Software Interfaces  Print-icon

caIntegrator caIntegrator is a web-based software package that allows researchers to set up custom, caBIG®-compatible web portals to conduct integrative research, without requiring programming experience. These portals bring together heterogeneous clinical, microarray and medical imaging data to enrich multidisciplinary research.  GenePattern is available through the caGrid analytical service.  For more information on caIntegrator and the caBIG project, please visit the caBIG Community website.
CellProfiler CellProfiler is free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. They have published papers on analyzing cell images and non-cell images.  CellProfiler can format and export image-based data as a GenePattern GCT file (.gct) through the ExportToSpreadsheet module or data tool.  For more information or to download CellProfiler, please visit
DREAM Project The DREAM (Dialogue for Reverse Engineering Assessments and Methods) Project poses fundamental questions about systems biology, and invites participants to propose solutions. The main objective is to catalyze the interaction between experiment and theory in the area of cellular network inference and quantitative model building in systems biology.  GenePattern will provide the computational infrastructure to support DREAM Challenge 2012.
Garvan Institute The Peter Wills Bioinformatics Centre at the Garvan Institute of Medical Research in Sydney, Australia, has set up a public GenePattern server here.
GenomeSpace The GenomeSpace Project brings together diverse computational tools, enabling scientists without programming skills to easily combine their capabilities through frictionless data transfers and cross-platform communication between tools.  GenomeSpace currently integrates 6 popular bioninformatics tools, including Cytoscape, Galaxy, Genepattern, Genomica, the Integrative Genomics Viewer, and the UCSC Genome Browser.  Other tools can be integrated either through a Java-based Client Development Kit or can communicate directly with a RESTful Web Services API.  More information is available at the GenomeSpace project website and at the Bitbucket project repository.
ImmPort logo The Immunology Database and Analysis Portal (ImmPort) system provides advanced information technology support in the production, analysis, archiving, and exchange of scientific data for the diverse community of life science researchers supported by the National Institute of Allergy and Infectious Diseases, Division of Allergy, Immunology, and Transplantation (NIAID/DAIT).
InSilico DB The InSilico project aims to make reuse and sharing of genomic datasets a reality for clinical researchers, expanding the possible research questions that can be answered, and providing a means for reproducible genomics research. They are developing user-friendly tools to access to gene-expression datasets by facilitating retrieval and necessary prepossessing.  InSilico DB allows users to export their data directly to the GenePattern public server for analysis.
NuGO NuGO has developed a Black Box environment that utilizes GenePattern as its preferred analysis tool and has deployed NuGO-modified versions of some GenePattern modules on the GenePattern servers installed on the Black Boxes. For more information about the NuGO NBX please visit The paper that describes the modules NuGO has contributed to GenePattern can be found here. Any comments or questions regarding the NuGO NBX and the NuGO GenePattern modules should be directed to sian.astley(at)
SMD The Stanford Microarray Database (SMD) provides an extensive microarray database and has integrated with GenePattern to provided tools for the analysis of the data. More information about SMD can be found at and the paper that describes the integration of GenePattern in their environment can be found here. Please send questions and comments regarding SMD to array(at)
StarBiogene is a set of visual and analytic software tools for the analysis of genomic gene expression data generated through microarray analysis.  It is developed at MIT as a part of the Software Tools for Academics and Researchers (STAR) program. The portal is a GenePattern server outfitted with a set of custom written modules to access and analyze hosted gene expression datasets.
Stemformatics Stemformatics is a portal to a series of public experiments describing mouse and human stem cells and how they differentiate to become mature cells, tissues and organs. Users can find data from leading stem cell laboratories in a format that is easy to search, easy to visualise and easy to export. User can also log in to the Workbench to run and save their own analyses.  These analyses are run on an integrated GenePattern server similar to the Stanford Microarray Database.  More information can be found at
University of Otago The Integrated Genomics group at the University of Otago in New Zealand also has a public GenePattern server deployed here.  More information about public resources from the Integrated Genomics group is available at their website:
Duke University IGSP The Nevens Lab at Duke University has set up a publicly accessible GenePattern server to support SIGNATURE, a web-based resource that uses Bayesian methods for processing gene expression data coupled with a curated database of gene expression signatures.  More information can be found at

Does your software interoperate with GenePattern? Or do you want your software to interoperate with GenePattern and need assistance? Contact us  at gp-help(at)

Updated on March 05, 2013 14:20