The Broad Institute has released GenePattern 3.1, which includes more than 100 modules for the analysis of gene expression, genetic variation, pathways, and proteomics data.
Protocols outline the steps to do clustering, classification, and marker selection on gene expression data, as well as SNP copy number and loss of heterozygosity determination. New modules include survival curve analysis and genetic network analysis algorithms.
In addition, the software is now hosted on the institute’s web site, allowing users to run large-scale analyses without downloading the software.
According to the Broad, there are more than 7,000 GenePattern users worldwide from over 500 institutions and more than 700 users have taken advantage of the hosted service since it was released earlier this spring.
Agilent Technologies has updated its CGH microarray software, DNA Analytics 4.0, to process more than 100 samples per experiment.
The new version also includes a genomic browser to enable data sharing, expanded copy number variation analysis functionality, and a probe database.
Kuala Lumpur-based Synamatix has released SynaWorks, its second-generation bioinformatics software. SynaWorks is a suite of applications specifically tailored to manage data generated from a variety of second-generation sequencers.
Rather than focus on handling, storing and archiving the data, Synamatrix says it offers a different approach with its data analysis pipeline, data mining and visualization tools.
The University of Texas at Austin has released Cellular Environment in Living Systems @ Home, or [email protected], a distributed computing software package for cell adhesion simulation, here.
According to its developers, the project has more than 1,000 contributors who are contributing their idle computer time to create a "virtual" supercomputer for calculating cellular interactions in different environments to help scientists explore the principles of cell migration and cancer cell metastasis.