User Guide to. Version 13. powered by UMETRICS

User Guide to Version 13 powered by UMETRICS 85037-541-19 Vers. 06 2013

powered by Umetrics 1992-2009 MKS Umetrics AB, all rights reserved The software, which includes information contained in any databases, described in this document is furnished under license agreement or nondisclosure agreement and may be used or copied only in accordance with the terms of the agreement. It is against the law to copy the software except as specifically allowed in the license or nondisclosure agreement. Umetrics patents and trade marks: OPLS/O2PLS, SWE-9802229-6, USA-6754543, OSC, SWE-0000563-7, USA-6853923 PLS-TREE, Pending SEQUENTIAL MODELING, USA-7523384 DESIGN SPACE, USA-8086327 MODDE, RED - MUP, VALUE FROM DATA, OPLS, O2PLS, O2-PLS, OPLS-DA, O2PLS-DA PLS-TREE, S-PLOT, EZinfo, SBOL, FABSTAT, BATCH FINGERPRINT, SIMCA. Sartorius trade marks: BioPAT In this document BioPAT MODDE, BioPAT SIMCA and BioPAT SIMCA-online can be synonymously read as MODDE, SIMCA and SIMCA-online. Screenshots may vary from the actual view, depending on the version you are using. For questions, comments and remarks please send an e-mail to: chemometrics@sartorius-stedim.com Or visit our webpage:www.sartorius-stedim.com Partner company: Sartorius Stedim Systems GmbH MKS Umetrics AB Robert-Bosch Str. 5-7 Sortoget 21 34302 Guxhagen, Germany SE-21134 Malmö, Sweden Phone +49.551.308.0 FAX +49.551.308.3289 www.sartorius-stedim.com

Welcome Welcome to BioPAT SIMCA-online 13.1. This is your guide to BioPAT SIMCA-online and its capabilities. It explains how to use the BioPAT SIMCA-online Client and Server and how to configure your system. This user guide does not include multivariate data analysis or how to use the offline software BioPAT SIMCA. For such information, see the book Multi- and Megavariate Data Analysis (ISBN-13: 978-91- 973730-2-9) and the BioPAT SIMCA user guide. Content The user guide is parted into 12 chapters and an appendix. 1. Installation and configuration - Installation and configuration instructions for the BioPAT SIMCA-online Client and Server. 2. Introduction to multivariate modeling - Introduction to BioPAT SIMCA-online and multivariate modeling and monitoring. 3. Using BioPAT SIMCA-online - Overview of the steps involved in using BioPAT SIMCAonline. 4. File - Description of all commands available on the File tab in the Client. 5. Quick Access Toolbar - Description of feature leaving favorite commands quickly accessible. 6. Home - Description of the most commonly used commands. 7. View - Description of the commands available on the View tab. 8. Tools - Description of plot and list tools. 9. Help - Short description of the Help menu. 10. Project administration - Instructions for the administrator on how to load SIMCA projects and configure hem for BioPAT SIMCA-online. 11. Customizing plots - Description of features to customize plots. 12. Maintenance - Description of how to maintain the BioPAT SIMCA-online system. Appendix A: General information - Information about error codes, endpoints, interfaces, terminology and feature changes, and tab and menu reference syntax.

Table of Contents Installation and configuration 1 Introduction... 1 License information... 1 What is in the package... 1 System requirements... 1 Installation... 1 DBMaker and DBView... 4 Configuration of the Server... 4 Background... 4 Opening the SIMCA-online Server options dialog... 4 Paths and directories... 4 Parameters to initiate communication with SimApi... 5 Miscellaneous settings... 5 Introduction to multivariate modeling 7 Introduction to SIMCA-online... 7 Process data analysis... 7 Batch evolution modeling in SIMCA... 8 Reorganization of the 3D table before import... 8 Modeling... 9 Batches with several phases... 10 Result variables... 10 Calculating limits to build control charts... 10 Batch level modeling in SIMCA... 11 Why batch level modeling... 11 Modeling batch level... 11 Hierarchical batch models... 11 The SIMCA approach... 11 Process data analysis... 11 Batch evolution analysis... 12 Batch level analysis... 12 Using SIMCA-online 13 Introduction... 13 Preparation... 13 Preparation by the administrator... 13 Server icons... 14 SIMCA-online physical overview... 14 SIMCA-online environment... 15 Monitoring the model... 16 To do by the user... 16 Plots for monitoring the new continuous data... 16 Plots for monitoring the evolution of new batches... 17 Plots for predicting results or classifying new batches... 18 Differences compared with SIMCA and unsupported features... 18 Terminology... 18 Client window... 19 Communication with the external system... 20 Connection to external database... 20 SIMCA-online Server handles communication... 21 SIMCA-online database stores all data... 21 File 23 Introduction... 23 Log in/log out... 23 Configuring network settings... 24 Open... 24 Open workspace... 25 Print, Print preview, Print setup... 25 Extract... 25 Extract Data - Select Tags... 25 Extract Data - Select Type... 26 i

BioPAT SIMCA-online User Guide Extract Data - Select Destination... 26 Administration... 27 Project administration... 27 Specifying tag out limits... 27 User administration... 28 Server audit trail... 31 Server log file... 33 Close... 33 SIMCA-online options... 34 SIMCA-online Options General tab... 34 Plot options... 35 Exit SIMCA-online... 39 Quick Access Toolbar 41 Introduction... 41 Customizing Quick Access Toolbar... 41 Removing buttons from Quick Access Toolbar... 41 Adding buttons to Quick Access Toolbar... 41 Moving the Quick Access Toolbar... 41 Minimizing the ribbon... 42 Home 43 Introduction... 43 Batch... 43 Batch evolution plots... 43 Batch level plots... 46 Properties group... 48 Regular... 53 Worm plot... 53 Scores... 53 DModX... 54 PModX... 54 Hotelling's T2Range... 54 Y Predicted... 55 Custom plots... 55 Empty instead of plot... 55 Properties group... 55 View 59 Introduction... 59 Data list... 59 Show or hide... 59 Project info... 60 Log... 60 Status bar... 60 Overview... 60 Plot Details... 62 Tabs... 62 Full screen... 62 Open... 62 Configuration audit trail... 62 Client log... 64 Report... 65 Window group... 68 Save workspace... 69 Tools 71 Introduction... 71 Select - Marking tool... 71 Deselecting/unmarking points... 71 Displaying properties of the item... 71 Creating contribution plots... 71 Zoom... 71 Zooming out... 72 Sort... 72 Drill down... 72 Contribution plots for batch projects... 72 Contribution plots for regular projects... 79 ii

Table Of Contents Adding notes... 82 Editing notes... 83 Deleting notes... 83 Create list... 83 Save as... 83 Help 85 Introduction... 85 Umetrics on the Web... 85 Support... 85 Project administration 87 Introduction... 87 Organize... 87 Access rights... 88 Add configuration for batch project... 88 Import configuration for the project... 89 Batch node... 89 Batch evolution... 90 Batch level... 100 Export the configuration to file... 104 Add configuration for regular project... 104 Import configuration for the project... 105 Model page... 106 Time ranges... 107 Tags... 107 Variable aliases... 108 Target values... 108 Alarms... 109 Write back... 110 Export the configuration to file... 112 Starting and stopping the execution... 112 Removing and restoring project configurations... 113 Manage data... 113 Configuration - view and modify... 113 Repredicting historical batches... 113 Repredicting data for continuous... 114 Deleting historical batches... 114 Workspaces... 115 Save workspace... 115 Delete workspace... 115 Customizing plots 117 Introduction... 117 Mini-toolbar... 117 Mini-toolbar for marked items... 117 Mini-toolbar for formatting... 118 Mini-toolbar for subplot... 118 Managing the mini-toolbar... 118 Show/Hide plot items... 119 Format plot... 119 Axis... 119 Gridlines... 123 Background... 123 Titles... 124 Legend... 125 Limits and Regions... 126 Label Style... 126 Error Bars... 127 Styles... 128 Multiplots... 131 Plot templates... 131 Saving plot formatting template... 132 Switching plot formatting templates... 132 Restoring to default plot formatting... 132 Maintenance 133 Introduction... 133 iii

BioPAT SIMCA-online User Guide Backup... 133 Restore... 133 Resource management... 133 What to do?... 133 Appendix A: General information 135 License reminder... 135 Error codes when starting the service... 135 Windows error codes... 135 Service-specific error codes... 135 Server endpoints... 136 SIMCA-online interfaces... 136 Terminology changes... 136 Discontinued features... 137 Menu and tab reference syntax... 138 Glossary Index 139 145 iv

Installation and configuration Introduction This chapter describes the installation of SIMCA-online and configuration of the BioPAT SIMCAonline Server. Content License information What is in the package System requirements Installation DBMaker and DBView Configuration of the Server License information Before installing the BioPAT SIMCA-online products, carefully read the license agreement included with your BioPAT SIMCA-online software package. In case you do not fully accept the terms of the license agreement, you should immediately return all parts of the package to your local supplier. What is in the package Your BioPAT SIMCA-online package holds the following: Installation files. License file. SimApi dll-file when applicable. BioPAT SIMCA-online User Guide (.pdf). Readme file. System requirements Installation The recommended system requirements for the BioPAT SIMCA-online Server are: Pentium based computer (PC) with a 2 GHz or faster processor. 2 GB RAM or more. 20 GB available hard disk space. Color graphics display with at least 1024x768 resolution. Microsoft Windows XP SP3, Windows Vista SP2, Windows 7 SP1, Windows 8, Windows Server 2003 SP2, Windows Server 2003 R2 SP2, Windows Server 2008 SP2, or Windows Server 2008 R2 SP1. The x64 version of BioPAT SIMCA-online requires a 64-bit operating system, a 64-bit SimApi DLL and a BioPAT SIMCA-online license that permits it to run on 64-bit Windows. SIMCA 13. Before installing, verify that the system requirements apply to your system. 1

BioPAT SIMCA-online User Guide Then follow the steps below. Action Illustration 1. Find the.msi-file, right-click it and select Open. 2. The first page displays the details of the software to install and whether it is 32 or 64- bit. In the welcome page, click Next. 3. Read the license agreement. To accept, select the I accept the terms in the License Agreement check box and click Next. 4. In the Custom Setup page, if you want to install the Client only on this computer, click Next and go to 6. To change from the default location, click Browse and change the destination folder. 5. To install the Server (or Client) on this computer: 1. Click the icon. 2. Select Will be installed on local hard drive or Entire feature will be installed on local hard drive. 3. Click Next. 2

Installation and configuration Action Illustration 6. The setup program is ready for installation. Click Install. While installing a progress bar is displayed. 7. When the installation is completed, click Finish. 8. When installing the server, the BioPAT SIMCA-online Server Options dialog opens up. For details about this dialog, see the Configuration of the Server section later in this chapter. 9. To be able to run the BioPAT SIMCA-online Server, import the license-file named SIMCAonline.$$$, delivered to you, by clicking the Import button in the Paths and directories page in BioPAT SIMCA-online Server Options dialog (see illustration in step 8), and browsing for the file. 10. To use a different SimApi DLL-file than the default, follow the instructions that came with the DLL, or in some cases simply copy the DLL from the BioPAT SIMCA-online package to the folder of the server executable. Then switch SimApi in the SimApi page in the BioPAT SIMCA-online Server Options dialog. Installed programs Find the program icons, under Start All Programs Umetrics BioPAT SIMCA-online 13. Tools: DBMaker and DBView. BioPAT SIMCA-online Client. BioPAT SIMCA-online Server Options. BioPAT SIMCA-online Server Monitor. Server Monitor opens an icon in the notification area in the taskbar. Right-click the icon and from the menu start the Server, launch the client, Server Options and Help. BioPAT SIMCA-online Help. 3

BioPAT SIMCA-online User Guide DBMaker and DBView DBMaker and DBView are installed in the same directory as the server. DBMaker is a small application that can be used to provide data from text or excel-files for testing purposes. It also supports Write Back. DBMaker is not intended (nor works) for real-world usage on production data. The SimApi DLL for DBMaker is installed automatically on the server on a new installation of BioPAT SIMCA-online. No further instructions for running DBMaker and DBView are available in this help. Configuration of the Server Background The BioPAT SIMCA-online Server handles the data transfer between the BioPAT SIMCA-online Client, the BioPAT SIMCA-online internal database (SDB), and the process database (PDB) and when present, the historical database (HDB). The last two databases are located in the external system, and the communication with the BioPAT SIMCA-online Server is done through the SimApi DLL. The Server performs all the project management, computation and execution of the multivariate models. The external system handles the PDB and HDB and runs the I/O drivers connected to the process. Opening the BioPAT SIMCA-online Server options dialog Before starting the Server the first time it has to be configured. The configuration is normally done during the installation. To configure, right-click the BioPAT SIMCA-online Server Monitor icon located in the notification area in the taskbar and select Server options. Alternatively open the BioPAT SIMCA-online Server Options from the Start menu. In the BioPAT SIMCA-online Server Options dialog the following tabs are available: Paths and directories, SimApi, and Miscellaneous. Details about these tabs follow. Paths and directories Use the Paths and directories page to: Enter or change the path to the BioPAT SIMCA-online database directory, where the copy of the SIMCA project file is placed when adding a project. Click Register to request a license file, if one was not provided with the installation package. Import the license file by clicking Import. After import, view the details of the imported license file. View the current directory for saving the internal configuration file (the file that stores all settings in Server Options). Clicking the Reset button removes the current server configuration file and re-configures the server. Note that this affects ALL tabs. 4

Installation and configuration Parameters to initiate communication with SimApi The SimApi DLL for some external databases may need some parameters in order to communicate with BioPAT SIMCA-online. These parameters should be specified in the documentation provided by the supplier of the SimApi DLL. Select the SimApi in the list and click the Change button to view and modify the settings. Note that some SimApi DLL may have other means of modifying the settings for the DLL. Installing SimApi DLLs - interfaces to external systems See the BioPAT SIMCA-online interfaces section in Appendix A: General Information to learn how to install SimApi DLL on your server for use with various external systems from which you want to obtain data. Miscellaneous settings Click an item to display the description and customize the settings as needed. Log file Under Log file, change or view, the maximum log file size in kb and minimum severity level to be logged by selecting Log level. Available log levels are: Debug, Information (default), Warning, Error, or Critical. Critical is the lowest level and logs the least information. Debug is the highest level and logs the most information. Each level is cumulative of the lower levels. Debug logs in great detail everything that happens including all communication and actual values read from the external database. Using this setting may slow down the system but provides the necessary details to know what the server is doing at all times. Recommended by Umetrics online support as soon as you want to identify problems. Information logs login, logout, project added, batch started etc. Warning logs incidents, such as a SimApi function being time consuming or a client being unexpectedly disconnected. Error logs errors in the server, such as failing to predict or failing to read from external database. Critical logs severe problems that will prohibit you from continuing to run BioPAT SIMCAonline, such as project crash or out of memory. 5

BioPAT SIMCA-online User Guide Server input files Under Server input files, view or change the path to the Plugin directory. Active Directory Under Active Directory settings, specify the authentication server to use if you want your users in BioPAT SIMCA-online to be authenticated by servers in your Windows network. Host name - Host name of the Active Directory server to connect to. Port number - The Active Directory port number to connect to. By default different depending on whether the SSL encryption is selected or not. If cleared the default port is 389 and if selected 636. SSL encryption - The Active Directory session will use SSL encryption when selected. Base - The Active Directory base for creating the users part of the distinguished name. Group filter - The Active Directory security group used for filtering the users in the Base. Server startup and timeout Under Server startup and timeout, view or change: The Listener port - listener TCP port used by the server. Default is 2371. The SimApi startup timeout (min). Default 60 minutes. The Project DB timeout (min). Default 60 minutes. The SimApi call timeout (s). Default is 2 seconds. Sound to be played after finished startup and close down. Default is not to play a sound. Resume execution is default selected. The execution of models starts automatically if they were executing when the server was shut down. Connection test interval (s) is how often the server should test the client connection. Default is 300 seconds. If the server does not get a response from a client, it will be disconnected and has to connect and login again to the server. Preload projects selected means that project configurations are loaded immediately when the server starts. When cleared project configurations are loaded when needed, that is when the execution is turned on or the project configuration is opened. Processor load In Processor load you can set a limit in Load warning percent for when to write in the log that The processor is working at a high load. Default is 80%. Averaging time (s) defines the time in seconds between checking the load. Set a time between 1-3600 seconds, default is 60. 6

Introduction to multivariate modeling Introduction to BioPAT SIMCA-online Sartorius-Stedim offline product SIMCA is used to create SIMCA projects (.usp files), and fit models for your data. SIMCA has no connections to real-time data, and a project can only be used by one person on one computer at a time. In BioPAT SIMCA-online you import the.usp file created in SIMCA, and configure it to be able to predict new data coming from an external data source. Multiple BioPAT SIMCA-online clients on many computers can connect to the same server and monitor how the process behaves. BioPAT SIMCA-online is a client-server solution where the server performs all the work, and the client is used to display the results and to manage the project configurations on the server. BioPAT SIMCA-online combines the SIMCA-4000 and SIMCA-Batch On-Line products into one, handling both continuous and batch data in the same product. Regular projects, created in SIMCA, imported in BioPAT SIMCA-online should contain process data. This means that the model describes the optimal state of the process and the data used for prediction in BioPAT SIMCA-online are not logically divided in parts but continuous over time. Batch projects, created in SIMCA, are built from data that are limited to batches. These batches represent the optimal state of the batch process and the data used for prediction is logically divided in batches. For more information about multivariate modeling than found in this chapter, see the SIMCA user guide and Sartorius-Stedim extensive training catalog. Content This chapter describes: Process data analysis Batch evolution modeling in BioPAT SIMCA Batch level modeling in BioPAT SIMCA The BioPAT SIMCA approach Process data analysis Any investigation of a real process or system is based on measurements (data). Fifty years ago, measurement devices were expensive and few, and consequently the amount of data, measured on processes, was limited; a temperature and a pressure here, a flow rate there. The monitoring, display, and analysis of these few data was relatively simple, and a few running charts of the data provided all available information about the state of the process. Today, batteries of sensors and on-line instruments are providing data from all parts of the process in various forms, often at very short intervals. The masses of data are fed into computers, re-computed into moving averages (per minute, hourly, daily, weekly, etc.) and displayed and stored. This change from a situation with few, fairly infrequent measurements, to many, almost continuously measured variables has still not affected the manner in which process data are treated, potentially leading to large losses of information. With appropriate multivariate analytical methods, such as Principal Components (PC) and Projection to Latent Structures (PLS) modeling in the BioPAT SIMCA software, the masses of process data can provide easy to grasp graphical information about the state of the process, and relations between important sets of process variables. These multivariate methods make efficient use of all pertinent data, with little loss of information. 7

BioPAT SIMCA-online User Guide Batch evolution modeling in BioPAT SIMCA With batch processes, K variables are measured on N batches at regular time intervals. This gives a J x K matrix for each batch (J time points (X) times K variables). Consequently, a set of N normal batches gives a 3 way matrix of dimension (N x J x K). Time One batch Batches Variables Figure 1. Three-way table of historical data of, for example, N batches with J time points, and K variables. Often the batches have different length (not shown in the picture) and may also be divided in phases. This section describes modeling of the batch evolution in BioPAT SIMCA. Reorganization of the 3D table before import To be able to import the dataset, the 3-way data table has to be unfolded to preserve the direction of the K variables (see figure 2). The resulting matrix has n obs = N x J observations (rows) and K columns. Hence this matrix, X, has the individual observation as a unit, and not the whole batches. X Variables Y Batches B1 B2 B3 Bn Time Recorded variables: Ethanol, Temperature, Molasses flow, NH3 feed, Air flow, Tank level, ph. Figure 2. The three-way matrix of figure 1 unfolded along the batch direction to give a two-way matrix with N x J rows and K columns. Each row has the data (x ijk ) from a single batch observation (batch i, time j, variable k). Reorganization with sub-batches Sub-batches are present when a batch is divided into multiple parts and individually run through the same equipment (unit). Each sub-batch has to be defined as a phase in BioPAT SIMCA. Therefore, in the case where you have sub-batches, each sub-batch needs a unique phase id at import. Sub-batches assumed identical When the sub-batches should be identical and interchangeable, the phase models must be made identical. There are a number of ways to avoid that variation in the sub-batches in the workset leads to different phase models. Currently, none of the ways are easily executed in BioPAT SIMCA. With small datasets, all sub-batch data can be copied and included in all phase models of that batch. This is illustrated in Figure 3. 8

Introduction to multivariate modeling 3a 3b Figure 3a and b. 3a displays the three-way matrix unfolded along the batch direction with sub-batches. 3b displays the permutation to certify that variations in sub-batches will not lead to different models. The following table explains figure 3: Original term Modified term Modification explanation Specifically in Figure 3 Data Permutated Data The subbatches have been permutated so that each subbatch is included in each phase once. In Figure 3a there are three batches and two phases. Phase 1 has three sub-batches while Phase 2 has no sub-batches. Now, let's look at Batch 1: in Figure 3b, through the permutation, each sub-batch (Sub-batch 1, 2, and 3) has been combined with each phase ID (Phase 1:1, 1:2, 1:3) leading to three unique batch IDs (Batch 1:1, 1:2, 1:3). For Phase 2, no permutation is necessary, therefore Phase 2 is only present in the first batch (Batch x:1). Real Phase ID Modified Phase ID Each sub-batch has to be imported as a phase, and therefore needs a unique phase ID. In Figure 3a, there are two phases, Phase 1 and Phase 2. In Figure 3b there are four phases Phase 1:1, 1:2, 1:3, and 2, so that all sub-batches have unique phase IDs. Real Batch ID Modified Batch ID After permutation of the subbatches, the Batch IDs must be unique before importing in BioPAT SIMCA. To let each sub-batch be included in each phase once, this demands 3x3 unique batch IDs. Modeling When importing the dataset in BioPAT SIMCA and no maturity (y-variable) has been specified, an index y-variable starting at 0 is constructed representing the "relative local batch time". The default model, after completed import in BioPAT SIMCA, is a PLS model for the centered and scaled X and "relative local batch time", y if no other y was specified. If a maturity variable, recorded relative to the start of each batch, was defined as y, that variable will be used as y by default. 9

BioPAT SIMCA-online User Guide When fitting the batch PLS model, Autofit will stop when 85% of X has been explained, but will also give at least 3 components (not exceeding N/2). This is necessary in order to ensure that much of the X- matrix is "explained". This results in an (n obs x A) score matrix, T, plus PLS weight and loading matrices W and P (of dimensions K x A). Batches with different length Alignment of data is done differently depending on configuration of the time/ maturity variables. For batches of similar length the impact is small. The default y configuration aligns the batch length by cutting the longer batches at median (or average) batch length. Batches that are shorter than the median (or average) batch are filled up with the last value up to the median batch length. The used length in average batch is the shorter of the median batch length and the average batch length rounded down. Batches with several phases When batches have several phases, observations are organized in classes, one class for every phase. Separate PLS class models are fitted for every phase. Result variables The score matrix T is a good summary of X, and PLS focuses this summary on y (local time). Hence the first column of t (t 1 ) will contain strong contributions of those X-variables that vary monotonically with y, i.e., either increase or decrease with time. The second component (t 2 ) is an aggregate mainly of those variables that change quadratically with time, i.e., first go up to a maximum, and then decrease, or first go down, and then up. The third component catches the variables having a cubic behavior, etc. The value of "local time" predicted by the PLS model (with the number of components determined by cross-validation ), y pred, is very suitable as a "maturity index" that can be used to indicate how far the batch has evolved, if it is ready for termination, etc. Calculating limits to build control charts To monitor the evolution of new batches, one calculates the typical evolution trace of a normal batch. This is in short done as follows: 1. Reorganization: First the scores of the batch evolution model are chopped up and reorganized so that the scores of one batch form one row vector (t 1 followed by t 2, followed by t 3, etc.) in a matrix S T. This matrix has N rows (one per batch) and A x J (AJ) columns from the A score vectors and the J "time points" per batch. When batches have phases, the scores of each batch are collected from the different PLS phase models. Batch t1 Average Avg + 3 sd StDev Avg 3 sd Time Figure 4. The score values for each batch are arranged as row vectors below each other, giving an N x (J x A) matrix, S T. Above we see only the first part of S T corresponding to the 1.st component (t 1 ). From this matrix one calculates the averages and standard deviations (SD:s) of the matrix columns, and then control intervals as the averages 3 SD. 2. Calculating tolerance limits for control charts: Now the matrix S T is used to derive minimum and maximum tolerated values at each time point (j) of t j1, t j2, t j3, t ja from the column averages and standard deviations of S T, as indicated in figure 4. In MSPC one would typically use tolerance intervals of the average 3 SD at each time point. Hence, we now have for each score vector an average trace with upper and lower tolerance limits. The corresponding actions are done when building the control charts for Predicted Y, DModX, and Hotelling's T2Range. 10

