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BioPathwise 2.0, Map Viewer, CLC Free Workbench 3.0, SimTK Simbody, SimTK ISIM, ToRNADo, CERF-Notebook, Jmol, International Protein Index, Unleashed Global Services, Experion 2.0


The BioAnalytics Group has released BioPathwise 2.0, a new version of its pathway-centric software and database system. The software includes a reaction repository and interface tools that allow users to pull in peer-reviewed information about specific reactions. Biologists can use the software to draw pathways and conduct virtual experiments, computational biologists and statisticians can view mathematical formulas that represent the processes at work, and programmers have access to tools that will enable them to integrate legacy data and third-party software packages.

The National Center for Biotechnology Information has released a re-annotation of the rat genome assembly, build 4.1, which includes annotation of the reference assembly of the BN/SsNHsdMCW genome and the January 2003 release of Celera Genomics' assembly from Brown Norway and Sprague-Dawley strains. The data can be viewed in Map Viewer at or downloaded by ftp at

CLC Bio has released CLC Free Workbench 3.0, a free bioinformatics analysis package, at The new version of the software enables analysis of multiple sequences in one step, improved restriction site analysis tools, and an improved history log.

Stanford University's Simbios (Physics-based Simulation of Biological Structures) program, one of the National Institutes of Health's National Centers for Biomedical Computing, has released a number of software tools through its website ( These include SimTK Simbody, a multi-body dynamics package, SimTK ISIM, an application for simulating the ionic environment of a macromolecule, ToRNADo, a visualization and manipulation tool for both coarse-grained and fine-grained representations of RNA molecules, and others.

Rescentris has released a new version of its CERF-Notebook software that runs on Intel-based Macintosh computers. Rescentris' CERF (Collaborative Electronic Research Framework) enables researchers to record and share their work across diverse applications and operating systems.

The National Heart, Lung, and Blood Institute's Laboratory of Computational Biology has upgraded its AD-ENM web server for analyzing dynamics of protein structures based on the elastic network model. The server, available at, now supports Jmol-based visualization and animation of protein structural models and their motions.

The European Bioinformatics Institute has released an updated version of the International Protein Index database at The database, compiled from UniProt, RefSeq, Ensembl, TAIR, and H-InvDB, includes protein data for human, mouse, rat, zebrafish, Arabidopsis, chicken, and cow.

Unleashed Informatics has launched Unleashed Global Services, a consulting and training group that will offer support services to commercial, academic, and governmental customers. Further information is available at

Bio-Rad has released Experion 2.0, a software upgrade for its Experion automated electrophoresis system. Features include a new e-gram overlay icon, chip compare, internal standards, and multi-instrument operation using a single computer. The 2.0 upgrade will be included with new Experion systems.

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The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.