GenePattern provides access to a broad array of computational methods used to analyze genomic data. Its extendable architecture makes it easy for computational biologists to add analysis and visualization modules. This ensures that GenePattern users have access to a continuously growing repository of new computational methods.
If you are new to GenePattern, begin with the basics:
To use GenePattern, you open a web browser and enter a URL. The URL that you enter is the address of a GenePattern server. For example:
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GenePattern public server. This URL connects you to the GenePattern server hosted at the Broad Institute. | |
GenePattern local server. You can download and install the GenePattern software,start your own GenePattern server and then use this URL to connect to your own GenePattern local server. For more information, see Starting Your Own GenePattern Server. | |
The URL for a networked server, for example: http://mycompany.com:8080/gp/ |
GenePattern networked server. A GenePattern administrator at your company or another institution, can install a GenePattern server and make it available for your use. You can then use the URL of the networked GenePattern server to connect to that server. |
For example, to use the GenePattern public server:
GenePattern prompts you to login:
Whether a GenePattern server requires passwords depends on how it is configured. The GenePattern public server requires passwords. By default, a local server does not.
Cannot connect to server: If the web browser cannot connect to the server, it displays a message such as “Unable to connect” or “Cannot display the webpage.”
To exit from GenePattern, click Sign Out in the top right corner of the title bar.
The GenePattern web site provides an overview of GenePattern and its analysis modules, as well as links to the GenePattern software and documentation. Click Documentation/Tutorials for a list of GenePattern tutorials and documentation, including:
If you would like, you can install your own local GenePattern server by downloading and installing the GenePattern software. You can install a local server on a standalone machine for your personal use or on a networked machine for use by several people or an entire organization. A local GenePattern server shared by several users is typically referred to as a networked GenePattern server.
For information about the pros and cons of using the GenePattern public server versus your own local GenePattern server, see Concepts:Servers.
To install a local GenePattern server, follow the instructions provided on the Download GenePattern page.
You use the same installation instructions regardless of whether you are installing a local GenePattern server for personal use or installing a networked server for use by an institution. The difference is in how you configure the server. If you are installing a local GenePattern server for personal use, the default server configuration is typically sufficient. If you are installing a networked server for use by an institution, see the Administrators Guide for instructions on how modify the default server configuration.
After installing a GenePattern server, you must start the server before you can use it.
Windows 7 |
To start the GenePattern server, right-click on StartGenePatternServer.exe and select Run as administrator. While the server is starting, the cursor displays as an hourglass. The server is ready when the cursor returns to normal. |
Other Operating Systems |
To start the GenePattern server, double-click the Start GenePattern Server icon (shown below). By default, installing GenePattern places this icon on your desktop. Windows: While the server is starting, the cursor displays as an hourglass. The server is ready when the cursor returns to normal. Mac OS X: While the server is starting, the server icon bounces in the Dock. The server is ready when the icon stops bouncing. Linux: The server starts silently. |
After starting your local GenePattern server, you can use it by opening a web browser and entering the URL for the server: http://localhost:8080/gp/.
Alternatively, you can click the GenePatternHome.html shortcut icon (shown below), to open a web browser and connect to your server. By default, installing GenePattern places this icon on your desktop.
If you did not install icons in your task bar or on your desktop, GenePatternHome.html can be found at the top level of your GenePattern install directory (for example, in C:\GenepatternServer\GenePatternHome.html or /Users/JDoe/Applications/GenePatternServer/GenePatternHome.html).
To shut down the GenePattern server, double-click the Stop GenePattern Server icon, shown below, or close the console window.
Windows: The GenePattern server exits silently.
Mac OS X: When you shut down the server, the GenePattern server icon disappears from the Dock.
Linux: The GenePattern server exits silently.
When first opened in your browser, GenePattern displays the home page. To return to this page at any time, click the GenePattern icon in the title bar or the Modules & Pipelines item in the navigation bar.
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The title bar includes:
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The navigation bar provides access to other GenePattern pages (see Navigation Bar). |
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Use the search box to quickly find a module or pipeline. |
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The Modules & Pipelines pane lists the analysis modules and pipelines that you can run. Modules and pipelines not installed from the Broad repository are shown in red.
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The center pane is the main display pane. GenePattern uses this pane to display information and to prompt you for input. Initially, the center pane contains a welcome page, which provides instructions for running common analysis protocols. To redisplay the welcome page, click the GenePattern icon in the title bar. |
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The far right pane provides access to several tabs:
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The navigation bar provides access to GenePattern pages and operations. When you log into a GenePattern server on which GenomeSpace is not enabled, you see the following navigation bar:
If you log into another GenePattern server, such as your own local GenePattern server or a GenomeSpace-enabled GenePattern server, you may see additional items in the navigation bar:
The following table describes all possible options in the navigation bar. Not all of these options are available on the GenePattern public server.
