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SBToolbox 2 for Matlab, SampleWare 3.0, Mobyle, SoftGenetics, MicrobesOnline

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This brief has been updated from a previous version to correct the name of the developer and host of SBToolbox.
 
Henning Schmidt of the Institute of Computer Science at Rostock University has released SBToolbox 2 for Matlab, an extensible environment for building models of biological systems. The toolbox includes a variety of specialized analysis tools and built-in Matlab functions. Users can define models using a simple syntax based on differential equations or based on biochemical reaction equations.

 

 

 
Biomatrica has released SampleWare 3.0, a database software system for storing and organizing sample information. The software includes tools for uploading, tracking, and retrieving sample data as well as a customizable database that allows users to match data to their specific sample types, and attach data and image files to corresponding samples, the company said.
 
SampleWare is available in three editions: Desktop, Network, and Basic, depending on the size and scale of the lab. SampleWare Desktop is a single-user version with “unlimited storage capacity,” Sampleware Network enables multi-user functionality with the purchase of additional network licenses, and SampleWare Basic is a single-user version limited to storage of 5,000 samples.
 

 
The Pasteur Institute has released a preliminary version of Mobyle, a portal for bioinformatics analysis, here. Mobyle is being designed to replace the institute’s Pise system.
 
Improvements over Pise include improved coding and design, a more extensible architecture, and new features such as an integrated menu of available programs, a search facility, improved data-entry features, and online interactive tutorials.
 
The next release will include grid access and workflow design, the institute said.
 

 
SoftGenetics said this week that it will preview a suite of new software analysis tools for next-generation sequencing systems at the Association for Biomolecular Facilities meeting in Salt Lake City Feb. 9-12. The company said the next generation software suite will include SNP mutation analysis, target sequence, and de novo assembly modules for data generated by Illumina’s Genome Analyzer, 454 Life Sciences’ Genome Sequencer FLX System, and Applied Biosystems’ SOLiD sequencing system.
 

 
The US Department of Energy’s Virtual Institute for Microbial Stress and Survival has released an updated version of MicrobesOnline, a resource for comparative and functional genomics.
 
This release includes new genome sequences from the National Center for Biotechnology Information’s RefSeq 22 database, functional genomic data sets, and an improved microarray expression interface that allows users to compare the expression patterns of selected genes as well as search for other genes with a similar expression profile. The system also includes a tool called TreeBrowser that allows users to evaluate genes within an evolutionary framework by browsing pre-computed phylogenetic trees.

Filed under

The Scan

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Just Make It

The New York Times writes that there is increased interest in applying gene synthesis to even more applications.

Nucleic Acids Research Papers on OncoDB, mBodyMap, Genomicus

In Nucleic Acids Research this week: database to analyze large cancer datasets, human body microbe database, and more.