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Windber, Strategic Medicine, Biobase, Integrated Genomics, Provid , Tripos, MIT, UCLA, Rosetta Biosoftware, Genedata, Thermo Fisher, Microsoft

Windber, Strategic Medicine, Biobase Collaborate on Clinical Data Analysis
Biobase, the Windber Research Institute, and Strategic Medicine „Ÿ a new firm created to commercialize technologies developed at the Windber Research Institute „Ÿ have entered a collaboration to analyze clinical breast cancer data, BioInform has learned.
Michael Liebman, executive director of the Windber Research Institute and managing director of Strategic Medicine, said that the project will focus on correlating the risk of disease co-occurrence with expression data. The goal, he said, is to identify biomarkers that will help physicians manage the treatment of breast cancer patients over the course of their lives.
Breast cancer is a chronic disease, Liebman noted, and often serves as a background for a range of other disorders that could be treated sooner if physicians can assess a patient’s likelihood for developing them. He added that the effort is an effort toward “personalized healthcare management” as opposed to “personalized medicine.”
Michael Tysiak, CEO and President of Biobase, told BioInform that the project will be the company’s first experience with clinical data. He said the company will primarily use its ExPlain gene expression analysis platform for the project, along with methods for promoter analysis and pathway analysis.

Integrated Genomics Sues Two Former Employees for Breaching Non-Compete Agreement
Integrated Genomics said this week that it has filed a lawsuit against two former employees for breach of non-competition and non-solicitation obligations under their employment contracts.
In the suit, IG claims that former director of bioinformatics Nikos Kyrpides, left the firm to join the US Department of Energy’s Joint Genome Institute and recruited other IG employees to accept positions at the JGI while he was still an IG employee.
In addition, the suit alleges that Kyrpides and Natala Ivanova, another IG employee who joined the JGI, developed a software product that competes with IG’s ERGO platform while at the JGI “in violation of their agreements not to engage in such activities.”
“This is not the option we wanted to pursue” said John Elling, president of IG, in a statement. “We have spent considerable time and resources for over a year trying to reach an amicable resolution to these issues.”
The suit was filed in the US District Court in Chicago, Illinois.

Provid May Lack Cash to Buy Tripos Discovery Research
Tripos said this week that a proposed deal to sell its Discovery Research branch to Provid Pharmaceuticals may fall through after Provid said it is unable to pull together the cash it needs to make the acquisition.
As a result, Tripos said it has begun talking with “other parties” that it said have shown interest in buying the DR business, although the company said it could not assure that another suitor could find the money either.
Tripos said in early January it intended to sell the research unit in a stock deal worth roughly $2 million as part of a liquidation plan. Tripos in November said it would sell its Discovery Informatics business to San Francisco-based Vector Capital for $26.5 million.
Tripos said this week that it is “doubtful” that Provid would be able to gather the necessary financing to complete the deal as planned but it would consider restructuring the terms of the deal to make it happen.

MIT’s CSBi Uses Star-P to Parallelize K-Means for Cell Image Analysis
Interactive Supercomputing said this week that researchers in the Massachusetts Institute of Technology’s Computational and Systems Biology Initiative are using its Star-P software to develop a parallel implementation of a cell image analysis program.
The agreement follows a similar project underway at the National Cancer Institute to parallelize an in-house array analysis program [BioInform 02023-07].
CSBi researchers have developed a desktop-based application based on K-means clustering to visualize and cluster cell images. They are currently using Star-P to develop a parallel version of the application that will run automatically on SGI Altix and Opteron-based parallel servers.
CSBi researchers are also “considering using Star-P for applications such as doing statistical analysis in preparation of cellular visualizations during high content imaging,” Interactive Computing said.

UCLA Cancer Center Licenses Rosetta's Resolver Software
Rosetta Biosoftware has licensed its Resolver software to the University of California, Los Angeles, the company said this week.
The university’s Jonsson Comprehensive Cancer Center will use the software to analyze gene expression data.

EU’s BaSysBio Project to Use Genedata’s Software
Genedata said this week that BaSysBio (Bacillus Systems Biology), a systems biology project involving 15 research organizations from nine European countries, will use its Phylosopher software as the “central management and infrastructure solution for sharing and interpreting the experimental data” generated within the consortium.
BaSysBio participants are studying the global regulation of gene transcription in Bacillus subtilis, a bacterium that is used in a wide range of industries to produce enzymes and metabolites. The project will also study two other bacteria, B. anthracis and Staphylococcus aureus.
The researchers will use Phylosopher to integrate and manage data from transcriptomics, proteomics, metabolomics, and cell-based assays.
BaSysBio was launched on Dec. 1, 2006, and is funded with €12 million ($15.8 million) from the European Union.

Thermo Fisher to Develop E-Lab Notebook on Microsoft .Net Platform
Thermo Fisher Scientific said this week that it is working with Microsoft to develop its upcoming Electronic Laboratory Notebook on the Microsoft platform.
Thermo, a member of Microsoft’s BioIT Alliance, said it has already built its Darwin LIMS on the Microsoft .Net platform and that it plans to use .Net 3.0 for the ELN system.

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The Scan

Pig Organ Transplants Considered

The Wall Street Journal reports that the US Food and Drug Administration may soon allow clinical trials that involve transplanting pig organs into humans.

'Poo-Bank' Proposal

Harvard Medical School researchers suggest people should bank stool samples when they are young to transplant when they later develop age-related diseases.

Spurred to Develop Again

New Scientist reports that researchers may have uncovered why about 60 percent of in vitro fertilization embryos stop developing.

Science Papers Examine Breast Milk Cell Populations, Cerebral Cortex Cellular Diversity, Micronesia Population History

In Science this week: unique cell populations found within breast milk, 100 transcriptionally distinct cell populations uncovered in the cerebral cortex, and more.