Introduction to multivariate modeling Batch level modeling in BioPAT SIMCA Why batch level modeling Batch level modeling may be advantageous in the case that the measurement of Y is laborious and time consuming, and one wishes to make an initial fast quality assessment before the real Y is available. This is often the case in biotechnological production, where extensive analysis and testing of the final products is made before acceptance (or rejection). The batch level model also allows the full interpretation of the batch data. Groups of batches may be discovered, outliers will be found, etc. Critical time periods will be indicated by "periods" of large weights, loadings, and VIP values. Analogously, important factors in the initial conditions will stand out. The "ideal" evolutionary trace corresponding to a desirable Y-profile can be deduced, and so on. Modeling batch level The objective of batch level modeling is to make a model of the whole batch in order to understand how Y is influenced by the combination of batch conditions and the batch evolution. This model will be based on (when available) the batch conditions (Z), the evolution trace matrix S T, and when applicable the properties and quality of the completed batch (Y), as shown in figure 5. The resulting model is used to predict Y for new batches from their batch conditions and their evolution traces. In the case that Y-values do not exist, the X-matrix can still be used to develop a PC model. This is the same type of model as the X-part of PLS in the batch evolution model. The difference is that in PCA the scores (T) are calculated to give an optimal summary of X, while in PLS this optimality is somewhat relaxed to make T scores better predictors of Y. The PC model can then be used to classify new batches as normal (similar = well fitting to the PC model) or non-normal (far from the model). X Y Back ground Data Scores t1, t2, t3 or original variables Final Results Data Z S T Figure 5. The data for batch level modeling. Each row has the data from one batch. The left matrix contains data describing initial conditions. The middle matrix contains the unfolded scores (or original variables or summary variables) which describe the evolution of each batch. The optional right matrix (Y) contains the responses, the properties of the complete batch such as yield, purity, activity, etc. Hierarchical batch models With batch level datasets you can fit hierarchical models of the whole batch, for different levels of completion: One model for each phase and component in the batch evolution model. One model for each phase. Sequential models covering parts of the batch completion, for example for 25%, 50%, 75% and 100% completion. These models can predict the final batch quality or classify the batch, before the batch is finished. The BioPAT SIMCA approach The BioPAT SIMCA project is the basis of the multivariate monitoring, describing the behavior of the process for good batches/optimal process behavior. In BioPAT SIMCA-online, you load projects, previously developed in BioPAT SIMCA. For batch data the BioPAT SIMCA approach includes analysis and monitoring of the batch data in two steps (levels): batch evolution analysis and batch level analysis. Process data analysis The model consists of optimal process behavior data. The steps in modeling and monitoring: 11

BioPAT SIMCA-online User Guide 1. Modeling the data in BioPAT SIMCA. 2. Predicting results of new process data in BioPAT SIMCA-online. Predictions: As the process is evolving, the data for monitoring are derived from applying the model to data from the external system and making predictions. Plots: Worm, Score, Hotelling s T2Range, and DModX are displayed with limits. For PLS models, predicted Y plots are displayed. Classify or predict result: You can classify the data as good or bad or predict their final quality. Contribution plots: If the values are outside the limits, contribution plots indicate which variables together are related to the deviations. Batch evolution analysis A batch evolution model, BEM, has many observations per batch. Modeling the batch evolution consists of: 1. Modeling the evolution of batches in the BEM in BioPAT SIMCA. 2. Monitoring the evolution of new batches in BioPAT SIMCA-online. Predictions: The batch evolution data of new batches, as they are evolving in real time, are projected on to the model plane or model planes (for batches with phases) of the batch evolution model developed off-line. This results in predicted scores (coordinates in the model plane), together with the distance between the new points and the model plane, DModX, and predicted maturity. Control charts: The predictions are plotted on control charts with limits calculated from the workset. These charts indicate whether the new batches are evolving normally or not. Contribution plots: If the values are outside the normal ranges, contribution plots based on the x-values of the average batch or the residuals (DModX) indicate which variables together are related to the deviations. Batch level analysis A batch level model, BLM, has one observation per batch. Modeling the whole batches consists of: 1. Modeling the whole batches in the BLM in BioPAT SIMCA. 2. Predicting results of whole new batches in BioPAT SIMCA-online. Predictions: As the batch is evolving, the data for monitoring the whole batch are derived from unfolding and aligning scores, original variables (raw data), or statistics for the original variables of the batch evolution data (raw data statistics). Plots: Score, Hotelling s T2Range, and DModX for the whole batch are displayed with limits. For PLS models, predicted Y plots are displayed. Classify or predict result: You can classify the finished batches as good or bad or predict their final quality. If you have made hierarchical models of the batch level at different percentage of completion, you can classify or predict the final quality of new batches as they are evolving when they reach the percent of completion of the models. Contribution plots: If the values are outside the limits, contribution plots indicate which variables together are related to the deviations. 12

Using BioPAT SIMCA-online Introduction BioPAT SIMCA-online version 13 is an execution module for models built with SIMCA version 13, in this user guide referred to as SIMCA. BioPAT SIMCA-online is designed as a client-server application. BioPAT SIMCA-online reads data from the process (referred to as external system or external database) at regular intervals through supported interfaces. BioPAT SIMCA-online executes multivariate models, thereby projecting new data, in real time, on to the model plane. This results in coordinates in the model plane, together with the distance between the new points and the model plane, DModX. The real time display of these results allow for an efficient monitoring of online process or batch data. Preparation Before using BioPAT SIMCA-online you must develop a project in SIMCA. This is done by building the models, for batch project batch evolution models and optionally batch level models, from data representing good process or batch behavior. For details on creating projects, see the SIMCA user guide. Content Preparation by the administrator BioPAT SIMCA-online physical overview BioPAT SIMCA-online environment Monitoring the model Differences compared with SIMCA and unsupported features Terminology Client window Communication with the external system Preparation by the administrator Before monitoring projects in the Client the following steps have to be conducted by the administrator. Step Action How More 1. Starting the BioPAT SIMCA-online Server Monitor. 2. Starting the BioPAT SIMCA-online Server. 3. Starting the BioPAT SIMCA-online BioPAT SIMCA-online Server Monitor is found on the start menu, or if it is already running in the notification area in the taskbar Right-click the BioPAT SIMCAonline Server Monitor icon, in the taskbar notification area, and select Start BioPAT SIMCAonline Server. A User Account control prompt may be displayed asking for administrative prilieges to start the server. The icon then changes into the BioPAT SIMCAonline - Running icon, and a message is displayed stating "Service start succeeded". Start the Client from the start menu. This can be done on the server If the message displayed is "Service start failed", see the section Error codes when starting the service in Appendix A: General information. 13

BioPAT SIMCA-online User Guide Step Action How More Client. computer or on another computer. 4. Logging on as administrator. 5. Adding a project. 6. Starting the execution. Select the server to connect to. Use the button next to the server to set up servers to connect to. Log on as Administrator with its password (default is empty). Click Connect. Add the SIMCA project and configure it from File Administration Project administration. In the Project Administration dialog, select the configuration and click the play button. For more, see the Log in/log out section in the File chapter. The Connect dialog is opened automatically when starting the client. For more, see the Add configuration for batch project and Add configuration for regular project sections in the Project administration chapter. For more, see the Starting and stopping the execution of the project section in the Project administration chapter. 7. Adding users Add user accounts and their privileges by clicking File Administration User administration. For more, see the User administration section. Now the project can be opened from any client connected to the server. Note: To stop the server, right-click the BioPAT SIMCA-online Server Monitor icon notification area, and click Stop server., in the taskbar Server icons The Server Monitor icon shows the state of the BioPAT SIMCA-online service. Icon Description The server is not running. Icon before starting and after stopping the server. The server is pending. Icon during starting and stopping of the server. The server is running and regularly checks for new data. The server has not been installed. BioPAT SIMCA-online physical overview The BioPAT SIMCA-online Server is running on a specific server computer. The server has copies of the SIMCA projects, and executes those, making multivariate predictions, for new data that the server obtains from a Data Source. To get the data from the data source the server uses a SimApi DLL. The server also stores all predictions locally on disk on the server. Clients connect to the server to view how the process evolves, by interacting with plots, etc. 14

Using BioPAT SIMCA-online Figure 7. The BioPAT SIMCA-online implementation. BioPAT SIMCA-online environment This subsection describes the different pieces of software that make up the BioPAT SIMCA-online environment: Client the software you use to view the execution of the models, the predictions, any alarms and such. Also used by administrators to import projects and set up configurations on the server. The client is the software that contains the user interface to interact with the server. There can be many clients running at the same time on different computers, all connecting to the same server. Server there is one server running on one computer which uses data from its data source to predict new results using the BioPAT SIMCA-models. These results can then be displayed in the Client. You never use the BioPAT SIMCA-online Server directly, you always work with it through the client software or any of the utilities listed below, for managing the server: Server Monitor a small icon and menu in the notification area in the taskbar of the server computer. It can be used to start and stop the server and provides quick access to the server log. The server monitor is optional, and doesn t need to run, because the server is running as a service which can be started or stopped as other windows services. 15

BioPAT SIMCA-online User Guide Server Options a small application that is run on the computer running the server. It is used to make settings controlling how the server runs; what folders to use, what SimApi's to use, and to specify the license file. In addition there are two programs that are used for demo or testing purposes: DBMaker a demo data source, see the DBMaker and DBView subsection. DBView a small tool to view data from DBMaker and from the internal databases of the BioPAT SIMCA-online Server, see the DBMaker and DBView subsection. Monitoring the model BioPAT SIMCA-online handles both regular (continuous) and batch projects in the same product. However, since batch projects need particular settings, as in SIMCA offline, they also need special configuration when they are added to BioPAT SIMCA-online. Furthermore, different plots and different functionality are available in the ribbon interface for regular and batch projects. For more about this, see the Add configuration for batch project and Add configuration for regular project sections in the Project administration chapter and the Batch and Regular sections in the Home chapter. Once the administrator has started the execution, the model starts to execute, i.e. read data in real time, at the specified interval, and computes the scores. For batch projects the new data is first used for predictions using the batch evolution model and then, as data becomes available, for the batch level models. To do by the user The table lists what the user needs to do in order to monitor a project. Step Action For more 1. Open a configuration known to the Server, in the Client. 2. Open plots. The plots are available on the Home tab. 3. Open contribution plots. When time points or batch points fall outside the limits, create contribution plots. For more, see the Open section in the File chapter. For more see the Home chapter. For more, see the Drill down section in the Tools chapter. Plots for monitoring the new continuous data The new data points, read from the external system, are inserted into the model, giving predicted values. If you only want predictions under certain conditions, use Prediction conditions to define when to predict. Worm plot The predicted values of the score line plot displaying t 1 vs. t 2, where the most recently predicted observation is displayed with a symbol that is larger than the other symbols. This plot also displays the Hotelling's ellipse, and workset observations, indicating whether the process is evolving normally or not. DModX, Hotelling's T2Range, and Y Predicted trend plots The predicted values of DModX, Hotelling's T2Range, and YPred values are plotted in trend plots. These plots indicate whether the process is evolving normally or not. Contribution plot If values are found outside the normal ranges, contribution plots based on the x-values of the average or the residuals (DModX) indicate which variables together are related to the deviations. 16

Using BioPAT SIMCA-online Plots for monitoring the evolution of new batches The batch evolution data for new batches, read from the external system, are inserted into the PLS model, giving predicted values. When batches have phases, the phase condition has to be defined for the correct PLS phase model to be used to predict the t scores of that phase. Score, DModX and Hotelling's T2Range control charts The predicted values of the score t 1 to t a, DModX, and Hotelling's T2Range values are plotted in control charts, with limits derived as described previously (trace level). These charts indicate whether the batches are evolving normally or not. Predicted maturity control chart The PLS model also gives predicted values of y (local time or maturity variable). Plotting y pred vs. y obs gives an indication of whether the batches are developing too quickly (over-mature, y pred > y obs ) or too slowly (under-mature, y pred < y obs ). Contribution plot If values are found outside the normal ranges, contribution plots based on the x-values of the average batch or the residuals (DModX) indicate which variables together are related to the deviations. Batch evolution plots background Batch evolution plots display a plot grid with many plots in the same window when there are units, phases, or sub-batches in the model. When the process includes several units, the plots for each unit are displayed beneath each other when the Layout selected is Units, see figure 6. Figure 6. This is an example of how BioPAT SIMCA-online presents units, unit groups, and sub-batches in a batch evolution plot. In the table, the notation in Figure 6 is explained. Unit Group Units Sub-batches Phases G G1, G2, G3. One sub-batch. In BioPAT SIMCAonline, each unit has to have at least one sub-batch. Therefore the single sub-batch in this unit is denoted Sub-batch 1 in the figure. Phase 1 and 2. D D1 and D2. Sub-batch 1 and 2. Phase 3 and 4. C One unit. In BioPAT SIMCAonline, each unit group has at least one unit. The single unit in this unit group is denoted C1 in the figure. One sub-batch. In BioPAT SIMCAonline, each unit has to have at least one sub-batch. Therefore the single sub-batch in this unit is denoted Sub-batch 1 in the figure. Phase 5. 17

BioPAT SIMCA-online User Guide Plots for predicting results or classifying new batches The batch evolution data must first be read by the server, and fitted to the PLS model to get the predicted scores. These scores get appended row wise to the batch conditions (Z) if present, once the batch (or with hierarchical models the model) is completed in batch evolution. The batch level PLS, PCA, and hierarchical models are used to predict quality of the final batch (Y), or classify the batch as normal good batch or bad batch. These plots are found in the Batch level plots group. Score scatter plot The Hotelling s T2 ellipse, by default at the 99% confidence interval, is drawn around the batch points in the batch level score scatter plot. When a batch is outside the ellipse limit, this indicates that this batch has some variables that are larger or smaller than the average batch. DModX When a batch is projected onto the model, BioPAT SIMCA-online computes also the distance of that batch to the model, DModX. DModX is proportional to the RSD (Residual Standard Deviation) of that batch in the X space. Larger DModX than the warning level indicates something unusual about the batch (different from the others) that was not captured by the model. Hotelling's T2Range For a given observation (batch) the Hotelling s T2Range is a combination of all the scores (t) for the selected components. Hence this plot is a summary of all the batch variables for the selected components and displays how far away from the center (target) the batch is along the PC model hyper plane. When a batch is outside the critical limit, this indicates that for this batch, the data vector has some variables that are larger or smaller than the average batch. Predicted Y plots The Predicted Y plots are displayed with confidence limits. Unusually large or small values in comparison with the others are interesting to display in a contribution plot. Contribution plot Contribution plots of points found outside the limits illustrate which variables differ between the marked point and average. When opening a contribution plot for a variable that is a score, the batch evolution contribution plot can be created by double-clicking the score variable. Differences compared with SIMCA and unsupported features Terminology BioPAT SIMCA-online, unlike SIMCA, typically receives data from the data source observation by observation (whereas SIMCA already has ALL data available when modeling). This fact, and that some functionality of SIMCA isn t meaningful in an online scenario, means that there are number of features available in SIMCA that are unsupported in BioPAT SIMCA-online or just executed differently. See the list below for details. A batch that meets the conditions for conditional exclude is available in BioPAT SIMCAonline but with missing instead of values. Generated variables that take into account future observations are not supported. Generated variables that take into account results from other models are not supported. Generated variables that lag variables. Date/Time variables are read as missing. Hotelling's T2Range is unavailable for OPLS models. Some features previously available in SIMCA-Batch On-Line or SIMCA-4000 are unavailable in BioPAT SIMCA-online. See the Discontinued features subsection for details. This section describes the basic terminology of BioPAT SIMCA-online. Project a Sartorius-Stedim SIMCA Project (USP-file), containing the models you want to execute on the BioPAT SIMCA-online server. Projects are uploaded (automatically copied) to the server from the client and then configured. For batch projects only one batch evolution model, BEM, may be present in the imported project. The single BEM may include several phases and the project may also include several batch level models, BLM. 18

Using BioPAT SIMCA-online Configuration or project configuration, is a specific instance of a SIMCA project configured to take data from certain tags in your data source, have specific alarms, and a range of other settings. A configuration can be executing the model for new data from the data source or it can be stopped (i.e. not reading new data). You can have multiple configurations for the same BioPAT SIMCA project. The configurations, for one particular SIMCA project, are managed independently from each other and can have totally different settings. The only thing they share is the same BioPAT SIMCA project. Batch node a node in the data source that contains the names, start and stop times for batches. Execution used for continuous configurations (non batch data) defined as follows: An execution starts when play-button for that configuration is clicked, and ends when the stop-button is clicked. Thus if the configuration s execution is started and stopped multiple times, it will result in multiple executions in the Overview window in the BioPAT SIMCA-online client. The execution is also stopped when the server is stopped. Repredict data the process of reading data from the data source again, and then repredicting it. This effectively first deletes data, then reads it again, and then finally predicts it again. Delete predicted data the process of deleting already predicted data for a configuration. Alarms alarms are triggered when certain user specified conditions are met. Alarms are used so that the user can be aware that something might have gone wrong with the process. Alarms can be displayed in plots as symbols, in the Plot Details window, the Report window, and in the Overview window which shows the global alarm state per model if alarms have been triggered. Only one alarm of a specific type (for a certain condition) can be triggered at the same time. Triggered (active) alarms can be reset (acknowledged). This means that the same alarm can be triggered again. These multivariate alarms are specified during the project configuration. Multivariate alarms use special trigger rules configured for them, which means that they are not triggered immediately when data is outside a limit, but rather after a certain number of observations outside the limits. Univariate Alarms on x- or y-variables can be specified in the Target values page in the project configuration. They are always triggered at first value outside the defined limits. Client window The BioPAT SIMCA-online client consists of the ribbon tabs, the Quick Access Toolbar, the help menu, tabs, and dockable windows. Plots and lists are displayed in the unused area between ribbon, dockable windows and status bar in client window. Note: You can have several clients open on the same computer. The table describes the parts of the client window. Item Description Default position More info Ribbon Displays the tabs File, Home, View, and Tools and the Help menu. Top of the screen. File, Home, View, Tools, and Help chapters. Quick Access Toolbar By default displays a few commonly used commands for easy access. Can be customized to hold your favorite commands. Toolbar positioned at the top above the tabs. Quick Access Toolbar chapter. Tabs Tabs to switch between open project configurations. Bottom of the screen. Tabs section in the View chapter. Dockable windows The dockable windows are: Project info, Log, Overview, and Plot Details. The Overview and Plot Details windows are placed to the right, while the others are placed to the left. Show or hide section in the View chapter. <empty area> The area where the plots are displayed. Center of the screen. Plots sections in the Home chapter. Figure: Explanation Client window for batch. 19

BioPAT SIMCA-online User Guide Figure: Explanation Client window for continuous. Communication with the external system In order to monitor BioPAT SIMCA project data, BioPAT SIMCA-online requires access to an external system, i.e. the process data, to read data and make predictions using the models. Process data comes from an interface (software) accessing the process databases on-line in real time. Connection to external database BioPAT SIMCA-online connects to the external database via a SimApi, and samples the data in real time. The process system, which we refer to as the external system, has a process database, PDB and often an historical database, HDB. The PDB is similar to a process buffer and contains only the current values of all the process variables. The HDB stores the historical values of the process variables. 20

Using BioPAT SIMCA-online BioPAT SIMCA-online Server handles communication The BioPAT SIMCA-online Server handles the communication with the external system - process PDB and HDB. The BioPAT SIMCA-online Server samples the PDB at regular intervals, the phase execution time, to extract the current value of the batch process. BioPAT SIMCA-online database stores all data The batch data read by BioPAT SIMCA-online as well as result variables computed by the model (output variables such as scores, distance to the model, predicted values, etc.), of both batch evolution models and batch level models, are stored in the BioPAT SIMCA-online database, SDB (internal database created by BioPAT SIMCA-online). The location of this database is specified in the BioPAT SIMCA-online Server Options application on the first tab. 21

File Introduction On File tab the following is available: Log in/log out and connect to server. Open project configurations and workspaces Print, Print preview, Print setup Extract data from the external database Administration with Project administration, Out limits, User administration, and Server log. About BioPAT SIMCA-online to display program and license information, version number, and copyright information. Close to close the current configuration. BioPAT SIMCA-online options to view and change settings. Exit BioPAT SIMCA-online to close the client. Recent files list with both recently opened project configurations and workspaces, with the possibility to pin favorites. Log in/log out When you start the Client the first time, it will automatically try to connect to a Server running on the same computer (the default Server). If the Server is running on a different computer, or the Server has not been started, the connection fails. You must then use File Log in to connect to a Server. To manually connect to a server, click File Log in. In the Log in dialog, click the arrow to see the list of servers known to the Client (i.e. you have specified their network settings). Default is the Server you were connected to last. Select one and click Connect. 23

BioPAT SIMCA-online User Guide Note: If the client is connected to a server and you want to switch servers, click File Log out and then connect to the new server. Clicking Log out closes all open projects and disconnects from the current Server. See the Configuring network settings subsection next on how to add, remove, and configure the Server. Configuring network settings In the Configure Network Settings dialog you can add new servers, remove servers, and configure the server port. Note: The server port has to be the same in the client as in the server configuration. The default server port is 2371. To open the Configure Network Settings dialog, click File Log in, then in the Log in dialog click the browse-button to the right of the Server box. Adding new server To add a new server, click the Add button. The Server Settings dialog opens with the default settings. Removing server To remove a server, mark it and click the Remove button. Editing the server configuration To change the configuration of a server, mark the server and click the Edit button. Use the Server Settings dialog to change the description, port number, and network address of the marked server. New server available When done adding, removing or configuring the servers, click OK in the Configure Network Settings dialog. In the Log in dialog, note that the names of all servers, including any new server, are displayed in the list of configured servers. Select the desired server and click Connect. Note: The client port is dynamic and set by the operating system. Open To open a project configuration or workspace known to the Server, click File Open. In this dialog all project configurations and saved workspaces are listed. 24

File For a project configuration to be known to the Server, it must have been added and configured in the Project Administration in the Client. For a workspace to be available, it must have been saved, either in the Project Administration dialog or by clicking Save workspace in the Windows group on the View tab. To close a project click File Close, or right-click the project tab and click Close. Open workspace To open a workspace, in the Workspaces section, mark the workspace and click Open. The Workspaces section is positioned below the Configurations section. Print, Print preview, Print setup Extract The standard print utilities are available by clicking File Print. Print preview is unavailable for lists. To extract data to spreadsheet or file, click File Extract and click through the wizard. The only difference between extracting to spreadsheet and extracting to file is the last page where you select how to extract. When extracting to file you can select to save as (*.dif) DIF Files (*.dif), Text Files (*.txt), or Matlab 4.x Files (*.mat). There are three pages in the wizard: Extract Data - Select Tags Extract Data - Select Type Extract Data - Select Destination Extract Data - Select Tags The external database holds only raw data, no calculated vectors. On the first page you must select which tags you want to extract data from in the external database: 1. Under Data Sources all data sources currently known are listed. Mark a node to view which tags are available. 2. The tags of the selected node appear under Tags to the right of the data sources. Mark the wanted tags and click the down-arrow. 25

BioPAT SIMCA-online User Guide 3. The selected tags are displayed in the Selected Tags list. Extract Data - Select Type To select which type of data and the time period including interval: Data Description Settings type Current data Historical data Batch data The last observation received from the external database. All observations (batch evolution or regular) with a time stamp within the range specified. Batch condition data with a time stamp within the range specified. No settings. From date/time and To date/time. Sampling interval also has to be specified and should be the same as the database. Number of points is updated automatically using the other settings. From date/time and To date/time. Number of points is updated automatically using the other settings. Then use the Time section to specify the range and sampling interval. Hint1: To change the date, click the arrow to display the calendar. Hint2: To change the time, start with the To time, position the cursor on the hours or minutes or seconds, and use the up and down arrows in the dialog or on your keyboard. Extract Data - Select Destination Select whether to extract to list or file by: Leaving Extract to list. 26

