Gemini Software Manual V4.0

Transcription

1 Gemini Software Manual V V4.0 Issued March 2002

2 Information provided by TECAN Software GmbH is believed to be accurate and reliable. However, the user is responsible for the proper and correct use of the product. No license is granted by acquisition of the product for any patent or patent rights of TECAN. If the user does not follow the instructions given in this Manual, TECAN does not take any responsibility for injuries or damages caused by the TECAN product. The information contained in this document is subject to change without notice. 2001, 2002 TECAN Software GmbH, all rights reserved.

3 TECAN Table of Contents Table of Contents 1 About This Manual Introduction Intended use of this product Related documentation Warning, cautions and notes Product Support System Setup System requirements Supported pipetting instruments Standard and advanced hardlocks Installation Upgrading to the latest software version Menus File menu New / Open / Close / Save / Save As Print / Print Preview / Print Setup Backup Data / Recover Data Data Explorer Recent files list Quit Gemini Edit menu Cut / Copy / Paste Edit / Delete / Insert New Command Setup menu Configuration Liquid Classes Setup & Service Te-MO Settings Arm initialization External Devices Execute menu Flush Instrument Drop DITIs Reset Options Fill System (ActiveTip) Switch on/off Doorlocks Send Firmware Command Set DITI Position Loading the Te-MO with racks Validate Start Pause Continue...26 March 2002 Gemini Software Manual V4.0 TOC - 1

4 Table of Contents TECAN Abort Start at line Undefined Variables View menu Log window Emergency Stop window Variables window Info window Toolbar Status Bar Command Bar Window menu Cascade Tile Arrange Icons Help menu Configuration Editor Basic concepts Introduction to carriers and racks Moving the arms Moving the LiHa Moving the RoMa Moving the PnP Moving the Te-MO Moving the PosID Configuring racks Rack coordinates Rack types Rack Wizard Configuring carriers Carrier dimensions and X/Y offsets Z offsets for carriers Custom objects Carrier Wizard Defining RoMa vectors RoMa Vector Wizard Defining PNP Vectors PnP Vector Wizard Configuring the LiHa Configuring the PosID Configuring the MPO/LICOS Configuring the ChemSystem Configuring Active tips Safety features for the Genesis instrument TOC - 2 Gemini Software Manual V4.0 March 2002

5 TECAN Table of Contents 5.17 Configuring the Doorlocks Liquid Classes Liquid Classes Editor Global parameters Type parameters Aspirate parameters Dispense parameters Calibration parameters Liquid classes for nanopipetting (NPS) Global parameters (NPS) Type parameters (NPS) Aspirate parameters (NPS) Dispense parameters (NPS) Calibration parameters (NPS) Commands for Gemini Scripts List of Gemini script commands Creating a Pipetting Script The Worktable window Adding carriers and racks to the worktable Assigning a label (or name) to the racks Specifying script commands Creating a Gemini script Example Script Typical application of a Gemini script Validating, Starting and Stopping a Script Validating a script Starting a script Pausing a script Continuing a script Stopping a script Starting a script at a certain line Undefined Variables option Sample scripts Advanced Programming Features Variables Defining and setting a variable Querying the value of a numeric variable during runtime Pre-defined variables CENTRIFUGE_RACK_CNT COPY_CNT DETECTED_VOLUME_x March 2002 Gemini Software Manual V4.0 TOC - 3

6 Table of Contents TECAN RACK_OFFSET RACK_VOLUME_X REPLICATE_CNT SAMPLE_CNT TUBE_CNT WELL_OFFSET Querying the value of a string variable during runtime Commands supporting string variables Expressions Commands supporting expressions Converting variables and expressions to a string Commands supporting variables and expressions converted to a string Validating a script containing variables Conditions (Condition command) Sub-routines Creating a sub-routine Sub-routine command Exchanging data with sub-routines Validating a script with sub-routines Log file for a script with sub-routines Loop options Description of selected commands Copy Plate command Replicates command Serial Dilution command Merge Plates command Transfer command Worklist command Worklist file format Worklist using rack labels Worklist using rack barcodes Worklist using tube barcodes Advanced worklist features Export Data command Report file format Worklist Import command RoMa vectors Defining a RoMa only carrier Defining a RoMa vector RoMa Vector command Move RoMa command Using a RoMa vector in a script Defining the home position for a RoMa PnP vectors Defining a PnP vector PnP Vector command Move PnP command TOC - 4 Gemini Software Manual V4.0 March 2002

7 TECAN Table of Contents Using a PnP vector in a script Defining the home position for a PnP Move LiHa command Te-Stack command Carousel commands Carousel Scan Barcodes command Carousel Retrieve command Carousel Return command Carousel Direct Movements command CAROUSEL settings in Gemini.opt Execute VB Script command Toolbar buttons for VB Scripts Set DiTi Position command Pick Up DITIs command Pickup ZipTip command Detect Liquid command Te-MO Relative Movements command PosID command Doorlocks command System command MIO command Execute Magellan Method command Execute WinWash Program command Centrifuge command Active WashStation command Error Handling Liquid error Clot error Instrument error Diluter error DITI Fetch error Lost DITI error Barcode error Grip error WRC/Te-MO error WRC Empty error WRC Overflow error Setup port for Magellan WinWash Plus Liquid Error March 2002 Gemini Software Manual V4.0 TOC - 5

8 Table of Contents TECAN Other WinWash Plus errors Te-Stack errors Appendices... A How to create a custom default worktable...a Standard options for carriers and racks...a How to create additional carriers...a Error messages...a Structure of the log files...a Structure of the Trace file...a Gemini directory structure and files...a Backing up your Gemini system and Gemini data...a Command line parameters...a Glossary of terms...a-13 List of Figures... A-27 List of Tables... A-31 Index... A-33 TOC - 6 Gemini Software Manual V4.0 March 2002

9 TECAN 1 - About This Manual 1 About This Manual 1.1 Introduction This manual describes the Gemini pipetting software for the GENESIS series of pipetting instruments. Gemini provides a graphical user interface for controlling the GENESIS instrument that facilitates the liquid handling needs of a wide range of diagnostic and life science applications, including both routine and research activities. Gemini can either be used stand alone for controlling Genesis and Genesis Freedom pipetting instruments or together with the Tecan dynamic scheduling software FACTS. The Gemini software allows the user to develop Gemini programs (which are normally called scripts) and to quickly visualize how a process can be implemented. Script commands are provided for a wide range of Tecan hardware options and the scripting system is designed for maximum flexibility when developing complex custom scripts. When the script is ready, Gemini controls the pipetting run by sending control signals to the GENESIS instrument through a data connection. If operator interaction is necessary, Gemini can display a dialog box on the display of the workstation which prompts for the information which is needed. The external programming interface which uses named pipes allows you to integrate Gemini into third party products or custom applications or to use Gemini components within other Tecan products running on the same computer or a different computer in the network. It is instructive for new users of Gemini to load the sample scripts which are provided and to work through each script by reviewing the on-line help (see also Glossary of terms on page A-13). This manual instructs the user how to: install the Gemini software, set up instrument and configuration data, define the worktable, define the pipetting scheme, start pipetting runs, and react to errors during pipetting. 1.2 Intended use of this product This product and manual is intended for laboratory specialists who need to develop programs (or scripts) for the GENESIS series of pipetting instruments. It is assumed that such specialists are already acquainted with standard laboratory procedures for handling and pipetting liquids as described in standard textbooks on this subject. March 2002 Gemini Software Manual V4.0 1

10 1 - About This Manual TECAN 1.3 Related documentation The following Tecan documentation provides additional information which can be useful when using this product: Te-MO Operating Manual - Doc ID , Command Set, PosID firmware - Doc ID Te-Flow Manual - Doc ID These manuals can be ordered from your nearest Tecan representative (see Product Support on page 3). 1.4 Warning, cautions and notes Three types of informational notices are used in this manual. They highlight important information or warn the user of a potentially dangerous situation. The following notices have the same level of importance throughout this manual. Warning: Indicates the possibility of severe personal injury, loss of life, or equipment damage if the instructions are not followed. Caution: Indicates the possibility of severe instrument damage or loss of data if instructions are not followed. Note: Gives helpful information about the equipment or situation. 2 Gemini Software Manual V4.0 March 2002

11 TECAN 2 - Product Support 2 Product Support How to get help Tecan and its representatives maintain a fully trained staff of technical specialists around the world. For any technical questions, contact your nearest Tecan representative. Addresses TECAN Sales Schweiz AG Seestrasse 103 CH-8708 Männedorf Switzerland Telephone Telefax Helpdesk [email protected] TECAN Regional Organizations: ASIA TECAN Asia (Pte) Ltd. 80, Marine Parade, # Singapore, Telephone Telefax [email protected] AUSTRIA TECAN Austria GmbH Untersbergstrasse 1a A-5082 Grödig / Salzburg Telephone Telefax Helpdesk [email protected] BELGIUM TECAN Benelux B.V.B.A. Vaartdijk 55 B-2800 Mechelen Telephone Telefax [email protected] FRANCE TECAN France S.A. Parc d Activités de Pissaloup Bâtiment B - Hermes II 27, Rue Edouard Branly F Trappes Telephone Telefax Helpdesk [email protected] GERMANY TECAN Deutschland GmbH Theodor-Storm-Straß e 17 D Crailsheim Telephone Telefax Helpdesk [email protected] March 2002 Gemini Software Manual V4.0 3

12 2 - Product Support TECAN GREAT BRITAIN TECAN UK Ltd. Theale Court, High Street Theale, Reading Berkshire RG7 5AH Telephone Telefax Helpdesk [email protected] ITALY TECAN Italia, S.r.l. Via F.Ili Cervi Palazzo Bernini Centro Direzionale Milano 2 I Segrate (MI) Telephone Telefax Helpdesk [email protected] JAPAN TECAN (Japan) Co. Ltd. Meiji Seimei Fuchu Building 10F 1-40 Miyamachi Fuchu City Tokyo 183 Telephone Telefax Helpdesk [email protected] NETHERLANDS TECAN Benelux B.V.B.A. Industrieweg 30 NL-4283 Giessen Telephone Telefax [email protected] USA TECAN US, Inc. P.O. Box Research Triangle Park, NC Telephone Telefax Helpdesk (800) TECAN-US, (800) [email protected] 4 Gemini Software Manual V4.0 March 2002

13 TECAN 3 - System Setup 3 System Setup This chapter describes the steps required to install and set up the Gemini software and to set up the Genesis instrument. 3.1 System requirements The Gemini software has the following minimum hardware and software requirements: An IBM-compatible computer with Microsoft Windows NT version 4.0, Service Pack 4 or later or Windows 2000 Service Pack 2 or later; Pentium 166 MHz or higher; at least 128 MB RAM; About 50 MB of hard disk space for the standard Gemini software, optional software components, scripts and log files; An SVGA monitor with a minimum resolution of 1024x768 pixels; to ensure correct display of the dialog boxes, we recommend you to configure your display settings in the Control Panel for Small Fonts; 100 MB of virtual memory; A Gemini hardlock (a copy protection device which is plugged into the parallel interface of the computer). This is often called a dongle; 1 parallel interface for the hardlock (you can connect a printer to the back of the hardlock if necessary); 1 unused serial interface for the data interface to the GENESIS instrument; additional serial interfaces are required by some of the instrument options (e.g. the Mettler balance); Printer (optional): March 2002 Gemini Software Manual V4.0 5

14 3 - System Setup TECAN 3.2 Supported pipetting instruments The Gemini software is designed for the following Tecan pipetting instruments: Genesis RSP, Genesis RWS, Genesis NPS and Genesis Freedom In addition, Gemini supports the following GENESIS options and systems: 4 or 8 tips Disposable Tips (DITIs) MonitoredPumpOption(MPO) Liquid Container Supervisor (LICOS) Low Volume Option Lower DITI Eject Te-VacS, the Tecan SPE Vacuum System Te-MagS, the Tecan Magnetic Bead Separator 6-way valve for different system liquids Vacuum assisted waste for viscous liquids NPS System (Nanopipetting System) Te-Shake (Orbital Shaker) Te-MO (Tecan Multipipetting Option) MIO (heated incubator with optional shaker hardware) Carousel Te-Stack (Tecan Microplate Stacker) Hettich Centrifuge H+P Variomag Connection Box for the Te-Flow option Tecan Magellan software (for Tecan Reader and Photometer) Tecan WinWash Plus software (for Tecan Plate Washers) Huber Recirculator Mettler Balance Symbol LS1220 Barcode Scanner Access/Status option (doorlocks and status lamps/siren unit) 6 Gemini Software Manual V4.0 March 2002

15 TECAN 3 - System Setup 3.3 Standard and advanced hardlocks Gemini is available with two different software feature levels. Whereas the software on the CD which is supplied is the same in both cases, the additional features provided by the advanced feature level are enabled by using the Advanced hardlock (sometimes called a dongle). The Standard hardlock does not support the following commands: Gemini commands Move ROMA, ROMA_VECTOR, Move PnP and PnP_VECTOR. Named-Pipe commands ROMA_GRIP, ROMA_MOVE, ROMA_RELATIVE, SET_ROMA_BARCODE, PNP_GRIP, PNP_MOVE, PNP_RELATIVE and SET_PNP_BARCODE. The hardlock version you are currently using is shown in the Gemini status bar (see Status Bar on page 28). See Gem_Pipe.pdf in the Gemini program directory for more information on the named pipes programming interface for Gemini. Note: Gemini runs in Simulation mode if no hardlock is detected. 3.4 Installation Please proceed as follows to install the Gemini software: Insert the Gemini CD into your CD-ROM drive. Click the Start button on your Windows task bar. Choose Run. Type D:\SETUP, where D: is the drive letter of your CD-ROM drive. Click OK. After the installation program has started please follow the instructions on the screen. Caution: You must use the Genesis Setup & Service software module to check the reference positions. Otherwise your rack and carrier coordinates might be wrong. See the Genesis Instrument Software Manual - Doc ID , Setup & Service Software Module for more information. March 2002 Gemini Software Manual V4.0 7

16 3 - System Setup TECAN Caution: The setup program overwrites existing Gemini installations. If you specify the same installation path which was used for an older version of Gemini, please back up your data first and copy it back after the installation is finished (see Backing up your Gemini system and Gemini data on page A-12 and Upgrading to the latest software version, below, for more information). 3.5 Upgrading to the latest software version The steps required to upgrade your Gemini software to the latest version are dependent in part on the GENESIS instrument version and system options which you are already using. For this reason upgrading is normally carried out by a Tecan representative. Please see the README.TXT file in the Gemini program directory and the upgrade notes supplied with the product for additional information. Where applicable, please observe your local regulations for certification of your GENESIS system. It is strongly recommended to backup up you system and data files before upgrading (see Backing up your Gemini system and Gemini data on page A-12). Gemini version 4.0 can read files created by Gemini version 3.2 or later. Files created with Gemini version 4.0 are generally not compatible with earlier versions of the software. Gemini configuration files and script files are now protected by checksums (see Data Explorer on page 10). When upgrading from an earlier version of Gemini, the Data Explorer will initially show that all files have incorrect checksums since earlier Gemini versions did not support the checksum feature. A warning is shown if an attempt is made to load a file with an missing checksum. A checksum is added automatically when the file is saved. Choose About Gemini in the Help menu if you want to check which version of Gemini you are using. 8 Gemini Software Manual V4.0 March 2002

17 TECAN 4 - Menus 4 Menus This chapter describes the main menu options which are provided by the Gemini software. Each menu will be discussed in more detail in subsequent chapters. 4.1 File menu This menu allows you to create a new Gemini script, to open an existing script, to print the contents of a script, to select a recent script or to quit Gemini Figure 4-1: File menu New / Open / Close / Save / Save As These menu items allow you to create, open and save Gemini scripts. Please note that Gemini script files have the extension.gem and are normally stored in the \Gemini\Data directory Print / Print Preview / Print Setup If you have a printer connected to your computer, these menu items allow you to print Gemini scripts. The following items are printed: The script March 2002 Gemini Software Manual V4.0 9

18 4 - Menus TECAN The path and filename of the script file The worktable layout Page number, time and date Gemini user name Backup Data / Recover Data Choose Backup to make backup copies of the Gemini configuration files and script files to your local hard disk.the following files are backed up: Carrier.cgf Gemini.cfg Gemini.set Gemini.opt LClasses.dat All script files (*.gem) Apart from Gemini.set, which is in the Gemini directory, from the Gemini/Data directory Gemini creates a new sub-directory in the Gemini directory for each backup. The name of the new sub-directory is BACKUP_YYYYMMDD_HHMMSS, where YYYYMMDD is the date and HHMMSS is the time of the backup. Choose Recover to recover previously backed up Gemini configuration files and script flies. This copies all of the backed up files to the Gemini/Data directory. A dialog box is shown to allow you to choose which backup version to recover. Choose Settings in the Setup menu to configure Gemini to make automatic backups at specified intervals. See Settings on page 16. Both backup and recovery operations are reported in the general trace file. See Backing up your Gemini system and Gemini data on page A-12 if you want to make an external backup of your Gemini installation Data Explorer The following Gemini configuration files and script files are protected by checksums: Carrier.cfg Gemini.cfg Gemini.set Gemini.opt LClasses.dat 10 Gemini Software Manual V4.0 March 2002

19 TECAN 4 - Menus All script files (*.gem) Log files Export files The trace file Choose Data Explorer to check whether these files have valid checksums. An incorrect checksum indicates that the file contents of the file may be corrupted or has been modified outside of Gemini by another program or process. Figure 4-2: Data Explorer dialog box A warning is shown if an attempt is made to load a file with an incorrect or missing checksum. The user can then choose to load the file or cancel. In the latter case, Gemini aborts with the exception of script files (*.gem). In this case, the file is not loaded but Gemini remains running. The incorrect checksum warning can be disabled in the Settings dialog box by a user with administrator status (see page 20). An entry is written to the log file each time an incorrect or missing checksum is found. When upgrading from an earlier version of Gemini, the Data Explorer will initially show that all files have incorrect checksums since earlier Gemini versions did not support the checksum feature. A warning is shown if an attempt is made to load a file with an missing checksum. Gemini automatically adds a checksum when the file is saved. If you select a configuration file or script, the Data Explorer also shows the date and time of the last modification to the file alongside the name of the user who modified it and a comment to explain the reason for the change. See Log Reason in the Settings dialog box on page 20 for additional information on this feature. March 2002 Gemini Software Manual V4.0 11

20 4 - Menus TECAN Recent files list Gemini keeps a list of up to 8 of the most recently opened scripts. You can load one of them by choosing it from the list or by opening the File menu and pressing the corresponding digit on the keyboard Quit Gemini This menu item closes all currently open scripts, de-initializes the instrument and quits Gemini. 12 Gemini Software Manual V4.0 March 2002

21 TECAN 4 - Menus 4.2 Edit menu This menu allows you to edit, insert and delete Gemini commands. The menu items are used when writing a Gemini script (see Creating a Gemini script on page 123). If you choose Insert new command, a floating menu appears with additional choices, as shown below: Figure 4-3: Edit menu You also get the floating menu if you click on the script window with the right mouse button Cut / Copy / Paste Gemini allows you to repeat script lines by using Copy & Paste. If you have more than one script opened at the same time, you can copy or move lines from one script to another Edit / Delete / Insert New Command These menu items are used to edit or delete existing commands (i.e. script lines) or to insert new commands. New commands are inserted below the currently selected command, which is highlighted in color (the default color is light yellow). You can select a command by clicking with the mouse or by using the cursor keys. If you select the first March 2002 Gemini Software Manual V4.0 13

22 4 - Menus TECAN line of the script, you will be asked whether to insert the new command above or below the current command. Note: You can also insert a command in your script by clicking on a button in the Command Bar or one of the commands toolbars, clicking with the right mouse button and choosing the command from the floating menu or by pressing the Insert key. 14 Gemini Software Manual V4.0 March 2002

23 TECAN 4 - Menus 4.3 Setup menu After opening a Gemini script, this menu allows you to configure the pipetting instrument (see Configuration Editor on page 33), set up liquid classes (see Liquid Classes on page 91) and to configure general settings: Figure 4-4: Setup menu Configuration See Configuration Editor on page Liquid Classes See Liquid Classes on page Setup & Service Te-MO See the Te-MO Operating Manual - Doc ID , Setup & Service for more information. March 2002 Gemini Software Manual V4.0 15

24 4 - Menus TECAN Settings This menu item lets you configure general settings for the Gemini software. The following dialog box is shown: Figure 4-5: Settings dialog box Paths panel Specify where Gemini should store its data files (Data), log files (Log) and output files (Output). Enter the required paths directly or click the Browse buttons and choose the required directories. Baud rate / COM-Port Specify the COM (V.24) port that the GENESIS instrument is connected to. You can also set the baud rate used for communication between Gemini and GENESIS. We recommend you to use a baud rate of 38,400 baud. See External Devices on page 21 for information on configuring COM ports for external devices such as the carousel or centrifuge. Simulation When running in simulation mode, Gemini pauses for a certain time after executing each pipetting command. You can set the duration of the pause here. Language Select the required language of the user interface (German (Deutsch) or English). 16 Gemini Software Manual V4.0 March 2002

25 TECAN 4 - Menus Initialising the instrument Gemini detects automatically whether the instrument needs to be initialized, and carries out initialization if necessary. If your instrument is equipped with a LiHa, during initialization it is moved above the left-most waste and all diluters are initialized. This can cause some liquid to drip from the tips. If you check the Deep in Waste checkbox, Gemini lowers the tips into the waste to minimize the risk of contamination during initialization. See also Arm initialization on page 20. Caution: Please check the coordinates of the waste before activating this option. Otherwise the tips might collide. User management User management is provided to restrict access to the Gemini software. Users are prompted to enter a user name and password during program start-up. Note that passwords are case-sensitive. When upgrading from an earlier version of Gemini, when the software is started for thefirsttimeyouwillbeforcedtocreateanewuserwithadministratorstatus(unless one was already created with the earlier software version). Click Change Password to change the password of the currently logged in user. Click Edit User to create new users or delete existing users. Gemini provides three user levels with the following rights: User has rights to: flush the instrument or drop DITIs specify the DITI position load, close or print a Gemini script validate or start a script handle errors during pipetting Since user level users are not allowed to create or modify scripts, the Command bar and various other program interface features used to create scripts are hidden or disabled. Table 4-1: Rights for users, managers and administrator March 2002 Gemini Software Manual V4.0 17

26 4 - Menus TECAN Manager same as User with additional rights to: create, modify and save Gemini scripts edit the Configuration edit the Liquid Classes edit the Settings edit the password skip timers during pipetting Administrator same as Manager with additional rights to: create or delete users Table 4-1: Rights for users, managers and administrator (Continued) Log off user after... Users are automatically logged out of Gemini after a specified time during which no keyboard or mouse-click activities have been detected. Specify the required interval in minutes in this field (range 1 to 1440 minutes). If the user is logged out while a script is running, the script continues to run. In addition, a dialog box containing a pause button is displayed in case it is necessary to stop the script. The dialog box also allows the user to log in again. All other Gemini functions are disabled until the user logs in again. Password has to be changed after... To maximize security, users can be forced to change their passwords at regular intervals. To activate this feature, check the checkbox and specify the interval in days. Maintenance panel Click Maintenance Settings to view the instrument s internal counters for LiHa, RoMa and PnP movements. Gemini gets this information by interrogating the instrument (the counters are all set to zero in simulation mode). Check the Active checkbox in the Maintenance panel of the Settings dialog box if you want to activate automatic warnings when predefined limits have been reached. In this case, the user is prompted to perform routine maintenance activities and the instrument will not start the pipetting run. See the specific instrument operating manual for information on the maintenance which is required. After carrying out the maintenance, click the Reset buttons to reset the internal counters to allow pipetting to resume. The predefined limits are specified in the Maximum allowed fields. You need to have Administrator rights to activate the maintenance check and/or set the predefined limits for the counters (see User Management in Settings on page 16). 18 Gemini Software Manual V4.0 March 2002

27 TECAN 4 - Menus After installing Gemini, the maintenance checkbox and button are initially disabled. To activate them, open the file Gemini.opt in the Gemini\data directory with a plain text editor such as Notepad and add the entry DISABLE_MAINTENANCE=0 to the [OPTIONS] section (or edit the existing entry accordingly). Display panel If required, you can choose an image such as a company logo to display as wallpaper in the background of the main Gemini window. Click the Browse button to choose the required file. The supported image file formats are.bmp,.dib,.gif,.jpg and.jpeg. Choose Center, Tile or Stretch as required to achieve the required effect. In addition, you can choose an image or movie file to display while a script is running. Click the Browse button to choose the required file. The supported image file formats are.bmp,.dib,.gif,.jpg and.jpeg. The supported video file formats are.avi,.mpg and.mpeg. Color of selected script line A colored background is used to indicate the script line which is currently selected. The default color is light yellow. If required click on the color and use the color picker to choose another color. When a script line is selected, the same color is used to highlight the associated object in the Worktable window. Log Files Gemini can write log files to document the pipetting, to record user inputs, to help you to check scripts in simulation mode and to find errors. You can activate three types of log files with different levels of logging detail, either individually or in combination: Check the Full checkbox to enable log files of type LOG. Check the Input checkbox to enable log files of type USR. Check the Error checkbox to enable log files of type ERR. See Structure of the log files on page A-5 for Information on each of these log file types. Caution: Gemini can write up to 100,000 individual log files, which can use up a lot of storage on your hard disk. Accordingly, it is recommended to delete or archive oldorunwantedlogfilesonaregularbasis. Even if you have not activated the Log Files option, you can view recent log entries by choosing Log Window in the View menu. The Log Window has the same structure as the log files and shows the last 1000 log entries when it is first opened. March 2002 Gemini Software Manual V4.0 19

28 4 - Menus TECAN Log Reason When saving one of the following files after making changes, users are forced to enter a comment to explain the reason for the changes: Carrier.cgf Gemini.cfg Gemini.set Gemini.opt LClasses.dat All script files (*.gem) Uncheck the Log Reason checkbox if you want to disable this feature (you need administrator status to do this). This setting can only be changed by a user with administrator status. Note: The user comment can be viewed in the Data Explorer (see page 10). Only the most recent comment is saved. Earlier comments are stored with earlier versions of these files, which are automatically backed up to the History sub-directory (see Gemini directory structure and files on page A-9). Evaluate file checksums Gemini configuration files and script files are protected by checksums, and a warning is shown if an attempt is made to load a file with an incorrect or missing checksum. Uncheck the Evaluate file checksums checkbox if you want to disable the warning (you need administrator status to do this). The validity of the checksums can be viewed in the Data Explorer (see page 10). Automatic data backup Check this checkbox and specify the duration in days to automatically back up Gemini configuration files and script files at regular intervals. Gemini creates a new sub-directory in the Gemini directory for each backup. See Backup Data / Recover Data on page 10 for more information Arm initialization When Gemini initializes the arms (LiHa, RoMa and PnP), a sequence of movements is carried out to determine the reference (zero) positions along the X, Y and Z axes. During the full initialization sequence which is carried out e.g. when Gemini is started after powering up the instrument, the arms need to move fully to the rear of the instrument to determine the zero position in the Y direction. Initialization mode: Standard With the GENESIS Freedom instrument, all arms move to the rear left of the worktable to initialize all axes. 20 Gemini Software Manual V4.0 March 2002

29 TECAN 4 - Menus With the GENESIS RSP instrument, during initialization the LiHa moves to the rear left of the worktable and the (optional) RoMa moves to the rear right of the worktable. With all instrument types, after initialization the arms move to their home (parking) positions if they have been defined (see Defining the home position for a RoMa on page 216 and Defining the home position for a PnP on page 224). Initialization mode: To the front If the rear left of the worktable is occupied by other objects, choose To the front to avoid a collision during initialization. In this case you must specify the grid position range in the From grid and To fields to indicate where it is safe to move the arms to the rear. Since the arms move one at a time to the rear in this case and then back to the front, the grid position range only needs to wide enough to accommodate one arm. When initialization is finished, all arms move to a parking position at the front left of the worktable. The initialization mode To the front is only available for the GENESIS Freedom instrument External Devices This menu item is used to select the COM ports to use for external devices such as the carousel or centrifuge. Gemini uses the following communication parameters for the serial interfaces: Device Baud rate Bits Stop Bits Parity Flow control Carousel Even None Carousel Scanner No None Waterbath No None Centrifuge Even None Variomag No None Balance Even DTR Barcode Scanner Even None Table 4-2: Configuration of the serial interfaces for external devices If Gemini is not able to successfully communicate with an external device, make sure that the device s serial interface has been correctly configured for the above communication parameters. Also make sure that you are using the correct serial interface cable. March 2002 Gemini Software Manual V4.0 21

30 4 - Menus TECAN 4.4 Execute menu This menu allows you to flush the instrument (you must first define the worktable; see The Worktable window on page 117), drop DITIs (you must first define the worktable), reset the Genesis options Te-VacS, Te-MagS, Te-Shake, set the DITI position (you must first define the worktable), validate and start a script. You can also start a script at a specified line. Figure 4-6: Execute menu Flush Instrument This menu item is used to flush the instrument (fill it with system liquid). Gemini prompts you for the volume and the location of the waste and cleaner on the worktable Drop DITIs This menu item is used to drop DITIs directly without running a script. Gemini prompts you for the location of the DITI waste on the worktable. 22 Gemini Software Manual V4.0 March 2002

31 TECAN 4 - Menus Reset Options This menu item is used to initialize the following hardware options for your GENESIS instrument manually. The hardware options are normally reset automatically at the appropriate time and a manual reset is only necessary under abnormal circumstances. Te-VacS Te-MagS Te-Shake Te-MO WRC Carousel The GENESIS instrument is interrogated for the presence of these options and the Reset Options menu item will be inactive (gray) if none of the options are detected or if Gemini is running in simulation mode. The following dialog box is shown if at least one of the options is present (the list of devices will change according to the installed options): Figure 4-7: Reset Options dialog box The device number is shown alongside the device name. Notes Te-VacS You can initialize the Te-VacS devices individually or all devices. Te-MagS You can initialize the Te-MagS devices individually or all devices. In addition, you can initialize the Te-MagS heaters individually. Te-Shake You can initialize the Te-Shake devices individually or all devices. March 2002 Gemini Software Manual V4.0 23

32 4 - Menus TECAN Te-MO WRC You can initialize the Te-MO WRC devices individually. This flushes the WRC with washing liquid #1 for 20 s using 50% pump power. This ensures that the tubing and the wash carrier is filled with liquid and free of bubbles. Carousel You can initialize the carousels individually. Click OK to initialize the selected device and close the dialog box. Click Cancel to close the dialog box without initializing Fill System (ActiveTip) If your instrument is fitted with ActiveTips, this menu item is used to fill the liquid system. A special procedure is necessary because of the very small inner diameter of the ActiveTips Switch on/off Doorlocks This menu item is used to open or close the doorlocks manually. This menu item is only available if your instrument is fitted with doorlocks and is not available in simulation mode. The doorlocks are normally opened and closed automatically at the appropriate time and you should only need to operate the doorlocks manually in special situations (e.g. during instrument configuration). See also Configuring the Doorlocks on page Send Firmware Command This menu item lets you send a firmware command directly to the instrument and is only intended for specialists. See the respective instrument manual for a list of firmware commands. Warning: Please be careful when using this feature. Sending the wrong commands can damage the instrument or objects in its workspace, hurt yourself or other people Set DITI Position If you are using DITIs, Gemini stores the position of the last fetched DITI. When starting a new run, the Get DiTis command starts picking up DITIs at the next available position. After loading new DITI racks onto the worktable, this menu item can be used to ensure that the next DiTi is fetched from position 1 rather than from the middle of the new rack. 24 Gemini Software Manual V4.0 March 2002

33 TECAN 4 - Menus You can specify the next location for each of the available DiTi types. You can also specify the next DiTi position during script runtime with the Set DiTi Position command. Figure 4-8: Set Next Available DiTi Position dialog box DiTi type Specify the DiTi type for which you want to specify the next location. Next DiTi position Specify the rack containing the next available unused DiTi of this type by clicking on the new DiTi tray in the Worktable window. Then specify the rack position (you should normally choose position 1) Loading the Te-MO with racks The Te-MO can be loaded with racks during script runtime using the RoMa. You can also load it manually before starting the script. Depending on their position in the TeMO, some of the sites may be difficult to access due to the position of the slides. This command is used to move a specified site to the RoMa exchange position (transfer position) manually to make it easier to exchange the rack. In this position, the LiHa or RoMa can access the specified site without colliding with the Te-MO pipetting head. March 2002 Gemini Software Manual V4.0 25

34 4 - Menus TECAN Choose the required slide and site in the Sites panel and click Move in the RoMa Exchange Position panel to move the site to the exchange position. Figure 4-9: Loading the Te-MO dialog box When the Te-MO reaches the RoMa exchange position and you are using an APC (Active Positioning Carrier), click Open in the APC panel to release the rack. Click Close in the APC panel to lock the rack in position again Validate See Validating a script on page Start See Starting a script on page Pause See Pausing a script on page Continue See Continuing a script on page Abort See Stopping a script on page Start at line... See Starting a script at a certain line on page Gemini Software Manual V4.0 March 2002

35 TECAN 4 - Menus Undefined Variables See Undefined Variables option on page View menu This menu allows you to view or hide the Log, Emergency-Stop, Variables and Info windows, to create custom toolbars and to view or hide the Status bar and the Command bar. Figure 4-10: View menu Log window This menu item lets you view or hide the Log window, a troubleshooting tool that tracks every command sent by the computer to the instrument, every response returned from the instrument to the computer and any user input. The content and format of the log corresponds to a Full log file of type LOG (see Structure of the log files on page A-5) Emergency Stop window This menu item is used to show or hide the Emergency Stop window (a quick access button that immediately stops the script, and thus the pipetting). The Emergency Stop window is always shown in the foreground to ensure that it is always available when March 2002 Gemini Software Manual V4.0 27

36 4 - Menus TECAN required. If you click the Emergency Stop button, the script is stopped and Gemini switches to simulation mode. Note: The Emergency Stop button is inactive in simulation mode Variables window This menu item is used to show or hide the Variables window, which shows the value of all defined variables during script runtime. This window is refreshed after every script line; changed variables are shown in red and unchanged variables are shown in black Info window This menu item is only available if you have a Te-VacS, Te-MagS and/or Te-Shake option connected to your instrument. During script runtime, the info window displays information such as pressure or temperature Toolbar This menu item lets you customize the standard toolbars and allows you to create and delete custom toolbars. You can also reset the toolbars to the default settings Status Bar Note: To rearrange toolbar buttons, press the Alt key and drag them with the mouse. You can remove a button by dragging it off of the toolbar. Select a toolbar in the Toolbars window and click Reset to restore the default button assignments. Double-click a toolbar (or drag the toolbar with the mouse) to switch between floating mode and docking mode. In addition, you can resize or reshape a toolbar by dragging its borders. This menu item is used to show or hide the status bar, which displays the following information: Figure 4-11: Status bar The Dongle Type fields show which Gemini feature level you are using. The feature level is dependent on the hardlock version you are using: REAL MODE = Real mode (normal operation), SIMULATION = Simulation mode STD = Standard Gemini hardlock, ADV = Advanced Gemini hardlock GEM = hardlock detected, DEMO = no hardlock detected See Standard and advanced hardlocks on page 7 for more information. 28 Gemini Software Manual V4.0 March 2002

37 TECAN 4 - Menus Command Bar This menu item allows you to display or hide the Command Bar, which lists all of the script commands in the same style as the element bar in Microsoft Outlook: The Command Bar is an alternative way of selecting script commands to the commands toolbars (see page 108). The commands in the Command Bar are grouped according to their function as follows: Pipetting commands (e.g. Aspirate) Advanced pipetting commands (e.g. Copy Plate) Script programming commands (e.g. Start Timer) Te-MO commands Commands for storage devices (e.g. Carousel) Commands for robotic devices (e.g. RoMa and PnP) Commands for optional devices or accessories (e.g. Vacuum Separator) Click on the group name button in the Command Bar to choose commands from the respective group. Right click on one of the commands to switch between large and small icons. Figure 4-12: Command Bar March 2002 Gemini Software Manual V4.0 29

38 4 - Menus TECAN 4.6 Window menu This menu allows you to display the currently open windows in cascade or tile style, or to arrange minimized icons. In addition, this menu lists all currently opened scripts and marks the currently active script with a check mark. Figure 4-13: Window menu Cascade If several script windows are open, this command arranges the script windows on top of each other Tile If several script windows are open, this command arranges the script windows as nonoverlapping tiles Arrange Icons If several script windows are open and minimized, this command arranges the icons along the bottom of the screen. 30 Gemini Software Manual V4.0 March 2002

39 TECAN 4 - Menus 4.7 Help menu This menu opens the online help (Help Topics) and identifies the version of Gemini you are using (About Gemini...). Figure 4-14: Help menu March 2002 Gemini Software Manual V4.0 31

40 4 - Menus TECAN 32 Gemini Software Manual V4.0 March 2002

41 TECAN 5 - Configuration Editor 5 Configuration Editor Gemini stores information on fixed and variable parts of the GENESIS pipetting instrument in the two configuration files CARRIER.CFG and GEMINI.CFG in the Gemini/ data directory, which are collectively called the configuration. The configuration also contains information on the dimensions of the racks and carriers which are available and parameters for optional accessories. The configuration is edited with the Configuration Editor, which is started when you choose Configuration in the Setup menu: Figure 5-1: Configuration editor Click the tabs at the top of the dialog box to choose the object type that you want to edit. Gemini then displays a list of the objects which are defined for the selected type. Then choose an item and click one of the following buttons: Edit Click this button to edit the properties of the selected item. Delete Click this button to delete the selected item. New Click this button to create a new item of the selected type, e.g. a new rack. Copy Click this button to copy the selected item. You will be prompted for the name of the copy. Name Click this button to change the name of the selected item. March 2002 Gemini Software Manual V4.0 33

42 5 - Configuration Editor TECAN Please proceed as follows when setting up a new GENESIS instrument: Use the Genesis Setup & Service software module to check the reference positions. See the Genesis Instrument Software Manual - Doc ID , Setup & Service Software Module for more information. Edit the settings for the LiHa (see Configuring the LiHa on page 82) If necessary, edit the settings for MPO/LICOS (see Configuring the MPO/LICOS on page 86) and ChemSystem (see Configuring the ChemSystem on page 87). Click OK to save the configuration and close the configuration editor. On delivery, the database of the Genesis software package already includes information on all standard Tecan carriers, racks and containers. I Caution: It is recommended not to change the properties of the predefined standard Tecan carriers, racks and containers. Copy the object and save it under a new name if you want to alter any of the properties. 34 Gemini Software Manual V4.0 March 2002

43 TECAN 5 - Configuration Editor 5.1 Basic concepts Introduction to carriers and racks Gemini allows you to define an object (e.g. a microplate rack) once only, and then to assign it to any required position on the worktable grid. This is handled by the Gemini software by storing the coordinates in a hierarchy: The rack coordinates are relative to the site on which the rack is placed. The site coordinates are relative to the carrier. The carrier offsets are relative to the grid position on the worktable (see also Figure 5-16 on page 64). The grid positions on the worktable have a periodic spacing of 25 mm. The hierarchy allows you to place a rack at any suitable site, carrier and worktable position without having to redefine its coordinates. The figure below shows the relationship between racks, carriers and the worktable. Figure 5-2: Rack, carrier and worktable March 2002 Gemini Software Manual V4.0 35

