The Institute for Genomic Research (TIGR) is a not-for-profit research institute whose primary research interests are the analysis of genomes and gene products from a wide variety of organisms. TIGR's bioinformatic research has produced new software for finding genes and for identifying other important biological features of genomes. One of these bioinformatics tools is TIGR Multiple Experiment Viewer (MEV) a software application used for gene expression analysis.
In October 2001, TIGR and DataNaut started a collaborative effort to build the next generation of TIGR MEV. TIGR MEV allows researchers to view representations of processed microarray slides and identify genes and expression patterns of interest. The first version of TIGR MEV was developed internally by TIGR in 2001 and welcomed in the microarray community as a powerful tool for researchers. However, as microarray technology and techniques quickly evolve it was clear that a completely new platform was needed to meet the demands of researchers.
The
goals for the next generation TIGR MEV were:
Develop an open source platform for
affordable microarray data analysis – in order to make
comprehensive microarray analysis available to everyone the
application had to be free and open source.
Handle large amounts of microarray
experiment data – TIGR will soon use microarray slides
that have 32,000 spots and researchers typically use
hundreds of slides for experiments. This results in data
sets approaching 500mb pushing the limits of a single PC.
High performance analysis - as data
sets increase and analysis algorithms become more complex a
new approach is need for computational analysis of
microarray data. An emerging approach to handle this problem
is grid computing where the processing power of many
computers is harnessed to work on a single task. Using a
grid would enable TIGR MEV users to get super computer
power for little or no cost.
Standards-based solution – the application should only use open source software that adheres to industry standards.
TIGR MEV was completed in June 2002 and took over 4000 man-hours to complete. The seven-person team was located in the U.S. and Russia collaborating with TIGR staff in Rockville, Maryland. The June release of the software delivered on all of the project goals although it was a tough road to success. The most time consuming task of the project was developing and testing the TIGR MEV computational grid that consumed 45% of overall project hours.
The remainder of this paper provides an
overview of microarrays and how they are used in genetics
research. Following that is a technical look at TIGR MEV and
issues faced while developing the system.
TIGR MEV is an open source bioinformatics system used for computational microarray analysis. Portions of
this software were developed by DataNaut Inc.; however, all rights and title in and to this software
are owned and retained by The Institute for Genomic Research. If you are interested in obtaining the
software visit the TIGR web site.
DataNaut provides software development consulting services with extensive expertise with microarray
technologies. Organizations that are interested in using DataNaut consulting services or having
TIGR MEV customized for specific research applications can send email to info@datanaut.com.
