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Downloads & Upgrades: Jun 26, 2009


CLC Bio plans to release its CLC Genomics Machine next week at the Intelligent Systems for Molecular Biology conference. The system includes a hardware platform, pre-installed software tools for next-generation sequence analysis and other applications, and "an enterprise level database," the company said.

According to the CLC Bio website, the hardware includes two quad-core Intel Xeon X5550 CPUs with 48 GB of RAM.

CLC said that initial performance benchmarks on the system indicate that the reference assembly of a one-fold coverage human genome can be completed "in about one hour." The system also includes an algorithm that can perform de novo assembly of human genomes and large plant genomes on one CLC Genomics Machine "in an astonishingly short time."

The system also includes several standard bioinformatics algorithms, including BLASTp, BLASTn, hmmsearch, hmmpfam, Smith-Waterman, and ClustalW. Performance benchmarks of these algorithms against "the best-selling off-the-shelf biocomputing FPGA solution" show "an impressive performance advantage," the company said.

SRI International has released BioCyc 13.1, which contains 507 genomes. Enhancements to EcoCyc 13.1 include four new metabolic pathways, 18 newly identified small proteins, and summaries for 170 transcription factors "that have at least one experimentally characterized binding site or interaction," according to an SRI statement. MetaCyc 13.1 contains 66 new and updated pathways.

The International Union of Basic and Clinical Pharmacology, or IUPHAR, has released a new ion channels database, covering both voltage-gated and ligand-gated ion channels, to add to its existing mammalian receptor database.

The IUPHAR database is hosted by the Centre for Cardiovascular Science at the University of Edinburgh. It is a curated resource that includes peer-reviewed information about pharmacological, chemical, genetic, functional, and patho-physiological properties of human, rat, and mouse genes that encode more than 354 non sensory G protein-coupled receptors.

A beta release for Biopython 1.51 is available for testing here.

The beta release includes support for writing features in GenBank files using Bio.SeqIO, extended SeqIO~s support for the FASTQ format to include files created by Illumina
1.3+, and a new set of application wrappers for alignment programs, among other enhancements.

Version 29 of the Reactome Knowledgebase is available here.

Version 29 of the curated resource of core pathways and reactions in human biology includes a new topic, axon guidance. Pathway topics updated with new curated events include: synaptic transmission, DNA repair, and pathways whose dysfunction plays a major role in the development of diabetes.

In addition, a new search tool and a beta version of a new pathway visualization tool are now available on the Reactome website.