44 5 - Configuration Editor TECAN When you set up the worktable for your Gemini script, you first choose a carrier with the required number of sites (see Configuring carriers on page 62). Each of the sites can hold a rack. If you cannot find the carrier you need in the Gemini database, you can define a new carrier (see Configuring carriers on page 62). You then choose the racks you want to use. If you cannot find the rack you need in the Gemini database, you can define a new rack (see Configuring racks on page 45). In the third step you position the carriers on the worktable and place the racks onto the carriers (see Adding carriers and racks to the worktable on page 118). 36 Gemini Software Manual V4.0 March 2002

45 TECAN 5 - Configuration Editor 5.2 Moving the arms Positions in Gemini are measured and verified by moving the LiHa, RoMa, PnP or Te- MO etc. to the required place by pressing keys on the numeric keypad. You can then store the current position coordinates in the dialog box for the object. Positions are defined in instrument steps, i.e. the smallest unit of movement of the servo motors (0.1 mm). The coordinate system of the instrument uses three axes for the LiHa (X, Y, and Z), five axes for the RoMa (X, Y, Z, R, and G), five axes for the PnP (X, Y, Z, R, and G), five axes for the Te-MO (X, Y1, Y2, Y3 and Z) and three axes for the PosID (X, Y and B) Moving the LiHa The LiHa (Liquid Handling Arm) is mounted on the X-slide and holds the pipetting tips. In Genesis, the origin of the LiHa coordinate system (X=0, Y=0, Z=0) is the rear left of the worktable with the pipetting tips raised. The three axes of the LiHa are defined as follows: X Y Z from left to right from rear to front tips from top to bottom Table 5-1: Movement axes for the LiHa March 2002 Gemini Software Manual V4.0 37

46 5 - Configuration Editor TECAN When editing an object for which a position has to be defined, an additional dialog box appears which helps you to specify certain movements. The LIHA tab shows the current position of the LiHa. If your instrument is not fitted with a LiHa, the LIHA tab is not displayed unless you are running in simulation mode. The Z-movements panel lets you select which tips should be moved in the Z-direction. You can specify the first tip to move and the total number of tips to move. The Adjust button is only available when editing racks. It is used to adjust the rack position for a specified, single site to compensate for small manufacturing inaccuracies without needing to switch to the carrier definition. To use the Adjust button, move the LiHa to the Z-max position above the first well of the rack while it rests on the required site. Then click the Adjust button to modify the carrier definition to match the current X, Y and Z coordinates. Figure 5-3: Move LIHA dialog box You can move the LiHa using the numeric keypad (make sure that NUM Lock key is pressed): 7 8 : rear (- Y) 9 :up(-z) 4 :left(-x) 5 6 :right(+x) 1 2 : front (+ Y) 3 :down(+z) Table 5-2: Moving the LiHa using the numeric keypad Each time you press one of these keys, the arm is moved by a single step. Keep the key pressed to move the arm by two steps per second. If you also press the CONTROL key, the arm is accelerated until it reaches a certain maximum speed. Note: You cannot use the cursor keys to move the arm since they have default functions in Windows applications. 38 Gemini Software Manual V4.0 March 2002

47 TECAN 5 - Configuration Editor Moving the RoMa The RoMa (Robotic Manipulator Arm) is a robotic arm with gripper fingers that can grip and move objects such as microplates. In Genesis, the origin of the RoMa coordinate system (X=0, Y=0, Z=0) is the rear left of the worktable with the gripper raised and pointing towards the front of the instrument. The five axes of the RoMa are defined as follows: X Y Z R G from left to right from rear to front from top to bottom clockwise rotation of the gripper when viewed from above from narrow to wide gripper distance Table 5-3: Movement axes for the RoMa When editing an object for which a position has to be defined, an additional dialog box appears which helps you to specify certain movements. The ROMA tab shows the current position of the RoMa. If your instrument is not fitted with a RoMa, the ROMA tab is not displayed unless you are running in simulation mode. Figure 5-4: Move RoMa dialog box March 2002 Gemini Software Manual V4.0 39

48 5 - Configuration Editor TECAN You can move the RoMa using the numeric keypad (make sure that NUM Lock key is pressed): 7 : clockwise (+R) 8 : rear (- Y) 9 :up(-z) 4 :left(+x) 5 6 :right(-x) 1 : counterclockwise (-R) 2 :front(+y) 3 :down(+z) 0 : narrow (-G), :wide(+g) Table 5-4: Moving the RoMa with the keys on the numeric keypad Each time you press one of these keys, the arm is moved by a single step. Keep the key pressed to move the arm by two steps per second. If you also press the CONTROL key, the arm is accelerated until it reaches a certain maximum speed. Note: You cannot use the cursor keys to move the arm since they have default functions in Windows applications Moving the PnP The PnP (Pick and Place) is a robotic arm with gripper fingers that can grip and move small objects such as tubes. In Genesis, the origin of the PnP coordinate system (X=0, Y=0, Z=0) is the rear left of the worktable with the gripper raised. The five axes of the PnP are defined as follows: X Y Z R G from left to right from rear to front from top to bottom clockwise rotation of the gripper when viewed from above from narrow to wide gripper distance Table 5-5: Movement axes for the PnP 40 Gemini Software Manual V4.0 March 2002

49 TECAN 5 - Configuration Editor When editing an object for which a position has to be defined, an additional dialog box appears which helps you to specify certain movements. The PnP tab shows the current position of the PnP. If your instrument is not fitted with a PnP, the PnP tab is not displayed unless you are running in simulation mode. Figure 5-5: Move PnP dialog box You can move the PnP using the numeric keypad (make sure that NUM Lock key is pressed): 7 : clockwise (+R) 8 :rear(-y) 9 :up(-z) 4 :left(+x) 5 6 : right (- X) 1 : counterclockwise (-R) 2 :front(+y) 3 :down(+z) 0 : narrow (-G), :wide(+g) Table 5-6: Moving the PnP with the keys on the numeric keypad Each time you press one of these keys, the arm is moved by a single step. Keep the key pressed to move the arm by two steps per second. If you also press the CONTROL key, the arm is accelerated until it reaches a certain maximum speed. Note: You cannot use the cursor keys to move the arm since they have default functions in Windows applications. March 2002 Gemini Software Manual V4.0 41

50 5 - Configuration Editor TECAN Moving the Te-MO Moving the Te-MO (Tecan Multipipetting Option) is similar to moving the LiHa or RoMa. The five axes of the Te-MO are defined as follows: X Y1 Y2 Y3 Z Head,lefttoright Left slide, rear to front Middle slide, rear to front Right slide, rear to front Head, top to bottom Table 5-7: Movement axes for the Te-MO You can move the Te-MO using the numeric keypad (make sure that NUM Lock key is pressed): 7 :Y1back 8 :Y2back 9 :Y3back - :Zup 4 :Xleft 5 : 6 :Xright + : Z down 1 :Y1front 2 :Y2front 3 :Y3front Table 5-8: Moving the Te-MO with the keys on the numeric keypad Each time you press one of these keys, the arm is moved by a single step. Keep the key pressed to move the arm by two steps per second. If you also press the CONTROL key, the arm is accelerated until it reaches a certain maximum speed. Note: You cannot use the cursor keys to move the arm since they have default functions in Windows applications. 42 Gemini Software Manual V4.0 March 2002

51 TECAN 5 - Configuration Editor When editing an object for which a position has to be defined, an additional dialog box appears which helps you to specify certain movements. The Te-MO tab shows the current position of the Te-MO. If your instrument is not fitted with a Te- MO, the Te-MO tab is not displayed unless you are running in simulation mode. To move the Te-MO to the transfer position, for example to test a RoMa vector, select a slide and site from the pop-up list and click Move to Transfer Position. In this position, the LiHa or RoMa can access the specified site without colliding with the Te-MO pipetting head. When the Te-MO reaches the transfer position and you are using an APC (Active Positioning Carrier), click Open APC to release the rack. Click Close APC to lock the rack in position again. Figure 5-6: Move Te-MO dialog box Moving the PosID The PosID (Positive Identification System) is a barcode scanner device. Moving the PosID is similar to moving the LiHa or RoMa. In Genesis, the origin of the PosID coordinate system (X=0, Y=0, B=0) is the rear left of the worktable with the carrier gripper near the front. The three axes of the PosID are defined as follows: X Y B PosID, from left to right PosID carrier gripper, rear to front PosID scanner head, top to bottom Table 5-9: Movement axes for the PosID You can move the PosID using the numeric keypad (make sure that NUM Lock key is pressed): 7 : 8 :back 9 : B counterclockwise 4 :Xleft 5 : 6 :Xright 1 : 2 :front 3 : B clockwise Table 5-10: Moving the PosID with the keys on the numeric keypad March 2002 Gemini Software Manual V4.0 43

52 5 - Configuration Editor TECAN Each time you press one of these keys, the arm is moved by a single step. Keep the key pressed to move the arm by two steps per second. If you also press the CONTROL key, the arm is accelerated until it reaches a certain maximum speed. Note: You cannot use the cursor keys to move the arm since they have default functions in Windows applications. When editing an object for which a position has to be defined, an additional dialog box appears which helps you to specify certain movements. The PosID tab shows the current position of the PosID. If your instrument is not fitted with a PosID, the PosID tab is not displayed. Figure 5-7: Move PosID dialog box 44 Gemini Software Manual V4.0 March 2002

53 TECAN 5 - Configuration Editor 5.3 Configuring racks A rack is an object such as a microplate which has one or more containers (wells) which are available for liquids or samples. Racks are placed on carriers. Carriers can be located at various positions on the worktable (see Figure 5-2 on page 35). Figure 5-8: Edit Rack dialog box The following explains the options in the Edit Rack dialog box. See Rack Wizard on page 53 for information on creating new racks. Caution: On delivery, the database of the Genesis software package already includes information on all standard Tecan carriers, racks and containers. It is recommended not to change the properties of the predefined standard Tecan objects. Copy the object to a new name if you want to alter any of the properties. Position panel This specifies the X, Y and Z coordinates of the wells in the rack (see Table 5-11 on page 48 for more information). The coordinates are normally set by manually moving the LiHa above the first and last positions on the rack and clicking the < buttons (see Teaching the rack coordinates on page 49). March 2002 Gemini Software Manual V4.0 45

54 5 - Configuration Editor TECAN Type panel Choose the rack type. See Rack types on page 51 for more information on this topic. Rack panel This specifies the well geometry: Wells (X): Specify the total number of wells in the X-direction (max. 128). Wells (Y): Specify the total number of wells in the Y-direction (max. 128). Color panel You can choose a unique color here to make it easier for you to identify this rack type in the Worktable window. The default rack colors are as follows: Microplate racks: blue Tube racks: green DiTi racks: red Washstation racks: yellow Default for all other rack types: blue Y-distance of wells Check that the Y-distance (the spacing between adjacent wells) which is shown graphically by the vertical bar lies within the green area (see Y-distance of wells on page 52). If the vertical bar lies within the red area, you may have specified the coordinates incorrectly or inaccurately. Well panel Tip-Touching Distance or X offset while pipetting This parameter is used when you activate tip touching for the liquid class in the pipetting script. When tip touching is activated, Gemini dispenses to the destination container in the normal way, but then moves the tips to the side of the well and back before retracting them. This helps to remove any drops which may be adhering to the tip. Gemini also uses this parameter if you select an offset (non-center) x-position for aspiration. This is done on the Aspiration tab of the liquid class and is mainly used for the Te-MagS. Tips per well This is used to enter the number of tips which can access the well at the same time. Specify 1 for normal wells. Specify the appropriate number for troughs (e.g. 8 for a Trough 100ml). 46 Gemini Software Manual V4.0 March 2002

55 TECAN 5 - Configuration Editor flat / round / v-shaped Select the shape of the bottom of the well. Depth of bottom For a well with a v-shaped bottom, specify the vertical distance in mm from the lowest point of the v (Z-max) to the beginning of the cylindrical part of the well. Area Specify the area of the well in mm². Click to display a dialog box which helps you to calculate the area from the diameter or from the length and the width. Note: Troughs are normally specified with length and width. To do this, click and press the Delete key to delete the diameter value. The length and width fields will then become active. Position during definition Specify the carrier, grid and site that you want to use to define the rack: Choose the carrier from the list, specify the grid position and the site. An easy way to choose the correct carrier, grid, site and rack is to click on the object in the Worktable window (this does not apply to RoMa only carriers, which are hidden). Caution: Please choose the correct site before specifying any coordinates. Otherwise the tips might move to the wrong position on the worktable. Allowed Carriers and Sites For each of the carriers which can be used with the rack, check the checkboxes alongside the allowed sites. Piercing panel If you activate this option, Gemini executes special movements for septum piercing when accessing the rack. It will pierce from Z-Travel to Z-Start and then retract from Z- Start to Z-Travel. Liquid level detection is not available with this option activated. Pierce with Specify the piercing speed in mm/s. Retract with Specify the retract speed after piercing in mm/s. March 2002 Gemini Software Manual V4.0 47

56 5 - Configuration Editor TECAN Precise Positioning panel If you activate this option, Gemini executes a special movement to increase positioning accuracy, e.g. for 1536 well plates. When accessing a rack for the first time in a sequence of pipetting commands, it makes a normal move to X-Start/Y-Start. It then makes a high resolution move to the actual pipetting position. This sequence of movements eliminates mechanical backlash and ensures the highest possible accuracy. X-Start should be set to ca. 0.4 cm to the left of the first well in the rack. Y- Start should be set to ca. 0.4 cm behind the first well in the rack. Note: The first well is at the rear left of the rack. X-Start Specify the required X-Start position for the precise X movement. Besides typing the position manually, you can teach the position with the < and M buttons. Y-Start Specify the required Y-Start position for the precise Y movement. Besides typing the position manually, you can teach the position with the < and M buttons. Move with Specify the speed for the precise positioning movement in mm/s Rack coordinates The following table describes the X, Y and Z coordinates for racks: Coordinate X,Y Z-Travel Z-Dispense Table 5-11: Position / Function At this position, the tip is situated above the well/tube of the first/last position on the rack. See Table 5-12 on page 51 for additional information on racks with offsets. Height at which the tip moves from one X/Y position to another. At this position, the tip should be above the highest point of the well/tube of the rack. Movements that cross different racks always use the highest Z-Travel value which is defined. Tip height at which liquid is dispensed. Gemini dispenses liquid into the rack at this position. It should be low enough to ensure that liquid cannot drop into the adjacent wells/tubes. X, Y and Z coordinates for racks 48 Gemini Software Manual V4.0 March 2002

57 TECAN 5 - Configuration Editor Coordinate Z-Start Position / Function Tip height at which the liquid detection (ILID) is switched on during a search for liquid operation. It is usually slightly above the rim of the liquid container. On the one hand, Z-Start should be chosen as low as possible for fast detection; on the other hand, Z-Start must be above the highest liquid level in the well/tube or the liquid will not be detected. Z-Max Table 5-11: This position is the lowest point of the well/tube of the rack and is the lowest possible position the tip is allowed to reach. During a search for liquid operation, the instrument will search for liquid from Z-Start down to Z-Max. X, Y and Z coordinates for racks (Continued) The figure below illustrates the different Z positions: Figure 5-9: Z positions for a tube Teaching the rack coordinates Teaching is the process of showing Gemini the required positions on the worktable by physically moving the LiHa (see the table Moving the LiHa using the numeric keypad on page 38) and then clicking the appropriate buttons in the dialog boxes. March 2002 Gemini Software Manual V4.0 49

58 5 - Configuration Editor TECAN The rack coordinates are shown in the Position panel of the Edit Rack dialog box. Next to the coordinates you can see several buttons labeled with < and M. Click the < buttons to copy the current LiHa coordinates (as shown in the LIHA tab of the Move dialog box) to the position fields in the Edit Rack dialog box. Tip: If you click the M buttons, this moves the LiHa to the coordinates shown in the Edit Rack dialog box. The tips first lift as far as possible, then the LiHa moves to the new position and the tips move back to the previous height. The LIHA tab of the Move dialog box will be updated accordingly. Proceed as follows to teach Gemini the X and Y coordinates of the rack: Specify the carrier, grid and site that you want to use to define the rack: Choose the carrier from the list, specify the grid position and the site. An easy way to choose the correct carrier, grid, site and rack is to click on the object in the Worktable window (this does not apply to RoMa only carriers, which are hidden). Move the LiHa above the first well of the rack (at the rear left of the rack) and click the corresponding < button. This copies the current LiHa X and Y coordinates to the position fields in the Edit Rack dialog box. Move the LiHa above the last well of the rack (at the front right of the rack) and click the corresponding < button. This copies the current LiHa X and Y coordinates to the position fields in the Edit Rack dialog box. For racks with offsets, you also need to move the LiHa above the first well of the second column and click the < button next to the field Y2 (column 2)". See Table5-12onpage51. Proceed as follows to teach Gemini the Z coordinates of the rack: Specify the carrier, grid and site that you want to use to define the rack: Choose the carrier from the list, specify the grid position and the site. An easy way to choose the correct carrier, grid, site and rack is to click on the object in the Worktable window (this does not apply to RoMa only carriers, which are hidden). Move the LiHa to the Z-Travel position above the first well of the rack and click the corresponding < button. This copies the current LiHa Z coordinate to the Z-Travel field in the Edit Rack dialog box. Repeat this process for the Z-Dispense, Z-Start and Z-Max positions. 50 Gemini Software Manual V4.0 March 2002

59 TECAN 5 - Configuration Editor Rack types The following table describes the two rack types supported by Gemini: Type Name Comment Rectangular rack Rectangular rack with offset This is a rack where the wells are arranged in rows and columns, e.g. a microplate. The first well is rear left; the last well is right front. This rack is similar to the rectangular type, but every second column is displaced in the +Y direction. The spacing of the wells in the Y direction are the same for all columns. In addition to the X and Y positions of the first and the last well, you must also specify the first well of the second column with Y2 (column 2). Table 5-12: Rack types When defining the rack type, you also have to select the intended usage of the rack. Gemini supports the following options: Cleaner Short (part of a wash station) Cleaner Long (part of a wash station) Waste (part of a wash station) DITIType1,DITIType2,DITIType3,DITIType4 DITI Waste Regular System Vac. Sep. (Vacuum Separator) Mag. Sep. (Magnetic Beads Separator) Shaker Cleaner NPS (part of NPS wash station) Cleaner LowVol (part of LowVol wash station) Te-MO DITI Te-MO Tipblock Te-MO DITI Waste Te-MO Wash station Te-MO Trough March 2002 Gemini Software Manual V4.0 51

60 5 - Configuration Editor TECAN When defining a DITI rack, you also have to specify DITI Capacity and DITI Offset. You can define up to four DITI types. When Gemini is first installed, DITI Type 1 is the 200 µl DITI, Type 2 is the 1000 µl DITI and Type 3 is the 10 µl Low Volume DITI. Type 4 can be used for custom DITI sizes and lengths. When defining a Te-MagS (Tecan magnetic bead separator device), you also have to specify Plate Type and Z-offset. The plate type ensures that the Te-MagS moves to the correct positions when performing an operation. When the Te-MagS moves to the incubation position, it slightly lifts the plate. This distance is specified in the Z-Offset field as a negative value. Y-distance of wells If the pipetting operation specifies the use of more than one tip, Gemini adjusts the spacing between the tips in the Y direction to allow pipetting to take place on several wells simultaneously if possible. The tips are spread by a servo motor on the LiHa and the spacing is subject to physical limitations. The minimum spacing between adjacent tips is 9 mm and the maximum spacing is 38 mm, as shown by the light green area in the middle of the indicator. Gemini calculates the Y-distance (the spacing between adjacent wells) from the rack coordinates and the number of wells you have specified. This is shown by a vertical line which is colored either dark green or dark red. To optimize pipetting speed, the vertical line should lie within the green area. If the vertical line lies within the red area, you may have specified the coordinates incorrectly or inaccurately. Alternatively, you are using a rack with a non-standard design. The yellow line shows half of the minimum Y-distance (i.e. 4.5 mm). If you are using microplates with 384 wells and choose this Y-distance, pipetting can take place simultaneously to every other well. 52 Gemini Software Manual V4.0 March 2002

61 TECAN 5 - Configuration Editor 5.4 Rack Wizard The Rack Wizard guides you through the process of creating a new rack for the Gemini Configuration. To start the Wizard, choose Configuration in the Setup menu, click the Racks tab and click New. Then enter a name of your choice for the new rack and click OK. Rack Wizard, step 1 of 5 This step specifies basic settings for the rack. Figure 5-10: Rack Wizard, step 1 of 5 Define the arrangement of the wells on your rack The following list illustrates the two rack types supported by Gemini: Type Name Comment Rectangular rack This is a rack where the wells are arranged in rows and columns, e.g. a microplate. The first well is rear left; the last well is right front. Table 5-13: Rack types March 2002 Gemini Software Manual V4.0 53

62 5 - Configuration Editor TECAN Rectangular rack with offset This rack is similar to the rectangular type, but every second column is displaced in the +Y direction. The spacing of the wells in the Y direction are the same for all columns. In addition to the X and Y positions of the first and the last well, you must also specify the first well of the second column with Y2 (column 2). Table 5-13: Rack types Select the intended usage of the rack See page 51 for a list of the supported options. When defining a DITI rack, you also have to specify DITI Capacity and DITI Offset. You can define up to four DITI types. When Gemini is first installed, DITI Type 1 is the 200 µl DITI, Type 2 is the 1000 µl DITI and Type 3 is the 10 µl Low Volume DITI. Type 4 can be used for custom DITI sizes and lengths. When defining a Te-MagS (Tecan magnetic bead separator device), you also have to specify Plate Type and Z-offset. The plate type ensures that the Te-MagS moves to the correct positions when performing an operation. When the Te-MagS moves to the incubation position, it slightly lifts the plate. This distance is specified in the Z-Offset field as a negative value. Select the worktable color of your rack You can choose a unique color here to make it easier for you to identify this rack type in the Worktable window. The default rack colors are as follows: Microplate racks: blue Tube racks: green DiTi racks: red Washstation racks: yellow Default for all other rack types: blue. 54 Gemini Software Manual V4.0 March 2002

63 TECAN 5 - Configuration Editor Rack Wizard, step 2 of 5 This step specifies well parameters for the rack. Figure 5-11: Rack Wizard, step 2 of 5 Define the number of wells on your rack Columns Specify the total number of wells in the X-direction (max. 128). Rows Specify the total number of wells in the Y-direction (max. 128). Select the shape of the wells on your rack flat / round / v-shape Select the shape of the bottom of the well. Height of v For a well with a v-shaped bottom, specify the vertical distance in mm from the lowest point of the v (Z-max) to the beginning of the cylindrical part of the well. March 2002 Gemini Software Manual V4.0 55

64 5 - Configuration Editor TECAN Definetheareaofthewellsonyourrack Specify the area of each well in mm². Click Calculate area to display a dialog box which helps you to calculate the area from the diameter or from the length and the width. Note: Troughs are normally specified with length and width. To do this, click Calculate area and press the Delete key to delete the diameter value. The length and width fields will then become active. Specify how many tips can access the well simultaneously Specify the number of tips which can access the well at the same time. Specify 1 for normal wells. Specify the appropriate number for troughs (e.g. 8 for a Trough 100ml). Set the tip-touching distance or the x-offset while pipetting This parameter is used when you activate tip touching for the liquid class in the pipetting script. When tip touching is activated, Gemini dispenses to the destination container in the normal way, but then moves the tips to the side of the well and back before retracting them. This helps to remove any drops which may be adhering to the tip. Gemini also uses this parameter if you select an offset (non-center) x-position for aspiration. This is done on the Aspiration tab of the liquid class and is mainly used for the Te-MagS. 56 Gemini Software Manual V4.0 March 2002

65 TECAN 5 - Configuration Editor Rack Wizard, step 3 of 5 This step specifies the rack coordinates. It also opens the Move dialog box (not visible in the Figure) to help you with positioning. Figure 5-12: Rack Wizard, step 3 of 5 Select the position on the worktable for teaching your rack Teaching is the process of showing Gemini the required positions on the worktable by physically moving the LiHa (see the table: Moving the LiHa using the numeric keypad on page 38) and then clicking the appropriate buttons in the dialog boxes. Specify the carrier, grid and site that you want to use to define the rack: Choose the carrier from the list, specify the grid position and the site. An easy way to choose the correct carrier, grid, site and rack is to click on the object in the Worktable window (this does not apply to RoMa only carriers, which are hidden). Teach the coordinates of the first and last well of your rack Move the LiHa above the first well of the rack (at the rear left of the rack) and click the corresponding Get button. This copies the current LiHa X and Y coordinates to the position fields in the dialog box. Move the LiHa above the last well of the rack (at the front right of the rack) and click the corresponding Get button. This copies the current LiHa X and Y coordinates to the position fields in the dialog box. See Rack coordinates on page 48 for more information on this topic. March 2002 Gemini Software Manual V4.0 57

66 5 - Configuration Editor TECAN For racks with offsets, you also need to move the LiHa above the first well of the second column and click the Get button next to the field Y2 (column 2)". See Table 5-12 on page 51. Tip: IfyouclicktheMove To buttons, this moves the LiHa to the X and Y coordinates shown in the dialog box. Y-distance of wells Check that the Y-distance (the spacing between adjacent wells) which is shown graphically by the vertical bar lies within the green area (see Y-distance of wells on page 52). If the vertical bar lies within the red area, you may have specified the coordinates incorrectly or inaccurately. Teach the Z coordinates of the wells in your rack Move the LiHa to the Z-Travel position above the first well of the rack and click the corresponding Get button. This copies the current LiHa Z coordinate to the Z-Travel field in the dialog box. Repeat this process for the Z-Dispense, Z-Start and Z-Max positions. See Rack coordinates on page 48 for more information on this topic. Tip: If you click the Move To buttons, this moves the LiHa to the Z coordinates shown in the dialog box. 58 Gemini Software Manual V4.0 March 2002

67 TECAN 5 - Configuration Editor Rack Wizard, step 4 of 5 This step specifies the carrier and site assignments for the rack. Figure 5-13: Rack Wizard, step 4 of 5 Define the allowed sites on the carriers for your rack For each of the carriers which will be used with the new rack, check the checkboxes alongside the allowed sites. March 2002 Gemini Software Manual V4.0 59

68 5 - Configuration Editor TECAN Rack Wizard, step 5 of 5 This step specifies settings for septum piercing and precise positioning. Figure 5-14: Rack Wizard, step 5 of 5 Define the septum piercing parameters for your rack Pierce through septum If you activate this option, Gemini executes special piercing movements when accessing the rack. It will pierce from Z-Travel to Z-Start and then retract from Z- Start to Z-Travel. Liquid level detection is not available with this option activated. Pierce with Specify the piercing speed in mm/s. Retract with Specify the retract speed after piercing in mm/s. Teach the start coordinates for precise positioning moves of your rack Precise Positioning If you activate this option, Gemini executes a special movement to increase positioning accuracy, e.g. for 1536 well plates. When accessing a rack for the first time in a sequence of pipetting commands, it makes a normal move to X-Start/Y- Start. It then makes a high resolution move to the actual pipetting position. This sequence of movements eliminates mechanical backlash and ensures the highest possible accuracy. X-Start should be set to ca. 0.4 cm to the left of the first well in the 60 Gemini Software Manual V4.0 March 2002

69 TECAN 5 - Configuration Editor rack. Y-Start should be set to ca. 0.4 cm behind the first well in the rack. Note: The first well is at the rear left of the rack. X-Start Teach the required X-Start position for the precise X movement: Move the LiHa above the X-Start position and click the corresponding Get button. This copies the current LiHa X coordinate to the X-Start field. Y-Start Teach the required Y-Start position for the precise Y movement: Move the LiHa above the Y-Start position and click the corresponding Get button. This copies the current LiHa Y coordinate to the Y-Start field. Move with Specify the speed for the precise positioning movement in mm/s. Finishing the configuration When you are finished, click Finish to store the new rack in the Gemini Configuration. March 2002 Gemini Software Manual V4.0 61

70 5 - Configuration Editor TECAN 5.5 Configuring carriers A carrier is an object such as a 3 position microplate carrier that sits on the worktable of the GENESIS instrument and can carry one or more racks. Carriers can be located at various positions on the worktable. Figure 5-15: Edit Carrier dialog box The following explains the options in the Edit Carrier dialog box. See Carrier Wizard on page 66 for information on creating new carriers. I: Caution: On delivery, the database of the Genesis software package already includes information on all standard Tecan carriers, racks and containers. It is recommended not to change the properties of the predefined standard Tecan objects. Copy the object to a new name if you want to alter any of the properties. Dimensions panel Specify the X and Y dimensions of the carrier outline in millimeters. See the illustration on page 64. Reference offsets panel The X reference offset is the distance in millimeters between the left edge of the carrier and the closest locating pin on the worktable below the carrier. The Y reference offset is the distance in millimeters between the rear edge of the carrier and the closest locating pin on the worktable below the carrier. The Z reference offset is the vertical distance in 62 Gemini Software Manual V4.0 March 2002

71 TECAN 5 - Configuration Editor millimeters between the top surface of the worktable and the bottom edge of a rack on the carrier. See the illustrations on page 64 and page 65. Barcode panel Specify the barcode ID for the carrier. This is the number shown on the barcode label at the end of the carrier. All standard Tecan carriers have a unique barcode ID. Only use barcode numbers in the range 500 to 999 for custom carriers. If the PosID cannot scan the carrier or racks on the carrier, e.g. due to a special carrier design, please set the barcode field to 0. You cannot specify a barcode for a RoMa only carrier. Sites panel Specify the number of sites on the carrier which are available for racks. Color panel You can choose a unique color here to make it easier for you to identify this carrier type in the Worktable window. The default color for carriers is gray. Type panel If the carrier is intended for a special device or option, choose the option from the popup list Type. The available options are Te-MO, Te-Stack, Carousel, Centrifuge and Reader (i.e. photometer). Otherwise you should leave this field at the default setting (blank). Check the For use with ROMA only checkbox if the carrier is only used by the RoMa or the PnP and not for pipetting with the LiHa. In this case, the carrier is no longer visible in the carrier list in the Worktable window and can only be used for defining RoMa and PnP vectors. Check the Hide from List of Carrier on worktable checkbox to remove the carrier from the carrier list in the Worktable window. This can be used to hide carriers that are not normally used. Site panel The X offset for sites is the distance in millimeters between the left edge of the carrier and the left edge of a rack at the respective site. The Y offset for sites is the distance in millimeters between the rear edge of the carrier and the rear edge of a rack at the respective site. The Z offset for sites is normally "0" and is only specified non-zero if the sites on the carrier are not at the same height. You can specify either negative or positive values in this case. X-Size and Y-Size are the outline dimensions of the site. See the illustrations on page 64 and page 65. Shape must always be Rectangle. March 2002 Gemini Software Manual V4.0 63

72 5 - Configuration Editor TECAN Carrier dimensions and X/Y offsets The figure below shows how to define the various dimensions for a carrier. The example is for the standard Tecan carrier Microplate, 3 Pos., landscape. As shown, this carrier design has a nose which extends beyond the rear edge. The locating pins shown in the figure are attached to the worktable and normally hidden from view by the carrier. Figure 5-16: Carrier dimensions and X/Y offsets 64 Gemini Software Manual V4.0 March 2002

73 TECAN 5 - Configuration Editor Z offsets for carriers The figure below shows how to specify the reference offset Z (the vertical distance in millimeters between the top surface of the worktable and the bottom edge of a rack on the carrier). The reference offset Z does not refer to the top edge of objects such as reagent troughs or racks which are placed on the carrier. Figure 5-17: Specifying the Z offset for carriers Custom objects Proceed as follows if you want to define a custom object which is neither a carrier nor a rack (i.e. it cannot be disassembled into a carrier and one or more racks). Define it as a new carrier and only specify X and Y Dimensions for the carrier and X and Y Size for the site. Then define a new rack, assign it to the site, specify the grid position and measure its coordinates as described in Moving the arms on page 37. Then save the configuration and use the custom object on the worktable anywhere where it is required. March 2002 Gemini Software Manual V4.0 65

74 5 - Configuration Editor TECAN 5.6 Carrier Wizard The Carrier Wizard guides you through the process of creating a new carrier for the Gemini Configuration. To start the Wizard, choose Configuration in the Setup menu, click the Carriers tab and click New. Then enter a name of your choice for the new carrier and click OK. Carrier Wizard, step 1 of 3 This step specifies basic settings for the carrier. Figure 5-18: Carrier Wizard, step 1 of 3 Define the dimensions of your carrier Specify the X and Y dimensions of the carrier outline in millimeters. See Carrier dimensions and X/Y offsets on page 64 for more information. Select the number of sites on your carrier Specify the number of sites on the carrier which will be available for racks. Select the worktable color of your carrier You can choose a unique color here to make it easier for you to identify this carrier type in the Worktable window. The default color for carriers is gray. 66 Gemini Software Manual V4.0 March 2002

75 TECAN 5 - Configuration Editor Carrier Wizard, step 2 of 3 This step specifies additional parameters for your carrier. Figure 5-19: Carrier Wizard, step 2 of 3 Define the barcode of your carrier Specify the barcode ID for the carrier. This is the number shown on the barcode label at the end of the carrier. All standard Tecan carriers have a barcode. Only use barcode numbers in the range 500 to 999 for custom carriers. If the PosID cannot scan the carrier or racks on the carrier, e.g. due to a special carrier design, please set the barcode field to 0. You cannot specify a barcode for a RoMa only carrier. Select the type of your carrier If the carrier is intended for a special device or option, choose the option from the popup list Type. The available options are Te-MO, Te-Stack, Carousel, Centrifuge and Reader (i.e. photometer). Otherwise you should leave this field at the default setting (blank). Specify the usage of your carrier Check the For use with ROMA only checkbox if the carrier is only used by the RoMa or the PnP and not for pipetting with the LiHa. In this case, the carrier is no longer visible in the carrier list in the Worktable window and can only be used for defining RoMa and PnP vectors. Check the Hide from List of Carrier on worktable checkbox to remove the carrier from the carrier list in the Worktable window. This can be used to hide carriers that are not normally used. March 2002 Gemini Software Manual V4.0 67

76 5 - Configuration Editor TECAN Carrier Wizard, step 3 of 3 This step specifies offsets and site parameters for your carrier. Figure 5-20: Carrier Wizard, step 3 of 3 Define the reference offsets for your carrier The X reference offset is the distance between the left edge of the carrier and the closest locating pin on the worktable below the carrier. The Y reference offset is the distance between the rear edge of the carrier and the closest locating pin on the worktable below the carrier. The Z reference offset is the vertical distance between the top surface of the worktable and the bottom edge of a rack on the carrier. See the illustrations on page 64 and page 65. Definethesiteparametersofyourcarrier The X offset for sites is the distance between the left edge of the carrier and the left edge of a rack at the respective site. The Y offset for sites is the distance between the rear edge of the carrier and the rear edge of a rack at the respective site The Z offset for sites is normally 0 and is only specified non-zero if the sites on the carrier are not at the same height. You can specify either negative or positive values in this case. X-Size and Y-Size are the outline dimensions of the site. See the illustrations on page 64 and page 65. Shape must always be Rectangle. Finishing the configuration When you are finished, click Finish to store the new carrier in the Gemini Configuration. 68 Gemini Software Manual V4.0 March 2002

77 TECAN 5 - Configuration Editor 5.7 Defining RoMa vectors The RoMa is a robotic arm with gripper fingers that can grip and move objects within the working area of the GENESIS instrument. It can be used to transport microplates, reagent blocks, deep well plates, etc. between carriers, incubators and storage positions (e.g. a RoMa shelf or carousel). Current GENESIS Freedom versions can be fittedwithuptotworomas. RoMa actions such as getting a plate from a RoMa hotel or putting it onto a carrier can be stored in the Configuration. Each RoMa action is called a RoMa vector, which is a predefined sequence of RoMa positions (called waypoints). RoMa vectors can consist of 1 to 10 waypoints. See RoMa vectors on page 208 for more information on defining RoMa vectors. Figure 5-21: Edit RoMa Vector dialog box The following explains the options in the Edit RoMa Vector dialog box. See RoMa Vector Wizard on page 73 for information on creating new RoMa vectors. Coordinates panel This shows the RoMa positions (waypoints) which are used for the RoMa vector. The following buttons can be used to edit, insert and delete waypoints. Buttons are also provided to move the RoMa along the specified waypoints: March 2002 Gemini Software Manual V4.0 69

78 5 - Configuration Editor TECAN << This button copies the current RoMa position (as shown in the ROMA tab of the Move dialog box) to the selected entry in the waypoint list. Move This button move the RoMa to the coordinates of the selected entry in the waypoint list. The ROMA tab of the Move dialog box will be updated accordingly. New This button inserts a new entry in the waypoint list above the currently selected entry. Delete This button deletes the currently selected entry in the waypoint list. move to Safe Position This button moves the RoMa along the defined waypoints from the selected waypoint to the Safe Position. move to End Position This button moves the RoMa along the defined waypoints from the selected waypoint to the final position of the RoMa vector. Note: The buttons <<, Move, New, Delete, move to Safe Position and move to End Position are only active after you have selected an entry (i.e. an entire row) in the waypoint list. To select an entry, click one of the buttons labeled 1 to 10 to the left of the entry. The Adjust button is only available if the carrier is only used for the RoMa and not for pipetting with the LiHa. It is used to adjust the RoMa position for a specified, single site to compensate for small manufacturing inaccuracies in a multi-site RoMa carrier without needing to switch to the carrier definition. To use the Adjust button, move the RoMa to the End Position of the specified site. Then click the Adjust button to modify the carrier definition to match the current X, Y and Z coordinates. Also see Defining the home position for a RoMa on page 216. XYZ Speed Specify the speed for x, y and z movements. Rotator speed Specify the speed for rotator movements. 70 Gemini Software Manual V4.0 March 2002

79 TECAN 5 - Configuration Editor Grip Parameters panel Grip Distance This is the distance in mm that the RoMa gripper closes to when gripping an object (range mm). It should be about 1-2 mm less than the width of the object. The minimum grip distance for the RoMa is 55 mm. Release Distance This is the distance in mm that the RoMa gripper opens to when releasing an object (range mm). It should be about 3-4 mm more than the width of the object. Force This is the force that the gripper uses when gripping an object. The force is specified by a number between 0 and 249. Higher numbers mean more force. Speed This is the speed in mm/s with which the gripper tries to grip an object. Grip If you click this button the gripper closes to the specified gripping distance. If the RoMa Is moved, the gripper remains at the specified gripping distance until the Release button is clicked. Release If you click this button the gripper opens to the specified release distance. Carrier panel Specify the carrier, grid and site that you want to use to define the RoMa vector: Choose the carrier from the list, specify the grid position and the site. An easy way to choose the correct carrier, grid, site and rack is to click on the object in the Worktable window (this does not apply to RoMa only carriers, which are hidden). Caution: Please choose the correct site before specifying any coordinates or using any of the movement buttons. Otherwise the RoMa might move to the wrong position on the worktable. Carrier Choose the required carrier. Grid Choose the grid position of the carrier. The Grid field is inactive (gray) if you have chosen a RoMa only carrier because it is not shown in the Worktable window. March 2002 Gemini Software Manual V4.0 71

80 5 - Configuration Editor TECAN Site Choose the site on the carrier. The Site field is inactive (gray) if the carrier only has one site. 72 Gemini Software Manual V4.0 March 2002

