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GenConnect 3.0, DrugMatrix Online 1.0, Ensembl 46, BioCyc 11.5, CodeQuest, PipeWorks

GenVault has announced the release of GenConnect 3.0, a software application offering enhanced tracking of biosamples and associated data from acquisition to analysis.
GenConnect's new "Storage Explorer" module, a navigation console within the application, enables researchers to store, track, and exchange biosamples along with related data and history across multiple sites.
GenConnect is designed to track samples, subjects and projects, and manage associated data through custom templates. Key GenConnect 3.0 features include the ability to create a central archive through networked collections at multiple sites, maintain record of sample status, details and history, and secure biosample data with project and role based user access.

Toxicogenomics shop Iconix Biosciences has introduced and sold its first license of DrugMatrix Online 1.0. This product provides web-based access to a full-featured version of the earlier version of DrugMatrix.
With the release of DrugMatrix Online, the Iconix DrugMatrix database content and customized tools are now available to a much broader group of customers, including medium-sized pharmaceutical and biotechnology companies, according to a company statement.
Researchers can access DrugMatrix Online remotely using a personal computer running Windows and Internet Explorer. DrugMatrix Online allows licensed users to securely upload Affymetrix gene expression data from the Rat 230 2.0, RAE230A or RGU34A GeneChips and obtain Drug Signature similarity scoring as well as extensive comparative data from reference information on rats treated with over 500 reference drugs and toxicants.

The Wellcome Trust Sanger Institute and European Bioinformatics Institute have released Version 46 of Ensembl with new and updated features including SequenceAlignView for Homo sapiens, Mus musculus, and Rattus norvegicus), as well as a new page enabling side-by-side comparison of sequence from different individuals or populations. This view currently only includes information on human, mice, and rat strains.
 Examples for Human and Mouse are accessible at:
Ensembl 46 includes a new genebuild based on the recently-released Zv7 Zebrafish assembly, in which gaps in the tiling path have been filled using sequence from a single Tuebingen, double haploid individual.
New databases for Platypus have also been added in Ensembl 46. The initial gene set has been extended using recently released DNA data from 454 sequencing, plus additional annotation from the Oxford Functional Genomics group.

SRI International has released version 11.5 of the BioCyc suite of databases includes pathway/genome databases for 374 organisms; pathway tools for software that serve as a local version of the web site; a new database scheme for regulatory information; and retrofitted Pathway tools for manipulating information about the regulation of transcription initiation to work with this new regulatory schema.
BioCyc is a collection of 260 pathway/genome databases for most
organisms whose genomes have been completely sequenced to aid systems biology research.
The new version also supports substrate-level regulation of enzyme activity, and pathway tools for supporting the representation, editing and display of electron transport information.
This release includes version 11.5 of downloadable BioCyc data files and of the BioCyc Web site, as well as version 11.5 of Pathway Tools.

In conjunction with the International Conference on Systems Biology, BioCyc will also present a tutorial on Oct 1, 2007, in Long Beach, Calif.
The tutorial on computational analyses across the BioCyc collection of Pathway/
Genome Databases will be moderated by Peter Karp and Suzanne Paley of SRI International.
 Expected outcomes and goals will be helping students to learn how to perform
 computational analyses across the large BioCyc collection of Pathway/
 Genome Databases.
 Prerequisites include basic familiarity with programming and databases and
 basic familiarity required with concepts in biology and metabolic
 pathways. More information is available here:

Time Logic, a brand of ActiveMotif has launched the CodeQuest biocomputing workstation that supports data analysis, oligo mapping and comparative metagenomics. By plugging in CodeQuest into a standard outlet, one can connect to a network and the entire lab can run Tera-Blast, Smith-Waterman, and HMM analyses.
CodeQuest also includes PipeWorks, a scientific workflow design tool. This allows one to automate database updates and build annotation workflows by dragging and dropping. Experts can include Perl snippets or wrap their own code for more comprehensive workflows.

Filed under

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Limited Rapid Testing

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Genome Research Papers on IPAFinder, Structural Variant Expression Effects, Single-Cell RNA-Seq Markers

In Genome Research this week: IPAFinder method to detect intronic polyadenylation, influence of structural variants on gene expression, and more.