GenePattern Team Blog

Creating a GenePattern Module

Posted on Saturday, December 15, 2012 at 11:36AM by The GenePattern Team

The following tutorial shows you how to create a new GenePattern module (in GenePattern 3.4 and up). Only the GenePattern team can create or install modules on the GenePattern public server. Therefore, to create a module, you need to have a local GenePattern server installed (see the download and installation page). You may also be interested in the video tutorial: Create a module in GenePattern.

In this tutorial, you will create a module named log_transform. The module invokes a perl script,, which log-transforms all positive values in a data set and sets all negative or zero values to zero. Before you begin, download the perl script and its documentation:

In GenePattern, to create the log_transform module:

  1. Click Modules & Pipelines>New Module. GenePattern opens the Module Integrator window.
    • Give it a Name: LogTransform
  2. Enter the following information in the Details fields:
    • Description: Log transform a data (gct)...

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Importing Data from caArray to GenePattern

Posted on Tuesday, October 30, 2012 at 12:36PM by The GenePattern Team


caArray is an open-source, web and programmatically accessible array data management system. caArray guides the annotation and exchange of array data using a federated model of local installations whose results are shareable across the cancer Biomedical Informatics Grid (caBIG®). caArray furthers translational cancer research through acquisition, dissemination and aggregation of semantically interoperable array data to support subsequent analysis by tools and services on and off the Grid.

To facilitate the importing of data from caArray repositories in GenePattern, a module named caArray2.3.0Importer is provided.


The CaArray2.3.0Importer imports data files from a caArray 2.x repository into GenePattern by connecting to a caArray 2.x repository and then retrieving all files of a given extension for a named experiment. The retrieved files are then collected into a single ZIP file archive which is returned as the module's output.

(Note: 2.x is used...

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October 2012 Java 6 update and GenePattern visualizer issues

Posted on Friday, October 26, 2012 at 02:47PM by David Eby

UPDATE MARCH 17, 2017 : Java applet visualizers no longer work in any browser. Please click here to read the blog post.

(Originally posted 2012-11-09)

Oracle recently released an update to their Java 6 platform which could cause problems for GenePattern users.  The update disables the underlying technologies used by several of GenePattern components, specifically the visualization modules (such as ComparativeMarkerSelectionViewer and HeatMapViewer) and the file uploader.  The GenePattern team is currently evaluating options to address this issue.

This update came out within the last couple of weeks, so you may or may not have already applied this change depending on the update policies of your organization and the settings on your own computer.  It is known by several different names, including at least the following:
  • Java SE 6 Update 37
  • JRE 6u37 or JDK 6u37
  • Java for Mac OS X 10.6 Update 11
  • Java for OS X 2012-006 (Mac OS X 10.7 or Later)
  • JRE...

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