81 TECAN 5 - Configuration Editor 5.8 RoMa Vector Wizard The RoMa Vector Wizard guides you through the process of creating a new RoMa vector for the Gemini Configuration. To start the Wizard, choose Configuration in the Setup menu click the RoMa Vectors tab and click New. Then enter a name of your choice for the RoMa vector and click OK. RoMa Vector Wizard, step 1 of 2 This step specifies basic settings for the RoMa vector. Figure 5-22: RoMa Vector Wizard, step 1 of 2 Define the carrier you are using for the definition of the RoMa vector Specify the carrier, grid and site that you want to use to define the RoMa vector: Choose the carrier from the list, specify the grid position and the site. An easy way to choose the correct carrier, grid, site and rack is to click on the object in the Worktable window (this does not apply to RoMa only carriers, which are hidden). Specify the grip parameters Grip Distance This is the distance in mm that the RoMa gripper closes to when gripping an object (range mm). It should be about 1-2 mm less than the width of the object. Release Distance This is the distance in mm that the RoMa gripper opens to when releasing an object (range mm). It should be about 3-4 mm more than the width of the object. March 2002 Gemini Software Manual V4.0 73

82 5 - Configuration Editor TECAN Force This is the force that the gripper uses when gripping an object. The force is specified by a number between 0 and 249. Higher numbers mean more force. Speed This is the speed in mm/s with which the gripper tries to grip an object. Check the grip parameters Grip If you click this button the gripper closes to the specified gripping distance. If the RoMa Is moved, the gripper remains at the specified gripping distance until the Release button is clicked. Release If you click this button the gripper opens to the specified release distance. 74 Gemini Software Manual V4.0 March 2002

83 TECAN 5 - Configuration Editor RoMa Vector Wizard, step 2 of 2 This step specifies the speed for movements and defines the waypoints. It also opens the Move dialog box (not visible in the Figure) to help you with positioning. Figure 5-23: RoMa Vector Wizard, step 2 of 2 Define the speed for x, y and z movements and for rotator movements XYZ Speed Specify the speed for x, y and z movements in mm/s. Rotator speed Specify the speed for rotator movements in degrees/s. Define the waypoints of the RoMa vector This shows the RoMa positions (waypoints) which are used for the RoMa vector. See page 69 for more information on coordinates and waypoints and a description of the buttons. Finishing the configuration When you are finished, click Finish to store the new RoMa vector in the Gemini Configuration. March 2002 Gemini Software Manual V4.0 75

84 5 - Configuration Editor TECAN 5.9 Defining PNP Vectors The PnP is a robotic arm with gripper fingers that can grip and move tubes within the working area of the GENESIS Freedom instrument, for example to transport tubes between racks. Current GENESIS Freedom versions can be fitted with up to two PnPs. PnP actions such as getting a tube from a rack can be stored in the Configuration. Each PnP action is called a PnP vector, which is a predefined sequence of PnP positions (called waypoints). PnP vectors can consist of 1 to 10 waypoints. See PnP vectors on page 217 for information on how to use PnP vectors in scripts. Figure 5-24: Edit PnP Vector dialog box The following explains the options in the Edit PnP Vector dialog box. See PnP Vector Wizard on page 79 for information on creating new PnP vectors. Coordinates panel This shows the PnP positions (waypoints) which are used for the PnP vector. The following buttons can be used to edit, insert and delete waypoints. Buttons are also provided to move the PnP along the specified waypoints: 76 Gemini Software Manual V4.0 March 2002

85 TECAN 5 - Configuration Editor << This button copies the current PnP position (as shown in the PnP tab of the Move dialog box) to the selected entry in the waypoint list. Move This button move the PnP to the coordinates of the selected entry in the waypoint list. The PnP tab of the Move dialog box will be updated accordingly. New This button inserts a new entry in the waypoint list above the currently selected entry. Delete This button deletes the currently selected entry in the waypoint list. move to Safe Position This button moves the PnP along the defined waypoints from the selected waypoint to the Safe Position. move to End Position This button moves the PnP along the defined waypoints from the selected waypoint to the final position of the PnP vector. Note: The buttons <<, Move, New, Delete, move to Safe Position and move to End Position are only active after you have selected an entry (i.e. an entire row) in the waypoint list. To select an entry, click one of the buttons labeled 1 to 10 to the left of the entry. Also see Defining the home position for a PnP on page 224. XYZ Speed Specify the speed for x, y and z movements. Grip Parameters panel Grip Distance This is the distance in mm that the PnP gripper closes to when gripping an object (range 7-28 mm). It should be about 1-2 mm less than the width of the object. Release Distance This is the distance in mm that the PnP gripper opens to when releasing an object (range 7-28 mm). It should be about 3-4 mm more than the width of the object. Grip If you click this button the gripper closes to the specified gripping distance. If the PnP is moved, the gripper remains at the specified gripping distance until the Release button is clicked. March 2002 Gemini Software Manual V4.0 77

86 5 - Configuration Editor TECAN Release If you click this button the gripper opens to the specified release distance. Carrier & Rack panel Specify the carrier, grid, site rack and rack position that you want to use to define the PnP vector: Choose the carrier from the list, specify the grid position, the site, rack and rack position. An easy way to choose the correct carrier, grid, site and rack is to click on the object in the Worktable window (this does not apply to RoMa only carriers, which are hidden). Caution: Please choose the correct site, rack and position before specifying any coordinates or using any of the movement buttons. Otherwise the PnP might move to the wrong position on the worktable. Carrier Choose the required carrier. Grid Choose the grid position of the carrier. The Grid field is inactive (gray) if you have chosen a PnP only or RoMa only carrier because it is not shown in the Worktable window. Site Choose the site on the carrier. The Site field is inactive (gray) if the carrier only has one site. Rack Choose the required rack. Position Choose the position of the tube in the rack (counting from rear to front). 78 Gemini Software Manual V4.0 March 2002

87 TECAN 5 - Configuration Editor 5.10 PnP Vector Wizard The PnP Vector Wizard guides you through the process of creating a new PnP vector for the Gemini Configuration. To start the Wizard, choose Configuration in the Setup menu click the PnP Vectors tab and click New. Then enter a name of your choice for the PnP vector and click OK. PnP Vector Wizard, step 1 of 2 This step specifies basic settings for the PnP vector. Figure 5-25: PnP Vector Wizard, step 1 of 2 Define the carrier and rack you are using for the definition of the PnP vector Specify the carrier, grid, site rack and tube position that you want to use to define the PnP vector: Choose the carrier from the list, specify the grid position, the site, rack and tube position. An easy way to choose the correct carrier, grid, site and rack is to click on the object in the Worktable window (this does not apply to RoMa only carriers, which are hidden). You must then specify the position of the tube in the rack (counting from rear to front). Specify the grip parameters Grip Distance This is the distance in mm that the PnP gripper closes to when gripping an object (range 7-28 mm). It should be about 1-2 mm less than the width of the object. Release Distance This is the distance in mm that the PnP gripper opens to when releasing an object (range 7-28 mm). It should be about 3-4 mm more than the width of the object. March 2002 Gemini Software Manual V4.0 79

88 5 - Configuration Editor TECAN Check the grip parameters Grip If you click this button the gripper closes to the specified gripping distance. If the PnP is moved, the gripper remains at the specified gripping distance until the Release button is clicked. Release If you click this button the gripper opens to the specified release distance. 80 Gemini Software Manual V4.0 March 2002

89 TECAN 5 - Configuration Editor PnP Vector Wizard, step 2 of 2 This step specifies the speed for movements and defines the waypoints. It also opens the Move dialog box (not visible in the Figure) to help you with positioning. Figure 5-26: PnP Vector Wizard, step 2 of 2 Define the speed for x, y and z movements XYZ Speed Specify the speed for x, y and z movements in mm/s. Define the waypoints of the PnP vector This shows the PnP positions (waypoints) which are used for the PnP vector. See page 76 for more information on coordinates and waypoints and a description of the buttons. Finishing the configuration When you are finished, click Finish to store the new PnP vector in the Gemini Configuration. March 2002 Gemini Software Manual V4.0 81

90 5 - Configuration Editor TECAN 5.11 Configuring the LiHa The LiHa (Liquid Handling Arm) is a Genesis component which is mounted on the X- slide and holds the pipetting tips. This dialog box is used to specify the properties of the LiHa: Figure 5-27: LIHA dialog box The parameters that can be adjusted for each tip are as follows: Tip Type Select between Fixed, Disposable Tips (DITI) and Active Tips. Gemini automatically sets the correct default value for the tip offset. If you want to use a combination of fixed and DITI tips, the fixed tips must have lower tip numbers (e.g. fixed tips at positions 1 to 4 and DITI tips at positions 5 to 8). Tip is Broken This is used to deactivate individual tips (including the corresponding diluters and valves) if they are broken. Note: Gemini will output an error message if you use a broken tip in a script. Accordingly, it is also necessary to deselect broken tips in the script. Low Volume In simulation mode, this is used to specify that the tip is equipped with the Low Volume option. In normal mode, Gemini automatically displays the options which are reported by the GENESIS instrument. 82 Gemini Software Manual V4.0 March 2002

91 TECAN 5 - Configuration Editor Tip Offset Specify the length of the tip in instrument steps (0.1 mm). Gemini uses these values to calculate the correct Z-coordinates when using different tips in a pipetting run. The offsets are measured relative to the Reference Tip in increments of 0.1 mm. A positive value indicates that this tip type is longer than the Reference Tip. For example, 390 for Standard Tip means that the tip is 3.9 cm longer than the Reference Tip. Tip offsets should be changed with great care and there is normally no need to modify them. Diluter Capacity This parameter is the maximum volume the diluter is able to dispense or aspirate with the current syringe size. System Capacity This parameter is the system volume, i.e., the contents of the tubing from the diluter valve to the tip. Gemini limits the maximum pipetting volume to the System Capacity or the Diluter Capacity, whichever is smaller. Max. Pipetting Speed This parameter limits the maximum flow rate of liquid through the diluter when pipetting. If you define higher speeds in the pipetting script, Gemini will limit them to this value. Max. Wash Speed This parameter specifies the maximum flow rate of liquid through the diluter when washing the tips. The absolute maximum diluter speeds (pipetting or washing) for different diluter capacities are as follows: Diluter capacity in µl below 100 Maximum speed 45 µl/s µl/s µl/s µl/s µl/s 2500 and above 2250 µl/s Table 5-14: Max. pipetting and washing speeds The following describes the global parameters that can be specified for the LiHa: March 2002 Gemini Software Manual V4.0 83

92 5 - Configuration Editor TECAN Number of Tips In simulation mode, this is used to specify the number of tips. In normal mode, this entry is disabled and displays the number of tips reported by the GENESIS instrument. Number of Grids In simulation mode, this is used to specify the number of grids (i.e. the size of the instrument). In real mode, this entry is disabled and displays the number of grids reported by the GENESIS instrument. Global Z-travel Gemini retracts the tips to this height when moving between different objects on the worktable. When it moves over a single object, it uses the respective Z-Travel value instead. During pipetting, Gemini has to retract the tips to a certain travel height when moving the LiHa in the X and Y directions. When two consecutive commands employ the same rack, the tips are moved to the Z-travel height defined for that rack. However, if two consecutive commands employ different racks, the tips are retracted to the Global Z-Travel height. This is done to speed up and optimize LiHa movements. Global Z-Travel is specified in instrument steps (0.1 mm) and is set by moving the LiHa to the highest place on the worktable. Caution: Set Global Z-Travel to 0 if your Genesis Freedom is equipped with a PosID. Otherwise the tips may collide with the PosID. 84 Gemini Software Manual V4.0 March 2002

93 TECAN 5 - Configuration Editor 5.12 Configuring the PosID This dialog box is used to specify custom parameters for the PosID (Positive Identification System), which is a barcode scanner device. Note: The allowed barcode types are configured with the PosID command (see page 248). Figure 5-28: PosID dialog box Commands for Custom Racks This is used to enter firmware commands which will be sent to the PosID before the script is started. This is normally only necessary for custom racks; standard Tecan racks are handled by the PosID automatically. The following example shows the three commands which are required to define a striprack with carrier code 500, which is similar to a standard striprack with code 016: SPS1,16,3,0,200,188,7,1 SPC1,1,0,0,1 SPA500,1,1 See the manual Command Set, PosID firmware - Doc ID for a list of firmware commands. The above commands only define the custom rack for the PosID device. You must also define it as a rack in Gemini to allow it to be used in a script. Only use barcode numbers in the range 500 to 999 for custom racks. March 2002 Gemini Software Manual V4.0 85

94 5 - Configuration Editor TECAN 5.13 Configuring the MPO/LICOS The MPO (Monitored Pump Option) consists of FAWA and LICOS. The FAWA option (Fast Wash) is used to pump a larger amount of liquid at higher speed through the system, normally to rinse the tips. The LICOS option (Liquid Container Supervisor) is a device which monitors the liquid level in the waste liquid and system liquid containers. This dialog box is used to set parameters for the MPO/FAWA and for LICOS. Figure 5-29: MPO dialog box MPOflowrate MPO is normally used for washing standard tips. This option allows you to reduce the default flow rate and thus the pressure in the tubing. This can be useful when special (smaller) tips are used. LICOS If you check this box, Gemini checks the current liquid levels when the tips are washed. You can also define the levels at which a warning is output. You must use the Genesis Setup & Service software module to calibrate the LICOS. See the Genesis Instrument Software Manual - Doc ID , Setup & Service Software Module for more information. 86 Gemini Software Manual V4.0 March 2002

95 TECAN 5 - Configuration Editor 5.14 Configuring the ChemSystem The ChemSystem option allows up to 6 different system liquids to be used in your GENESIS instrument. It consists of a 6-way valve to select the required system liquid, a nitrogen valve and the vacuum assisted waste option (not available for GENESIS Freedom). The following dialog box is used to set the parameters for the ChemSystem: Figure 5-30: ChemSystem dialog box System Liquids Enter the names of the system liquids you want to use in the System Liquids panel and click OK. The available system liquids are then shown as blue/green rectangles at the bottom right of the worktable. When you specify a script command which involves aspiration, click on the blue/ green rectangle(s) if you want to aspirate the system liquid. If you need to aspirate large volumes of the system liquid, this avoids having to place a large container on the worktable. This does not allow you to choose which of the system liquids you want to aspirate. If necessary, choose the required system liquid in advance with the System command (see System command on page 252). After clicking on the blue/green rectangle(s), the gray (inactive) field in the dialog box of the pipetting command then shows System instead of a rack name. March 2002 Gemini Software Manual V4.0 87

96 5 - Configuration Editor TECAN 5.15 Configuring Active tips An Active Tip is an electrically activated tip which aspirates and dispenses very small quantities of liquid. Dispensing is metered by the active tip rather than by the diluter. Active Tips are a key component of the Tecan Nanopipetting System (NPS). This dialog box is used to set global parameters for the NPS option. These settings configure the global control parameters for each of the ActiveTips and are used to compensate for manufacturing tolerances. Tips without an Active Tip mounted are shown in gray (inactive). In simulation mode, you can specify the tip type in the LiHa dialog box. In normal mode, Gemini automatically displays the options which are reported by the GENESIS instrument. Figure 5-31: Active Tips dialog box Each Active Tip is individually tested and is supplied with its individual control parameters which are required for proper functioning. Please specify the parameters supplied with each Active Tip in the following fields: Voltage Specify the drive voltage (between 20 and 120 Volts). Frequency Specify the drive frequency (between 50 and 5000 Hz). Pulse Width Specify the drive pulse width (between 10 and 250 µs). All tips are the same If you activate this option, the parameters of all tips are set to the same values as the first tip fitted with an Active Tip. 88 Gemini Software Manual V4.0 March 2002

97 TECAN 5 - Configuration Editor 5.16 Safety features for the Genesis instrument The Access/Status option for the Genesis instrument consists of up to four electricallyoperated doorlocks for safety cabinets or safety screens which surround the instrument to prevent access while the instrument is operating and a status lamps/siren unit which can be mounted next to or above the instrument at a conspicuous position to ensure that it is visible to the operator from some distance away. The doorlocks can be manually opened and closed by choosing Doorlocks in the Execute menu. They can also be controlled from within a script using the Doorlocks command. Gemini controls the status of the status lamps/siren unit as follows: Green, red and siren are off: Gemini is idle (not executing a script). Green is continuously lit: A script is running and everything is ok. Green is flashing: The script command "User prompt", "Set Variable" with user query or "Set String variable" with user query is currently waiting for user input. Red is flashing and the siren is on: An error message is being displayed. March 2002 Gemini Software Manual V4.0 89

98 5 - Configuration Editor TECAN 5.17 Configuring the Doorlocks Gemini supports up to four doorlocks and the doorlocks are arranged in groups. This dialog box is used to assigned each of the doorlocks to one of the four available groups. The doorlocks of all groups are closed automatically when starting or re-starting a script. The doorlocks of all groups are opened automatically when finishing, stopping or pausing the script. Use the Doorlocks command in your script to open the doorlocks in a specified group while the script is running to allow the operator to access to the instrument. Figure 5-32: Doorlocks dialog box Groups panel Specify the required doorlock group assignment for each of the doorlocks by choosing the required group from the list. Choose the blank entry instead if the doorlock is not fitted to your instrument. 90 Gemini Software Manual V4.0 March 2002

99 TECAN 6 - Liquid Classes 6 Liquid Classes A liquid class is a set of liquid handling parameters. It specifies speeds, airgaps, detection modes, etc. Gemini contains a number of predefined liquid classes which are based on the extensive experience of the Tecan liquid handling specialists. Gemini stores the liquid classes for all scripts in a single file (LClasses.dat in the Gemini/Data directory) and has an editor for displaying, creating and deleting liquid classes. 6.1 Liquid Classes Editor Choose Liquid Classes in the Setup menu to open the liquid classes editor: Figure 6-1: Liquid classes editor The left side of the window shows a list of standard liquid classes ( liquid classes which you have defined ( ). ) and the custom Note: You cannot change the properties of the predefined standard liquid classes. However, you can define a new custom class with the same properties and then change them. March 2002 Gemini Software Manual V4.0 91

100 6 - Liquid Classes TECAN Each liquid class is divided into subclasses. Click the + symbol in front of a liquid class or double-click the liquid class name to show its subclasses. The + symbol then changes to a - symbol. Click the - symbol to hide the subclasses again. A subclass is characterized by the tip type and volume range for which its parameters are defined. During script runtime, Gemini selects the liquid class and subclass that best matches the liquid class name, the currently used tip type and the pipetting volume. If you choose an item in the liquid classes list, Gemini displays one or more parameter pages in the right side of the window. The parameter pages are described in more detail in the following chapters. New Class Click this button to create a new liquid class using one of the existing classes as a template. New Entry Click this button to create a new subclass. Delete Click this button to delete the currently selected liquid class or subclass. Print Click this button to print information on the currently selected liquid class (including every subclass) or subclass (single page) as a report. You are first shown a print preview window. Click the Printer button in the menu bar of the print preview window to print the report. 92 Gemini Software Manual V4.0 March 2002

101 TECAN 6 - Liquid Classes Global parameters Gemini uses these parameters for all subclasses of the selected liquid class. Figure 6-2: Global parameters for liquid classes Name Specify the name of the liquid class. Liquid Detection Specify the liquid detection parameters. Specify the Detection Mode, the Liquid Conductivity, the Detection Speed and the Double Distance (only necessary when a detection mode with double detection is selected). Clot Detection Specify the clot detection parameter. Specify the Detection Speed and the Clot Limit. March 2002 Gemini Software Manual V4.0 93

102 6 - Liquid Classes TECAN Type parameters Gemini uses these parameters to select the best suited subclass for a specified tip type and pipetting volume. Figure 6-3: Type parameters for liquid classes Tip Type Select the tip type from the available choices: Standard, DITI, Std. & Low Vol. (standard tips with low volume option), DITI & Low Vol. (disposable tips with low volume option), Active Tips (tips for the GENESIS NPS Instrument), Te-MO Fixed tips and Te-MO DITI tips. Volume Range If you check the Use for All Volumes checkbox, the Aspirate, Dispense and Calibration parameters for this subclass are valid for all pipetting volumes. If this box is not checked, you must specify the Minimum Volume and Maximum Volume. Gemini will then use this subclass during pipetting if the following expression is true: Minimum Volume pipetting volume < Maximum Volume 94 Gemini Software Manual V4.0 March 2002

103 TECAN 6 - Liquid Classes Aspirate parameters Gemini uses these parameters when aspirating or mixing. The illustrations in the top right of the window show graphically the current settings for single and multi pipetting. Vol. stands for the pipetted volume. Figure 6-4: Aspirate parameters for liquid classes Aspiration Speed Specify the aspiration speed. Delay Specify the delay after aspiration. System Trailing Airgap (STAG) Specify the volume of the system trailing airgap. Gemini uses the aspiration speed specified for the leading airgap for the system trailing airgap, too. Leading Airgap (LAG) Specify the volume, aspiration speed, and delay after aspiration. Click the to edit aspiration speed and delay after aspiration. button March 2002 Gemini Software Manual V4.0 95

104 6 - Liquid Classes TECAN Trailing Airgap (TAG) Set the volume, aspiration speed, and delay after aspiration. Click the edit aspiration speed and delay after aspiration. button to Excess Volume Specify the excess Volume (in µl or %). Click the button to select the position to use for discarding the excess volume (Discardtowasteor Back to vessel). Specify a digit in the Replace after field to discard the excess volume after re-using it several times (e.g. to save costs). This only applies if excess volume > 0 and if you are using multi-pipetting. Conditioning Volume Specify the Conditioning Volume here. Click the use for discarding the excess volume. button to select the position to Use Pinch Valve This is used to activate the Low Volume option if your GENESIS instrument is fitted with this option. Use Liquid Detection Check this box if you want to activate liquid detection. Gemini uses the detection mode, liquid conductivity, detection speed and double distance settings which you defined on the Global dialog box for the liquid class. Liquid detection during aspiration is necessary e.g. to ensure minimal tip contamination by limiting the submersion depth. Aspiration Position Specify the Z-position and the offset of the tips when aspirating. A positive value for the offset lowers the tip. You can also specify the x-position during aspiration: Center: as defined for the rack which is used Left: left of center, offset as defined in X offset while pipetting for the rack which is used Right: right of center, offset as defined in X offset while pipetting for the rack which is used Left / Right: left of center for odd columns, right of center for even columns of the rack which is used Right / Left: right of center for odd columns, left of center for even columns of the rack which is used On Detection Error Select the required error handling if Gemini detects no liquid or not enough liquid. 96 Gemini Software Manual V4.0 March 2002

105 TECAN 6 - Liquid Classes Use Clot Detection Check this box to activate Clot Detection. Gemini uses the Detection speed and Clot Limit which you defined on the Global dialog box for the liquid class. On Clot Error Select the required error handling if Gemini detects a clot. Mix before Aspiration Check this box if you want Gemini to mix the liquid before aspirating it. You can define the number of mix cycles, the mix volume, the Z-position and the offset. Retract Tips to Specify the Z-position and offset to which the tips should retract after aspirating. A negative value for the offset raises the tips. Retract Speed Specify the retract speed Dispense parameters Gemini uses these parameters when dispensing or mixing. Figure 6-5: Dispense parameters for liquid classes March 2002 Gemini Software Manual V4.0 97

106 6 - Liquid Classes TECAN Dispense Speed Specify the maximum dispense speed. Breakoff Speed Specify the final dispense speed (breakoff speed). Delay Specify the delay after dispensing. Trailing Airgap after each Dispense Gemini lets you aspirate a trailing airgap after each dispense command in order to avoid droplets forming on the tip. This is done using the Trailing Airgap parameters from the Aspirate dialog box. Use Pinch Valve This is used to activate the Low Volume option if your GENESIS instrument is fitted with this option. Use Liquid Detection Check this box if you want to activate liquid detection. Gemini uses the detection mode, liquid conductivity, detection speed and double distance settings which you defined on the Global dialog box for the liquid class. Liquid detection during dispensing is necessary e.g for submerged dispensing. Dispense Position Specify the Z-position and the offset of the tips when aspirating. A positive value for the offset lowers the tip. You can also specify the x-position during aspiration: Center: as defined for the rack which is used Left: left of center, offset as defined in X offset while pipetting for the rack which is used Right: right of center, offset as defined in X offset while pipetting for the rack which is used Left / Right: left of center for odd columns, right of center for even columns of the rack which is used Right / Left: right of center for odd columns, left of center for even columns of the rack which is used Tip Touching Activate the tip touching function if required and specify the direction of the movement. Tip touching is a special movement when dispensing a liquid. When tip touching is activated, Gemini dispenses to the destination container in the normal way, but then moves the tips to the side of the well and back before retracting them. This helps to remove any drops which may be adhering to the tip. 98 Gemini Software Manual V4.0 March 2002

107 TECAN 6 - Liquid Classes Speed Specify the tip touching speed. Delay after touching Specify the delay between the tip touching the well and moving back to the middle of the well. Mix after Dispense Check this box if you want Gemini to mix the liquid after dispensing it. You can define the number of mix cycles, the mix volume, the Z-position and the offset. Retract Tips to Specify the Z-position and offset to which the tips should retract after aspirating. A negative value for the offset raises the tips. Retract Speed Specify the retract speed. March 2002 Gemini Software Manual V4.0 99

108 6 - Liquid Classes TECAN Calibration parameters Gemini uses these parameters to ensure that the specified net volumes are pipetted accurately. The two curves in the dialog box show graphically the current settings for single and multi pipetting. Figure 6-6: Calibration parameters for liquid classes Gemini uses the following expression to calculate the diluter movement from the net volume specified in the pipetting script: Diluter movement = (net volume * factor) + offset 100 Gemini Software Manual V4.0 March 2002

109 TECAN 6 - Liquid Classes 6.2 Liquid classes for nanopipetting (NPS) The Tecan Nanopipetting System (NPS) uses ActiveTips for dispensing very small quantities of liquid. The ActiveTip M tip system consists of a micropump with a piezo-actuated pump chamber. It is able to form droplets in the nl (nanoliter) size range depending on the electrical actuation parameters (voltage, frequency and pulse width). As a result of the functional principle, the liquid classes for nanopipetting differ somewhat from the liquid classes for use with other tip types Global parameters (NPS) See Global parameters on page 93. Names of liquid classes for nanopipetting (NPS) are prefixed with Micro Type parameters (NPS) See Type parameters on page 94. March 2002 Gemini Software Manual V

110 6 - Liquid Classes TECAN Aspirate parameters (NPS) See Aspirate parameters on page 95 Trailing Airgap and Pinch Valve are not applicable for ActiveTips. The illustrations at the top right of the window show graphically the current settings for single and multi pipetting. Figure 6-7: Aspirate parameters for NPS liquid classes Dispense parameters (NPS) The dispense speed for ActiveTips is a function of the tip calibration parameters (see Calibration parameters (NPS) on page 103). ActiveTips normally use a synchronized start and stop of the ActiveTip piezo and the diluter. For advanced liquid handling you can specify the following delays to achieve an asynchronous behavior: Piezo Delay Specify the delay before starting and/or after stopping the diluter. If you specify a value other than 0, you can t specify the corresponding diluter delay. 102 Gemini Software Manual V4.0 March 2002

111 TECAN 6 - Liquid Classes Diluter Delay Specify the delay before starting and/or after stopping the piezo of the ActiveTip. If you specify a value other than 0, you can t specify the corresponding piezo delay. Note: The delay parameters should only be changed by specialists. Tip Touching should not be used for ActiveTips; Mix after Dispense is not applicable to ActiveTips. Figure 6-8: Dispense parameters for NPS liquid classes See Dispense parameters on page 97 for details of the other parameters Calibration parameters (NPS) When using the Nanopipetting System, the required dispense volume is delivered by the ActiveTip as a number of very small droplets of defined size. The volume of the droplets is dependent on the calibration parameters (voltage, frequency and pulse width) and must be specified in the Drop Volume field. Each Active Tip is individually tested and comes with its individual drive parameters which are specified globally in the March 2002 Gemini Software Manual V

112 6 - Liquid Classes TECAN Active Tips tab of the instrument configuration (see Configuring Active tips on page 88). The calibration values for each ActiveTip are calculated from the global drive parameters and the offset and factor which you specify in the Calibration tab (Figure 6-9). This ensures that the calibration values are automatically updated if an ActiveTip is replaced by another one with different drive parameters. Figure 6-9: Calibration parameters for NPS liquid classes Offset / Factor Specify an offset and/or factor to be applied to the global parameters in the instrument configuration. The calibration values are then calculated using the following expression: Parameter (Voltage, Frequency or Pulse Width) = (drive parameters * factor) + offset. The offset and factor values must be chosen to ensure that the droplets dispensed by the ActiveTip match the volume entered in the Drop Volume field. The global parameters for each tip are shown in the table in gray. Separate Calibration Check these checkboxes if you want to specify custom values for the drive parameters for one or more tips (custom values may be necessary for special 104 Gemini Software Manual V4.0 March 2002

113 TECAN 6 - Liquid Classes liquids). If the checkboxes are unchecked, the values you see in gray are the global parameters for each tip. Voltage Specify the custom drive voltage (between 20 and 120 Volts). Frequency Specify the custom drive frequency (between 50 and 5000 Hz). Pulse Width Specify the custom drive pulse width (between 10 and 250 µs). In this case, the parameters which are used for the ActiveTip are no longer based on the global values in the instrument configuration and are not updated if the latter are changed. March 2002 Gemini Software Manual V

114 6 - Liquid Classes TECAN 106 Gemini Software Manual V4.0 March 2002

115 TECAN 7 - Commands for Gemini Scripts 7 Commands for Gemini Scripts After creating a worktable and choosing/defining the carriers and racks that you want to use, you create a Gemini script by selecting commands from the Command Bar or one of the commands toolbars. The following figure shows the pipeting commands in the Command Bar: The commands in the Command Bar are grouped according to their function as follows: Pipetting commands (e.g. Aspirate) Advanced pipetting commands (e.g. Copy Plate) Script programming commands (e.g. Start Timer) Te-MO commands Commands for storage devices (e.g. Carousel) Commands for robotic devices (e.g. RoMa and PnP) Commands for optional devices or accessories (e.g. Vacuum Separator) Click on the group name button in the Command Bar to choose commands from the respective group. Right click on one of the commands to switch between large and small icons. Figure 7-1: Command Bar March 2002 Gemini Software Manual V

116 7 - Commands for Gemini Scripts TECAN The following figure shows the standard commands toolbars: Figure 7-2: Standard commands toolbars The commands toolbars can be configured to meet your personal preferences. You can also create custom toolbars (see Toolbar on page 28). Note: You can also insert a command in your script by choosing Insert new Command in the Edit menu, by clicking with the right mouse button and choosing the command from the floating menu or by pressing the Insert key. 7.1 List of Gemini script commands The available script commands are shown in Table 7-1, below. The third column of the table shows the toolbar to which the commands are normally assigned. The same groups are used in the Command Bar: P: Pipetting commands (e.g. Aspirate) A: Advanced pipetting commands (e.g. Copy Plate) S: Script programming commands (e.g. Start Timer) T: Te-MO commands C: Commands for storage devices (e.g. Carousel) R: Commands for robotic devices (e.g. RoMa and PnP) 108 Gemini Software Manual V4.0 March 2002

117 TECAN 7 - Commands for Gemini Scripts D: Commands for optional devices or accessories (e.g. Vacuum Separator) Aspirate - The Aspirate command is used to pick up liquid from specified positions on the worktable using appropriate tips. You can see an example of the Aspirate command on page 124. Dispense - The Dispense command is used to dispense liquid to specified positions on the worktable. Mix - The Mix command performs a mix operation by aspirating and then dispensing at the same position. Wash Tips - The Wash Tips command instructs the system to wash the tips in a wash station at the specified waste and cleaner positions. Periodic Wash - The Periodic Wash command instructs the system to wash the tips in a wash station at regular intervals. Get DITIs - The Get DITIs command lets you pick up DiTis (disposable tips) of the specified capacity from a DITI rack. Gemini keeps track of their position on the worktable and automatically chooses the next available unused DiTi. You can see an example of the Get DITIs command on page 125. See also Set DiTi Position command on page 239. Drop DITIs - The Drop DITIs command lets you discard the specified DiTis at the specified DITI waste position. Set DiTi Position - The Set DiTi Position command is used to specify the location of the next DiTi which should be used by the Get DiTis command. See Set DiTi Position command on page 239. new pix Pick Up DITIs - The Pick Up DITIs command lets you pick up DITIs, which have already been used and put back into the DiTi rack with the Set DITIs Back command. You must specify the DiTis you want to pick up. See Pick Up DITIs command on page 240. Set DITIs Back - The Set DITIs Back command lets you return used DITIs to specified positions on a DiTi rack for later use. This command requires the Lower DiTi Eject option. Pickup ZipTip - The Pickup ZipTip command is used to pick up ZipTips. See Pickup ZipTip command on page 242. pix Detect Liquid - The Detect Liquid command is used to carry out liquid detection without pipetting and reports the liquid volume for each of the chosen wells in the rack. See Detect Liquid command on page 244. pix P P P P P P P P P P P P Table 7-1: List of commands which can be used in Genesis scripts March 2002 Gemini Software Manual V

118 7 - Commands for Gemini Scripts TECAN Copy Plate - The Copy Plate command is used to make a specified number of identical copies of the source plate (complete or partial copies, 1 to 1 Copy mode). It also gives you the option to transfer selected wells from a source to a destination plate (Pick Hits mode). See Copy Plate command on page 181. Replicates - The Replicates command is used to pipette sample and dispense reagents in replicate. This command only creates horizontal replicates. See Replicates command on page 184. Serial Dilution - The Serial Dilution command is used to perform a serial dilutionintwoormoresteps.eachdilutionstephasthesamedilution ratio. See Serial Dilution command on page 187. Merge Plates - The Merge Plates command is used to create a destination rack (e.g. a 384 well plate) by merging together one or more source racks (e.g. four 96 well plates). See Merge Plates command on page 190. Transfer - The Transfer command is used to pick up liquid from specified positions on the worktable using appropriate tips and transfer it to destination positions See Transfer command on page 193. pix Worklist - The Worklist command is used to load and run external text files containing commands which tell the instrument what and where to pipette. The file contains information on source and destination positions and the pipetted volumes. See Worklist command on page 195. Export Data - The Export Data command is used to create report files for selected racks or for all racks on the worktable. The report files contain information about the pipetting which has been carried out. See Export Data command on page 200. Worklist Import - The Worklist Import command is used to create a Gemini worklist from an Excel file stored in CSV format. See Worklist Import command on page 206. Start Timer - The Start Timer command starts one of 100 internal clocks. A A A A A A A A S Wait for Timer - The Wait for Timer command instructs the instrument to wait until a specified number of seconds have expired since a specified timer was started. You can see an example of the Wait for Timer command on page 126. Execute Application - The Execute Application command instructs the system to start an external program. You can see an example of the Execute Application command on page 127. S S Table 7-1: List of commands which can be used in Genesis scripts (Continued) 110 Gemini Software Manual V4.0 March 2002

119 TECAN 7 - Commands for Gemini Scripts Comment - The Comment command lets you insert a comment for a special command or for some other reason. It is an informational command that is not executable but serves to annotate an item in the script. User Prompt - The User Prompt command is an informational command that displays a prompt on the screen as a reminder to the operator to execute a function or to perform a special action. Begin Loop - The Begin Loop command instructs Gemini to repeat a command or a set of commands (i.e. a loop) a specified number of times until an End Loop command is encountered in the script. End Loop - The End Loop command terminates the loop initiated by the Begin Loop command. Set Variable - The Set Variable command is used to assign a value to a variable. You can also prompt the operator for the value. See Variables on page 161 for more information. Set String Variable The Set String Variable command is used to assign a string to a variable. You can also prompt the operator for the string. See Variables on page 161 for more information. Condition - The Condition command is used to jump to a selected line in the script if a specified condition is true. See Conditions (Condition command) on page 175 for more information. Sub-Routine - The Sub-Routine command executes another script as part of the current script. See Sub-routines on page 176 for more information. Execute VB Script The Execute VB Script command is used to execute a Visual Basic (VB) script from within a Gemini script.see Execute VB Script command on page 236. Notification - The Notification command is used to send an from within a script (e.g. to inform an operator in another room that a certain process has finished). It can also be used to send an automatic if an error occurs during script execution. The Notification command requires the MAPI service. MAPI is included with many programs, e.g. Microsoft Outlook. Te-MO Aspirate The Te-MO Aspirate command is used to pick up liquid from specified positions on the Te-MO using appropriate tips. It is analogous to the Aspirate command for the LiHa. See the Te-MO Operating Manual - Doc ID , Te-MO Aspirate for more information. S S S S S S S S S S T Table 7-1: List of commands which can be used in Genesis scripts (Continued) March 2002 Gemini Software Manual V

120 7 - Commands for Gemini Scripts TECAN Te-MO Dispense The Te-MO Dispense command is used to dispense liquid to specified positions on the Te-MO. It is analogous to the Dispense command for the LiHa. See the Te-MO Operating Manual - Doc ID , Te-MO Dispense for more information. Te-MO Mix The Te-MO Mix command performs a mix operation by aspirating and then dispensing at the same Te-MO position. It is equivalent to the Mix command for the LiHa. See the Te-MO Operating Manual - Doc ID , Te-MO Mix for more information. Te-MO Wash The Te-MO Wash command instructs the system to wash the tips at the specified wash position (the WRC position) on the Te-MO. See the Te-MO Operating Manual - Doc ID , Te-MO Wash for more information. Te-MO Get DITIs The Te-MO Get DITIs command lets you pick up disposable tips of the specified capacity from a specified position on the Te-MO. See the Te-MO Operating Manual - Doc ID , Te-MO Get DITIs for more information. Te-MO Drop DITIs The Te-MO Drop DITIs command lets you discard the disposable tips at a specified location. See the Te-MO Operating Manual - Doc ID , Te-MO Drop DITIs for more information. Te-MO Get Tip Block The Te-MO Get Tip Block command lets you pick up a tip block from a specified position on the Te-MO. It is analogous to the Te-MO Get DITIs command. See the Te-MO Operating Manual - Doc ID , Te-MO Get Tip Block for more information. Te-MO Drop Tip Block The Te-MO Drop Tip Block command lets you set down the tipblock at a specified position. It is analogous to the Te-MO Drop DITIs command. See the Te-MO Operating Manual - Doc ID , Te-MO Drop Tip Block for more information. Te-MO Refill Trough - The Te-MO Refill Trough command is used to control the Refill option for the Te-MO. Te-MO Te-Stack Drop Rack - The Te-MO Te-Stack Drop Rack commandisusedtodroparackfromthete-mostackeroptionontothe Te-MO. Te-MO Te-Stack Pickup Rack - The Te-MO Te-Stack Pickup Rack command is used to pick-up a rack from the Te-MO and put it into the Te- MO Stacker option. T T T T T T T T T T Table 7-1: List of commands which can be used in Genesis scripts (Continued) 112 Gemini Software Manual V4.0 March 2002

