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mpiBlast-pio, Marvin 5, JChem 5, Glycine max, ACD/Analytical Automation Suite, BioVenn

Version 1.5.0 of mpiBlast-pio (parallel input/output) is available from the mpiBlast development team here.
New features include a portable high-performance input/output that works on serial and parallel file systems; scalable database pre-distribution; and in-memory caching of database fragments. The software is distributed with an NCBI toolbox and has been “stress tested” on more than 12,000 cores, according to the development team.

ChemAxon has released Marvin 5 and JChem 5.
New features in Marvin 5 include a customizable graphical user interface, the ability to copy and paste live objects to Word, Excel, and other programs, new chemical features for drawing coordinative bonds and Markush features, and new calculator plug-ins for IUPAC name generation and Markush enumeration.
New features in JChem 5 include new table types for storing query substructures and Markush libraries, performance improvements, faster return of database search results, and support for much larger input sets.

The Department of Energy’s Joint Genome Institute has released a preliminary assembly and annotation of the soybean genome, Glycine max, here.
The current assembly, which represents 7.23x coverage, is a “preliminary release” based on a partial dataset, JGI said. The institute expects to replace this with an improved, chromosome-scale "Glyma1" version by the end of 2008.

ACD/Labs has launched ACD/Analytical Automation Suite, a modular software package for processing and interpreting spectral and chromatographic data with “minimal human involvement,” according to the company.
ACD/Analytical Automation Suite allows users to automate processing, data interpretation, reporting, and storage of spectral and chromatographic results from multiple analytical techniques and numerous vendors.

Radboud University Nijmegen’s Center for Molecular Life Sciences has released BioVenn, a web application for summarizing the overlap between two or three lists of identifiers using area- proportional Venn diagrams.

Filed under

The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.