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NIH Bioinformatics Cooperative

Bioinformatics software and databases are essential tools for biomedical research at NIH, yet these resources are costly and out of reach for many Labs. Pooling the efforts of four ICs, we provide access to a growing list of microarray analysis tools. These include:


Affymetrix LIMS database – A secure, convenient location to store, analyze and retrieve Affymetrix GeneChip data. This database is hosted at CIT and is available to investigators in participating Institutes. It is a great alternative to managing your own pile of Zip disks, CD-ROMs, Jaz disks, etc. The NIHLIMS database is hosted in a controlled machine-room environment with 24x7 operation, automated backups, and a high level of system security. View more information about Affymetrix. Obtain library files from Affymetrix.

MSCL Analyst's Toolbox

MSCL Analyst’s Toolbox– This toolbox includes a set of scripts for database access and analysis of Affymetrix data. The scripts run in the JMP statistical package available to NIH users. See below.


Affymetrix Netaffx annotation files – in JMP table form.


GO-SCAN – Gene Ontology for Significant Collection of Annotations: GO-SCAN is a bioinformatics tool that selects and presents relevant Gene Ontology (GO) annotations for a gene “hit” list from an Affymetrix microarray experiment.


A-SCAN 3.0 – NIH BC’s web interface for retrieving and analyzing LIMS data.

JMP NIH site licence

JMP NIH site license – For more information about downloading a copy of JMP under the NIH site license, go to

More information about JMP

Partek Pro

Partek Pro – A full-scale microarray analysis package with strong statistical analysis capabilities. Visit for more information.

Shared licenses are available to investigators in ICs participating in the NIH Bioinformatics Cooperative and NIDDK.

Download new Partek GS (build 6.06.0517 from May 17th 2006) version.


NIAID software: DAVID – Database for Annotation, Visualization and Integrated Discovery


NIAID software: EASE – the Expression Analysis Systematic Explorer


GeneSpring – Shared licenses are no longer available.

In addition, the Mathematical and Statistical Computing Lab of CIT collaborates with investigators on analysis of studies involving all aspects of microarray expression analysis, especially of Affymetrix data.

LIMS information:

Currently participating ICs:

  • Clinical Center/CCMD - Dr. Robert Danner
  • NHLBI – Dr. Eric Billings
  • NINDS – Dr. Lynn Hudson
  • CIT – Dr. Peter Munson

Contact Peter Munson ( or Steve Bailey ( for more information.

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This page last reviewed: November 09, 2011