GenePattern News, January 2005, Number 1

In This Issue:

1. Announcements
2. New Modules
3. Updated Modules
4. User Resources
5. Training and Events

1. Announcements: GenePattern 1.3

A new version of GenePattern was released on December 13. GenePattern version 1.3 includes the following major features:

Reproducible Research

GenePattern modules and pipelines support reproducible research by assigning unique identifiers to each version of a module or pipeline. This functionality allows you to do the following:
- Specify which version of a module to use in an analysis. Even if the code for that algorithm changes later, you can still refer to the version you used to obtain a result, guaranteeing that you can obtain that result at any time in the future.
- Record all changes made to a module or pipeline. All changes to modules and pipelines are recorded, so you can refer to any previous version
- Automatically determine which modules are required to run an analysis. GenePattern uses the Life Sciences Identifier (LSID) to identify modules used in an analysis pipeline. If your GenePattern server requires a new module (or an updated version of a module it already has), it will automatically detect and install that module.

Online module repository

A repository at the Broad Institute Web site allows you to identify and install new modules and updates of current modules.

New Programming Language Environments

GenePattern now offers programming environments for Java, MATLAB, and R. These consist of libraries that allow programmers to call any GenePattern module from within one of those languages. Users can also convert a pipeline to its equivalent code in Java, MATLAB, or R.

Pipeline and module view mode

View a concise description of pipelines and modules, with control over the level of detail displayed.

Batch analyses

Select a folder instead of a single file as input to a module, and the analysis will run on all of the files within that folder.

The GenePattern 1.3 software and a comprehensive list of new features and fixes can be found on the GenePattern Web site,

2. New Modules:

Several new GenePattern modules are available on the GenePattern module repository. You can view comprehensive documentation at and can install them by clicking on “Install/Update” in the Admin frame of your local GenePattern server.

MAGE-ML Import Viewer and MAGE-ML Converter

These modules convert expression data to MAGE-ML format compatible with current microarray repositories such as ArrayExpress and GEO.

GEO Importer

This module imports an expression file from the Gene Expression Omnibus (GEO) repository. It generates GenePattern formatted files automatically from a GEO series record.


The GeneCruiser module allows users to retrieve comprehensive annotations for identifiers of microarray data. Users can convert Affymetrix probe IDs to corresponding information in GenBank, UniGene, SwissProt, LocusLink, Gene Ontology (GO), RefSeq, and TIGR databases. GeneCruiser is also available as a Web application at and as a Web service at

Download URL

Downloads text from a URL and saves it to a file. This module is useful in pipelines which use a file as input to multiple steps, as the file can be retrieved only once and the local copy used in later steps.

3. Updated Modules:

The following modules have been released with significantly updated functionality:

Prediction Results Viewer

This viewer now provides a graphical representation of the results of prediction algorithms, in addition to a detailed tabular results panel.

Feature Summary Viewer

This viewer now provides a graphical representation of the results of cross-validation analyses, in addition to a detailed tabular results panel.

Gene List Significance Viewer

This viewer now provides a graphical representation of the results of marker selection algorithms, in addition to a detailed tabular results panel.

4. User Resources: GenePattern Users' Forum

A new forum is available for public discussion of microarray analysis and methodologies using the GenePattern package. The GenePattern Users' Forum, at, is intended to allow the community of over 600 GenePattern users to communicate directly with one another. The GenePattern team regularly reads the forum and responds.

5. Training and Events:

GenePattern workshops have been extremely popular. We will be scheduling the next round of workshops shortly. Watch our website for updates, or sign up to be notified immediately at