Modules & Pipelines |
Display the GenePattern home page. |
Create a pipeline. |
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Create a module. |
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Install a module or pipeline from the Broad repository. |
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Install a module or pipeline from a ZIP file. |
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Display installed modules or pipelines; delete modules or pipelines. |
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Suites |
Display the Manage Suites page. |
Create a suite. |
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Install a suite from the Broad repository. |
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Install a suite from a ZIP file. |
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Display installed suites; delete suites. |
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Job Results |
Display the Results Summary page. |
Display jobs run on the server; delete jobs. |
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Resources |
Display an overview of the resources. |
Mailing List |
Display the form you use to join a low-traffic GenePattern mailing list. |
Report Bugs |
Display the form you use to contact the GenePattern team to report bugs, provide feedback, or ask questions. |
Contact Us |
Display a form, which you can use to send questions and comments to the GenePattern team. |
Downloads |
Display an overview of the available downloads. |
Programming Libraries |
Download and install GenePattern libraries for use with Java, MATLAB, or R. |
Public Datasets |
Download sample datasets for use with GenePattern. |
GParc1 | Display the GenePattern Archive web site, which is a repository and community where users can share and discuss their own GenePattern modules. |
Administration1 |
Display the Server Settings page. |
Modify settings that affect the GenePattern server. |
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Help |
Display the GenePattern home page. |
Tutorial |
Display the Tutorial, which provides a comprehensive hands-on tour of GenePattern. |
Video Tutorials |
Display the list of GenePattern training videos. |
User Guide |
Display this guide, which describes how to use GenePattern. |
Programmers Guide |
Display the Programmers Guide, which provides guidelines for writing modules and instructions for accessing GenePattern from the Java, MATLAB, and R programming environments. |
Module Documentation |
Display a list of the modules and pipelines installed on your server, with brief descriptions and links to the module/pipeline documentation. |
File Formats |
Display the File Formats Guide, which describes all file formats and provides instructions for creating input files. |
Release Notes |
Display the Release Notes, which describes new features and known issues in this release. |
FAQ |
Display the GenePattern list of Frequently Asked Questions. |
About |
Display the release date and build number of the GenePattern server. |
GenomeSpace | Display the GenomeSpace menu options: Login (to GenomeSpace), GenomeSpace UI, Register (a new GenomeSpace account), and About (GenomeSpace). A GenomeSpace-enabled GenePattern installation includes several elements that help move data files from GenomeSpace and analysis results to GenomeSpace. For more information, see www.genomespace.org. |
1Not available on the public GenePattern server.
When you run an analysis, GenePattern displays the job results in the Recent Jobs tab:
Click the icon next to the job name to display a menu of commands for working with that job. For more information, see Working with Analysis Results.
Download |
Download a zip file containing all analysis result files for this job. |
Terminate |
Stop the job. This menu item appears only while the job is running. |
Reload |
Display the analysis and its parameters in the center pane, with the parameters set to the values used for this analysis job. |
Delete |
Delete the analysis job and its analysis result files from the GenePattern server. |
Info |
Display the parameter values and the analysis result files for this job. |
View Java Code |
Display the command line that you would use to run this job in the Java, MATLAB, or R programming environments. These commands are useful for programmers who want to access GenePattern from one of these programming environments or from their own applications. |
When you run an analysis, GenePattern displays the job results in the Recent Jobs tab:
Click the icon next to the file name to display a menu of commands for working with that file. For more information, see Working with Analysis Results.
Delete |
Delete the file from the GenePattern server. |
Save |
Download the file from the GenePattern server. |
Send to <input-file-parameter> |
Specify this file as the input file for the selected parameter. (Only appears when a module is selected.) |
Create Pipeline |
Create a GenePattern pipeline that includes the modules and parameters necessary to reproduce this result file. |
List of modules |
List of modules that accept this type of file as an input parameter. Select an analysis to display its parameters in the center pane. This result file is specified as the first input parameter. |
The Uploads pane lists files that you have uploaded to the GenePattern server: (Please note that as of GenePattern 3.8.0 this is now the Files tab)
Click the icon next to the uploads directory, or a subdirectory or file in that directory, to display a menu of commands for working with that directory or file. For more information, see Running Modules and Pipelines.
