Skip to main content
Premium Trial:

Request an Annual Quote

Bioinformatics Briefs: Dec 3, 2001



The Pharmaceutical Research and Manufacturers of America Foundation has added a new Center of Excellence in Integration of Genomics and Informatics to its informatics awards program, which was announced earlier this year [BioInform 10-08-01].

The new center will be awarded $350,000 per year for up to three years, with a funding start date of July 1, 2002.

The center will address the increasingly complex and sophisticated technologies and skills required for computational exploitation of genome-related data. “The intent is to promote the close integration of computational approaches with the results of bench research, rather than novel informatics technology for its own sake,” according to a statement on the PhRMA Foundation’s website.

Candidate institutions must already have comprehensive ongoing research activities in genomics, as well as a capacity to provide training in both biological and computational sciences. Plans for effective interactions with industry are encouraged.

Detailed application information is available on the PhRMA Foundation website,



A request for proposal for a “Bioinformatics Integration Support Contract” has been issued by the NIH’s National Institute of Allergy and Infectious Diseases. The RFP, NIH-NIAID-DAIT-02-16, is available from the NIAID Contract Management Branch website: Further information is available from contracting officer Cyndie Cotter at 301-402-0641 or [email protected].



Hitachi has extended its distribution deal with DoubleTwist for an additional year.

The agreement extends a deal made last year when Tokyo-based Hitachi agreed to purchase licenses to DoubleTwist’s bioinformatics products with DoubleTwist granting the company exclusive rights to market and distribute the products in the Asia-Pacific region.

John Couch, CEO of DoubleTwist, told BioInform’s sister publication GenomeWeb that the deal gave DoubleTwist an upfront payment, though he would not divulge the exact amount. “It’s significant, it’s cash,” Couch said.


Gene Logic has obtained an exclusive commercial license to BioCarta’s signal transduction pathway information, which it intends to include in the next release of the GeneExpress software system.

About 150 of BioCarta’s collection of diagrams representing molecular and cellular signal transduction pathways will be available through GeneExpress, making it the sole commercial database product with this particular set of pathway models, according to Gene Logic.

BioCarta has agreed to update the pathway collections for Gene Logic and provide hundreds of additional charts in the future. Under BioCarta’s “Proteomic Pathway Project,” updates and additional pathway contributions are provided on an “open source” model, whereby an online community of researchers contributes to maintaining and improving pathway information collected on a public website.



Fujitsu is the latest company to jump on the XML bandwagon, endorsing LabBook’s BSML standard for communicating genomic information. Fujitsu of Tokyo joins the European Bioinformatics Institute, IBM, Bristol-Myers Squibb, John Wiley & Sons, Ohio Supercomputer Center, NetGenics, Celestar Lexico-Sciences, ApoCom Genomics, National Foundation for Cancer Research, and other BIO member companies in its support of the standard.

EBI, along with BioTools, Sun, and the Weizmann Institute, also supports the AGAVE XML standard for genomic information developed by DoubleTwist.

The BSML standard is freely available from



Cambridge, Mass.-based bioinformatics consulting firm 3rd Millennium has completed its custom bioinformatics system for Biogen, also of Cambridge.

As part of the project, 3rd Millennium designed a proprietary laboratory information management system to support the integration, workflow, and analysis requirements of Biogen’s core gene expression facility.

“We looked at the product alternatives available to us and found that none of them sufficiently addressed our critical requirements,” said Rainer Fuchs, Biogen’s senior director of research informatics, in a statement. “We are very pleased with the system they developed which, importantly, they delivered on time and on budget.”

Filed under

The Scan

Cell Signaling Pathway Identified as Metastasis Suppressor

A new study in Nature homes in on the STING pathway as a suppressor of metastasis in a mouse model of lung cancer.

Using Bees to Gain Insights into Urban Microbiomes

As bees buzz around, they pick up debris that provides insight into the metagenome of their surroundings, researchers report in Environmental Microbiome.

Age, Genetic Risk Tied to Blood Lipid Changes in New Study

A study appearing in JAMA Network Open suggests strategies to address high lipid levels should focus on individuals with high genetic risk and at specific ages.

Study Examines Insights Gained by Adjunct Trio RNA Sequencing in Complex Pediatric Disease Cases

Researchers in AJHG explore the diagnostic utility of adding parent-child RNA-seq to genome sequencing in dozens of families with complex, undiagnosed genetic disease.