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March 5, 2009 | Critical Path Director Rachel Behrman Provides Update
FDA’s four-year-old Critical Path Initiative (CPI) may not be the transformational force many hoped, but it’s pushing forward steadily. In 2008 the congressional funding for CPI supported a total of 46 different Agency-wide research projects. Research ranges from efforts to develop new technologies for personalizing cancer treatment and therapies for Alzheimer's to improving FDA's ability to respond to emergency food contaminations. Behrman, Associate Commissioner for Clinical Programs and Director, Office of Critical Path Programs, provides a snapshot of progress in this interview. Read more.  

Ohio Supercomputer Center to Boost Bioscience Activity
The Ohio Supercomputer Center today announced the purchase of a $4 million expansion of its flagship supercomputing system that will more than double the Center’s current computing power and memory and significantly increase the Center’s computational capacity dedicated to Ohio’s bioscience and research efforts.

The expansion will integrate a new generation of IBM hardware into OSC’s IBM Cluster 1350. Expected to be fully operational by summer, the total expanded system will increase in computing capacity from 22 teraflops to 75 teraflops and more than double available memory, from 8.4 terabytes to 24 terabytes. The expansion will add 5,328 processing cores housed within 600 nodes; combined, there will be more than 9,500 processing cores. Qualified researchers interested in obtaining an OSC account to access the new system can visit:

“The Ohio Supercomputer Center has fostered close ties with the state’s bioscience research
community, especially within bioinformatics and biomedical sciences,” said Anthony Dennis,
president and CEO of BioOhio. An example of OSC’s partnerships includes work with Nationwide Children’s Research Institute on the innovative Virtual Microscopy to Microarray cancer identification project, which has garnered attention from national oncology groups, and OSC’s partnership with the Ohio State University Medical Center’s Department of Biomedical Informatics, working on its caGrid infrastructure. For more information. 

Stocks Dip for Most Tool Companies; Nine Buck the Trend
Stocks of most of the 38 firms that comprise the GenomeWeb Daily News Index fell during the month of February, mirroring a drop for the tech-heavy Nasdaq market, according a GenomeWeb report. “Only nine of the companies in the Index closed the month up compared to January's close. Orchid Cellmark gained around 30 percent to close at $.70, while other notable gainers included CombiMatrix (+15 percent), Illumina (+15 percent), and Life Technologies (+14 percent)” Illumina also reported a 43 percent increase in fourth-quarter revenues. Read GenomeWeb report.

Genstruct, Gene Logic Strike Tox Collaboration
As part of the collaboration Gene Logic (an Ocimum Biosolutions company) will provide extensive toxicology databases and data on specific compounds. Genstruct will apply its Causal Network Modeling platform for systems biology to create network models that fully capture the toxicity potential of any compound.

“In Genstruct’s work with pharmaceutical clients, we have characterized complex and poorly understood mechanisms of toxicity such as idiosyncratic drug-induced liver injury and hemangiosarcoma,” said Keith Elliston, president and CEO, Genstruct, in a release. “We can now evaluate a new compound's potential to elicit these types of reactions in man based on data from simple animal studies. Partnering with a highly regarded data provider like Gene Logic, we can now offer pharmaceutical clients of both companies tremendous additional value in toxicity evaluation.” Elliston was the CSO of Gene Logic in its early days.

Gene Logic CEO Anuradha Acharya noted, “As the global pharma landscape is changing, collaborations which create integrated solutions for our customers give us an edge. This strategic partnership will be pivotal in providing integrated solutions spanning across different stages of the discovery value chain to our valuable customers.” Genstruct and Gene Logic will participate in co-marketing initiatives to extend each other’s offerings to current and potential clients. The two companies say they intend to collaborate in other areas, including personalized or individualized oncology therapy. Read release.

Science 2.0 or Science Without Borders 
India’s Department of Science and Technology (DST) has devised a plan to tackle lack of adequate research into drugs for key diseases amounts to just that, according to an article in the Business Standard.

