Skip to main content
Premium Trial:

Request an Annual Quote

TIGR Releases Suite of Open Source Microarray Informatics Tools


The NCICB isn't the only bioinformatics group hoping to make its software available to a wider audience. Last week, TIGR's array software team released its informatics suite, TM4, under an open source license in order to “democratize microarray analysis,“ according to TIGR investigator John Quackenbush. “We're basically giving state-of-the-art data management and analysis tools to everyone who wants them for free. That way, people in small labs can collect and analyze data like the big guys without breaking the bank — or overspending their grants,“ Quackenbush told BioInform via e-mail.

TM4 comprises four packages: MIDAS (Microarray Data Analysis System), a microarray data normalization and filtering tool; MADAM (Microarray Data Manager), an application designed to load microarray data into a database in a MIAME-compliant manner; Spotfinder, an image processing program; and MultiExperiment Viewer (MeV), a data mining and visualization tool.

Quackenbush said that MeV supersedes ArrayViewer, a program TIGR released three years ago for visualizing and normalizing data from a single two-color array. The MeV package was given a complete overhaul before its first source code release in June, with new features including a number of new algorithms and a well-defined API. Plans for future releases include a client/server model and a metabolic pathway viewer module. Developers from biotech firms DataNaut and Syntek contributed free support to TM4 development, Quackenbush said.

Response to the package has been fairly strong so far, according to Quackenbush. MADAM and MIDAS, which were released on August 23, have each been downloaded 29 times. Source downloads for MADAM and MIDAS number 4 and 3, respectively. Since June, 1,256 users outside of TIGR have downloaded MeV, with 63 downloads for source.

The choice to release the source for the TM4 suite wasn't purely altruistic, however. Quackenbush said he recognized that “there are a lot of people out there who are smarter than me who are developing new methods for analyzing array data.“ The TIGR informatics team is seeking to build a community of developers working on a common microarray analysis platform. “We are hoping that this could be that platform,“ he said. In addition, Quackenbush pointed out, “If 1,300 people license our software instead of some $3,000 commercial package, that saves the funding agencies $3.9 million that can be spent directly on research. I think that funding a few people to continue to enhance and maintain the system makes sense in that context.“

— BT

Filed under

The Scan

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.

Circulating Tumor DNA Linked to Post-Treatment Relapse in Breast Cancer

Post-treatment detection of circulating tumor DNA may identify breast cancer patients who are more likely to relapse, a new JCO Precision Oncology study finds.

Genetics Influence Level of Depression Tied to Trauma Exposure, Study Finds

Researchers examine the interplay of trauma, genetics, and major depressive disorder in JAMA Psychiatry.

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.