File Clicking Extract to file and specifying the file to extract to. The path to the file is then displayed in the Path field. Administration Use Administration to access: Project administration Out limits User administration Server audit trail Server log Note: If you cannot see the Server log in the backstage menu, click the small arrow at the bottom of the backstage. Project administration In the Project Administration dialog the projects and configurations currently known to the Server are listed and an administrator with configure management permissions can do the following: 1. Add, configure, and remove batch project configurations and regular project configurations. 2. Start and stop the execution of a project configuration. 3. Repredict and delete predicted data. 4. Save workspaces. For details, see the Project administration chapter. Specifying tag out limits Out limits for tags define the valid range of a tag. Outside these limits, the value of a tag is set to missing. To add an out limit, click the Add tag-button and select the tag to add the out limit for (see below). 27

BioPAT SIMCA-online User Guide Then enter the out limit values. Managing the out limits To exclude a tag and replace it with missing, select Yes in the Exclude column for that row. This can be useful when an instrument is malfunctioning. To include the tag again, select No in the Exclude-column. Turn on or off the usage of out limits by selecting/clearing the Use out limits check box. Note: Out limits are global and independent of configurations and take action before the data reaches the clients. Shortcut menu You can copy, paste, and delete the values in the spreadsheet using the shortcut menu. Right-clicking and clicking Print prints the spreadsheet. User administration For a BioPAT SIMCA-online client to connect to the BioPAT SIMCA-online Server, the user must first log in to the server using a user name and password. The Server keeps lists of users allowed to log on to the server, groups of users, and their rights to perform various tasks. By default the account Administrator is created with an empty password. This account has full rights to the server and can import projects and create configurations on the Server. Note: It is recommended practice that the password for the Administrator account is changed from the default. After installation of the software, the administrator has to set up other user accounts with passwords for the individuals that will use the system. These new users may have other permissions, for example cannot delete projects from the server or cannot add new users. Adding users with roles and group belonging is done using the tabs: Users Groups Roles 28

File Users page The Users page in the User Administration dialog displays the users present in the system, which groups the marked user is a member of and the role the user has. By default there is one user, the Administrator which is member of the groups Everyone and Administrators. To add a new user, do as follows: 1. Click New. 2. Enter the User name and password, for a Normal user or a Domain user. A normal Normal user is authenticated by BioPAT SIMCA-online using the specified password. A domain Domain user is authenticated using Active Directory services. When selecting to add a domain user, the Distinguished name needs to be specified. 3. Click OK and in the Users page, specify the groups the new user should be a member of. 4. Repeat this procedure as needed. In case you misplace the master administrator password, contact Sartorius-Stedim support. Groups page The Groups page in the User Administration dialog displays the groups present in the system and which members the marked group has. By default there are two groups, Everyone and Administrators, both with one member: Administrator. To add a new group, do as follows: 1. Click New. 2. Enter the new group Name in the Add Group dialog and click OK. 3. Repeat this procedure as needed. 29

BioPAT SIMCA-online User Guide Using groups When groups have been specified, access rights can be specified using the Access rights button in the Project Administration dialog. Note: Access rights is only available for folders. Roles page The Roles page in the User Administration dialog displays the available roles and their permissions. By default there are two roles present, Administrator and User, and the possible Permissions: alarm management - alarms can be reset. configuration management - the Project administration is available for adding and updating configurations. extract data - extracting data using File Extract. note management - notes can be added and removed. out limits - out limits can be specified. purge configurations - configurations can be permanently removed. user administration - can add/remove users, change/add/remove roles and groups of users and modify permissions. workspace management - can add and remove workspaces. By default the Administrator has all the permissions and the User has none. Change permissions for the marked role by selecting or clearing the Permission check boxes. To add a new role, do as follows: 1. Click New. 2. Enter the new role Name in the Add Role dialog and click OK. 3. Repeat this procedure as needed. 30

File Server audit trail The server audit trail records events on the server. Here all events in the Server audit trail are listed with details about the event. Note: All events are accompanied by date and time. All events but the first 4 in the list below are accompanied by a session ID. Project ID includes the project name. Event Description Event details 1. audit_integrity_warning The audit trail may have been compromised. 2. server_starting The server is initialized. The application name, version and platform. 3. server_started The server has started. 4. server_stopped The server has stopped. The path and name of the used server ini-file including inifile content. SimApi name and path. License information including license number, user, company, features and expiration date. Local server information including port and network address. Database directory path. 5. folder_created 6. folder_deleted 7. folder_renamed 8. folder_moved The folder <folder name> has been created. The folder <folder name> has been deleted. The folder <folder name> has been renamed <new folder name>. The folder <folder name> has been moved to <parent folder ID of new position>. FolderID, ParentFolderID, FolderName FolderID FolderID, NewFolderName FolderID, ParentFolderID 9. folder_group_access_gra nted The access rights to <folder name> have been granted for the current group. FolderID, GroupID 31

BioPAT SIMCA-online User Guide Event Description Event details 10. folder_group_access_rev oked The access rights to <folder name> have been revoked for the current group. FolderID, GroupID 11. project_created 12. project_deleted 13. project_restored 14. project_purged 15. project_initialized 16. project_moved 17. configuration_created 18. configuration_deleted 19. configuration_restored 20. configuration_purged 21. configuration_renamed 22. configuration_updated 23. workspace_created 24. workspace_deleted 25. workspace_renamed 26. role_created 27. role_deleted 28. role_permission_granted 29. role_permission_revoked 30. user_created The user has commenced the import of a BioPAT SIMCA project. <project name> has been deleted. <project name>,which was previously deleted, has been restored. <project name>,which was previously deleted, has been permanently deleted. A BioPAT SIMCA project has been imported and copied. A unique project ID has been assigned. <project name> has been moved to <folder name>. A new configuration has been created defining how a BioPAT SIMCA project should be handled in BioPAT SIMCA-online. <configuration name> has been deleted. <configuration name>, which was previously deleted, has been restored. <configuration name>, which was previously deleted, has been permanently deleted. <configuration name> has been renamed <configuration new name>. <configuration name> has been changed. A workspace has been created. A workspace has been deleted. <workspace name> has been renamed <workspace new name>. A new user role has been created in the User Administration. A user role has been deleted. <permission ID> has been granted for <role name>. <permission ID> has been revoked for <role name>. <user name> has been added to the user list. ProjectID, ParentFolderID ProjectID ProjectID ProjectID ProjectID ProjectID, ParentFolderID ConfigurationID, ParentProjectID, ConfigurationName ConfigurationID ConfigurationID ConfigurationID ConfigurationID, NewConfigurationName ConfigurationID, version and comment added to summary. WorkspaceName WorkspaceName WorkspaceName, NewWorkspaceName RoleID RoleID RoleID, PermissionID RoleID, PermissionID UserID 31. user_deleted <user name> has been UserID 32

File Event Description Event details removed from the user list. 32. user_password_changed 33. user_role_changed The password for <user name> was changed. The user role for <user name> was changed to <role name>. UserID UserID, RoleID 34. user_distinguished_name _changed The distinguished name for <user name> was changed. UserID, DistinguishedName 35. group_created 36. group_deleted 37. group_user_added 38. group_user_removed 39. out_limits_enabled 40. out_limits_disabled 41. out_limits_updated 42. user_session_started 43. user_session_ended <group name> has been added to the groups list. <group name> has been deleted from the groups list. A user has been added to a group. A user has been removed from a group. The Use Out Limits check box was selected in the File Administrators Out limits dialog. The Use Out Limits check box was cleared. The out limits were updated. <user name> has logged on to the server. <user name> has logged off the server. GroupID GroupID GroupID, UserID GroupID, UserID Settings For details about the interface, see the Audit trail toolbar features subsection in the View chapter. Server log file The Server log displays information about the server the Client is connected to. The content of the Server log file depends on the severity level selected in the Server options Miscellaneous settings. To open the server log file, you need to have configuration management permissions. Open it by clicking File Administrator Server log. Close To close the current project in the BioPAT SIMCA-online Client, click File Close. 33

BioPAT SIMCA-online User Guide BioPAT SIMCA-online options In the BioPAT SIMCA-online Options dialog various options for the Client are available. An explanation to each option is displayed at the bottom of the window when an option is clicked. The options are organized in two tabs: General Plot options BioPAT SIMCA-online Options General tab In the BioPAT SIMCA-online Options General tab various options for the Client are available. An explanation to each option is displayed at the bottom of the window when an option is clicked. The options available are: Paths Ini file view or change the Client Ini file path. Log file Log file size (kb) view or change the maximum Client Log file size. Log level - view or change the minimum severity Log level for messages that should be written to the client log file. Server log file Max display size (kb) view or change the Max display size which is the maximum log file size that will be displayed. If the log file exceeds the limit, the last max size part will be displayed. Text editor - View or change the current Text editor when opening the log file. Miscellaneous Info tip show level - View or change the Info tip show level, which is the minimum importance level of server messages to the Client, also shown as info tips. Startup - Select what to do on Startup: (a) Show Connect to BioPAT SIMCA-online Server dialog (default), (b) Show Empty Environment which results in that the client does not connect to the last server and does not display the Connect to Server dialog box. Interface Tabs view or change whether the tabs are configurations or windows: One tab per window to view all open windows as tabs. Grouped (default) to view all open project configurations as tabs. Using this mode one tab for each project configuration is displayed. 34

File Rolling view When enabled, rolling view behaves as a screen saver, and is activated after a given number of seconds (default 60) if the user doesn t move the mouse or press a key on the keyboard. When Rolling view is selected the client will loop through all open workspace tabs at a given interval, by default 15 seconds. Audit trail comparison tool To see what differs between two versions of the configuration, use the Audit trail comparison tool: In File comparison utility select the file comparison utility to use. ExamDiff is automatically installed and the default. For more about ExamDiff, visit http://www.prestosoft.com/edp_examdiff.asp. The Command line parameters content specifies the command line parameters sent to the file comparison utility. Change this according to the documentation of the specified File comparison utility if changed from the default utility. $File1 and $File2 are expanded to the full paths of the files to compare. The comparison tool is opened by clicking the Compare button after marking one or two versions in the configuration or server audit trails. When marking only one version, clicking the Compare button compares with version 1. Plot options Use File BioPAT SIMCA-online options to view or change: Limit settings in Plot defaults. Batch control chart settings in Plot defaults - batch evolution. Batch level plot defaults in Plot defaults - batch level. The Identifiers to be listed in plots and lists The Batches box content in the Properties group. Plot defaults Plot defaults general for regular project models, BEM and BLM are found in the Plot defaults section. 35

BioPAT SIMCA-online User Guide Show alarm limits To display the alarm limits specified in the project configuration, in the plots for which alarm limits were specified, select the Show alarm limits check box. Read how to specify alarm limits in the Alarms for batch evolution and Alarms for batch level sections in the Project administration chapter. Show control limits For continuous, select the Show control limits check box to display DCrit, T2Crit, Hotelling's ellipse, and standard deviation in the relevant plots. Show annotation To display notes for points or batches for which a note has been added, select the Show annotations check box. Plot defaults - batch evolution The Plot defaults - batch evolution section holds default settings for visualization of the batch evolution model control charts. Layout In the Layout box, select to default display the batch evolution control charts by Units or by Phases. See also the Layout box section in the Home chapter. Automatic zooming Select the Automatic zooming check box to automatically zoom in the subplot displaying the phase of the currently active batch. Note that this option requires that Phases is selected in the Layout box. Note that automatic zooming cannot be selected in the properties of the individual plot. Show recent batches Select to display respective not display recent batches by selecting respective clearing the Show recent batches check box. How many batches are considered recent is specified in the configuration. 36

File Show target values Select the Show target values check box to display the target values specified in the project configuration, in the plots for which target values were specified. Read how to specify target values in the Specifying Target Values section in the Project administration chapter. Show subheader Select the Show subheader check box to display the subheaders for all plots in multiplots. Plot defaults - batch level The Plot defaults - batch level section holds settings for visualization of the batch level plots. Layout In the Layout box, select for the plots to display Individual models or Combined by default. Show recent batches Select to display respective not display recent batches by selecting respective clearing the Show recent batches check box. How many batches are considered recent is specified in the configuration. Show significance limits Select to display the significant limits in the score scatter plot, DModX plot, and Hotelling's T2Range plot by selecting the Show significance limits check box. Significance level In the Significance level field enter the significance level to use in the score scatter plot, DModX plot, and Hotelling's T2Range plot. Show standard deviation limits Select to display the standard deviation limits in the score plot displaying one component by selecting the Show standard deviation limits check box. Number of standard deviations In the Number of standard deviations field, enter the number of standard deviations to display in the score plot displaying one component. Show subheader Select the Show subheader check box to display the subheaders in all plots. Identifiers Select the way you want variable and batch identifiers to be displayed in plots and lists. The details of the variable and batch IDs are displayed in the header row. Variable ID For regular projects In the Variable ID box select: a. One of the available IDs to display the primary or secondary ID as in BioPAT SIMCA. b. Alias to display the Alias specified in the project configuration. 37

BioPAT SIMCA-online User Guide Use the Start at and Length fields to define which part of the names to display. For information about how to specify aliases, see the Tags page in Configure dialog subsection in the Project administration chapter. Batch evolution In the Batch evolution section In the Variable ID box select: a. One of the available IDs to display the primary or secondary ID as in BioPAT SIMCA. b. Alias to display the aliases specified in the project configuration. Use the Start at and Length fields to define which part of the names to display. For information about how to specify aliases, see the Phase tags page in Configure dialog subsection in the Project administration chapter. Batch level In the Batch level section In the Variable ID box, select: a. One of the available IDs to display as listed in the dataset spreadsheet in BioPAT SIMCA. b. Phase to display the phase ID. c. Maturity to display the maturity of the variable. When the batch level holds summary variables, the maturity is the name of the function, for instance MIN or MAX. d. Source to display the source of the batch level variable, for instance t[1] or variable id. Use the Start at and Length fields to define which part of the names to display. Batch ID For batch level plots displaying the batch ID, use the Start at and Length fields to define which part of the identifiers to display. Batches box The active batches are always by default displayed. In the Batches box section, select the batches to be displayed in the Batches box in the Properties group on the Home tab: 1. Active batches are always displayed. 2. Select whether to Include recent batches. The number of batches considered recent is specified in the configuration. 3. Select whether to Include workset batches. When the Include workset batches check box is selected the button is available. Click the browse-button and select which of the workset batches to display. By default all workset batches are included. 38

File Selecting which workset batches to display Clicking the browse button opens a dialog displaying all workset batches available. All batches are by default selected. To exclude batches, clear the Select all check box and then clear the check boxes of the batches to exclude. Note: Multi selection is available in the Select Batches dialog. Consequently, if you mark several batches and then select or clear one of them, all marked batches will be selected or cleared. Exit BioPAT SIMCA-online To close the BioPAT SIMCA-online Client, click File Exit BioPAT SIMCA-online. 39

Quick Access Toolbar Introduction The Quick Access Toolbar is by default positioned at the top above the tabs and allows you to have your favorite commands easily accessible. The Quick Access Toolbar is standard in Windows software with ribbons. The Quick Access Toolbar in BioPAT SIMCA default displays the following features: Open (Ctrl+O) - to open a configuration or workspace. Project administration - to open the Project Administration dialog. Copy (Ctrl+C) - to copy the active plot or selection. Customizing Quick Access Toolbar You can add buttons to and remove buttons from the Quick Access Toolbar and also reposition the Quick Access Toolbar to below the ribbon. Quick Access Toolbar menu Quick Access Toolbar shortcut menu Removing buttons from Quick Access Toolbar To remove a button from the Quick Access Toolbar use one of the following methods: Right-click the button and click Remove from Quick Access Toolbar. Click the arrow to the right of the available Quick Access Toolbar buttons and clear the relevant check box. Adding buttons to Quick Access Toolbar To add a button to the Quick Access Toolbar, right-click the button on the ribbon and click Add to Quick Access Toolbar. Moving the Quick Access Toolbar To position the Quick Access Toolbar closer to the workspace you can select to position it below the ribbon by clicking the Show Below the Ribbon in the Quick Access Toolbar menu. Click Show Above the Ribbon to move it back to its original position. 41

BioPAT SIMCA-online User Guide Minimizing the ribbon To maximize the workspace you can minimize the ribbon so that it folds away like a menu. The Minimize the Ribbon command is available: When you right-click a button in the Quick Access Toolbar. In the Quick Access Toolbar menu. When you right-click a button in the ribbon. 42

Home Introduction The Home tab holds the commands most commonly used. On the Home tab you can: Create plots for batch and regular projects. Change the properties of the active plot in the Properties group. If you have the right privileges: View or update the configuration, Repredict data, and Delete predicted data in Manage data. For details, see the Modifying configuration section in the Project administration chapter. All plots, except for the variable plots, display predicted values. Batch On the Home tab, view/update the configuration, select the plots to display, and change the properties of the open plot. All plots, except for those displaying individual variables, display predicted values. There are four groups on the Home tab: Manage with Configuration, Repredict data and Delete predicted data. Only available for users with configuration management permissions. The Batch evolution plots group with the available batch evolution plots. The Batch level plots group with the available batch level plots. The Properties group which allows changing the properties of the active plot. Batch evolution plots In the Batch evolution plots group, find the control charts: Scores, DModX, Hotelling s T2, Variable, and Y Predicted. The Dual Variable Plot is found by clicking the Variable menu. Batch evolution plots display active and historical batches and the appropriate limits for the respective plots. Batches with observations outside the limits are in some way different from the workset batches. Score Batch Evolution control chart for the scores (T) of the active batches. The default is to display scores for the first component, t[1]. 43

BioPAT SIMCA-online User Guide Displaying triggered alarms When alarms have been defined, triggered alarms are displayed as described in the Alarm visualization section in View chapter. For more, see the Plot defaults subsections in the BioPAT SIMCA-online Options section in the File chapter. DModX Batch Evolution control chart of the distance to the model, DModX, after the last component. Hotelling s T2Range Batch Evolution control chart of Hotelling s T2Range. The default is to display from component 1 to the last component. Variable Batch Evolution control chart of the individual variables. By default the first variable available is displayed. Use the Variable box in the Properties group on the Home tab to switch variables. 44

Home Dual variable Batch Evolution control chart of two variables. By default the first and second variables available are displayed. Use the Variable boxes in the Properties group on the Home tab to switch variables. The plot is opened by clicking Variable and then Dual Variable in the Batch evolution plots group on the Home tab. Y Predicted Batch Evolution control chart of predicted maturity (Y). Empty instead of plot When the space where you expected a plot is empty, the reason is one of the following: There is no data to display. The plot cannot be displayed since some of the necessary variables and/or components are missing. Can happen for subplots. The x-axis annotation is too large. To switch variable or component, use the Properties group. 45

BioPAT SIMCA-online User Guide Batch level plots In the Batch level plots group on the Home tab, find Scores, DModX, Hotelling s T2, Variable, and Y Predicted. The Score Scatter plot can be opened from the Score menu and the All Y Predicted plot from the Y Predicted menu. The batch level plots by default display the completed batches (Recent Batches) in a plot grid with one plot for each model. Using the Layout box, the plot can be displayed one for each plot type so that the prediction for each model is displayed for each batch. See also the Layout box for batch level subsection later in this chapter. With hierarchical models or partial models, you can also display the active batches as they are still evolving in the batch evolution level. Without hierarchical or partial models, active batches are unavailable in the batch level plots. How many batches are considered recent is specified in the configuration. Scores The Batch Level Score plot is a scatter plot of a score vector; scores for the first component are shown by default, t[1]. The plot can be displayed Combined (default) and as Individual models using the Layout box to switch. Figure: Batch Level Score plot Combined Score scatter plot The Batch Level Score Scatter plot displays the scores. The default is to display t[1] vs. t[2]. The plot can be displayed Combined (default) and as Individual models using the Layout box to switch. When Individual models is selected the Hotelling s T2 ellipse (99%) is also displayed. Figure: Batch Level Score Scatter plot Combined The plot is opened by clicking Score and then Score Scatter in the Batch level plots group on the Home tab. DModX The Batch Level DModX plot is a scatter plot displaying the distance to model after the last component. DModX is proportional to the RSD (Residual Standard Deviation) of batches in the X space. The plot can be displayed Combined (default) and as Individual models using the Layout box to switch. Figure: Batch Level Distance to Model X plot Combined 46

Home Hotelling s T2 The Batch Level Hotelling s T2Range plot is a scatter plot displaying the distance from the origin in the model plane (score space) for each selected batch. The default is to display from component 1 to the last component. The plot can be displayed Combined (default) and as Individual models using the Layout box to switch. Figure: Batch Level Hotelling's T2Range plot Combined Variable plot The Batch Level Variable plot is a scatter plot displaying the selected variable. By default the first variable in the variable list is displayed. Use the Variable box in the Properties group on the Home tab to switch variables. The plot can be displayed Combined (default) and as Individual models using the Layout box to switch. Figure: Batch Level Variable plot Combined. Y Predicted The Batch Level Y Predicted plot is a scatter plot, default displaying the predictions of the first y- variable. The plot can be displayed Combined (default) and as Individual models using the Layout box to switch. Figure: Batch Level Y Predicted plot Combined. 47

BioPAT SIMCA-online User Guide The confidence intervals displayed in this plot were derived from Jack-knifing. For details about Jackknifing, see the BioPAT SIMCA user guide. All Y Predicted The Batch Level All Y Predicted plot displays the predictions of all y-variables in the same plot. The predictions of all y-variables are displayed for each batch in this plot. Figure: Batch Level All Y Predicted plot. The plot is opened by clicking Y Predicted and then All Y Predicted in the Batch level plots group on the Home tab. Empty instead of plot When the space where you expected a plot is empty, the reason is one of the following: There is no data to display. The plot cannot be displayed since some of the necessary variables and/or components are missing. Can happen for subplots. The x-axis annotation is too large. To switch variable or component, use the Properties group. Properties group Use the Properties group to change the relevant parameters of the plot, such as variables, components, batches and layout. Access the properties by using the arrow keys on your keyboard. Pressing: UP and DOWN switches the component or variable in the first property box for the next or previous. RIGHT and LEFT switches the content of the second property box for the next or previous. PAGE UP and PAGE DOWN switches the content of the third property box for the next or previous. Customize the display of the active batch plot by changing the properties in the displayed boxes 48

Home opening the Properties dialog using one of the methods described in the Plot Properties section later in this chapter. For other and more customization, see the sections Plot Properties later in this chapter and Format Plot in the Customizing plots chapter. Note: The selected change will affect only the active plot. If you want to customize the default settings for the plots, click File BioPAT SIMCA-online options. Batches box Select from the Batches box the batches to display in the active plot. The Batches box is available for all plots for batch evolution and batch level models. Batches box content In the Batches box, find the groups Active Batches and Recent Batches (historical) and the list of named selected batches. For the batch level score scatter plot there is also a group named Workset Batches to enable displaying all workset batches with one click. Beneath these groups, the Active Batches, Recent Batches and Workset Batches are listed. Reference batches To display certain workset or historical batches as reference batches, along with the active batches, select them in the Batches box under the respective headers. Named batches selected in the Batches box are displayed until cleared. So to continue to display a certain active batch, click the Batches box and select the batch from the list. Note: Any specific batch selected from the Batches box is referred to as a reference batch. You can select to display several reference batches. Customizing Batches box The content of the Batches box can be customized in the Batches box section in the BioPAT SIMCAonline options dialog. For details see the Batches box subsection in the BioPAT SIMCA-online options section in the File chapter. The number of batches considered recent is specified in the Time ranges page in the Configure dialog. Selecting components In plots displaying scores or T2Range you can select for which components to display the plot. In the Y- axis/from/to box in the Properties group on the Home tab; all score vectors available for the active plot are listed. In the table, the first column shows the plots for which the components can be changed and the second column contains the available boxes. Plot Boxes to select components from Score plots Score Scatter plot for batch level Hotelling s T2Range Plots Y-axis X-axis and Y-axis From and To The component to display for the Distance to Model X plots cannot be changed. The DModX plot is always displayed after the last component of the model. The Y Predicted plot is displayed using all components. 49

