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Entelos, Pfizer, Organon, Ingenuity, SAS, Compendia, Mitrionics, NIAID, Genencor, Biosoft, PamGene, GenoLogics, DSM, Ludesi, Chugai, Genedata

Entelos Extends Agreements with Pfizer, Organon
Entelos said this week in separate announcements that it has extended collaborations with Pfizer and Organon.
Pfizer has agreed to continue using the Entelos Cardiovascular PhysioLab platform, which the companies built under a collaboration.
Additional details of the agreement were not provided.
Meanwhile, Organon, a business unit of Akzo Nobel, has signed a two-year extension of the companies’ ongoing rheumatoid arthritis collaboration.
“The collaboration with Entelos has generated candidate targets and biomarkers which will be pursued under the extension of our collaboration”, said David Nicholson, executive vice president of R&D at Organon, in a statement.
Organon and Entelos have collaborated since 2001 to develop the Entelos Rheumatoid Arthritis PhysioLab platform, a large-scale, mathematical model that includes more than 700 biological functions or pathways.

Ingenuity Signs Integration Agreements with SAS, Compendia
Ingenuity Systems said this week that it will integrate its Ingenuity Pathway Analysis software with the JMP Genomics software from SAS and the Oncomine cancer gene expression database.
The agreement with SAS will enable users to upload the results of JMP Genomics analysis directly into IPA for interpretation within the context of biological pathways.
JMP is a business unit of SAS. JMP Genomics includes statistical analysis capabilities from the SAS and JMP platforms with additional analytical features for large genetics, microarray, and spectral data sets.
The Compendia agreement, announced separately, is expected to help researchers discover and validate biomarkers for cancer by mapping gene expression data to biological pathways.

Mitrionics Begins Development of FPGA-Accelerated BlastP for FPGA Platform
FPGA supercomputing firm Mitrionics said this week that it has begun development of an accelerated version of BlastP that will run on the Mitrion Virtual Processor operating in FPGA-based computer systems.
BlastP is the second open source application the company is developing under its Mitrion-C Open Bio Project. The company launched its first accelerated Blast product, NCBI BlastN, last fall [BioInform 11-10-06].
The company said it expects the BlastP application to enter beta testing in the second quarter.
“Customer interest for our first accelerated Blast application has been very strong worldwide, and we're excited to begin development on our second application under the Mitrion-C Open Bio Project,” said Anders Dellson, CEO of Mitrionics, in a statement.

NIAID-Funded Researchers Deposit Sequence for 2,000 Flu Genomes in GenBank
Researchers have deposited genome sequence data for more than 2,000 influenza viruses in GenBank, the National Institutes of Health said this week.
The genomes were sequenced under the Influenza Genome Sequencing Project, funded by the National Institute of Allergy and Infectious Diseases.
The project, which began in 2004, has been carried out at the NIAID-funded Microbial Sequencing Center managed by The Institute for Genomic Research.
Other project collaborators include the National Center for Biotechnology Information, the Centers for Disease Control and Prevention, and several academic and clinical research institutions.
According to an NIH statement, “growing sequencing capacity has enabled the production rate to increase to more than 200 viral genomes per month.”
Additional information about the project can be found here.
In a related project, NIAID has also funded the BioHealthBase Bioinformatics Resource Center, which is being developed by researchers at the University of Texas Southwestern Medical Center and Northrop Grumman Information Technology's Life Sciences division. The goal of the center is to provide the scientific community with bioinformatics and software tools and a “robust” portal for accessing influenza genomic and related data.
BioHealthBase has recently begun a collaboration with the Influenza Sequence Database at Los Alamos National Laboratory to provide influenza researchers with computational data-management and analysis resources, NIH said. 

Genencor Licenses Integrated Genomics' Ergo Platform
Genencor has licensed Integrated Genomics’ Ergo genome-analysis platform to help it develop microbial products, IG said this week.
Ergo integrates data from genomics biochemistry, gene-expression studies, and the scientific literature, and is used to analyze genome sequences, annotate genes, and perform metabolic reconstructions and other comparative functions.
Genencor develops microbial products for use in the cleaning, textiles, fuel, and chemical industries. 

Premier Biosoft to Develop Custom Software for PamGene's MLPA Array
Premier Biosoft said this week that it will develop customized software for PamGene’s microarrays.
The company said the software will be used by customers of PamGene’s multiplex ligation-dependent probe-amplification microarrays.
MLPA is used to speed up “a number of genomic assays” and assesses gene copy number changes, SNPs, insertions, deletions, and methylation markers in one reaction tube, Premier Biosoft said.
Premier Bio said researchers would use the customized software to develop new multiplex genomic assays.

Hospital for Sick Children to Use GenoLogics' Geneus Software
The Hospital for Sick Children Research Institute in Toronto will use GenoLogics’ Geneus software for collaborative stem cell research projects involving nine other labs, GenoLogics said this week.
Sick Kids will install an early version of the software some time in the first half of the year and use it to manage microarray, flow Cytometry, and RNA-preparation information, GenoLogics said. It will also use it to track data from samples and projects.

DSM to Use Ludesi's 2D Gel Analysis Services
Swedish bioinformatics company Ludesi said this week that it will provide its 2D gel image-analysis software services to DSM, a manufacturer of nutritional and pharmaceutical ingredients.
The software will help DSM streamline the protein quantification step in its proteomics pipeline for studying microbial metabolism, the company said.

Chugai Using Genedata's Screening Software in Tokyo Labs
Genedata this week said that Chugai Pharmaceuticals is using its Screener software to analyze high-throughput screening data.
Under the agreement, Genedata said its Tokyo-based staff has helped Chugai integrate its AssayAnalyzer and Condoseo modules to review screening data and to evaluate compounds.
Genedata said Chugai has been using the software to help it develop drugs for cancer and for joint and bone diseases.

Filed under

The Scan

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Researchers Find Gene Affecting Alkaline Sensitivity in Plants

Researchers from the Chinese Academy of Science have found a locus affecting alkaline-salinity sensitivity, which could aid in efforts to improve crop productivity, as they report in Science.

International Team Proposes Checklist for Returning Genomic Research Results

Researchers in the European Journal of Human Genetics present a checklist to guide the return of genomic research results to study participants.