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W3C, Eidogen-Sertanty, Rosetta Biosoftware, Incogen, NCGR, Tripos, Ariadne, ABI


GeneGo Readies MetaCore 3.0 Release for End of Month

GeneGo will release the next version of its MetaCore pathway informatics system at the end of September, a company official told BioInform last week.

Julie Bryant, vice president of business development and sales at GeneGo, said that the company will launch the new version, MetaCore 3.0, at the end of the month.

The release will include 5,000 new metabolites, and a total of 400 metabolic maps, as well as a number of features that Bryant claimed are not available in other pathway informatics platforms, such as the ability to import and visualize user-generated metabolomics data from a range of mass spec instruments.

In addition, the new release will enable users to integrate metabolic and signaling networks. Bryant said that GeneGo curators addressed this challenge by replacing EC numbers in the scientific literature with the proteins that are most significant for each reaction. This work led to 84 new metabolic maps that the company released in March. The company has since added this information to its central database, which enables it to merge metabolic and signaling networks "on the fly," Bryant said.

MetaCore 3.0 will also include more than 10 network-building algorithms "because each researcher asks different questions," Bryant said.

W3C Seeks Comments on Initial Draft of SWLS Charter

The Worldwide Web Consortium's Semantic Web for Life Sciences working group has drafted an initial version of a charter for a proposed "Semantic Web for Healthcare and Life Sciences Interest Group" (HCLSIG), which will work under the umbrella of the W3C.

The draft, available at, states that the HCLSIG will "develop and support the use of Semantic Web technologies to improve collaboration, research and development, and innovation adoption in the of healthcare and life science domains," and will be chartered for eighteen months, beginning this month.

Specific work areas outlined in the charter include the development of core vocabularies, the identification of guidelines and best practices for resource identification, and the provision of guidelines for scientific and scholarly publication.

The working group is seeking comments from the life science informatics community on the charter.

Eidogen-Sertanty Expands Agreement with CTC, Licenses Database to Medisyn

Eidogen-Sertanty said in August that it has expanded its existing distribution agreement with CTC Laboratory Systems of Tokyo to include its full suite of informatics products.

Eidogen-Sertanty announced separately that it has licensed its Kinase Knowledgebase to Medisyn Technologies, an early-stage drug discovery company.

The Kinase Knowledgebase includes more than 160,000 structure-activity relationship data points and more than 390,000 kinase compounds mined from scientific literature and patents.

FDA Evaluates Rosetta Resolver for VGDS Program

Rosetta Biosoftware said last month that the US Food and Drug Administration's Center for Drug Evaluation and Research will evaluate its Rosetta Resolver gene-expression data management and analysis system.

CDER is evaluating the system for use as part of its Voluntary Genomics Data Submissions (VGDS) program, Rosetta said. CDER will use the system "to better understand, learn from, and reproduce analyses conducted by pharmaceutical companies who voluntarily submit genomics data," Rosetta said in a statement.

Iowa State Receives $3M Grant for Bioinformatics Education

The National Science Foundation has awarded Iowa State University a five-year, $3 million grant for graduate studies in computational molecular biology, the university said in August.

The grant was awarded to a faculty team led by Daniel Voytas, professor of genetics development and cell biology. It continues a $2.6 million education grant awarded in 1999, which helped launch the university's computational biology program.

More than 80 faculty currently conduct bioinformatics, computational biology, and biological statistics research at ISU, said Robert Jernigan, director of the Laurence H. Baker Center for Bioinformatics and Biological Statistics, in a statement.

Incogen Awarded $500K SBIR, Inks Co-Marketing Deal with Apple

Incogen said last month that it has received a $500,000 Phase II Small Business Innovation Research grant from the National Science Foundation to create an educational version of its VIBE bioinformatics analysis workflow platform.

The new software, called VIBE Education Edition, or VIBE-Ed, will be co-marketed with Apple Computer, the company said. A beta version of the software is expected to be ready by the end of the year.

The grant is a follow-on to a Phase I SBIR award the company received in 2004. During the Phase I project, VIBE was evaluated in university classrooms and compared with current methods of bioinformatics education. "The Phase I project made it clear that there is a tremendous need for more sophisticated tools to adequately train the next generation of bioinformaticists," said Maciek Sasinowski, Incogen's CEO, in a statement.

USDA-ARS Awards NCGR More than $1M for Legume Informatics Development

The National Center for Genome Resources has been awarded two grants worth more than $1 million from the United States Department of Agriculture's Agricultural Research Service to develop informatics systems for legume research.

USDA-ARS awarded NCGR and its partners $790,000 to continue the development of its existing Legume Information System (LIS), and $225,000 to develop a new Legume Information Network (LIN).

NCGR said that LIS currently supports research at around 125 distributed legume research labs. The new funding will allow expansion of LIS to integrate experimental genomic and genetic information from all legumes, and the development of new interfaces.

NCGR will collaborate with USDA-ARS at Ames Iowa and the Center for Computational Genomics and Bioinformatics at the University of Minnesota to develop the Legume Information Network, which will integrate distributed legume information resources.

Legume crops, such as beans, soybeans and peanuts, contribute more than $30 billion annually to US agricultural productivity and are grown on more than 75 million acres in the US, NCGR said.

The LIN will be based on emerging middleware technology platforms such as BioMOBY, and will also provide mechanisms for other information resource providers to join the network.

