Spyglass Portal Manual v.20140214

Spyglass Portal Manual v.20140214 Spyglass Portal Manual... 1 Getting Started... 2 Pre- mission... 3 As a user, I want to create and download a mission for the ESP... 3 Define default setting (phasecfg.rb)... 3 Create ESP device... 4 Creating a mission... 5 Download a mission... 8 As a user, I want to provide feedback... 9 Post- mission... 10 As a user, I want to upload log file and images... 10 Upload files... 10 As a user, I want to auto- upload the log file and images from a folder... 13 Upload files... 13 As a user, I want to create a standard curve... 15 Upload files... 15 Analyze Log File... 17 As a user, I want to analyze the data in the operational dashboard... 17 Analyze Images... 18 As a user, I want to upload and analyze images, and see concentration values... 18 Prepare GAL file... 18 Process image... 19 Map Image with GAL file... 20 Review brightness and concentration values... 20 As a user, I want to analyze the data in research dashboard... 22 As a user, I want to see the concentration values on the landing page... 23 Spyglass Portal Manual, v2014-02- 14 1

Getting Started Access the site at http://portal.spyglasswater.com/espdev. Log in with your account. Follow the use cases in this guide. For more information, see the detailed online manual available at the top right of any page (the small book icon). Spyglass Portal Manual, v2014-02- 14 2

Pre- mission As a user, I want to create and download a mission for the ESP Steps: 1. Log into the Postal 2. Define default setting (phasecfg.rb) 3. Create ESP device 4. Create a new mission from the landing page 5. Fill in mission information e.g. starting tube, mission setting, image setting, phase 6. Download mission.rb and phasecfg.rb Define default setting (phasecfg.rb) Access global default setting from the top menu. This global setting is specific to a user; making changes to this setting will affect the mission that you are going to create in the next step. Figure 1. Access global default settings Here you can edit mission start time, sample volume for each protocol, archive volume for each protocol, email setting, and image setting. Spyglass Portal Manual, v2014-02- 14 3

Figure 2 Enter start time, volume, and archival default settings for a new mission. For image setting, you can add as many settings as you want by clicking (+) Add protocol button then specify protocol, resolution, and exposure time. Figure 3 Add image settings for each protocol. When you finish editing the global default setting, click the Save button on the top of the form. Create ESP device Access the menu to manage ESP device from the top menu. Figure 4 Add an ESP device. In ESP Management page, you can add a new ESP or edit an exising ESP. The ESP device Spyglass Portal Manual, v2014-02- 14 4

listing here belongs to a particular user. Figure 5 Add details about a specific ESP. Creating a mission To create a new mission, you can use either the top menu Add new mission or the bottom menu + -> ESP Mission. Figure 6 Create a new mission. When creating a new mission, you have to specify all required fields, i.e. mission name, starting tube, and ESP device. Spyglass Portal Manual, v2014-02- 14 5

Figure 7 Enter basic settings for a new mission. If you provide information such as Project, Instrument, and Location, you can use the text facets on the All Data Source or My Data page to filter your data set. Note that you can edit the default configuration Project and Instrument categories on the Facet Management page. Figure 8 Access the "Facets management" page However, please be careful while editing the Facet Management page because entries in this page are shared across all users in Spyglass Portal. Spyglass Portal Manual, v2014-02- 14 6

Figure 9 Modify the taxonomy for faceted browsing, such as organizations, instruments When you finish filling in mission information, click the Next button on the top of the form. Figure 10 Access the next page of details for a new mission. Then you will see the popup for creating a mapping between Protocol, GAL (Gene Array Layout) file, Organism, and Standard curve. You can skip it for now. We will come back to this later. Click the Cancel button to close this window. Figure 11 Specify the details required interpret brightness of spots on an image and concentration of cells: Protocol - GAL file - Organism - Standard Curve Now you can add a phase to your mission. You can manually create each phase or use the Repeat This Phase? option to create multiple phases at once. You can choose to use the mission default setting or override it. When you finish, click (+) Add phase button. You will see the newly created phase in the Phase List table. Spyglass Portal Manual, v2014-02- 14 7

Figure 12 Add additional phases to a mission. Download a mission When deploying a mission, we will need to export both mission.rb and phasecfg.rb. Figure 13 Download the files used to configure an ESP for a mission. Click Export mission.rb to download mission file. Click Export phasecfg.rb to download the default setting file. Spyglass Portal Manual, v2014-02- 14 8