121 TECAN 7 - Commands for Gemini Scripts Te-MO Relative Movements - The Te-MO Relative Movements command is used to perform Te-MO movements with an offset. For example it can be used to specify a serial dilution with the Te-MO. see See Te-MO Relative Movements command on page 246. Te-Stack - The Te-Stack command is used to control the Te-Stack option (stand-alone stacker device). See Te-Stack command on page 228. Carousel Scan Barcodes The Carousel Scan Barcodes command is used to scan the barcodes on the plates in the carousel. See Carousel Scan Barcodes command on page 230. Carousel Retrieve The Carousel Retrieve command is used to retrieve plates from the carousel according to a condition which you specify, e.g. retrieve a plate with a specified barcode. See Carousel Retrieve command on page 231. Carousel Return The Carousel Return command is used to return plates to the carousel according to a condition which you specify, e.g. return a plate to position 1 in tower 3. See Carousel Return command on page 232. Carousel Direct Movements The Carousel Direct Movements command is used to control the carousel directly, e.g. initialize the carousel or rotate the carousel to a specified tower. See Carousel Direct Movements command on page 233. Move RoMa - The Move RoMa command instructs the instrument to execute simple RoMa movements. See Move RoMa command on page 212. RoMa Vector - The RoMa Vector command instructs the instrument to execute a RoMa vector, which is a predefined sequence of RoMa positions. You can also specify gripper actions. RoMa Vector command on page 211. Move PnP - The Move PnP command instructs the instrument to execute simple PnP movements. See Move PnP command on page 220. PnP Vector - The PnP Vector command instructs the instrument to execute a RoMa vector, which is a predefined sequence of RoMa positions. You can also specify gripper actions. See PnP Vector command on page 219. T C C C C C R R R R Table 7-1: List of commands which can be used in Genesis scripts (Continued) March 2002 Gemini Software Manual V

122 7 - Commands for Gemini Scripts TECAN Move LIHA - The Move LIHA command is used to move the liquid handling arm from one position to another without performing an Aspirate or Dispense operation. See Move LiHa command on page 226. Send a Command - The Send a Command command allows you to send a string command directly to the GENESIS instrument. PosID - The PosID command is used to read tube and rack barcodes on the indicated objects on the worktable. Your GENESIS instrument must be equipped with the PosID option. Barcode Scanner - The Barcode Scanner command is used to control the Symbol LS1220 barcode scanner option, which allows you to read barcodes on plates or tubes without using the PosID. The Symbol LS1220 requires a RoMa or PnP to present the plates or tubes to the scanner. Doorlocks TheDoorlockscommandisusedtoopenorclosethe doorlocks of the GENESIS instrument. See Doorlocks command on page 251. Vacuum Separator - The Vacuum Separator command controls the SPE vacuum separation option (Te-VacS) for the GENESIS instrument. Magnetic Separator - The Magnetic Separator command controls the Magnetic Beads Separator option (Te-MagS) for the GENESIS instrument. System - The System command lets you switch between 6 different system liquids. Your instrument must be equipped with the ChemSystem option (6-way valve). See System command on page 252. Waste - The Waste command lets you control the vacuum-assisted wasteoptionforthegenesisinstrument. Variomag The Variomag command controls the H+P Variomag. R R D D D D D D D D Shaker The Shaker command is used to control the Tecan Orbital Shaker (Te-Shake). Connection Box The Connection Box command is used to control the connection box for the Te-Flow option. MIO The MIO command is used to control the Tecan Monitored Incubator Option (a heated incubator with optional shaker hardware). See MIO command on page 253. D D D Table 7-1: List of commands which can be used in Genesis scripts (Continued) 114 Gemini Software Manual V4.0 March 2002

123 TECAN 7 - Commands for Gemini Scripts Execute Magellan Method The Execute Magellan Method command is used to control Tecan microplate readers (i.e. photometers) using the Magellan data collection and reduction software. Execute Magellan Method command on page 255. Execute WinWash Program - The Execute WinWash Program command is used to control Tecan Plate Washers using the WinWash Plus software. Execute WinWash Program command on page 259. Waterbath Control The Waterbath Control command is used to control the waterbath for the Te-Flow option, which provides support for the Situ Hybridization method. Centrifuge The Centrifuge command lets you start and stop the centrifuge, open and close the hatch and configure settings for the centrifuge. See Centrifuge command on page 262. Balance - The Balance command is used to read a weight from a Mettler balance and store it in a variable. Active WashStation The Active WashStation command is used to control the pressure pump of the Active WashStation. It is mainly intended for ZipTips. See Active WashStation command on page 264. D D D D D S Table 7-1: List of commands which can be used in Genesis scripts (Continued) March 2002 Gemini Software Manual V

124 7 - Commands for Gemini Scripts TECAN 116 Gemini Software Manual V4.0 March 2002

125 TECAN 8 - Creating a Pipetting Script 8 Creating a Pipetting Script This chapter describes the steps which are required to create a pipetting script for the GENESIS instrument. You need a user level of Manager or Administrator to create scripts. First of all, start the Gemini software and click New. This opens a new window for the Gemini script which will specify the pipetting operations. You will also see the worktable and one or more toolbars with buttons for the script commands. The Worktable and scripts windows are initially empty, and the title bar shows a generic name for the script, e.g. Prog1. After saving the script, the title bar shows the chosen script name. Initially, the Worktable is also empty (i.e. it does not contain any carriers or racks etc.). You can arrange the toolbars on the screen to suit your requirements. Toolbars can also be hidden or docked onto the menu bar (see Toolbar on page 28). 8.1 The Worktable window The Worktable window represents the working surface (deck) of the GENESIS instrument. Before programming your pipetting operations, you need to place the carriers and racks etc. which you want to use on the worktable. Carriers can only be placed on the worktable at specified grid positions which correspond to the locating pins on the worktable. One grid unit is 25.0 mm. The choice and the positions of carriers and racks is based on your application needs. You can change the carrier positions later by dragging with the mouse without needing to change your script, for example if it turns out that the carriers are too close together to position additional objects in between. However, the final positions you choose must correspond to the actual positions of the physical objects on the GENESIS instrument. March 2002 Gemini Software Manual V

126 8 - Creating a Pipetting Script TECAN The worktable window in Gemini looks similar to the following before you add any objects: Figure 8-1: The worktable with no objects defined You can change the size of the worktable window by moving the mouse over an edge or corner until the double arrow cursor appears. Then press the left mouse button and drag until the required size has been reached. The next step is to add carriers and racks to the worktable layout and assign labels (i.e. names) to the racks. Note: Each script has its own worktable layout, and the worktable layout is automatically saved with the script Adding carriers and racks to the worktable To create the required Worktable layout, click on the Carriers tab, select the carrier you want to use and drag it onto the worktable at the required position. When positioning the carrier, the current grid position is shown in the small yellow tab at the bottom left. Then click on the Racks tab, select the rack you want to use and drag it onto the carrier on top of the required site. Repeat this process to add all of the racks and carriers to the worktable that you need. The choice and the positions of the racks and carriers is based on your application needs. When you select a carrier, a graphical representation of the carrier is shown to the right of the list. After selecting a carrier, the list of racks only shows racks which are suitable for use with that carrier. When you select a rack, a graphical representation of the rack 118 Gemini Software Manual V4.0 March 2002

127 TECAN 8 - Creating a Pipetting Script is shown on the carrier at the allowed site or sites. You can test this feature e.g. by choosing racks for a 2-position DiTi carrier. See Configuring racks on page 45 and Configuring carriers on page 62 for information on how to define custom racks and/or carriers which are not contained in the Gemini database. To move a carrier to a new worktable position, click the body of the carrier to select it and drag to the required position. When dragging the carrier, the current grid position is shown in the small yellow tab at the bottom left. The final position you choose must correspond to the actual, physical position on the GENESIS instrument. To move a rack to a new site, click on the rack to select it and drag to the required position.to delete a carrier or rack, click on it and drag it off of the worktable. When adding, deleting or moving carriers and racks, a special cursor is shown to indicate the action you are performing ("add", "del" or "move").. Note: For information on how to create custom carriers and racks, see How to create additional carriers on page A-1. March 2002 Gemini Software Manual V

128 8 - Creating a Pipetting Script TECAN The following is an example of a worktable filled with: a MTP 3 Pos. landscape carrier containing two Microplate landscape racks, a DiTi200 2 Pos. carrier containing two new tray DiTi Tip racks and a DiTi Waste position a 100ml 3 Pos. Trough carrier containing three 100ml racks, a Wash station containing 8 Pos. deep and shallow Cleaner and Waste racks. Figure 8-2: Typical worktable with several objects Racks and carriers can be assigned unique colors in the Gemini configuration make it easier for you to identify them in the Worktable window (see page 46 and page 63). In addition, racks can be assigned labels (names) to make them easier to identify in the Worktable window. Check the Label checkbox to show the rack labels that you have assigned. The label is shown in yellow. Check the Barcode checkbox to show the rack barcode. The barcode is shown in green. Rack barcodes are only shown after you have run a script which scans the rack with the PosID device. In simulation mode, the PosID command prompts you to enter the barcodes manually. You can also activate a 3D effect to give a spatial impression of the worktable layout. To do this, move the 3D slider at the right of the window until the desired effect is achieved. 120 Gemini Software Manual V4.0 March 2002

129 TECAN 8 - Creating a Pipetting Script Assigning a label (or name) to the racks You can assign a label (i.e. name) to each rack by double clicking on the rack in the Worktable window and typing the required name in the Name field of the Edit Rack Name dialog box. The label is shown in yellow. Rack labels can be used in scripts and worklist files to make them easier to understand for other persons (see Worklist command on page 195). They are also used by Gemini in log files and by the Tecan dynamic scheduling software FACTS. If you don t specify rack labels, the scripts, worklists and log files contain the generic rack name instead, e.g. Microplate, landscape. For example, you can label the racks on the example worktable above with source and destination names as follows: Figure 8-3: Specifying labels for objects on the worktable The worktable should appear as follows after the labels have been assigned: Figure 8-4: Worktable showing labels for racks March 2002 Gemini Software Manual V

130 8 - Creating a Pipetting Script TECAN 8.2 Specifying script commands After creating a worktable and choosing/defining the carriers and racks that you want to use, you create a Gemini script by selecting commands from the Command Bar or one of the commands toolbars. The following figure shows the pipeting commands in the Command Bar: The commands in the Command Bar are grouped according to their function as follows: Pipetting commands (e.g. Aspirate) Advanced pipetting commands (e.g. Copy Plate) Script programming commands (e.g. Start Timer) Te-MO commands Commands for storage devices (e.g. Carousel) Commands for robotic devices (e.g. RoMa and PnP) Commands for optional devices or accessories (e.g. Vacuum Separator) Click on the group name button in the Command Bar to choose commands from the respective group. Right click on one of the commands to switch between large and small icons. Figure 8-5: Command Bar Please see page 108 for information on the commands toolbars. Please see List of Gemini script commands on page 108 for a full list of the script commands. 122 Gemini Software Manual V4.0 March 2002

131 TECAN 8 - Creating a Pipetting Script 8.3 Creating a Gemini script The commands in the Command Bar will now be used to create a pipetting program (or script). Because Gemini normally executes a script in a linear sequence, you should write it in the exact order that you want it to be executed. Each script is associated with its own worktable, which must be specified before writing the script. The example script is described in Example Script, starting on page 129. The following pages first discuss general principles and give a few examples of script commands. When you select a command by clicking on its button, a dialog box is shown where you can complete all of the information needed to define the command. When you are finished, click OK in the dialog box to add the command to the script. The new command is inserted below the currently selected command, which is highlighted in color (the default color is light yellow). You can select a command by clicking with the mouse or by using the cursor keys. When a script line is selected, the same color is used to highlight the associated object in the Worktable window. If you select the first command in the script, you will be asked whether to insert the new command above or below the current command. Another way to add a command to the script is to click the script window with the right mouse key. A floating menu will appear with all available commands. Select the required command with the mouse or navigate using the cursor keys and press Enter. Note: You can also insert a command in your script by clicking on a button in one of the commands toolbars, by choosing Insert new Command in the Edit menu or by pressing the Insert key. The Cut, Copy, andpaste functions in the Edit menucanalsobeusedwhencreatinga script. When the script is complete, you can use the Validate function (blue check mark button in the File toolbar) to look for mistakes (see Validating a script on page 157). March 2002 Gemini Software Manual V

132 8 - Creating a Pipetting Script TECAN The Aspirate, Dispense and Mix commands have similar screens. The following figure shows an example of the Aspirate command: Figure 8-6: Example of the Aspirate command The above example aspirates 25 µl using standard tips (see Configuring the LiHa on page 82 for information on configuring the liquid handling arm) and a tip spacing of 2 (i.e. every other well). To select the required source plate, click in the Worktable window on the appropriate rack. We will now show examples of several other Gemini commands. 124 Gemini Software Manual V4.0 March 2002

133 TECAN 8 - Creating a Pipetting Script Example of the Get DITIs command Figure 8-7: Example of the Get DiTis command The above example of the Get DITIs command picks up four DiTi200 tips. Note: You can only specify disposable tips (DITIs) in the Get DITIs and Drop DITIs commands if the LiHa has been configured with DITIs. See Configuring the LiHa on page 82 for information on configuring DITIs. March 2002 Gemini Software Manual V

134 8 - Creating a Pipetting Script TECAN Example of the Timers command Figure 8-8: Example of the Wait for Timer command The above example of the Timers command specifies a delay of 60 seconds for Timer 1. After the aspirate and dispense operations have finished, the system waits until 60 seconds have elapsed since Timer 1 was started (in the first script line) before proceeding with line 5 of the script. Note that the specified delay will have already elapsed if the aspirate and dispense operations take longer than 60 seconds. 126 Gemini Software Manual V4.0 March 2002

135 TECAN 8 - Creating a Pipetting Script Example of the Execute command Figure 8-9: Example of the Execute Application command The above example of the Execute command starts the RDROLE.EXE program after the second aspirate/dispense cycle. March 2002 Gemini Software Manual V

136 8 - Creating a Pipetting Script TECAN Copy Plate command Figure 8-10: Example of the Copy Plate command The above example of the Copy Plate command copies the source plate five times into destinations 1 to 5. See Copy Plate command on page 181 for more information. 128 Gemini Software Manual V4.0 March 2002

137 TECAN 9 - Example Script 9 Example Script This chapter describes the steps required to create a Gemini script for a typical pipetting application. 9.1 Typical application of a Gemini script The following pages illustrate how to develop a script for a typical Gemini application. The chosen exercise is a column overlapping pooling application involving single pipetting using only standard tips. The purpose of the script is to pool two columns of the source plate into one column of the destination plate using single pipetting. The initial volume in the source plate is 200 µl and the pipetting volume is 50 µl (final total of 100 µl) per well in the destination plate. You must first specify the worktable which is required. One microplate serves as the source plate and another microplate serves as the destination plate. Both plates are placed in the landscape orientation on the same MTP (microtiter plate or microplate) carrier. The application uses one wash station with shallow cleaner and waste. Figure 9-1: Example script, step 1 March 2002 Gemini Software Manual V

138 9 - Example Script TECAN For all normal applications using standard tips, it is necessary to start with a wash command. Click the Wash Tips button in the commands toolbar. Note: Alternatively, press the Insert key on the keyboard and choose Wash Tips or choose Insert new Command in the Edit menu and choose Wash Tips. On the Wash dialog box that appears, select tips 1-8 (or click All Tips) and fill in the remaining fields as appropriate (appropriate values have already been chosen). Click OK to add the properly defined Wash Tips command to your script. Figure 9-2: Example script, step 2 Now click the Aspirate button in the commands toolbar. On the Aspirate dialog box that appears, select tips 1-8 (or click All Tips), specify 50 µl as the volume for all tips and click the source rack in the Worktable window. The source rack should then be highlighted in color. Now click on the first column in the Aspirate dialog box. Tips Gemini Software Manual V4.0 March 2002

139 TECAN 9 - Example Script should then be highlighted in green. Click them to select them and they will become green. The dialog box should now appear as follows: Figure 9-3: Example script, step 3 Note: You can customize the tip selection and tip spacing in the Aspirate and Dispense dialog boxes by clicking on the tips you want to use and choosing the spacing as required. For example, a tip spacing of 2 will select every other well. March 2002 Gemini Software Manual V

140 9 - Example Script TECAN Click OK to add the properly defined Aspirate command to your script. The program window should now appear as follows: Figure 9-4: Example script, step 4 Now click the Dispense button in the commands toolbar. On the Dispense dialog box that appears, select tips 1-8 (or click All Tips), specify 50 µl as the volume for all tips and click the destination rack in the Worktable window. The destination rack should then be highlighted in color. Now click on the first column in the Dispense dialog box. Tips Gemini Software Manual V4.0 March 2002

141 TECAN 9 - Example Script should then be highlighted in green. Click them to select them and they will become green. The dialog box should now appear as follows: Figure 9-5: Example script, step 5 March 2002 Gemini Software Manual V

142 9 - Example Script TECAN Click OK to add the properly defined Dispense command to your script. The program window should now appear as follows: Figure 9-6: Example script, step 6 Now click the Wash Tips button in the commands toolbar. On the Wash dialog box that appears, select tips 1-8 (or click All Tips) and fill in the remaining fields as 134 Gemini Software Manual V4.0 March 2002

143 TECAN 9 - Example Script appropriate (suitable values are filled in automatically). The dialog box should now appear as follows: Figure 9-7: Example script, step 7 March 2002 Gemini Software Manual V

144 9 - Example Script TECAN Click OK to add the properly defined Wash Tips command to your script. The program window should now appear as follows: Figure 9-8: Example script, step Gemini Software Manual V4.0 March 2002

145 TECAN 9 - Example Script Now click the Begin Loop button in the commands toolbar. On the Begin Loop dialog box that appears, specify the number of loop cycles as 11 and give the loop the name Cycle 1. Figure 9-9: Example script, step 9 March 2002 Gemini Software Manual V

146 9 - Example Script TECAN Click OK to add the Begin Loop command to your script. The program window should now appear as follows: Figure 9-10: Example script, step 1 You must now define which actions have to be repeated 11 times. Because an Aspirate step should be executed first, click the Aspirate button in the commands toolbar and select tips 1-8 (or click All Tips), specify a pipetting volume of 50 µl, select the source rack and specify rack column 1 for the aspirate position. 138 Gemini Software Manual V4.0 March 2002

147 TECAN 9 - Example Script Additional loop options must now be defined. In this example, we will increase the rack column by +1 for every cycle in the loop. Figure 9-11: Example script, step 11, showing loop options March 2002 Gemini Software Manual V

148 9 - Example Script TECAN Click OK to add the properly defined loop options for the Aspirate command to your script. The program window should now appear as follows: Figure 9-12: Example script, step 12 The next action to be executed inside the Loop Cycle 1 is a Dispense command. Click the Dispense button in the commands toolbar, select tips 1-8 (or click All Tips), specify a pipetting volume of 50 µl, select the destination rack and specify rack 140 Gemini Software Manual V4.0 March 2002

149 TECAN 9 - Example Script column 2 for the dispense position. Additional loop options must now be defined. In this example, we will increase the rack column by +1 for every cycle in the loop. Figure 9-13: Example script, step 13 March 2002 Gemini Software Manual V

150 9 - Example Script TECAN Click OK to add the properly defined loop options for the Dispense command to your script. The program window should now appear as follows: Figure 9-14: Example script, step 14 The next action to be executed inside the Loop Cycle 1 is another Wash Tips command. Click the Wash Tips button in the commands toolbar, select tips 1-8 (or click All Tips), and fill in the remaining boxes in the Wash dialog box as appropriate (suitable values are filled in automatically). After the Wash Tips command has been 142 Gemini Software Manual V4.0 March 2002

151 TECAN 9 - Example Script fully specified (see the examples above in steps 1 and 4), click OK to add the command to your script. The program window should now appear as follows: Figure 9-15: Example script, step 15 The Wash Tips command is the last command you need in the loop Cycle 1. Click the End Loop button in the commands toolbar to add the End Loop command to the March 2002 Gemini Software Manual V

152 9 - Example Script TECAN script. The End Loop command automatically refers to the previous Begin Loop command in the script. The program window should now appear as follows: Figure 9-16: Example script, step 16 The Begin Loop Cycle 1 command (step 5) instructs the instrument to begin 11 cycles of the first loop of the script, which consists of steps 6-8 in the script. This instructs the instrument to aspirate from column 1 of the source rack, dispense to column 2 of the destination rack, aspirate from column 2 of the source rack, dispense to column 3 of the destination rack, and so on, until it aspirates from column 11 of the source rack and dispenses to column 12 of the destination rack. Now click the Aspirate button in the commands toolbar. On the Aspirate dialog box that appears, select tips 1-8 (or click All Tips), specify an Aspirate volume of 50 µl, 144 Gemini Software Manual V4.0 March 2002

153 TECAN 9 - Example Script select the source rack, and the position on the rack (column 12). The dialog box should now appear as follows: Figure 9-17: Example script, step 17 March 2002 Gemini Software Manual V

154 9 - Example Script TECAN Click OK to add the properly defined Aspirate command to your script. The program window should now appear as follows: Figure 9-18: Example script, step 18 Now click the Dispense button in the commands toolbar. On the Dispense dialog box that appears, select tips 1-8 (or click All Tips), specify a Dispense volume of 50 µl, 146 Gemini Software Manual V4.0 March 2002

155 TECAN 9 - Example Script select the destination rack, and the position on the rack (column 1). The dialog box should now appear as follows: Figure 9-19: Example script, step 19 March 2002 Gemini Software Manual V

156 9 - Example Script TECAN Click OK to add the properly defined Dispense command to your script. The program window should now appear as follows: Figure 9-20: Example script, step 20 The next step is to add another Wash Tips command. Since this Wash Tips command is exactly the same as the Wash Tips commands defined previously, you can select (click on) the previously defined Wash Tips command in the script (it will be highlighted in color) and copy it using the Copy function in the Edit menu (or click the Copy button in the File toolbar). Then click the last line of the script (Dispense command, line 11) and choose Paste in the Edit menu (or click the Paste button in 148 Gemini Software Manual V4.0 March 2002

157 TECAN 9 - Example Script the File toolbar). This adds another Wash Tips command to the end of the script. The program window should now appear as follows: Figure 9-21: Example script, step 21 Now click the Begin Loop button in the commands toolbar to add a new loop. On the Begin Loop dialog box that appears, specify the number of loop cycles as 11 and March 2002 Gemini Software Manual V

158 9 - Example Script TECAN give the loop the name Cycle 2. ClickOK to add the Begin Loop command to your script. The program window should now appear as follows: Figure 9-22: Example script, step 22 You must now define which actions have to be repeated 11 times. Because an Aspirate step should be executed first, click the Aspirate button in the commands toolbar and select tips 1-8 (or click All Tips), specify a pipetting volume of 50 µl, select the source rack and specify rack column 2 for the aspirate position. Additional 150 Gemini Software Manual V4.0 March 2002

159 TECAN 9 - Example Script loop options must now be defined. In this example, we will increase the rack column by +1 for every cycle in the loop. The dialog box should now appear as follows: Figure 9-23: Example script, step 23 March 2002 Gemini Software Manual V

160 9 - Example Script TECAN Click OK to add the properly defined loop options for the Aspirate command to your script: Figure 9-24: Example script, step 24 The next action to be executed inside the loop Cycle 2 is a Dispense command. Click the Dispense button in the commands toolbar, select tips 1-8 (or click All Tips), specify a pipetting volume of 50 µl, select the destination rack and specify rack column 2 for the dispense position. Additional loop options must now be defined. In 152 Gemini Software Manual V4.0 March 2002

161 TECAN 9 - Example Script this example, we will increase the rack column by +1 for every cycle in the loop. The dialog box should now appear as follows: Figure 9-25: Example script, step 25 March 2002 Gemini Software Manual V

162 9 - Example Script TECAN Click OK to add the properly defined loop options for the Dispense command to your script. The program window should now appear as follows: Figure 9-26: Example script, step 26 The next item to add to the script is another Wash Tips command. To do this, click the Wash Tips button in the commands toolbar or copy a previous Wash Tips 154 Gemini Software Manual V4.0 March 2002

163 TECAN 9 - Example Script command to this line of the script as described above. The program window should now appear as follows: Figure 9-27: Example script, step 27 The Wash Tips command is the last command you need in the loop Cycle 2. Click the End Loop button in the commands toolbar to add the End Loop command to the March 2002 Gemini Software Manual V

164 9 - Example Script TECAN script. The End Loop command automatically refers to the previous Begin Loop command in the script. The program window should now appear as follows: Figure 9-28: Example script, step 28 The Begin Loop Cycle 2 command (step 13) instructs the instrument to begin 11 cycles of the second loop of the script, which consists of steps in the script. This instructs the instrument to aspirate from column 2 of the source rack, dispense to column 2 of the destination rack, aspirate from column 3 of the source rack, dispense to column 3 of the destination rack, and so on, until it aspirates from column 12 of the source rack and dispenses to column 12 of the destination rack. 156 Gemini Software Manual V4.0 March 2002

165 TECAN 10 - Validating, Starting and Stopping a Script 10 Validating, Starting and Stopping a Script This chapter describes how to validate a script, locate errors in a script and start, pause, continue and stop a script Validating a script To validate a script (i.e. to check for errors), click the Validate button (blue check mark in the File toolbar) or choose Validate in the Execute menu.thevalidatefunctionwill then list any obvious errors. You can test the Validate function with the sample script script4.gem. The following error messages will then be shown in the Gemini Errors window when you click the Validate button: Figure 10-1: Validating a script, step 1 Each error is identified by a line number and a description of the error. When you click the error, the cursor jumps to the faulty line in the script so that you can modify it as appropriate. After correcting the faulty command(s), click OK to close the Gemini Errors window. Please refer to Error messages on page A-3, which lists all of the error messages which can be output by the Validate function. March 2002 Gemini Software Manual V

166 10 - Validating, Starting and Stopping a Script TECAN The following dialog box will be shown instead if there are no errors in your script: Figure 10-2: Validating a script, step Starting a script To start running the current script, click the Start button (green triangle in the File toolbar) or choose Start in the Execute menu. The script will first be validated, and will then start running if there are no errors. The script line which is currently executing is highlighted in color. The default color is light yellow. The same color is used to highlight the associated object in the Worktable window Pausing a script To pause the current script, click the Pause button (red parallel bars in the File toolbar) or choose Pause in the Execute menu Continuing a script To resume running a script which has been paused, click the Continue button (green parallel bars in the File toolbar) or choose Continue in the Execute menu. 158 Gemini Software Manual V4.0 March 2002

167 TECAN 10 - Validating, Starting and Stopping a Script 10.5 Stopping a script To stop the script from running, click the Stop button(redstopsigninthefiletoolbar)or choose Abort in the Execute menu Starting a script at a certain line To start running the current script at a specified line, click the StartatLinebutton (green triangles in the File toolbar) or choose Startatlinein the Execute menu. You will be prompted for the first and the last line of the script that you want to run. The script will first be validated, and will then start running if there are no errors Undefined Variables option If this option is activated, Gemini allows you to use undefined variables when validating a script. It then prompts you to enter values for the variables during runtime, directly before their use. This can be useful if you want to validate and execute just a part of a script. If this option is not activated, the Variable not defined error will be displayed if an undefined variable is found. To activate the Undefined Variables option, click the Undefined Variables button in the File toolbar or choose Undefined Variables in the Execute menu. A tick is shown alongside the menu item when it is activated. Repeat the same actions to disable the Undefined Variables option again Sample scripts Gemini is provided with a number of sample scripts to illustrate various aspects of script programming. It is instructive for new users of Gemini to load the sample scripts which are provided and to work through each script by reviewing the on-line help. For learning purposes, many of the scripts can also be run in simulation mode. Note that if you change the default Gemini Configuration for the LiHa, the scripts may no longer run without errors. For example, if you configure the LiHa for DITIs, the script must fetch the DiTis before they can be used. script4.gem contains intentional errors to illustrate the use of the Validate function. March 2002 Gemini Software Manual V

168 10 - Validating, Starting and Stopping a Script TECAN 160 Gemini Software Manual V4.0 March 2002

169 TECAN 11 - Advanced Programming Features 11 Advanced Programming Features 11.1 Variables Gemini allows you to use variables in scripts. This lets you modify the execution of the script during runtime. You can use variables for pipetting volumes, timers and time durations, string commands, names of external applications and loop counters etc. Gemini also supports expressions, which are a combination of variables and basic mathematical operators such as add or multiply. The following paragraphs discuss the definition and use of variables in more detail Defining and setting a variable You can only use a variable after it has been defined (declared) with one of the following commands: Icon Command Description Aspirate Copy Plate Dispense Merge Plates Mix Replicates The LiHa pipetting commands automatically define variables if liquid detection was used. One variable is provided for each tip on the LiHa. The detected volume is reported in µl for each tip. The variable names are as follows: DETECTED_VOLUME_1... DETECTED_VOLUME_8. The value -1 is reported as the detected volume if the tip was used with liquid detection disabled or was not part of the pipetting command. Serial Dilution Transfer Balance This command lets you store a measured weight in a variable. Table 11-1: Commands which support variables March 2002 Gemini Software Manual V

170 11 - Advanced Programming Features TECAN Barcode Scanner Begin Loop Detect Liquid Execute Application Execute VB Script PosID Send a Command Set String Variable Set Variable This command lets you store a scanned barcode in a string variable. The Begin Loop command automatically defines a variable with the name LOOP_x, where x is the name of the loop. Gemini sets this variable to the current cycle number for the loop, e.g. to 1 to 12 for a loop with 12 cycles. The Detect Liquid command returns the detected volumes in a set of variables DETECT_VOLUME_X, where X is the tip number. This command lets you write the return value of the specified application to a variable. The Execute VB Script command can assign values to variables for subsequent use in the Gemini script. However, you must declare the variables in advance in the Gemini script before calling the Execute VB Script command. See Execute VB Script command on page 236. The PosID command automatically defines a counter variable with the name TUBE_CNT which is incremented each time a tube is successfully scanned. This command lets you write the response of the specified command to a variable. The returned error codecanalsobewrittentoavariable. The Set String Variable command is used to assign a string to a variable. You can also prompt the operator for the string. The Set Variable command is used to assign a value to a variable. You can also prompt the operator for the value. See Querying the value of a numeric variable during runtime on page 164. Table 11-1: Commands which support variables 162 Gemini Software Manual V4.0 March 2002

171 TECAN 11 - Advanced Programming Features Move RoMa RoMa Vector The Move RoMa and RoMa Vector commands automatically define a counter variable with the name CENTRIFUGE_RACK_CNT which is incremented each time a plate is placed into the centrifuge and decremented each time a plate is removed from the centrifuge. Please note that the RoMa Vector you use to load and unload the centrifuge must be based on a carrier of type "Centrifuge". The carrier should have 4 sites (one for each centrifugation bucket). See Centrifuge command on page 262 for more information. Table 11-1: Commands which support variables After being defined, the variable is accessible until the script terminates. Variable names can be 1 to 64 characters in length and must not begin with a digit. Variable names are case-insensitive and numeric variables are treated as floating point numbers, except when used in a Send a Command command (see also Commands supporting expressions on page 171). March 2002 Gemini Software Manual V

172 11 - Advanced Programming Features TECAN Querying the value of a numeric variable during runtime The Set Variable command ( button) can be used to prompt the operator for the value of a numeric variable during runtime. To do this, check the User Query checkbox when you specify the command and specify the user prompt which should appear on the screen. You can also specify a default value and check that the value which is entered by the operator lies within a specified range. The following example prompts the operator for a volume and sets the admissible range to 10 to 100 µl. In addition, a default value of 50 µl is suggested. Figure 11-1: Querying the operator for a value during script runtime During runtime, the value which is input by the operator is validated and a warning is output if it does not lie within the specified range. The user can also be prompted for a string variable during runtime. This is done with the Set String Variable command. See Querying the value of a string variable during runtime on page Gemini Software Manual V4.0 March 2002

173 TECAN 11 - Advanced Programming Features Pre-defined variables Gemini has some pre-defined variables which allow the same script to be used for different numbers of samples or contain useful information CENTRIFUGE_RACK_CNT This counter variable is incremented by the Move RoMa and RoMa Vector commands each time the RoMa places a plate into the centrifuge and is decremented each time the RoMa removes a plate from the centrifuge. It is intended for use in a sub-routine to avoid possible mechanical imbalance by always placing racks in the centrifuge in pairs. Please note that the RoMa Vector you use to load and unload the centrifuge must be based on a carrier of type "Centrifuge". The carrier should have 4 sites (one for each centrifugation bucket). See Centrifuge command on page 262 for more information COPY_CNT This counter variable lets you limit the number of copied source wells in Copy Plate commands. If you assign a value to COPY_CNT, Gemini will copy up to the specified number of source wells for all following Copy Plate commands. COPY_CNT is ignored if its value is larger than the number of source wells specified in the Copy Plate command. You cannot deactivate COPY_CNT for a part of the script, but you can assign a large number (e.g. 1000) to it, so that the well selection in the Copy Plate command is used instead DETECTED_VOLUME_x The LiHa pipetting commands automatically define variables if liquid detection was used. One variable is provided for each tip on the LiHa. The detected volume is reported in µl for each tip. The variable names are as follows: DETECTED_VOLUME_1... DETECTED_VOLUME_8. The value -1 is reported as the detected volume if the tip was used with liquid detection disabled or was not part of the pipetting command RACK_OFFSET This variable lets you change the specified rack for the basic commands Aspirate, Dispense, Mix and Move LIHA. If e.g. RACK_OFFSET equals 1, Gemini searches for the next rack of the same type on the worktable. The search direction is from rear to front, left to right of the worktable. Negative values in RACK_OFFSET cause Gemini to March 2002 Gemini Software Manual V

174 11 - Advanced Programming Features TECAN search in the opposite direction. You can deactivate RACK_OFFSET by setting its valueto RACK_VOLUME_X The Te-MO does not support liquid detection. To emulate liquid detection for the Te- MO, specify the volume for the wells of the rack you are using by assigning a value to this variable. This ensures that the tips are not lowered too far into the wells of the Te- MO. Replace the X in the variable name with the rack name, e.g. use RACK_VOLUME_SOURCE if you named the rack SOURCE. Note: For mechanical reasons, the pipetted volume for the Te-MO is the same for all wells REPLICATE_CNT This counter variable lets you limit the number of pipetted destination wells in Replicates commands. If you assign a value to REPLICATE_CNT, Gemini will pipette up to the specified number of destination wells for all following Replicates commands. REPLICATE_CNT is ignored if its value is larger than the number of destination wells specified in the Replicates command. You cannot deactivate REPLICATE_CNT for a part of the script, but you can assign a large number (e.g. 1000) to it, so that the well selection in the Replicates command is used instead SAMPLE_CNT Gemini normally executes a script in its entire length. If you want to use a different number of samples in each run, you would need to modify the script accordingly each time you use it. The SAMPLE_CNT counter variable allows you to write a script for the maximum number of samples and to limit the script during runtime according to the actual number of samples. SAMPLE_CNT is intended for use in loops in combination with basic pipetting commands such as Aspirate, Dispense, Mix, Get DITIs and Drop DITIs. This feature is activated by assigning a positive value to SAMPLE_CNT. If SAMPLE_CNT is set to a value larger or equal to 0, Gemini keeps a count of how many different tips are used in each cycle of the following loop(s). The loop is then terminated the next time End Loop is executed when the number of tips used reaches SAMPLE_CNT. If SAMPLE_CNT is not a multiple of the number of tips used in one cycle of the loop(s), Gemini modifies the tip selection in the final cycle of the loop. 166 Gemini Software Manual V4.0 March 2002

175 TECAN 11 - Advanced Programming Features The following figure shows an example of using the SAMPLE_CNT variable: Figure 11-2: Using the SAMPLE_CNT variable The example script copies 10 µl from the source rack to the destination rack. The loop is programmed for a maximum of 96 samples or wells. If SAMPLE_CNT is set to 13, the script is executed as follows: Wash tips 1-8, Aspirate with tips 1-8 from column 1 of the source rack, Dispense with tips 1-8 into column 1 of the destination rack, Wash tips 1-8, Aspirate with tip 1-5 from column 1 of the source rack, Dispense with tips 1-5 into column 1 of the destination rack, Wash tips 1-8. Assign -1 to SAMPLE_CNT to deactivate the feature again TUBE_CNT After executing a PosID command, Gemini writes the number of tubes scanned in the script so far to TUBE_COUNT WELL_OFFSET This variable lets you modify the well selection for the basic commands Aspirate, Dispense, Mix and Move LIHA. Gemini shifts the well selection in the rack by the number of wells defined in WELL_OFFSET. If e.g. A1 to H1 of a microplate have been March 2002 Gemini Software Manual V

176 11 - Advanced Programming Features TECAN selected in the script and WELL_OFFSET is set to 8, Gemini will pipette in A2 to H2. When applying the offset, Gemini shifts from rear to front and then from left to right. Negative values of WELL_OFFSET shift the selection in the opposite direction. You can deactivate WELL_OFFSET by setting its value to Querying the value of a string variable during runtime Besides numeric variables Gemini also supports string (text) variables. These can be used to generate file names, barcodes etc. The Set String Variable command ( button) can be used to prompt the operator for thevalueofastringvariableduringruntime.todothis,checktheuser Query checkbox when you specify the command and specify the user prompt which should appear on the screen. You can also specify a default value. The following shows a Gemini script which uses string variables and numerical variables to generate a worklist file name. Figure 11-3: Using string variables to generate worklist file names Commands supporting string variables The following list shows all commands which support string variables: Icon Command Parameter name Balance Store weight in variable Carousel Direct Movements Send String Command Table 11-2: Commands which support string variables 168 Gemini Software Manual V4.0 March 2002

177 TECAN 11 - Advanced Programming Features Icon Command Parameter name Carousel Retrieve Barcode Centrifuge Avoid imbalance through sub-routine Condition If variable Execute Application Execute Magellan Method Execute VB Script Path & Name & Command line Workspace-Filename and Method Path & Name Execute WinWash Program Notification Program Profile, Address, Subject and Message Send a Command Command Set String Variable Value Set Variable Value Sub-Routine Path & Name User Prompt Text Worklist Worklist (Path and Name) Worklist Import Import Worklist and Generated Gemini Worklist Table 11-2: Commands which support string variables (Continued) March 2002 Gemini Software Manual V

178 11 - Advanced Programming Features TECAN Expressions In addition to using variables and constants, certain commands also allow you to specify a mathematical expression (see Commands supporting expressions on page 171). An expression is constructed from floating point numbers, variables and operators. The following operators are available: Sign Function + addition - subtraction * multiplication / division % division remainder ( ) parenthesis, specifies evaluation order Table 11-3: Expressions which can be used with variables Examples of valid expressions: volume volume volume * 2 volume + (samples * 2) 3+4*5 Spaces in expressions are ignored. Multiplication and division have precedence over addition and subtraction. 170 Gemini Software Manual V4.0 March 2002

179 TECAN 11 - Advanced Programming Features Commands supporting expressions The following list shows all commands which support expressions. Icon Command Parameter Aspirate Volume or Individual Volumes Begin Loop Number of loops Carousel Direct Movements Carousel Retrieve Tower Tower, Position Carousel Return Tower, Position Carousel Scan Barcode Condition Tower Both sides of the comparison operator Copy Plate Volume Dispense Volume or Individual Volumes Merge Plates Volume Mix Volume or Individual Volumes Periodic Wash Period PnP Vector Grid, site and positioninrack Replicates Volume Table 11-4: Commands which support expressions March 2002 Gemini Software Manual V

180 11 - Advanced Programming Features TECAN Icon Command Parameter RoMa Vector Grid and site Serial Dilution Volume Set DITI Position Gride, Site, Position in rack Set Variable Value Start Timer Timer Te-MO Relative Movements Te-MO Aspirate Offset Volume Te-MO Dispense Volume Te-MO Mix Volume Te-MO Te-Stack drop rack Te-MO Te-Stack pickup rack Vacuum Separator Wait for Timer Plate type Plate type Pressure Timer and time span Wash Tips Volume in Waste and Volume in Cleaner Table 11-4: Commands which support expressions (Continued) Converting variables and expressions to a string Certain commands (e.g. User Prompt) allow you to specify a numeric variable or a mathematical expression instead of a string, e.g. for displaying the value of the variable 172 Gemini Software Manual V4.0 March 2002

