Working with Modules  

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.

• Basic Operations
• Displaying Module Properties
• Creating Modules
• Editing Modules

Basic Operations

The following table summarizes the different ways you can work with GenePattern modules.

Displaying Module Properties

To view the definition of a module, display its properties:

1. Click Modules & Pipelines to display the GenePattern home page.
2. Select the module to display.
3. When GenePattern displays the module parameters, click Properties. GenePattern displays the module properties:

Clicking the help icon displays brief descriptions of each field:

• Name. Name of the module.
• LSID. The Life Science Identifier (LSID) used to uniquely identify a GenePattern module.
• Description. Brief description of the module.
• Author. The author's name and affiliation (company or academic institution).
• License. The End-User license agreement for the module. (This is an optional property and will therefore usually be empty.)
• Privacy. Modules may be marked as public or private:
  • Public modules may be accessed by anyone using the GenePattern server.
  • Private modules may be accessed only by the person who installed or created the module (or by an administrator).
• Quality level. One of three terms that indicates the author’s confidence in the robustness of the module: development, preproduction, and production.
• Documentation. Help file that describes the module and provides instructions for its use.
• Command line. Command line used to launch the module. Values enclosed in angle brackets are replaced by specific values before the command executes.
• Module category. Category under which to list this module. Categories are used to organize modules and pipelines on the GenePattern home page. Pipelines are always assigned to the category name pipeline.
• CPU type. Indicates the type of CPU required to run the module, or any if the module runs on any type of CPU.
• Operating system. Indicates the operating system required to run the module, or any if the module runs on any operating system.
• Language. Indicates the programming language used to implement the module.
• min. language version. Indicates the version of the programming language used to implement the module.
• Version comment. Describes changes made to the module in this version.
• File format(s). Lists the file formats of any output files generated by the module.
• Current files: Lists the support files packaged with the module, such as executable programs, documentation, and so on.
• Parameters: Lists the module parameters, including the file formats of any input files required by the module.

Creating Modules

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:

1. Find or write a program that executes the desired function. Any program that can be executed from the command line can be run as a GenePattern module. If you are writing the program, you can use any programming language. For example, you can use a compiled language, such as C, to create an executable or use a scripting language, such as Perl, to create a script that is run by an interpreter. The Programmers Guide provides guidelines for writing programs that will be run as GenePattern modules.
2. Use GenePattern to create a module that invokes the program that you have written. It takes just a few minutes to enter the necessary information. Once you have done so, you can run the module. You can decide which parameters from the algorithm to expose to the user and can replace command line parameter names that are hard to remember with names that are self-explanatory. You can also create drop-down list choices for parameters to reduce the possibility of invoking the module with incorrect values.

To create a module that invokes the program that you have written (or otherwise obtained):

1. Click Modules & Pipelines>New Module. GenePattern displays the module integrator.
2. Define the module.
3. Click Save to create the module.

For more information about creating modules and using the module integrator, see the Programmers Guide.

Editing Modules

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:

1. Click Modules & Pipelines  to display the GenePattern home page.
2. Display the module properties page in one of the following ways:
   • Select a module that you created. When GenePattern displays the module parameters, click Edit. GenePattern displays the module integrator.
   • Select a public module. When GenePattern displays the module parameters, click Properties. When GenePattern displays the module properties, click Clone to create a copy of the module. You created the copy, so you can edit it.
3. Edit the module.
4. Click Save to create a new version of the module.

For more information about editing modules and using the module integrator, see the Programmers Guide.

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