BioPAT SIMCA-online User Guide Selecting variables When the active plot is a Variable plot, or a Y Predicted plot from batch level, the Variable box displays the list of available variables. When the active plot is a Dual Variable plot for a batch evolution model, an additional variable box, Variable 2, displays the list of available variables. Click the Variable box and select the desired variable. Properties group for the Variable plot and Y Predicted plot. Layout for batch evolution plots In the Layout box, select whether to view the plot by Phase or by Unit (default). When displaying the plot by Phase the phases are displayed one after the other from left to right in the model order. When displaying the plot by Unit the cells are displayed to visualize the system at hand. See also the Plot defaults - batch evolution subsection in the BioPAT SIMCA-online options section in the File chapter. Layout for batch level plots In the Layout box, select whether to view the plot as Individual models (default) or Combined in one plot. When the plot displays Individual models (subplots), the predictions for each batch level model are displayed in one plot. When displaying the plot Combined, the plot is reorganized to display the predictions for all models for each batch. The batches are displayed on the x-axis, one after the other from left to right, in the order the batches were executed. See also the Plot defaults - batch level subsection in the BioPAT SIMCA-online options section in the File chapter. Individual models Combined 50

Home Plot Properties Use the Plot Properties dialog to customize what is displayed in the current plot. The Plot Properties dialog the current plot is opened by: clicking the plot and clicking Properties in the mini-toolbar. clicking the Properties group dialog dispatch launcher on the Home tab or right-clicking the plot and clicking Properties. The Plot Properties dialog can have the following tabs: Select batches, Plot options and Selected observations (contribution plot only). These tabs are described in the sections that follow. For other customization, see the section Customizing plots chapter. Note: The selected change will affect only the active plot. If you want to customize the default settings for the plots, click File BioPAT SIMCA-online options. Plot options The Plot options tab has a number of options depending on the open plot.. Show alarm limits To show or hide the alarm limits of the current plot, select or clear the Show alarm limits check box. To show or hide the alarm limits by default, see the BioPAT SIMCA-online options section in the File chapter. Note: When displaying plots by clicking in the Overview window, the created plots always display the alarm limits. Show annotations To display an envelope icon for points or batches for which a note has been entered, select the Show annotations check box. Read how to specify notes in the Add note subsection in the Tools chapter. Show subheader To hide or display the subheaders in the subplots, the Show subheader check box has to be cleared or selected. Control limits for batch evolution plots 51

BioPAT SIMCA-online User Guide In Control limits, select the limits to display: +3, +2, +1, -1, -2, -3 std. dev. (standard deviations), Average (batch). Default is to display +3 standard deviations and the Average. The current selection is displayed on the header row. To add/change limits to choose from, see the Control limits subsection in the Project administration chapter. Show significance limits for batch level plots Select to display or hide limits in the current plot by selecting or clearing the Show significance limit check box. To change the significance level from the default 0.01, enter a new value in the Significance level field, available when the Show significance limits check box is selected This feature is available for the batch level DModX and Hotelling's T2Range plots. Show standard deviation limits for batch level score plot Select to display or hide limits in the batch level score plot by selecting or clearing the Show standard deviation limits check box. To change the number of standard deviations, by default '3', enter a new number in the Number of standard deviations field, available when the Show standard deviation limits check box is selected. Plot options for Contribution In the Plot Properties dialog of the Contribution plot there is a Selected observations page, a Plot options page with the Sort feature described here and for continuous a Time page. By default the contribution plot is not grouped nor sorted. To sort the contribution plot: 1. Select the Sort check box. 2. Select Absolute Value (default), Value, or Name. Select batches By default the most recent historical batches are plotted in the background. The number of recent batches displayed is specified in the Time ranges page in the Configure dialog. Change which batches are displayed in the current plot by specifying a new time range in the Select batches tab in the Plot Properties dialog. 52

Home Selected observations Contribution plots are displayed for one point/group of points versus another point/group of points/average. In the case with groups, use the Selected observations page to see which points were included in the group. Regular On the Home tab, view/update the configuration, select the plots to display, and change the properties of the open plot. All plots, except for those displaying individual variables, display predicted values. The number of observations displayed is specified in the Configure dialog on the Time ranges page. There are four groups on the Home tab: Manage with Configuration and Repredict data. Only available for users with configuration management permissions. The Trend plots group with the available predefined trend plots. The Custom plots group with the fully customizable trend and scatter plots. The Properties group which allows stepping backwards and forwards or pause the active plot. Worm plot The Worm Plot displays: Scores, default t1 vs. t2, as a line plot. Head (larger circle) of the worm (line). The workset observations. Hotelling s T2 ellipse. Scores Trend plot displaying scores (T). The default is to display t[1]. 53

BioPAT SIMCA-online User Guide DModX Trend plot of the distance to the model, DModX, after the last component. From the DModX menu, the trend plots for DModX+, PModX and PModX+ can be displayed. PModX Trend plot of the probability that each point belongs to the model. Available both for regular PModX and PModX+. Display the PModX and PModX+ plots by clicking DModX and the respective vector name. Hotelling's T2Range Trend plot of Hotelling's T2Range. The default is to display from component 1 to the last component. For OPLS this plot is unavailable. 54

Home Y Predicted Trend plot of observed and predicted y-variables. By default the first y-variable is displayed. See also the Data vectors and Plot options subsections later in this chapter. Custom plots Use Trend and Scatter to create plots using any combination of vectors. Trend and Scatter are found in the Custom plots group on the Home tab for regular projects. When clicking Trend or Scatter a dialog opens allowing you to select which vectors to plot. Identifiers are displayed according to plot defaults in BioPAT SIMCA-online options. Note: To switch component or variable, click the (blue) number/variable ID and select another one. Empty instead of plot When the space where you expected a plot is empty, the reason is one of the following: There is no data to display. The plot cannot be displayed since some of the necessary variables and/or components are missing. Can happen for subplots. The x-axis annotation is too large. To switch variable or component, use the Properties group. Properties group The Properties group for continuous processes contains the stepping buttons and the Pause button. Pausing affects only the current plot and not the execution as such. Stepping is done in steps of 10% of the total window length. The Plot Properties dialog the current plot is opened by: clicking the plot and clicking Properties in the mini-toolbar. clicking the Properties group dialog dispatch launcher in the Home tab or right-clicking the plot and selecting Properties. Plot options Specify whether to show limits and annotations in the Plot Options page. 55

BioPAT SIMCA-online User Guide Note: Changes in options in the Plot Properties dialog apply to the current plot only. When opening a new plot, the Properties settings are reset to default. To change for future plots, change in Plot options in the File BioPAT SIMCA-online Options dialog. Show alarm limits To show or hide the alarm limits of the current plot, select or clear the Show alarm limits check box. To show or hide the alarm limits by default, see the BioPAT SIMCA-online options section in the File chapter. Note: When displaying plots by clicking in the Overview window, the created plots always display the alarm limits. Show control limits Select to display or hide limits in the plots by selecting or clearing the Show control limits check box. Depending on plot, the relevant critical limit or standard deviation limits are displayed. Show annotations To display an envelope icon for points or batches for which a note has been entered, select the Show annotations check box. Read how to specify notes in the Add note subsection in the Report section in the View chapter. Plot options for Contribution In the Plot Properties dialog of the Contribution plot there is a Selected observations page, a Plot options page with the Sort feature described here and for continuous a Time page. By default the contribution plot is not grouped nor sorted. To sort the contribution plot: 1. Select the Sort check box. 2. Select Absolute Value (default), Value, or Name. 56

Home Selected observations Contribution plots are displayed for one point/group of points versus another point/group of points/average. In the case with groups, use the Selected observations page to see which points were included in the group. Data vectors In the Data vectors page you can change vectors to display, remove vectors, add new vectors, and change components.. Actions available: Remove all vectors by clicking the Delete All-button in the header. Remove a vector by clicking the delete-button. Time Add a vector by clicking the new-button at the bottom of the list. In the Type column, change the displayed vector by clicking the vector and selecting a new vector in the list that expands. In the Vector column, change components or variables by clicking the blue item to change. In the Vector column, display all components or variables by right-clicking the blue item and clicking Expand. In the Time page you can select to display a specific interval in time by changing the From and To dates and times. This applies only to the current plot. The default is to Automatically update to show the latest available data on the server. 57

View Introduction On the View tab, find following features: Data list. Show/Hide group with Project info, Overview, Log, Plot details, Status bar, Tabs and Full screen. Open group with Configuration audit trail, Client log, and Report. Window arrangements in the Window group including Save workspace. Data list The data in the internal database can be listed by clicking Data list on the View tab. In the dialog that appears, select the data to display in the spreadsheet using the From and To date and time fields. For batch projects you can also select among the batches listed for the specified interval. In the table below, the content of the tabs in the created list are described. Sheet What is listed Batch Evolution Data Batch Level Data Batch Condition Data. Local Centering Data Continuous Trend Data Original measured variables plus the computed parameters, scores, DModX, etc available in the selected batch evolution model. Original measured variables plus the computed parameters, scores, DModX, etc available in the selected batch level model. Batch condition variables. Local centering data used in the selected batch evolution model. Original measured variables plus the computed parameters, scores, DModX, etc available in the selected model. Show or hide The Show or hide group includes the following features: The dockable windows Project info, Overview, Log and Plot details. The Status bar check box. The Tabs check box. Full screen 59

BioPAT SIMCA-online User Guide Project info The Project info dockable window displays, the project name, the projects original location, the time the project was added to the Server, and whether the execution is On or Off for each open project. The Project info dockable window is opened by selecting the Project info check box in the Show or hide group on the View tab. Log The Log dockable window displays: Administrator actions, such as log on or off. Project failures, such as failing to initialize, to connect, or to create a data source. If the processor works at high load, this is also logged here. A license reminder message when the license is about to expire. The Log dockable window is opened by selecting the Log check box in the Show or hide group on the View tab. Status bar The Status bar, found at the bottom of the screen, displays a description, coordinates, and connection status for the server. In the table, see which type of information and where in the Status bar it is displayed: Action Position Displays Marking a menu item (for ex. File Print) or hovering over a button. Left The description of a menu item or button. When nothing is marked the Status bar displays 'Ready' When holding the cursor over Print. Hovering in a plot. Middle The coordinates of the cursor in a plot. None. Right The user currently logged on and the status of the connection to the server (Connected/Disconnected/Server busy). Overview The Overview dockable window displays the status of the active batch or execution. The header row displays the batch ID/execution start time, and current overall status for the batch/execution: OKAY and green when no alarm has been triggered, WARNING (yellow) and CRITICAL (red) when the respective alarm has been triggered. Below the header row the Start and Stop times are displayed. If the batch/execution is still active, the stop time is Active. Each model is represented by a color coded box with its model number and title, or for phases, phase ID. The box is green when there is an active batch or execution but no alarm has been triggered, yellow when a warning alarm has been triggered, red when a critical alarm has been triggered, and uncolored before data has reached that model. 60

View The progress of an active batch can be followed through these color coded boxes to completion. Note: For phases with normalized maturity, alarms are displayed during the evolution of the batch, but are not final until after phase completion. When clicking one of the models, Reset alarms, Display triggered alarms and Display configured alarms are displayed. Reset alarms returns the color for the model to green until the next alarm is triggered. Display triggered alarms opens the triggered vectors zoomed in on the subplot with the triggered alarm for the model. These plots also display the specified alarm limits, warning limits in yellow and critical limits in red. Display configured alarms opens plots displaying all alarms specified in the configuration. These plots also display the specified alarm limits, warning limits in yellow and critical limits in red. In the Alarm visualization section next, see details about the visualization of the alarms. See also the Adding alarms section in the Project Administration chapter. Alarm visualization When alarms are specified, triggered alarms are displayed in: Overview window. Plots displaying the vector with the specified alarm. Plot Details window when a plot with a triggered alarm is active. The Report window. The table describes the color coding and symbols displayed concerning alarms. Alarm Overview window color Plot, Plot Details and Report No alarm triggered and the model is not executing No alarm triggered and the model is currently executing Alarm triggered due to point outside a warning limit (Lo/Hi). Alarm triggered due to point outside a critical limit (LoLo/HiHi). Uncolored Green Yellow Red Plots display nothing, Plot Details displays No alarms or notes and the Report displays: Plots display the default plot symbols, Plot Details displays No alarms or notes and the Report displays: The triggered point displays a yellow warning sign: Resetting the alarm results in that the symbol changes to: The triggered point displays a red circle with a cross. Resetting the alarm results in that the symbol changes to: Note: After resetting an alarm the Overview window again displays a green box while the plots, Plot Details window and the Report display the symbol for reset alarms. 61

BioPAT SIMCA-online User Guide Plot Details The Plot Details dockable window displays all triggered alarms and all notes present in the active plot. In the Plot Details window you can reset alarms and edit notes by double-clicking the respective rows. You can also delete notes by marking and pressing DELETE. Tabs To display or hide tabs for all open project configurations or windows, on the View tab, in the Show or hide group select the Tabs check box. Whether the tabs show project configurations or all windows depends on the settings in File BioPAT SIMCA-online Options under the Interface header in the General tab. The tabs are color coded signaling status. In the example below: The left configuration is not receiving data, thus the tab is uncolored. For the middle one a critical alarm was triggered, thus the tab is colored red. When a warning alarm has been triggered the tab is colored yellow. The right configuration is running and no alarms have been triggered, thus colored green. When selecting to display the individual windows, all windows are colored according to the description above for the configuration they were created from. Full screen To maximize the plot area, leaving only the minimized ribbon and the plot area, on the View tab, click Full screen. To return to normal, again click Full screen. Open The Configuration audit trail, Client log, and Report are all available in the Open group on the View tab. Configuration audit trail In BioPAT SIMCA-online the Audit trail is always turned on. The actions and incidents listed in the table are recorded in the audit trail with time and date stamp: Open the audit trail by clicking Audit trail in the Open group on the View tab. The audit trail of the current configuration is then opened. 62

View Event Description Event details 1. configuration_updated 2. execution_started 3. execution_stopped 4. execution_resumed 5. execution_aborted <configuration name> has been updated to version <version number>. The execution of <configuration name> has started. The execution of <configuration name> has stopped. The execution of <configuration name> has resumed (started again after being stopped). The execution of <configuration name> was interrupted, for instance error when reading from external data source. UserSessionID, Version number and comment added to Summary UserSessionID, ExecutionID UserSessionID, ExecutionID ExecutionID ExecutionID 6. repredict_started Repredict has started. ExecutionID 7. repredict_stopped Repredict was stopped. ExecutionID 8. batch_started <batch ID> has started. BatchID 9. batch_finished <batch ID> has finished. BatchID 10. batch_deleted 11. batch_discarded 12. phase_started 13. phase_finished 14. note_created 15. note_deleted 16. note_updated <batch ID> has been deleted from the server. <batch ID> has been discarded. Happens when a batch is not read to completion. <phase name> has started. <phase name> has finished. A note has been created at with <content>. <note ID> has been deleted. <note ID> has been updated to hold <content>. UserSessionID, BatchID BatchID, Reason BatchID, PhaseNumber BatchID, PhaseNumber UserSessionID, Severity, NoteID, note text and point ID (Batch ID, Phase Number, time point) added to summary. UserSessionID, Severity, NoteID, note text and point ID (Batch ID, Phase Number, time point) added to summary. UserSessionID, Severity, NoteID, note text and point ID (Batch ID, Phase Number, time point) added to summary. 17. alarm_triggered The alarm <triggered alarm ID> has been TriggeredAlarmID, Severity, vector, point ID 63

BioPAT SIMCA-online User Guide Event Description Event details triggered for <vector>. (Batch ID, Phase Number, time point) added to summary. 18. alarm_elevated 19. alarm_reset The alarm <triggered alarm ID> has been elevated to critical for <vector>. The alarm <triggered alarm ID> has been reset for <vector>. TriggeredAlarmID, Severity, vector, point ID (Batch ID, Phase Number, time point) added to summary. UserSessionID, TriggeredAlarmID, Severity, vector, point ID (Batch ID, Phase Number, time point) and user entered reset-comment added to summary. In the audit trail, use the toolbar to organize, select range, compare configuration versions, view configurations, roll back to a previous version of a configuration and filter search. The table describes the different features available for batch and regular projects. Toolbar features Result Organize - see the Organize in the audit trails subsection later in this chapter. From To Refresh Compare View configuration Roll back Filter field Select the event to start from. Negative values indicate how many events backing up from the value in To to back up. The last event displayed. Last means the last event at all times. Updates the audit trail window. Has to be clicked to update after changes in the From and To fields. Displays what differs between the two marked versions of the configuration using a File comparison utility. When only one version is marked, the comparison is made versus version 1. For options, see the BioPAT SIMCA-online Options - General topic. Opens the marked version of the configuration. No changes can be made in the dialog. Creates a new version with the content of the marked version. The content of the audit trail is filtered to only display rows matching the filter field. Organize In the Organize button the following features are available: Show system events - In addition to showing regular events, system events are displayed. Show details - Displays details of the events currently displayed in the audit trail. Field chooser - displays the columns currently not displayed in the audit trail. Drag headers from the Field chooser to the audit trail to add columns. To remove a column, drag the header down from the header row. Copy - is available when something is marked in the audit trail and then copies the selection. Select all - selects all contents of the audit trail thus allowing all contents to be copied. Expand all groups - expands all groups when some or all collapsed. Groups are created by dragging a header to the area above the headers. Collapse all groups - collapses all groups in the case when some or all are expanded. Groups are created by dragging a header to the area above the headers. Client log The Client log lists information such as: - Connection/disconnection to server. 64

View - Log level specified in BioPAT SIMCA-online options. - Days until license expires. The Client log is available in the Open group on the View tab. Report The Report displays a summary of all triggered alarms and notes, in the current configuration for the selected time period/batches. In the Report you can reset alarms and add, edit and remove notes. Note: After resetting alarms or adding/editing/removing notes, you have to refresh to see modifications. The table describes the features available in the report. Report features Description Toolbar features Saving of the report Group Shortcut menu See the Report toolbar features subsection. Can be done by printing it to pdf or copying to clipboard. Drag a column header above the header row to group by that property. The report for batch configurations is grouped by batch and model by default. The shortcut menu allows you to: Select more/other columns in Columns. Group by this field adding a group to the group area. Hide column to not display the right-clicked column. Sort ascending according to the right-clicked column. Sort descending according to the right-clicked column. Copy the selection. Select all items in the report. Print the content in the report. The Report is available in the Open group on the View tab. Report toolbar features In the Configuration audit trail and Server audit trail use the toolbar to organize, select range, display plots, reset alarms, and add/modify notes. The table describes the different features available for batch and regular projects. Toolbar features Result Organize - see the Organize subsection later in this section. Select batches Select time range Display triggered alarms Reset alarm Add note, Edit note, Delete note Enter filter text here Refresh 1. Click Select batches/select time range 2. Specify the From and To dates and times. 3. For batch projects, mark the batches to display in Available Batches and click ->. Plots displaying the triggered alarms marked in the Report are opened. See the Reset alarms subsections later in this section. See the Add note and Adding note to batch/phase/model subsections later in this section. The content of the report is filtered to only display rows matching the filter field. Updates the Report window. 65

BioPAT SIMCA-online User Guide Adding notes Notes can be added to a point marked in a plot or in the Report as follows: Plot: mark a point and click Add note: in the mini-toolbar, in the Marked items group on the Tools tab or on the shortcut menu. Report: mark the row and click Add note in the toolbar or in the shortcut menu. When adding a note the following dialog appears. In the Add Note: Specify Severity and Text dialog, select the Severity level, and enter the text for the note in the Comment field. The Severity levels available are: Low, Medium (default), or High where they result in different note symbols in the plot, in the Plot Details window, and in the Report: Low - Medium - High - Editing notes To modify a note use one of the following methods: In the plot, mark the point with the note and click Add note. In the Report, mark the note and click Edit note in the toolbar. In the Plot Details window, double-click the note. Deleting notes To remove a note use one of the following methods: Mark the note in the Report and click Delete note in the toolbar. In the Plot Details window, mark the note and press DELETE on your keyboard. Adding Note in Note wizard Notes can also be added to a batch, phase model, batch level model or observation using a wizard in the Report. To add a note to an entire batch: 1. In the Report mark a row that does not relate to maturity. 2. Click the Add note-button. 3. In the Add Note: Select Note Type window, select Batch, Phase/Model, or Observation. a. With Batch selected you must select a batch. b. With Phase selected you must select a batch and a phase or batch level model. c. With Observation selected you must select a batch, a phase, and an observation. 4. After stepping through the wizard making selections according to step 3 the Add Note: Specify Severity and Text page opens allowing you to enter severity and text. For more about this page, see the Add note subsection earlier in this chapter. 66

View Reset alarms Triggered alarms can be reset in three places: In the Overview window by clicking the model with the triggered alarm and clicking Reset alarms in the menu. In the Plot Details window by double-clicking the triggered alarm. In the Report by marking a triggered alarm row and clicking the Reset alarms button in the toolbar. In the Reset Alarms dialog the user must enter a text in the Comment field to enable the Reset button. Alarm symbols after resetting: Warning level: Critical level: Organize In the Organize button the following features are available: Show alarms - results in that all alarms triggered during the time period are displayed. By default selected. Show reset alarms - results in that triggered alarms during the time period that were reset are displayed. By default selected. Show phases/models with no alarms - displays all phases and models for the time period even if no alarms were triggered and no notes added for them. By default selected and only available for batch models. Show notes - displays all added notes for the time period. By default selected. Field chooser - displays the columns currently not displayed in the Report. Drag headers from the Field chooser to the Report to add columns. To remove a column, drag the header down from the header row. Copy - is available when something is marked in the Report and then copies the selection. Select all - selects all contents of the Report thus allowing all contents to be copied. Expand all groups - expands all groups when some or all collapsed. Groups are created by dragging a header to the area above the headers. Collapse all groups - collapses all groups in the case when some or all are expanded. Groups are created by dragging a header to the area above the headers. Save layout - saves the current column headers and groups as the default for next time the report is opened. Load saved layout - opens the saved layout for column headers and groups. Restore default layout - removes any customization of the layout and displays the Umetrics default layout. Note: Save layout does not save changes to the selection in Organize. Report columns description The columns in the Report window are described in this subsection. 67

BioPAT SIMCA-online User Guide To add columns, use the Organize Field chooser from the toolbar, or Columns on the shortcut menu. To remove columns, just drag the column from the header row. The default layout is different depending on whether the project is batch or regular, but the columns available are the same. Column Description and illustration Icon signaling severity: Severity - a HiHi/LoLo alarm was triggered, then reset: - a Hi/Lo warning was triggered, then reset: - a note was added, here displayed with increasing importance: Icon signaling importance: Importance - no alarms were triggered or there is a note of low importance : - a warning alarm was triggered or a medium importance note was added: nothing. - a critical alarm has been triggered or a high severity note has been added: - reset alarm: Icon signaling which type of event has happened: Type - an alarm: - a note: Model Vector Observation Model name from SIMCA, for instance "M1, Process under control". Vector that the alarm was triggered in, for instance 'YPred'. Time the alarm was triggered or note was added. Batch specific Batch Maturity Batch start time Batch stop time Phase start time Phase stop time Batch ID from the external database The maturity value at the triggered alarm or note. Start time, in the external database, for the batch. Stop time, in the external database, for the batch. Start time, in the external database, for the phase. Stop time, in the external database, for the phase. Window group The Window group contains the window commands Cascade, Tile horizontally, Tile vertically, Close, Save workspace and Switch windows. Clicking the Window group dialog box launcher opens the Arrange Windows dialog. 68

View Save workspace The configuration of the Client's open projects and plots can be saved as a workspace. All workspaces are saved on the Server. Workspaces can be opened by any user, while only an administrator with workspace management permissions can save or delete workspaces. To save a workspace, open the projects and plots that you want the workspace to contain, on the View tab, in the Window group, click Save workspace, give the workspace a unique name, and then click Save. Note: Only open configurations and plots are saved in workspaces. See also the Workspaces section in the Project administration chapter. 69

Tools Introduction The Tools tab holds the buttons: Select, Zoom, Zoom out, Sort, Drill down, Add note, Create list, and Save as. Select - Marking tool The Select-button is used to select which type of marking to use. Click the small arrow below the button and click the type of marker from the menu. The available marking types are: Free-form selection: Allows marking to take any shape (default). Rectangular selection: Marks in a rectangular shape. Select along the X-axis: Marks as a vertical bar. Select along the Y-axis: Marks as a horizontal bar. Note: To keep the marked points marked, while marking new points, hold down CTRL. The marked points then belong to the same group of marked items. Deselecting/unmarking points To deselect points in a plot, click a white area in the plot. To deselect points in a list, mark the first row. Displaying properties of the item When positioning the cursor on an item in a plot, the marker behaves as a pointer and displays the name and coordinates of the observation or variable. Creating contribution plots With any marker: 1. Double-click an observation in a score plot for instance. The contribution plot opens, comparing the variable values of the selected observation to the average of all the observations in the workset. This plot indicates why the selected observation is different from the average. 2. Click the first observation, and then double click the second observation. The resulting contribution indicates why the first observation differs from the second. For more about creating contribution plots, see the Drill down section in the Tools chapter. Zoom To zoom in a plot, click the Zoom tool in the Zoom group. By default Zoom in is selected. 71