Upload Files |
Upload a file to the uploads directory on the GenePattern server. |
Create Subdirectory |
Create a subdirectory under the uploads directory on the GenePattern server. |
Delete |
Delete the file/directory from the uploads directory on the GenePattern server. |
Save |
Download the file from the uploads directory on the GenePattern server. |
Send to <input-file-parameter> |
Specify this file as the input file parameter. |
Send Batch to <input-file-parameter> |
Specify this directory as the input file parameter. This creates a batch job to analyze each file in the directory. |
List of modules |
List of modules that accept this type of file as an input parameter. Select an analysis to display its parameters in the center pane. This file is specified as the first input parameter. |
Click Suites>Manage to display the currently installed suites:
Click the icon next to the suite name to display a menu of commands for working with that suite. For more information, see Working with Suites.
Edit |
Available only for suites that you have created. Display the Edit GenePattern Suite page, which you can use to modify your suite. |
Delete |
Delete the suite from the GenePattern server. |
Export excluding dependents |
Create a ZIP file that contains the definition of the suite, but not the modules or pipelines in the suite. The ZIP file can be used to install the suite on another GenePattern server (see Exporting and Installing Suites Using ZIP Files). Installing the suite from this ZIP file will not install any modules or pipelines in the suite; they must already be installed on the GenePattern server or be installed separately. |
Export including dependents |
Create a ZIP file that contains the definition of the suite, as well as the modules and/or pipelines in the suite. The ZIP file can be used to install the suite on another GenePattern server (see Exporting and Installing Suites Using ZIP Files). Installing the suite from this ZIP file will also install the modules and pipelines in the suite (unless they are already installed on the GenePattern server). |
Use My Settings to change your GenePattern account information:
An analysis module runs a single analysis. A pipeline runs a series of analysis modules. If you are unfamiliar with GenePattern modules and pipelines, see Concepts.
To run a module or pipeline:
Alternative: A module or pipeline can also be run from an analysis result file or uploaded file. When GenePattern displays such files (for example, in the Recent Jobs tab, the Uploads tab, or the Job Status page), click the icon next to the file of interest, as shown below. GenePattern displays the file menu, which lists all modules that accept this type of file as an input file parameter. Select the module or pipeline. GenePattern displays its parameters in the center pane, setting the input file parameter to the file of interest.
Some modules or pipelines may have associated end-user license agreements (EULAs). When you first run a licensed module/pipeline, you will be shown a window containing the license terms, where you can read the terms and choose to accept them or not. (Note: The license terms will differ depending on the module. The terms shown in this image are only an example.)
When you click OK to accept the license agreement, your acceptance is logged in a database maintained at the Broad. You will not be asked to accept the license terms when you use that particular module/pipeline again until and unless a new version of the module/pipeline is released.
If you choose not to accept the license agreement, you will be unable to run the licensed module or pipeline.
To view a license you have already accepted, click the properties link on the licensed module or pipeline page. The modules properties page contains a link to the full-text license.
On the pipeline properties page, the link appears above the pipeline listing.
When you select a module or pipeline, GenePattern displays its parameters:
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Most modules require one or more input files. There are several ways to choose an input file:
In general, uploading a file using drag-and-drop or the Upload File button is fine. However, if you are focused on a particular dataset, it may be faster to upload your files to the Uploads tab and then analyze the uploaded files. Just be aware that if you delete the uploaded files, you cannot rerun the analyses. If you have extremely large datasets, consider using file paths. You can save a significant amount of time by avoiding file transfers. |
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Specify other parameter values using the drop-down lists and entry fields:
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Version of the module. If multiple versions of the module are installed on the server, GenePattern displays the latest version by default. Select a different version from the version number drop-down menu. |
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The Documentation link displays the module or pipeline documentation. The Gear icon
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To rerun an analysis:
See the video tutorial: Using the GenePattern Uploads Tab
Uploading files to the GenePattern server provides the following benefits:
To upload files:
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Add files to the applet window. Click the icon to display a file browser from which you can select files. Alternatively, drag-and-drop files directly onto the window. |
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Remove files from the applet window. Click the icon to display a menu from which you can choose to delete selected, pending, finished, failed, or all files from the window. |
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Pending. When you have added files to the window, but have not yet clicked Upload, the files are pending. |
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Queued. When you click Upload, all pending files are added to the applet's upload queue. |
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Finished. Files that have been successfully uploaded to the GenePattern server are marked as finished. |
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Failed. Files that could not be uploaded to the GenePattern server are marked as failed. |
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Upload. Start uploading all pending files. |
To delete an uploaded file from the server:
Partial uploads: If an upload fails to complete (because you stopped the upload or because of a server error or network interruption), the file is marked as '(Uploading)' in the Uploads tab. To reload the file, delete the partially uploaded file and upload it again.
