Downloads & Upgrades
Accelrys has released Insight II 2005, an updated version of its biomolecular modeling, simulation, and visualization software. New features include a ZDockpro interface; an updated CHARMm interface; nucleic acid typing; updates to the DelPhi, CHARMm, and Modeler computational engines; support for both SGI Irix and Red Hat Enterprise Linux; and support for IBM T42p Thinkpads. The company said that it will release an Insight II 2005 interface to the GOLD protein-ligand docking algorithm from the Cambridge Crystallographic Data Center later this month.
Accelrys also released MacVector 8.0.2, an upgrade for its sequence analysis tool for the Macintosh. The release offers improved user interactivity and sequence confirmation functionality, and includes "numerous bug fixes," the company said. Existing 8.0 or 8.0.1 users can download a free updater at http://www.accelrys.com/products/macvector/patches.html.
The Plant Ontology Consortium has released the first version of the Developmental Ontology for flowering plants at http://www.plantontology.org/amigo/. The ontology includes terms that describe the developmental stages of organs and organ systems of a generic flowering plant, and is designed for use by plant databases and researchers to describe the effects of genes, mutations and environmental permutations on plant structure and growth using a standardized terminology.
The European Bioinformatics Institute has released InterPro 11.0, which contains 12,295 entries and covers 77.5 percent of UniProt (1,620,653 of 2,090,735 proteins), at http://www.ebi.ac.uk/interpro/.
EBI has also released version 13 released of the ChEBI (Chemical Entities of Biological Interest) small-molecule database, which contains 5,549 curated compounds, at http://www.ebi.ac.uk/chebi/.
The Gladstone Institute of Cardiovascular Disease has released a GenMAPP gene database and MAPP (Map Annotator and Pathway Profiler) archives for Canis familiaris at http://genmapp.org/. Updated gene databases for all supported species human, mouse, rat, dog, yeast, worm, fruit fly, and zebrafish are also available for download. Several additional species databases are also available on request, including mosquito, honey bee, fugu, chicken, chimpanzee, and pufferfish.
The Blueprint Initiative has released a new version of it BIND interaction viewer, version 3.51, which includes support for SOAP as well as for vector graphics formats like PostScript, Adobe Acrobat PDF, Scalable Vector Graphics, and bitmap formats like JPG, PNG, and RAW files.
SCOP (Structural Classification of Proteins) 1.69 is available at http://scop.mrc-lmb.cam.ac.uk/scop. The release includes 25,973 PDB entries and 70,859 domains.
The BioPAX Consortium has posted a BioPAX Level 2 release candidate, which covers molecular interactions, at http://www.biopax.org/Downloads/Level2v0.91/biopax-level2.zip. A feedback page is available at http://biopax.sf.net/cgi-bin/moin.cgi/Level_2_Release_Candidate_Feedback.
People in the News
Loralyn Mears has joined Gene Logic as vice president of genomics alliances. Mears most recently led Sun Microsystems' life sciences program as segment manager for life sciences market development. At Gene Logic, Mears will report to Dennis Rossi, senior vice president and general manager of the company's genomics and toxicogenomics business unit. Mears said in an e-mail to BioInform that she will be responsible for "establishing new alliances to broaden Gene Logic's selling and marketing efforts through indirect channels and looking to in-license new and innovative technologies, solutions and products to augment existing genomics offerings."