Working with Modules  Print-icon

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

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.

Display module properties

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.

Send module to other users

Zip files provide a convenient way to send modules to other GenePattern users:

  • To export a module to a zip file, click Modules & Pipelines and select the module to export. When GenePattern displays the module parameters, click Export.
  • To install a module from a zip file, click Modules & Pipelines>Install from zip.

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.

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:

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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Updated on May 20, 2013 20:32