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PathwayArchitect, VIBE-Ed, ImmPort, UCSC Genome Browser, REDDB, COR (Cellular Open Resource), Synopsis, Mary Lipscomb, Stephen Kingsmore, Jack Anthony


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Stratagene has launched PathwayArchitect, a pathway-analysis software package that includes a database of more than a million biological interactions. The software uses a new method called the Relevance Interaction Network to predict interactions, Stratagene said. The method begins with a protein list "and identifies the network of proteins and small molecules which are most statistically related to the biology of the protein list," the company said. The algorithm can be used to identify binding complexes, transcriptional regulation networks, and small molecules. PathwayArchitect currently supports MySQL and will "shortly" support Oracle databases, Stratagene said. The software can be installed on the desktop or deployed as an enterprise-level solution, and is compatible with Mac, Windows, and Linux.

Incogen has released a beta version of its VIBE-Ed Bioinformatics Education Software, which was funded with a $500,000 National Science Foundation Phase II SBIR award in September [BioInform 09-12-05]. The software is based on Incogen's VIBE (Visual Integrated Bioinformatics Environment) workflow software, but is "specifically developed for bioinformatics education," Maciek Sasinowski, Incogen's CEO, said in a statement. VIBE-Ed will be beta-tested at several universities, including Northwestern University, the College of William and Mary, Harvard University, and University of Delaware.

Biomind said that it has begun rolling out its ImmPort web portal for enterprise-level analysis of microarray expression and other biological databases. ImmPort was developed in collaboration with Northrop Grumman, UT Southwestern, and other partners, and will be available to immunology researchers funded under the National Institute of Allergy and Infectious Disease. The company said that it has released the portal to "select research groups," with a broader launch planned for later in the year.

The Genome Bioinformatics Group at the University of California, Santa Cruz, has released the latest Drosophila yakuba assembly through the UCSC Genome Browser. This version, Release 2.0, was sequenced and assembled by the Genome Sequencing Center at Washington University School of Medicine in St. Louis. Downloads are available from the UCSC FTP server ( or Downloads page (

REDDB (the RESP ESP charge database) is available from the University of Picardie Jules Verne at The database includes RESP (restrained electrostatic potential) or ESP (electrostatic potential) atomic charge values for small structures or model systems. REDDB can also be used to reproduce, compare, and improve different RESP and ESP models.

The Department of Physiology, Anatomy, and Genetics at the University of Oxford has released COR (Cellular Open Resource), a Windows environment for cellular and multi-cellular modeling, for academic use at COR is built around a "slightly limited" version of CellML, according to its developers, and offers access to a large database of single-cell models.

Ananomouse has released Synopsis, a genome-visualization and -browsing tool. The company offers two versions of the software: the Professional edition for research by individual investigators and small groups; and the Enterprise edition, which can be integrated into existing proprietary bioinformatics systems. A free demonstration version of the Synopsis software is available for download at

People in the News

The National Center for Genome Resources has appointed Mary Lipscomb as chairman of its board of directors. Lipscomb is chair of the department of pathology at the University of New Mexico. She replaces Miguel Rios, CEO of Orion International Technologies, who was appointed chairman emeritus. Rios has served on the NCGR board since 1995 and was elected chairman in 2001. Rios also served as acting president and CEO from that time through January 2004, when Stephen Kingsmore joined as president and CEO.

NCGR also elected Kingsmore to the board, as well as several new members: Donald Armstrong of the Memorial Sloan-Kettering Cancer Center; Charles Arntzen, co-director of the Center for Infectious Diseases & Vaccinology at the Biodesign Center of Arizona State University; William Beavis, chief scientific officer of NCGR; Michael Cawley, president and CEO of the Samuel Roberts Noble Foundation; Mark Chandler, chairman and CEO of Biophysical Corp.; Keith Joiner, dean of the College of Medicine at the University of Arizona; Stuart Kauffman, director of the Institute for Biocomplexity and Informatics at the University of Calgary; Teresa Leger de Fernandez, managing partner of Nordhaus Law Firm; Rick Lyons, director of the Center for Infectious Disease and Immunity at the University of New Mexico; Michael Martin, president of New Mexico State University; Marvin Miller, chairman of Onconova Therapeutics; Van Romero, vice president for research at New Mexico Tech; Gloria Sarto, director of the University of Wisconsin Center for Women's Health at Meritor Hospital; Jonathan Soderstrom, managing director of the Office of Cooperative Research at Yale University; and Terry Yates, vice president of research and economic development at the University of New Mexico.

Pharmix, a startup using molecular modeling and bioinformatics to engineer pharmaceuticals, has named Jack Anthony as president and CEO. Anthony was most recently senior vice president of business development at Saegis Pharmaceuticals. Prior to that, he was senior vice president of business and commercial development at Tularik. He has also held senior-level business development and marketing positions at FibroGen, Cell Therapeutics, Inhale Therapeutics (now Nektar), and Applied Immune Sciences (now part of Sanofi-Aventis).

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