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SimBiology, Cytoscape 2.3, Agilent Literature Search, GSnet, Integrated Microbial Genomes, Cancer Cell Map, Image-Pro Express 6.0


The MathWorks has released SimBiology, a graphical system for simulating, modeling, and analyzing biochemical pathways. SimBiology is built on the company's Matlab engine and includes a drag-and-drop interface that allows nonprogrammers to create, edit, and view models of pathways. Biologists can simulate modeled reactions and then analyze the resulting data in SimBiology or perform custom analysis with Matlab. Commercial US pricing starts at $3,000 per seat.

Cytoscape 2.3, an open-source software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other data, is available at New features include a high-performance rendering engine that supports networks with more than 100,000 nodes and edges, the ability to save a session, support for network attributes, an improved command line interface, an enhanced ontology server wizard, greater flexibility in expression data loading, and other improvements.

Agilent Technologies has released version 2.3 of the Agilent Literature Search plug-in for Cytoscape 2.3 at Agilent Literature Search automatically queries multiple text-based search engines in order to extract associations among genes or proteins of interest. These associations are grouped into a network that is viewed and manipulated in Cytoscape. Enhancements in version 2.3 include improved file-based lexicon management and a paged results view.

GSnet, a Cytoscape plug-in, is available from the Korean Bioinformation Center at GSnet visualizes a network graph of a given enriched gene set with protein-protein interaction and Gene Ontology term enrichment. Protein-protein interactions are estimated with the Agilent literature search engine and the Biomolecular Interaction Network Database.

Version 1.5 of the Integrated Microbial Genomes data-management system is available from the US Department of Energy's Joint Genome Institute at IMG 1.5 contains 741 genomes (435 bacterial, 32 archaeal, 15 eukaryotic genomes and 259 bacterial phages), of which 602 are finished and 139 are draft genomes.

The Computational Biology Center at Memorial Sloan-Kettering Cancer has released the Cancer Cell Map, a selected set of human cancer focused pathways, at The map enables users to browse and search cancer pathways and view gene expression data on any pathway. All pathways can be downloaded in BioPAX format for global analysis, and a web service API is available for software developers.

Media Cybernetics has released Image-Pro Express 6.0. The latest version of the scientific image processing and analysis software includes new tools that allow users to uncover more details within their images, including edge filters for improved object identification. The software also includes new measurement tools for metrology, thickness measurement, and edge detection.

Filed under

The Scan

WHO Seeks Booster Pause

According to CNN, the World Health Organization is calling for a moratorium on administering SARS-CoV-2 vaccine boosters until more of the world has received initial doses.

For Those Long Legs

With its genome sequence and subsequent RNAi analyses, researchers have examined the genes that give long legs to daddy longlegs, New Scientist says.

September Plans

The New York Times reports that the US Food and Drug Administration is aiming for early September for full approval of the Pfizer-BioNTech SARS-CoV-2 vaccine.

Nucleic Acids Research Papers on Targeting DNA Damage Response, TSMiner, VarSAn

In Nucleic Acids Research this week: genetic changes affecting DNA damage response inhibitor response, "time-series miner" approach, and more.