181 TECAN 11 - Advanced Programming Features during runtime (see Commands supporting variables and expressions converted to a string on page 174) The expression or variable is enclosed within tilde characters ~. Gemini then replaces the expression with the value of the expression during runtime. The following shows a Gemini script and its user prompt during runtime: Figure 11-4: Gemini script with user prompt Figure 11-5: User prompt message box The next example passes a variable to an external application: Figure 11-6: Passing a variable to an external application March 2002 Gemini Software Manual V

182 11 - Advanced Programming Features TECAN Commands supporting variables and expressions converted to a string The following list shows all commands which support variables and expressions converted to text: Icon Command Parameter name Carousel Retrieve Barcode Execute Application Send a Command Set String Variable Path & Name & Command line Command (the expression is converted to an integer value before converting it to a string) Query Set Variable Query User Prompt Text Table 11-5: Commands which support variables and expressions converted to a string Validating a script containing variables When validating a script, Gemini uses default values for variables which are set during run-time, e.g. from operator prompts or return codes. Gemini might otherwise not be able to detect problems during validation. 174 Gemini Software Manual V4.0 March 2002

183 TECAN 11 - Advanced Programming Features The following list shows the default values which are used during validation for all commands which can set variables: Icon Command Variable and value used during validation Execute Application Return value = 0 Send a Command Answer = (empty string), error code = 0 Set String Variable Variable = default string specified with Value Set Variable Variable = default string specified with Value Table 11-6: Commands with default values for variables for use during script validation See also Undefined Variables on page Conditions (Condition command) The Condition command lets you continue script execution at a specified line which is based on the value of a variable or expression. Four different comparison operators are provided: is equal to is not equal to is bigger than islessthan The Condition command lets you specify an expression on both sides of the comparison operator. If the comparison is true, Gemini continues at the script line specified with then goto line. Gemini uses Comment commands as jump destinations for the Condition command. When specifying a Condition command, all comments defined in the script are shown in a pop-up list. You can also specify a name for the jump destination in the Condition command in advance and add the corresponding comment to the script later. Note: When a script is validated, Gemini uses default values for the variables as shown in Validating a script containing variables on page 174. Please note that errors might thus go undetected and that the behavior of the script could be unexpected. March 2002 Gemini Software Manual V

184 11 - Advanced Programming Features TECAN 11.3 Sub-routines Sub-routines are Gemini scripts (*.gem files) which can be used as parts of another script. They allow you to shorten complex scripts and to build libraries of pipetting procedures (e.g. serial dilutions) which you want to use repeatedly. The differences between separate scripts and sub-routines are: a sub-routine uses the same worktable as the main script, variables names and timers are shared between sub-routine and main script, loop names and line markers for conditions are not shared between sub-routines and the main script Creating a sub-routine To create a sub-routine, simply write a Gemini script and then store it. You must use the same worktable layout as in the main script Sub-routine command InsertaSub-routinecommandatthepositioninthemainscriptwhereyouwantthesubroutinetobeexecuted:. Figure 11-7: Sub-Routine command The parameters of the Execute VB Script command are as follows: Path & Name This edit field shows the filename and location of the sub-routine you want to run. Edit: Click this button to edit the specified sub-routine. Browse: Click this button to look for existing Gemini scripts and to choose the one you want to use as a sub-routine. 176 Gemini Software Manual V4.0 March 2002

185 TECAN 11 - Advanced Programming Features Execute sub-routine and wait for it to finish This starts the specified sub-routine; the main script waits for the sub-routine to finish before continuing. Start sub-routine and continue This starts the specified sub-routine but continues the main script without waiting for the sub-routine to finish. The sub-routine must contain only these commands : Move ROMA ROMA Vector MOVE PnP PnP Vector Te-Stack Carousel - Scan Barcodes Carousel - Retrieve Carousel - Return Carousel Movements Wait for previously started sub-routine to finish The main script waits for the specified, previously started sub-routine to finish before continuing. Note: You can also start a sub-routine from within another sub-routine by including a Sub-Routine command within the sub-routine Exchanging data with sub-routines Variables are shared between the main script and the sub-routine and can be used to exchange data. To feed in data into the sub-routine, set a variable in the main script and use the same variable in the sub-routine (e.g. for volumes or loops). To get data back from a sub-routine (e.g. error codes), write the data to a variable in the sub-routine and use the same variable in the main script Validating a script with sub-routines If Gemini finds an error during script validation, it displays a window with the line number and a description of the error. If a problem is detected in a sub-routine, Gemini only shows the line number of the main script and not that of the sub-routine. To correct the error, you have to open and correct the file containing the sub-routine manually. March 2002 Gemini Software Manual V

186 11 - Advanced Programming Features TECAN Log file for a script with sub-routines Gemini reports the currently executed script line in the log window and in the log file. A typicallineinthelogfileisasfollows: E 11:55:42 Line 1 : Aspirate When Gemini executes a sub-routine, it displays the line number in the main script and the line number in the sub-routine, separated by a slash /. A typical line then looks like this (line 2 of the main script, line 1 of the sub-routine, Aspirate command): E 11:55:42 Line 2/1 : Aspirate If you are using sub-routines nested inside of other sub-routines, the log file shows the line numbers of all levels, separated by slashes Loop options Many of the standard pipetting commands allow you to specify loop options, which let you to use a different column, row, well and/or rack for each loop cycle if you are using the command in a script loop. In the dialog box for the command, click Loop Options to view, define or modify the loop options: Figure 11-8: Loop Options dialog box The fields of the Loop Options dialog box are as follows: 178 Gemini Software Manual V4.0 March 2002

187 TECAN 11 - Advanced Programming Features In every cycle of loop... Choose the name of the loop to which the loop options refer. The popup list shows all of the loops in the current script. Note: Loop names are defined in your script with the Begin Loop command. Vary, for Specify how to modify the current well selection in each cycle of the loop. Choose column, row, well or rack from the vary popup list and specify the increment in the for field. A positive value in the for field increases the chosen parameter (e.g. use the next column) and a negative value decreases it. Gemini interprets a positive value in the for field as follows: Column Row Well Rack Left to right Rear to front Rear to front, then left to right Rear to front on same carrier, then the next carrier to the right Add option Click this button to add the current loop settings to the list of defined loop options. Defined loop options This shows you all of the currently defined loop options for the pipetting command. Delete option Click this button to delete the currently selected loop option from the list. March 2002 Gemini Software Manual V

188 11 - Advanced Programming Features TECAN 180 Gemini Software Manual V4.0 March 2002

189 TECAN 12 - Description of selected commands 12 Description of selected commands 12.1 Copy Plate command This command is used to make a specified number of identical copies of the source plate (complete or partial copies, 1 to 1 Copy mode). It also gives you the option to transfer selected wells from a source to a destination plate (Pick Hits mode). When copying racks, Gemini always proceeds from rear to front and from left to right. Figure 12-1: Copy Plate command The parameters of the Copy Plate command are as follows: Tip Selection Select the tips you want to use. Note: The Copy Plate command does not allow you to use a mixed tip configuration (mixture of standard / active tips and DITIs). March 2002 Gemini Software Manual V

190 12 - Description of selected commands TECAN Additional Commands When using fixed or active tips for the Copy Plate command, you must also specify a Wash command. It is executed automatically at the beginning and at the end of the sequence and between aspirations from different source wells. Click the Wash button and click on the waste and cleaner positions of the wash station you want to use in the Worktable window. If only one wash station is present, it is chosen automatically. Appropriate default settings for the Wash command are chosen automatically. When using multi-pipetting mode, Gemini uses the defined waste for discarding the excess volume before aspirating again from the same source. When using DITIs for the Copy Plate command, you must also specify the Get DITI and Drop DITI commands which are used at the beginning and at the end of the sequence and between aspirations from different source wells. Check the Don t wash first checkbox to skip the wash which normally is executed at the beginning of the sequence. Don t change DITIs first is shown instead if you selects DITIs, and works in the same way. Copies Select the number of copies you want to make from the source rack. The allowed range is from 1 to 16. Mode With 1 to 1 Copy mode, you must select the same number of samples for the source and copy (copies). With Pick Hits mode, you can select more wells on the copy (copies) than are selected on the source. This mode allows you to pick individual wells (hits) in the source and specify a group of wells on the copies where the hits should be placed. You can choose multi-pipetting if the number of copies is >1. Otherwise, Gemini will default to single pipetting mode. Copies per Aspiration When copying in multi-pipetting mode, you can limit the number of wells that are dispensed after one aspiration. The allowed range is from 2 up to the number of copies to be made. Location Select a rack for the source by clicking the Source tab and clicking on the rack in the Worktable window. Then click on the required source well(s). Select a rack for the firstcopybyclickingthecopy 1 tab and clicking on the rack in the Worktable window. Then click on the required copy well(s). Repeat this procedure for each of the other copies. The gray (inactive) field at the top right of the tab shows the label 182 Gemini Software Manual V4.0 March 2002

191 TECAN 12 - Description of selected commands (name) of the racks that you have selected (it shows a generic name if you have not assigned a rack label). Note: You can select and deselect individual wells (by clicking with the mouse while holding down the Ctrl key) or select one or more rows of wells (by clicking and dragging with the mouse). The latter operation can also be combined with the Ctrl key. Cursor (x,y) You can also select specific wells or ranges of wells by entering values for the x coordinates (from left to right) and y coordinates (from top to bottom) instead of by clicking with the mouse. Note: the cursor shows the x and y coordinates for each well as it moves over the rack in the Location panel. Select: Click this button to select the wells you have specified in the Cursor (x,y) field. Deselect: Click this button to deselect the wells you have specified in the Cursor (x,y) field. Volume You can select a different volume for each copy. Gemini automatically calculates the necessary aspiration volume for the source rack. However, Gemini does not automatically handle volumes that exceed the diluter or DITI capacity. Liquid Class You can choose a different liquid class for the source rack and for each copy. Click the Editor buttontostarttheliquidclasseseditorifyouwanttocreateanewclassor modify an existing class (see Liquid Classes on page 91). Furthermore you can customize an existing liquid class for use with this command only (click the Customize button). March 2002 Gemini Software Manual V

192 12 - Description of selected commands TECAN 12.2 Replicates command This command is used to pipette sample and dispense reagents in replicate. It only creates horizontal replicates. Figure 12-2: Replicates command The parameters of the Replicates command are as follows: Tip Selection Select the tips you want to use. Note: The Replicates command does not allow you to use a mixed tip configuration (mixture of standard / active tips and DITIs). Additional Commands When using fixed or active tips for the Replicates command, you must also specify a Wash command. It is executed automatically at the beginning and at the end of the sequence and between aspirations from different source wells. Click the Wash button and click on the waste and cleaner positions of the wash station you want to use in the Worktable window. If only one wash station is present, it is chosen 184 Gemini Software Manual V4.0 March 2002

193 TECAN 12 - Description of selected commands automatically. Appropriate default settings for the Wash command are chosen automatically. When using multi-pipetting mode, Gemini uses the defined waste for discarding the excess volume before aspirating again from the same source. When using DITIs for the Replicates command, you must also specify the Get DITI and Drop DITI commands which are used at the beginning and at the end of the sequence and between aspirations from different source wells. Check the Don t wash first checkbox to skip the wash which normally is executed at the beginning of the sequence. Don t change DITIs first is shown instead if you selects DITIs, and works in the same way. Copies Select the number of copies you want to make from the source rack. The allowed range is from 1 to 16. Mode This is used to set the placement and direction on the destination rack(s) and the pipetting mode: With AB to AABB, Gemini pipettes all replicates of the first source column onto the destination, and then proceeds with the replicates of the second source column. With AB to ABAB, Gemini pipettes a single replicate of the first column and then a single replicate of the second column, and so on. With AB to BABA, Gemini proceeds from right to left instead of from left to right. Replicates per Aspiration You can limit the number of wells that are dispensed after one aspiration. The allowed range is from 2 to 24, but Gemini will use a lower value than specified if necessary. Location Select a rack for the source by clicking the Source tab and clicking on the rack in the Worktable window. Then click on the required source well(s). Select a rack for the first copy by clicking the Copy 1 tabandclickingontherackintheworktable window. Then click on the required copy well(s). Repeat this procedure for each of the other copies. The gray (inactive) field at the top right of the tab shows the label March 2002 Gemini Software Manual V

194 12 - Description of selected commands TECAN (name) of the racks that you have selected (it shows a generic name if you have not assigned a rack label). Note: You can select and deselect individual wells (by clicking with the mouse while holding down the Ctrl key) or select one or more rows of wells (by clicking and dragging with the mouse). The latter operation can also be combined with the Ctrl key. Gemini calculates the number of replicates per sample by dividing the number of the destination columns by the number of source columns. Cursor (x,y) You can also select specific wells or ranges of wells by entering values for the x coordinates (from left to right) and y coordinates (from top to bottom) instead of by clicking with the mouse. Note: the cursor shows the x and y coordinates for each well as it moves over the rack in the Location panel. Select: Click this button to select the wells you have specified in the Cursor (x,y) field. Deselect: Click this button to deselect the wells you have specified in the Cursor (x,y) field. Volume You can select a different volume for each copy. Gemini automatically calculates the necessary aspiration volume for the source rack. However, Gemini does not automatically handle volumes that exceed the diluter or DITI capacity. Liquid Class You can choose a different liquid class for the source rack and for each copy. Click the Editor button to start the liquid classes editor if you want to create a new class or modify an existing class (see Liquid Classes on page 91). Furthermore you can customize an existing liquid class for use with this command only (click the Customize button). 186 Gemini Software Manual V4.0 March 2002

195 TECAN 12 - Description of selected commands 12.3 Serial Dilution command This command is used to perform a serial dilution in two or more steps. Each dilution step has the same dilution ratio. Figure 12-3: Serial dilution command The parameters of the Serial Dilution command are as follows: Tip Selection Select the tips you want to use. Note: The Serial Dilution command does not allow you to use a mixed tip configuration (mixture of standard / active tips and DITIs). Additional Commands When using fixed or active tips for the Serial Dilution command, you must also specify a Wash command. It is executed automatically at the beginning and at the end of the sequence and between aspirations from different source wells. Click the Wash button and click on the waste and cleaner positions of the wash station you want to use in the Worktable window. If only one wash station is present, it is chosen March 2002 Gemini Software Manual V

196 12 - Description of selected commands TECAN automatically. Appropriate default settings for the Wash command are chosen automatically. When using DITIs for the Serial Dilution command, you must also specify the Get DITI and Drop DITI commands which are used at the beginning and at the end of the sequence and between the dilution steps. Check the Don t wash first checkbox to skip the wash which normally is executed at the beginning of the sequence. Don t change DITIs first is shown instead if you selects DITIs, and works in the same way. Destination Racks Select the number of destination racks needed for diluting all selected samples. The allowed range is from 1 to 16. Mode The Serial Dilution command can handle the diluent in two different ways: With Diluent for Each Step, the Serial Dilution command will only aspirate diluent for a single dilution step. With Diluent for All Steps, the Serial Dilution command will aspirate sufficient diluent for all following dilution steps in a single operation. The Serial Dilution command normally proceeds from left to right on the destination rack(s). Check the Pipette from Right to Left checkbox to dilute from right to left instead. Copies per Aspiration This value determines for how many dilution steps Gemini should aspirate the diluent in a single operation. This option is only available if you select the Diluent for all Steps mode. Location Select a rack for the diluent by clicking the Diluent tab and clicking on the rack in the Worktable window. Then click on the required diluent well(s). Select a rack for the source by clicking the Source tab and clicking on the rack in the Worktable window. Then click on the required source well(s). Select a rack for the first destination by clicking the Destination 1 tab and clicking on the rack in the Worktable window. Then click on the required destination well(s). Repeat this procedure for each of the other destination racks. The gray (inactive) field at the top right of the tab shows the label (name) of the racks that you have selected (it shows a generic name if you have not assigned a rack label). Note: You can select and deselect individual wells (by clicking with the mouse while holding down the Ctrl key) or select one or more rows of wells (by clicking and dragging with the mouse). The latter operation can also be combined with the Ctrl key. 188 Gemini Software Manual V4.0 March 2002

197 TECAN 12 - Description of selected commands Gemini calculates the number of dilution steps by dividing the number of destination wells by the number of source wells. Cursor (x,y) You can also select specific wells or ranges of wells by entering values for the x coordinates (from left to right) and y coordinates (from top to bottom) instead of by clicking with the mouse. Note: the cursor shows the x and y coordinates for each well as it moves over the rack in the Location panel. Select: Click this button to select the wells you have specified in the Cursor (x,y) field. Deselect: Click this button to deselect the wells you have specified in the Cursor (x,y) field. Volume Specify a volume for the source and destination racks. The latter volume determines the amount of liquid left in the destination well after the Serial Dilution command has executed. The ratio between the source and the sum of source and destination volume is the dilution ratio. Note: The Serial Dilution command allows you to enter 0 µl for a destination rack. You can use this feature to implement a serial dilution by first dispensing the diluent into all wells using the Replicates command. Liquid Class You can choose a different liquid class for the diluent rack, the source rack and for each copy. Click the Editor button to start the liquid classes editor if you want to create a new class or modify an existing class (see Liquid Classes on page 91). Furthermore you can customize an existing liquid class for use with this command only (click the Customize button). March 2002 Gemini Software Manual V

198 12 - Description of selected commands TECAN 12.4 Merge Plates command This command is used to create a destination rack (e.g. a 384 well plate) by merging together one or more source racks (e.g. four 96 well plates). When merging racks, Gemini always proceeds from rear to front and from left to right. Figure 12-4: Merge Plates command The parameters of the Merge Plates command are as follows: Tip Selection Select the tips you want to use. Note: The Merge Plates command does not allow you to use a mixed tip configuration (mixture of standard / active tips and DITIs). Additional Commands When using fixed or active tips for the Merge Plates command, you must also specify a Wash command. It is executed automatically at the beginning and at the end of the sequence and between aspirations from different source wells. Click the Wash button and click on the waste and cleaner positions of the wash station you want to use in the Worktable window. If only one wash station is present, it is chosen 190 Gemini Software Manual V4.0 March 2002

199 TECAN 12 - Description of selected commands automatically. Appropriate default settings for the Wash command are chosen automatically. When using DITIs for the Merge Plates command, you must also specify the Get DITI and Drop DITI commands which are used at the beginning and at the end of the sequence and between aspirations from different source wells. Check the Don t wash first checkbox to skip the wash which normally is executed at the beginning of the sequence. Don t change DITIs first is shown instead if you selects DITIs, and works in the same way. Sources Select the number of source racks you want to merge into the destination rack. The allowed range is from 1 to 16. Mode Check the High Density checkbox to optimize the LiHa movements when using a high-density rack (e.g. a 384 well plate) for the destination rack. Distance of destination wells These two parameters specify where Gemini dispenses adjacent source wells on the destination rack. Please note the following examples: Example 1 merging 4 landscape microplates into 1 landscape 384 well plate With X and Y set to 1, the four source racks will occupy the four quadrants of the destination rack: Example 2 merging 4 landscape microplates into 1 landscape 384 well plate March 2002 Gemini Software Manual V

200 12 - Description of selected commands TECAN With X and Y set to 2, the corresponding wells from the different source racks are grouped together on the destination rack: Location Select a rack for the first source by clicking the Source 1 tab and clicking on the rack in the Worktable window. Then click on the required source well(s). Repeat this procedure for each of the other source racks. Select a rack for the destination by clicking the Destination tab and clicking on the rack in the Worktable window. Then click on the required destination well(s). The gray (inactive) field at the top right of the tab shows the label (name) of the racks that you have selected (it shows a generic name if you have not assigned a rack label). Note: You can select and deselect individual wells (by clicking with the mouse while holding down the Ctrl key) or select one or more rows of wells (by clicking and dragging with the mouse). The latter operation can also be combined with the Ctrl key. Cursor (x,y) You can also select specific wells or ranges of wells by entering values for the x coordinates (from left to right) and y coordinates (from top to bottom) instead of by clicking with the mouse. Note: the cursor shows the x and y coordinates for each well as it moves over the rack in the Location panel. Select: Click this button to select the wells you have specified in the Cursor (x,y) field. Deselect: Click this button to deselect the wells you have specified in the Cursor (x,y) field. Volume You can select a different volume for each source. Gemini automatically calculates the necessary dispense volume for the destination rack. However, Gemini does not automatically handle volumes that exceed the diluter or DITI capacity. Liquid Class You can choose a different liquid class for each source rack and for the destination rack. Click the Editor button to start the liquid classes editor if you want to create a new class or modify an existing class (see Liquid Classes on page 91). Furthermore you can customize an existing liquid class for use with this command only (click the Customize button). 192 Gemini Software Manual V4.0 March 2002

201 TECAN 12 - Description of selected commands 12.5 Transfer command This command is used to pick up liquid from specified positions on the worktable using appropriate tips and transfer it to destination positions. It is equivalent to a combination of Aspirate, Dispense and Wash commands (or a combination of Get DITIs, Aspirate, Dispense and Drop DITIs commands if you are using DITIs). Figure 12-5: Transfer command The parameters of the Transfer command are as follows: Tip Selection Select the tips you want to use. Note: The Transfer command does not allow you to use a mixed tip configuration (mixture of standard / active tips and DITIs). March 2002 Gemini Software Manual V

202 12 - Description of selected commands TECAN Additional Commands When using fixed or active tips for the Transfer command, you must also specify a Wash command. It is executed automatically at the beginning and at the end of the sequence and between aspirations from different source wells. Click the Wash button and click on the waste and cleaner positions of the wash station you want to use in the Worktable window. If only one wash station is present, it is chosen automatically. Appropriate default settings for the Wash command are chosen automatically. When using DITIs for the Transfer command, you must also specify the Get DITI and Drop DITI commands which are used at the beginning and at the end of the sequence. Volume Specify the volume that you want to transfer. Click Individual Volumes if you want to select a different volume for each tip. Location SelectarackforthesourcebyclickingtheAspirate tab and clicking on the rack in the Worktable window. Then click on the required source well(s). Select a rack for the destination by clicking the Dispense tab and clicking on the rack in the Worktable window. Then click on the required destination well(s). The gray (inactive) field at the right of the tab shows the label (name) of the racks that you have selected (it shows a generic name if you have not assigned a rack label). Liquid Classes You can choose a different liquid class for the source and destination racks. Click the Editor button to start the liquid classes editor if you want to create a new class or modify an existing class (see Liquid Classes on page 91). Furthermore you can customize an existing liquid class for use with this command only (click the Customize button). Loop options If you are using the command in a script loop, click this button if you want to specify loop options. This allows you to use a different column, row, well and/or rack for each cycle of the loop. You can choose different loop options for the source and the destination. See Loop options on page Gemini Software Manual V4.0 March 2002

203 TECAN 12 - Description of selected commands Spacing The Spacing parameter controls the distance between adjacent pipetting tips for this command. You can choose a different tip spacing for the source rack and the destination rack. Tip spacing is only relevant if you have specified the use of more than one tip. A tip spacing of 1 means that the tips will be spread to match the distance between adjacent wells in the rack. A tip spacing of 2 will select every other well in the rack. You can only choose values for tip spacing which are meaningful for the rack geometry. Cursor (x,y) You can also select specific wells by entering values for the x coordinates (from left to right) and y coordinates (from top to bottom) instead of by clicking with the mouse. Note: the cursor shows the x and y coordinates for each well as it moves over the rack in the Location panel. Select: Click this button to select the wells you have specified in the Cursor (x,y) field Worklist command This command is used to load and run external text files containing commands which tell the instrument what and where to pipette. Worklist files contain information on source and destination positions and the volumes to pipette. Figure 12-6: Worklist command The parameters of the Worklist command are as follows: Mode If you want to execute a worklist in a Gemini script, you must first load it before you can do this. Insert a Worklist command in your script and click Load Worklist to load a worklist file and specify additional parameters for the pipetting operations. Then insert an additional Worklist command in another line of your script and click Execute loaded worklist(s) to run the worklist which has already been loaded. In this case, all March 2002 Gemini Software Manual V

204 12 - Description of selected commands TECAN other parameters in the command are disabled cannot be modified. You can load several worklists by inserting several Load Worklist commands in your script. In this case, a single Execute loaded worklist(s) command runs all of the worklists which you have loaded. Gemini keeps a track of the worklists which have been run, and a second Execute loaded worklist(s) command will not run them again unless you have reloaded them. Worklist (Path and Name) Specify the path and name of the worklist file (*.gwl). Enter the path and file name directly or click the Browse button and choose the required file. Tip Selection Select the tips you want to use. Note: Gemini does not allow a mixed tip configuration (both standard / active tips and DITIs) when using a worklist. Additional Commands When using standard tips for the Worklist command, you also must specify a Wash command. It should be used between aspirations from different source wells and is specified with the W record. When using DITIs for the Worklist command, you must specify Get DITI and Drop DITI commands to be used for every W entry in the worklist file. Liquid Class You can choose a different liquid class for each source rack and for the destination rack. Click the Editor button to start the liquid classes editor if you want to create a new class or modify an existing class (see Liquid Classes on page 91). Furthermore you can customize an existing liquid class for use with this command only (click the Customize button) Worklist file format A worklist file is a text (ASCII) file. The worklist commands consist of individual lines (or records). Six different record types are available: Aspirate, Dispense, Wash / Change DITI, Flush, Break and Comment. Each record starts with a single character indicating the type and is followed by one or more parameters. The parameters are separated by semicolons. Some of the parameters are optional (see later) and some record types have no parameters. The Aspirate record has the following structure: A;RackLabel;RackID;RackName;Position;TubeID;Volume;LiquidClass;TipType;Tip Mask 196 Gemini Software Manual V4.0 March 2002

205 TECAN 12 - Description of selected commands The Dispense record has the following structure: D;RackLabel;RackID;RackName;Position;TubeID;Volume;LiquidClass;TipType;Tip Mask The Wash / Change DITI record has the following structure: W; There are no parameters (the Wash or Change DITI position is specified in the Worklist command). The Flush record has the following structure: F; It discards the contents of the tips without washing them or dropping DITIs. The Break record forces the execution of previously specified aspirate, dispense or wash actions which have not yet been executed. It has the following structure: B; If you don t specify a Break command, Gemini normally executes pipetting commands in groups to optimize the efficiency. For example, if you have specified four tips, Gemini will queue Aspirate commands until four commands are ready for execution. Specify the Break command if you want to execute the commands without waiting. The Comment record (ignored by Gemini) has the following structure: C;Comment The parameters are as follows: Parameter Range Explanation RackLabel Max. 32 characters This is the user-configurable name which can be assigned to a rack (visible as yellow labels). RackID Max. 32 characters This is the barcode of the rack. RackName Max. 32 characters This is the configuration name of the rack. Position 1.. number of wells This is the position in the rack. The position starts with 1 and increases from rear to front and left to right. TubeID Max. 32 characters This is the barcode of the tube. Volume This is the volume in µl. LiquidClass Max. 32 characters This optional parameter is the name of a liquid class. If specified, it overwrites the liquid class name specified in the Worklist command. Table 12-1: Parameters for a worklist file March 2002 Gemini Software Manual V

206 12 - Description of selected commands TECAN Parameter Range Explanation TipType Reserved, must be omitted. TipMask This optional parameter is the tip you want to use. The tip number is bit-coded, i.e. Tip 1 = 1, Tip 2 = 2, Tip 3 = 4; Tip 4 = 8 and so on. Please note that you can only use a tip which has been enabled with Tip Selection in the Worklist command. If you do not specify TipMask, Gemini uses one of the tips specified with Tip Selection in the Worklist command. Table 12-1: Parameters for a worklist file The following paragraphs describe how to create files for three different types of worklist Worklist using rack labels Use this worklist format if you want to use rack labels to specify source and/or destination positions in the worklist. This is necessary if your instrument does not have a PosID option or your racks do not carry a barcode. In this case, you only need to define the following parameters in an Aspirate or Dispense record: A;RackLabel;;RackName;Position;;Volume D;RackLabel;;RackName;Position;;Volume Parameter RackName is optional. When specified, Gemini checks whether the rack with the RackLabel is of the given configuration name. If no match is found, Gemini displays an error message. The following worklist example aspirates 10.1 µl from well A2 in rack S1, dispenses 6 µl into well A1 in rack D1, dispenses 4 µl into well B1 in rack D1 and then washes the tip / changes the DITI: A;S1;;Microplate, landscape;9;;10.1 D;D1;;Microplate, landscape;1;;6 D;D1;;Microplate, landscape;2;;4 W; Note that Gemini counts wells from rear to front and then from left to right and a Microplate, landscape rack has eight wells in each column. Accordingly, well A2 is specified in the above worklist as Gemini Software Manual V4.0 March 2002

207 TECAN 12 - Description of selected commands Worklist using rack barcodes Use this worklist worklist format if you want to use rack barcodes to specify source and/ or destination positions in the worklist. To use this worklist format, your instrument must be equipped with a PosID option and you must scan the rack (with a PosID command) in advance of the Execute Worklist command. In this case, you only need to define the following parameters in an Aspirate or Dispense record: A;;RackID;RackName;Position;;Volume A;;RackID;RackName;Position;;Volume The following worklist example aspirates 10 µl from well H12 in the rack with barcode 1234, dispenses 10 µl into well A12 into the rack with barcode 5678 and then washes the tip / changes the DITI: A;;1234;Microplate, landscape;96;;10 D;;5678;Microplate, landscape;89;;10 W; Worklist using tube barcodes Use this worklist worklist format if you want to use tube barcodes to specify source and/ or destination positions in the worklist. To use this worklist format, your instrument must be equipped with a PosID option and you must scan the rack (with a PosID command) in advance of the Execute Worklist command. In this case, you only need to define the following parameters in an Aspirate or Dispense record: A;;;RackName;;TubeID;Volume A;;;RackName;;TubeID;Volume The following worklist example aspirates 10 µl from the tube with barcode S0001, dispenses 10 µl into the tube with barcode D0002 and then washes the tip / changes the DITI: A;;;Tube 10*100mm, 16 Pos.;;S0001;10 D;;;Tube 16*100mm, 16 Pos.;;D0002;10 W; Advanced worklist features Gemini allows you to use most of the script commands in a worklist too. See Gem_Work.pdf in the Gemini program directory for information on the advanced worklist features. March 2002 Gemini Software Manual V

208 12 - Description of selected commands TECAN 12.7 Export Data command This command is used to create report files for selected racks or for all racks on the worktable. The report files contain information about the pipetting which has been carried out. Figure 12-7: Export data command The parameters of the Export Data command are as follows: Rack to be exported This panel shows the racks for which Gemini will create output files. A separate report file is created for each rack. Add a rack to the list by clicking on the rack in the Worktable window. To remove an entry, select the line in the list and click Delete rack from list. Check the Export all racks on worktable checkbox to creates reports for all racks on the worktable. In this case, the list of racks you have specified is ignored. File Formats This panel is used to select one or more file formats for the report. Gemini uses the path you have specified in Setup > Settings >Output. The file name for a rack report file (e.g. Microplate, landscape) is: rack barcode + extension for selected file format (e.g. WKS) 200 Gemini Software Manual V4.0 March 2002

209 TECAN 12 - Description of selected commands The file name for a striprack report file (e.g. Tube 13*75mm, 16 Pos.) is: carrier barcode + extension for selected file format (e.g. WKS) Please note that Gemini replaces the slash / in the carrier barcode with an underscore _. Significant pipetting step for Magellan If you plan to use a Tecan Microplate Reader (photometer) in your script, specify which pipetting step is relevant to the Magellan photometer software if the same well is pipetted several times. See Execute Magellan Method command on page 255 for further information. Don't export already exported data later again If you output report files for a rack several times from within the same script, check this checkbox if you don t want to export data again which has already been exported. Create only one record per well Gemini normally outputs one record for each Aspirate or Dispense command for each well. If you check this checkbox, Gemini only writes one record for each well which contains the accumulated errors (bitwise addition of all error codes), the accumulated total pipetting volume (the sum of dispense volumes, i.e. positive values and aspirate volumes, i.e. negative values) and the maximum detected volume Report file format The following is an example of an output file in Excel format (file XLS): Time Detect Vol Tip Number SiteOnGrid Grid Pos SRCRackID Error Volume SRC Tube ID SRC Pos SRCRack Scan Error Tube ID Pos. Version Microplate FB Tube 13*85mm 3 0 Tube 13*85mm 5 0 Tube 13*85mm 7 0 Tube 13*85mm _ :55: _ :55: _ :55: _ :55:42 Table 12-2: Sample Excel file produced with the Export Data command March 2002 Gemini Software Manual V

210 12 - Description of selected commands TECAN The first line contains the column headers, which are the same for all formats (except that some formats only support upper-case characters for column headers). The second line contains information about the rack or striprack for which the report file was created. The second line also contains information which is relevant to the Magellan (photometer) option. The third and following lines refer to wells of the rack or tubes of the striprack. Dispense commands are indicated by a positive value in the volume column and aspirate commands are indicated by a negative value. The columns contain the following information: Column Range Explanation Position 1.. number of wells Position of the well in the rack. The numbering sequence is rear to front and then left to right. TubeID Max. 32 characters This column is only used for stripracks if the tube barcodes were scanned with a PosID command. In line 2, this column shows the Gemini software version. ScanError This column shows barcode scanning errors (if any). See Table 12-4, below. In line 2, this column shows the serial number of GENESIS instrument. SRCRack Max. 32 characters For dispense commands, this column shows the configuration name of the source rack. In line 2, this column shows the configuration name of the rack for which the report file was created. SRCPos 1.. number of wells For dispense commands, this column shows the position in the source rack where the liquid came from. In line 2, this column shows the total number of wells in the rack in the x direction. SRCTubeID Max. 32 characters If the source for a dispense command was a striprack, this column shows the barcode of the source tube. In line 2, this column shows the total number of wells in the rack in the y direction. Table 12-3: Parameters in the report file output by the Export Data command 202 Gemini Software Manual V4.0 March 2002

211 TECAN 12 - Description of selected commands Column Range Explanation Volume This column contains the volume in µl which was dispensed (positive value) or aspirated (negative value). In line 2, this column shows which pipetting step is relevant to the Magellan photometer software if more than one has been carried out on the same well; see Significant pipetting step for Magellan on page 201 for further information. Error This column shows pipetting errors (if any). See Table 12-5, below. In line 2, this column shows scanning errors for the rack for which the report file was created. SRCRackID max. 32 characters For dispense commands, this column shows the source rack barcode. In line 2, this column shows the barcode of the rack for which the report file was created. GridPos For dispense commands, this column shows the grid position of the source rack. In line 2, this column shows the grid position of the rack for which the report file was created. SiteOnGrid For dispense commands, this column shows the carrier site of the source rack. In line 2, this column shows the carrier site of the rack for which the report file was created. TipNumber This column shows the tip number which was used for pipetting into / from this well. In line 2, this column contains the 4-character checksum for the file. This is used to check whether the file is corrupted or has been modified outside of Gemini (see Data Explorer on page 10). DetectVol If liquid detection was used, this column shows the detected volume in the well before the aspirate / dispense command. Time This is the time (hh:mm:ss) when the pipetting was carried out on the well. In line 2, this column shows the date that the report was created. Table 12-3: Parameters in the report file output by the Export Data command (Continued) March 2002 Gemini Software Manual V

212 12 - Description of selected commands TECAN The following table shows possible codes in the ScanError column. Please note that the ScanError entry is bit-coded. Accordingly, if several errors occurred, the value shown is the sum of several error codes. Code (decimal) Code (hex) Caused by Explanation Instrument A barcode could not be read by the PosID scanner User The user entered the barcode manually after a scanning error User The user chose Retry after a barcode scanning error User The user chose Ignore after a barcode scanning error. Table 12-4: Scanning error codes in the report file output by the Export Data command The following table shows possible codes in the Error column. The value is bit-coded. If several errors occurred, the value shown is the bitwise addition of the individual error codes. Code (decimal) Code (hex) Caused by Explanation 1 1 Instrument No liquid was detected. 2 2 Instrument Not enough liquid was detected. 4 4 Instrument Clot was detected. 8 8 Instrument A diluter error occurred during pipetting User The diluter was initialized after a diluter error User The diluter was deactivated after a diluter error User The user chose Retry after a clot-detection error User The user chose Ignore after a clot-detection error User The user chose Continue after a clot-detection error User The user chose Retry after a liquid-detection error User The user chose Pipette Air after a liquid-detection error User The user chose Go to Z-Max after a liquid-detection error. Table 12-5: Error codes used in the report file output by the Export Data command 204 Gemini Software Manual V4.0 March 2002

213 TECAN 12 - Description of selected commands Note: Gemini does not report a well in an output file if Pipette Nothing was chosen after a liquid detection or clot error. March 2002 Gemini Software Manual V

214 12 - Description of selected commands TECAN 12.8 Worklist Import command This command is used to import a Gemini worklist which has been stored in Excel CSV (comma-separated) format. Worklists are described in Worklist command on page 195. Figure 12-8: WorklistImportcommand The parameters of the Worklist command are as follows: Import Worklist (Path and Name) Specify the path and name of the CSV file to import. Enter the path and file name directly or click the Browse button and choose the required file. Column Separator Choose the separator which is used between the fields (columns) in each of the records (i.e. lines) of the import file. The default is Comma. Start with line Conversion normally starts with the first line of the import file. Specify a value which is higher than 1 to skip one or more lines at the beginning of the file. Source Rack Choose the source rack type for which the generated worklist will be used. 206 Gemini Software Manual V4.0 March 2002

215 TECAN 12 - Description of selected commands Destination Rack Choose the destination rack type for which the generated worklist will be used. Content The Import Worklist command can handle up to 11 different input parameters in the import file (rack name, rack barcode, tube barcode, worktable position for both source and destination carrier; volume, liquid class, and tip). For each column (field) of the import file, specify the assignment to one of the 11 parameters by choosing from the drop-down list. Alternatively, leave the Content field empty to skip the field because it is empty or contains irrelevant data. An error message is output if you assign the same parameter to more than one column of the input file or make a meaningless or contradictory assignment. Generated Gemini Worklist (Path and Name) Specify the required path and name of the worklist file (*.gwl). Enter the path and file name directly or click the Browse button and choose the required file. The Import Worklist command overwrites the previous contents of the file each time it is executed. OK Click OK to insert the Worklist Import command in your script. Cancel Click Cancel to close the dialog box without inserting the command. Help Click Help or press ALT-H to get online help. When your script is validated (by clicking the Validate button or automatically when you run the script), an error message is output if the worklist file specified in a Worlist command is not found. The Worklist Import command does not create a worklist file during the validation run. Accordingly, we recommend you to create an empty (dummy) worklist file using an editor such as Notepad before validating the script for the first time. March 2002 Gemini Software Manual V