BioPAT SIMCA-online User Guide Use the Zoom menu to select the type of zoom from the drop down menu: Zoom in: Magnifies a rectangular region Zoom X: Magnifies a region along the x-axis Zoom Y: Magnifies a region along the y-axis Zoom subplot: Magnifies a subplot in a multi-plot display. Then mark the desired region, or subplot, of the plot to zoom. Note: With any zooming type selected, double-clicking a subplot automatically zooms the subplot. Zooming out Click Zoom out to revert zoom to original scale in the steps taken when zooming. Sort The contribution column plots can be sorted ascending or descending. To sort 1. Open the contribution plot. 2. On the Tools tab, click Sort. The resulting plot is sorted by absolute value with the largest absolute column to the left. By clicking the Sort arrow, you can select to: Sort by absolute value (default when clicking Sort) - see above. Sort by value - leaving the plot sorted with the largest positive column to the left and the smallest value to the right. Sort by name - leaving the plot sorted alphabetically using the displayed variable ID. Original sort order - reverting the sorting to standard order, that is, the variables are displayed in the same order as the BioPAT SIMCA workset. Drill down The Drill down button becomes available in the Marked Items group, on the Tools tab, after marking one or more points. The table lists, the different results possible when using the Drill down button. Marked points Drill down result Time points for regular or batch evolution. Batch points in batch level. Contribution column for regular or batch evolution. Score (t) contribution column in batch level. Contribution column for a batch condition in batch level. Contribution column that is not score and not a batch condition, in batch level. A contribution plot. A contribution plot of the points vs. average batch. A variable plot. A batch evolution contribution plot. A batch level variable plot. A batch evolution variable plot. Contribution plots for batch projects When a time point or batch point deviates from the expected, a contribution plot displays which variables that have contributed to the deviation. 72

Tools In the table, the types of contribution plots available are listed. Plot type Using Drill down One point compared to the average. One point compared with another point. A group of points compared to the average. One point compared to a group of points. A group of points compared to another group of points. Mark a point and click the Drill down button. Click on one point and then on the other. Note that they are marked in different colors. Click the Drill down button. Mark all points in the group by circling them or by holding down the CTRL key and clicking the points. Then click the Drill down button. Mark all points in the group by circling them and then click the single time point (without holding down the CTRL key). Click the Drill down button. Mark all points in the first group by circling them or by holding down the CTRL key and clicking the points. Then mark all points in the second group by circling them or by holding down the CTRL key and clicking the points. Click the Drill down button. Note: When marking a group of points and then clicking Drill down, the Select Observations dialog opens. To not include all points when calculating the contribution plot, clear the relevant boxes. Contribution plots not available The following contribution plots cannot be created in BioPAT SIMCA-online batch projects Contribution plots of time points in different phases or sub-batches in batch evolution. Display a contribution or variable plot To display a contribution or variable plot, use one of the following methods: Double-click the point or column. Mark and click Drill down in the mini-toolbar. Mark and on the Tools tab, in the Marked items group, click Drill down. Mark, right-click, and click Drill down. Marking first one point or group and then another, in a score or y predicted plots, results in a contribution plot of the first marking vs. the second marking. When marking in a contribution plot of a regular or batch evolution model, and using the Drill down, the result is a variable plot. When marking in a batch level contribution plot, where the model was built from score variables from the batch evolution model, the resulting plot is a batch evolution contribution plot. Contribution plot for time points outside the limits For batch evolution models, the active batches are projected in control chart plots as they are evolving. When a batch time point is outside the limit, this indicates that at this time point the batch data vector has some variables that are larger or smaller than the variable of the average batch computed from the workset in BioPAT SIMCA offline. Contribution score plots When a point is found outside the limits, double-click the selected time point to display the contribution plot. 73

BioPAT SIMCA-online User Guide The contribution plot displays the difference between the variables of the active batch at the selected time point and the variables of the average batch at that same time point, weighted by the loading p of the corresponding dimension. Trend plot of the variable Double-click the variable with the large value in the contribution plot to display the dynamic trend plot of that variable. This plot is also updated in real time as the active batch evolves. Contribution DModX plots When a time point has a DModX or DModX+ outside the critical limit, double-click the time point to display the contribution plot. The contribution plot shows the variables residuals for the selected time point weighted by the variable importance in the model RX. Trend plot Double-click a variable to display its trend plot. 74

Tools Contribution Hotelling's T2Range plots When the value for Hotelling's T2Range is outside the limit, double-click the time point to display the contribution plot. The contribution plot shows the deviations for the selected time point weighted by the loading p of the corresponding dimensions. Trend plot Double-click a variable to display its trend plot. Contribution Y Predicted plots When a time point in the Y Predicted plot is outside the limits, double-click the time point outside the limits to display the contribution plot. 75

BioPAT SIMCA-online User Guide The contribution plot shows the deviations for the selected time point weighted by CoeffCS. Trend plot Double-click a variable to display its trend plot. Contribution plot of the difference between batches at a selected time point To display the contribution plot between the active batch at a selected time point and a reference batch, do the following: 1. Select the reference batch from the Batches box. 2. Mark the two points by clicking one, and then the other. 76

Tools 3. Click Drill down in the Marked items group on the Tools tab. 4. Double-click the variable if you want to display the trend plot. Contribution plot for batch points outside the limits When the last observation of a new batch or model has been read from the server, the batch level observation for that batch is created and the batch is displayed in the batch level plots. When a batch point is positioned outside the limit, this indicates that the batch differs from the batches used in the workset in BioPAT SIMCA offline. Contribution score plots When a batch is found outside the ellipse in the score scatter plot, mark the batch, and click the Drill down button to display the contribution plot. The batch level score contribution plot shows the difference in the X variables between the selected batch and the model center, weighted by the loadings p[1] & p[2] for PCA and w*[1] & w*[2] for PLS. Contribution DModX plots Double-click the deviating batch in the DModX plot to display the contribution plot. The batch level DModX contribution plot shows the variable residuals for the selected batch weighted by the variable importance in the model RX. 77

BioPAT SIMCA-online User Guide Contribution Hotelling's T2Range plots Double-click a deviating batch in the Hotelling's T2Range plot to display the contribution plot. The batch level Hotelling's T2Range contribution plot shows the deviations for the selected batch weighted by the loading p of the corresponding dimensions. Contribution Y Predicted plots When a value is large or small in comparison with the others in the Y Predicted plot, this indicates something unusual about that batch. Double-click the batch to display the contribution plot. The contribution plot shows the deviations for the selected batch weighted by CoeffCS. 78

Tools Batch evolution contribution from batch level contribution When the variables in the batch level model are scores from the batch evolution model, the variables displayed in the batch level contribution plots are scores, t1, t2 etc over the evolution of the batch. Doubleclicking a score column in the batch level contribution plot then opens the batch evolution contribution plot. The plot displayed here was created by double-clicking a column in the Batch Level DModX Contribution plot found in the section Contribution DModX plots subsection earlier in this chapter. Contribution plots for regular projects When a point deviates from the expected, a contribution plot displays which variables have contributed to the deviation. In the table, the types of contribution plots available are listed. Plot type Using Drill down One point compared to the average. One point compared with another point. A group of points compared to the average. One point compared to a group of points. A group of points compared to another group of points. Mark a point and click the Drill down button. Mark one point and then the other. Note that they are marked in different colors. Click the Drill down button. Mark all points in the group by circling them or by holding down the CTRL key and clicking the points. Then click the Drill down button. Mark all points in the group by circling them and then click the single time point (without holding down the CTRL key). Click the Drill down button. Mark all points in the first group by circling them or by holding down the CTRL key and clicking the points. Then mark all points in the second group by circling them or by holding down the CTRL key and clicking the points. Click the Drill down button. Note: In the DModX contribution plot, the columns indicate the deviations from the normal correlation structure (model), NOT from the average point or another reference point. The dominating columns indicate which variables deviate most from the correlation structure, and the sign of the column (down = minus and up = plus) indicate in which direction the variables deviate. Display a contribution or variable plot To display a contribution or variable plot, use one of the following methods: Double-click the point or column. Mark and click Drill down in the mini-toolbar. Mark and on the Tools tab, in the Marked items group, click Drill down. 79

BioPAT SIMCA-online User Guide Mark, right-click, and click Drill down. Marking first one point or group and then another, in a score or y predicted plots, results in a contribution plot of the first marking vs. the second marking. When marking in a contribution plot of a regular or batch evolution model, and using the Drill down, the result is a variable plot. When marking in a batch level contribution plot, where the model was built from score variables from the batch evolution model, the resulting plot is a batch evolution contribution plot. Contribution plot for deviating points The points in the process are projected in plots as they are evolving. When a time point deviates from normal behavior, this indicates that at this time point the data vector has some variables that are larger or smaller than the variable of the average computed from the workset in BioPAT SIMCA offline. Independent of which type of contribution that is being created, when more than one point is marked (a group is marked) the Select Observation dialog opens enabling revision of the selection. Contribution plot of the difference between selected time points To display the contribution plot between a selected point and another point: 1. In the relevant plot, mark the two points by clicking one, and then the other. 2. Mark and then click Drill down in the Marked items group on the Tools tab. 3. Double-click the variable if you want to display the trend plot. Contribution score plots When a point deviates, double-click the selected time point to display the contribution plot. The contribution plot displays the difference between the variables of the marked point and the variables at the workset average, weighted by the loading w* of the corresponding dimension. 80

Tools Contribution DModX plots When a time point has a DModX that deviates, double-click the time point to display the contribution plot. The contribution plot shows the variables residuals for the selected point weighted by the variable importance in the model RX. Note: When DModX+ is displayed in the plot, the resulting plot is a plot displaying Hotelling's T2Range and DModX since these plots reveal which of the two, if not both, is responsible for the deviating observation. Contribution Hotelling's T2Range plots When the value for Hotelling's T2Range deviates, double-click the time point to display the contribution plot. The contribution plot shows the deviations for the selected time point weighted by the loading w* of the corresponding dimensions. Trend plot 81

BioPAT SIMCA-online User Guide Double-click a variable to display its trend plot. Contribution Y Predicted plots When a point in the Y Predicted plot deviates, double-click it to display the contribution plot. The contribution plot shows the deviations for the selected point weighted by CoeffCS. Note: For models with only one y-variable, w*[1] is used as weight in the contribution plot. Adding notes Notes can be added to a point marked in a plot or in the Report as follows: Plot: mark a point and click Add note: in the mini-toolbar, in the Marked items group on the Tools tab or on the shortcut menu. Report: mark the row and click Add note in the toolbar or in the shortcut menu. When adding a note the following dialog appears. 82

Tools Editing notes In the Add Note: Specify Severity and Text dialog, select the Severity level, and enter the text for the note in the Comment field. The Severity levels available are: Low, Medium (default), or High where they result in different note symbols in the plot, in the Plot Details window, and in the Report: Low - Medium - High - To modify a note use one of the following methods: In the plot, mark the point with the note and click Add note. In the Report, mark the note and click Edit note in the toolbar. In the Plot Details window, double-click the note. Deleting notes Create list To remove a note use one of the following methods: Mark the note in the Report and click Delete note in the toolbar. In the Plot Details window, mark the note and press DELETE on your keyboard. The data in each plot can be displayed as a list with tabs by clicking Create list on the Tools tab. This list includes data for dynamic limits. For multiplots, the data from each subplot is found in a tab named by the phase ID. Save as Note: Creating a list can also be done by pressing CTRL+L or right-clicking the plot and clicking Create list. On the Tools tab, click Save as to save the active plot or list to a specific file name and path. 83

BioPAT SIMCA-online User Guide Plots can be saved as Bitmap files (*.bmp), EMF files (*.emf), JPEG files (*.jpg), or PNG files (*.png). Lists can be saved as DIF Files (*.dif), Matlab Files (*.mat), or Text Files (*.txt). To save a plot: 1. Display it and make sure it is active. 2. On the Tools tab, click Save as. The Save Plot dialog is displayed. 3. In the Size box you can choose between - Custom - A) 600x375 (Suitable for portrait (A4, US Legal, etc.)) - B) 300x300 (Square, fits two side by side) - C) 600x600 (Square) - D) 755x465 (Suitable for PowerPoint, one per slide) - E) 755x270 (PowerPoint, fits two above and below) - F) 370x465 (PowerPoint, fits two side by side) - G) 800x600 (4:3 format) - H) 1024x768 (4:3 format) - I) 1280x720 (16:9 format, HD 720) - J) 1920x1080 (16:9 format, HD 1080) - Original size 4. In the dialog select the Keep aspect ratio check box to keep the proportions of the plot as on the screen (Original size) or according to a predefined plot size. 5. Click OK when done. 6. Select location, file name, and file type. Click Save. To save a list: 1. Display it and make sure it is active. 2. On the Tools tab click Save as. The Save dialog is then displayed. 3. Select location, file name, and file type. Click Save. 84

Help Introduction The Help menu holds the standard help menu commands. Clicking the?-button opens the help file, as does clicking Help View help. Sartorius-Stedim on the Web Support If you have an Internet connection, you can visit the web page of Sartorius-Stedim (www.sartorius- Stedim.com) to get the latest news and other information by clicking Sartorius-Stedim on the Web on the Help menu. Click Help Support to open the Support page on the Sartorius-Stedim website. 85

Project administration Introduction In the Project Administration dialog, opened by clicking File Administration Project administration, the projects and configurations currently known to the Server are listed. Users with configure management privileges can view and change the settings of the Project Administration dialog. Organize In the Project Administration dialog, the following features are available: Organize with Show deleted items, New folder, Delete, Rename, and Save workspace allowing flexible organization of configurations. Upload BioPAT SIMCA project to import the BioPAT SIMCA project and add project configurations for BioPAT SIMCA-online. The Configure dialog is automatically opened after selecting a SIMCA project. Save workspace to save the currently open project configurations and plots as a workspace. Only available when no folder, project or configuration is marked. Access rights for folders. Permissions to access folders and their content can be specified per group. Restore and Purge projects and configurations. After a project or configuration has been deleted it can be restored, which means that it returns as it was, or it can be purged, which means that it is permanently deleted. Open/Close depending on whether the marked project configuration is currently open or not. See also the Open subsection in the File chapter. Add configuration, see the Add configuration for batch project and Add configuration for regular project sections. Manage data with Configuration, Repredict data and Delete predicted data. In Organize the following features are available: Show deleted items - Displays also deleted items that have not been purged. New folder - Create a new folder and group configurations/workspaces as desired. Delete - Delete the marked configuration or workspace. Rename - Rename a configuration, workspace or folder. Save workspace - Save the currently open project configurations and plots as a workspace. 87

BioPAT SIMCA-online User Guide Access rights The Access rights feature controls which folders group members can see and open. To specify access rights, mark a folder and click Access rights. Note: Permissions are controlled by the role specified for the individual user in the User administration dialog. Add configuration for batch project To import a new batch project and configure it: 1. Click Upload BioPAT SIMCA project (available when a project or the Type: Configurations line is marked). 2. Select the BioPAT SIMCA project and click Open. The configuration wizard opens. When loading a BioPAT SIMCA project, the following files are created specific to that project: Static information of the BioPAT SIMCA project (.solproject). A copy of the BioPAT SIMCA project (.usp). When adding a configuration for a batch project, the following files are created: Current project and configuration id (.solconfig). Current configuration settings and history plus audit trail content (.solconfig.db). Databases for local centering for each phase (_LC_Pn.db and _LC_Pn.sbdb). Databases for the results for each phase and sub-batch combination (_LL_Sn.db and _LL_Sn.scdb). Databases for the results for each batch level model (_UL_Mn.db and _UL_Mn.sbdb). Databases for batch conditions (_BC.db and _BC.sbdb). The configuration wizard for a batch project includes the following pages: Import configuration - to import an already created configuration-file. Batch node - to specify the batch node of the current configuration. Batch evolution - to specify Execution interval. Time ranges - to specify scanning time period in search of incomplete batches and time range that specifies a batch as recent. Unit groups - to specify how the process is set up. Phase conditions - to specify phase and sleep conditions and the batch tag. Phase tags - to associate the variables to the correct tags in the database. Variable aliases - to optionally specify aliases to display in plots. Local centering - to specify the tag supplying local centering information. Target values - to specify target and limits for specific variables to display in plots and trigger univariate alarms. 88

Project administration Control limits - to specify default limits in the batch evolution plots. Alarms for batch evolution - to specify multivariate alarms for the batch evolution models. Alarm triggers for batch evolution -to specify trigger event. Write back - to specify batch evolution information to be written back to the database. Batch level - to specify which batch level models to include. Batch conditions - to specify tags for batch condition variables. Alarms for batch level - to specify multivariate alarms for the batch level models. Write back - to specify batch level information to be written back to the database. Export configuration - to save the configuration to file. Import configuration for the project If you have a BioPAT SIMCA-online configuration file you want to use, click the Import configuration button, in the Import configuration page, and select the.bcg-file. After importing the configuration file, the Description section displays the name of the selected configuration file warnings if there are obvious mismatches between the selected project and the imported configuration file. To start configuring, or view/modify the configuration in the case where you have imported a configuration file, click Next. To save the configuration for import, on the Export configuration page of the Configure wizard click the Export configuration button and specify where to save it and under which name. Importing configuration file from previous version You can import a.bcg-file from a previous version. However some configurations are not imported. When converting a SIMCA-P+ batch project with both observation and batch level, the converted project will rename the batch level models. For instance, in the previous version the batch level model could be M1, in BioPAT SIMCA 13 a batch level model can never be M1. Thus, when importing a.bcg-file created in a previous version, the batch level model settings are not imported, nor are export settings (write back) or execution intervals for phases. Batch node The batch node contains information about start and stop times of the batches. On the Batch node page, select the node that contains information about the active and historical batches of the project you are configuring. Then click Next. If no node is listed here you need to check the SimApi configuration, see the subsection Parameters to initiate communication with SimApi in the Configuration of the Server section in the Installation and configuration chapter. Nodes that are unavailable in the external system are displayed in red. If the external system was started after the server, stopping the server and restarting it might solve the issue. 89

BioPAT SIMCA-online User Guide The Batch identifier filter field enables batch selection by batch ID. For instance, if the Batch ID contains the recipe used by the batch, entering that recipe will result in using this selection of batches in the predictions in BioPAT SIMCA-online. Wild card symbols '?', and '*' are allowed in specifying batch IDs. For example?lh* selects batches with IDs such as SLH2 or QLHSW, etc. Batch evolution Specifying execution interval for phases When there are phases in the project, you have to specify the execution interval for each phase in the Batch evolution page. The unit of the Execution interval is seconds. The execution interval is the sampling interval of the BioPAT SIMCA-online Server, i.e. how often the Server samples the PDB for batch data and executes the models. Note: The execution interval in BioPAT SIMCA-online must be the same as the sampling interval used in the SIMCA model. After filling in all execution intervals, click Next. Time ranges Catch-up Catch-up can be performed if a batch was started but not finished, while running BioPAT SIMCAonline. In the Catch-up time range field, enter the time in minutes (default), hours, or days that BioPAT SIMCA-online should retrieve in the database in search for uncompleted batches. Leaving the default '0' disables the catch-up function. 90

Project administration When enabling the catch-up function by entering a time allowance, the recommendation is to enter a value that is twice the length of the average batch. Recent batches The value in the Recent batch time range field defines batches that are considered recent batches and thus are displayed when selecting the Recent batches check box in the Batches box and in the Overview window. Unit groups A unit group is a process step, for instance a granulator. The unit group contains one or more identical units. Each unit is a physical equipment/machine/vessel that processes a batch or sub-batch. A sub-batch is a part of a batch. Sub-batches are present when an entire batch cannot be processed in a single unit. Each batch passes through one or more phases. When a unit group is marked use the Add unit group, Remove unit group and Rename unit group buttons to organize the unit groups. When a unit is marked, use the Add unit, Remove unit and Rename unit buttons to organize the units. If some part of the batch process separates batches in sub-batches, right-click and click Show subbatches. When there are phases in the project, you have to specify in which unit and sub-batch the phase will be executed by selecting the respective phase check box in that unit group or sub-batch. Note: Expand all or Collapse all unit groups by right-clicking the dialog box. 91

BioPAT SIMCA-online User Guide When all unit groups, units, and sub-batches have been defined and phases selected, click Next. Phase conditions In the Phase conditions page, the tags in BioPAT SIMCA-online must be connected with the corresponding tags in the server. For phases, this includes defining all phase conditions. The following needs to be connected and configured: Batch Identifier Tag with the batch identifying variable (Batch ID). Optionally Sleep Condition. Phase Conditions. Configuring phase and sleep conditions The phase conditions have to be configured to enable prediction using the correct phase model. Optionally you can configure sleep conditions to not include nor display observations satisfying the entered sleep condition expression. In the example here, GranulatorPhase1 is running when the G1:Granulator1Phase (the first phase condition tag) text is equal to P1. For each phase, mark the phase and click the Configure-button to open the configure condition dialog. 1. In Tag name, select the tag holding the trigger or part of the trigger. 2. Select the type of trigger in Logical expression and enter a value in the Value field. 3. Click the And, Add, or Or button and note that the selected tag trigger is displayed in the Expression field. 4. Repeat 1-3 to add another condition. If the phase should be triggered when both expressions are true, click the And button. If the phase should be triggered when either one of the expressions is true, click the Or button. Under Expression the complex expression is displayed. 5. When done click OK or Next. Adding sleep triggers is done in the same manner, using the dialog displayed here: 92

Project administration After cross referencing all tags, click Next. Configure condition dialog explanation The configure condition dialog works as follows. Logical expression box In the table, the available logical expressions are listed. Logical expression Value equal to Value not equal to Value less than Value less than or equal to Value greater than Value greater than or equal to Text equal to Text not equal to Text starts with Text ends with Text contains Triggers when The numerical tag value equals the value entered in Value. The numerical tag value does not equal the value entered in Value. The tag value is smaller than the value entered in Value. The tag value is smaller than, or equal to, the value entered in Value. The tag value is greater than the value entered in Value. The tag value is greater than, or equal to, the value entered in Value. The tag value equals the text entered in Value. The tag value does not equal the text entered in Value. The tag starts with the text entered in Value. The tag ends with the text entered in Value. The tag contains the text entered in Value. Use when A phase is running when a variable equals a certain value. A phase is running when a variable does not equal a certain value. A phase is running when a variable decreases below a certain value. A phase is running when a variable decreases to or below a certain value. A phase is running when a variable increases above a certain value. A phase is running when a variable reaches or increases above a certain value. A phase is running when a variable equals a certain text. A phase is running when a variable does not equal a certain text. A phase is running when a variable starts with a certain text. A phase is running when a variable ends with a certain text. A phase is running when a variable contains a certain text. Value field In the Value field, enter the value that triggers the phase. And and Or buttons When using more than one logical expression to trigger a phase: Click the And button when both expressions have to be true to trigger the phase. Click the Or button when either expression being true triggers the phase. Expression field 93

BioPAT SIMCA-online User Guide In the Expression field, the currently added trigger expression is displayed. In addition standard mathematical and some logical operations are available by typing in this field. For more, click the question mark. Phase tags On the Phase tags page, each variable of each phase from SIMCA has to be associated with the correct variable from the database. By default the tag associations are done for <All Phases>. Select a single phase if you want the associations to apply to that phase only. To associate: 1. Mark the cell 2. In the list of notes, mark the correct node 3. In the Tags list, double-click the variable. For all methods to associate tags, see the Associating tags subsection next. Use Tag filter field above the Tags list to search in the variable list. Use the shortcut menu to facilitate the association. After associating variable IDs from the BioPAT SIMCA models with the tags in the external database, click Next. Associating tags The variables are associated by clicking the cell in the spreadsheet, and then entering the name by one of the following methods: 1. Double-clicking the variable from the database in the Tags list. Alternatively, right-clicking the variable in the Tags list and clicking Associate tag. 2. Typing the name. 3. Pasting the name. Using the Tag filter field The Tag filter field, found above the Tags list in the dialog, is not case sensitive, meaning that a and A are perceived as the same character. Typing in the Tag filter field instantly loops the available variables in the Tags list to match each new character, leaving all variables matching the string marked. 94

