Implementation of GenePattern within the Stanford Microarray Database

Abstract

Hundreds of researchers across the world use the Stanford Microarray Database (SMD; http://smd.stanford.edu/) to store, annotate, view, analyze and share microarray data. In addition to providing registered users at Stanford access to their own data, SMD also provides access to public data, and tools with which to analyze those data, to any public user anywhere in the world. Previously, the addition of new microarray data analysis tools to SMD has been limited by available engineering resources, and in addition, the existing suite of tools did not provide a simple way to design, execute and share analysis pipelines, or to document such pipelines for the purposes of publication. To address this, we have incorporated the GenePattern software package directly into SMD, providing access to many new analysis tools, as well as a plug-in architecture that allows users to directly integrate and share additional tools through SMD. In this article, we describe our implementation of the GenePattern microarray analysis software package into the SMD code base. This extension is available with the SMD source code that is fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD with an enriched data analysis capability.

Figure 1.

Accessing GenePattern microarray data analysis package from a publication record in SMD. Clicking on the red gear icon in a publication record will take the user to the SMD data retrieval pipeline. At any point after the data are retrieved, the user will be able to download the data files or click on the ‘Analyze with GenePattern’ option. GenePattern is launched with the data already loaded into the PCL to GCT conversion module.