216 12 - Description of selected commands TECAN 12.9 RoMa vectors The RoMa is a robotic arm with gripper fingers that can grip and move objects within the workingareaofthegenesisinstrument.itcanbeusedtotransportmicroplates, reagent blocks, deep well plates, etc. between carriers, incubators and storage positions (e.g. a RoMa shelf or carousel). Current GENESIS versions can be fitted with up to two RoMas. RoMa actions such as getting a plate from a RoMa hotel or putting it onto a carrier can be stored in the Configuration. Each RoMa action is called a RoMa vector, which is a predefined sequence of RoMa positions (called waypoints). RoMa vectors are executed in your script with the RoMa Vector command. RoMa vectors can consist of 2 to 10 waypoints. The first point is called the safe position and the last point is called the end position. The safe position should be chosen such that the RoMa can move to the safe position of another RoMa vector or to the RoMa home position without causing it to collide. The end position is where the RoMa grips or releases the object (e.g. a microplate). Also see Defining the home position for a RoMa onpage216. Like racks, RoMa vectors are stored in the Configuration and use the same carrier concept as racks. In other words, a RoMa vector is relative to a carrier, and if the carrier is moved on the worktable, the RoMa vector moves along with the carrier and does not need to be redefined. Accordingly, you only have to define a RoMa vector once and you can then re-use it for any worktable position or carrier of the same type. In addition, if your instrument is fitted with is fitted with two RoMas, the same RoMa vector can be used by either RoMa. RoMa vectors can be assigned to regular carriers (e.g. a microplate carrier), which are also used by the LiHa for pipetting. You can also define special RoMa only carriers (e.g. a RoMa hotel or shelf) which are only used by the RoMa or the PnP. RoMa only carriers are used to store (i.e. park) objects such as racks, e.g. for use in subsequent pipetting operations. They are not shown in the Worktable window. Also see the For use with ROMA only checkbox in Configuring carriers on page 62. RoMa vectors can be used directly in Gemini or in combination with the Tecan dynamic scheduling software FACTS Defining a RoMa only carrier Gemini is provided with an extensive database of carrier definitions. However, the database only contains regular carriers for use in pipetting and does not include any RoMa only carriers since there are too many individual designs. This section explains how to define a RoMa only carrier and uses a Tecan RoMa shelf with 8 positions as an example. Note that the 8 position Tecan RoMa shelf is installed at the back of the GENESIS instrument and can only be fitted at a single position. The following section, 208 Gemini Software Manual V4.0 March 2002

217 TECAN 12 - Description of selected commands Defining a RoMa vector on page 210 then explains how to create a RoMa vector for microplates placed on this carrier. The following figure shows one possible definition for an 8 position RoMa shelf, which has 8 sites for microplates. Figure 12-9: Specifying a RoMa only carrier Please note that only the fields for the X-offset of the different sites have been specified. This is permitted because: Gemini does not need to draw the shelf on the screen because RoMa shelves are not shown in the Worktable window. Accordingly, the dimensions and the X-size and Y-size of the sites can all be set to 0, due to physical limitations of size, you can only fit one 8 position RoMa shelf to the GENESIS instrument (and thus the reference offsets can be set to 0), all 8 sites are in a horizontal line (and thus the Y and Z offsets are 0). March 2002 Gemini Software Manual V

218 12 - Description of selected commands TECAN Defining a RoMa vector Based on the 8 position Tecan RoMa shelf described above, this section explains how to define a RoMa vector to move microplates to and from the sites of the carrier. The following figure shows the completed definition of the RoMa vector with three waypoints (intermediate positions of the RoMa): Figure 12-10: Defining a RoMa vector As shown in Carrier panel, the currently shown RoMa coordinates are for site 8 (on the right side of the shelf). If you select a different site, all coordinates will be recalculated accordingly. Because the sites in the example carrier only differ in the X offsets, only the X coordinates of the three waypoints of the vector will change in this case. However, this can lead to collisions if the same vector is assigned to a RoMa carrier which has different sites in the Y or Z direction. This can be avoided by using the same safe position for all sites. This is done by checking the checkbox in the Abs. (absolute) column for the first waypoint. In this case, Gemini only recalculates the X coordinate according to the selected site or grid and does not change Y, Z and R coordinates for the safe position. If necessary, you can check the Abs. checkbox for additional waypoints (but not for the end position of course). 210 Gemini Software Manual V4.0 March 2002

219 TECAN 12 - Description of selected commands See Defining RoMa vectors on page 69 for information on the other elements in the Edit RoMa Vector dialog box. Caution: Please make sure that the correct carrier and site has been chosen before specifying any coordinates or using any of the movement buttons. Otherwise the RoMa might move to the wrong position on the worktable RoMa Vector command This command instructs the instrument to execute a RoMa vector, which is a predefined sequence of RoMa positions. You can also specify gripper actions at the Safe and End positions: Figure 12-11: RoMa Vector command The parameters of the RoMa Vector command are as follows: PnP-No. Choose the required RoMa if your instrument is fitted with more than one (range: 1-2). UseRoMaVector Choose the RoMa vector you want to use for the RoMa movement. The popup list shows the RoMa vectors which you have defined in the Configuration. Then specify the grid position and the site on the carrier. The Grid field is inactive (gray) if you March 2002 Gemini Software Manual V

220 12 - Description of selected commands TECAN have chosen a RoMa only carrier in the RoMa vector definition because it is not shown in the Worktable window. Move along RoMa Vector Choose the required direction of the RoMa movement. Click And back if you want the RoMa to return to the Safe position after reaching the End position. Gripper action Choose the gripper action which should executed at the Safe position and at the End position. Speed Specify whether you want the PnP to move at its maximum speed (click Maximum) or at the speed defined in the PnP vector (click Slow) Move RoMa command This command instructs the instrument to execute simple RoMa movements: Figure 12-12: Move RoMa command The parameters of the Move RoMa command are as follows: ROMA-No. Choose the required RoMa if your instrument is fitted with more than one (range: 1-2). Open Gripper This opens the gripper to the specified width (range: 55 to 140 mm). 212 Gemini Software Manual V4.0 March 2002

221 TECAN 12 - Description of selected commands Close Gripper This closes the gripper to the specified width (range: 55 to 140 mm) using the specified force (range 0 to 249). A Grip Error message is output if no corresponding resistance is detected. Move to home position This moves the RoMa to the specified home position. After completing a sequence of movements with the RoMa, you should move it back to its home (parking) position, out of the way of other objects on the worktable (see Defining the home position for a RoMa on page 216). Move relative to current position This moves the RoMa relative to its current position. The movements in A and B are not aligned with the instrument axes, but with the current rotator position (angle). Specify the relative distances (range: -400 to 400 mm) and whether the RoMa should move at a particular speed (range: 0.1 to 400 mm/s) or with maximum speed. The movement in A is perpendicular to the gripper. Example #1: If the gripper points to the front (angle = 0 ) and the A value is positive, then the RoMA will move to the left. Example #2: If the gripper points to the left (angle = 90 ) and the A value is positive, then the RoMA will move to the back. The movement in B is in line with the gripper. Example #1: If the gripper points to the front (angle = 0 ) and the B value is positive, then the RoMA will move to the front. Example #2: If the gripper points to the left (angle = 90 ) and the B value is positive, then the RoMA will move to the left. This ensures compatibility between the Gemini software and the Tecan dynamic scheduling software FACTS Using a RoMa vector in a script The following script fetches a microplate from site 8 of the shelf, puts it onto site 7 of the same shelf and then moves the RoMa back to the home (parking) position: Figure 12-13: Using a RoMa vector in a script March 2002 Gemini Software Manual V

222 12 - Description of selected commands TECAN The following figure shows the settings which are necessary for line 1 of the example script: Figure 12-14: Specifying line 1 of the RoMa script 214 Gemini Software Manual V4.0 March 2002

223 TECAN 12 - Description of selected commands The following figure shows the settings which are necessary for line 2 of the example script: Figure 12-15: Specifying line 2 of the RoMa script The last line of the script moves the RoMa back to the home (parking) position, out of the way of other objects on the worktable. This is done with the Move RoMa command: Figure 12-16: Specifying line 3 of the RoMa script March 2002 Gemini Software Manual V

224 12 - Description of selected commands TECAN Defining the home position for a RoMa After completing a sequence of movements with the RoMa, you should move it back to its home (parking) position, out of the way of other objects on the worktable. Otherwise it might obstruct the movement of other arms such as the LiHa, which will cause script execution to halt without displaying an error message. The RoMa moves to the home position if you specify Move to home position with the Move RoMa command, when you exit the Gemini Configuration dialog box and when Gemini is terminated. The home position for a RoMa is normally at the extreme left or right of the worktable, and should be chosen to be out of the way of other objects on the worktable. The home position is specified by creating a special RoMa vector with the name HOME1, which moves the RoMa to the chosen safe position. If your instrument is fitted with two RoMas, the home position for RoMa 1 is normally at theextremeleftoftheworktableandthehomepositionforroma2isnormallyatthe extreme right of the worktable. The home position for RoMa 2 is specified by creating a special RoMa vector with the name HOME2. Proceed as follows to define a home vector for the RoMa: Identify a route across the worktable from right to left (for RoMa 1) or left to right (for RoMa 2) along which the RoMa can safely move without colliding with other objects. Then specify a RoMa vector for this route with at least five waypoints and name the vector HOME1 or HOME 2 accordingly. If you specify Move to home position with the Move RoMa command, during script runtime Gemini automatically determines the closest waypoint of the home vector to the current RoMa position. The RoMa then moves to this waypoint and along the home vector until the home (parking) position has been reached. 216 Gemini Software Manual V4.0 March 2002

225 TECAN 12 - Description of selected commands PnP vectors The PnP is a robotic arm with gripper fingers that can grip and move tubes within the working area of the GENESIS Freedom instrument. Current GENESIS Freedom versionscanbefittedwithuptotwopnps. PnPactionssuchasgettingatubefromarackcanbestoredintheConfiguration.Each PnP action is called a PnP vector, which is a predefined sequence of PnP positions (called waypoints). PnP vectors are executed in your script with the PnP Vector command. PnP vectors can consist of 1 to 10 waypoints. The first point is called the safe position and the last point is called the end position. The safe position should be chosen such that the PnP can move to the safe position of another PnP vector or to the PnP home position without causing it to collide. The end position is where the PnP grips or releases the tube. Also see Defining the home position for a PnP on page 224. Like racks, PnP vectors are stored in the Configuration and use the same carrier concept as racks. In other words, a PnP vector is relative to a carrier, and if the carrier is moved on the worktable, the PnP vector moves along with the carrier and does not need to be redefined. Accordingly, you only have to define a PnP vector once and you can then use it any worktable position or carrier of the same type. In addition, if your instrument is fitted with is fitted with two PnPs, the same PnP vector can be used by either PnP. PnP vectors can be assigned to regular carriers (e.g. a microplate carrier), which are also used by the LiHa for pipetting. You can also define special RoMa only carriers (e.g. a RoMa hotel or shelf) which are only used by the RoMa or the PnP. RoMa only carriers are used to store (i.e. park) objects such as racks, e.g. for use in subsequent pipetting operations. They are not shown in the Worktable window. Also see the For use with ROMA only checkbox in Configuring carriers on page 62. March 2002 Gemini Software Manual V

226 12 - Description of selected commands TECAN Defining a PnP vector This section explains how to define a PnP vector to move tubes between stripracks. The following figure shows the completed definition of the PnP vector with three waypoints (intermediate positions of the PnP): Figure 12-17: Defining a PnP vector As shown in Carrier & Rack panel, the currently shown PnP coordinates are for the first position in a striprack (the well at the rear of the worktable). If you select a different grid or position, all coordinates will be recalculated accordingly. Because the positions in the example rack only differ in the Y offsets, only the Y coordinates of the three waypoints of the vector will change in this case. However, this can lead to collisions if the same vector is assigned to a PnP carrier which has different sites in the X or Z direction. This can be avoided by using the same safe position for all sites. This is done by checking the checkbox in the Abs. (absolute) column for the first waypoint. In this case, Gemini only recalculates the X coordinate according to the selected site or grid and does not change Y, Z and R coordinates for the safe position. If necessary, you can check the Abs. checkbox for additional waypoints (but not for the end position of course). 218 Gemini Software Manual V4.0 March 2002

227 TECAN 12 - Description of selected commands See Defining PNP Vectors on page 76 for information on the other elements in the Edit PnP Vector dialog box. Caution: Please make sure that the correct carrier and site has been chosen before specifying any coordinates or using any of the movement buttons. Otherwise the PnP might move to the wrong position on the worktable PnP Vector command This command instructs the instrument to execute a PnP vector, which is a predefined sequence of PnP positions. You can also specify gripper actions at the Safe and End positions: Figure 12-18: PnP Vector command The parameters of the PnP Vector command are as follows: PnP-No. Choose the required PnP if your instrument is fitted with more than one (range: 1-2). Use PnP Vector Choose the PnP vector you want to use for the PnP movement. The popup list shows the PnP vectors which you have defined in the Configuration. Then specify March 2002 Gemini Software Manual V

228 12 - Description of selected commands TECAN the grid position, the site on the carrier and the position of the tube. The Grid field is inactive (gray) if you have chosen a RoMa only (PnP only) carrier in the PnP vector definition because it is not shown in the Worktable window. Move along PnP Vector Choose the required direction of the PnP movement. Click And back if you want the PnP to return to the Safe position after reaching the End position. Gripper action Choose the gripper action which should executed at the Safe position and at the End position. Speed Specify whether you want the PnP to move at its maximum speed (click Maximum) or at the speed defined in the PnP vector (click Slow) Move PnP command This command instructs the instrument to execute simple PnP movements: Figure 12-19: Move PnP command The parameters of the Move PnP command are as follows: PnP-No. Choose the required PnP if your instrument is fitted with more than one (range: 1-2). Open Gripper This opens the gripper to the specified width (range: 7 to 28 mm). 220 Gemini Software Manual V4.0 March 2002

229 TECAN 12 - Description of selected commands Close Gripper This closes the gripper to the specified width (range: 7 to 28 mm) using the specified force (range 0 to 249). A Grip Error message is output if no corresponding resistance is detected. Move to home position This moves the PnP to the specified home position. After completing a sequence of movements with the PnP, you should move it back to its home (parking) position, out of the way of other objects on the worktable (see Defining the home position for a PnP on page 224). Move relative to current position This moves the PnP relative to its current position. Specify the relative distances (range: -400 to 400 mm) and whether the PnP should move at a particular speed (range: 0.1 to 400 mm/s) or with maximum speed Using a PnP vector in a script The following script fetches a tube from position 1 of a striprack (at grid 1), puts it into position 16 of an adjacent striprack (at grid 2) and then moves the PnP back to the home (parking) position: Figure 12-20: Using PnP vectors in a Genesis script March 2002 Gemini Software Manual V

230 12 - Description of selected commands TECAN The following figure shows the settings which are necessary for line 1 of the example script: Figure 12-21: Specifying line 1 of the PnP script 222 Gemini Software Manual V4.0 March 2002

231 TECAN 12 - Description of selected commands The following figure shows the settings which are necessary for line 2 of the example script: Figure 12-22: Specifying line 2 of the PnP script March 2002 Gemini Software Manual V

232 12 - Description of selected commands TECAN The last line of the script moves the PnP back to the home (parking) position, out of the way of other objects on the worktable. This is done with the Move PnP command: Figure 12-23: Specifying line 3 of the PnP script Defining the home position for a PnP After completing a sequence of movements with the PnP, you should move it back to its home (parking) position, out of the way of other objects on the worktable. Otherwise it might obstruct the movement of other arms such as the LiHa, which will cause script execution to halt without displaying an error message. The PnP moves to the home position if you specify Move to home position with the Move PnP command, when you exit the Gemini Configuration dialog box and when Gemini is terminated. The home position for a PnP is normally at the extreme left or right of the worktable, and should be chosen to be out of the way of other objects on the worktable. The home position is specified by creating a special PnP vector with the name HOME1, which moves the PnP to the chosen safe position. If your instrument is fitted with two PnPs, the home position for PnP 1 is normally at the extreme left of the worktable and the home position for PnP 2 is normally at the extreme right of the worktable. The home position for PnP 2 is specified by creating a special PnP vector with the name HOME2. Proceed as follows to define a home vector for the PnP: Identify a route across the worktable from right to left (for PnP 1) or left to right (for PnP 2) along which the PnP can safely move without colliding with other objects. Then 224 Gemini Software Manual V4.0 March 2002

233 TECAN 12 - Description of selected commands specify a PnP vector for this route with at least five waypoints and name the vector HOME1 or HOME 2 accordingly. If you specify Move to home position with the Move PnP command, during script runtime Gemini automatically determines the closest waypoint of the home vector to the current PnP position. The PnP then moves to this waypoint and along the home vector until the home (parking) position has been reached. March 2002 Gemini Software Manual V

234 12 - Description of selected commands TECAN Move LiHa command This command is used to move the liquid handling arm (LIHA) from one position to another without performing an Aspirate or Dispense operation. Figure 12-24: Move LiHa command The parameters of the Move LiHa command are as follows: Tip Selection Select the tips you want to use. Type of movement You can either move the LIHA to the rack at maximum speed (Positioning with Global Z-Travel or Positioning with local Z-Travel) or you can move one axis of the LIHA with a specified speed (X-Move, Y-Move and Z-Move). Loop options If you are using the command in a script loop, click this button if you want to specify loop options. This allows you to use a different column, row, well and/or rack for each cycle of the loop. See Loop options on page Gemini Software Manual V4.0 March 2002

235 TECAN 12 - Description of selected commands Z-Position If you choose Positioning in the Type of Movement field, you can specify to which Z- Position the tips should be lowered at the end of the LIHA movement. Choose the required Z-position and then specify a Z offset if required. A positive value for the offset lowers the tips. Location Select the rack which you want to check by clicking the rack in the Worktable window. Then click on the required well(s). The gray (inactive) field at the right of the panel shows the label (name) of the rack that you have selected (it shows a generic name if you have not assigned a rack label). Tip Spacing The Tip Spacing parameter controls the distance between adjacent pipetting tips for this command. You can choose a different tip spacing for the source rack and the destination rack. Tip spacing is only relevant if you have specified the use of more than one tip. A tip spacing of 1 means that the tips will be spread to match the distance between adjacent wells in the rack. A tip spacing of 2 will select every other well in the rack. You can only choose values for tip spacing which are meaningful for the rack geometry. Cursor (x,y) You can also select specific wells by entering values for the x coordinates (from left to right) and y coordinates (from top to bottom) instead of by clicking with the mouse. Note: the cursor shows the x and y coordinates for each well as it moves over the rack in the Location panel. Select: Click this button to select the wells you have specified in the Cursor (x,y) field. March 2002 Gemini Software Manual V

236 12 - Description of selected commands TECAN Te-Stack command This command is used to control the stand-alone stacker (Te-Stack option) for the GENESIS instrument (the Te-MO stacker is controlled by the Te-MO Te-Stack Drop Rack and Te-MO Te-Stack Pickup Rack commands). Stackers are used to store a stack of racks and to present them to the instrument for pipetting operations. The Te-Stack command lets you get a rack from a specified stack and place it onto a moveable carrier for accessing by the LiHa or RoMa. It also lets you put the rack back into the stack. An optional barcode reader lets you scan rack barcodes. Gemini uses the barcodes e.g. in output files. The Te-Stack command supports a maximum of four stackers. Gemini assigns the logical addresses 1 to 4 automatically according to the device address (stacker 1 has the lowest address and Q-address devices are assigned before S-address devices). Figure 12-25: Te-Stack command The parameters of the Te-Stack command are as follows: Present Plate This positions the moveable carrier to allow the LiHa or RoMa to access it. Stacker-No.: Choose the required stacker If your instrument is fitted with more than one. 228 Gemini Software Manual V4.0 March 2002

237 TECAN 12 - Description of selected commands Drop Plate This drops a rack from the specified stack onto the moveable carrier. Stacker-No.: Choose the required stacker If your instrument is fitted with more than one. Stack-No.: Choose the required stack. The Te-Stack command supports a maximum of two stacks per stacker. Selected plate type: Specify the plate (rack) type (from 1 to 25). This tells the stacker the plate dimensions and how to handle the plate correctly. Available plate types: The pop-down list shows the available plate types and lets you choose the one you want to use; Gemini gets this list by interrogating the stacker firmware. Labels (names) can be assigned to plate types to make it easier to choose the correct plate type in the Selected plate type field. The labels are assigned using the Genesis Setup + Service software module and are stored in the stacker firmware (see Genesis Instrument Software Manual - Doc ID for more information). Scan barcode: Check this checkbox to read the barcode of the picked up rack using the barcode scanner on the stacker. Gemini uses the barcode e.g. in output files. Pick-up Plate This picks up a rack from the moveable carrier and puts it into the specified stack. See Drop Plate, above for a description of the parameters. March 2002 Gemini Software Manual V

238 12 - Description of selected commands TECAN Carousel commands The carousel is a motor-driven magazine system which used as storage for racks (plates). Each carousel can have 1 to 9 towers. The racks are removed from the carousel and re-inserted using the RoMa. Each of the Carousel commands supports a maximum of four carousels. Gemini assigns the logical addresses 1 to 4 automatically according to the COM port number (carousel 1 has the lowest COM port number). Please note that the RoMa Vector you use to load and unload the carousel must be based on a carrier of type "Carousel". The carrier should have as many sites as you have carousels installed. If you want to access carousel #2 in your script, choose site 2 in the RoMa Vector command. This allows Gemini to track the racks and their barcodes correctly Carousel Scan Barcodes command The Carousel Scan Barcodes command is used to scan the barcodes on the plates in the carousel. Gemini uses the barcodes e.g. in output files. Figure 12-26: Carousel Scan Barcodes command The parameters of the Carousel Scan Barcodes command are as follows. Carousel No. Choose the required carousel if your instrument is fitted with more than one (range: 1-4). Whole Carousel Scans the barcodes of all plates in the carousel. Individual Tower Scans the barcodes of the plates in one tower. Specify the required tower in the Tower field (range: 1-9). 230 Gemini Software Manual V4.0 March 2002

239 TECAN 12 - Description of selected commands Configuring the barcode types which will be accepted Choose the barcodes types which will be accepted by the carousel barcode scanners using the Barcode types tab of the POSID command, but do not choose any racks. Insert the POSID command in your script before the Carousel Scan Barcodes command. (see PosID command on page 248). If you configure barcode types with the PosID command but do not choose any racks in the Scan tab, the chosen barcode types are used to configure all of the carousel barcode scanners instead and apply to subsequent Carousel Scan Barcodes commands. The information on the barcode types is stored in the carousel barcode scanners until they are switched off or re-configured with another POSID command Carousel Retrieve command The Carousel Retrieve command is used to retrieve plates from the carousel according to a condition which you specify, e.g. retrieve a plate with a specified barcode. Figure 12-27: Carousel Retrieve command The parameters of the Carousel Retrieve command are as follows: Carousel No. Choose the required carousel if your instrument is fitted with more than one (range: 1-4). Plate with Barcode... Retrieves the plate with the specified barcode from the carousel. March 2002 Gemini Software Manual V

240 12 - Description of selected commands TECAN At Individual Position Retrieves the plate from a particular position from the carousel, specified with the parameters Tower (range: 1-9) and Position in the tower (range: 1-21). Next retrieve start position Specifies the first position from which the command Retrieve from next position starts. Retrieve from next position can be used to program a loop. Retrieve from next position Every time this command is selected, the carousel takes a plate from the next position in the tower Carousel Return command The Carousel Return command is used to return plates to the carousel according to a condition which you specify, e.g. return a plate to position 1 in tower 3 Figure 12-28: Carousel Return command The parameters of the Carousel Return command are as follows: Carousel No. Choose the required carousel if your instrument is fitted with more than one (range: 1-4). To Source Returns the plate to its original position in the carousel. 232 Gemini Software Manual V4.0 March 2002

241 TECAN 12 - Description of selected commands At Individual Position Returns the plate to a particular position in the carousel, specified with the parameters Tower (range: 1-9) and Position in the tower (range: 1-21). Next return start position Specifies the first position from which the command Return to next position starts. Return to next position can be used to program a loop. Return to next position Every time this command is selected, the carousel returns a plate to the next position in the tower Carousel Direct Movements command The Carousel Direct Movements command is used to control the carousel directly, e.g. initialize the carousel or rotate the carousel to a specified tower. Figure 12-29: Carousel Direct Movements command The parameters of the Carousel Direct Movements command are as follows: Carousel No. Choose the required carousel if your instrument is fitted with more than one (range: 1-4). Initialize Carousel Initializes the carousel. This must be done once only before the carousel is used for the first time in the script. Move to individual tower Rotates the carousel to a particular tower which is specified with the Tower parameter (range: 1-9). March 2002 Gemini Software Manual V

242 12 - Description of selected commands TECAN Send String Command This option lets you send a firmware command directly to the carousel. Enter the required command in the edit field. It will be send during the execution of the Gemini script. See the respective instrument manual for a list of firmware commands. Warning: Please be careful when using this feature. Sending the wrong commands can damage the instrument or objects in its workspace, hurt yourself or other people. End Move Completes the current carousel movement, e.g. return a plate to the carousel. This command is necessary after each Carousel Retrieve and Carousel Return command CAROUSEL settings in Gemini.opt In the default configuration, Gemini assumes that all carousels have 9 towers, that each tower has 21 slots and that the slots are cm in height. However, the rails in the carousel slots can be removed or re-positioned to accommodate very high racks. In addition, you may want or need to use less than 9 towers or 21 slots. To specify a non-standard carousel configuration, open the file Gemini.opt in the Gemini\data directory with a plain text editor such as Notepad and add the following entries to the [CAROUSELx] section (where x is the carousel number) or edit an existing entry. [CAROUSEL1] MAX_TOWER=9 TOWER01_SLOT_SIZE=1925 TOWER02_SLOT_SIZE=1925 TOWER03_SLOT_SIZE=1925 TOWER04_SLOT_SIZE=1925 TOWER05_SLOT_SIZE=1925 TOWER06_SLOT_SIZE=1925 TOWER07_SLOT_SIZE=1925 TOWER08_SLOT_SIZE=1925 TOWER09_SLOT_SIZE=1925 TOWER01_MAX_SLOT=21 TOWER02_MAX_SLOT=21 TOWER03_MAX_SLOT=21 TOWER04_MAX_SLOT=21 TOWER05_MAX_SLOT=21 TOWER06_MAX_SLOT=21 TOWER07_MAX_SLOT=21 TOWER08_MAX_SLOT=21 TOWER09_MAX_SLOT= Gemini Software Manual V4.0 March 2002

243 TECAN 12 - Description of selected commands The values in the example are for CAROUSEL1 and correspond to the default carousel configuration. You can specify non-standard settings for additional carousels (CAROUSEL2 to CAROUSEL4) analogously. March 2002 Gemini Software Manual V

244 12 - Description of selected commands TECAN Execute VB Script command This command is used to execute a Visual Basic (VB) script from within a Gemini script. Refer to the standard Microsoft documentation for more information on VB scripts. Visit e.g. and search for Visual Basic Scripting Edition. Provision is made to allow you to transfer numerical and string variables from the VB script to the Gemini script and vice versa. The VB script can include any of the Gemini named pipe commands. For information on the named pipe commands see Gem_Pipe.pdf in the Gemini program directory. When validating a Gemini script, it is not possible to execute or validate VB scripts which are called by the main script. If the main script uses variables from the VB script, youmustdeclarethem(assignvalues)inthemainscriptbeforethevbscriptiscalledto avoid the Variable not defined error during validation. If required, you can run several VB scripts simultaneously by using the Execute VB Script command more than once in your Gemini script.. Figure 12-30: Execute VB Script command The parameters of the Execute VB Script command are as follows: Path & Name This edit field shows the filename and location of the VB script you want to run. Edit: Click this button to edit the specified VB script in the Notepad editor. Browse: Click this button to look for existing VB scripts and to choose the one you want to use. Gemini script waits for end of VB script This starts the specified VB script; the Gemini script waits for the VB script to finish before continuing. 236 Gemini Software Manual V4.0 March 2002

245 TECAN 12 - Description of selected commands Gemini script continues This starts the specified VB script but continues the Gemini script without waiting for the VB script to finish. Gemini script waits for a previously started VB script The Gemini script waits for the specified, previously started VB script to finish before continuing. The VB script feature in Gemini provides a new VB object "GEMINI" with the following five functions: GetDoubleVariable: This function accepts the name of the Gemini variable as a string argument and returns a numerical value. Example: Gemini.GetDoubleVariable("volume") SetDoubleVariable : This function accepts the name of the Gemini variable as a string and its new numerical value as arguments. Example: Gemini.SetDoubleVariable "volume",10.5 GetStringVariable: This function accepts the name of the Gemini variable as a string argument and returns a string value. Example: Gemini.GetStringVariable("barcode") SetStringVariable: This function accepts the name of the Gemini variable as a string and its new string value as arguments. Example: Gemini.SetStringVariable "barcode","012345" SendNamedPipeCommand: This function accepts a complete named pipe command as a string argument. Example: Gemini.SendNamedPipeCommand("INIT_RSP;") See the Gemini/Data/VBscripts directory for examples of VB scripts. The scripts are plain text files and contain a description of their intended application Toolbar buttons for VB Scripts Gemini scans the Gemini/Data/VBscripts directory for VB scripts and associated bitmaps. The bitmaps can be used as buttons on the toolbars to allow the VB scripts to be executed manually outside of a script. The bitmaps must be BMP files which are 24 pixels wide and 22 pixels high and have the same filename as the associated VB script (e.g. testvb.vbs and testvb.bmp). Adding a button for a VB script to a toolbar Choose Toolbar in the View menu and click Customize. Click the Commands tab. A VB scripts entry will be visible in the list if Gemini has found VB scripts and matching bitmaps the Gemini/Data/VBscripts directory. March 2002 Gemini Software Manual V

246 12 - Description of selected commands TECAN Click the VB scripts entry and drag the button for the VB script to the required Gemini toolbar (the toolbar must be visible on the screen to do this). We recommend you to use the File toolbar for VB script buttons. 238 Gemini Software Manual V4.0 March 2002

247 TECAN 12 - Description of selected commands Set DiTi Position command If you are using DITIs, Gemini stores the position of the last fetched DITI. When starting a new run, the Get DiTis command starts picking up DITIs at the next available position. After loading new DITI racks onto the worktable during script runtime (e.g. using the RoMa), this command can be used to ensure that the next DiTi is fetched from position 1 rather than from the middle of the new rack. You can specify the next location for each of the available DiTi types. You can also specify the next DiTi position manually before the script is started with Set DiTi Position in the Execute menu. Figure 12-31: Set DiTi Position command The parameters of the Set DiTi Position command are as follows: DiTi type Choose the DiTi type for which you want to specify the next location. The available DiTi types are defined in the rack configuration. Next DiTi position Specify the grid, site and rack position of the next available unused DiTi of this type. You can enter either a numeric constant or a variable. The specified grid and site must contain a DiTi tray. An error message will result during runtime if another rack type is present. March 2002 Gemini Software Manual V

248 12 - Description of selected commands TECAN Pick Up DITIs command This command lets you pick up DITIs which have already been used and put back into the DiTi rack with the Set DITIs Back command. You must specify the DiTis you want to pick up. Figure 12-32: Pick Up DITIs command The parameters of the Pick Up DITIs command are as follows: Tip Selection Select the tips you want to pick up. You can only choose tips which are configured for DITIs in the configuration of the LiHa. Loop options If you are using the command in a script loop, click this button if you want to specify loop options. This allows you to use a different column, row, well and/or rack for each cycle of the loop. See Loop options on page 178. DiTi Type Choose the required DiTi type (1, 2, 3 or 4). The available DiTi types are defined in the rack configuration. Location Select the rack which you want to use by clicking the rack in the Worktable window. Then click on the required well(s). The gray (inactive) field at the top of the panel 240 Gemini Software Manual V4.0 March 2002

249 TECAN 12 - Description of selected commands shows the label (name) of the rack that you have selected (it shows a generic name if you have not assigned a rack label). March 2002 Gemini Software Manual V

250 12 - Description of selected commands TECAN Pickup ZipTip command This command is used to pick up ZipTips. ZipTips are disposable tips which are prefilled with liquid and thus do not need an aspirate command. The Pick Up ZipTip command automatically aspirates a specified volume of air before picking up the tips. The same volume should be chosen in the subsequent Dispense command, which then ejects the pre-filled liquid into the well. Figure 12-33: PickupZipTipcommand The parameters of the Pickup ZipTip command are as follows: Tip Selection Select the tips you want to pick up. You can only choose tips which are configured for DITIs in the configuration of the LiHa. Loop options If you are using the command in a script loop, click this button if you want to specify loop options. This allows you to use a different column, row, well and/or rack for each cycle of the loop. See Loop options on page 178. ZipTip Type Choose the required DiTi type (1, 2, 3 or 4). The available DiTi types are defined in the rack configuration. 242 Gemini Software Manual V4.0 March 2002

251 TECAN 12 - Description of selected commands Airgap Choose the required size of the airgap in µl and the aspiration speed for the airgap in µl/s. Location Select the rack which you want to use by clicking the rack in the Worktable window. Then click on the required well(s). The gray (inactive) field at the top of the panel shows the label (name) of the rack that you have selected (it shows a generic name if you have not assigned a rack label). March 2002 Gemini Software Manual V

252 12 - Description of selected commands TECAN Detect Liquid command Liquid detection is one of the options available for aspirating and dispensing and can be individually defined for each liquid class. The Detect Liquid command is used to carry out liquid detection without pipetting and reports the liquid volume for each of the chosen wells in the rack. The volumes are returned in a set of variables DETECT_VOLUME_X, where X is the tip number. Figure 12-34: Detect Liquid command The parameters of the Detect Liquid command are as follows: Tip Selection Select the tips you want to use. Loop options If you are using the command in a script loop, click this button if you want to specify loop options. This allows you to use a different column, row, well and/or rack for each cycle of the loop. See Loop options on page 178. Liquid Class Choose the required liquid class. Click the Editor button to start the liquid classes editor if you want to create a new class or modify an existing class (see Liquid Classes on page 91). 244 Gemini Software Manual V4.0 March 2002

253 TECAN 12 - Description of selected commands Location Select the rack which you want to check by clicking the rack in the Worktable window. Then click on the required well(s). The gray (inactive) field at the right of the panel shows the label (name) of the rack that you have selected (it shows a generic name if you have not assigned a rack label). Tip Spacing The Tip Spacing parameter controls the distance between adjacent pipetting tips for this command. You can choose a different tip spacing for the source rack and the destination rack. Tip spacing is only relevant if you have specified the use of more than one tip. A tip spacing of 1 means that the tips will be spread to match the distance between adjacent wells in the rack. A tip spacing of 2 will select every other well in the rack. You can only choose values for tip spacing which are meaningful for the rack geometry. Cursor (x,y) You can also select specific wells by entering values for the x coordinates (from left to right) and y coordinates (from top to bottom) instead of by clicking with the mouse. Note: the cursor shows the x and y coordinates for each well as it moves over the rack in the Location panel. Select: Click this button to select the wells you have specified in the Cursor (x,y) field. March 2002 Gemini Software Manual V

254 12 - Description of selected commands TECAN Te-MO Relative Movements command This command is used to perform Te-MO movements with an offset. The Te-MO (Tecan Multipipetting Option) is normally used to perform pipetting operations on all of the wells of a rack simultaneously, whereby the Te-MO pipetting head is positioned directly above the rack. However, it can also be used to carry out operations such as serial dilution. In this case, pipetting takes place to one column or one row of the rack at a time. This is achieved by only picking up DITIs for a single column or row and positioning the Te-MO head with an offset to align the DITIs with the required wells. For fixed tips, you can use a special tip block which only has tips fitted to one row or column. The Te-MO head can only be positioned within the working area of the Te-MO. Accordingly, fit the tips to the column on the left side of the head if you want to access all of the columns of a rack on the left slide. Fit the tips to the column on the right side of the head if you want to access all of the columns of a rack on the right slide. If you fit the tips to the front row of the Te-MO head, you can access all rows of racks on the left or the right slide. Note: The center slide is not normally used for pipetting with relative movements. To fit DITI tips to the required column or row of the Te-MO head, load tips into only one column or row of the new DITI tray and then use the Te-MO Get DITIs command in the normal way (with an offset of 0). Figure 12-35: Te-MO Relative Movements command The parameters of the Te-MO Relative Movements command are as follows: Row offset (tips are on front side of Te-MO head) This option is used to pipette to rows of a rack on on the left or right slide. Specify the required row offset. Fit the tips to the front row of the Te-MO head. The offset for the front row is 0. The offset for the second row (from front to back) is Gemini Software Manual V4.0 March 2002

255 TECAN 12 - Description of selected commands Column offset (tips are on left side of Te-MO head) This option is used to pipette to columns of a rack on the left slide. Specify the required column offset. Fit the tips to the left column of the Te-MO head. The offset for the left column is 0. The offset for the second column (from left to right) is 1. Column offset (tips are on right side of Te-MO head) This option is used to pipette to columns of a rack on the right slide. Specify the required column offset. Fit the tips to the right column of the Te-MO head. The offset for the left column is 0. The offset for the second column (from left to right) is 1. Switch off offset This cancels a previously specified offset (row or column) and has the same effect as specifying a column offset of 0 with the option Column offset (tips are on left side of Te-MO head). You cannot specify a row and a column offset simultaneously. If you specify a row offset, this cancels a previously specified column offset. It is recommended to use the Te-MO Relative Movements command to switch off the offset before fetching the DITIs with the Te-MO Get DITIs command. In addition, it is recommended to use the Te-MO Relative Movements command to switch off the offset when you no longer want to use Te-MO offsets in your script. The Te-MO does not support liquid detection. If the liquid class configuration specifies liquid detection, it must be emulated for the Te-MO using a special variable (see RACK_VOLUME_X on page 166). March 2002 Gemini Software Manual V

256 12 - Description of selected commands TECAN PosID command This command is used to read the barcodes of one or more racks using the POSID device (barcode scanner). The Scan tab lets you choose the racks you want to scan and the Barcode types tab is used to configure the barcode types which the POSID scanner will accept for the chosen racks. Figure 12-36: PosID command, Scan The parameters of the POSID command are as follows (Scan tab): Racks to be scanned This shows the racks which Gemini will scan with this command. You can add racks to the list by clicking on the racks in the Worktable window. Delete rack from list To remove a rack from the list, select the corresponding line and click this button. Scan worktable with Choose a scanning speed between 30 and 300 mm/s. Choose slower speeds if the barcodes are difficult to read or very small and to prevent spilling of the liquid in the wells as the scanner carrier is positioned. No prompt for scan errors If this option is enabled, Gemini does not display an error message if a barcode could not be read. If a carrier barcode isn't readable, all tubes or racks on this carrier won't be scanned either and keep their default barcodes. The default barcode is the grid position followed by an underscore (_) and then the site number. If a rack or tube barcode isn't readable, Gemini assigns a default barcode of three stars (***). 248 Gemini Software Manual V4.0 March 2002

257 TECAN 12 - Description of selected commands Write file with scan results If this option is enabled, Gemini creates a report file which lists the scanned barcodes. The filename is SCAN.CSV and it is created in the Gemini output directory (default path Gemini\Output). Existing files with the same filename are overwritten. The file contains one line per scanned rack or tube barcode. Each line contains the following parameters, separated by semicolons: Grid;Site on Carrier;Position in Rack (for Tubes only);configuration name of rack or tube;rack label on worktable;carrier barcode;scanned barcode. POSID command, Barcode types tab The Barcode types tab of the POSID command is used to configure the barcode types which the POSID scanner will accept. If you configure barcode types with the POSID command but do not choose any racks in the Scan tab, the chosen barcode types are used to configure all of the carousel barcode scanners instead and apply to subsequent Carousel Scan Barcodes commands. The information on the barcode types is stored in the carousel barcode scanners until they are switched off or re-configured with another POSID command. Figure 12-37: PosID command, Barcode types The parameters of the POSID command are as follows (Barcode types tab): Type Choose the barcodes types which will be accepted by the barcode scanner from the popup lists. Some of the barcode types have additional settings. Note: The barcode scanner will report an error if it finds barcode types which you have not chosen. Length 0 do not check the length of the barcode March 2002 Gemini Software Manual V