Project administration Shortcut menu Use the spreadsheet shortcut menu to Copy, Cut, Paste, Select all, Find and replace, Add prefix, or Add suffix. Variable aliases In the Variable aliases page you can optionally specify alternative IDs for your variables. Note: Identifiers entered in the Alias column are by default displayed in plots and lists. Local centering When a phase in your offline model has used local centering, i.e. the variables for batches in that phase have been centered with values read from a file at import, you can specify tags containing new values for these variable centers on the Local centering page. Mark the empty cell in the Tag column and associate with the appropriate variable in the Tags list. Batches with no values for local centered variables, are centered using the average value for that variable in the workset. 95

BioPAT SIMCA-online User Guide Target values On the Target values page, enter low, target, and high limits in the Lo Limit, Target, and Hi Limit cells respectively. These limits will be displayed in plots but do not trigger alarms when the Alarms cell is left empty. Note: For batch projects with phases, you must select for which phase the target values should be displayed/trigger alarms. By default the target values are displayed/triggered for <All Phases>. Alarms Use the Alarms column to let the Target values page not only specify limits to display in plots but also univariate alarms. You can select: Missing - the alarm is triggered when missing value is read for the variable. Outside - the alarm is triggered when the read value is either below the Lo Limit or above the Hi Limit. Outside or missing - the alarm is triggered when a missing value is read or the read value is either below the Lo Limit or above the Hi Limit. Control limits In the Control limits page, select which limits to default display in all batch evolution control charts. The Variable box has a list of the batch evolution variables and a <Default> entry. The limits that you specify as default will apply to all batch evolution control charts where you have NOT specified individual limits for the displayed variable. If you want more, or other, levels than +/- 1, 2, 3 standard deviations, e.g. also 1.5 standard deviations, click the Add button and enter the limit. To remove one of the added limits, click the Remove button and type the limit to remove. Note: Only user added limits can be removed. 96

Project administration Limits for specific variables To specify which limits to be displayed for a specific variable, select the variable in the Variable box, then select the desired limits in the Control limits box. Note: You can always switch limits in an open plot by right-clicking it and selecting Properties. Alarms for batch evolution The Overview window normally displays all batches in green. By configuring alarms, the color of a batch or phase can be changed to yellow (warning) or red (critical) when the values of specific batch vectors fall outside a set of predefined limits for a certain number of observations in the batch. In the plots, triggered alarms are illustrated using a colored alarm symbol. There are two degrees of limits: Lo Limit and Hi Limit representing the lower severity (warning), and LoLo Limit and HiHi Limit representing the higher severity (critical). For each vector in each phase, you can define any combination of limits. This section describes batch evolution alarms. For details about batch level alarms, see the Batch level alarms section later in this chapter. Vectors The table below shows the vectors for which alarms can be added. Vector Component Default Limit DModX No component. +3 and 4 standard deviations. t One specific component. ±3 and 4 standard deviations. T2Range From and To components. T2Crit at 0.05 and 0.01 significance level. Note: Univariate alarms can be added for individual variables in the Target values page. 97

BioPAT SIMCA-online User Guide Adding an alarm 1. In the Phase box, select a phase or leave <All phases> selected. 2. Select Vector and, when applicable, component. 3. Set the Hi Limit and/or HiHi Limit. The Lo Limit and LoLo Limit are automatically filled in as the negatives of the Hi Limit and HiHi Limit. The HiHi limit must be numerically larger than the Hi limit. 4. Click Add and note that the alarm is added to the list in the dialog. Removing an alarm Mark the alarm, and click Remove. Updating an alarm Mark the alarm, change the settings, and then click Update. Update is only available for specific phases, not for <All phases>. Note: An alarm can be added for each component for t and for each component combination for T2Range. Alarm triggers After specifying the alarms in batch evolution alarms the Alarms page, the Alarm triggers have to be specified. Triggers are events that activate the alarm. There are two types of triggers: Consecutive activates when X observations in a row are outside the limit. Total activates when Y observations are outside the limit during a phase. The default values for X and Y are 3 and 10 respectively. To change these values, enter new values in the Consecutive and Total columns. Note: Alarm triggers cannot be left empty when alarms have been specified. Write back The PDB can retrieve the current values of all output variables (computed by the model) for storage in the HDB. When you configure the PDB you must define blocks for the output variables you want to connect. The PDB is a global database so if you are executing several projects you will have, for example, per project, DModX for the batch evolution and batch level models. In the PDB you should give these DModX from different projects unique names. In the Write back pages for the batch evolution and batch level respectively define which predictions, limits and information to automatically export to the process database. Figure: Write back page for batch evolution. The page is identical for batch level but Phase is Model. 98

Project administration Connect the vectors to the tags as follows: 1. In the Vector box select the vector to export. 2. When applicable, select the relevant component or variable in the From, To, Component, and Variable boxes. 3. Click the Add button. 4. Associate the appropriate tag to the added item. For more about how to connect to the tags, see the Associating tags section earlier in this chapter. Use the Tag filter field to help you find the desired tag. See also the shortcut menu to facilitate the association. Result variables for batch evolution Available prediction results that can be exported for batch evolution are: Name in dialog Description Result exported Predictions DModX Distance to Model DModXPS t Scores tps T2Range Hotelling's T2Range T2RangePS YPred Predicted Y YPredPS Maturity Observed maturity YVar(as WS) treated as the y in the model. Limits T2RangeCrit Critical limit for T2Range T2Crit for significance level 0.01.* DModXAverageBatch DModX for average batch DModX for average batch. DModXStdDevBatch Standard deviation for DModX Standard deviation for DModX. T2RangeAverageBatch T2Range for average batch T2Range for average batch. T2RangeStdDevBatch Standard deviation for T2Range Standard deviation for T2Range. TAverageBatch Scores for average batch t for average batch. TStdDevBatch Standard deviation for scores Standard deviation for t. YPredAverageBatch Y Predicted average batch YPred for average batch. YPredStdDevBatch Y Predicted standard deviation Information Standard deviation of YPred. AlarmStatus Batch evolution alarms 0 when no alarm was triggered. 1 when one or more warning alarms were triggered. 2 when one or more critical alarms were 99

BioPAT SIMCA-online User Guide Name in dialog Description Result exported triggered. BatchID Batch identifier BatchID for the active batch. ConfigurationName Configuration name Configuration name, by default project name plus model title. ConfigurationUniqueID Configuration identifier Internal project configuration identifier. ModelID Model identifier Model in the BioPAT SIMCA project, for ex M1. ModelNumber Model number Model number for the model. PhaseID Phase identifier Phase ID from the SIMCA project. PhaseNumber Phase number Phase number in the SIMCA project. ProjectName Project name BioPAT SIMCA project name. ProjectUniqueID Project identifier Internal project identifier. SineTime Variable used to signal that the server is running. Sine of the current time. Results in values ranging between -1 and 1. *Always 0.01 significance level. To export alarms, associate the alarms for each unit and phase with the appropriate external variable. Vector box content Batch level On the Batch level page, select which batch level models you want to include. Under Batch level model prediction in the lower part of this dialog, select when to predict for the batch level models. You can select to: Predict at model finish Predict at model finish and repredict at batch finish Predict at batch finish 100

Project administration Batch conditions When the offline batch level model has batch conditions, there is a Batch conditions page in the wizard. Associate the batch condition tags in the Batch condition page, by marking the empty cell in the Tag column and associating it with the appropriate variable in the Tags list. Alarms for batch level The Overview window normally displays all batches in green. By configuring alarms, the color of a batch or phase can be changed to yellow (warning) or red (critical) when the values of specific batch vectors fall outside a set of predefined limits. In the plots, triggered alarms are illustrated using a colored alarm symbol. This section describes batch level alarms. For details about alarms for batch evolution models, see the Alarms for batch evolution section earlier in this chapter. 101

BioPAT SIMCA-online User Guide There are two degrees of limits: Lo Limit and Hi Limit representing the lower severity (warning), and LoLo Limit and HiHi Limit representing the higher severity (critical). For each vector in each model, you can define any combination of limits. Vectors The table below shows the vectors for which alarms can be added. Vector Component/Variable Default Limits DModX No component. DCrit at 0.05 and 0.01 significance level. t One specific component. ±3 and 4 standard deviations. T2Range From and To components. T2Crit at 0.05 and 0.01 significance level. YPred Selected variable. ±3 and 4 standard deviations. Note: Alarms cannot be added for batch level variables. Adding an alarm 1. In the Phase box, select a phase or leave <All phases> selected. 2. Select Vector and, when applicable, component. 3. Set the Hi Limit and/or HiHi Limit. The Lo Limit and LoLo Limit are automatically filled in as the negatives of the Hi Limit and HiHi Limit. The HiHi limit must be numerically larger than the Hi limit. 4. Click Add and note that the alarm is added to the list in the dialog. Removing an alarm Mark the alarm, and click Remove. Updating an alarm Mark the alarm, change the settings, and then click Update. Note: An alarm can be added for each component for t, for each component combination for T2Range, and for each y-variable for YPred. Write back The PDB can retrieve the current values of all output variables (computed by the model) for storage in the HDB. When you configure the PDB you must define blocks for the output variables you want to connect. The PDB is a global database so if you are executing several projects you will have, for example, per project, DModX for the batch evolution and batch level models. In the PDB you should give these DModX from different projects unique names. In the Write back pages for the batch evolution and batch level respectively define which predictions, limits and information to automatically export to the process database. 102

Project administration Figure: Write back page for batch evolution. The page is identical for batch level but Phase is Model. Connect the vectors to the tags as follows: 1. In the Vector box select the vector to export. 2. When applicable, select the relevant component or variable in the From, To, Component, and Variable boxes. 3. Click the Add button. 4. Associate the appropriate tag to the added item. For more about how to connect to the tags, see the Associating tags section earlier in this chapter. Use the Tag filter field to help you find the desired tag. See also the shortcut menu to facilitate the association. Result variables batch level and regular Available prediction results that can be exported for batch level and regular are: Name in dialog Description Result exported Predictions DModX Distance to Model DModXPS t Scores tps T2Range Hotelling's T2Range T2RangePS YPred (available when applicable) Predicted Y YPredPS. Limits DCrit Critical distance for DModX DCrit*. TMean TCrit Center of the hotelling's ellipse in the score scatter plot. The radius of the hotelling's ellipse in the score scatter plot. Average of the score vector for the selected component. TCrit for the selected component. TStdDev Standard deviation of t. Standard deviation of t. T2RangeCrit Critical distance in the Hotelling's T2Range plot. Information T2RangeCrit* is the critical limit in the Hotelling's T2Range-plot. AlarmStatus Batch level alarms 0 when no alarm was triggered. 1 when one or more warning alarms were triggered. 2 when one or more critical alarms were triggered. BatchID Batch identifier BatchID for the active batch. (batch only) 103

BioPAT SIMCA-online User Guide Name in dialog Description Result exported ConfigurationName Configuration name Configuration name, by default project name plus model title. ConfigurationUniqueID Configuration identifier Internal project configuration identifier. ModelID Model identifier Model in the BioPAT SIMCA project, for ex M1. ModelNumber Model number Model number for the model. ProjectName Project name BioPAT SIMCA project name. ProjectUniqueID Project identifier Internal project identifier. SineTime Variable used to signal that the server is running. Sine of the current time. Results in values ranging between -1 and 1. *Always 0.01 significance level. To export alarms, associate the alarms for each model with the appropriate external variable. Vector box content Export the configuration to file On the last page of the wizard, click the Export configuration-button to export the configuration to file (.bcg). This is useful when adding more than one project with a similar configuration. To save the configuration to file after completing the configuration, see the Configuration subsection later in this chapter. Add configuration for regular project To import a new regular project and configure it: 104

Project administration 1. Click Upload BioPAT SIMCA project (available when a project or the Type: Configurations line is marked). 2. Select the BioPAT SIMCA project and click Open. The configuration wizard opens. When loading a BioPAT SIMCA project, the following files are created specific to that project: Audit trail for the project (.audit). Static information of the BioPAT SIMCA project (.solproject). A copy of the BioPAT SIMCA project (.usp). When adding a configuration for a regular project, the following files are created: Audit trail for the configuration (.audit). Configuration settings for audit trail (.bcg). Current configuration settings (.solconfig). This file is the internal configuration file and cannot be imported when configuring another project. Database for triggered alarms and notes (.solconfig.db) Database for the results for the model (_Mn.db and _Mn.scdb) The configuration wizard for a regular project includes the following pages: Import configuration - to import an already created configuration-file. Model - to specify model, execution interval and prediction condition. Time ranges - to specify the time range displayed in the Overview window and in plots. Tags - to associate the variables to the correct tags in the database. Variable aliases - to optionally specify aliases to display in plots. Target values - to specify target and limits for specific variables to display in plots and trigger univariate alarms. Alarms - to specify multivariate alarms. Write back - To select project results and limits to send to external database. Export configuration - to save the configuration to file. Import configuration for the project If you have a BioPAT SIMCA-online configuration file you want to use, click the Import configuration button, in the Import configuration page, and select the.bcg-file. After importing the configuration file, the Description section displays the name of the selected configuration file warnings if there are obvious mismatches between the selected project and the imported configuration file. To start configuring, or view/modify the configuration in the case where you have imported a configuration file, click Next. To save the configuration for import, on the Export configuration page of the Configure wizard click the Export configuration button and specify where to save it and under which name. 105

BioPAT SIMCA-online User Guide Importing configuration file from previous version You can import a.bcg-file from a previous version. However some configurations are not imported. When converting a SIMCA-P+ batch project with both observation and batch level, the converted project will rename the batch level models. For instance, in the previous version the batch level model could be M1, in BioPAT SIMCA 13 a batch level model can never be M1. Thus, when importing a.bcg-file created in a previous version, the batch level model settings are not imported, nor are export settings (write back) or execution intervals for phases. Model page Use the Model page of the configuration to specify model, execution interval and prediction condition. The settings in the Model page are described in the table below. Setting Description Selected model Execution interval Prediction condition The selected model using the model number and title from the BioPAT SIMCA project file. The execution interval is how often process data tags are read. Enter the desired execution interval. Recommended is to use the execution interval of the BioPAT SIMCA project. Prediction condition, when used, specifies the condition under which predictions will be performed. When the prediction condition is not fulfilled, there is no prediction result. Leaving Prediction condition empty results in continuous predictions of all incoming data. Click the button to the right of the Prediction condition field and in the Configure Prediction Condition dialog: 1. Click the Tag name field button and select the tag to enter the condition for. 2. Select a Logical expression and enter a value in the Value field. 3. Click Add/And/Or as desired. When clicking OK the condition is automatically added to the Prediction condition field. 106

Project administration Time ranges The values in the fields in the Time ranges page specify catch-up, what is displayed in the Overview window and in the plots. The Catch-Up time range value specifies the time period (backing up from current) that will be predicted if the execution is stopped and then resumed. If the Catch-Up time range value is '0', predictions will only be made for current values when the execution resumes. The Default plot time range value specifies the time range displayed in the plots. The Overview time range value specifies the time range displayed in the Overview window. These values can be changed as desired but the fields may not be left empty. Tags On the Tags page, each variable from the BioPAT SIMCA model has to be associated with the correct variable from the database. To associate: Mark a (red) cell and double-click the variable in the Tags list. For all methods to associate tags, see the Associating tags subsection next. Use the Tag filter field at the bottom of the page to search in the variable list. Use the shortcut menu to facilitate the association. After associating variable IDs from the SIMCA models with the tags in the external database, click Next. Associating tags The variables are associated by clicking the cell in the spreadsheet, and then entering the name by one of the following methods: 1. Double-clicking the variable from the database in the Tags list. Alternatively, right-clicking the variable in the Tags list and clicking Associate tag. 2. Typing the name. 3. Pasting the name. 107

BioPAT SIMCA-online User Guide Using the Tag filter field The Tag filter field, found above the Tags list in the dialog, is not case sensitive, meaning that a and A are perceived as the same character. Typing in the Tag filter field instantly loops the available variables in the Tags list to match each new character, leaving all variables matching the string marked. Shortcut menu Use the spreadsheet shortcut menu to Copy, Cut, Paste, Select all, Find and replace, Add prefix, or Add suffix. Variable aliases In the Variable aliases page you can optionally specify alternative IDs for your variables. Note: Identifiers entered in the Alias column are by default displayed in plots and lists. Target values On the Target values page, enter low, target, and high limits in the Lo Limit, Target, and Hi Limit cells respectively. These limits will be displayed in plots but do not trigger alarms when the Alarms cell is left empty. Note: For batch projects with phases, you must select for which phase the target values should be displayed/trigger alarms. By default the target values are displayed/triggered for <All Phases>. Alarms Use the Alarms column to let the Target values page not only specify limits to display in plots but also univariate alarms. You can select: Missing - the alarm is triggered when missing value is read for the variable. 108

Project administration Outside - the alarm is triggered when the read value is either below the Lo Limit or above the Hi Limit. Outside or missing - the alarm is triggered when a missing value is read or the read value is either below the Lo Limit or above the Hi Limit. Alarms The Overview window displays each model in green. When configuring alarms, the color of a model changes to yellow (warning) or red (critical) when the values of a specific model fall outside a set of predefined alarm limits for a certain number of observations. In the plots, triggered alarms are illustrated using a colored alarm symbol. Triggers Triggers are events that activate the alarm. There are two types of triggers: Trigger 1 activates when X observations in a row are outside the limit. Trigger 2 activates when Y observations are outside the limit. The default values for X and Y are 3 and 10 respectively. To change these values, enter new values in the Triggers section of the Alarms window. Note: Trigger fields cannot be empty. There are two levels of limits: Lo Limit and Hi Limit which are warning, and LoLo Limit and HiHi Limit which are critical. For each vector, you can define any combination of limits. The Lo limits are automatically filled in as the negatives of the Hi limits. Vectors The table below shows the vectors alarms can be added for. Vector Component/Variable Default Limit DModX No component. DCrit at 0.05 and 0.01 significance level. DModX+ No component. DCrit at 0.05 and 0.01 significance level. PModX No component. 0.01 and 0.05. PModX+ No component. 0.01 and 0.05. 109

BioPAT SIMCA-online User Guide Vector Component/Variable Default Limit t One specific component. + 3 and 4 standard deviations. T2Range From and To components. T2Crit at 0.05 and 0.01 significance level. YPred Y-variable. + 3 and 4 standard deviations displayed in real values. Note: Univariate alarms can be added for individual variables in the Target values page. Adding an alarm 1. Set the trigger values in the Triggers section (or use the default settings). 2. Select Vector and, when applicable, component. 3. Set the Hi Limit and/or HiHi Limit. The Lo Limit and LoLo Limit are automatically filled in as the negatives of the Hi Limit and HiHi Limit. The HiHi limit must be numerically larger than the Hi limit. 4. Click Add and note that the alarm is added to the list in the dialog. Removing an alarm Mark the alarm, and click Remove. Updating an alarm Mark the alarm, change the settings, and then click Update. Note: An alarm can be added for each component for t, for each component combination for T2Range, and for each y-variable for YPred. Write back The PDB can retrieve the current values of all output variables (computed by the model) for storage in the HDB. When you configure the PDB you must define blocks for the output variables you want to connect. The PDB is a global database so if you are executing several models you will have, for example, one DModX per model. In the PDB you should give these DModX from different models unique names. In the Write back page, define which predictions, limits and information to automatically export to the process database. Connect the vectors to the tags as follows: 1. In the Vector box select the vector to export. 2. When applicable, select the relevant component or variable in the From, To, Component, and Variable boxes. 3. Click the Add button. 4. Associate the appropriate tag to the added item. For more about how to connect to the tags, see the Associating tags section earlier in this chapter. Use the Tag filter field to help you find the desired tag. See also the shortcut menu to facilitate the association. 110

Project administration Result variables batch level and regular Available prediction results that can be exported for batch level and regular are: Name in dialog Description Result exported Predictions DModX Distance to Model DModXPS t Scores tps T2Range Hotelling's T2Range T2RangePS YPred (available when applicable) Predicted Y YPredPS. Limits DCrit Critical distance for DModX DCrit*. TMean TCrit Center of the hotelling's ellipse in the score scatter plot. The radius of the hotelling's ellipse in the score scatter plot. Average of the score vector for the selected component. TCrit for the selected component. TStdDev Standard deviation of t. Standard deviation of t. T2RangeCrit Critical distance in the Hotelling's T2Range plot. Information T2RangeCrit* is the critical limit in the Hotelling's T2Range-plot. AlarmStatus Batch level alarms 0 when no alarm was triggered. 1 when one or more warning alarms were triggered. 2 when one or more critical alarms were triggered. BatchID Batch identifier BatchID for the active batch. (batch only) ConfigurationName Configuration name Configuration name, by default project name plus model title. ConfigurationUniqueID Configuration identifier Internal project configuration identifier. ModelID Model identifier Model in the BioPAT SIMCA project, for ex M1. ModelNumber Model number Model number for the model. ProjectName Project name BioPAT SIMCA project name. ProjectUniqueID Project identifier Internal project identifier. SineTime Variable used to signal that the server is running. Sine of the current time. Results in values ranging between -1 and 1. *Always 0.01 significance level. To export alarms, associate the alarms for each model with the appropriate external variable. 111

BioPAT SIMCA-online User Guide Vector box content Export the configuration to file On the last page of the wizard, click the Export configuration-button to export the configuration to file (.bcg). This is useful when adding more than one project with a similar configuration. To save the configuration to file after completing the configuration, see the Configuration subsection later in this chapter. Starting and stopping the execution When logged on as administrator of the program, you can start and stop the execution by marking a project configuration and clicking the play and stop-buttons respectively in the Project Administration dialog, opened from File Administration Project administration. Projects can execute in the background without being opened. Depending on whether a project is executing or not, the status according to the buttons is displayed to the left of the configuration name. 112

Project administration - the configuration is not executing. - the configuration is executing. - the configuration is repredicting but not executing. - the configuration is repredicting while executing. - the configuration is unavailable. Removing and restoring project configurations Manage data To remove a project or a configuration from the Server, mark it in the Configurations section, in the Project Administration dialog, and press the DELETE-button on your keyboard. If you answer Yes in the displayed dialog, the project/configuration will no longer be displayed in the dialog. After deleting the project or configuration you can restore it by marking it and clicking Restore. To permanently delete, click Purge. Then the project/configuration and all associated files will be removed from the Server, while the original BioPAT SIMCA.usp files remain. To be able to purge projects and configurations you need to have purge configurations permissions. The Manage data button includes: Configuration - open the current configuration. Repredict data - to repredict selected batches or the specified time range for continuous. Delete predicted data - to delete selected batches. These features are available for users with configuration management privileges only, and in the following locations: Manage on the Home tab. Manage in the Project Administration dialog. Configuration - view and modify You can modify previously added project configurations. Before modifying a project, the execution has to be stopped. To re-configure a project: 1. Log on as a user with configure management privilege. 2. If the project is executing, File Administration Project administration and click the stopbutton for the project configuration you want to update. Make sure the configuration is marked and not executing, then click Manage. 3. Start the re-configuration. In the Configure dialog, all pages from the configuration wizard are available as tabs. For more about these tabs, see the sections Add configuration for batch project or Add configuration for regular project earlier in this chapter. Note: The configuration done on the Batch evolution, Unit groups, and Batch level pages for batch and Model for regular cannot be modified. To make such changes, add a new configuration for the project. Repredicting historical batches When the BioPAT SIMCA-online server is turned off, it does not receive any data for new batches. If an entire batch has passed while the server has been turned off you can use Repredict data to monitor that batch once the server is running again. Note: Repredicting batches can take a while and the server may become unresponsive. To repredict do as follows: 1. Enter the From date/time and To date/time that contain the (missed) batches. 2. Click the Show batches button. The batches that match the specified time limits are displayed with their start and stop times and current status. The status can be: 113

BioPAT SIMCA-online User Guide a. Missing - The batch has not been predicted. b. Repredicting - The batch is currently repredicting. c. Predicted - Predicted results exist for the batch. d. Workset duplicate - A batch with the same name exists in the workset and cannot be predicted. 3. In the list, select the (missed) batches. Note: To multiselect, mark and press <SPACE>. 4. Click the Repredict button. Note: All batches within the date/time range will be displayed when clicking the Show batches button, including batches already displayed in plots. However, the batches may display different status. Repredicting data for continuous When the BioPAT SIMCA-online server is turned off, it does not receive any data. Use Repredict data to monitor the data not predicted once the server is running again. Note: Repredicting data can take a while and the server may become unresponsive. To repredict do as follows: 1. Enter the From date/time and To date/time that specifies the time range to repredict. 2. Click the Repredict button. Note: All data within the date/time range will be predicted when clicking the Repredict button, including data already displayed in plots. Deleting historical batches Historical batches can be deleted from the server. After deleting a batch, it can no longer be displayed in plots or lists. To delete historical batches, click the Delete Batches tab, select the batches to delete, and click the Delete button. 114

