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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.

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The Scan

Genetic Tests Lead to Potential Prognostic Variants in Dutch Children With Dilated Cardiomyopathy

Researchers in Circulation: Genomic and Precision Medicine found that the presence of pathogenic or likely pathogenic variants was linked to increased risk of death and poorer outcomes in children with pediatric dilated cardiomyopathy.

Fragile X Syndrome Mutations Found With Comprehensive Testing Method

Researchers in Clinical Chemistry found fragile X syndrome expansions and other FMR1 mutations with ties to the intellectual disability condition using a long-range PCR and long-read sequencing approach.

Team Presents Strategy for Speedy Species Detection in Metagenomic Sequence Data

A computational approach presented in PLOS Computational Biology produced fewer false-positive species identifications in simulated and authentic metagenomic sequences.

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.