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Downloads and Upgrades : Mar 11, 2011

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This week, the Netherlands Bioinformatics Centre released e-Galaxy, an application that aims to make Galaxy and Taverna2 more interoperable.

According to the developers, the application allows users to automatically generate a Galaxy tool from a Taverna2 workflow that can then be installed in a Galaxy server allowing the Taverna workflow to become part of a Galaxy pipeline.


Velvet 1.0.19 is now available here.

The release includes a -noHash option to Velveth and the Solaris-specific files are now in the distribution, among other changes.


This week, Vanderbilt-Ingram Cancer Center launched a web-based personalized cancer decision-support tool, called My Cancer Genome, to keep researchers and physicians up to date on the latest developments in personalized cancer medicine as well as to connect their patients to clinical research trials.

According to developers, the tool, which is linked to VU’s StarPanel electronic medical record database, is designed to educate clinicians on the rapidly expanding list of genetic mutations that impact different cancers and at the same time, enable them to more easily research various treatment options based on specific mutations.


The European Nucleotide Archive said this week that EMBL-Bank Release 107 is now available from the European Bioinformatics Institute's FTP servers and other verified mirror sites.

Full release notes are available here and here.


RefSeq 46 is now available via FTP from the National Center for Biotechnology Information.

This full release incorporates genomic, transcript, and protein data available as of March 8 and includes 16,998,463 records, 12,167,392 proteins, and sequences from 11,734 different organisms.


This week, Proteome Software released Scaffold PTM, a post-translational modification site assignment tool for MS/MS analysis and PTM visualization and validation for proteomics researchers.

The tool, which relies on the open data source format mzIdentML, includes several features for site determination of phosphorylation and other PTMs and enables the comparison of peptide modification rates from multiple samples in a dataset. Additional search engine supports enable researchers to gain access to PTM data processed by Scaffold, Mascot, or any other software tool that supports the mzIdentML format.

The software is priced at $7,000 for commercial users and $6,000 for academics, with additional discounts available for customers with other Proteome Software offerings.


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.