GenePattern and GPARC Integration  Print-icon

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.

How to Install a Module or Pipeline from GPARC

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.

How to Submit a Module or Pipeline to GPARC from GenePattern

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:

  1. Exporting and downloading a .zip of the module
  2. Submiting to GPARC, which takes the module author to the GPARC submission page.

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.

New Features (June 2014)

Note that prior users will have received an email asking them to set a new password. Please contact us if you have any trouble.

A note on Curation and Quality

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.

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Updated on June 19, 2014 15:10