“Drugs and diseases are split into haves and have-nots when it comes to attracting funds for research. So, while 399 drugs for treating cancer are under development and a total of 136 drugs are being developed for cardio-vascular conditions, only six drugs have been developed for tuberculosis (TB), which affects a third of the global population. And all of these six drugs were discovered in 50s and 60s. The reason for this is that a poor man’s disease fetches little money and a TB drug with a $300-million market does not lure drug companies, which won’t invest anything in a market that is worth less than a billion dollars, say scientists.

“So, the DST’s Council of Scientific and Industrial Research (CSIR) is resorting to open source drug research for TB through its Open Source Drug Discovery (OSDD) Project. It has created a web-based platform that taps scientists, students and researchers across the world, creating a global laboratory that is as fenceless as a paddy field, as its mentor, Dr Samir Brahmachari, director-general of CSIR and former director of Institute of Genomics and Integrative Biology (IGIB), puts it.” Read article.

GenoLogics Completes $5M Financing 
The latest round of financing was led by OVP Venture Partners of Seattle with support from Growth Works and Yaletown Venture Partners of Vancouver. The funds will be used to accelerate development and global deployment of an end-to-end informatics solution for organizations pursuing translational research initiatives.
“We feel positive that the growth GenoLogics has experienced will continue as they expand their footprint in the life sciences software market,” said Chad Waite, Managing Director at OVP Venture Partners. “We’ve already seen GenoLogics make significant inroads by establishing collaborative partnerships with leading organizations that are looking for ways to achieve their translational research outcomes.”
Last year GenoLogics announced a new product suite for biorepositories and biomedical informatics to help customers better manage their clinical information. GenoLogics has developed this product suite in collaboration with the Fred Hutchinson Cancer Center, Windber Research Institute and the University of Texas Medical Branch. When the biomedical products are deployed in combination with the GenoLogics’ research informatics solutions, clients have a comprehensive bench-to-bedside informatics platform to enable their translational research initiatives. Read release.
Gilman Joins GNS Board
Gene Network Sciences named Michael Gilman, founder and CEO of Stromedix, Inc. and former EVP of research at Biogen Idec, to its Board of Directors. Read release. 

Genedata Expands Syngenta Collaboration
Syngenta has added the Genedata Expressionist Refiner MS module for LC-MS and GC-MS metabolomic raw data processing and analysis to their existing Genedata Expressionist system. Refiner MS expands Expressionist to process and analyze metabolomic raw MS data separately and in conjunction with microarray data, which Genedata says dramatically improves efficiency and enhances the biomarker discovery process at Syngenta.

“Syngenta’s decision to use the Genedata Expressionist system for our metabolomics research is based on the ability of Refiner MS to capture very large data sets directly from a wide range of instruments quickly and efficiently and to visualize and manipulate data from a wide variety of mass spectrometry experiment,” said David Portwood, Head of Metabolomics, Syngenta, in a release. Read more.

IO Informatics Adds to its PM Working Group
Joining the group are Kathy Gibson (Helios Consulting), Uwe Christians (University of Colorado and Eurofins Medinet Denver), Herb Fritsche (MD Anderson) and Dan Crowther (Wyeth). More information.

BI Licenses Genomatix Next Gen Analysis Tools
Boehringer Ingelheim has installed a Genomatix Mining Station (GMS) and a Genomatix Genome Analyzer (GGA) at its Pharma Research Center in Biberach, Germany. GMS and GGA combine built high performance hardware and terabytes of proprietary databases and software technology. Read release.

Biodesix Chooses Sapio LIMS
Sapio Sciences reports Biodesix has selected Sapio Sciences’ Exemplar LIMS as its Laboratory Information Management Solution (LIMS).More information. 

New Computational Method for Predicting PTMs
Daniel Schwartz and coworkers in George Church's laboratory at Harvard Medical School report developing a novel computational approach to predicting post-translational modifications (PTM) which cannot ordinarily be identified by mass spec methods. Their paper appears in Molecular & Cellular Proteomics, where the authors report they were able to identify novel phosphorylation and acetylation sites across several organisms. Read article in ProteoMonitor or the paper. 

This article first appeared in Bio-IT World’s Predictive Biomedicine newsletter. Click here for a free subscription. 

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