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Tripos, Semantic Web, IBM, Scripps, Applied InSilico, Ariadne Genomics, KeyMolnet, Rosetta Resolver, NHLBI

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Pfizer Opts to End Tripos Collaboration; Informatics Business Not Affected

Tripos said last week that Pfizer will not renew a four-year file-enrichment collaboration that began in 2001.

Tripos received around $90 million over the project, in which it designed, synthesized, and purified a library of drug-like compounds for the pharmaceutical firm. The collaboration will end next month.

The wind-down of the agreement has had a negative affect on Tripos' revenues for the past two quarters. In October, John McAlister, president and CEO of Tripos, warned analysts that "there is no guarantee that we will continue to work with Pfizer" beyond 2005. [BioInform 10-31-05]

Last week, McAlister said in a statement that Tripos remains "committed to our Discovery Research business," but added that "a reorganization of Tripos Discovery Research may be necessary."

He said that the company will "carefully review staff levels to ensure we can continue to deliver the highest-quality service without impacting our existing and developing collaborations."

McAlister added that the company's discovery informatics business "is not impacted by the Pfizer file enrichment contract completion, and existing informatics contracts with Pfizer are unaffected."


W3C Launches Semantic Web for Life Sciences Interest Group

The World Wide Web Consortium said last week that it has launched a new group that will focus on applying semantic web technology to data-integration challenges in the health care and life science industries.

The group, called the Semantic Web for Health Care and Life Sciences Interest Group (HCLSIG), aims to deploy "standardized semantic web specifications into specific services defined by a user community," and marks the first such domain-centric initiative for the W3C.

"This new venture puts W3C specifications through the paces of a dynamic, multifaceted, and interdependent set of communities," said Tim Berners-Lee, director of the W3C, in a statement. "We have a remarkable opportunity to listen to the area experts, to see how our work meets their needs, and to serve their future requirements."

The W3C envisions the semantic web as the next generation of the current web, in which content will be embedded with semantic meaning that computers can recognize in order to automate linking across documents.

In the health care and life sciences domains, the W3C said it expects embedded semantics to provide researchers with "better access to the knowledge required to effectively find cures to diseases, make drugs safer and more affordable, and enable health-care providers to offer individualized clinical management to patients."

The HCLSIG will develop use cases that "demonstrate the value to business of adopting semantic web technology, core vocabularies and ontologies, guidelines and best practices for unique identifiers," the W3C said.

The group's charter runs through Sept. 30, 2007.


IBM, Scripps to Use World Community Grid for AIDS Drug Docking Study

IBM said today last week it is partnering with the Scripps Research Institute to find new AIDS therapies with the World Community Grid — an international community of 100,000 computer users who have donated cycle time on more then 170,000 PCs by registering at http://www.worldcommunitygrid.org.

The project, called [email protected], will be the second large-scale computational biology project to run on the so-called "virtual supercomputer." In the first, announced a year ago, IBM partnered with the Institute for Systems Biology, United Devices, and the University of Washington to predict the three-dimensional structure of 120,000 protein domains that could not be characterized using traditional approaches.

The goal of [email protected] is to design new therapeutic approaches to treat AIDS, which poses a considerable challenge because the HIV virus evolves rapidly to acquire new mutations that confer drug resistance.

"The computational challenges in approaching this problem are the vast number of possible mutations that may occur, and the huge number of possible chemical compounds that might be tested against them," said Arthur Olson of the Department of Molecular Biology at Scripps, in a statement.

Olson said that the World Community Grid project will run "millions upon millions" of docking computations to evaluate potential interactions between compounds and mutant viral proteins.


Applied InSilico to Provide Microarray Analysis Services for OGT

Oxford Gene Technology said last week that Applied InSilico will use its ELE (Evolutionary Learning Environment) software platform to analyze data generated from OGT's microarray technology and services.

As part of the agreement, the two companies will also collaborate on several projects "designed to deliver a range of new products and services for life science research."

Further details of the proposed projects were not provided, but Clive Briant, Applied InSilico's vice president of business development, said in a statement that both companies are "interested in the possibilities surrounding predictive diagnostics and creating intelligent medical devices."


Merck to Use Ariadne's MedScan Text-Mining Software

Ariadne Genomics said last week that Merck has taken a corporate-wide license for its MedScan natural language processing software.

MedScan extracts pathway-related information from the scientific literature and converts it into a database of protein functional relationships.

Financial details of the agreement were not provided.


FDA to Integrate IMMD's KeyMolnet with ArrayTrack

The Institute of Medicinal Molecular Design (IMMD), based in Tokyo, said last week that the US Food and Drug Administration has licensed its KeyMolnet pathway informatics platform.

The FDA will integrate KeyMolnet with its ArrayTrack system for reviewing pharmacogenomic data submissions, IMMD said.

KeyMolnet is a manually curated database of relationships among genes, molecules, diseases, pathways and drugs.

ArrayTrack, a microarray data-management system, was developed by the FDA's Center for Toxicoinformatics at the National Center for Toxicological Research.

The FDA has also integrated Ingenuity Pathway Analysis and PathArt from Jubilant Biosys into the system.


FGCZ Licenses Rosetta Resolver

Rosetta Biosoftware said last week that the Functional Genomics Center of Zurich (FGCZ) has licensed the Rosetta Resolver system.

The FGCZ will use Resolver to analyze and store cross-platform microarray data generated from hundreds of regional functional genomic projects.


NHLBI Sets Aside $24.3M RFA for Systems Biology Research

The National Heart, Lung, and Blood Institute last week issued a request for applications for collaborative research projects combining computational modeling and simulation approaches with experimental validation of model predictions to improve understanding of heart, lung, blood, and sleep disorders.

The NHLBI said it plans to award $24.3 million over the next five years to support nine new cluster grants, three in each of the next three years, focused on developing systems biology approaches to "explaining and predicting complex cellular and physiological phenomena of living organisms in terms of underlying physical and chemical processes and accompanying feedback regulations at molecular, cellular, tissue, or whole organ levels" in the context of heart, lung, blood, and sleep physiology and pathophysiology.

Examples of research topics that fall under this request include, but are not limited to: networks involved in regulating oxygen delivery, including regulation of hemoglobin levels though control of red cell production, changes in vascular tone, and regulation of distribution of blood flow in different vasculatures; electrical and structural simulations of the heart, including expression of ion channel genes, that predict occurrence of arrhythmias and responses to potential treatments; and the role of inflammation in the development of pulmonary, thrombotic, and cardiovascular diseases and responses to pharmacological intervention, targeting NSAID therapy.

Letters of intent are due by Feb. 8, 2006, with final applications due by March 10, according to the NHLBI. The RFA expires on March 11. Additional details about the funding opportunity can be found at http://grants.nih.gov/grants/guide/rfa-files/RFA-HL-06-004.html.

Filed under

The Scan

For Better Odds

Bloomberg reports that a child has been born following polygenic risk score screening as an embryo.

Booster Decision Expected

The New York Times reports the US Food and Drug Administration is expected to authorize a booster dose of the Pfizer-BioNTech SARS-CoV-2 vaccine this week for individuals over 65 or at high risk.

Snipping HIV Out

The Philadelphia Inquirer reports Temple University researchers are to test a gene-editing approach for treating HIV.

PLOS Papers on Cancer Risk Scores, Typhoid Fever in Colombia, Streptococcus Protection

In PLOS this week: application of cancer polygenic risk scores across ancestries, genetic diversity of typhoid fever-causing Salmonella, and more.