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Briefs from the Systems Biology Community

July 16, 2008

Ingenuity/CHDI Work on Huntington’s Disease Tool
Ingenuity Systems and CHDI Foundation, a non-profit focused on discovering and developing drugs to treat Huntington’s disease, announced a multi-year agreement for CHDI to use Ingenuity’s IPA to integrate Ingenuity-curated information relevant to Huntington’s disease. CHDI researchers will be able to leverage this knowledge using the complete set of analysis tools and structured knowledge already available in IPA.

Ingenuity is advancing the development of disease-specific solutions by allowing organizations such as CHDI to use IPA as a platform to access both internal documents and disease-specific knowledge. This new type of solution addresses longstanding information management challenges by providing a uniform platform to capture and access diverse information resources, allowing for more efficient knowledge management and improved business value.

Robert Pacifici, chief scientific officer for CHDI, said, “Using IPA provides us with a single entry point for Huntington’s disease-specific content so that this knowledge is leveraged effectively across our organization.” CHDI’s virtual pharma approach is designed to bring the right collaborators together to identify and address critical scientific issues and move drug candidates to clinical evaluation as quickly as possible.

Genomatix Releases Genome Analyzer
Genomatix Software announced availability of the Genomatix Genome Analyzer GGA, which the company says is the first integrated hardware / software solution for in-depth analysis of data generated by next-generation sequencing (NGS) devices as provided by Illumina, Roche (454), Applied Biosystems (SOLiD) and Helicos.

Terabytes of locally installed data integrated with Genomatix powerful analysis technology facilitate easy extraction of relevant biological knowledge from mammalian ChIP-seq and transcriptome studies. A typical analysis of a ChIP-seq experiment with 10 million reads takes only two hours, and results contain important information such as clustered and classified enriched regions, transcription factor (TF) over-representation and TF associations.

In addition, genome-wide correlations with genomic features as well as meta-analysis with genome-wide chromatin modification, methylation state, expression levels or any data derived by other NGS experiments can be added with a few mouse clicks. Identification of phylogenetically conserved functional elements adds another dimension of analytic power. The GGA is driven by an easy-to-use, integrated browser-based interface. Alternatively, all database structures, scripts, and tools are open and accessible to the bioinformatics specialist for re-arrangement or integration of his or her own procedures.

Physiomics Expands Support of Lilly's Oncology Programs
Physiomics extended its collaboration with Eli Lilly to perform two in silico simulation projects in the field of oncology. This follows the successful completion earlier this year of a project studying cancer cellular processes for drugs targeting the cell cycle. The first new project’s goal is to provide a rationale for the identification of patient subpopulations that could benefit from an undisclosed target inhibitor. Physiomics will work to identify the mechanisms underlying the response of cells with different genetic backgrounds.

The second project entails delivering a model that integrates various biomarkers currently being investigated by Lilly as functional readouts for proprietary, undisclosed target inhibitors. The model will provide a mechanistic understanding of the involvement of these biomarkers in the functional response to the inhibitors. Physiomics develops computational systems biology models to predict and understand cancer drug efficacy from pre-clinical research to clinical development.

ISMB Kicks Off in Toronto
On July 20-23, 2008, scientists from around the world will gather in Toronto for the 16th annual international conference on Intelligent Systems for Molecular Biology (ISMB, held at the Metro Toronto Convention Centre. It’s one of the premier meetings in the field of computational biology, organized by the International Society for Computational Biology (ISCB --, and includes eight keynote addresses ( from the most sought-after and innovative research leaders of the field, including the two major ISCB award winners for 2008 (, and over 160 additional presentations selected as the best results and brightest innovations from among some 600 submissions.

At a press conference to be held on Monday, July 21, at 2:30 p.m., local Toronto steering committee member Shoshana Wodak of the Hospital for Sick Children in Toronto ( will be joined by keynote speaker Gene Myers of Howard Hughes Medical Institute Janelia Farm Research Campus (, ISCB 2008 Overton Prize winner Aviv Regev of the Broad Institute of MIT and Harvard (, as well as conference chair Burkhard Rost of Columbia University (, and conference co-chairs Jill Mesirov of the Broad Institute of MIT and Harvard (, and Michal Linial of the Hebrew University of Jerusalem (

Finnish Red Cross Licenses Pathway Studio
The Finnish Red Cross has licensed Ariadne Genomics’ Pathway Studio Enterprise for pathway, biological process, and disease modeling. Finnish Red Cross scientists will use Pathway Studio Enterprise to extract information from text, create custom cell type-specific, ICD10 disease-specific, and organism-specific databases, and use them for disease etiology research and risk group identification.

