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Accelrys, Genedata, QBioCom, CASP6, Molecular Connections, HPC Benchmarks, Institute for Bioinformatics, Iconix, Optive, Daylight, Strand Genomics, European Bioinformatics Institute, 3DGenome


Accelrys Gains Exclusive Rights to Commercialize BU’s ZDock and RDock

Accelrys last week said that it had signed an exclusive agreement with Boston University to distribute the ZDock and RDock protein-protein interaction algorithms developed by BU’s Zhiping Weng.

Accelrys has exclusive rights to market the software to the commercial market, while BU retains rights to use the software in academic collaborations, according to an Accelrys spokesman.

The software will be available as part of the Insight II molecular modeling suite, and also as standalone packages, in about six months, the spokesman said.

Genedata Signs Co-Marketing Deal with MWG Biotech ...

Genedata and MWG Biotech have agreed to jointly market MWG’s experimental services and Genedata’s data analysis capabilities, the companies said last week.

Under the terms of the agreement, MWG said it will integrate data from sequencing, microarray-, or siRNA-based projects into Genedata’s Phylosopher analysis platform so that Genedata can offer “extended biological analysis of the generated data.”

... And Licenses Software to Degussa

Genedata said last week that Degussa’s Feed Additives Business Unit in Dusseldorf, Germany, had licensed “tailored editions” of its Expressionist and Phylosopher software packages to support its metabolic engineering R&D process.

Financial terms of the agreement were not provided.

EPO to Use QBioCom’s MPSRCH for Patent Sequence Searching

QBioCom said last week that the European Patent Office had licensed its MPSRCH sequence search software for analyzing biological sequences that are included within patent applications.

MPSRCH, an accelerated version of the Smith-Waterman algorithm, was originally developed by Aneda (formerly Edinburgh Biocomputing Systems), which QBioCom acquired last year. The company claims that MPSRCH can reach speeds “comparable” to heuristic methods like Blast, but with increased reliability. It runs on both Intel and Alpha platforms under Linux and Tru64.

The deal marks the EPO’s second major bioinformatics purchase this year. In February, the EPO licensed another sequence search software tool — GenomeQuest — from Gene-IT [BioInform 02-09-04].

CASP6 Organizers Seeking Targets

Organizers for the Sixth Critical Assessment of Techniques for Protein Structure Prediction (CASP6), to be held Dec. 4-8 in Gaeta, Italy, are seeking assistance in lining up an “adequate supply” of targets for the structure prediction experiment.

A recent message on the CASP6 listserv urged prediction groups to approach “at least one” experimentalist, “and make a direct, strong, personal plea that they provide a target, explaining why it is important.” The organizers are looking for details of structures that protein crystallographers and NMR spectroscopists expect to have solved before Sept. 1.

Information about target submission and release and the submission form are at

Molecular Connections Licenses NetPro to UCLA

Molecular Connections said last week that it has licensed its NetPro curated database of protein interactions to the DOE Institute for Genomics and Proteomics at the University of California, Los Angeles.

Financial terms of the licensing agreement were not disclosed.

First Results of New HPC Benchmarks Released: Cray Comes out on Top

The first results of a new set of benchmarking guidelines are in, and a 252-processor Cray X1 supercomputer at Oak Ridge National Laboratory had the highest overall test scores of any other participating system, as of June 10.

The new set of tests, called the HPC Challenge benchmark suite, was co-sponsored by the Defense Advanced Research Project Agency’s HPCS (High Productivity Computing Systems) program, the US Department of Energy, and the National Science Foundation. It was introduced at the SC2003 conference last November as a means to test multiple attributes that can contribute to the performance of HPC systems.

The suite of tests includes the Linpack benchmark, the processor performance test that is the basis for the semi-annual Top500 supercomputer ranking, in addition to six additional tests that asses the processors as well as the memory system and the interconnect.

In a statement, Jack Dongarra, a professor of computer science at the University of Tennessee and one of the organizers of the Top500 supercomputing list, called the new benchmarks “a better indicator of how an HPC system will perform across a spectrum of real-world applications.” Thomas Zacharia, ORNL’s associate director for computing and computational sciences, said “We look forward to widespread adoption of this new measurement tool by the global HPC community.”