Duplicate names: The server prevents you from uploading multiple files with the same name. If two different files have the same name, rename the file before uploading it to GenePattern.
Sharing uploaded files: As of GenePattern 3.6, you cannot share uploaded files with other users. We plan to implement this feature in a future GenePattern release.
Upload window stalls: On rare occasions, the upload window may remain blank or not fully load. If this occurs, close the applet and click Upload Files to reopen the applet. In extremely rare cases, you may need to restart your web browser or reboot your machine. This behavior appears to be caused by known compatibility issues between web browsers (specifically Firefox on Macs) and Java applets.
Note: For security reasons, file paths are not enabled on the GenePattern public server.
When file paths are enabled on a GenePattern server, you can use file paths to identify input files for modules and pipelines. The GenePattern server can directly access the files stored on your local or networked drives; therefore, the files do not have to be transferred to or stored on the GenePattern server. Avoiding file transfers can save significant upload time and avoiding file storage can save significant amounts of disk space. Therefore:
When file paths are enabled, the module/pipeline run page includes the Add Path or URL option. To use a file path as an input file parameter:
The Adminstrators Guide provides instructions on how to enable file paths on your GenePattern server.
See the video tutorial: Batch Execution in GenePattern 3.3.3
Batch processing provides an automated method of running several files through a module or pipeline in parallel.
As of GenePattern 3.8.0 you can drag in a list of files to batch over, or run over a directory, as before. For more information on dragged in lists, please see the 3.8.0 release notes.
To run a batch job from a directory in the Files tab:
To provide multiple input files for a module or pipeline, identify each set of files to be processed by giving them the same name (excluding file extension). For example, to run ComparativeMarkerSelection as a batch job, give each .gct or .res file the same name (excluding file extension) as its matching .cls file. For example: test1.gct, test1.cls, test2.gct, test2.cls. You can place all of the files in one subdirectory or create a separate subdirectory for each input file parameter (for example, one subdirectory for .gct files and another for .cls files). GenePattern processes each set of matching files, ignoring any other files in the directory.
Tip: You do not have to wait for the job to complete. You can move off of the Job Results Summary page and continue working or even log out of GenePattern. If you choose to wait for the jobs to complete, periodically refresh the Job Results Summary page to update the status of the jobs.
Please Note: Currently, batch processing may only be applied to input file parameters. It can not be applied to any other parameter type.
To create and run a batch job using an upload subdirectory:
To create and run a batch job using a file path subdirectory:
When you run a module or pipeline, GenePattern runs the analysis job on the GenePattern server. Analysis results are stored on the GenePattern server for a period of time (by default, one week) and then deleted. If you are unfamiliar with how GenePattern runs modules and pipelines, see Concepts.
The following table summarizes ways to work with analysis results:
Display analysis results |
Click a job ID number to display the Job Status page, which lists the input parameters and analysis results for that analysis job. (Recent jobs are listed on the GenePattern home page. To display all jobs, click Job Results>Results Summary.) |
By default, analysis results are private. To share results with other GenePattern users, click the |
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Save analysis results |
To save results persistently (beyond the period of time they are stored on the server), download the analysis result files to a more permanent location:
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Delete analysis results |
If you no longer need your analysis results, you can delete the files from the server:
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When you run a module or pipeline, the files generated by the module/pipeline are stored on the GenePattern server. The module author determines the content and format of the generated files; however, by convention, each module generates the following files:
When you run a module or pipeline, GenePattern sends the analysis job to the server and displays the Job Status page. This page displays complete information for an analysis job, including its status, input files, parameter values, and (when the job completes) result files. After starting an analysis, you can continue working. You do not have to leave the Job Status page displayed.
GenePattern offers several ways to redisplay a Job Status page:
The following figure shows the Job Status page for a pipeline job. The Job Status page for a module job is similar.
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Click the ![]() |
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Icons indicate whether this is an ![]() ![]() |
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Click the ![]() |
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Show/hide execution log files. |
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Click the ![]() An ![]() |
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Click the ![]() |
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Icons indicate whether the job is ![]() ![]() ![]() |
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For a pipeline, each section of the colored line beneath the job name represents a step in the pipeline. As each step completes, its section of the line changes from green to blue. |
An Email Reminder check box is visible while the job is running. For long running jobs, select the check box to have GenePattern send you email when the job completes. Continue working in GenePattern or exit from GenePattern. When you receive the email indicating that the job is finished, display the Job Status page to review the analysis results.
