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Systems Biology Roundup


By John Russell

March 1, 2008 | Naama Barkai of the Weizman Institute of Science in Rehovot, Israel, has won the first FEBS/EMBO Women in Science Award. She is being recognized for her work in mathematical modeling of biological systems, in particular around the design and function of biological networks. It’s more evidence that systems biology is becoming an accepted part of the lexicon of modern life science research.

The FEBS/EMBO Women in Science Award is a joint initiative of European Molecular Biology Organization and the Federation of European Biochemical Societies intended to honor distinguished women researchers in life sciences. Barkai will be presented the award and a prize of 10,000 euros at the 2008 FEBS Congress in Athens, Greece, where she will deliver a special plenary lecture.

Barkai’s credentials are impressive. She is an associate professor at the departments of Molecular Genetics and Physics of Complex Systems at the Weizmann. She was visiting professor at Harvard University (2005-2006) and a Robert H. Dicke Fellow at Princeton University where she worked with Stanislas Leibler on the theoretical analysis of biochemical networks. She received her Ph.D. in Physics at the Hebrew University (1995) for research on statistical mechanisms of learning. Congratulations.

Optimata’s Short List
Moving from academia to commercial systems biology, biosimulation specialist Optimata and pathway tool provider GeneGo each had important developments this month.

Optimata, which recently shifted its business emphasis (See Optimata: Eyes on the Prize, Bio•IT World, October 2007) from research collaboration to oncology drug repositioning, arranged for $1.5 million in new financing to help drive its new business model.

“After closely examining more than 100 drug candidates, we have short-listed several that we believe have good prospects for repurposing and renewed clinical development,” says Guy Malchi, Optimata’s CEO, “We plan in the next few months to make a final selection of one or two compounds and then to use our technology to significantly improve the compounds’ safety and efficacy profiles.”

The cash infusion will also fund an upgrade to Optimata’s computational infrastructure including, says Malchi, “installation of a distributed computing farm hosting multiple computer engines based on Intel Quad cores which provides best CPU/$ ratio. The computing farm will have the capability to grow modularly. The existing SW platform that already supports distributed simulation and optimization will be enhanced to allow for increased flexibility and more automation.”

Optimata is one of many companies betting on repositioning previously shelved compounds. So far no one has hit the jackpot.

Disease-Specific Analysis
Bio-simulation providers like Optimata have long targeted specific diseases. Optimata targets cancer. Entelos, another bio-simulation specialist, has several PhysioLabs for specific diseases. For example, Entelos recently announced that UCB Pharma would use its Rheumatoid Arthritis PhysioLab, which is a predictive computer model that simulates arthritic patients and drug effects.

But pathway tool providers have delved less deeply into individual diseases. Now, after close collaboration with the Cystic Fibrosis Foundation Therapeutics (CFFT), GeneGo has launched MetaMiner CF, a disease-specific tool embedded in GeneGo’s MetaCore pathway database and analysis platform. The new tool contains rich information about cystic fibrosis and represents an important expansion by GeneGo into disease-specific areas.

“[T]he information is current and based upon the latest understanding of disease mechanism. For instance, there has been a shift in the understanding of how TLR4 receptors in lung epithelium are involved in generating an inflammatory response to bacteria,” says Jerry Wright, a project collaborator and researcher at Johns Hopkins Medical Institutions Department of Physiology. “Five or ten years from now it would be generally accepted but would be difficult to pick out by a non-expert from current literature. This knowledge is reflected in the GeneGo maps connections and the information on record justifying why this connection exists and why it disagrees with previously published studies.”

At the beginning of the CF collaboration last summer, Bryant noted it would be “the first in the series of disease-centered Meta-Miner projects.” That the project was able to be completed so quickly bodes well for future disease-centered efforts. Stay tuned.

 

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 This article appeared in Bio-IT World Magazine.
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