Figure 14 Preview the files used to configure an ESP for a mission. As a user, I want to provide feedback In the top menu bar, click the Email of the current logged in user and select the Feedback menu. Figure 15 Access the Portal feedback form. Enter your name and your message, and then click the Send Feedback button. Figure 16 Fill out and send the feedback to Spyglass. Spyglass Portal Manual, v2014-02- 14 9

Post- mission As a user, I want to upload log file and images Steps: 1. Log into the Portal 2. Select mission from top menu 3. Go to Data dashboard 4. Upload log file and images Upload files Access the Data dashboard page from the top menu. Make sure you selected a mission first otherwise this menu will not be available. Figure 17 Access the "Data dashboard" page in the menu. In the Data Dashboard, you can manage all ESP related files here. You can manually upload CTD data (.csv), Can data (.csv), Log file (.out,.txt), and Image (.zip). For image, it must be an archive (.zip) of images (.tif). Figure 18 An example of a CTD data file (.csv), which contains data from a CTD sensor attached to the ESP. This is an example of Can data (.csv) Spyglass Portal Manual, v2014-02- 14 1 0

Figure 19 An example of a Can data file, which contains data from sensors monitoring the status of the ESP. Note that when you upload a log file (.out), the CTD and Can data will be automatically extracted (if available), as well as the phases associated with images. Figure 20 The toolbar menu for uploading images, log files, CTD and Can data files. Online documentation can be accessed in the upper right. It may take several minutes per megabyte to process the log file. You will see a flash message notification at the top of the page when the processing is finished. Spyglass Portal Manual, v2014-02- 14 1 1

Figure 21 The progress bar shown when uploading a log file. Spyglass Portal Manual, v2014-02- 14 1 2

As a user, I want to auto- upload the log file and images from a folder Steps: 1. Log into the Portal 2. Select mission from top menu 3. Go to Data dashboard 4. Upload log file and images Upload files Access the Data dashboard page from the top menu. Make sure you selected a mission first otherwise this menu will not be available. Figure 22 Access the "Data dashboard" to manage mission files. You can sync files from a remote directory. This function is for fetching images and log files from a remote directory to the Spyglass Portal. The watch folder configuration needs to be set only one time, after that you will get a notification whenever new files are available in your watch folder. Figure 23 Select the folder icon to create a new watch folder. Spyglass Portal Manual, v2014-02- 14 1 3

You have to fill in information about the remote directory e.g. IP address, Port, Username, Password, and Path to the directory storing files. You can click the View all button to preview files in the specified directory. Then click the Save button. It may take awhile for files to be synced to the Spyglass Portal. You will receive a notification message when it finishes. Figure 24 Configure the network settings to connect to the remote folder. Select View all to test the connection, and Sync to start the automatic synchronization between the watch folder and the Portal. The log file will be automatically parsed and made available in the Operational Dashboard page. Images will be automatically processed only if the GAL mapping is defined when you created a mission. Spyglass Portal Manual, v2014-02- 14 1 4

As a user, I want to create a standard curve Steps: 1. Log into the Portal 2. Select mission from top menu 3. Go to Standard Curve page 4. Upload log file and images Upload files Access Standard Curve page from the top menu. Figure 25 Access the "Standard curve" page. This page shows the standard curves that you have created. The standard curve belongs to a particular user, ESP device, protocol, and target organism. You can create a new standard curve by clicking the (+) Add new standard curve button, or delete it by clicking the trash icon. Figure 26 Add a new standard curve to the Portal. When creating a new standard curve, you have to specify an equation for the curve. Please refer to in-page documentation for more details. Spyglass Portal Manual, v2014-02- 14 1 5

Figure 27 Specify the variables of the linear equation for the standard curve. Spyglass Portal Manual, v2014-02- 14 1 6

Analyze Log File As a user, I want to analyze the data in the operational dashboard Steps: 5. Log into the Portal 6. Select mission from top menu 7. Upload log file 8. Go to Operational Dashboard Access the Operational Dashboard from the top menu. Figure 28 Access the "Operational dashboard" page. To use this page, please refer to in-page documentation (in top navigation bar). Figure 29 The Operational dashboard visualizes events and data from the log file. Spyglass Portal Manual, v2014-02- 14 1 7