“MedScan is the only existing tool that allows flexible concentration of biomedical text and extraction of knowledge, e.g., after a batch download of full-text articles or Google Scholar full text queries into a database amenable for further analysis,” said Pauli Ojala, bioinformatician at Finnish Red Cross. “Pathway Studio Enterprise allows us to easily add and update databases, expand the database content, and work with our own and third-party data."

Linguamatics Joins BioIT Alliance
Linguamatics joined the Microsoft BioIT Alliance, an association of life science organizations and informatics companies whose focus is to enhance collaboration and accelerate the pace of drug discovery and development. “As a leader in knowledge discovery from text, we look forward to working with other alliance members to explore new ways in which the immense value of text mining can be exploited across complex, multidisciplinary organizations like pharmaceutical companies.” said Roger Hale, COO and co-founder of Linguamatics.

Formed in 2006, the BioIT Alliance is a cross-industry group working to integrate science and technology in order to accelerate the pace of drug discovery and realize the potential of personalized medicine. Founding members include Accelrys Software Inc., Affymetrix, Inc., Agilent Technologies Inc., Amylin Pharmaceuticals, Inc., Applied Biosystems, The BioTeam Inc., Digipede Technologies LLC, Discovery Biosciences Corporation, Geospiza Inc., Hewlett-Packard Development Company, L.P., Illumina Inc., InterKnowlogy, Microsoft Corporation, Sun Microsystems Inc., The Scripps Research Institute, VizX Labs LLC and other key companies in the pharmaceutical, biotech, hardware and software industries. Additional information about the BioIT Alliance can be found on the BioIT Alliance Web site at

Genego Works with Yale Microarray Center
GeneGo reported the Keck Microarray Center at Yale has become a certified GeneGo Center of Excellence (COE). Yale researchers will have access to GeneGo’s MetaCore, training and advanced support. The W. M. Keck Foundation Biotechnology Resource Laboratory (Keck Lab), one of the largest biotechnology laboratories of its kind in academia. TheYale Microarray Center is one of four national centers which together form a Consortium that provide gene expression and genotyping services at significantly reduced costs to approximately 10,000 NIH-funded neuroscientists from 15 branches of NIH that are part of the NIH-Neuroscience Blueprint.

“Neurosciences is one of the key diseases we have chosen to focus on this year and working with Yale is important to GeneGo as they are a leader in this field,” said Julie Bryant, GeneGo’s VP of Business development. “We are very pleased to have them as a GeneGo Center of Excellence.” Separately, the company VTT has licensed MetaCoreT. VTT develops novel high-throughput methods for cancer research, drug discovery and diagnostics. VTT will utilize MetaCore and MetaDrug in high-throughput compound screening, RNA interference experiments, cell biology and bioinformatics projects to identify pathways and networks important in translational cancer research.

Compugen Reports in Vivo Study Results
Compugen said it had positive results from a recently completed in vivo study of CGEN-25007, a novel peptide antagonist of the gp96 protein. The data indicate that CGEN-25007 has immunosuppressive effects and therapeutic potential for the treatment of various inflammatory diseases and other immune related pathologies. CGEN-25007, which has been shown to bind to recombinant gp96 in a dose dependent manner, was initially predicted using the Compugen’s DAC blockers platform.

The Blockers of Disease-Associated Conformation (DAC Blockers) is designed for the prediction and selection of peptides that block proteins from adopting their disease-associated conformations. This is accomplished through the use of a series of proprietary algorithms to identify segments in proteins of interest that, if introduced as synthetic peptides, would prevent the proteins from adopting disease-associated conformations and related activities and thus could have therapeutic benefits.

Genedata Inks Deal with Axxam
Genedata and CRO Axxam have signed a multi-year contract for the implementation of the Genedata Screener data analysis and management platform into Axxam`s high-throughput screening process. Dr. Stefan Lohmer, CEO of Axxam, said, “Establishing flexible and efficient working practices to ensure client satisfaction is our top priority as a reputable service provider. Genedata`s consistently high performance and data quality along with their expertise and profound scientific knowledge enable us to meet that goal on a daily basis.”

Pharsight Added to Russell Microcap
Pharsight Corporation, a provider of software and services to optimize clinical drug development was been added to the Russell Microcap Index when Russell Investments reconstituted its comprehensive family of U.S. and global equity indexes on June 27, 2008. Membership in the Russell Microcap, which remains in place for one year, means automatic inclusion in the appropriate growth and value style indexes.


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