Project administration Note: To multiselect, mark and press <SPACE>. Workspaces A workspace holds information about the Client's open projects and plots. This selection can be saved as a workspace. All workspaces are saved on the Server and can thus be opened by all clients connected to the Server. Workspaces can be opened by any user, while workspace management privilege is needed to save or remove workspaces. Save workspace To save the current selection of projects and plots as a workspace, on the View tab, in the Window group, click Save workspace. Alternatively use the Project Administration dialog: 1. With the Type: Workspaces section active. 2. Click Save workspace. Delete workspace To remove a workspace from the server: 1. On the View tab, in the Window group, click Save workspace. 2. Mark the unwanted workspace. 3. Press DELETE, or click the Organize button and click Delete. Alternatively use the Project Administration dialog: 1. Mark the unwanted workspace in the Type: Workspaces section. 2. Press DELETE, or click the Organize button and click Delete. Note: No lists are saved in workspaces. 115

Customizing plots Introduction The plots in BioPAT SIMCA-online can be customized using Properties or Format Plot. Commonly used features in the Format Plot dialog can be accessed from the mini-toolbar. The Format Plot dialog can be opened from the mini-toolbar or by right-clicking the plot. Applying and organizing the templates saved using the Format Plot dialog is done from Plot templates on the shortcut menu. Properties or Plot Properties can be opened by right-clicking the plot or by clicking the Properties group dialog box launcher. The content of the (Plot) Properties dialog is described in the sections describing the Properties group on the Home tab for batch and regular respectively. Mini-toolbar Content This chapter describes the following features: Mini-toolbar - for quick access to common commands regarding the content or marking in the plot. Show/Hide - to quickly show/hide text outside the plot area. Format plot - customize plots using Format Plot. Changes in Format Plot can be saved to a template. Plot templates - save, load and manage the plot templates. When you click or mark points the mini-toolbar automatically appears. The mini-toolbar helps you to customize the attributes of the plot, create contribution plots and to add notes to marked points. It also appears with the menu when you right-click. To hide the mini-toolbar, see the Managing the mini-toobar subsection. Mini-toolbar for marked items Mini-toolbar for marked items: (cogwheel appears only when right-clicking) Note: When clicking a symbol, that symbol is marked and the mini-toolbar for marked items appears. Features available when marking items are described in the table. Mini-toolbar button Description Drill down. Add note. Mini-toolbar options Opens a contribution/variable/t2range&dmodx plot. For details, see the Drill down section in the Tools chapter. Opens the Add note dialog. For details see the Add note subsection in the Tools chapter. When right-clicking the marking, the cogwheel appears allowing you 117

BioPAT SIMCA-online User Guide Mini-toolbar button Description to select the behavior of the mini-toolbar. For details see the Managing the mini-toolbar subsection later in this section. Mini-toolbar for formatting The mini-toolbar contents change when you click on different items in the plot. When no other mini-toolbars are available the standard mini toolbar is displayed. This mini-toolbar contains the Format Plot and Properties commands as well as commands to toggle zooming and selecting modes. Mini-toolbar for formatting, after clicking a text-field in the plot or an empty area: Mini-toolbar for formatting: Features available when clicking in plots are described in the table. Click in plot area An empty area in the plot area. A line. A limit. Mini-toolbar features in order of appearance Format Plot, Properties and zooming. Format Plot dialog, line width, style, and color of that specific line when the Marked items mini-toolbar is not enabled.. Format Plot dialog, line width, style, color and fill color of that specific line. The last button allows saving the current settings as default for the limit type. Features available when clicking in the legend are described in the table. Click in legend Mini-toolbar features in order of appearance Symbol Line Column Format Plot dialog, hide series, symbol style, size and color. Format Plot dialog, hide series, line width, style, and color of that specific line. Format Plot dialog, hide series, color. Features available when clicking in a text box are described in the table. Click in text box Mini-toolbar features in order of appearance Any text box (header, footer, axis title, etc.) Format Plot dialog, hide selected, font face, font size, grow font, shrink font, bold, italic, font color and save as default style. Mini-toolbar for subplot Mini-toolbar for subplot that zooms in or out depending on current plot state: Managing the mini-toolbar The mini-toolbar is always displayed with the menu when right-clicking. Clicking the cogwheel of this mini-toolbar opens the Mini-toolbar options where you can select to: Show mini-toolbars - the appropriate mini-toolbar is displayed when clicking in the plot. When cleared the mini-toolbars are only displayed above the shortcut menu. Enable 'Format Plot' mini-toolbar - when clicking on text, lines etc. the plot, common plot formatting features/commands/buttons are displayed. Enable 'Marked Items' mini-toolbar - when marking points, the drill down and add notesbutton are displayed. Enable 'Zoom Subplot' mini-toolbar - when the plot has subplots, this mini-toolbar shows up in the upper right corner of each subplot. Figure: Default mini-toolbar options. 118

Customizing plots Mini-toolbar for formatting, after clicking a text-field in the plot when Enable 'Format Plot' minitoolbar was selected in the Mini-toolbar options: Show/Hide plot items To quickly show/hide the Header, Footer, Legend, Axis titles, Axes, or Timestamp, right-click the plot, click Show/Hide and select/clear the relevant items. When done, click outside the menu or click Done at the bottom of the menu. Maximize plot area is also available here. Maximize plot area hides everything but the plot area. Format plot Use the Format Plot dialog to change the most common attributes of the axes, plot area, and header and footer. To open the Format Plot dialog right-click the plot and click Format plot. This dialog can also be opened by clicking a plot and then clicking the Format plot button in the Mini-toolbar or double-clicking on the axes, axis titles, header or on the footer. To save the new settings, click the Save Settings button in the settings dialog, or right-click the plot and click Plot templates Save as default. Axis The properties under the Axis node apply to the selected axis: Axis X, Axis Y, Axis Y2 (second Y-axis) etc. In the Format Plot dialog, Axis node, click: The respective axis to customize the scaling of the selected axis, annotation rotation etc. Leave the node marked to introduce changes for all axes. Axis General to access the following pages: 1. Axis General to customize color, width and other properties of all axes. 2. Tick Marks to select how to display major and minor tick marks. 119

BioPAT SIMCA-online User Guide Individual axes 3. Axis Font to customize the font of the axis annotation. 4. Title Font to customize the font of all axis titles. The content for the individual axes is described in the table below: Field/button name Displays Axis Result after entering a new value and clicking Apply Show axis Default selected. If cleared, that axis is not displayed. Minimum Maximum Auto adjust scales for suitable limits and step size Start point for the selected axis when the values are displayed in regular order. For time-variables the page is adjusted, see the Time axis subsection. End point for the selected axis when the values are displayed in regular order. Default selected. The new start point is used for the selected axis. The new end point is used for the selected axis. If cleared, enables the Step size field. Step size Default disabled. The entered value defines the major tick mark spacing for the selected axis. Reverse axis Default cleared. If selected, the scale is displayed with the highest number to the left and the lowest to the right. Annotation Rotation Default No Rotation. Selecting 90 degrees displays the annotation turned 90 degrees. Title Show title Default selected. If cleared, the axis title is not displayed. Title The vector name. The new title. Title changes cannot be saved. Note that the distance between the tick marks is constant. When you have more than one series in a plot, you can select to display more than one y-axis. For more, see the Multiple Y axes subsection later in this chapter. Time axis The content for the Axis X and Axis X Title pages for a time variable is described in the table below: Field/button name Displays Time Axis section Result after entering a new value and clicking Apply 120

Customizing plots Field/button name Displays Result after entering a new value and clicking Apply Show axis Default selected. If cleared, that axis is not displayed. Minimum Maximum Auto adjust scales for suitable limits and step size Start point in time units. Change by typing in the field. End point in time units. Change by typing in the field. Default selected. The new start point is used for the selected axis. The new end point is used for the selected axis. If cleared, enables the Step size field. Step size Default disabled. The entered value defines the major tick mark spacing for the selected axis. unit The unit of the step size. Switching between units updates the step size automatically. Format section Time format Default ISO 8601, YYYY-MM- DD HH:mm:ss. The entered time format specifies the annotation on the marked time axis. Rotation under Annotation Show title under Title Default No Rotation. Default selected. Axis X Title tab Selecting 90 degrees displays the annotation turned 90 degrees. If cleared, the axis title is not displayed. Title The vector name. The new title. Title changes cannot be saved. Note that the distance between the tick marks is constant. Axis General In Axis General the following features are available and are applied for all axes: Axis Color and Width. Always recalculate scales - when selected all axes are autoscaled. Clearing it makes the current ranges of the axes stick even if the vector displayed is switched except when the new vector range goes outside the minimum or maximum. Show arrows - when selected the arrows are displayed at the end of the axes. Arrow Color - Automatic here means the same as the axis color. Annotation Color and Distance from axis. Axis title Color. 121

BioPAT SIMCA-online User Guide Tick Marks Use the Tick Marks page to specify how the tick marks should be oriented and how long they should be. Under Major tick marks and Minor tick marks the same boxes are available: Tick mark type - where None is no tick mark, Outside is to have the tick mark outside the axis, Inside is to have the tick mark inside the axis and Cross is to have the tick mark on both sides of the axis. Tick mark size is the length of the tick mark. Font Use the respective font pages, to select the Font, Font style, Size, and Effects for the annotation, title, etc. Section Font Font style Size Preview Anti aliased Description Displays the currently selected font. Click another font to switch. Displays the current font style. Select to display the text Regular (default), Bold, Italic, or Bold Italic. Displays the current size. Select another size as desired. Displays a preview of the expected text according to the selections above. Allows selecting to display the text Anti aliased or not. 122

Customizing plots Section check box Description Gridlines Use the Gridlines page to customize the gridlines and grid stripes. The gridlines are placed on the major tick marks. Grid stripes are the areas between the gridlines, where every second such area can be colored. Note: Gridlines and grid stripes can be specified individually for Vertical and Horizontal. Specification using the node applies to both. The following is available: Option/Box/Field Description No gridlines Gridline Gridline Color Width No grid stripes Grid stripe Solid fill Grid stripe Color Grid stripe Gradient fill Grid stripe Color 2 No gridlines are displayed when No gridlines is selected. When selecting Gridline you can select to display the lines Solid, Dashed, Dotted, Dash dot or Dash dot dot. The color of the grid, by default gray. The width of the gridlines. No grid stripes are displayed when No grid stripes is selected. When selecting Solid fill the grid stripes are displayed in the selected color. Displays the current color and allows selecting a new color. When selecting Gradient fill you can select to display the stripes Horizontal, Vertical, Forward diagonal, Backward diagonal, Radial, Horizontal bar, Vertical bar. Displays the current color and allows selecting a new second color for Gradient fill. Background The Background node controls the attributes of the background displayed in the plot. Note: The background fill and border can be specified individually for the Window area and Plot area. Specification using the node applies to both. The table describes the available options: Option/Box/Field Description Fill No fill Sold fill Gradient fill No background is displayed when No fill is selected. When selecting Solid fill the background is displayed in the selected color. When selecting Gradient fill you can select to display the background Horizontal, 123

BioPAT SIMCA-online User Guide Option/Box/Field Color Color 2 Description Vertical, Forward diagonal, Backward diagonal, Radial, Horizontal bar, Vertical bar. Displays the current color and allows selecting a new color for the background. Displays the current color and allows selecting a new second color for Gradient fill. Border No border Solid line Color Width No border around the background area is displayed when No border is selected. When selecting Solid fill, the background is displayed in the selected color. Displays the current color and allows selecting a new color for the border. The width of the border. Titles Use the Format Plot dialog to customize the items available in the Titles node. When customizing, the changes apply to the selected item, Header/Footer/Timestamp/Subheader. Note: Changing color, font and size of the Header/Footer/Timestamp/Subheader can be done directly in the plot by clicking and using the mini-toolbar for formatting. 124

Customizing plots On the Titles page: Select to hide or show by selecting or clearing the Is Visible check box. Select where to display the title in the Anchor box, when applicable. Customize the text displayed by changing or typing in the field. Align the text right, center, or right by clicking the appropriate alignment button. Customize the color of the text in the Text color box. Customize the background color by clicking the Background color box. Select to display a border by selecting the Is visible check box in the Border section. With it selected you can customize Color, Margin (to the text) and Width of the border. On the Font page you can select the Font, Font style, Size, and Effects. See also the Font subsection earlier in this chapter. Legend The Legend page controls the attributes of the legend, such as placement, color, and border. The table describes the available options: Option/Box/Field Description Placement section Show legend Position Orientation Text alignment The legend is displayed when the Show legend check box is selected. By default the legend is positioned Top right. To change from the default, click one of the available placement options. The orientation is by default Vertical. Horizontal is the other option. Alignment of the text in the legend is by default Left. Right and Center are the other options. Color section Text color Background color By default the text is black. To customize text color of the legend, click the Text color box. The default background color is white. To select another color, click the Background color box. Border section Is visible Color Margin Width By default the border is not displayed. To display the border around the legend, select the Is visible check box. To customize the border color of the legend, click the Color box in the Border section. To specify the margin to the text, change the value in the Margin field. To increase or decrease the width, enter a new number in the Width field. 125

BioPAT SIMCA-online User Guide Limits and Regions There are a number of limits available in plots in BioPAT SIMCA-online, for instance the ellipse in the score scatter plot, the DCrit limit in the DModX plot etc. Additionally there are regions, such as the background active batches for a batch level plot with partial models. The attributes of the limits and regions can be modified individually for each limit and region type under the Limits and Regions node in the Format Plot dialog, in the respective Region Style pages. The Region Style page is described in this section. For multiplots, the limit pages are positioned last in the Format Plot dialog under Plot 1, Plot 2, Plot 3, etc. For batch evolution plots, the limit pages are positioned under Styles. Customizing Limits and Regions The selected limit or region can be customized in the Region Style page. Feature Description Line Style Width Color Select between the available line styles. Increase or decrease as desired. Displays the current color and allows selecting a new color. Fill Type Style Gradient Color 1 Color 2 Select to fill the area Over or Under the limit, or select No fill. Select the fill to be Solid or Gradient. Selecting Solid enables the Color 1 box and selecting Gradient enables the Gradient, Color 1 and Color 2 boxes. When selecting Gradient you can select to display the fill Horizontal, Vertical, Forward diagonal, Backward diagonal, Radial, Horizontal bar, Vertical bar. Displays the current color and allows selecting a new color. Displays the current color and allows selecting a new color. Available when the Style is Gradient. Font tab - see the Font subsection. Label Style - see the Labels subsection. Label Style The Labels pages control the attributes of the displayed plot marks. Color, alignment, font and rotation apply to all labels in a given series. The tabs available in the Labels node, Label Style, Font and General, are described in the table. Option/Box/Field Description Label section in Label Styles Position The default position of the label in reference to the point is Right To position the 126

Customizing plots Option/Box/Field Offset Rotation Description label in another direction, click the Position box and make a new selection. The offset defines the distance between the label and what it labels in the direction of the selected Position. To increase or decrease the distance between the label and item, enter a new value in the Offset field. The default rotation of the labels is 0. To rotate the label, enter a new value in the Rotation field. Note that this field is unavailable when Avoid overlapping labels has been selected in the General tab. Color section in Label Styles Text color Background color Displays the current color of the text in the label and allows selecting a new color. Automatic displays the text in the same color as the symbol fill. The background color of the label is default transparent. To select a color, click the Color box and make the selection. Border section in Label Styles Is visible Color Margin Width Draw connection line By default, no border for the label is displayed. To display a border around the label select the Is visible check box. Displays the current color of the border and allows selecting a new color. The margin between the text and the border can be customized in the Margin field. To increase or decrease the width, enter a new number in the Width field. Draw connection line is by default cleared. Selecting it will display a thin line between the label and its point. Font tab - see the Font subsection. General tab Avoid overlapping labels With Avoid overlapping labels selected, point labels will try not to overlap each other. A high specified limit in the Limit field in combination with many labels can be quite time consuming. Error Bars The Error Bars page controls the attributes of the error bars displayed in the Y Predicted plot for batch level plots. The settings available are: Is visible - hides the error bars when cleared. Color of the error bars - by default black. To display the error bars in any other color, click the Color box. Line width of the vertical and horizontal lines. To display wider error bars, enter a new number in the field. Error bar width is how wide the horizontal line is compared to the column. 127

BioPAT SIMCA-online User Guide Styles In the Styles node the attributes of the series, and for batch evolution plots limits, can be customized. The available pages in the Styles node, different depending on which plot is open, are: Category coloring Marking Style Line Style Fill Style - See Customizing limits Fill section. Y-Axis Font Category coloring In Category coloring you can specify colors for the batches. 128

Customizing plots Marking style In the Marking Style page you can change the marking colors by marking and selecting a new color in the color box to the right. Symbol Style The Symbol Style page controls the attributes of the symbols displayed in the plot. The table describes the available options: Option/Box/Field Description Shape The shapes of the series can be changed by: 1. Marking a series. 2. Selecting a new shape in the Shape box. With None selected, no symbols are displayed. Size To increase or decrease the size, enter a new number in the Size field. For the Worm plot for continuous, the size of the head of the worm is sized proportionally. Fill No fill Solid fill Gradient fill Color Color 2 Results in symbols transparent inside the outline. Displays the color selected in Color. Allows you to select to display the symbol with a gradient fill of type Horizontal, Vertical, Forward diagonal, Backward diagonal, Radial, Horizontal bar, Vertical bar. Displays the current color. To display another color, click the Color box, and then select a new color. Displays the current second color for Gradient fill and allows selecting a color. Outline No outline Solid line Color Width No outlining contour of the symbols. The outline of the symbol is displayed. Color of the outline. Automatic results in an outline in the same color as the symbol but in a darker shade. Width of the outline. Glow Use glow Color Width When selected an area outside the outline is colored for a glowing effect. Color of the glow. Automatic results in the same color as fill color. Width of the glow. 129

BioPAT SIMCA-online User Guide Line Style The Line Style page controls the attributes of the lines displayed in the plot. The table describes the available options: Option/Box/Field Description Pattern Width Color Smoothed line (Bezier) Change the pattern of the line by clicking the Pattern box and selecting another pattern. The available types are: Solid, Dashed, Dotted, Dash dot, and Dash dot dot. To increase or decrease the width, enter a new number in the Width field. To display another color, click the Color box, and then select a new color. Select Smoothed line (Bezier) to smooth out the edges of the line. Note: Filling is available in the Fill Style tab. See the Customizing limits subsection for details. Column and Column Style The Column and Column Style pages control the attributes of the columns displayed in the plot. The Column page, found above the Styles node, displays the current Column width and allows adjusting it. The Fill and Border options are described in the Symbol Style subsection earlier in this chapter; Border is there named Outline 130

Customizing plots Multiple Y axes When you have more than one series in a plot, you can select to display more than one y-axis and linking it to one of the series. To display multiple y-axes: 1. Click the Styles node and click the series you want on the second y-axis. 2. Click the Y Axis tab. 3. In the Attach to Y Axis box, select Axis Y2. Steps 1-3 can be repeated for more series. Multiplots For multiplots there are Plot nodes beneath the Styles node, named Plot 1, Plot 2, etc. In these plots specific nodes the Sub Title and Plot area of the individual plots can be customized as described in Titles and Background respectively. Plot templates The Plot templates command on the shortcut menu holds features pertaining to handling of the templates. The following features are available and described in this section: Load described in the Switching plot formatting templates subsection. Save as and Save as default described in Saving plot formatting template subsection. Open templates folder - opens the folder holding the templates when clicked. Restore default settings described in Restoring to default plot formatting subsection. The Format Plot dialog itself is described in the self titled section earlier in this chapter. 131

BioPAT SIMCA-online User Guide Saving plot formatting template After customizing the plots using Format Plot you can save the settings of some attributes, such as fonts, gridlines, symbol type etc, to a template. To save a template, with the plot open, right-click the plot, click Plot template and then, under the Save template header click Save as default or Save as and specify a name. Note: Only the formatting available in the current plot is saved to the customized plot formatting configuration. All other formatting will remain default. This means that formatting of headers, footers etc. apply to all plot types (e.g. scatter, column, line) while default line color, default symbol shape are plot specific and need to be specified with that plot type open. Switching plot formatting templates After having added customized plot formatting templates, these templates can be selected by right-clicking the plot, clicking Plot template and then selecting it under the Load template header. After loading a new template, that template is applied to the open plot and future plots. Restoring to default plot formatting To restore to the Umetrics default plot formatting template, with the plot open, right-click the plot, click Plot template and then, under Manage templates click Restore default settings. Clicking Restore restores the Default plot formatting to the Umetrics default plot formatting and switches to it. Under the Manage templates header you can also select to Open templates folder to view and delete templates. 132

Maintenance Introduction This chapter contains instructions and routines for the administrator on how to maintain the BioPAT SIMCA-online system. Content Backup and restore Resource management Backup Restore 1. Stop the server. 2. Backup the database directory and subdirectories. 3. Backup the configuration file. 4. Backup the license file. 5. Backup the plugin directory. 6. Backup the SimApi files and settings. 7. Start the server. 1. Stop the server. 2. Restore the database directory and subdirectories. 3. Restore the configuration file. 4. Restore the license file. 5. Restore the plugin directory. 6. Restore the SimApi files and settings. 7. Start the server. Resource management Several data structures are used by BioPAT SIMCA-online for keeping information about predicted results, their identifiers and when they executed, triggered alarms, added notes and such. Over time these data structures grow in size. These data structures are stored in a database that increases over time, sometimes to an unsustainable level. It is therefore important to include regular checks on available disk space on the server computer. What to do? When the available disk space becomes low, you have to free up disk space on your computer. To free disk space, you may remove project configurations or delete historical batches. 133

Appendix A: General information License reminder A license reminder will be issued and written to the log dockable window once a day starting 60 days prior to license expiration. The last 10 days prior to license expiration a tooltip will also be displayed once a day. Error codes when starting the service Windows error codes Error 3: Possible cause: Solution: The system cannot find the path specified. The installation of the BioPAT SIMCA-online service is incomplete. Reinstall from installation package. Error 5: Possible cause: Solution: Access denied. Application does not have sufficient permissions to complete the operation. Start application as administrator. Error 1069: Possible cause: Solution: The service did not start due to a logon failure. The Windows password for the selected user is incorrect. In Control Panel, click Administrative Tools, and then Services. Locate the BioPAT SIMCAonline Server service, right-click and click Properties. Click the Log On tab, and enter the correct password for the specified account. Service-specific error codes Error 42: Solution: General error code often referring to the initialization of the SimApi. When running the demoversion, this means that DBMaker needs to be started before the server. For more information, review the server log file, or if the log file does not exist, the Windows event log. The server log file is named SIMCAonlineserver.log and positioned in the database folder specified in the Server configuration page Paths and directories. Error 1001: Possible cause: The path to the configuration file is unavailable. The server configuration has not been done. Solution: Open BioPAT SIMCA-online Server Options from Umetrics BioPAT SIMCA-online 13 and review the settings. Error 1002: The path to the database directory is unavailable. 135

BioPAT SIMCA-online User Guide Service-specific error codes Possible cause: The server configuration has not been done correctly. Solution: Open BioPAT SIMCA-online Server Options from Umetrics BioPAT SIMCA-online 13, tab Paths and directories and review the settings. Error 1003: Possible cause: The path to the SimApi file is unavailable. The server configuration has not been done correctly. Solution: Open BioPAT SIMCA-online Server Options from Umetrics BioPAT SIMCA-online 13, tab SimApi and review the settings. Error 1004: Possible cause: There is a problem with the license file. The license has expired or the license file cannot be found. Solution: Open BioPAT SIMCA-online Server Options from Umetrics BioPAT SIMCA-online 13, tab Paths and directories. Click the Import button and browse to the license file. For more information, review the server log file, or if the log file does not exist, the Windows event log. The server log file is named SIMCAonlineserver.log and positioned in the database folder specified in the Server configuration page Paths and directories. Error 1005: Possible cause: Could not create the log file. The account the database directory used for the server has too low permissions. Solution: Open BioPAT SIMCA-online Server Options from Umetrics BioPAT SIMCA-online 13, tab Paths and directories and review the settings. Error 1006: Possible cause: The network settings are unavailable. The server configuration has not been done correctly. Solution: Open BioPAT SIMCA-online Server Options from Umetrics BioPAT SIMCA-online 13, tab Network Settings and review the settings. Server endpoints TCP/IP is the only supported protocol. The default port is 2371. BioPAT SIMCA-online interfaces BioPAT SIMCA-online is available with an interface to OPC, OSIsoft PI, ODBC, AspenTech IP21 and more. Please contact you sales representative for more information. Terminology changes With the rearrangement of BioPAT SIMCA-online into ribbons, features were moved, some renamed, others found obsolete. In this section the basic terminology changes are listed in alphabetical order of the previous version terminology. 136