BII to Modify Pattern-Recognition Software for Protein Biomarker Discovery

The Biosystems Informatics Institute and its commercial trading arm, Turbinia, said in August that they have secured exclusive rights to pattern-recognition software from Pattern Expert, a software firm based in Borsdorf, Germany.

BII plans to modify the software for the discovery and validation of protein biomarkers.

To date, the Pattern Expert software has been used by the German police force during forensic analysis of hit-and-run accidents. BII and Turbinia said that they have applied this same discovery engine as a biomarker software tool to improve the quality of mass spectrometry data.

The product will be "market ready" at the end of September, said Ian Humphrey-Smith, CEO of BII, in a statement.

Tripos, CambridgeSoft to Integrate Software

Tripos and CambridgeSoft have agreed to integrate Tripos' Benchware suite of laboratory informatics products and CambridgeSoft's ChemOffice application suite, including the ChemDraw chemical-sketching tool, the companies said last month.

Under the terms of the agreement, CambridgeSoft will provide Tripos with support and development licenses of its ChemOffice suite. CambridgeSoft has also joined the Tripos Alliance Program as a software and content partner.

Tripos said that it would feature ChemDraw as a "preferred" chemical rendering tool for Benchware.

RTI International Wins Two NCI Bioinformatics Contracts Worth $5.6M

RTI International's Partnerships for Genomics and Molecular Epidemiology group has won two bioinformatics contracts from the National Cancer Institute worth a total of $5.6 million, the Research Triangle Park, NC-based organization said last month.

Under a four-year, $4.3 million contract, RTI will provide bioinformatics support for the NCI's Breast and Colon Cancer Family Registries. RTI will manage the informatics support center, which facilitates data and sample collection from more than 20,000 cancer patients and family members. RTI will also help researchers design studies and analyze data. Research partners in this project include Alpha Gamma Technologies and Duke University.

Under a three-year, $1.3 million contract, RTI will support the management of several bioinformatics projects under the NCI's Center for Bioinformatics. Specifically, RTI will help with a proteomics biomarker discovery project, a multi-center trial called I-SPY, and the Cancer Biomedical Informatics Grid, caBIG.

Simulations Plus Acquires Assets of Sage Informatics

Simulations Plus has acquired the assets of chemistry software firm Sage Informatics of Santa Fe, NM.

Financial details of the acquisition were not disclosed.

Sage Informatics markets the ChemTK series of computational chemistry software.

The president of Sage Informatics, David Miller, will join Simulations Plus on Oct. 1 as senior scientist and product manager for the ChemTK product line.

Strand Genomics Changes Name to Strand Life Sciences

Strand Genomics said on Sept. 1 that it has changed its name to Strand Life Sciences, effective immediately.

"The change in corporate identity reflects the expanding focus of the company. Our portfolio of products now extends beyond functional genomics into computational chemistry," said Vijay Chandru, CEO and chairman of Strand Life Sciences.

Synamatix Licenses Bioinformatics Service to Beatson Institute via MGRC

Synamatix said last week that its Kuala Lumpur-based Malaysian Genomics Resource Center has licensed online bioinformatics services based on Synamatix technology to UK-based Beatson Institute for Cancer Research.

All MGRC applications are based on Synamatix's SynaSuite bioinformatics tools and are built on the company's core IP, SynaBase, a structured network database for storing biological data.

The MGRC service will be used to support cancer research being led by Keith Vass, head of bioinformatics at the Beatson Institute, the company said.

Financial terms of the deal were not disclosed.

Bioalma Licenses Text-Mining Tool to EMBL

Bioalma has licensed its almaKnowledgeServer biological text-mining and data storage software to the European Molecular Biology Laboratory, the company said last week.

In addition, Bioalma and EMBL will jointly tailor the software to the specific needs of EMBL, Bioalma said.

The almaKnowledgeServer uses text mining to annotate and detect biological entities in documents, and stores the annotated documents in a biological knowledge base.

Financial details were not disclosed.

Bayer Licenses Ariadne's MedScan

Ariadne Genomics said last week that Bayer HealthCare has licensed its MedScan text-mining suite for the development of an internal molecular interaction database.

MedScan uses natural language processing technology to extract pathway-related facts from the scientific literature.

Financial terms of the agreement were not disclosed.

"Bayer HealthCare recognizes the importance of using pathway analysis tools for interpretation of experimental results and hypotheses validation. But to make these tools truly efficient, we need an internal integrated database of pathways and molecular networks, containing all most recent information", said Michael Seewald, a bioinformatician at Bayer HealthCare, in a statement.

ABI Developing New Protein Identification Software

Researchers at Applied Biosystems are developing a new protein identification software called ProGroup that could result in a 20 to 50 percent increase in protein identification from mass spectra, according to ABI researcher Sean Seymour.

Seymour, who gave a presentation on the new software at the Seventh International Symposium on Mass Spectrometry in the Health and Life Sciences in August, said that ProGroup focuses on the inference of protein identifications from peptide identifications, rather than on peptide scoring.

"Most of the heavy algorithm work in conventional protein identification software goes into scoring peptides," said Seymour. "But there's a limit to better scoring functions, because not all peptides fragment well. What we've done is focus on the protein inference problem. ProGroup takes a different approach to protein identification."

Seymour said the ProGroup software is currently in the research stage, and he does not know when it might be released.

Filed under

The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.