Results for all participating systems are available at

Bioinformatics Center Planned for Northeast England

The UK’s Department for Trade and Industry and One NorthEast, a regional economic development organization, last week announced a £3.8 million ($4.6 million) funding package to establish the Institute for Bioinformatics in Northeast England.

The regional consortium will include the University of Dunham, the University of Sunderland, the University of Newcastle, the University of Teesside, Northumbria University, and Newcastle-based bioinformatics firm Nonlinear Dynamics. It is expected to create up to 20 new graduate-level jobs in its first phase, according to One NorthEast.

Taisho Pharma to Use Iconix Chemogenomics Database

Iconix Pharmaceuticals said last week that Taisho Pharmaceutical will use its DrugMatrix chemogenomics reference database and informatics system in its lead selection and optimization activities.

Under the terms of the agreement, Iconix said it will perform a preliminary chemogenomics profiling and analytical study for a compound in Taisho’s drug discovery pipeline using its Drug Signature library of predictive biomarkers. In addition, Taisho will “explore” integrating the company’s in vivo and in vitro chemogenomics technology into its drug discovery efforts.

Optive, Daylight Pledge to Integrate Computational Chemistry Tools

Optive Research and Daylight Chemical Information Systems said last week that they have entered into a strategic partnership to integrate their cheminformatics platforms “in response to customer requests.”

Under the terms of the partnership, Optive will ensure that its Discovery Engine and Benchware software products for computer-assisted drug discovery are interoperable with Daylight’s DayCart chemical information management system and related toolkits.

Daylight is now a strategic partner in Optive’s alliances program and DayCart will become a supported chemical information database platform for Optive’s suite of discovery informatics products.

The first integrated product available as a result of the collaboration is Optive’s DiverseSolutions software package, which now uses the Daylight Fingerprint Toolkit to offer chemical fingerprint-based functionality.

Strand Signs Hitachi Software Engineering as Japanese Distributor

Strand Genomics has entered into a distribution agreement with Hitachi Software Engineering for its Avadis microarray analysis software package, the company said last week.

Last month, Strand signed on UBI as its distributor in Canada, and said it was “close” to signing a Japanese distribution deal [BioInform 05-31-04].

The company has distributors in Singapore, Malaysia, the UK, France, Germany, Switzerland, Austria, the US, Canada, China, Hong Kong, Thailand, Indonesia, and the Philippines.

EC Funds Bioinformatics PhD Fellowships at EBI

The European Commission is supporting a limited number of PhD studentships at the European Bioinformatics Institute under the EU’s Marie Curie Training Sites Fellowship program, EBI said last week.

Fellows will receive a subsistence allowance of €1,200 ($1,450) per month, and the program will reimburse travel expenses between the applicant’s present country of activity and EBI.

The application deadline for the program is July 30.

EU Awards €2.2M for 3D DNA Map Project

The European Union has awarded €2.2 million ($2.7 million) to a group of seven academic institutions who plan to create a three-dimensional map of DNA.

The project, called 3DGenome, is coordinated by Roel van Driel of the Swammerdam Institute for Life Sciences of the University of Amsterdam in the Netherlands. The researchers will use microscopic techniques and data analysis software to create the 3D map, which will then be related to gene regulation patterns, according to the project organizers.

The funds have been awarded under the four-year EU Sixth Framework program, which has a total budget of €17.5 billion, with €2.3 billion earmarked for life sciences.


Filed under

The Scan

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.

Circulating Tumor DNA Linked to Post-Treatment Relapse in Breast Cancer

Post-treatment detection of circulating tumor DNA may identify breast cancer patients who are more likely to relapse, a new JCO Precision Oncology study finds.

Genetics Influence Level of Depression Tied to Trauma Exposure, Study Finds

Researchers examine the interplay of trauma, genetics, and major depressive disorder in JAMA Psychiatry.

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.