Symyx Technologies has released Isentris 3.1. The new version of the informatics platform enables the creation, management, and sharing of searchable local databases with full insert, update, and delete capabilities. Other new features include molecule and reaction clustering; chemical structure searching in Excel spreadsheets; molecule- and reaction-based enumeration of results into Isentris for Excel; support for polymers, mixtures, and formulations; and writable .NET controls for inserting, updating, and deleting data.
IMG, IMG/M, IMG/EDU, Biopython 1.48, OpenMM, BASE 2.8, Milliplex Analyst, RefSeq 31, Isentris 3.1
The Department of Energy’s Joint Genome Institute has updated its Integrated Microbial Genomes data-management system, updated the content of its IMG/M metagenome data management and analysis system, and launched an educational companion site, IMG/EDU.
Version 2.6 of IMG includes new microbial genomes from RefSeq 29. IMG 2.6 includes 4,207 genomes consisting of 1,078 bacterial, 56 archaeal, and 40 eukaryotic genomes, 2,230 bacterial phages, and 803 plasmids that did not come from a specific microbial genome sequencing project.
IMG/M now includes three additional metagenome datasets: a microbial community from Lake Washington in Seattle (Nature Biotechnology, August 2008), a hypersaline microbial mat (Molecular System Biology 4, June 2008), and the airborne metagenome in an indoor urban environment (PLoS One 3, April 2008).
IMG/EDU, developed to support JGI's Education Program in Microbial Genome Annotation, was designed to teach microbial genome analysis and annotation using specific microbial genomes in the comparative context of all the genomes available in IMG.
Details and downloads for all three resources are available here.
Biopython 1.48 is available here. The release includes support for several new file formats in the Bio.SeqIO and Bio.AlignIO modules, including reading and writing "tab" format, writing "nexus" files, reading "pir" files, and basic support for writing "genbank" files. It alsos includes some updates to the Bio.Sequencing parsers.
Simbios, a National Center for Biomedical Computing based at Stanford University, has released a preview of OpenMM here.
OpenMM is an API written in C++ for executing molecular dynamics simulations on high performance computer architectures, such as GPUs or computer clusters communicating over a network. According to a statement from Simbios, the OpenMM “will make it easier for molecular dynamics code to benefit from hardware acceleration, such as with GPUs.”
The preview release provides reference code only and is intended to give people a “first look” at the API and to solicit feedback, Simbios said.
The center said it plans to release Gromacs code using the API on Dec. 1.
Millipore and its development partner VigeneTech have launched Milliplex Analyst, a software package that is integrated with the xPONENT software that controls Luminex multiplexed bioassay instruments.
Milliplex Analyst includes “unique algorithms and analytics” that enable rapid processing of multiplex data sets, the companies said. The software complements Millipore’s Milliplex MAP kits, a set of analytes for multiplexing using the Luminex xMAP platform.
Sweden's University of Lund has released BASE (BioArray Software Environment) 2.8, a free database for microarray data, here.
New features include several batch import/update plug-ins that allow users to import data more easily than prior versions of the software.
The National Center for Biotechnology Information has released RefSeq 31.
The release includes genomic, transcript, and protein data available as of Aug. 30, and includes 9,145,702 records, 5,859,648 proteins, and sequences from 5,513 different organisms.