Appendix A: General information SIMCA-Batch On-Line SIMCA-4000 Autocolor Active Batches dockable window Alarms dockable window Batch level Batch level project (model) BM Default plot action Distance to Model, DModXPS, DModXPS+ Hotelling s T2Range Observation level Observation level project (model) PS-vectors, for example DModXPS Recent Batches dockable window SIMCA-P+ Toolbars BioPAT SIMCA-online Autoformat Overview dockable window Overview dockable window Batch level, BL Batch level model, BLM BEM. BM includes BEM and optionally BLM. Drill down on the Tools tab. DModX, DModX+ Hotelling s T2, Hotelling's T2 Range Batch evolution, BE Batch evolution model, BEM The letters PS in the vector name of the predicted vectors is no longer displayed. Overview dockable window BioPAT SIMCA The features of the toolbars have been split to different parts of the software, some are available on the Home tab, others on the Tools tab. Discontinued features Discontinued features when comparing BioPAT SIMCA-online 13 to SIMCA-Batch On-Line 3.4 and SIMCA-4000 12 are: Four overview plots - the plots can be opened one by one and tiled. Use workspaces to specify project configurations and plots to open. Plots displaying model results: Score Plot, Loading Plot, Variable Importance Plot (VIP), and Coefficient Plot. Insert plot label. Coordinate reader - The Status Bar displays the plot coordinates. Regression line. Shewhart, EWMA and CUSUM Control Charts. Administrator Message. Connected Clients. Server Info dockable window - info available in the Project Info and Log windows and in the Status bar. Lag Multiplier in the configuration of projects. When the sample time between consecutive observations in BioPAT SIMCA offline was different from the online execution time, you could use the Lag Multiplier field to address this. In BioPAT SIMCA-online the sampling and execution times have to correspond. Model Description in the configuration of projects. To alter the name of a configuration from the default (project: model title), in the Project Administration dialog, right-click the configuration, click Rename and introduce the change. Averages box allowing removal of average and normalization of batch evolution plots. Time Sync setting. Was deemed unnecessary. Show Overview Status select to show the status of all open projects in the Active Batches dockable window. Currently displayed by coloring the project configuration tab. Grouping of observations in combination with sort for contribution plots. 137

BioPAT SIMCA-online User Guide Workset observations can no longer be hidden in for regular (continuous) projects. Scaling of plots for regular projects to 0-1, previously available in the Properties dialog Scale page, was discontinued. Connect to Last Server on Startup was discontinued. The Log in dialog is displayed when opening the Client. Alarm zones for continuous. Manually specifying contribution weight for continuous. Dynamic, automatically updated, lists for continuous. Prediction list for continuous. Repredict and catch-up for continuous. Delete predicted data for continuous. Adaptive predictions for continuous.. The following features in the Active Batches and Recent Batches dockable windows: 1. Open Projects Overview - showed the overall status of all open projects. 2. Observation Level Overview and Batch Level Overview - showed the status of the overall status of the current project for the respective batch project types. These two are combined in one, just showing the overall alarm status of the configuration in the color of the configuration tab. 3. Unit Overview - unavailable, the models are just displayed in the order in BioPAT SIMCA. 4. Individual observation level overview - unavailable, the models are just displayed in the order in BioPAT SIMCA. 5. Create DModX Plot and Create Score Plot were deemed unnecessary. 6. Shortcut menu. Menu and tab reference syntax In this user guide we use the following syntax when referring to the File tab commands: Click Tab Command. An example: Click File Print. On the Tab tab, click Command. An example: On the File tab, click Print. Click Command on the Tab tab. An example: Click Print on the File tab. In this user guide we use the following syntax when referring to tab commands/buttons: On the Tab tab, in the Group group, click Command. An example: On the View tab, in the Window group, click Save workspace. Click Command, in the Group group, on the Tab tab. An example: Click Save workspace in the Window group on the View tab. Click Tab Command Menu item. An example: Click View Close Close all windows. 138

Glossary Active batches: The Active Batches (previously named current) are the batches that are being predicted by the server currently. The active batches are displayed as they are evolving in the batch evolution control charts and in the Overview window. After completion, batch or model wise, active batches are also displayed in the batch level plots. Note: when repredicting a batch it will also briefly show up as active during the time it is being predicted. Automatic classification: Option available in previous versions. In the current version there is no automatic classification. Phase belonging of new observations is identified using the phase condition. Average batch: The average batch is the average at each time point, computed over all batches in the model. Batch hibernation: Batch hibernation was available in a previous version. In the current version, batch hibernation is only available between phases when a phase condition for any phase not yet has been fulfilled. Batch node: The batch node contains information about start and stop times of the batches. The batch node is created and updated by the external system. Batch process: A batch process is a finite duration process. The batch starts, evolves, and stops. Catch up: The model reads all observations since the last execution or since the specified time point. Class: A class is a subset of similar observations from a dataset. Concurrent batches: The ability to run and monitor several batches at once. Contribution: The contribution is a measure of the differences in variable values between two observations. The differences are normally weighted by model loadings or modeled variability. Critical limit: When points are found outside the critical limit the resulting product is likely to be of poor quality. Cross-validation: In cross-validation, parameters are estimated on one part of a matrix and the goodness of the parameters tested in terms of its success in the prediction of another part of the matrix. Current batches: See Active batches. Data source: See SimApi. Dataset: A dataset is the base of all multivariate data analysis, often also called a data matrix. It is made up of values of several different variables for a number of observations. The data are collected in a data matrix (data table) of N rows and K columns, often denoted X. The N rows in the table are termed observations. The K columns are termed variables. Dependent variables: See Y-variable. Discriminant analysis: Discriminant analysis is a method for allocating observations to one class of a given set of classes by means of a decision rule based on a function of the data. The function is derived from data for a reference set of individuals where it is known which class each individual belongs to. A B C D Endpoint: See Port. E 139

BioPAT SIMCA-online User Guide Factor: Factor is a term often used in experimental design. It signifies controlled and varied variable. Also a term for one model dimension in factor and bilinear models. See also: X-variable. Factor analysis: Factor analysis has an aim similar to PCA, but assumes an underlying model with a specified number of factors which are linear combinations of the original variables. The analysis is more concerned with 'explaining' the covariance structure of the variables rather than with 'explaining' the variances. HDB: HDB is the abbreviation for Historical DataBase. The HDB contains observations from the past. Hi limit: Hi and Lo limits are used as warning limits. This means that when the process is inside these limits it is under control. HiHi limit: HiHi and LoLo limits are used as critical limits. This means that when the process is outside one of these limits it is out of control. Historical batch: A historical batch is a batch that was not part of the workset of the model, was previously monitored, has finished, and sits in the database. Least squares estimate: The least squares estimate is a method to estimate model parameters by minimizing the sum of squares of the differences between the actual response value and the value predicted by the model. Lo limit: Hi and Lo limits are used as warning limits. This means that when the process is inside these limits it is under control. Loading vector: The loading vector is the direction coefficients of a PC or PLS component axis. LoLo limit: HiHi and LoLo limits are used as critical limits. This means that when the process is outside one of these limits it is out of control. Missing value: Missing values are elements in a data matrix without defined values. As a rule of thumb, each observation and variable should have more than five defined values per principal component. Observations (or variables) with missing values that show up as outliers should be treated with suspicion. Model: A model is: 1) An approximation of reality. A good model preserves all properties of interest. 2) A hyperplane, with limited extension, that approximates the variable space spanned by a class of observations. MSPC: Multivariate Statistical Process Control. The use of multivariate methods to characterize the state of a process with respect to known states. The state is determined from model score plots and distance to model plots. See also: SPC. Multivariate analysis: Multivariable analysis is a group of statistical methods, which are appropriate when measurements are made on several variables for each of a large number of individuals or observations. Multivariate data: Multivariate data consist of observations on several different variables for a number of individuals or observations. Indeed, the vast majority of data is multivariate, although introductory statistics courses naturally concentrate on the simpler problems raised by observations on a single variable. F H L M NIPALS: Non-linear Iterative Partial Least Squares N Observation space: The space spanned by the observation vectors of a data matrix. Each variable vector is represented as a point in that space. Outlier: An outlier is a batch or time point found outside a critical limit, e. g. DCrit. O 140

Glossary Partial Least Squares: Partial Least Squares Projection to Latent Structures. See PLS. Partial models: In workset of the batch level model, where the batch evolution model has phases, there is a Create partial models for each phase box. After selecting this box, the models fitted are cumulative over the phases. That is, the first model contains the first phase, the second the first and second phases, etc. and the last contains all phases. PC: Principal Component. A PC is a one model dimension of a PC model. Often also used as a term for the scores t. PC modeling: Principal Component modeling. PC modeling is: 1) The use of PCs to define a model. 2) The approximation of a matrix by a model, defined by averages and a relatively small number of outer vector products. The components can often be used in place of the original variables for plotting, regression, clustering and so on. PCA: Principal Component Analysis. PCA is the technique for finding a transformation that transforms an original set of correlated variables to a new set of uncorrelated variables, called principal components. The components are obtained in order of decreasing importance, the aim being to reduce the dimensionally of the data. PDB: PDB is the abbreviation for Process DataBase, a database in the external system. PLS: Partial Least Squares Projection to Latent Structures. PLS is a generalization of PCA where a projection model is developed predicting Y from X via scores of X. Can also be seen as a generalized multiple regression method that can cope with multiple collinear X and Y variables. Port: The communication channel that is used by the server and client. Also named Endpoint. BioPAT SIMCA-online uses TCP ports. Prediction set: A dataset used together with an established model in order to obtain model predictions for each of the observations in the set. See also Test dataset. Predictor variable: See X-variable. Principal component: See PC. Principal component analysis: See PCA. Principal component modeling: See PC modeling. Principal factor analysis: See: Principal component analysis. Projection: 1) The act of projecting. 2) Something that has been projected, i.e. the 'picture' of orthogonally projected points on a line, plane or hyperplane. Projection methods: Projection methods are a group of methods that can efficiently extract the information inherent in MVD. They give results that are easy to interpret because they can be presented as pictures. Such methods are efficient for pattern recognition, classification, and predictions. The most commonly used methods are PC and PLS modeling. Projection point: The projection point is a point, along a line or in a plane or hyperplane (created by approximating data in k-space as a low dimensional hyperplane), which is closest to the original point. Projection to Latent Structures: See PLS. PS: Prediction Set. Denotes that the vector displays results for predictions. Recent batches: Recent Batches are the most recent batches that have finished executing. The time range that defines recent batches can be modified in the Time ranges page of the project configuration for each project. Reference batch: A reference batch is any historical or workset batch that you select to display alongside the active batches. You select a reference batch by marking it in the Batches box. A reference batch is by default displayed as line without symbols alongside the active batches. Reference dataset: The term 'Reference dataset' is used for datasets with known properties and origin, often used to define models. Synonyms: Calibration dataset, Training dataset, Workset. Regression: In mathematics Y is called a function of X, but in statistics the term regression of Y on X is generally used to describe the (sound, approximate) relationship. Regression analysis: Regression analysis is the fitting of an equation to a set of values. The equation predicts a response variable from a function of regressor variables and parameters, adjusting the parameters such that a measure of fit is optimized. P R 141

BioPAT SIMCA-online User Guide Residual: The residuals are the left-over; un-modeled part of a dataset; the mismatch between the observed and modeled values. Response variable: See Y-variable. Score: The score is: (1) The distance from the origin, along a loading vector, to the projection point of an observation in K- or M-space. (2) The coordinates of a point when it is projected on a model hyperplane. Score vector: The score vector is the observation coordinates along a PC or PLS component axis. Scores for all observations for one model dimension (component). SDB: SDB is the abbreviation for BioPAT SIMCA-online DataBase. SDB is the internal database created by BioPAT SIMCA-online to store results. Selected batch: See Reference batch. SimApi: Short for BioPAT SIMCA Application Programming Interface. A data source and a programming interface for data access specified by Umetrics. Version 2 is the latest version used by BioPAT SIMCA-online. SimApi DLL: An implementation of the SimApi for a specific external system. Used by BioPAT SIMCA-online to obtain data from the external system. Sartorius-Stedim provides the DBMaker SimApi DLL for demo purposes, and there are implementations for OPC, PI, ODBC. BioPAT SIMCA: The Sartorius-Stedim offline software used to create projects to use in BioPAT SIMCA-online. See the System requirements section for version. Singular value decomposition: See: Principal component analysis Sleep: Sleep is used to inform BioPAT SIMCA-online of skipped observations. Sleep was used in versions before 3.0 of SBOL to inform SBOL of skipped phases. SPC: Statistical Process Control. The behavior of a process is characterized using data when the process is operating well and is in a state of control. In the monitoring phase the new incoming, measured, data are used to detect whether the process is in control or not. See also: MSPC. Sub-batch: When a batch is partitioned into several physical parts, each part is a sub-batch. Sublot: See sub-batch. Tag: Tag is another name for variable. TCP/IP: TCP/IP is the standard internal protocol. BioPAT SIMCA-online uses TCP. Test dataset: See Prediction set. Trend plot: Variable plot that is displayed over time. Trigger: An act or event that initiates a reaction such as raising an alarm. Unit: A unit is a physical equipment/machine/vessel that processes a sub-batch. Unit group: A unit group is a process step, for instance a granulator. The unit group contains one or more identical units. Warning limit: When points are found outside the warning limit the process has left its controlled state and some parameters should probably be adjusted. Workset: The workset contains the batches used to build models in SIMCA. Synonyms: Training dataset, training set. Workspace: A workspace consists of one or more open project configurations and the positioning of all open plots as arranged when the workspace was saved. S T U W X 142

Glossary X-variable: X-variables are used to 'explain' the variation in the dependent variables (y). Synonyms: predictor variables or explanatory variables. Y-variable: Y-variables are modeled as dependent on other variables. These other variables are often named predictor variables or X-variables. Synonyms: dependent variables, response variables. Y 143

Index 145

A Adding Alarms... 140, 147, 159 Note... 96, 97, 120 Project... 125 Unit groups... 131 Workspaces... 168 Administrator preparation... 22 Alarm Adding batch evolution... 140 Adding batch level... 147 Adding for regular... 159 Alarm triggers for BEM... 142 Coloring... 88 Displaying triggered alarms... 62 Export... 143, 149, 162 Show limits... 74 All Y Predicted Plot... 69 Associating tags... 136, 156 Audit Trail... 46, 91 Axis... 175, 178 B Background... 181 Batch Box... 70 Box in BioPAT SIMCA-online options57 Classification... 29 Conditions... 146 Data visualization... 11 Deleting... 168 Evolution... 12 Model selection... 145 Monitoring... 26 Node... 129 Repredict... 166 Batch evolution Contribution plots... 107 Overview... 87 Plots... 62 Properties... 74 Batch filter... 129 Batch level Alarms... 147 Combined... 72 Contribution plots... 112 Layout box... 72 Model selection... 145 Overview... 87 Properties... 81 Variables... 115 Box Batches... 70 Components... 71 Layout... 72 Variable... 72 Button Add note... 96, 97, 120 Drill down... 105 Starting, stopping execution... 164 Zooming in, out... 104 C Catchup... 130, 155 Catch-up... 130 Changing Color... 174 Configuration... 166 Classifying new batches... 29 Client window... 31 Close project configuration... 37 Color Background... 181 Customization... 174 Combined... 72 Communication parameters... 7 Configuration Audit trail... 91 Export... 151, 164 Import... 128, 153 Loading... 128, 153 Saving... 151, 164 Server... 6 Configuring Network settings... 36 Old project... 166 Phase conditions... 132 Project... 127, 152 Server... 5 Connect batch conditions to tags... 146 local centering to tags... 138 output variables to the process database142, 148, 161 SIMCA variables to tags... 135 tags and configuring phase conditions132 to Server... 36 Context menu... 137, 157, 171 Contribution plot batch evolution Difference between... 111 Display... 106, 116 DModX... 108 Hotelling's T2Range... 109 Score plot... 107 Y Predicted... 110 Contribution plot batch level Display... 106, 116 DModX... 113 Hotelling's T2Range... 113 Score plots... 112 Y Predicted... 114 Control charts Defining... 139 Limit calculation... 16 Control Tags... 132 Create Contribution plot... 106, 116 List... 121 Variable plot... 106, 116 Critical limit... 140, 147 Customizing Plots with Format plot... 174 Plots with Properties... 74, 81 Databases D 146

Index Directory... 6 HDB... 33 PDB... 33 SDB... 33 DBMaker... 5 DBView... 5 Default Port... 201 Default Properties... 52 Defining batch conditions... 146 control chart limits... 139 Delete Historical batches... 168 Project configuration... 165 Workspace... 168 Deleting Historical batches... 168 Project configurations... 165 Workspace... 168 Diagnostics... 106 Directories... 6 Disconnect... 36 Display a contribution or variable plot106, 116 Distance to Model Contribution plot... 108, 113, 118 Plot... 63, 67, 78 DModX Contribution plot... 108, 113, 118 Plot... 63, 67, 78 Dockable windows... 86, 87, 90 Drill down... 105, 106 Dual Variable... 64 E Empty plot... 65, 69, 81 Environment... 24 Error codes... 199 Execution Interval... 130, 154 Start... 164 Stop... 164 Exit... 58 Export Alarms... 143, 149, 162 To external database... 142, 148, 161 To spreadsheet or file... 38 External database communication142, 148 Extract data... 38 F File tab... 35 Find... 136, 137, 157 Footer... 174, 182 Format Plot... 174 H HDB... 33 Header... 174, 182 Help menu... 123 Hi Limit... 140, 147 Hierarchical batch models... 18 HiHi Limit... 140, 147 Historical batch deletion... 168 Hotelling's T2 Range Contribution plot... 109, 113, 118 Plot... 63, 67, 79 I Initiate communication... 7 Installation... 2 Interface Option page... 51 To external system... 201 L Layout box... 72 License File... 6 Info... 1 Reminder... 199 Limits Alarm... 140, 147 Calculate control charts... 16 In options... 54, 55 Lo, LoLo, Hi, HiHi... 140, 147 Specify variable out limits... 41 Line Style... 191 Lo Limit... 140, 147 Load warning percent... 7 Local centering tags... 138 Log File... 7, 51 Log in/log out... 36 LoLo Limit... 140, 147 M Magnify... 104 Maintenance... 197 Marker... 103 Menu reference syntax... 204 Minimizing the ribbon... 60 Mini-toolbar Formatting... 172 Managing... 173 Marked items... 172 Subplot... 173 Miscellaneous page... 7, 51 Modeling batch evolution... 12, 15 batch level... 17 why batch level... 17 Monitoring evolution... 27 project... 26 Multiple Y Axes... 192 147

BioPAT SIMCA-online User Guide N New batch classification... 29 project configuration... 127, 152 Not available... 65, 69, 81 Notes... 96, 97, 120 O ODBC... 201 Open Overview window... 87 Project configuration... 37 Workspace... 101, 168 Organize In Project Administration dialog... 126 In the audit trails... 94 In the Report... 98 OSI PI... 201 Outliers... 17, 107, 116 Overview window... 87 P Partial models... 18 Paths... 6, 51 PDB... 33 Phase conditions... 132 Phase tags... 135 Physical overview... 24 Plot Batch evolution plots... 62 Batch level... 65 Combined... 72 Default batch evolution... 54 Default batch level... 55 Drill down... 105 Formatting... 174 Labels... 56 Options... 74, 75, 82, 83 Regular... 77 Templates... 193 Plot labels... 56 Plot options... 52 Plot templates... 194 Pop-up menu... 137, 157, 171 Port... 201 Predict batches... 29 Predicted Maturity Contribution plot... 110 Plot... 65 Preparation by administrator... 22 Print... 38 Print preview... 38 Print setup... 38 Processor load... 7 Project administration... 41, 125 Project Configuration New... 127, 152 Old... 166 Project DB Max Time... 7 Properties Batches... 70 Components... 71 Layout... 72 Plot Properties dialog... 74 BioPAT SIMCA-online options... 50 Variable... 72 What is... 70, 81 Properties group Batch... 70 Continuous... 81 Plot Properties dialog... 74 Protocol... 201 Q Quick Access Toolbar... 59 R Real time on-line batch data... 33 Re-configuring old project... 166 Removing Historical batches... 168 Project configuration... 165 Workspace... 168 Reorganization of table before import13 Report... 94 Repredict... 166, 167 Reset alarms... 97 Result variables... 16, 143, 149, 162 Rolling view... 51 S Save As... 122 Configuration... 151, 164 Plot formatting... 193, 194 Workspace... 101, 168 Save as... 122 Score Contribution plot... 107, 112, 117 Plot... 62, 66, 78 SDB... 33 Select batches... 76 Sequential models... 18 Server Administration... 41, 125 Audit trail... 46 Configuration... 5 Endpoints... 201 Installation... 2 Log file... 50, 51 Several phases... 15 Shortcut menu... 137, 157 Significance level... 55 SimApi Call timeout... 7 148

Index Configuration... 7 Max time... 7 Parameters... 7 BioPAT SIMCA approach... 18 BioPAT SIMCA-online interfaces201 BioPAT SIMCA-online options.. 50 General... 51 Plot options... 52 BioPAT SIMCA-online Server.. 2, 5 Sleep condition... 132 Sleep trigger... 132 Sort... 105 Specify Alarms... 140, 147, 159 Limits... 74 Variable out limits... 41 Start Client... 22 Execution... 164 Server... 22 Status bar... 87 Stop Execution... 164 Server... 22 Sub-batches... 13 Subplot Empty... 65, 69, 81 Subheader... 74 Zoom... 104 Switch plot formatting... 194 Symbol Style... 190 System requirements... 2 T T2 Range Contribution plot... 109, 113, 118 Plot... 63, 67, 79 Tabbed mode... 86, 90 Tabs Description... 90 Interface... 51 Tag Association... 136, 156 Batch condition... 146 Condition dialog... 134 Local centering... 138 Page in Configure dialog... 156 Phase conditions... 132 Phases... 135 Tag filter field... 136, 157 Target values... 138, 158 TCP/IP... 201 Terminology... 30 Time... 84, 177 Time ranges... 130, 155 Title... 174, 182 Toolbars Audit trail... 93 Report... 95 Status bar... 87 Tools tab... 103 U Unit groups... 131 Unsupported features... 30 User administration... 42 Groups page... 44 Roles page... 45 Users page... 43 Using BioPAT SIMCA-online... 21 Tag filter... 136, 157 V Variable Aliases...137, 157 batch evolution... 64 batch level... 68 display plot... 106, 116 Dual plot... 64 from contribution... 106, 115, 116 Identifiers... 56 View by phase... 72 149

BioPAT SIMCA-online User Guide W Warning limit... 140, 147, 159 Window group... 100 Workbook Interface... 51 Tabs... 90 Workspace Open... 37 Save... 101 Worm plot... 77 Y Y Predicted Contribution plot... 110, 114, 119 Plot... 65, 68, 80 Z Zoom Automatic... 54 In and out... 104 150

Sartorius Stedim Systems GmbH Robert-Bosch-Str. 5 7 34302 Guxhagen, Germany Phone +49.551.308.0 Fax +49.551.308.3289 www.sartorius-stedim.com Copyright by Sartorius Stedim Biotech GmbH, Goettingen, Germany. All rights reserved. No part of this publication may be reprinted or translated in any form or by any means without the prior written permission of Sartorius Stedim Biotech GmbH. The status of the information, specifications and illustrations in this manual is indicated by the date given below. Sartorius Stedim Biotech GmbH reserves the right to make changes to the technology, features, specifications and design of the equipment without notice. Status: June 2013, Sartorius Stedim Biotech GmbH, Goettingen, Germany Printed in Germany on paper that has been bleached without any use of chlorine. W Publication No.: SBI6012-e13061 Ver. 06 2013