258 12 - Description of selected commands TECAN the length of the barcode must match this value (the checksum and start/stop code are also counted). Barcodes with different lengths will be ignored. Check Mode empty evaluate / transmit evaluate / don't transmit Start/Stop empty transmit don't transmit do not check the checksum. the checksum is checked and is reported to Gemini as part of the barcode. the checksum is checked but not reported. a start/stop code is not required. a start/stop code is required and is reported to Gemini as part of the barcode. a start/stop code is required but not reported. 250 Gemini Software Manual V4.0 March 2002

259 TECAN 12 - Description of selected commands Doorlocks command This command is used to open or close the doorlocks of the GENESIS instrument. Gemini supports up to four doorlocks and the doorlocks are arranged in groups. The doorlocks of all groups are closed automatically when starting or re-starting a script. The doorlocks of all groups are opened automatically when finishing, stopping or pausing the script. Use the Doorlocks command in your script to open the doorlocks of a specified group while the script is running to allow the operator to access to the instrument. Figure 12-38: Doorlocks command Open Doorlocks Specify this option to open all of the doorlocks in the group. Specify the required group by choosing it from the list. Close Doorlocks Specify this option to close all of the doorlocks in the group. Specify the required group by choosing it from the list. See Configuring the Doorlocks on page 90 for information on how to assign the doorlocks to one of the four available groups. March 2002 Gemini Software Manual V

260 12 - Description of selected commands TECAN System command If your GENESIS instrument is fitted with the ChemSystem option, you can choose the required system liquid in your script with the System command. This causes the instrument to drain off the currently used system liquid and replace it with another one. It is first necessary to configure the ChemSystem to specify the additional system liquids (see Configuring the ChemSystem on page 87). The available system liquids are shown as blue/green rectangles at the bottom right of the worktable and in the System command dialog box. In the following example, three system liquids are defined (System. DMSO and Aqua. Dest.): Figure 12-39: System command The parameters of the System command are as follows: Switch to system liquid... Select the system liquid you want to use. Flush instrument Specify the waste position on the worktable which should be used to drain off the currently used system liquid from the tubing. Choose the required waste from the list or click on the waste position in the Worktable window. Specify the volume of system liquid which is necessary to refill the tubing. See Configuring the ChemSystem on page 87 for information on how to aspirate the current system liquid in your script. 252 Gemini Software Manual V4.0 March 2002

261 TECAN 12 - Description of selected commands MIO command The MIO command is used to control the Tecan Monitored Incubator Option, which consists of a heated incubator with optional shaker device. The MIO command supports a maximum of four incubators. Gemini assigns the logical addresses 1 to 4 automatically according to the device address (incubator 1 has the lowest address and O-address devices are assigned before T-address devices). Figure 12-40: MIO command The parameters of the MIO command are as follows: MIO-No. Choose the required MIO If your instrument is fitted with more than one. Close Doors This command closes the doors of the MIO slots. Start Shaking This command starts the shaking process. Speed: Specify the shaking speed (range: Hz). Stop Shaking This command stops the shaking process. Heat Slots This command is used to heat the slots of the MIO. Check the Slots checkbox for each of the slots that you want to heat. Alternatively, check All Slots to heat all slots. Then specify the required temperature of each slot in the Temperature fields alongside each slot (range: C). March 2002 Gemini Software Manual V

262 12 - Description of selected commands TECAN Deactivate Slots This command is used to deactivate the slots (switch off the heating). Check the Slots checkbox for each of the slots that you want to deactivate. Alternatively, check All Slots to deactivate all slots. Only the selected slots will be deactivated. 254 Gemini Software Manual V4.0 March 2002

263 TECAN 12 - Description of selected commands Execute Magellan Method command The Execute Magellan Method command is used to control Tecan microplate readers (i.e. photometers) using the Magellan data collection and reduction software. This command gets important information it requires from a rack report file which is output by the Export Data command. Your script must include an Export Data command for the rack in advance of the Execute Magellan Method command. The Export Data command must be configured to create the rack report file in CSV format. The rack to be scanned is placed in the Tecan microplate reader using the RoMa. The associated RoMa vector must position the rack on a special carrier of type "Reader". This is a RoMa only carrier which is only visible in the Configuration and not in the Worktable window. When the Execute Magellan Method command is started, it is given the barcode of the rack which was placed on the special carrier. This allows the correct rack report file to be used. Reports prepared by the Magellan Method identify which wells which have been scanned (e.g. using the sample barcode). If several pipetting steps have been carried out on the same well or wells, the Magellan Method needs to know which of them can be used as a unique identifier for the samples. Information on the relevant step is contained in the rack report file and must be configured in the accompanying Export DatacommandinthefieldSignificant pipetting step for Magellan. March 2002 Gemini Software Manual V

264 12 - Description of selected commands TECAN The Execute Magellan Method command lets you edit, create or execute a Magellan method. Figure 12-41: Execute Magellan Method command The parameters of the Execute Magellan Method command are as follows: Start Magellan This option starts the measurement sequence in the microplate reader. Workspace Filename: Specify a name for the Magellan workspace file. If you don t enter a filename, a default Magellan workspace file will be used instead. Delete content if workspace exists: Measurement data recorded earlier in the workspacefilewillbeoverwrittenbythenewdata. Append new values if workspace exists: The new data will be appended to measurement data which was recorded earlier. Method: Name.mth Browse: Clickthisbuttontolookforexistingmethodfilesandtochoosetheoneyou want to use. 256 Gemini Software Manual V4.0 March 2002

265 TECAN 12 - Description of selected commands New Method: Click this button to start the Magellan Wizard. The wizard is used to create a new method file or to edit an existing one. Note: The error message "Magellan server could not be created" will be shown if the Magellan software is not installed. Constants Set no constants during execution: Do not set any Magellan constants during execution of the Magellan method. Query Magellan constants during execution: A dialog box is opened during script run time to allow the operator to specify a value for each of the Magellan constants as a numeric value, numeric variable or Gemini expression. Set Magellan constants during execution: This allows you to specify a value or variable for each of the Magellan constants when writing the script. The constants are set to the actual variable values during script run time. Click Show constant dialog to specify the values of the Magellan constants as follows: Figure 12-42: Edit Magellan Constants dialog box Name: Name of the Magellan constant. Value: Specify a numeric value, numeric variable or Gemini expression for the Magellan constant. Refer to the Magellan manual for additional information. Required: This indicates whether the Magellan constant is obligatory or optional. Wait for end of method Gemini normally continues with subsequent commands in the pipetting script even if the microplate reader is still busy. This option causes the pipetting script to wait until the Magellan method has completed. March 2002 Gemini Software Manual V

266 12 - Description of selected commands TECAN Warning Display and interrupt script: If a warning is encountered, display it on the screen and stop the script. Write warning to log file without interrupting script: If a warning is encountered, write a message to the log file but do not stop the script. Note: The script is always stopped if an error is encountered. In addition, the error message is displayed on the screen. Move plate out This option moves the plate out of the microplate reader. Move plate in This option moves the plate into the microplate reader. 258 Gemini Software Manual V4.0 March 2002

267 TECAN 12 - Description of selected commands Execute WinWash Program command The Execute WinWash Program command is used to control Tecan Plate Washers using the WinWash Plus software. WinWash Plus is an MS Windows-based program which is supplied with Tecan Plate Washers. It lets you specify wash programs and download and upload wash programs to/from the plate washer via the RS232 interface. It also functions as the software interface between Gemini and the plate washer hardware. Figure 12-43: Execute WinWash Program command The parameters of the Execute WinWash Program command are as follows. Washer selection Choose the plate washer type which is fitted to your instrument. Execute WinWash This option starts a wash program on the Tecan Plate Washer. You can only start wash programs that have already been downloaded to the washer using the WinWash Plus software or created and stored in the washer manually. The plate washer must be primed before using it for a wash program (see below). March 2002 Gemini Software Manual V

268 12 - Description of selected commands TECAN Number of Strips: This parameter is only needed by the Columbus plate washer. Choose the number of strips that you want to wash in the rack (range: 1 to 32). Browse: Click this button to see a list of wash programs which are currently stored in the plate washer and to choose the one that you want to use. Gemini gets this list by interrogating the plate washer. Note: The error message "WinWash server could not be created" will be shown if the WinWash Plus software is not installed. Start Prime Priming is used to prepare the Plate Washer for use in a wash program. Priming can take several minutes; you can start priming with this command at an early stage in your script to make sure that the washer is ready when you want to use it. Channel: Select the channel containing the wash buffer liquid you want to use for the following wash program. Mode: Choose Short if you only want to flush the washer dispense tips (the washer tips used to dispense the wash buffer liquid). If you choose Full, first of all the washer dispense tips are flushed. Then the waste container is filled with liquid. After that the washing head is lowered into the liquid and the washer aspirate tips are flushed as well. Time: Specify the number of seconds that the prime procedure should run. To ensure proper filling of the system, it is recommended to choose not less than 5 seconds and not more than 15 seconds. Start Rinse Channel: Select the channel containing the liquid you want to use for the rinse procedure. Mode: Choose Day (short) if the plate washer has only been out of use for a short period of time (e.g.the lunch break of the operator). This procedure is normally performed using the wash buffer liquid. After cleaning the washing head, all washer tips are soaked in the wash buffer liquid to prevent blockages. The Night (long) procedure should be used instead If the instrument will not be used for a longer period of time. Choose Night (long) at the end of each working day to clean the washing head. This procedure is normally performed using distilled water (lab grade). After the cleaning step, all washer tips are soaked in distilled water. This procedure is repeated every 6 hours to compensate for evaporation and to ensure that all washer tips remain soaked in distilled water. 260 Gemini Software Manual V4.0 March 2002

269 TECAN 12 - Description of selected commands Time: Specify the number of seconds that the rinse procedure should run (range 5 to 15 seconds). The soaking step continues indefinitely until it is interrupted by the Stop Rinse command. The instrument is then switched back to standby mode. Wait for end of program or end of prime Gemini normally continues with subsequent commands in the pipetting script even if the plate washer is still busy. This option causes the pipetting script to wait until the wash program or end of priming has finished. Stop Rinse The rinsing procedure is an endless process and the soaking step continues indefinitely until it is interrupted by the Stop Rinse command. The instrument is then switched back to standby mode. March 2002 Gemini Software Manual V

270 12 - Description of selected commands TECAN Centrifuge command This command is used to control the centrifuge option. Please note that the RoMa Vector you use to load and unload the centrifuge must be based on a carrier of type "Centrifuge". The carrier should have 4 sites (one for each centrifugation bucket). If you want to access bucket #2 in your script, use the Centrifuge command to move the rotor to position 2 and then choose site 2 in the following RoMa Vector command. Figure 12-44: Centrifuge command The parameters of the Centrifuge command are as follows: Open Hatch This opens the hatch to allow a rack to be inserted into or removed from the centrifuge using the RoMa. Close Hatch This closes the hatch. The hatch must be closed to allow centrifuging to start. Move Rotor to Position This turns the centrifuge rotor to allow the rack to be inserted or removed at the specified rotor position (1 to 4). Start Centrifugation This starts centrifuging with the specified parameters: 262 Gemini Software Manual V4.0 March 2002

271 TECAN 12 - Description of selected commands Time in s (seconds): Duration of the centrifuging. Speed rpm: Speed of the centrifuging. Ramp up: Choose the required ramp for accelerating the centrifuge to the working speed (range 1-9). Ramp down: Choose the required ramp for decelerating and stopping the centrifuge when centrifuging is finished (range 1-9). Temperature C: Choose the temperature required during centrifuging (range -20 C to +40 C). Abort Centrifugation This stops the centrifuging prematurely. Normally, centrifuging stops when the specified time has elapsed. Avoid possible imbalance through sub-routine Click this radio button if you want to use a sub-routine to avoid mechanical imbalance by always placing racks in the centrifuge in pairs. The sub-routine is only executed if an odd number of racks is placed in the centrifuge. You can determine the number of racks in the centrifuge by checking a pre-defined Gemini variable (see CENTRIFUGE_RACK_CNT on page 165). The sub-routine should be designed to place an additional rack in the centrifuge in the proper place to avoid the imbalance. Browse Specify the path and name of the balance sub-routine file (*.gem). Enter the path and file name of the file directly or click the Browse button and choose the required file. Edit This opens the balance sub-routine in a new window to allow you to edit it. OK Click OK to insert the Worklist Import command in your script. Cancel Click Cancel to close the dialog box without inserting the command. Help Click Help or press ALT-H to get online help. March 2002 Gemini Software Manual V

272 12 - Description of selected commands TECAN Active WashStation command This command is used to control the pressure pump of the Active WashStation. It is mainly intended for ZipTips. Standard tips are washed in a wash station using the Wash Tips command, which moves the LiHa over the wash station and flushes the system liquid through the tips and into the waste. ZipTips cannot be flushed and are washed after use in an Active WashStation, which has its own pump. In this case, you must move the LiHa over the Active WashStation with a Move Liha command before executing the Active WashStation command. Figure 12-45: Active WashStation command The parameters of the Active WashStation command are as follows: Time of activation in seconds Specify the time of pump activation in seconds (range seconds). Wait until termination of command Gemini normally continues with subsequent commands in the pipetting script even if the pressure pump is still busy. This option causes the pipetting script to wait for the pressure pump to finish before continuing. Continue with script without waiting for termination The Gemini script continues without waiting for the pressure pump to finish. 264 Gemini Software Manual V4.0 March 2002

273 TECAN 13 - Error Handling 13 Error Handling This chapter discusses common error messages which can be displayed by the Gemini software. See Error messages on page A-3 for a list of the more common error messages Liquid error Gemini displays the following dialog box when the instrument reports a liquid detection error. The dialog box shows the respective tip or tips and its status. The last column display the detected volume: Figure 13-1: Liquid Error dialog box The buttons in the dialog box are as follows: Retry detection Gemini retries the liquid detection. Move tips to Z (Max) Gemini moves the tips to Z-Max and then tries to aspirate the specified volume again. Pipette nothing Gemini aspirates nothing and dispenses nothing in the following commands until the next Wash Tips/Change DITIs. Affected wells will not appear in the output files. March 2002 Gemini Software Manual V

274 13 - Error Handling TECAN Aspirate air instead of the liquid Gemini aspirates air instead of the liquid and treats it the same way. Abort The pipetting run is aborted. Help Click Help or press ALT-H to get online help. 266 Gemini Software Manual V4.0 March 2002

275 TECAN 13 - Error Handling 13.2 Clot error Gemini displays the following dialog box when the instrument reports a clot detection. It shows the respective tip or tips and its status: Figure 13-2: Clot Error dialog box The buttons in the dialog box are as follows: Dispense back into vessel, then retry Gemini dispenses the aspirated volume back into the vessel and retries the liquid detection, volume aspiration, and clot detection. Dispense back into vessel, then pipette nothing Gemini dispenses the aspirated volume back into the vessel and omits the following pipetting commands until the next Wash Tips/Change DITIs. Affected wells will not appear in the output files. Go on with clot Gemini resumes pipetting, clot error reported in output file(s). Continue, ignore clot error Gemini resumes pipetting, clot error not reported in output file(s). Help Click Help or press ALT-H to get online help. March 2002 Gemini Software Manual V

276 13 - Error Handling TECAN 13.3 Instrument error Gemini displays the following dialog box when the instrument reports an error that is not handled automatically by Gemini. The dialog box shows the error number, a brief description of the error, and the instrument device and command that caused the error. Figure 13-3: Instrument Error dialog box The buttons in the dialog box are as follows: Retry Gemini resends the command to the instrument. Ignore Gemini ignores the error and resumes operation. Please be careful with this button, because ignoring errors can lead to further errors. Abort Gemini switches to simulation mode. Help Click this button or press ALT-H to get online help. 268 Gemini Software Manual V4.0 March 2002

277 TECAN 13 - Error Handling Send This button lets you send a firmware command directly to the instrument and is only intended for specialists. Specify the required command in the Command field (e.g. A1PIZ to initialize the tips in the Z-direction) and click Send (see the respective instrument manual for a list of firmware commands). The response from the instrument and a subsequent error (if any) will be shown in the Answer and Error fields. Warning: Please be careful when using this feature. Sending the wrong commands can damage the instrument or objects in its workspace, hurt yourself or other people. March 2002 Gemini Software Manual V

278 13 - Error Handling TECAN 13.4 Diluter error Gemini displays the following dialog box when the instrument reports a diluter error. The dialog box shows the respective diluter or diluters and its error: Figure 13-4: Diluter Error dialog box The buttons in the dialog box are as follows: Initialise Gemini moves the LiHa above the left-most waste and tries to initialize the diluter(s). If an error occurs again, the dialog box is displayed again. If the initialization is successful, pipetting continues, but all commands up to the next wash or DITI change are marked with a liquid error. Deactivate This switches off the affected diluter. It is not used any further for the pipetting and is marked as broken in the Configuration for the LiHa. Help Click Help or press ALT-H to get online help. 270 Gemini Software Manual V4.0 March 2002

279 TECAN 13 - Error Handling 13.5 DITI Fetch error Gemini displays the following dialog box if a DITI could not be fetched. It shows the respective tip or tips and its status: Figure 13-5: Error Fetching DITI dialog box The buttons in the dialog box are as follows: Retry at same position Gemini tries to fetch a DITI at the same position again. Try at next position Gemini tries to fetch a DITI at the next available location in the DITI rack. Abort The pipetting run is aborted. Help Click Help or press ALT-H to get online help. March 2002 Gemini Software Manual V

280 13 - Error Handling TECAN 13.6 Lost DITI error Gemini displays the following dialog box if a DITI has been lost directly before or after a pipetting command. It shows the respective tip or tips and its status: Figure 13-6: Lost DITI Error dialog box The buttons in the dialog box are as follows: Continue, but pipette nothing with lost DITI Gemini continues the pipetting, but does not do anything with the lost DITI (or the corresponding DITI adapter) until the next Drop DITI command. Abort The pipetting run is aborted. Help Click Help or press ALT-H to get online help. 272 Gemini Software Manual V4.0 March 2002

281 TECAN 13 - Error Handling 13.7 Barcode error Gemini displays the following dialog box if the instrument reports an error while scanning a barcode. It shows the error which was returned: Figure 13-7: Error Reading Barcodes dialog box The buttons in the dialog box are as follows: Retry Gemini scans the barcode again. Enter The user can enter the barcode manually. Cancel The run is aborted. Ignore Gemini ignores the error. This may lead to further errors. Help Click Help or press ALT-H to get online help. March 2002 Gemini Software Manual V

282 13 - Error Handling TECAN 13.8 Grip error Gemini displays the following dialog box if the RoMa could not grip a plate or if the PnP could not grip a tube: Figure 13-8: Grip Rack Error dialog box The buttons in the dialog box are as follows: Retry Gemini tries to grip the plate or tube again. Ignore Gemini ignores the error. Abort The pipetting run is aborted. Help Click Help or press ALT-H to get online help. 274 Gemini Software Manual V4.0 March 2002

283 TECAN 13 - Error Handling 13.9 WRC/Te-MO error Gemini displays the following dialog box if the Te-MO or the Wash and Refill Center (WRC) reports an error, with the exception of the errors WRC overflow and WRC empty, which are described later. The dialog box shows the error number and a brief description of the error: Figure 13-9: WRC/Te-MO Error dialog box The buttons in the dialog box are as follows: Retry Gemini resends the command to the instrument. Ignore Gemini ignores the error and resumes operation. Please be careful with this button, because ignoring errors can lead to further errors. Abort Gemini switches to simulation mode. Help Click Help or press ALT-H to get online help. Send This button lets you send a firmware command directly to the instrument. Specify the required command in the Command field (e.g. A1PIZ to initialize the tips in the Z- direction) and click Send (see the respective instrument manual for a list of firmware commands). The response from the instrument and a subsequent error (if any) will be shown in the Answer and Error fields. Warning: Please be careful when using this feature. Sending the wrong commands can damage the instrument or objects in its workspace, hurt yourself or other people. March 2002 Gemini Software Manual V

284 13 - Error Handling TECAN WRC Empty error Gemini displays the following dialog box during a wash cycle if the wash station of the Wash and Refill Center (WRC) is empty. You will be asked if you want the wash station to be refilled: Figure 13-10: Washstation Error error dialog box The buttons in the dialog box are as follows: OK The pumps will be started, and run until the liquid reaches the specified level or the user stops the pumps. Ignore Gemini ignores the error and resumes operation. Please be careful with this button, because ignoring errors can lead to further errors. Abort The pipetting script will be stopped. 276 Gemini Software Manual V4.0 March 2002

285 TECAN 13 - Error Handling WRC Overflow error Gemini displays the following dialog box during a wash cycle if the wash station of the Wash and Refill Center (WRC) has overflowed. You will be asked if you want to empty the wash station: Figure 13-11: Washstation Overflow Error dialog box The buttons in the dialog box are as follows: OK The vacuum pump will be started, and runs until the liquid reaches the specified level or the user stops the pump. Ignore Gemini ignores the error and resumes operation. Please be careful with this button, because ignoring errors can lead to further errors. Abort The pipetting script will be stopped. March 2002 Gemini Software Manual V

286 13 - Error Handling TECAN Setup port for Magellan The Magellan option contains special software for Tecan photometers. Gemini displays the following dialog box if the photometer cannot be connected. This can happen if the photometer is switched off, the wrong photometer is selected or the wrong port is selected: Figure 13-12: Magellan Port Setup dialog box The buttons in the dialog box are as follows: Instrument Choose the connected reader or choose Find any. Port Choose the port to which the instrument is connected or choose Find any. OK Gemini tries to connect to the reader again. If this fails, the dialog box will be displayed again. Cancel The pipetting run is aborted. Help Click Help or press ALT-H to get online help. 278 Gemini Software Manual V4.0 March 2002

287 TECAN 13 - Error Handling WinWash Plus Liquid Error WinWash Plus is the control software for the Tecan Plate Washers. Gemini displays the following dialog box when executing a script containing WinWash commands if one or more of the bottles is empty: Figure 13-13: WinWash Liquid Error dialog box The buttons in the dialog box are as follows: OK Gemini resends the command to the instrument. Ignore Gemini ignores the error and resumes operation. Please be careful with this button, because ignoring errors can lead to further errors. Cancel The pipetting run is aborted. Help Click Help or press ALT-H to get online help Other WinWash Plus errors The following general errors can also occur: COM-Library could not be initialized! Possible reason: WinWash Plus is not installed. WinWash server could not be created! Possible reason: WinWash Plus is not installed. The washer could not be connected! Possible reason: Washer not switched on or washer not connected to the PC. March 2002 Gemini Software Manual V

288 13 - Error Handling TECAN The following error can occur when defining the WinWash command in your script: Error during wash program selection! Internal WinWash error. A problem occurred when choosing the WinWash program. The following errors can occur when validating a script with WinWash: WinWash: Stop Rinse has to be inserted first! You must insert a Stop rinse command in your script prior to the current script line. WinWash: Wait for end of program has to be inserted first! You must insert a Wait for end of program or end of prime command in your script prior to the current script line. WinWash: Wait for end of Prime has to be inserted first! You must insert a Wait for end of program or end of prime command in your script prior to the current script line. 280 Gemini Software Manual V4.0 March 2002

289 TECAN 13 - Error Handling Te-Stack errors Gemini displays the following message box if the Te-Stack (stand-alone stacker) or the Te-MO Stacker reports an error. Figure 13-14: Te-Stack Errors message box The following errors can occur: Stack not in position You must insert a stack into the stacker (both Te-MO stacker and Te-Stack). Stack empty The stack is empty, you must insert racks (both Te-MO stacker and Te-Stack). Carrier position not empty The drop position is already occupied, you must remove the rack from the drop position (Te-Stack only). Carrier position empty The position for picking up the rack is empty, you must place a rack onto the carrier at the pick up position (Te-Stack only). No barcode detected The rack barcode could not be scanned (e.g. damaged barcode, or wrong barcode format). You should check the barcode and/or the scanner. March 2002 Gemini Software Manual V

290 13 - Error Handling TECAN Gemini displays the following dialog box if the Te-Stack reports an error which is not listed above. The dialog box shows the error number and a brief description of the error, such as Te-Stack collided with an obstacle or time-out error : Figure 13-15: Te-Stack Error dialog box The buttons in the dialog box are as follows: Retry Gemini resends the command to the instrument. Ignore Gemini ignores the error and resumes operation. Please be careful with this button, because ignoring errors can lead to further errors. Abort The pipetting run is aborted. Help Click Help or press ALT-H to get online help. Send This button lets you send a firmware command directly to the instrument. Specify the required command in the Command field (e.g. Q4PIS to initialize the tips in the Z- direction) and click Send (see the respective instrument manual for a list of firmware commands). The response from the instrument and a subsequent error (if any) will be shown in the Answer and Error fields. Warning: Please be careful when using this feature. Sending the wrong commands can damage the instrument or objects in its workspace, hurt yourself or other people. 282 Gemini Software Manual V4.0 March 2002

291 TECAN 14 - Appendices 14 Appendices 14.1 How to create a custom default worktable When you create a new script, Gemini starts by opening the $$NEW$$.GEM script, which is in the Gemini/Data directory. To define a custom default worktable, open this file, specify the default worktable as required, and save the $$NEW$$.GEM script Standard options for carriers and racks When Gemini is first installed, the Worktable window lists all of the standard carriers which are defined in the Gemini database. After selecting a carrier, the list of racks only shows racks which are suitable for use with the carrier. See also the description of the Hide from List of Carrier on worktable and For use with ROMA only checkboxes in Adding carriers and racks to the worktable on page How to create additional carriers New carriers are normally specified in the carrier configuration dialog box of the Gemini software (see Configuring carriers on page 62). In certain cases, you may need to create a custom carrier or rack in the Carrier/Rack/ Container (CRC) database of the GENESIS Instrument Software and to import the new carrier into the Gemini configuration file (CARRIER.CFG). This can be done with the ReadWat tool: Create the new carrier in the CRC Editor of the Genesis instrument software (refer to the Genesis Instrument Software Manual - Doc ID for more information). Make a backup copy of the existing CARRIER.CFG file. It is contained in the Gemini/ Data directory Start READWAT.EXE on the computer where the CRC Editor is installed. It is contained in the Gemini directory) You will see a list of all defined carriers and racks. When you click with the mouse onto a carrier in the carrier list, the assigned rack(s) will be highlighted. Specify the path that READWAT.EXE should use for writing CARRIER.CFG (the path defaults to the current Gemini data path, which is normally the Gemini/Data directory). When you only want to import new carriers, activate the option Displayonlycarriers which are not already defined in Gemini. Otherwise, READWAT.EXE will convert the entire CRC database and overwrite all of the rack and carrier data in Gemini, including racks you may have subsequently modified. March 2002 Gemini Software Manual V4.0 A-1

292 14 - Appendices TECAN Click the Write CFG button. Click OK to quit READWAT.EXE. If necessary, copy CARRIER.CFG to the desired location. Note: You can only import carriers and racks, not worktables or applications. Gemini contains another tool for importing new carriers and racks. The ImpMan tool impman.exe lets you copy individual objects (carriers, racks, liquid classes and RoMa vectors) from one Gemini data directory to another. Please see Impman.pdf in the Gemini directory for a description of the ImpMan tool. A-2 Gemini Software Manual V4.0 March 2002

293 TECAN 14 - Appendices 14.4 Error messages The following list describes the more common error messages that can be output when running a script. See also Error Handling on page 265 for additional information on errors. Variable variablename not defined The variable variablename is not defined in your script. See Defining and setting a variable on page 161. DITI waste not defined This message is output if a Drop DITI command does not define a DITI waste (or a valid one). Low Volume command without Low Volume device This message is output when using a Liquid Class if the Use Pinch Valve option has been chosen and the GENESIS instrument has no Low Volume option installed. The following messages are related to Loop Options and appear if Gemini detects that a range has been violated after evaluating a Loop Option. Column larger than... The calculated column number exceeds the number of columns in the rack being used. Column less than 1... The calculated column number is a negative value or zero. Internal error: too many elements in liquid column Gemini allows up to 200 elements in its internal virtual liquid column. Gemini keeps track of the contents of all tips, and every airgap and volume element is counted. Invalid rack number This message appears if there is an internal problem with a Copy Plate, Replicates or Serial Dilution command. Next rack not defined There is no following rack for a rack loop with an increment. Previous rack not defined There is no preceding rack for a rack loop with a decrement. Row larger than... The calculated row number exceeds the number of rows in the rack being used. Row less than 1... The calculated row number is a negative value or zero. March 2002 Gemini Software Manual V4.0 A-3

294 14 - Appendices TECAN Too many files open This message appears if there is an internal problem with a Copy Plate, Replicates or Serial Dilution command. Too many nested loops Gemini allows up to 100 nested loops. A-4 Gemini Software Manual V4.0 March 2002

295 TECAN 14 - Appendices 14.5 Structure of the log files Gemini can write log files to document the pipetting, to record user actions, to help you to check scripts in simulation mode and to find errors. As described below, you can activate three types of log files with different levels of logging detail, either individually or in combination. Choose Settings in the Setup menu to configure the log file options (see Settings on page 16). The log files are written to the specified log files directory (default Gemini/LogFiles). Log files are protected by checksums which are stored in the file. Caution: Gemini can write up to 100,000 individual log files, which can use up a lot of storage on your hard disk. Accordingly, it is recommended to delete or archive oldorunwantedlogfilesonaregularbasis. Even if you have not activated the Log Files option, you can view recent log entries by choosing Log Window in the View menu. The Log Window has the same structure as the log files and shows the last 1000 log entries when it is first opened. Full log file (type LOG) A log file of type LOG contains the highest level of detail. It contains the record types A to G in Table 14-1 on page A-7. A new log file is written to the Gemini\LogFiles directory each time you run a script. The filename is LOGxxxxx.LOG, where xxxxx is a five digit number. The following is an example of part of a full log file (the structure is explained below): E 11:55:20 Line 1 : Aspirate tip 1 : aspirate 51.95µl 1, 1 Tube 13*85mm, 16 Pos. [1,1] 50.00µl "Water" Standard <all volumes> Single tip 2 : aspirate 51.95µl 1, 2 Tube 13*85mm, 16 Pos. [1,1] 50.00µl "Water" Standard <all volumes> Single tip 3 : aspirate 51.95µl 1, 3 Tube 13*85mm, 16 Pos. [1,1] 50.00µl "Water" Standard <all volumes> Single tip 4 : aspirate 51.95µl 1, 4 Tube 13*85mm, 16 Pos. [1,1] 50.00µl "Water" Standard <all volumes> Single F 11:55:20 > A1,SHZ2090,2090,2090,2090,2090,2090,2090, A1,0 > A1,PAA0,-32,188,1415,1415,1415,1415,2090,2090,2090,2090 F 11:55:22 - A1,0 > M1,GFC - M1,0 > D1,OV420P60M0R > D2,OV420P60M0R March 2002 Gemini Software Manual V4.0 A-5

296 14 - Appendices TECAN > D3,OV420P60M0R > D4,OV420P60M0R > M1,GSC - M1,0 - D1,0 - D2,0 - D3,0 - D4,0 > A1,SDM2,1 - A1,0 > A1,SSL600,600,600,600,,,, - A1,0 > A1,STL1325,1325,1325,1325,,,, - A1,0 > A1,SML490,490,490,490,2100,2100,2100, A1,0 > A1,SBL20,20,20,20,,,, - A1,0 > A1,MDT15,,,,5,5,5,5,0,0,0,0 F 11:55:26 * A1,11 > A1,REE - A1,0,@@@@K@@@@@@ C 11:55:26 tip 1 : OK / automatic handling tip 2 : not enough liquid tip 3 : OK / automatic handling tip 4 : OK / automatic handling D 11:55:40 button "pipette air" has been pressed F 11:55:40 > A1,RPZ0 - A1,0,506,2090,882,611,2090,2090,2090,2090 > A1,SSS14,,14,14,,,, - A1,0 > M1,GFC - M1,0 > A1,MRZ-5,0,-5,-5,0,0,0,0 > D1,V900P156M50R > D2,V900P156M50R > D3,V900P156M50R > D4,V900P156M50R > M1,GSC - M1,0 F 11:55:41 - D1,0 A-6 Gemini Software Manual V4.0 March 2002

297 TECAN 14 - Appendices - D2,0 - D3,0 - D4,0 - A1,0 > A1,RPZ0 - A1,0,501,2090,877,606,2090,2090,2090,2090 > A1,SSS200,,200,200,,,, - A1,0 > A1,MAZ556,,932,661,,,, - A1,0 > M1,GFC - M1,0 > D1,OV420P30M0R > D2,OV420P30M0R > D3,OV420P30M0R > D4,OV420P30M0R > M1,GSC - M1,0 F 11:55:42 - D1,0 - D2,0 - D3,0 - D4,0 Each line has the following structure: Column Explanation 1 Alpha character which symbolizes the type of logged information: A = internal event B = dialog was opened C = message appeared on the screen D = user action E = pipetting command F = serial command (send to the instrument or response from instrument) G = named pipe command or response 2 Space character The time in the format hh:mm:ss 11 Space character 12.. End of Line Additional information depending on the type of information Table 14-1: Structure of the log files March 2002 Gemini Software Manual V4.0 A-7

298 14 - Appendices TECAN Please note that some of the columns 1 to 10 are filled with space characters if the type of information or the time has not changed since the previous line. The additional information which is shown for a pipetting command, taken from the above example of a log file, is as follows: E 11:55:20 Line 1 : Aspirate tip 1 : aspirate 51.95µl 1, 1 Tube 13*85mm, 16 Pos. [1,1] 50.00µl "Water" Standard <all volumes> Single "Line 1 : Aspirate " Line 1 of the Gemini script was executed. It contains an Aspirate command. "tip 1 : aspirate 51.95µl 1, 1 Tube 13*85mm, 16 Pos. [1,1]" Tip 1 executes an Aspirate command which aspirates µl (the net volume of liquid after applying calibration factor and offset from the liquid class) from 1,1 (X and Y position) of rack Tube 13*85mm, 16 Pos. (the configuration name of the rack). The rack is placed at [1,1] (grid 1 and site 1 of the carrier). "50.00µl "Water" Standard <all volumes> Single " The net volume (without calibration) is µl. The liquid class Water and subclass Standard <all volumes> was used. The command is a single pipetting command. User log file A log file of type USR contains information on pipetting commands and user inputs. It contains the record types D and E in Table 14-1 on page A-7. A new log file is written to the Gemini\LogFiles directory each time you run a script. The filename is USRxxxxx.TXT, where xxxxx is a five digit number. Error log file A log file of type ERR contains information on pipetting commands, user inputs and errors/warnings. It contains the record types C, D and E in Table 14-1 on page A-7. A new log file is written to the Gemini\LogFiles directory each time you run a script. The filename is ERRxxxxx.TXT, where xxxxx is a five digit number. The error file is empty (except for the checksum at the beginning) if no errors took place Structure of the Trace file The trace file (Trace.txt) contains information on all Gemini files which have been created, edited or saved. Each entry in the trace file specifies the date and time, user name (except for log files) and path/file name. The trace file is written to the Gemini/ Data directory. A-8 Gemini Software Manual V4.0 March 2002

299 TECAN 14 - Appendices 14.6 Gemini directory structure and files This section describes Gemini s directory structure and its files. The following structure is used if you choose the installation defaults: Figure 14-1: Directory structure The main directory of the Gemini installation contains the following files: File Carrier.cfg Collision Avoidance in Gemini 3.5.pdf ConvMan.exe Gem_Pipe.pdf Gem_Work.pdf Gemini.cnt Gemini.exe Gemini.hlp Gemini.jpg Gemini.opt Gemini.set Genfirm.hlp Hldinst.exe ImpMan.exe ImpMan.pdf Install.log Description Default carrier, rack, RoMa vector and PnP vector data. Description of the arm collision avoidance procedures in Gemini. Utility to convert liquid class files to the new Gemini 3.20 file format. Documentation for Gemini s named pipes (remote control) interface. Documentation for Gemini s advanced worklist features. Online help contents. Gemini application. Online help file. Default background image to display as wallpaper. Template (read only) for the Gemini options file. Gemini settings file. Online help for instrument firmware commands. Tool to install / de-install dongle drivers. Tool to extract configuration data and liquid classes from another Gemini data directory. Brief documentation for ImpMan.exe. Log file of setup application. Used by Unwise.exe. Table 14-2: Files contained in the Gemini directory March 2002 Gemini Software Manual V4.0 A-9

300 14 - Appendices TECAN File LClasses.dat Opnx32.dll PipeClnt.exe ReadMe.txt ReadWat.exe Revision.pdf Tecan.jpg Unwise.exe Vpex32.dll Table 14-2: Description Template (read only) for the Gemini liquid classes. Library. Tool to test remote-control interface (named pipe). ReadMe file of setup application. Tool to extract carrier and rack data from the Genesis Setup + Service database. Revision history of Gemini. Default run-time image to display when a script is running. De-installation application. Library. Files contained in the Gemini directory (Continued) The Data sub-directory contains the following files: File $$NEW$$.gem AllCmd.gem Kinetic.gem Loop.gem Transfer.gem Script1.gem... Script8.gem Carrier.cfg Gemini.cfg Gemini.opt LClasses.dat *.gem Trace.txt Description This default script is loaded when you choose New in the File menu (see How to create a custom default worktable on page A-1). Sample scripts. Carrier, rack, RoMa vector and PnP vector data. LIHA, PosID, MPO/LICOS and RoMa data. Gemini options file containing dialog defaults and other internal data. Liquid classes. Your scripts. This file contains information on all Gemini files which have been created, edited or saved. Table 14-3: Files contained in the Gemini/Data directory The Backup... sub-directories contain backup copies of Gemini configuration files and script files. See Backup Data / Recover Data on page 10. A-10 Gemini Software Manual V4.0 March 2002

301 TECAN 14 - Appendices The Data/VBscripts sub-directory contains sample VB scripts as follows: File Example1.vbs Example1.bmp Example2.vbs Example2.bmp Example3.vbs Example3.bmp Description First VB script example. Toolbar bitmap for first VB script example. Second VB script example. Toolbar bitmap for second VB script example. Third VB script example. Toolbar bitmap for third VB script example. Table 14-4: Files contained in the Gemini/Data/VBscripts directory The Data/History sub-directory is used for storing previous versions of the following files: Carrier.cgf Gemini.cfg Gemini.set Gemini.opt LClasses.dat All script files (*.gem) The previous version is stored each time one of these files is modified and saved. The date and time is appended to the original filename as follows: name.extension.yymmdd.hhmmss, where YYMMDD is the date and HHMMSS is the time of the backup, e.g.: Carrier.cfg The LogFiles sub-directory contains log and error files (see Settings on page 16 and Structure of the log files on page A-5). Caution: Gemini can write up to 100,000 individual log files, which can use up a lot of storage on your hard disk. Accordingly, it is recommended to delete or archive oldorunwantedlogfilesonaregularbasis. The Output sub-directory is used for storing the files which are generated by the Export Data command. See Export Data command on page 200 for information on the file naming conventions. March 2002 Gemini Software Manual V4.0 A-11

302 14 - Appendices TECAN 14.7 Backing up your Gemini system and Gemini data If you want to make an external backup of your entire Gemini installation, copy the Gemini directory including all subdirectories onto your backup device. If you just want to save your Gemini data, you only need to copy the entire Gemini/Data directory and the GEMINI.SET file from the Gemini directory. ChooseBackupDataintheFilemenu(seepage10)tomakeabackupoftheGemini configuration files and script files to your local hard disk instead Command line parameters Gemini supports the following command line options: Specify -u User -w Password to allow Gemini to start without requiring the user name and password to be entered manually in the Gemini Login dialog box. Specify the path and filename of a script file which should be loaded at start-up. Specify -sim in the command line Gemini to start up in simulation mode. Gemini starts with the most recently used script if you do not specify a script in the command line. The following example starts Gemini with the user login David and loads the script test.gem: gemini.exe./data/test.gem -u David -w Long A-12 Gemini Software Manual V4.0 March 2002

