Thursday, March 17, 2005

Bioinformatics, Microarrays, and Understanding the Functioning of the Cell

Recently, I had the opportunity to meet with Orly Alter, a researcher at the University of Texas in Austin, to discuss the issues and challenges in the world of Bioinformatics. According to Orly, the primary challenge in Bioinformatics is the visualization of data and clustering data into meaningful sets. The visualization of data needs to be interactive with multiple views and multiple queries as there are many unknowns and thus cannot be automated yet. She also raised the issue of data integration and analysis since data comes from microarrays stations locally as well as publicly available databases. Finally, large data sets can require grid computing and other CPU-intensive resources. Orly indicated that Bioinformatics today is in the same place astronomy was in the 17th century. Lots of data points and efforts are underway but the broad-based principles remain to be discovered.

I also met with Jim Collett, who is a graduate student at the University of Texas. He is using BASE, an open source tool for microarray analysis. He has a background in lab automation and is familiar with the challenge of automating the reading of microplates. Jim is interested in linking databases, open source bioinformatics tools, and mathematical software into a cohesive whole the better models the functioning of a cell. He pointed out Sydney Brenner , a Nobel prize winner of 2002, as a leader in the field. Brenner described the ideal environment for modeling the functioning of a cell over time and under various conditions as one which includes an object oriented, graphical environment with mathematical tools, simulation capability, and a visualization environment. Finally, Jim pointed out an effort at MIT called Synthetic Biology which focuses in this area. You can see their take on it at this site.

Microsoft had an interesting take on the subject with this site. This is all food for thought as we take Virtual Instrumentation into new fields. It appears the Bioinformatics may be a fertile field.

If you are working in the Bioinformatics area, I would like to share more thoughts with you. You can reach me at

Best regards,
Hall T. Martin


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