The GenePattern home page lists your most recent jobs. The Job Results Summary page lists all of your analysis jobs.
To display the Job Results Summary page, click Job Results>Results Summary. If a job is still running, refresh the page periodically to update its status.
To sort the job results, click a column header. You can sort jobs by status, job ID, module name, submit date, or completion date. Within jobs, you can sort files by file size or file output date.
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Filter the display:
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Show/hide the execution log files. |
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Icons indicate whether the job is |
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Click the job ID to display the Job Status page. |
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Delete jobs and/or files: (1) select the check boxes of the jobs and/or files to delete and (2) click the delete link in the column header to delete them. Selecting a job selects all of its files. Selecting the check box in the column header selects/clears all check boxes. |
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Name of the module that was run and the name of each result file. Click the arrow next to the Module Name header to hide/show all result files. Click the arrow next to a module name to hide/show its result files. |
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Size of each file and the total job size (combined file size). |
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Time the job was submitted. |
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Time the job was completed and time each file was last saved. |
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Name of the person who ran the job. Or, more precisely, the GenePattern user name of the account that ran the job. |
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Your access to the job. You have read/write access to jobs that you have run. You have either read or read/write access to shared jobs. Write access gives you permission to delete a job or any of its result files. |
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Share status: |
When you run an analysis job, by default, it is private: only you (and GenePattern administrators) can view or delete the job. Sharing job results gives other GenePattern users access to the job, including its input files, parameter values, and result files.
To share job results or modify the share status of a job:
Sharing input files: In GenePattern, you can specify the output file from one analysis as the input file for a subsequent analysis. For example, you might use the output file from PreprocessDataset as the input file for ComparativeMarkerSelection. In this case, if you share the ComparativeMarkerSelection job, the other user can view the result files but cannot view the input file (which is from the PreprocessDataset job) or rerun the job. To share the ComparativeMarkerSelection job and its input file, either (1) share both the ComparativeMarkerSelection and PreprocessDataset jobs or (2) save the output file from PreprocessDataset, rerun ComparativeMarkerSelection using the saved file, and share the resulting ComparativeMarkerSelection job.
Creating groups: To create a group or add members to a group, contact the GenePattern administrator. If you are an administrator, see Creating Groups and Administrators for more information.
Analysis and visualization modules are at the heart of GenePattern. Analysis modules provide computational methods and tools for gene expression analysis, proteomics data analysis, SNP analysis, RNA-seq analysis, flow cytometry, and data preprocessing and conversion. Visualization modules display your data and analysis results graphically. If you are unfamiliar with GenePattern modules and pipelines, see Concepts.
The following table summarizes the different ways you can work with GenePattern modules.
Run a module |
Select a module, enter its parameters, and click Run. For more information, see Running Modules and Pipelines. |
Module properties include the author, the command line used to invoke the module, and the programs used to execute the module. If a module has an end-user license agreement associated with it, you can view the license via the module properties page. To display a module’s properties, click Modules & Pipelines and select the module. When GenePattern displays the module parameters, click Properties. |
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Send module to other users |
Zip files provide a convenient way to send modules to other GenePattern users:
For more information, see Exporting and Installing Modules & Pipelines Using Zip Files. |
Install modules from the repository |
The Broad Institute maintains a repository of modules, pipelines, and suites. To install modules from the Broad repository, click Modules & Pipelines>Install from Repository. For more information, see Installing Modules & Pipelines from the Repository. |
Create modules |
An analysis module invokes a program that executes the desired function. To create a module, you must write the program that implements the analysis and then create the GenePattern module that invokes that program. For more information, see Creating Modules. |
Edit modules |
You can edit a module that you have created or copy a public module and edit your copy of the public module. For more information, see Editing Modules. |
Delete modules |
To delete a module from your GenePattern server, click Modules & Pipelines>Manage. For more information, see Managing Modules & Pipelines. |
To view the definition of a module, display its properties:
Clicking the help icon displays brief descriptions of each field:
Only the GenePattern team can create, edit, or install modules on the GenePattern public server. Therefore, to create a module, you must have a local GenePattern server installed (see Starting Your Own GenePattern Server).
Creating a GenePattern module is a two-step process:
To create a module that invokes the program that you have written (or otherwise obtained):
For more information about creating modules and using the module integrator, see the Programmers Guide.
Only the GenePattern team can create, edit, or install modules on the GenePattern public server. Therefore, to edit a module, you must have a local GenePattern server installed (see Starting Your Own GenePattern Server).
