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Microsoft Research, Linguamatics, GeneGo, Ingenuity, Definiens, Genostar

Microsoft Research Awards More than $850K to GWAS Software Development Projects
Microsoft Research this week said it has awarded more than $850,000 to six research projects under its “Computational Challenges of Genome Wide Association Studies" program, an initiative that it launched last July [BioInform 07-20-07].
The six projects were selected from 40 proposals submitted from 39 academic institutions worldwide. The goal of the program is to encourage “the development of computer-science solutions to improve data access, standardization, visualization, and tools to help scientists study the human genome,” Kristin Tolle, program manager for biomedical computing on the External Research & Programs team at Microsoft Research, said in a statement.
Funded projects include:
  • "PGRx: An Interactive Software System for Integrating Clinical Genotyping with Prescription Drug Safety Assurance," led by Michael Kane and John Springer at Purdue University. The project aims to develop a software system to predict and prevent adverse drug responses, and to provide training for physicians and pharmacists to better understand pharmacogenomics.
  • "A Universal Data Format for Genotype Microarrays," led by John Pearson at the Translational Genomics Research Institute. Pearson plans to develop a data format that would “accommodate multiple vendor platforms into a single file and software library.”
  • "Genome Wide Association Study of Amyotrophic Lateral Sclerosis in Finland," led by Bryan Traynor at the National Institutes of Health and Johns Hopkins Hospital. The goal of this project is to discover genes that are relevant to the development of ALS by studying 489 Finnish ALS cases.
  • "Pathway-Based Association: A New Paradigm for Genome Wide Association Studies," led by Trey Ideker and Richard Karp in the Department of Bioengineering at the University of California, San Diego. Ideker and Karp plan to develop computational tools “that help explain linkages between signaling, regulatory, and metabolic pathways to the genes that are associated with a disorder.”
  • "Phenotypic Pipeline for Genome-wide Association Studies," led by George Hripcsak of Columbia University. This project aims to develop informatics methods to convert raw health records data into “usable research information.”
  • "Data Quality Management for Model Improvement in GWAS," led by Raul Ruggia and Hugo Naya of the University of the Republic of Uruguay, the Pasteur Institute University of the Republic of Uruguay, and the Pasteur Institute at Montevideo. The goal of the project is to develop a data-quality management environment that will allow users to define and evaluate “biological-oriented data-quality properties.”

Pfizer to use Linguamatics Text-Mining Software in New Biotherapeutics and Bioinnovation Center
Text-mining software provider Linguamatics said this week that it has extended an existing collaboration with Pfizer.
Under the terms of the extended agreement, Pfizer will use the software within its Biotherapeutics and Bioinnovation Center, a new “entrepreneurial” R&D center that the company created last fall with the goal of advancing translational research via internal development as well as in-licensing and incubating new technologies and research tools.
Financial details of the agreement were not disclosed.
David de Graaf, director of systems biology at Pfizer, said in a statement that the company was previously using I2E “for focused knowledge discovery from large document collections in a variety of R&D applications.”
Under the extended agreement, he said, Pfizer is using the platform “to inform research decisions” within the Biotherapeutics and Bioinnovation Center as well as in other areas of the company’s business.

Scripps Institute Joins GeneGo's Cardiac Pathways Group
GeneGo said this week that the Scripps Translational Science Institute has become the first member of a consortium that the company is building to develop a systems biology software and database platform for cardiovascular diseases.
The company plans to add other members from the pharmaceutical and academic communities to the MetaMiner Cardiac Consortium. The members of the consortium will have a say in what cardiac-specific ontologies and pathway maps the company will incorporate into the MetaMiner product.
Scripps and any future consortium members, in return, will have free access to the product GeneGo develops. The company plans to commercialize product six to 12 months after the consortium members have access to it, Julie Bryant, GeneGo’s VP of business development and marketing, told BioInform sister publication GenomeWeb Daily News.
Cardiac Consortium memberships last for three years, and the company should be ready to release a MetaMiner Cardiac product within one to two years, Bryant said.

Pfizer to Use Ingenuity's Pathway Software in Rx Programs
Ingenuity Systems said this week that Pfizer will use its pathway informatics software under a multi-year, enterprise-wide licensing agreement.
Under the agreement, Pfizer will integrate the Ingenuity Pathway Analysis software and related content from Ingenuity’s biological and chemical knowledgebase with other informatics solutions that Pfizer uses throughout its organization, Ingenuity said.
Ingenuity CEO Jake Leschly said in a statement that the company also has tailored “a suite of powerful capabilities” specifically for Pfizer.
Financial terms of the agreement were not released.

Servier To Use Definiens Software at Two R&D Sites
Definiens said this week that French pharmaceutical firm Servier plans to use its image-analysis software in its discovery research facilities in Suresnes and Croissy-sur-Seine.
Servier is using the company’s Enterprise Image Intelligence software to automate its molecular pathology analysis.
Financial terms of the agreement were not provided.

Merial To Use Genostar's Metabolic Pathway Software
Bioinformatics developer Genostar said this week that animal health company Merial has purchased its data mining and analysis software.
Genostar said Merial will use its IOGMA 3.4 Metabolic Pathway Builder software for use in its studies of pathogens focused on viral, bacterial, and parasitic diseases in domestic and wild animals.
The company said the software includes three modules: GenoAnnot, ProteoAnnot, and PathwayExplorer. These are used together to analyze high-throughput bacterial omics data.
The platform also includes the microB database, which includes omics information sourced and standardized from a number of reference databases on over 450 microbial organisms.
The software also comes in a client-server version that allows collaborations using the same data, Genostar added.

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