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Bioinformatics Briefs: Dec 10, 2001

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GRID COMPUTING

French bioinformatics company Genomining has developed software based on the Smith-Waterman algorithm for a “Decrypthon” grid computing project that will compare over 500,000 known proteins of humans, animals, and plants using a network of tens of thousands of consumer PCs.

Genomining joins Platform Computing, headquartered in Markham, Ont., the French Myopathy Association (AFM), and IBM in its support of the Decrypthon, which will launch as part of France’s National Telethon, December 7-8.

Platform will integrate its Platform LSF and LSF ActiveCluster distributed computing software with IBM’s hardware and software solutions and Genomining’s software to power the Decrypthon. The AFM and Genomining will have access to the protein database generated by the project.

The Decrypthon application will compare sequential patterns of proteins and classify them in families of equivalent proteins. Users can download the Decrypthon software from www.telethon.fr.

 

Entelos of Menlo Park, Calif., has also chosen to integrate Platform’s distributed computing software with its PhysioLab disease simulation platform.

Entelos will use Platform LSF to manage the workload across its server farms and will use LSF ActiveCluster for distributed desktop processing.

 

INTEGRATION

Cleveland-based NetGenics has completed the installation if its DiscoveryCenter product at Paradigm Genetics, based in Research Triangle Park, NC.

Paradigm is using DiscoveryCenter to integrate its proprietary data with public information about genes, proteins, pathways, and organisms. The company also plans to integrate DiscoveryCenter into its FunctionFinder Bioinformatics System.

 

EDUCATION

Baylor College of Medicine, Rice University, the University of Houston, the University of Texas Health Science Center at Houston, the University of Texas Medical Branch at Galveston, and the University of Texas M.D. Anderson Cancer Center have banded together as the Gulf Coast Consortium — a research and education initiative funded in part by a $3.5 million grant from the W. M. Keck Foundation of Los Angeles.

The grant will support the expansion of the Keck Center for Computational Biology, which was initiated in 1990 by Keck Foundation funding to Baylor College of Medicine and Rice University.

The GCC will involve 90 faculty from a number of disciplines at the six institutions, who will train more than 100 students in computational, mathematical, physical, and chemical biology.

 

The Insight Computer Training Center of Brighton, Mass., is offering a Bioinformatics Certification Program for life science or IT professionals. The program is designed to help students prepare for the certified bioinformatics specialist exams sponsored by the Bioinformatics Institute (www.bioinfoinstitute.com) and begins January 6, 2002.

 

The University of Calgary has been selected as a Sun Microsystems Center of Excellence for Visual Genomics. Stefan Unger, business development manager for computational biology at Sun, said that University of Calgary professor of biochemistry and molecular biology Christoph Sensen’s work was instrumental in the decision. Sensen is building a CyberCell — a three-dimensional representation biological system with a Java-3D enabled CAVE — using a SunFire 6800.

 

ONTOLOGIES

Ardais has selected medical terminology tools from Apelon of Ridgefield, Conn., to help link its bioinformatics and clinical informatics efforts.

Ardais, based in Lexington, Mass., said it would use Apelon’s Terminology Development Environment tool to create an ontology of concepts unique to human clinical materials classification and management and would link this data to its existing applications with Apelon’s Distributed Terminology System servers.

According to Ardais, the new ontology will enable its researchers to associate allele expression in tissues and genomics data with clinical samples and clinical information about those samples.

 

CUSTOMIZATION

Ardais has also christened its new custom bioinformatics system, designed by 3rd Millennium of Cambridge, Mass.

The proprietary LIMS system supports Ardais’ high-throughput pathology lab operations. At its core is Ardais’ BIGR Library of clinical materials, which it provides to its external clients along with medical, pathology, and outcomes data and proprietary bioinformatics tools.

 

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