303 TECAN 14 - Appendices 14.9 Glossary of terms 6-way valve Option which allows the use of up to 6 different system liquids. It is a component of the ChemSystem option. Active Tips An Active Tip is an electrically activated tip which aspirates and dispenses very small quantities of liquid. Dispensing is metered by the active tip rather than by the diluter. Active Tips are a key component of the Tecan Nanopipetting System (NPS). The ActiveTip system consists of a micropump with a piezo-actuated pump chamber. It is able to form droplets in the nl (nanoliter) size range. The drop size depends on the electrical control parameters (voltage, frequency and pulse width). Each Active Tip is individually tested and is supplied with its individual control parameters which are required for proper functioning. Airgaps Airgaps are necessary for separation of different liquid segments inside tubing and tips. In order to avoid disintegration, airgaps should be kept below 30 µl. For the same reason, the airgap aspiration speed should not exceed 70 µl/second. Aspiration speed In general, a decrease of the aspiration speed will increase precision and accuracy. Very low aspiration speeds (30-70 µl/second) are required when pipetting small volumes (< 25 µl) or when pipetting liquids with high viscosity or low boiling point. Liquids with a viscosity higher than that of water may also require an aspiration delay. Calibration volume Use of the Calibration tool requires knowledge of the actual absolute pipetting volume error. Carousel Motor-driven magazine system used as storage for racks. The carousel can have one or more towers. The racks are removed from the carousel and re-inserted using the RoMa. Carrier Holder for the racks on the worktable (see Figure 14-2 on page 24). Carrier unit See Grid Unit. March 2002 Gemini Software Manual V4.0 A-13

304 14 - Appendices TECAN ChemSystem ChemSystem is an option which allows you to use up to 6 different system liquids in your GENESIS instrument. It consists of a 6-way valve to select the required system liquid, a nitrogen valve and the vacuum assisted waste option. Cleaner Well in which a tip is positioned in order to wash both its interior and exterior surfaces by dispensing system liquid through the tip. Clot detector Script function which outputs a message if the difference between the liquid levels measured before and after sample aspiration does not correspond to the calculated level difference, indicating that clots are attached to the tip. The liquid detector works in both directions, i.e., when moving into a liquid and when retracting again. This dip-out or bi-directional feature allows detection of aspirated blood clots. The principle is simple. The software stores the position at which the dip-in signal occurred. The volume aspirated and the vial diameter are known. The software can thus calculate the point at which the dip-out signal should occur. If the dip-out signal occurs at a much higher position, it can be assumed that a clot is attached to the tip. A tolerance for cohesion effects must be taken into consideration (clot limit). Connection box (Te-Flow) Valve box for use with the Te-Flow option. Command string (firmware command) Combination of user-entered parameters which instructs the Robotic Sample Processor (RSP) to perform different actions. The commands must follows the rules and syntax of the GENESIS command set. Command strings can also be sent specific devices such as the POSID. Conditioning volume Volume of excess liquid that is aspirated together with the liquid to be distributed and immediately discarded (usually in the source container) before the dispense process starts. It serves to create a controlled state of the system. The use of a conditioning volume will help to dispense the first portion of a multi pipetting distribution under conditions most similar to those of the subsequent portions. This is because the mechanical backlash of the diluter drive is eliminated after dispensing the conditioning volume. Configuration Gemini stores information on fixed and variable parts of the GENESIS pipetting instrument in the two configuration files CARRIER.CFG and GEMINI.CFG in the Gemini/data directory, which are collectively called the Configuration. The Configuration also contains information on the dimensions of the racks and carriers which are available and parameters for optional accessories. The Configuration is A-14 Gemini Software Manual V4.0 March 2002

305 TECAN 14 - Appendices edited with the Configuration Editor, which is started when you choose Configuration in the Setup menu. Container Individual well or tube which is used to contain liquid (see Figure 14-2 on page 24). CRC Editor Carrier/Rack/Container editor (part of the GENESIS Instrument Software). It is used to edit the CRC database. See the Genesis Instrument Software Manual - Doc ID for more information. CRC (checksum) Cyclic redundancy check. A method which used to calculate a checksum for files or data. Gemini uses a CRC checksum to check whether configuration files have been corrupted or modified outside of Gemini. Deep-well plate A type of microplate with a capacity of more than 400 µl for each well. Mainly used for predilution and/or for storage of serum. Detection speed Speed at which the liquid level is detected. Because automatic liquid detection on the GENESIS RSP is based on measurement of the capacitance, the correct detection speed is dependent on the conductivity of the liquid used as well as on the well geometry. The normally used liquid detection speed ( mm/s) must be reduced when pipetting small volumes of distilled water or organic solvents. Diluter Precision pump used to aspirate and dispense exactly defined volumes of liquid by means of motor-driven syringes. The GENESIS Diluter XP 3000 consists of a syringe pump and a 3-way valve that is connected through flexible tubing to the pipetting tip and a system liquid reservoir. Dispense speed/breakoff The dispense speed never should be set below 250 µl/second to guarantee laminar liquid flow at the tip face and to avoid droplets forming on the tip when dispensing from above the liquid surface. The maximum dispense speed may be limited by foam formation as well as by the shape and size of the destination container. When pipetting very small volumes, the speed of the liquid flow often is limited by the diluter drive s maximum acceleration. DiTis Disposable tips. They are normally only used once (e.g. to avoid contamination) and are discarded after use to the DiTi waste. Dongle See hardlock. March 2002 Gemini Software Manual V4.0 A-15

306 14 - Appendices TECAN Error handling mode Identifies the system reaction (e.g., stop instrument and call operator, or aspirate at Z-max, or skip sample, etc.) which is triggered by an error condition. Excess volume Used for multi pipetting. Volume of excess liquid that is aspirated together (not separated by an airgap) with the liquid to be distributed. It is not dispensed anywhere, but is discarded to waste (or to a special position) after use. Use of an excess volume ensures that the volume of the last portion of a multi pipetting distribution is the same as previous portions. To a certain extent, excess volume can also help to prevent the pipetted sample from being diluted by the system liquid. FACTS Tecan dynamic scheduling software (option). FAWA Abbreviation for Fast Wash. This is used to pump a larger amount of liquid at higher speed through the system, normally to rinse the tips. The Monitored Pump Option consists of FAWA and LICOS. Flush Procedure that rinses the entire liquid system for the purpose of removing air pockets or exchanging the system liquid. Free dispensing Dispensing without the tip touching the liquid. The opposite of free dispensing is submerged dispensing. Freedom GENESIS Freedom instrument. Global Z-travel Gemini retracts the tips to this height when moving between different objects on the worktable. When it moves over a single object, it uses the respective Z-Travel value instead. Grid, grid position Objects such as carriers are held in place by a grid of locating pins (clips). This ensures that they are accurately positioned at discrete positions on the worktable. The locating pins are spaced 25.0 mm apart in the X direction. Grid position 1 is on the left of the worktable. In Gemini, you can only position objects at grid positions and not in between. Grid unit Unit of measurement (25.0 mm, not 1 inch) on the worktable of the GENESIS instrument. Corresponds to the spacing between the locating pins in the X direction. A-16 Gemini Software Manual V4.0 March 2002

307 TECAN 14 - Appendices Hardlock Software copy protection device (or dongle) which is plugged into the parallel port of the computer (printer port). Different hardlock versions enable different Gemini software feature levels (see Standard and advanced hardlocks on page 7). ILID Integrated LIquid Detector. Electronic device mounted on the liquid handling (LiHa) arm. The ILID monitors the capacitance between the pipetting tip and electrical ground (worktable) and generates a signal when there is a sudden change in capacitance caused by the pipetting tip coming in and out of contact with an ionic solution. The signal is used for liquid and clot detection. Instrument step Smallest unit of movement for the servo motors on the GENESIS instrument (0.1 mm). ISH In Situ Hybridization method, requires the Te-Flow option. Initialization Term used to describe the calibration of one or more axes of the RSP (robotic sample processor= Genesis). The axes are offset to a predefined position. if no wash station is predefined on the worktable, the X, Y and Z coordinates are set to 0, 0 and Z-global when the instrument is fully initialized. The RSP operates using an absolute coordinate system that requires an X/Y/Z calibration. LICOS Liquid Container Supervisor. The LICOS option is a device which monitors the liquid level in the waste liquid and system liquid containers. Liquid class Set of properties defining a theoretical model for a particular type of liquid. Liquid classes are identified by a generic name (e.g., Serum, Buffer, Ethanol, etc.) and include all liquid handling parameters required to process liquids of that type. The liquid classes can be edited with the Liquid Class Editor. Liquid handling arm (LIHA) RSP component mounted on the X-slide which holds the pipetting tips. Liquid handling parameters Set of parameters that influence the liquid distribution process (e.g., aspirate and dispense speeds, delays, liquid detection, tracking, etc.). Liquid system All instrument modules and parts that contain or directly influence liquid (tubing, diluters, valves, tips, etc.). March 2002 Gemini Software Manual V4.0 A-17

308 14 - Appendices TECAN Locating pin (positioning pin) Objects such as carriers are held in place by a grid of locating pins (clips). This ensures that they are accurately positioned at discrete positions on the worktable. The locating pins are spaced 25.0 mm apart in the X direction. Also see Grid position. Low volume option The Low Volume option allows pipetting of small volumes as low as 0.5 µl with free dispensing, i.e. the tips are not touching the liquid. Even smaller volumes can be dispensed if tip touching is used. The main components of the Low Volume option are the pinch valve, the low volume pipetting tubing, the thinner low volume tips, and the pressure relief valve, which reduces the pressure in the tubing system. Impulses in the pinch valve drive tiny droplets out of the tip. The Low Volume option can only be used with a system liquid of water. Lower DITI Eject Option to discard DITIs at a lower height, e.g. to minimize contamination due to aerosols. This option is required by the Set DiTis Back command. Magellan Software for Tecan photometers. Microplate Plate (or "rack") of standardized size, typically containing 96 containers (wells) or more. MIO Monitored Incubator Option. Consists of a heated incubator with optional shaker device. MPO Monitored Pump Option (consists of FAWA and LICOS). The MPO is used to pump a larger amount of liquid at higher speed through the system, normally to rinse the tips. MTP Microtiter plate, usually called a microplate. Multi-pipetting Pipetting mode where one aspiration is performed for dispensing (aliquoting) into several destination positions. NPS Tecan Nanopipetting System. It uses ActiveTips for dispensing very small quantities of liquid. A-18 Gemini Software Manual V4.0 March 2002

309 TECAN 14 - Appendices Pinch valve Used by the Low Volume option. Allows small quantities of liquid to be dispensed accurately. Plate See rack or microplate. Plate washer Tecan Plate Washer. Requires WinWash Plus control software. PosID The PosID (Positive Identification System) is a barcode scanner device. Bar codes can also be scanned by the Symbol LS1220 barcode scanner option. Position Physical coordinates of the pipetting tip which define a location on the worktable. The position is expressed as X, Y, and Z in mm from the initialization position. PnP or P&P (Pick and Place) The PnP is a robotic arm with gripper fingers that can grip and move small objects within the working area of the GENESIS Freedom instrument, for example to transport tubes between racks. Current GENESIS Freedom versions can be fitted with up to two PnPs. PnP vector A predefined sequence of PnP positions (called waypoints) which define an action like getting a tube from a rack. Pre-dilution Technique in which a liquid (e.g., sample, control) is first diluted with additive or system liquid. Some of the resulting mixture is processed further in a follow-up distribution. The remainder of the mixture is usually discarded. Rack Generic name for a collection of containers. i.e. wells, tubes, troughs, etc. (see Figure 14-2 on page 24). A microplate is a common rack type. Reference Tip Alignment tool used to calibrate the Liquid Handling Arm (LiHa). Retract Speed The retract speed can be critical if you want to pipette liquids with a high viscosity. You must make certain that the tip retracts slowly enough to prevent any subsequent droplet formation. RMP GENESIS RMP instrument (not supported by Gemini). March 2002 Gemini Software Manual V4.0 A-19

310 14 - Appendices TECAN RoMa (Robotic Manipulator Arm) The RoMa is a robotic arm with gripper fingers that can grip and move objects within the working area of the GENESIS instrument. It can be used to transport microplates, reagent blocks, deep well plates, etc. between carriers, incubators and storage positions (e.g. a RoMa shelf or carousel). Current GENESIS versions can be fitted with up to two RoMas. Standard arm versions can handle objects on or above the worktable. Long arm (long z) versions can also access objects which are positioned lower than the worktable. RoMa hotel, RoMa shelf Device (e.g. metal shelf) used to store (i.e. park) objects such as racks which can then be picked up by the RoMa for placing in carriers. RoMa only carrier A RoMa only carrier (e.g. a RoMa hotel or shelf) ia a carrier which is only used by the RoMa or the PnP. RoMa only carriers are used to store (i.e. park) objects such as racks, e.g. for subsequent pipetting operations. They are not shown in the Worktable window. RoMa vector Sequence of movements of the RoMa. RSP GENESIS Robotic Sample Processor instrument. RWS GENESIS Robotic Work Station instrument. Script A script (or program) is a set of Gemini commands which are specific to a worktable layout. A script is normally performed in a sequential manner. Serial Dilution Technique in which a fraction of the liquid dispensed into a destination position is reaspirated and then dispensed together with additive or system liquid into a further destination position. This can be repeated several times if necessary. Shaker Abbreviation for the Tecan Orbital Shaker (Te-Shake). Single Pipetting Pipetting mode where each aspiration is performed for dispensing into just one destination position. Also see Multi-Pipetting. Site Position on a carrier which can hold an object such as a rack. For example a Microplate 3 pos. landscape carrier can hold three 384 well landscape racks. A-20 Gemini Software Manual V4.0 March 2002

311 TECAN 14 - Appendices Source Rack Rack holding container(s) out of which liquid is aspirated. SPE Solid Phase Extraction option (Te-Vacs). Stacker Stackers are used to store a stack of racks and to present them to the instrument for pipetting operations. The racks can then be returned to the stacker for subsequent actions. Genesis supports several types of stacker, e.g. the Te-MO stacker (which is installed above the Te-MO) and the Stand-alone stacker (which is attached to the side of the instrument alongside the worktable). Standard Liquid containing a defined concentration of the substance to be tested. It is used to create a standard curve allowing the concentration of the analyte in the samples to be determined. The properties of the standard are well known and stable. Stand-alone stacker option Stackers are used to store a stack of racks and to present them to the instrument for pipetting operations. The racks can then be returned to the stacker for subsequent actions. The Stand-alone stacker (or Te-Stack) is attached to the side of the instrument alongside the worktable. Striprack Tecan rack which has a single column of wells. Submerged dispensing Dispensing where the tip is submerged in the liquid. The opposite of submerged dispensing is free dispensing. Symbol LS1220 Barcode scanner option. Bar codes can also be scanned by PosID (Positive Identification System). System Liquid Liquid (e.g. water) that fills the liquid system. It can be used as a washing fluid and/or can be added to selected samples, analogously to an additive. The use of a system liquid (and the absence of air bubbles) is also important for pipetting accuracy. The ChemSystem option allows you to switch between up to 6 different system liquids. Te-Flow option The Te-Flow option provides support for the Situ Hybridization method. Te-MO Tecan Multipipetting Option (not to be confused with multi-pipetting mode). March 2002 Gemini Software Manual V4.0 A-21

312 14 - Appendices TECAN Te-MO stacker option Stackers are used to store a stack of racks and to present them to the instrument for pipetting operations. The racks can then be returned to the stacker for subsequent actions. The Te-MO stacker is installed above the Te-MO. Te-MagS Magnetic bead separator device with optional heater (instrument option). Te-Shake Orbital shaker (instrument option). Te-Stack (Tecan microplate stacker option) Stackers are used to store a stack of racks and to present them to the instrument for pipetting operations. The racks can then be returned to the stacker for subsequent actions. The Te-Stack option (also called Stand-alone stacker) is attached to the side of the instrument alongside the worktable. Te-VacS SPE (Solid Phase Extraction) vacuum system (instrument option). Tip Touching Tip touching is a special movement when dispensing a liquid. When tip touching is activated, Gemini dispenses to the destination container in the normal way, but moves the tips to the side of the well and back before retracting them. This helps to remove any drops which may be adhering to the tip. Tracking Speed Refers to the speed at which the tip moves up or down to follow the liquid level during aspiration and dispensing operations. Vacuum assisted waste Option for viscous liquids which creates a partial vacuum in the waste bottle. Variomag H+P Variomag. Device from the H+P company consisting of magnetic stirrers for tubes and a thermostatically-controlled heater. Volume Calibration Function Software function by which the volumes actually pipetted can be calibrated in order to correspond exactly to the intended volume. Wash Technique of aspirating system liquid from the diluent reservoir and dispensing it through the pipetting tips into the wash position in order to clean the inside and the outside of the tips. A-22 Gemini Software Manual V4.0 March 2002

313 TECAN 14 - Appendices Wash/Waste Station Refers to the combination of a cleaner position and a waste position. The GENESIS Wash/Waste Station is used for discarding waste liquid that has been aspirated but which is not needed anymore. It is also used for cleaning the tips. Waste Position in the wash/waste carrier into which a tip is placed for washing its interior. The system liquid is dispensed through the tip and then into the outer cavity of the wash/waste carrier. The waste liquid then flows off through the waste tubing into the waste container. Waypoint (in RoMa or PnP vectors) A vector is a sequence of movements of the RoMa or PnP. Each of the intermediate positions is called a waypoint. WinWash Plus Control software for Tecan Plate Washers. WRC Wash and Refill Center. Supporting device for the Te-MO. Well One of the containers in a microplate. Work area The instrument area that can be accessed by the pipetting tips and the RoMa. Worktable Work surface (or deck) of the GENESIS instrument where carriers are placed for access by the liquid handling arm (LiHa). The Worktable window in the Gemini March 2002 Gemini Software Manual V4.0 A-23

314 14 - Appendices TECAN software is a graphical representation of the instrument worktable (see illustration below and The Worktable window on page 117): Figure 14-2: Example worktable showing carriers, racks and rack labels When specifying an aspirate operation, click on the blue/green rectangle(s) at the bottom right of the worktable if you want to aspirate the system liquid. If you need to aspirate large volumes of the system liquid, this avoids having to place a large container on the worktable. See Configuring the ChemSystem on page 87 for further information. Y-distance of wells The spacing between adjacent wells in the rack in the Y direction (front to back). Z-Dispense Tip height at which liquid is dispensed. Gemini dispenses liquid into the rack at this position. It should be low enough to ensure that liquid cannot drop into the adjacent wells/tubes. See Figure 5-9 on page 49. Z-Max This position is the lowest point of the well/tube of the rack and is the lowest possible position the tip is allowed to reach. During a search for liquid operation, the instrument will search for liquid from Z-Start down to Z-Max. If the tip reaches Z-max without finding liquid, the instrument reacts according to the selected liquid detection error mode. See Figure 5-9 on page 49. Z-Start Tip height at which the liquid detection (ILID) is switched on during a search for liquid operation. It is usually slightly above the rim of the liquid container. A-24 Gemini Software Manual V4.0 March 2002

315 TECAN 14 - Appendices On the one hand, Z-Start should be chosen as low as possible for fast detection; on the other hand, Z-Start must be above the highest liquid level in the well/tube or the liquid will not be detected. See Figure 5-9 on page 49. Z-Travel Height at which the tip moves from one X/Y position to another. At this position, the tip should be above the highest point of the well/tube of the rack. Movements that cross different racks always use the highest Z-Travel value which is defined. See Figure5-9onpage49. March 2002 Gemini Software Manual V4.0 A-25

316 14 - Appendices TECAN A-26 Gemini Software Manual V4.0 March 2002

317 TECAN List of Figures List of Figures Figure 4-1: File menu... 9 Figure 4-2: Data Explorer dialog box Figure 4-3: Edit menu Figure 4-4: Setup menu Figure 4-5: Settings dialog box Figure 4-6: Execute menu Figure 4-7: Reset Options dialog box Figure 4-8: Set Next Available DiTi Position dialog box Figure 4-9: Loading the Te-MO dialog box Figure 4-10: View menu Figure 4-11: Status bar Figure 4-12: Command Bar Figure 4-13: Window menu Figure 4-14: Help menu Figure 5-1: Configuration editor Figure 5-2: Rack, carrier and worktable Figure 5-3: Move LIHA dialog box Figure 5-4: Move RoMa dialog box Figure 5-5: Move PnP dialog box Figure 5-6: Move Te-MO dialog box Figure 5-7: Move PosID dialog box Figure 5-8: Edit Rack dialog box Figure 5-9: Z positions for a tube Figure 5-10: Rack Wizard, step 1 of Figure 5-11: Rack Wizard, step 2 of Figure 5-12: Rack Wizard, step 3 of Figure 5-13: Rack Wizard, step 4 of Figure 5-14: Rack Wizard, step 5 of Figure 5-15: Edit Carrier dialog box Figure 5-16: Carrier dimensions and X/Y offsets Figure 5-17: Specifying the Z offset for carriers Figure 5-18: Carrier Wizard, step 1 of Figure 5-19: Carrier Wizard, step 2 of Figure 5-20: Carrier Wizard, step 3 of Figure 5-21: Edit RoMa Vector dialog box Figure 5-22: RoMa Vector Wizard, step 1 of Figure 5-23: RoMa Vector Wizard, step 2 of Figure 5-24: Edit PnP Vector dialog box Figure 5-25: PnP Vector Wizard, step 1 of Figure 5-26: PnP Vector Wizard, step 2 of Figure 5-27: LIHA dialog box Figure 5-28: PosID dialog box Figure 5-29: MPO dialog box Figure 5-30: ChemSystem dialog box Figure 5-31: Active Tips dialog box March 2002 Gemini Software Manual V4.0 A-27

318 List of Figures TECAN Figure 5-32: Doorlocks dialog box Figure 6-1: Liquid classes editor Figure 6-2: Global parameters for liquid classes Figure 6-3: Type parameters for liquid classes Figure 6-4: Aspirate parameters for liquid classes Figure 6-5: Dispense parameters for liquid classes Figure 6-6: Calibration parameters for liquid classes Figure 6-7: Aspirate parameters for NPS liquid classes Figure 6-8: Dispense parameters for NPS liquid classes Figure 6-9: Calibration parameters for NPS liquid classes Figure 7-1: Command Bar Figure 7-2: Standard commands toolbars Figure 8-1: The worktable with no objects defined Figure 8-2: Typical worktable with several objects Figure 8-3: Specifying labels for objects on the worktable Figure 8-4: Worktable showing labels for racks Figure 8-5: Command Bar Figure 8-6: Example of the Aspirate command Figure 8-7: Example of the Get DiTis command Figure 8-8: Example of the Wait for Timer command Figure 8-9: Example of the Execute Application command Figure 8-10: Example of the Copy Plate command Figure 9-1: Example script, step Figure 9-2: Example script, step Figure 9-3: Example script, step Figure 9-4: Example script, step Figure 9-5: Example script, step Figure 9-6: Example script, step Figure 9-7: Example script, step Figure 9-8: Example script, step Figure 9-9: Example script, step Figure 9-10: Example script, step Figure 9-11: Example script, step 11, showing loop options Figure 9-12: Example script, step Figure 9-13: Example script, step Figure 9-14: Example script, step Figure 9-15: Example script, step Figure 9-16: Example script, step Figure 9-17: Example script, step Figure 9-18: Example script, step Figure 9-19: Example script, step Figure 9-20: Example script, step Figure 9-21: Example script, step Figure 9-22: Example script, step Figure 9-23: Example script, step Figure 9-24: Example script, step Figure 9-25: Example script, step Figure 9-26: Example script, step A-28 Gemini Software Manual V4.0 March 2002

319 TECAN List of Figures Figure 9-27: Example script, step Figure 9-28: Example script, step Figure 10-1: Validating a script, step Figure 10-2: Validating a script, step Figure 11-1: Querying the operator for a value during script runtime Figure 11-2: Using the SAMPLE_CNT variable Figure 11-3: Using string variables to generate worklist file names Figure 11-4: Gemini script with user prompt Figure 11-5: User prompt message box Figure 11-6: Passing a variable to an external application Figure 11-7: Sub-Routine command Figure 11-8: Loop Options dialog box Figure 12-1: Copy Plate command Figure 12-2: Replicates command Figure 12-3: Serial dilution command Figure 12-4: Merge Plates command Figure 12-5: Transfer command Figure 12-6: Worklist command Figure 12-7: Export data command Figure 12-8: Worklist Import command Figure 12-9: Specifying a RoMa only carrier Figure 12-10: Defining a RoMa vector Figure 12-11: RoMa Vector command Figure 12-12: Move RoMa command Figure 12-13: Using a RoMa vector in a script Figure 12-14: Specifying line 1 of the RoMa script Figure 12-15: Specifying line 2 of the RoMa script Figure 12-16: Specifying line 3 of the RoMa script Figure 12-17: Defining a PnP vector Figure 12-18: PnP Vector command Figure 12-19: Move PnP command Figure 12-20: Using PnP vectors in a Genesis script Figure 12-21: Specifying line 1 of the PnP script Figure 12-22: Specifying line 2 of the PnP script Figure 12-23: Specifying line 3 of the PnP script Figure 12-24: Move LiHa command Figure 12-25: Te-Stack command Figure 12-26: Carousel Scan Barcodes command Figure 12-27: Carousel Retrieve command Figure 12-28: Carousel Return command Figure 12-29: Carousel Direct Movements command Figure 12-30: Execute VB Script command Figure 12-31: Set DiTi Position command Figure 12-32: Pick Up DITIs command Figure 12-33: Pickup ZipTip command Figure 12-34: Detect Liquid command Figure 12-35: Te-MO Relative Movements command Figure 12-36: PosID command, Scan March 2002 Gemini Software Manual V4.0 A-29

320 List of Figures TECAN Figure 12-37: PosID command, Barcode types Figure 12-38: Doorlocks command Figure 12-39: System command Figure 12-40: MIO command Figure 12-41: Execute Magellan Method command Figure 12-42: Edit Magellan Constants dialog box Figure 12-43: Execute WinWash Program command Figure 12-44: Centrifuge command Figure 12-45: Active WashStation command Figure 13-1: Liquid Error dialog box Figure 13-2: Clot Error dialog box Figure 13-3: Instrument Error dialog box Figure 13-4: Diluter Error dialog box Figure 13-5: Error Fetching DITI dialog box Figure 13-6: Lost DITI Error dialog box Figure 13-7: Error Reading Barcodes dialog box Figure 13-8: Grip Rack Error dialog box Figure 13-9: WRC/Te-MO Error dialog box Figure 13-10: Washstation Error error dialog box Figure 13-11: Washstation Overflow Error dialog box Figure 13-12: Magellan Port Setup dialog box Figure 13-13: WinWash Liquid Error dialog box Figure 13-14: Te-Stack Errors message box Figure 13-15: Te-Stack Error dialog box Figure 14-1: Directory structure...a-9 Figure 14-2: Example worktable showing carriers, racks and rack labels...a-24 A-30 Gemini Software Manual V4.0 March 2002

321 TECAN List of Tables List of Tables Table 4-1: Rights for users, managers and administrator Table 4-2: Configuration of the serial interfaces for external devices Table 5-1: Movement axes for the LiHa Table 5-2: Moving the LiHa using the numeric keypad Table 5-3: Movement axes for the RoMa Table 5-4: Moving the RoMa with the keys on the numeric keypad Table 5-5: Movement axes for the PnP Table 5-6: Moving the PnP with the keys on the numeric keypad Table 5-7: Movement axes for the Te-MO Table 5-8: Moving the Te-MO with the keys on the numeric keypad Table 5-9: Movement axes for the PosID Table 5-10: Moving the PosID with the keys on the numeric keypad Table 5-11: X, Y and Z coordinates for racks Table 5-12: Rack types Table 5-13: Rack types Table 5-14: Max. pipetting and washing speeds Table 7-1: List of commands which can be used in Genesis scripts Table 11-1: Commands which support variables Table 11-2: Commands which support string variables Table 11-3: Expressions which can be used with variables Table 11-4: Commands which support expressions Table 11-5: Commands which support variables and expressions converted to a string Table 11-6: Commands with default values for variables for use during script validation Table 12-1: Parameters for a worklist file Table 12-2: Sample Excel file produced with the Export Data command Table 12-3: Parameters in the report file output by the Export Data command Table 12-4: Scanning error codes in the report file output by the Export Data command Table 12-5: Error codes used in the report file output by the Export Data command 204 Table 14-1: Structure of the log files...a-7 Table 14-2: Files contained in the Gemini directory...a-9 Table 14-3: Files contained in the Gemini/Data directory...a-10 Table 14-4: Files contained in the Gemini/Data/VBscripts directory...a-11 March 2002 Gemini Software Manual V4.0 A-31

322 List of Tables TECAN A-32 Gemini Software Manual V4.0 March 2002

323 TECAN Index Index Numerics 3D effect in the worktable window way valve A-13 A Access/Status option 89 Active Tips 88, A-13 Administrator level (user management) 17 Advanced hardlock 7, 28 Advanced worklist features 199, A-9 Airgaps A-13 API using named pipes 1, 7, 236, A-9 Aspirating the system liquid 87 Aspiration speed A-13 B Background image 19 Backing up files 10, A-12 Barcode Barcode Scanner command 114 checkbox in the worktable window 120 PosID command 248 C Calibration volume A-13 Carousel A-13 settings for non-standard devices 234 Carrier A-13 Carrier colors in the Worktable window 63, 66 Carrier hidden (invisible) A-20 Carrier type 63 Carrier unit A-13 Carrier Wizard 66 Carrier/Rack/Container (CRC) database A-1 Centrifuge avoiding imbalance 165, 263 Checksum incorrect 8, 11, 20 Checksums for files 10, 20 ChemSystem 87, 252, A-14 Cleaner A-14 Clot detector A-14 Collision avoidance procedures A-9 Color of selected script line and worktable object 19, 158 Colors for carriers in the Worktable window 63, 66 Colors for racks in the Worktable window 46, 54 COM interface configuration settings for external devices 21 Command Bar 29, 107, 122 Command string (firmware command) A-14 Commands Active WashStation 115, 264 Aspirate 109 example 124 Balance 115 Barcode Scanner 114 Begin Loop 111 Carousel Direct Movements 113, 233 Carousel Retrieve 113, 231 Carousel Return 113, 232 Carousel Scan Barcodes 113, 230 Centrifuge 115, 262 Comment 111 Condition 111, 175 Connection Box 114 Copy Plate 110, 181 example 128 Detect Liquid 109, 244 Dispense 109 Doorlocks 114, 251 Drop DITIs 109 End Loop 111 Execute Application 110 example 127 Execute Magellan Method 115, 255 Execute VB Script 111, 236 Execute WinWash Program 115, 259 Export Data 110, 200 Get DITIs 109 example 125 Magnetic Separator 114 Merge Plates 110, 190 MIO 114, 253 Mix 109 Move LiHa 114, 226 March 2002 Gemini Software Manual V4.0 A-33

324 Index TECAN Move PnP 113, 220 Move RoMa 113, 212 Notification 111 Periodic Wash 109 Pick Up DITIs 109, 240 Pickup ZipTip 109, 242 PnP Vector 113, 217, 219 PosID 114, 248 Replicates 110, 184 RoMa Vector 113, 211 Send a Command 114 Serial Dilution 110, 187 Set DITI Position 109, 239 Set DITIs Back 109 Set String Variable 111, 168 Set Variable 111, 164 Shaker 114 Start Timer 110 Sub-Routine 111 System 114, 252 Te-MO Aspirate 111 Te-MO Dispense 112 Te-MO Drop DITIs 112 Te-MO Drop Tip Block 112 Te-MO Get DITIs 112 Te-MO Get Tip Block 112 Te-MO Mix 112 Te-MO Refill Trough 112 Te-MO Relative Movements 113, 246 Te-MO Te-Stack Drop Rack 112 Te-MO Te-Stack Pickup Rack 112 Te-MO Wash 112 Te-Stack 113, 228 Transfer 110, 193 User Prompt 111 Vacuum Separator 114 Variomag 114 Wait for Timer 110 example 126 Wash Tips 109 Waste 114 Waterbath Control 115 Worklist 110, 195 Worklist Import 110, 206 Commands toolbars 108 Commands, full list of 108 Conditioning volume A-14 Configuration (instrument) A-14 Configuration files (for instrument) A-14 Connection box (Te-Flow) A-14 Container A-15 CRC (checksum) for files 10, A-15 CRC database A-1 CRC Editor A-1, A-15 Custom object for worktable, defining 65 D Deep-well plate A-15 Detection speed A-15 Diluter A-15 Dispense speed/breakoff A-15 Dispensing free A-16 submerged A-21 DITI types 52, 240, 242 DITIs A-15 Dongle 7, 28, A-15 E Error handling mode A-16 Error messages 265, A-3 checksums 10 Magellan 257 Variable not defined 236 WinWash 260 Worklist 207 Example scripts 159 Excess volume A-16 External devices configuration settings for the serial interface 21 F FACTS dynamic scheduling software 1, 121, 208, 213, A-16 FAWA A-16 Feature level (of the Gemini software) 7, 28 Firmware command (glossary) A-14 Firmware command, sending 24, 85, 269, 275, 282 First well of the rack 50, 57 A-34 Gemini Software Manual V4.0 March 2002

325 TECAN Index Flush A-16 Free dispensing A-16 Freedom A-16 G GEM hardlock 7, 28 Gemini script commands, full list of 108 Global Z-travel 84, A-16 Grid A-16 Grid position A-16 Grid unit A-16 H Hardlock 7, 28, A-17 Hidden carrier A-20 Home position for a PnP 217, 224 Home position for a RoMa 208, 216 I ILID A-17 Imbalance centrifuge 165, 263 ImpMan tool A-2 Incorrectchecksum8,11,20 Initialization A-17 Instrument step A-17 Invisible carrier A-20 ISH A-17 L Label checkbox in the worktable window 120 for rack 121 Last well of the rack 50, 57 LICOS A-17 LiHa A-17 origin of coordinate system 37 positioning manually with the cursor keys 37 Liquid class A-17 Liquid column, virtual A-3 Liquid detection 93, 96, 98 Detect Liquid command 244 Te-MO 166, 247 Liquid handling arm A-17 Liquid handling parameters A-17 Liquid system A-17 Locating pin A-18 Log file type ERR A-8 type LOG A-5 type USR A-8 Long arm RoMa (long z) A-20 Loop options 178 example 139 Low volume option A-18 Lower DITI Eject A-18 M Magellan photometer software 255, A-18 Manager level (user management) 17 MAPI service (required by Notification command) 111 Measuring the position of the LiHa, RoMa, PnP and Te-MO 37 Microplate A-18 Microtiter plate A-18 MIO (option) A-18 Move LIHA dialog box 38 Moving the LiHa, RoMa, PnP and Te-MO 37 MPO (option) A-18 MTP A-18 Multi-pipetting mode A-18, A-21 Multiple wells, selecting 183 N Name (label) for rack, assigning 121 Named pipes programming interface 1, 7, 236, A-9 Nanopipetting System (NPS) 88, 101, A-13 New Genesis instrument setting up 34 NPS 101, A-13, A-18 P P&P A-19 Pick and Place A-19 Pinch valve A-19 Plate A-19 Plate Washer 279, A-19 PnP A-19 origin of coordinate system 40 March 2002 Gemini Software Manual V4.0 A-35

326 Index TECAN positioning manually with the cursor keys 40 PnP only carrier 208, 217 PnP vector moving to a specified waypoint 76 PnP Vector Wizard 79 PosID A-19 origin of coordinate system 43 positioning manually with the cursor keys 43 Position A-19 Positioning pin A-18 Pre-defined variables 165 Pre-dilution A-19 R Rack A-19 assigning a label 121 Rack colors in the Worktable window 46, 54 Rack label (rack name) 121 Rack Wizard 53 ReadWat tool A-1 Reference tip A-19 Retract speed A-19 Revision history A-10 RMP instrument A-19 RoMa origin of coordinate system 39 positioning manually with the cursor keys 39 RoMa (Robotic Manipulator Arm) A-20 RoMa exchange position for Te-MO slides 25, 43 RoMa hardlock 7, 28 RoMa hotel A-20 RoMa only carrier 208, 217, A-20 RoMa shelf A-20 RoMa vector A-20 moving to a specified waypoint 69 RoMa Vector Wizard 73 RoMa vectors 208 RSP instrument A-20 Run-time image or movie 19 RWS instrument A-20 S Safety features for GEMINI Status lamps 89 Sample scripts 159 Saving the worktable layout 118 scan.csv report file 249 Script A-20 Script commands, full list of 108 Script execution halts without displaying an error message 216, 224 Scripts 1 Selected script line, changing the background color 19 Serial dilution A-20 Serial interface configuration settings for external devices 21 Setting up a new Genesis instrument 34 Shaker A-20 Simulation mode 7, 28 Single pipetting A-20 Siren 89 Site A-20 Source rack A-21 Spacing of tips 52 SPE A-21 Stacker A-21 Stand-alone stacker A-21 Standard A-21 Standard hardlock 7, 28 Status bar 28 Stop script execution halts without displaying an error message 216, 224 Striprack A-21 Submerged dispensing A-21 Sub-routines 176 Symbol LS1220 A-21 System Liquid A-21 System liquid choosing 114 System liquids 87, 252 aspirating 87 T Teaching the coordinates of a rack 49, 57 Tecan Microplate Stacker A-22 Tecan Multipipetting Option (Te-MO) A-21 Te-Flow A-21 Te-MagS A-22 A-36 Gemini Software Manual V4.0 March 2002

327 TECAN Index Te-MO A-21 coordinate system 42 loading racks 25, 43 positioning manually with the cursor keys 42 Te-MO Stacker option A-21, A-22 Te-Shake A-22 Te-Stack A-22 Te-VacS A-22 Tip spacing 52, 124, 131, 195, 227, 245 TiptouchingA-22 Toolbars 28, 108 Command Bar 29, 107, 122 TracefileA-8 Tracking Speed A-22 Transfer position for Te-MO slides 25, 43 Type of carrier 63 U Undefined variables 159, 236 Upgrading to the latest software version 8, 17 User level (user management) 17 V Vacuum assisted waste A-22 Variable not defined error 159, 236 Variables pre-defined 165 Variomag A-22 VB (Visual Basic) 111 VB (Visual Basic) script 236 Virtual liquid column A-3 Visual Basic 111 Visual Basic script 236 Volume Calibration Function A-22 PnP Vector Wizard 79 Rack Wizard 53 RoMa Vector Wizard 73 Work area A-23 Worklist advanced features 199, A-9 Worktable A-23 defining a custom worktable A-1 Worktable layout, saving 118 Worktable window 3D effect 120 barcode checkbox 120 changing the size 118 label checkbox 120 WRC A-23 Y Y-distance of wells 52, A-24 Yellow label (rack name) 121 Z Z-Dispense A-24 ZipTip 242, 264 Z-Max A-24 Z-Start A-24 Z-Travel A-25 W Wash A-22 Wash/Waste Station A-23 Waste A-23 Waypoints in PnP vectors 76 Waypoints in RoMa vectors 69, A-23 Well A-23 WinWash Plus software 259, 279, A-23 Wizards Carrier Wizard 66 March 2002 Gemini Software Manual V4.0 A-37

328 Index TECAN A-38 Gemini Software Manual V4.0 March 2002