To edit a module:
For more information about editing modules and using the module integrator, see the Programmers Guide.
A GenePattern pipeline defines a sequential series of modules to be run. Modules run from a pipeline work exactly the same as those run directly from GenePattern. If you are unfamiliar with GenePattern pipelines, see Concepts.
The following table summarizes the different ways you can work with GenePattern pipelines.
Run a pipeline |
Select a pipeline, enter its parameters, and click Run. For more information, see Running Modules and Pipelines. |
Pipeline properties include the pipeline’s author, the modules to be run and their parameters. If a pipeline has an end-user license agreement associated with it, you can view the license via the pipeline properties page. To display pipeline properties, click Modules & Pipelines, select the pipeline, and click Properties. For more information, see Displaying Pipeline Properties. |
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Send pipelines to other users |
Zip files provide a convenient way to send pipelines to other GenePattern users.
For more information, see Exporting and Installing Modules & Pipelines Using Zip Files. |
Install pipelines from the repository |
The Broad Institute maintains a repository of modules, pipelines, and suites. To install pipelines from the Broad repository, click Modules & Pipelines>Install from Repository. For more information, see Installing Modules & Pipelines from the Repository. |
Create pipelines |
You can create an empty pipeline and add modules to it, create a pipeline by cloning an existing pipeline, or start with an analysis result file and have GenePattern create a pipeline that recreates that analysis result file. For more information, see Creating Pipelines. |
Edit pipelines |
You can edit a pipeline that you have created or clone a public pipeline and edit your copy of the public pipeline. For more information, see Editing Pipelines. |
Delete pipelines |
To delete a pipeline, click Modules & Pipelines>Manage. For more information, see Managing Modules & Pipelines. |
To view the definition of a pipeline, display its properties:
On this page, you can:
You can create a pipeline in several ways: from an analysis result file, from an existing pipeline, or from scratch (beginning with an empty pipeline).
To create a pipeline from an analysis result file:
GenePattern adds modules to the pipeline based on the following logic: add the module that created the result file; check the module’s input file parameters; if the input file for the module was the output file of a previous module, add the previous module; check that module’s input file parameters; continue to walk back through the chain of modules, adding modules to the pipeline, until reaching the initial input file.
To create a new copy of an existing pipeline:
To create a pipeline from scratch:
To edit a pipeline:
See the video tutorial: Exploring the New GenePattern Pipeline Designer.
When you create or edit a pipeline, GenePattern displays the pipeline designer:
From left to right:
The pipeline diagram toolbar provides the following options:
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Displays the basic pipeline properties in the Editing Pipeline panel, as shown here. For more information, see Editing Basic Pipeline Properties. |
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Saves your changes without closing the designer. |
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Saves your changes, closes the designer and runs the pipeline. |
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Loads the last saved version of the pipeline, overwriting any unsaved changes. |
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Displays this section of the GenePattern documentation. |
The remaining topics in this section describe how to use the pipeline designer:
To edit basic pipeline properties:
The Editing Pipeline panel displays the following properties:
To supply a help file, click Attach Documentation and select a (previously created) documentation file. GenePattern uploads the documentation file to the server and displays its name in the pipeline properties panel. Only one help file can be attached to the pipeline. To select a different file, click Attach Documentation.
License: To supply a text file containing an end user license agreement to the pipeline, click Attach License. Anyone using the pipeline will be prompted to accept or decline the license terms when they first run the pipeline, and their acceptance will be tracked in a database maintained at the Broad Institute. They will not have to accept the terms again unless and until a new version of the pipeline is created. Only one license file can be attached to the pipeline. To select a different license file, click Attach License. This is an optional property; as such it will often be empty.
Prompt When Run: Most modules in a pipeline have one or more parameters. You can supply values for these parameters or mark them as prompt-when-run. When the pipeline runs, GenePattern prompts the user for all prompt-when-run parameters. By default, GenePattern prompts the user for a parameter by displaying its name and description. Optionally, you can supply alternate text for the prompt. Click Display Prompt When Runs to view all prompt-when-run parameters in the pipeline and, optionally, modify the prompt text. For more information about setting parameter values, see Editing Module Properties and Setting File Input Parameters.
To add a module to the pipeline:
Note: If you add a module with an end-user license to your pipeline, users who have not accepted that module's license terms will be presented with a license-acceptance window before the pipeline will run.
