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Mac Vector, PathwayStudio Central, COPASI, PySCeS, Ensembl 31, Ontologizer, GPCR SARfari

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Accelrys has written a patch for its Mac Vector software to run on Apple's OS X 10.4 "Tiger" operating system, Dave Edwards, director of computational biology, told BioInform last week. The patch will be released through the company's website in the near future, he said.


Ariadne Genomics has released PathwayStudio Central, a client-server software system for visualizing and analyzing biological pathways and gene regulation networks. The software, which comes with the company's ResNet database of more than 500,000 functional relationships and its MedScan tool for automatic extraction of information from scientific literature, is available for a free 20-day trial at http://www.ariadnegenomics.com.


The Virginia Bioinformatics Institute has released build 13 of its COPASI biochemical simulator, at http://www.copasi.org. COPASI is the successor to VBI's Gepasi biochemical simulator, but is still considered a "test version" of the software, according to its developers. The current release includes stochastic time course simulation, deterministic time course simulation, steady-state analysis, linear stability analysis, metabolic control analysis, elementary mode analysis, mass conservation analysis, parameter scans, and other features. COPASI is free for non-commercial use. Commercial use is "negotiable through specific licensing agreements."


PySCeS (Python Simulator for Cellular Systems), a toolkit for analyzing the dynamic behavior of reaction networks in living cells, has been released at http://pysces.sourceforge.net. The software was developed by the Triple-J group for Molecular Cell Physiology at Stellenbosch University. It was designed with a command-line interface that allows it either to be used interactively in a Python console or as part of a Python-based modeling script.


Ensembl 31 is available at http://www.ensembl.org. The release includes Ciona intestinalis (assembly v1.95 from the Joint Genome Institute); new assemblies for honeybee (assembly Amel_2.0) and C. elegans (imported from Wormbase 140); and a complete set of paralog data for all Ensembl species.


A new version of the Ontologizer is available from Institute of Medical Genetics of the Charité University Hospital in Berlin at http://www.charite.de/ch/medgen/ontologizer. The software analyzes lists of genes, such as clusters from microarray data, and produces an overview of GO annotations together with a statistical analysis of over-representation of terms based on their hypergeometric distribution.


Inpharmatica has launched GPCR SARfari, a database of chemical, natural ligand, structural, and biological information on all 297 human rhodopsin-like G-protein coupled receptors. The resource also includes protein sequences, proprietary 3D structures, corresponding natural ligands, and more than 60,000 drug-like compounds derived from Inpharmatica's StarLite database of medical chemistry and pharmacology.

(See "Bioinformatics News Briefs from the Bio-IT World Conference Floor," this issue, for additional product releases.)

Filed under

The Scan

Interfering With Invasive Mussels

The Chicago Tribune reports that researchers are studying whether RNA interference- or CRISPR-based approaches can combat invasive freshwater mussels.

Participation Analysis

A new study finds that women tend to participate less at scientific meetings but that some changes can lead to increased involvement, the Guardian reports.

Right Whales' Decline

A research study plans to use genetic analysis to gain insight into population decline among North American right whales, according to CBC.

Science Papers Tie Rare Mutations to Short Stature, Immunodeficiency; Present Single-Cell Transcriptomics Map

In Science this week: pair of mutations in one gene uncovered in brothers with short stature and immunodeficiency, and more.