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Downloads & Upgrades: EBI; Bowtie 2 2.0.0-beta 4; Labguru; Opera; IDBS; PDB; Lipid Structures App

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The European Bioinformatics Institute said this week that it plans to phase out several alternative splicing databases in 2012.

The EBI is discontinuing its Alternative Splicing Database, the Alternative Transcript Diversity Database, the Alternative Exon database, and the Alternative Splicing and Transcript Diversity Database.

In future, researchers will be able to retrieve data on alternatively spliced transcripts in model organisms from Ensembl. Additionally, they will have access to archived data from all four projects on the EBI ftp site.

Separately, the EBI released version 86 of the Chemical Entities of Biological Interest small-molecule database, which contains 26,724 fully annotated compounds.


Bowtie 2 2.0.0-beta 4 is available here.

The release includes accuracy and speed improvements and several bug fixes among other updates.


This week, BioData launched Labguru, a research management web application for use in academic labs.

The tool helps researchers plan experiments; track progress; annotate and share results, figures, protocols, and papers; manage inventories; and organize related documents, protocols, and data. It also lets users locate reagents and samples and schedule use of shared equipment.

Labguru is free for individual use. For a monthly fee, researchers can access features related to collaboration, order management, and equipment scheduling.


Researchers at the Genome Institute of Singapore have released a computational tool, dubbed Opera, which provides a systematic approach to reconstruct DNA sequences. According to the developers, the method guarantees the quality of the solution and scales to large datasets.


This week, IDBS released a free 'real-time' publication capability that lets research chemists publish chemistry data and send it directly to the ChemSpider database from the company's E-WorkBook software.

The new application lets users access ChemSpider’s chemistry content directly from E-WorkBook and explore physical and biological properties, spectra, suppliers, links, and safety information about compounds prior to using the compounds in their experiments. It also lets researchers share and reuse their work.


The Protein Databank has made several updates to its website.

The new features include tools to support molecular surfaces to aid in the display of quaternary structure, protein-protein interactions, and binding sites; improved Jmol visualization, information about subcomponents, and links to DrugBank have been added to Ligand Summary pages; and binding affinity data from PDBbind has been added to the external ligand annotations widget on structure summary pages.


Elsevier and the Lipid Maps Structure Database consortium have launched a beta version of the Lipid Structures app on Elsevier's SciVerse Applications website.

According to the developers, the tool identifies and links lipid names or synonyms to articles in the SciVerse ScienceDirect website. The application draws on the LMSD to provide information on things like common and systematic names, formula, exact mass, InChIKey, classification hierarchy, and links to other public databases.


Filed under

The Scan

Self-Reported Hearing Loss in Older Adults Begins Very Early in Life, Study Says

A JAMA Otolaryngology — Head & Neck Surgery study says polygenic risk scores associated with hearing loss in older adults is also associated with hearing decline in younger groups.

Genome-Wide Analysis Sheds Light on Genetics of ADHD

A genome-wide association study meta-analysis of attention-deficit hyperactivity disorder appearing in Nature Genetics links 76 genes to risk of having the disorder.

MicroRNA Cotargeting Linked to Lupus

A mouse-based study appearing in BMC Biology implicates two microRNAs with overlapping target sites in lupus.

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.