To specify a file as input to a module in the pipeline, you must first add the file to the pipeline diagram. To add a file to the diagram:
The pipeline diagram uses color to distinguish between files, modules, and pipelines. Connections between objects show the flow of data through the pipeline. The following diagram shows a file, a module and a pipeline. The file (all_aml_train.gct) is used as an input file parameter (input.file) for the module. To delete an object and all of its connection, click its delete icon.
To edit a module's properties:
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By default, a pipeline runs the most recent version of a module. The drop-down list shows all versions of the module that are installed on the GenePattern server. To have the pipeline run a different version of the module, select it from the list. |
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The Life Science Identifier (LSID) for this module. You cannot create or edit LSIDs. The GenePattern server automatically assigns an LSID to each version of a module. |
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Click the Documentation button to display the module documentation. |
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Warnings shown here must be addressed before you can save the pipeline. GenePattern highlights all parameters affected by the warnings. |
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All module parameters are listed here. Input file parameters are critical and are generally listed first. They control the flow of data through the pipeline. For more information, see Setting Input File Parameters. |
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Click the check box next to a parameter to mark it prompt-when-run. When the pipeline runs, GenePattern prompts the user for all prompt-when-run parameters in the pipeline. By default, GenePattern prompts the user for a parameter by displaying its name and description. Optionally, click Set Prompt When Run Display Settings to supply alternate text for the prompt. |
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For most parameters, you enter a value, select a value from a drop-down list, or use the default value supplied by GenePattern. |
In the pipeline diagram, the connections between modules show the flow of data through the pipeline. You modify the flow of data by modifying the input file parameters. The connections in the diagram are a graphical representation of the input file parameter settings. When you click on the module, the editing panel provides a textual representation of the same input file parameter settings.
You can supply the file for an input file parameter in one of three ways:
The following pipeline diagram uses the ComparativeMarkerSelection module to illustrate the different ways of supplying input file parameters:
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For the input.file parameter, use the output file generated by the PreprocessDataset module.
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For the cls.file parameter, prompt the user for input.
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For the confounding.variable.cls.file, specify the file all_aml_train_confound.cls.
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The method you use to set the input file parameter depends on how you plan to supply the file:
Click Save or Save & Run to save your changes.
Occasionally, a pipeline requires that the same input file be specified for multiple parameters. For example, consider a pipeline with two modules:
You want to use the same input file for both the ComparativeMarkerSelection.input.file parameter and the ExtractComparativeMarkerResults.dataset.filename parameter. If the input file that you want to use is either the output file generated from another module (perhaps an expression dataset generated by the PreprocessDataset module) or an uploaded file, this is not a problem. You can connect the file that you want to use to both the ComparativeMarkerSelection.input.file parameter and the ExtractComparativeMarkerResults.dataset.filename parameter.
However, what happens if you want to prompt the user for the expression dataset file? If you mark the ComparativeMarkerSelection.input.file parameter as a prompt-when-run parameter, you still need an input file for ExtractComparativeMarkerResults.dataset.filename parameter. If you mark both parameters as prompt-when-run, you have to rely on your user to submit the same expression dataset file for both parameters. The workaround is to add the ConvertLineEndings module to your pipeline:
GenePattern orders modules in a pipeline based on their position in the diagram. The diagram is read from left to right and top to bottom, as you would read a book written in English.
You can reorder the modules in a pipeline by repositioning the modules in the diagram. Similarly, you can insert a module into a pipeline simply by adding it to the diagram and dragging it to the appropriate location. However, in either case, you are changing the flow of the data and, therefore, must delete and recreate any affected connections.
To reposition a module in the pipeline:
GenePattern includes close to 200 analysis and visualization modules, and the list is constantly growing. With so many modules, it's helpful to have shortcuts for finding your favorites. Suites can help you organize modules in much the same way playlists help you organize music. Each suite is a themed collection of user-selected modules. You can create as many suites as you like. The GenePattern team has created several suites, which are included on the GenePattern public server. For example, the ClusteringSuite contains the HierachicalClustering, KMeansClustering, and SOMClustering modules. If you are unfamiliar with GenePattern suites, see Concepts.
The following table summarizes the different ways you can work with GenePattern suites.
To display the suite definition:
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Send suites to other users |
Zip files provide a convenient way to send suites to other GenePattern users.
