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Bristol-Myers Squibb, Ingenuity, BASF Plant Science, Genedata, MD Anderson Cancer Center, GeneGo, University of Tennessee, Waters, BioIT Alliance, Microsoft, Life Biosystems, Fraunhofer Institute, Premier Biosoft, NYU, natural History Museum

Bristol-Myers Squibb Renews License for Ingenuity Systems Software
Ingenuity said this week that Bristol-Myers Squibb has renewed its license for Ingenuity Pathway Analysis for use in genomics and proteomics research aimed at advancing its drug discovery programs.
Under the agreement, Bristol-Myers Squibb gains enterprise-wide access to the Ingenuity Pathways Analysis software for modeling, visualization, and interpretation of genomics and proteomics data. BMS has been an Ingenuity customer since 2004.
The IPA software supports data from a variety of experimental platforms and at “all stages of the drug discovery and development process,” including biomarker discovery, target identification and validation, pharmacogenomics, metabolomics, and molecular toxicology, Ingenuity said.
Financial terms of the agreement were not released.

BASF Plant Science Licenses Genedata's Expressionist Software
Genedata said this week that BASF Plant Science has licensed its Expressionist bioinformatics software for use in its genetic screening programs across North America and Europe. Financial terms of the agreement were not released.
Some of BASF’s projects include increasing plant yield and enhancing the nutritional value of plants, which entails analyzing large volumes of molecular profiling data, Genedata said.
Juergen Logemann, vice president of technology management at BASF Plant Science, said in a statement that the company selected Expressionist after “a thorough market evaluation” for its ability to process and analyze "large amounts" of expression profiling data in a high-throughput manner.
Genedata said that Expressionist is used for quality assessment and pre-processing of a range of ‘omics data types, including microarray and PCR data, and allows researchers to integrate molecular profiling data from transcriptomics, proteomics, and metabolomics applications.

MD Anderson To Use GeneGo’s Metacore
GeneGo announced that the MD Anderson Cancer Center has licensed GeneGo’s MetaCore data analysis suite for use throughout the institution. No financial details were disclosed.
The St. Joseph, Mich.-based company said MD Anderson will apply the platform, which includes training and support, as a central data repository, as a management and collaboration platform for clinical ‘omics data, and for integrative pathway analysis.
MD Anderson pathologist Mary Edgerton said in a statement that she is using the MetaCore platform to infer networks from the analysis of gene expression array data in lung, brain, and breast cancer. She said she also uses the curated pathways to develop mathematical models of molecular networks that “predict tumor behavior using multi-scale modeling.”

NSF Awards UT Knoxville $16M to Create Mathematics and Biology Center
The National Science Foundation has awarded the University of Tennessee at Knoxville $16 million to create the National Institute for Mathematical and Biological Synthesis, or NIMBioS, to be directed by Louis Gross, professor of mathematics, ecology, and evolutionary biology.
Funding for the institute will be used to create a high-tech center on the campus that will draw researchers to take part in working groups, workshops and conferences focusing on mathematics and modeling of complex biological problems

Waters Joins Microsoft’s BioIT Alliance
Waters this week announced that it has joined Microsoft’s BioIT Alliance, a cross-industry group formed in 2006 with the aim of speeding drug discovery and personalized medicine efforts.
Waters said that its informatics business will work with other participants to develop standard conventions for sharing scientific data based on Microsoft technology.
The BioIT Alliance currently has more than 80 members in the pharmaceutical, biotech, lab instrument, and software development fields.

Life Biosystems Licenses Fraunhofer Software
German biomedical software company Life Biosystems has licensed entity recognition software from the Fraunhofer Institute for Algorithms and Scientific Computing for its text-mining infrastructure. The partners plan to develop information extraction algorithms for clinical research but did not elaborate on the financial terms of the agreement.
The work will include identifying and modelling therapeutically relevant information from clinical/lexical data, with a particular emphasis on drug mode of action and clinical outcomes, according to a statement.
Life Biosystems Director of In Silico Discovery David Jackson said that the collaboration will help the company “efficiently bridge the gap between the clinical and molecular information domains,” permitting innovations in analysis and application of patient-derived data.

Premier Biosoft Completes Software-Development Project for DxTerity Diagnostic
Bioinformatics firm Premier Biosoft said this week that it has delivered the final part of a contracted software module to DxTerity Diagnostic, a firm that provides genomic testing.
DxTerity hired Premier to design a probe-design software module for its NEAT genomic testing platform, which replaces enzymatic amplification techniques with a chemical reaction.
“The software module allows customers to quickly adapt the NEAT technology to their individual needs, allowing the rapid development of robust genomic assays,” Premier said in a statement.
The company said that the contract started in December 2007 and proceeded “in phases with periodic deliveries” until July.

NYU, Natural History Museum to Use $1.6M NSF Grant for Plant Proteome Bioinformatics Research
The National Science Foundation has given three scientists at New York University and at the American Museum of Natural History a $1.6 million grant to study the proteomes of two plants and to develop a database to house the information, NYU said this week.
The investigators will use the three-year grant to study the structure, evolution, and function of the proteomes of Arabidopsis thaliana, a small flowering plant that was the first plant to have its genome sequenced, and the rice plant Oryza sativa.
The scientists will map information about the evolutionary importance of certain parts of genes and study how proteins are encoded into the genomes. The researchers will run their analysis on the World Community Grid, an IBM-supported computing platform that involves 400,000 volunteer computers worldwide.
NYU said that scientists at its Courant Institute of Mathematical Sciences, which is run by Bonneau, have already used the grid to perform structure prediction for more than 150 genomes.
These methods will be useful for annotating proteins that have unknown functions, and which currently have no detectable similarity to another protein with a known structure.
The project also will be linked to a continuing education program at NYU’s Steinhardt School for Culture, Education, and Human Development to train teachers how to use bioinformatics in high school science classes.

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