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Bayer HealthCare, Ariadne’s Pathway Studio, Agilent Technologies, Klee Group, Monarch LifeSciences, GeneGo, RFS Pharma, Genoscience Pharma, Ryoka Systems, BiosolveIT, Simulations Plus, Gene Network Sciences, Weill Cornell Medical College, GenoLogics, Illu

Bayer Renews License for Ariadne Pathway Studio, MedScan Technology
Ariadne said this week that Bayer HealthCare will renew and expand its license for Ariadne’s Pathway Studio software till the end of 2010. Bayer will use the software for pathway research, toxicology studies, and microarray data analysis.
Pathway Studio analyzes pathways, signaling networks, and microarray data. The software is based on the company’s MedScan natural language processing technology, which extracts pathway-related information from biomedical literature, including PubMed.
Under the terms of the extended agreement, Bayer HealthCare has added additional research sites to its license and has gained early access to a MedScan extension for extracting toxicology data from text.

Agilent Technologies Acquires Kalabie ELN from Klee Group
Agilent Technologies said this week that it has acquired the Klee Group's Kalabie Electronic Laboratory Notebook.
Agilent said that the focus for the product, its Agilent's first electronic lab notebook, will be the pharmaceutical market and some chemical applications.
Financial details of the acquisition were not disclosed.
Kalabie ELN is a highly configurable software solution for the R&D sector, used by pharmaceutical and dermo-cosmetic companies since 2004.
A digital laboratory notebook, Kalabie ELN provides a foundation for knowledge and process management as well as intellectual property protection within laboratories, Agilent said. Kalabie ELN centralizes and secures all data from experimental work with a high level of traceability. Kalabie ELN can be deployed as a standard packaged solution or it can be configured to meet customers' specific needs.
Agilent's current portfolio of laboratory software includes OpenLAB — a laboratory operating system. Agilent plans to integrate the Kalabie ELN product into OpenLAB in the next six months to provide customers with the ability to manage computing resources in the laboratory.
The acquisition comes at a time of heightened adoption of ELNs in the bioinformatics market [BioInform 06-15-07].

Monarch LifeSciences Partners with GeneGo to Provide Pathway Analysis Services
Monarch LifeSciences will use the 1-2-3 Workflow technology from systems biology software shop GeneGo in order to offer pathway analysis services to its clients, GeneGo said this week.
Monarch, a contract research organization with expertise in protein biomarker discovery, development, and validation, will use 1-2-3 Workflow to upload proteomics data; identify and compare data sets; conduct enrichment analysis in multiple ontologies such as diseases, canonical pathways and functional processes; and calculate relevant networks and focal hub proteins. The end product is a comprehensive Word report.

RFS Pharma and Genoscience Pharma to Jointly Discover and Develop Protease Inhibitors
RFS Pharma and Genoscience Pharma have announced the formation of a drug discovery joint venture to develop protease inhibitors for the treatment of life-threatening viral infections.
Under the agreement, the companies will collaborate on the discovery, optimization, and development of therapeutic agent compounds.
Genoscience uses two proprietary software platforms to support its work on antiviral therapies. The first, GenMol, “enables the development of highly targeted molecules, taking into account the phenomenon of resistance,” the company said. Its PredictSearch software is used to identify biomarkers for monitoring antiviral therapies and for prognosis.

Ryoka Systems and BiosolveIT Sign Distribution Contract
Ryoka Systems, a subsidiary of Mitsubishi Chemical of Tokyo, has signed a software distribution agreement with cheminformatics provider BioSolveIT of St. Augustin, Germany.
Under the terms of the agreement, Ryoka will distribute BioSolveIT's software in the Japanese market and will handle distribution, local contact, and support.
Ryoka also distributes Chemical Computing Group’s MOE drug design and modeling platform in Japan, and plans to integrate BioSolveIT's portfolio of applications with MOE.
All major integration work between BioSolveIT products and MOE is planned to be made available worldwide free of charge.