For more information, see Exporting and Installing Suites Using Zip Files. |
Install suites from the repository |
The Broad Institute maintains a repository of modules, pipelines, and suites. To install suites from the Broad repository, click Suites>Install from Repository. For more information, see Installing Suites from the Repository. |
Create suites |
To create a suite, click Suites>New. For more information, see Creating Suites. |
Edit suites |
You can edit a suite that you have created or copy a public suite and edit your copy of the public suite. For more information, see Editing Suites. |
Delete suites |
To delete a suite from your GenePattern server, click Suites>Manage. For more information, see Managing Suites. |
To display the definition of a suite:
From this page, you can:
To create a suite:
To view or edit a suite:
An analysis module runs a single analysis. A pipeline runs a series of analysis modules. Suites group modules and pipelines into packages that have related functionality, which helps you to organize and work with modules and pipelines. If you are unfamiliar with GenePattern modules, pipelines, and suites, see Concepts.
The Broad Institute maintains a repository of modules and pipelines that are freely available to the public. Most of these modules and pipelines are available on the GenePattern public server. To install these modules and pipelines on your local GenePattern server:
Use the top section of the form to find the modules to install. To update the list of modules/pipelines, select the modules/pipelines to search for and click Update View:
Show new modules: Displays modules and pipelines that are in the repository and not on your server.
Show updates to currently installed modules: Displays modules and pipelines where the repository contains a more recent version than the version installed on your server.
Show latest versions of all modules: Displays all modules and pipelines in the repository, whether or not they are installed on your server.
Operating system: Filters the search results to display only modules and pipelines that run the selected operating system platform(s).
Note: To install an older version of a module already installed on your server, check the "Show latest versions of all modules" box under Filtering Options, then Update View. This will show all modules in the repository. The checkbox underneath Update View and next to "Name (Version)" allows you to select/deselect all modules in the displayed list. Then you can use the dropdown under the module to select the version you wish to install.
For each module and pipeline, GenePattern displays similar information:
Zip files provide a convenient means of sending your modules and pipelines to other GenePattern users. You can export a module or pipeline to a zip file. The zip file can then be used to install the module or pipeline on another GenePattern server.
To export a module or pipeline to a zip file:
To install a module or pipeline from a zip file:
Click Modules & Pipelines>Manage to display the Manage Modules & Pipelines page. From this page, you can
The Broad Institute maintains a repository of suites that are freely available to the public. To install these suites on your GenePattern server:
Use the top section of the form to find the suites to install. To update the list of suites, select the suites to search for and click Search:
For each suite, GenePattern displays similar information:
Zip files provide a convenient means of sending your suites to other GenePattern users. You can export a suite to a zip file. The zip file can then be used to install the suite on another GenePattern server.
To export a suite to a zip file:
To install a suite from a zip file:
Click Suites>Manage to display the Manage Suites page. From this page, you can
GPARC is a repository and community where GenePattern users can share and discuss their own modules. These modules have not been tested by the GenePattern team, but recognizing their value to the community, GenePattern now offers increased visibility and ease of integration with the GPARC repository.
GenePattern versions 3.6.1 and higher offer the ability to install a module directly from GPARC. Users must first be granted the permission to install modules by the server administrator. On the Install Modules page, the user can choose a repository from a drop-down menu. A description of the selected repository explains the curation and quality level of the modules it contains.
For more information on GPARC modules, including the community discussion and ranking features, a link to the GPARC website is also provided in the navigation bar under Downloads.
From the Module Integrator, a module author now has a new button labeled “Submit to GPARC.” Selecting this button displays instructions for the two-step process:
The dialog also checks to be sure that the latest edits to the module have been saved, and that the module has documentation attached - a requirement for GPARC submission. The module author will either need to log in or create a new GPARC account in order to submit their module.
Underneath the Submit to GPARC button is a link to an explanation of what GPARC is and its use to the GenePattern user community.
Note that prior users will have received an email asking them to set a new password. Please contact us if you have any trouble.
Curated modules have been developed or tested by the GenePattern team at the Broad Institute. The GenePattern team offers two curated repositories. The GenePattern production repository includes modules that have completed development and testing, and the team determines which modules meet the requirements for production use. The GenePattern beta repository includes modules that have completed development, and some amount of testing, but have not completed the testing process. Modules in the GPARC repository are user-submitted, and not considered to be curated by the GenePattern team. Occaionally modules from the GPARC respository, are selected for installation on the GenePattern Production server. If you have questions about the quality level of a GPARC module, please contact the module author.
GenePattern now provides information about a module or pipeline’s source in several places. On the Job Submit page, the Manage Modules page, or the Job Status page, an icon and summary description will indicate whether a module or pipeline was installed from the production repository, beta repository, GPARC repository, uploaded from .zip, or created on the server.
GenePattern server administrators can configure which repositories their users can access, as well as the names, descriptions, and icons to display on the pages listed above.