IMG, accessible to the public at http://img.jgi.doe.gov/, is a collaborative effort between DOE JGI and the Lawrence Berkeley National Laboratory Biological Data Management and Technology Center.
Instant JChem 2.0, Taverna 1.6, Researchers' Digest, Reactome Knowledgebase Version 22, IMG Version 2.3
Instant JChem 2.0 has been released by ChemAxon, a software solutions provider in the cheminformatics space. This desktop application supports work with chemical and other data on local and remote databases.
This release brings forms and form building, relational data support, advanced query building and multi-user access. Instant JChem Personal Edition features the vast majority of functionality and is free for all users.
For software developers and IT architects, Instant JChem includes its own application programming interface for extensibility and customization, and with the underlying JChem toolkits, offers highly scalable research informatics platforms, according to the company.
Taverna 1.6 was released August 20. It includes several improvements, including GUI support for many processors/ports and a more readable color of nested workflows. It also includes a critical bug fix for multi-threaded nested workflows and an alternative view on the logbook using the data lineage browser, previously introduced as an
update for the Logbook plugin.
Workflows can now be executed remotely using the Taverna remote execution service. The service can be installed in any Tomcat container and allows remote execution of workflows from within Taverna using a plugin.
The service includes a web administration interface for the system administrator and for monitoring the job without starting Taverna.
Taverna 1.6.0 is available here: http://taverna.sourceforge.net/index.php?doc=download.html.
Researchers’ Digest has been released and is freely available at: http://bioinfogp.cnb.csic.es/tools/digest/index.php as a conversion list for grouping genes into functional clusters via text-mining techniques.
Users can paste a table of up to 1000 gene IDs and desxcriptions to ascertain the values of gene expression patterns.
Version 22 of the Reactome Knowledgebase has been released and is accessible here: http://www.reactome.org/!
The curated knowledgebase covers human biological processes ranging from metabolic pathways to hormonal signaling and apoptosis.
Reactome is a curated knowledgebase developed and maintained by the Reactome Knowledgebase team, Lincoln Stein's group at Cold Spring Harbor Lab with Ewan Birney's group at European Bioinformatics Institute.
New material is peer-reviewed and revised as necessary before publication to the web. Reactome entries are linked to corresponding ones in NCBI, Entrez Gene, RefSeq, OMIM, Ensembl genome annotations, HapMap, UCSC Genome Browser, KEGG, ChEBI and Gene Ontology (GO).
Topics discussed in Version 22 include botulinum neurotoxicity, Membrane trafficking and Metabolism of vitamins, pathways for HIV Nef protein interactions (HIV infection pathway), immunoregulatory interactions (immune signaling pathway) and AMPK regulation of fatty acid oxidation.
A new tool, Reactome Mart, is available for comprehensive datamining. Reactome Wiki is available for editing documentation by the user community. As before, Reactome data can be exported in SMBL, Protégé, and BioPAX level 2 formats.
The US Department of Energy’s Joint Genome Institute’s Integrated Microbial Genomes data management system has been upgraded. It now includes new microbial genomes from the Version 2.3 release of the National Center for Biotechnology Information Reference Sequence collection.
The upgraded tool now offers access to fungi, protests, and plant genomes to enhance the breadth of comparative analysis. A new addition of particular interest to DOE is Pichia stipitis CBS 6054, a fungus with the exceptional capability to ferment xylose, five-carbon wood sugar, and yield high levels of ethanol.
The new version of IMG contains a total of 2,878 genomes consisting of 729 bacterial, 46 archaeal, 40 eukaryotic, and 1,661 bacterial phage genomes, and 402 plasmids that did not come from a specific microbial genome sequencing project. Among these genomes, 2,609 are finished and 269 are draft genomes. IMG 2.3 contains 236 microbial genomes sequenced at DOE JGI, consisting of 157 finished and 79 draft genomes.