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Proteomweaver, GenomatixSuite, KEM, HapMap, UCSC Genome Browser, BioWarehouse, Jmol, BAMarray, SafeBase 2.5, BioRuby 0.6.2

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Definiens has released version 3.0 of its Proteomweaver 2D gel analysis software. The release includes improved metadata handling to annotate experiments, gels, and spots with information on species, tissue, experimenter, sample preparation, staining, sequence, and mass spec data, the company said.


Genomatix has released an updated version of its GenomatixSuite, which now includes 11 genomes via the ElDorado genomic annotation engine: human, mouse, rat, chimp, dog, chicken, Drosophila, Anopheles, Plasmodium, Arabidopsis, and rice.


Ariana Pharma has launched KEM (Knowledge Extraction and Management), an AI-based computational tool that is available for service and collaboration projects. Ariana said that KEM can integrate and mine multiple data sources and suggest improved compounds for use in pharmaceutical applications.


HapMap 14 is at http://www.hapmap.org. It includes 956,730 SNPs genotyped in CEPH, 412,669 SNPs in Han Chinese, 412,608 SNPs in Japanese, and 432,523 SNPs in Yoruba.


The University of California Santa Cruz Genome Bioinformatics Group has added three more Drosophila genomes — initial assemblies of D. ananassae, D. virilis, and D. mojavensis — to the UCSC Genome Browser at http://genome.ucsc.edu/cgi-bin/hgGateway?org=D.+ananassae.


SRI International’s Bioinformatics Research Group has released version 3.0 of BioWarehouse, an open-source toolkit for constructing bioinformatics database warehouses, at http://bioinformatics.ai.sri.com/biowarehouse/. BioWarehouse integrates multiple public and in-house bioinformatics databases into a common relational database management system.


Jmol version 10.00, an open source replacement for the Chime plug-in, is available at http://www.jmol.org.


Case Western Reserve University has released BAMarray, a statistical software package for analyzing gene expression data, at http://ora.ra.cwru.edu/bamarray. BAMarray is based on the Bayesian analysis of variance for microarrays methodology.


TheraStrat of Allschwil, Switzerland, has released SafeBase 2.5, which includes a database of structural and genetic factors that predispose individuals to adverse drug reactions, along with several analysis tools.


BioRuby 0.6.2 is available at http://bioruby.org/archive/bioruby-0.6.2.tar.gz. The release includes support for Sim4, Spidey, and Blat.

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The Scan

Mosquitos Genetically Modified to Prevent Malaria Spread

A gene drive approach could be used to render mosquitos unable to spread malaria, researchers report in Science Advances.

Gut Microbiomes Allow Bears to Grow to Similar Sizes Despite Differing Diets

Researchers in Scientific Reports find that the makeup of brown bears' gut microbiomes allows them to reach similar sizes even when feasting on different foods.

Finding Safe Harbor in the Human Genome

In Genome Biology, researchers present a new approach to identify genomic safe harbors where transgenes can be expressed without affecting host cell function.

New Data Point to Nuanced Relationship Between Major Depression, Bipolar Disorder

Lund University researchers in JAMA Psychiatry uncover overlapping genetic liabilities for major depression and bipolar disorder.