Simulations Plus Wins SBIR to Commercialize ADMET Prediction Software
Simulations Plus, a provider of software for pharmaceutical discovery and development, this week said that it has received a $100,000 Small Business Innovation Research grant from the National Cancer Institute to help improve the predictive capabilities of its ADMET Predictor software product.
ADMET Predictor calculates quantum atomic and molecular descriptors for new drug molecules in order to predict their interactions with each other and their environment.
The grant will support the development of new ADMET calculation methods that are “orders of magnitude faster” than current methods “and yet accurate enough to provide improved prediction of a number of properties for new drug-like molecules,” Robert Fraczkiewicz, team leader for ADMET cheminformatics for Simulations Plus and principal investigator for the grant, said in a statement.
Fraczkiewicz said that preliminary studies show a speed improvement that “reduces the calculation time from over 700 CPU-days to just minutes.”

Gene Network Sciences Collaborates with Weill Cornell Medical College on Cancer Treatment Study
Gene Network Sciences said this week that it is collaborating with the Weill Cornell Medical College on a project that will use GNS’s simulation software to study the interactions between two classes of cancer drugs.
Financial terms of the agreement were not disclosed.
In the project, researchers from GNS and Weill Cornell will use the company’s reverse engineering and forward simulation, or REFS, software platform to characterize the molecular mechanisms of action for the combination of farnesyl transferase inhibitors and taxanes.
"Phase I and II clinical trials have shown that the combination of FTIs and taxanes have clinical activity in taxane-refractory cancer patients," said Paraskevi Giannakakou, Weill Cornell's principal investigator for the collaboration, in a statement.
He added that the project could “pave the way towards identifying subsets of patients likely to benefit from this drug combination and will assist the rational development of therapeutic strategies able to overcome clinical drug resistance."
WCMC will generate molecular-level data from the use of these drugs in model cancer systems and GNS will use the REFS technology to build computational models containing FTIs and taxanes together. The researchers will use these models to study the drugs' “synergistic mechanisms” of efficacy, toxicity, biomarkers, and other biological characteristics.

GenoLogics Joins IlluminaConnect Program
GenoLogics said this week that it has joined IlluminaConnect, a partnership program that Illumina launched last month for third-party bioinformatics providers.
GenoLogics said that it will integrate its Geneus software with Illumina’s BeadArray technology and software for both gene expression and genotyping applications.
Other participants in the IlluminaConnect program include Biocomputing Platforms, GeneSifter, Golden Helix, Ingenuity Systems, Partek Genomics, Rosetta BioSoftware, Sapio Sciences, SAS, and Stratagene.

Spain’s Integromics to Use Ingenuity Pathway Analysis in Andalusian Core Facility
Ingenuity Systems said this week that it has signed a five-year contract with Integromics, a life science IT company based in Granada, Spain, and the service provider to the Genomics, Proteomics and Bioinformatics Core Facility of Andalusia in Malaga, Spain.
Under the terms of the agreement, Ingenuity will be the sole pathways analysis provider for the core facility and all of its academic member organizations, the company said.
The Ingenuity Pathway Analysis platform “provides a great complementarity with other tools for functional analysis of genomic data like Integromic's ArrayUnlock,” said Pedro de Alarcon, business development director of Integromics, in a statement. “Additionally, IPA provides a remarkable add-on to our portfolio in secondary analysis as it is integrated with our Spotfire DecisionSite modules for microarray analysis.”
Financial terms of the agreement were not provided.

NHGRI Offers Access to Cancer Sequencing Data
The National Human Genome Research Institute is granting access to datasets from cancer sequencing projects through open-access and controlled-access programs, NHGRI said last week.
Researchers will be able to access controlled information from the Medical Sequencing Program by downloading individual-level genotype and assembled DNA-sequence data, NHGRI said.
Most of the data in the open category are available through the National Cancer Institute’s Center for Bioinformatics. DNA sequences may be accessed through the National Center for Biotechnology Information’s trace archive.
NHGRI also said it plans to announce procedures for accessing individual-level data for the Cancer Genome Atlas program separately.
NHGRI’s Medical Sequencing Program also is supporting investigations of other diseases besides cancer, and data from those studies may be found in the NCBI’s Genotype and Phenotype database.
Further information on accessing this data is available here.

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The Scan

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