Analyze Images As a user, I want to upload and analyze images, and see concentration values Steps: 1. Log into the Portal 2. Select mission from top menu 3. Upload image (either manual upload or auto sync from remote directory) 4. Prepare GAL file 5. Select image, define mapping with GAL file 6. Process image 7. Review brightness and concentration values Prepare GAL file Access the GAL page from the top menu. Figure 30 Access the "GAL" management page for Gene Array Layout (GAL) files. GAL files here are global to all users. You can use existing GAL files or upload a new GAL file. For more detailed documentation, please use the link in the top navigation bar. Figure 31 Add and visualize the layout of GAL files. This is an example of a GAL file. Spyglass Portal Manual, v2014-02- 14 1 8

Figure 32 Example content of a GAL file, showing spot numbers, source wells, and spot locations. Process image Access the Image Analysis page from the top menu. Figure 33 Access the "Image analysis" dashboard. In this page you can upload new images, process, delete, exclude, and download images. You can also view details of test spots inside each image. For more detailed documentation, please use the link in the top navigation bar. Figure 34 The Image Analysis dashboard shows the mission images and related brightness data. Spyglass Portal Manual, v2014-02- 14 1 9

Exclude is useful when you do not want to show the result of this image in the Brightness and Cell count graphs. You will still see this excluded image in Image Analysis page. Delete is useful when you want to remove this image from graphs and the Image Analysis page. To restore the deleted image, go to the Data Management page, check Trash, and click the Restore button. Map Image with GAL file Click on images to select, then click Process images button. You will see the Sourcewell Mapping popup. You can use an existing mapping, edit an existing mapping, or define a new mapping. Then click Process images. Figure 35 The Sourcewell mapping allows you to link the spots on an image to a standard curve, and then process the image to automatically derive cell concentration values. Note that if you modify an existing mapping and click Process images, other images associated with this mapping will also be re-processed. The selected image will be processed in a background job. You will be notified via the flash message at the top of the page when the processing is done. Review brightness and concentration values After images have been processed, you can see the overview of brightness in the bottom of this page. You can filter the brightness graph by using organisms and background subtraction models. To analyze each image in detail, you can click buttons under each image. Spyglass Portal Manual, v2014-02- 14 2 0

Figure 36 The Brightness graph summarizes the brightness values from images over the course of a mission. The checkboxes on the left will filter organisms or background subtraction models. In this page, you will see image details, test spot brightness, cell density, and cell concentration (if the standard curve is defined). You can also exclude outlier spots and immediately see the new cell concentration. Figure 37 The image detail page provides interactive visual analysis of an image. As shown in Figure 37, spot locations are overlaid on the image (upper left), spot statistics are shown in graphical (upper right) and tabular (lower right) form. Summary statistics and cell concentrations are shown in the lower left. Spyglass Portal Manual, v2014-02- 14 2 1

As a user, I want to analyze the data in research dashboard Steps: 1. Log into the Portal 2. Select mission from top menu (assuming images have been uploaded and processed already) 3. Go to Research Dashboard page, see cell count, brightness, and image detail. Access the Research Dashboard page from the top menu. Figure 38 Access the "Research dashboard" page. In this page, you can see CTD data as well as the image associated with each phase. For more details, please see the in-page documentation in the top menu. Figure 39 The Research Dashboard summarizes the data collected over the course of a mission. If there is CTD data collected with the mission, then the tabs will show interactive visualizations (horizon, calendar, histogram+timeline, scatterplot, and tabular previews) of the data. Spyglass Portal Manual, v2014-02- 14 2 2

As a user, I want to see the concentration values on the landing page Steps: 1. Log in to Spyglass Portal 2. Select mission from top menu (assuming images have been uploaded and processed already) 3. Go to My Data or All data sources page. From the Parameter facet, select Cell Concentration. From result table, select a mission that contains the processed images and standard curve. Figure 40 The Portal landing page supports interactive filtering and visualization of mission data and open- data sources. The My Data page only shows data that you have loaded to the Portal. The All data sources contains data from your missions, data shared with you, and data from open sources that you add to the portal (such as OPeNDAP servers). For more information about these advanced features, consult the online documentation or contact Spyglass (info@spyglasswater.com). Spyglass Portal Manual, v2014-02- 14 2 3