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Expressionist, EMBL Nucleotide Sequence Database, Ingenuity Pathways Analysis, Pathway Tools, Pegasys, Genomorama, HelixTree v3.1, Lasergene v6.1

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Genedata has released a new version of its Expressionist platform, which includes support for biomarker discovery, analysis of metabolic and signal transduction pathways, and in silico prediction of toxicity and compound mode-of-action. The software complies with the FDA’s 21 CFR Part 11 regulations.


Release 82 of the EMBL Nucleotide Sequence Database is available from ftp://ftp.ebi.ac.uk/pub/databases/embl/release/ (UK) and mirror sites. The file size is about 43 GB (compressed), and 241 GB (uncompressed).


Ingenuity has released a new “Sharing and Workgroups” capability for its Ingenuity Pathways Analysis platform. The new functionality enables researchers to share analysis results and is available immediately to all customers. The company said that it plans to release a new pathway-editing function for the platform this summer that will allow users to customize networks and share them with colleagues.


SRI International has released version 9.0 of the BioCyc databases and Pathway Tools software at http://www.biocyc.org. The BioCyc database collection includes 145 new databases, bringing the collection to 165 total databases. In addition, a new BioCyc Open Chemical Database, which collects chemical compound data from many BioCyc databases into one dataset, is available at http://biocyc.org/open-compounds.shtml. A new horizontal genome browser is also available.


Version 0.5 of Pegasys, workflow management software for biological sequence analysis, is available from the University of British Columbia Bioinformatics Center at http://bioinformatics.ubc.ca/pegasys/.


Genomorama, a software program for interactively displaying multiple genomes, is available from Los Alamos National Laboratory at http://snp.lanl.gov/genomorama. Genomorama runs natively on OS X, Windows, and Linux.


Golden Helix has released HelixTree v3.1 for OS X. The software includes a recursive partitioning data analysis engine for locating genetic and environmental subpopulations. Capabilities include linkage-disequilibrium analysis, haplotype and diplotype estimation, Hardy-Weinberg equilibrium analysis, regression-based haplotype association techniques, and SNP tagging.


DNAStar has released Lasergene v6.1. The release addresses “some usability and performance issues identified by customers after the release of Lasergene 6.0 in November 2004,” the company said.

 

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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.