Blogging the biotechnology revolution

Systems Biology is changing the way biology is done. Is it a fad or is it effective? This blog tracks current happenings and helps you stay on top of the field. You can find a list of relevant papers at systems biology paper watch Have you heard a talk or read a paper in bioinformatics / systems biology you would like to tell other people about? Email: and get the word out!

Tuesday, August 29, 2006

Applied Biosystems makes file formats open source

Back when I was outside the academic sector I remember the groans and moans over working with the ubiquitous ABI sequencing/genotyping/rt-pcr machines and their crazy proprietary file formats. We had to invent ways to get around the restrictions imposed by the software that we had to use because of their almost monopolistic hold of the market share (in all fairness they were the best machines at the time).

Either way, they have made their ABI file formats open source, so now who knows what is possible. One interesting use would be to associate specific read data with published SNP data so that the quality of the data can be assessed.

Thanks to Colin who made me aware of this story!

Monday, August 14, 2006

Systems Biology companies

Lately ive been hearing gripes that there are no bioinformatics/systems biology companies and that within industry the only jobs you can hope for are within a progressive big pharma company. Recently i read an interview with the CEO of GeneStruct Keith Ellison who talked about tools, strategies and companies driving systems biology. Here he mentions that this new paradigm of drug discovery follows any natural order, with early adopters, conservatives and larrards in the mix. He mentions alot of systems and pathway companies that are often overlooked when thinking about bioinformatics in industry. I recap them here:

Ariadne - software for pathway analysis and automated science text processing
Jubilant - curated databases and visualization of interactions
BG Medicine - formerly beyond genomics, predictive toxicology drug company
Predix Pharmaceuticals
Entelos -modeling through a mathmatics approach
Compugen -drug discovery through proteins and diagnostic marker pipeline
Optimata -improving drug testing schedules
Gene Logic-data driven drug development?
GenStruct - knowledge drive discovery

Hope you guys find this list interesting! Feel free to add more

Also at Bio-IT World is a listing of 50 top life science firms (biased toward those with a Pro-IT stance)

Tuesday, August 08, 2006

Few papers that have come out recently that are of interest (some to be reviewed later)

A yeast-one-hybrid approach for mapping p-dna binding in vitro in elegans ( specied where chip/chip doesnt work)
A gene-centered C. elegans protein-DNA interaction network.
Cell 2006

This one talks about the stability of using arrays for classification
Reliable gene signatures for microarray classification: assessment of stability and performance.

Talks about designing drugs specifically toward protein-protein interactions
Rational drug design via intrinsically disordered protein. Trends in Biotechnology 2006

A direct comparison of protein interaction confidence assignment schemes. BMC Bioinformatics
Suthram S, Shlomi T, Ruppin E,Sharan R, Ideker T