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


Downloads & Upgrades

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.


People in the News

Tom Humphreys, professor of cell and molecular biology at the John A. Burns School of Medicine at the University of Hawaii at Manoa, has been tapped to lead research initiatives for the university's new Center for Genomics, Proteomics and Bioinformatics.

Humphreys has been on the faculty at Manoa for 34 years. During that time, he organized the first recombinant DNA lab in Hawaii, led a reorganization of the UH Cancer Research Center of Hawaii, established the graduate program in cell and molecular biology and founded Hawaii Biotech, the state's biotech venture. He has accepted a three-year appointment as director of the center, effective July 1.

Filed under

The Scan

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With data for more than 1,900 individuals affected by a range of genetic conditions, researchers compared facial phenotype-based diagnoses informed by 2D or 3D images in the European Journal of Human Genetics.

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Investigators surveyed dozens of genetic counselors working in clinical or laboratory settings, uncovering attitudes around VUS reporting after multigene cancer panel testing in the Journal of Genetic Counseling.

Study Points to Tuberculosis Protection by Gaucher Disease Mutation

A mutation linked to Gaucher disease in the Ashkenazi Jewish population appears to boost Mycobacterium tuberculosis resistance in a zebrafish model of the lysosomal storage condition, a new PNAS study finds.