Nikos Kyrpides on a GSC Global Genome Census at GSC8

submitted by: JGI

Nikos Kyrpides of the DOE Joint Genome Institute discusses the notion of a global genome census at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

Field on GEM Catalogue and Sansone on ISA-GCDML workshop at GSC8

submitted by: JGI

Dawn Field of the NERC Centre for Ecology & Hydrology briefly introduces the GEM Catalogue, followed by Susanna Sansone of the European Bioinformatics Institute who talks about the ISA-GCDML workshop at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

Vaughan on INSDC submission and Kaye on Sequencing Pipelines at GSC8

submitted by: JGI

Bob Vaughan of EMBL on submitting MIGS/MIMS/MIENS information to EMBL-EBI's system, followed by a brief talk from Jon Kaye of the Gordon and Betty Moore Foundation on standards and the foundation's sequencing pipelines at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

The ELIXIR Database Provider Survey

submitted by: cdsouthan

How biological databases are used in the European Union.

BioHDF - Toward Scalable Bioinformatics Infrastructures

submitted by: mark_welsh

The huge volume of data produced by novel sequencing technologies presents significant challenges around data transmission, storage, bioinformatics analysis, visualization, and archiving. Widespread adoption of Next Generation DNA Sequencing (NGS) will be hindered if bioinformatics software cannot scale to meet these challenges.

Source Organism and Molecule Information at INSDC and the Trace Archives

submitted by: dougramsey
Guy Cochrane, European Nucleotide Archive, EMBL-European Bioinformatics Institute, Welcome Trust Genome Campus The databases of the International Nucleotide Sequence Database Collaboration (INSDC, DDBJ/EMBL/GenBank) and of the Trace and Short Read Archive collaborations between the NCBI and the EBI provide free and comprehensive access to nucleotide sequencing information, from raw sequencing machine output through to functional annotation. As well as offering a direct public portal into...

Antibody-protein interactions: benchmark datasets and prediction tools evaluation

linked profile(s): juliap
submitted by: apryl
Background The ability to predict antibody binding sites (aka antigenic determinants or B-cell epitopes) for a given protein is a precursor to new vaccine design and diagnostics. Among the various methods of B-cell epitope identification X-ray crystallography is one of the most reliable methods. Using these experimental data computational methods exist for B-cell epitope prediction. As the number of structures of antibody-protein complexes grows, further interest in prediction...
Authors: Julia v Ponomarenko, Philip e Bourne

SDSC is Data Centric

linked profile(s): Fran
submitted by: apryl

Fran Berman discusses SDSC's data centric focus and their three key leadership areas.: data-oriented high performance computing, data-storage and preservation, empowering data-oriented communities. Originally posted by SDSC on SDSC's CI Channel at: www.cichannel.org

Structural Evolution of the Protein Kinase–Like Superfamily

linked profile(s): Phil
submitted by: escheeff
The protein kinase family is large and important, but it is only one family in a larger superfamily of homologous kinases that phosphorylate a variety of substrates and play important roles in all three superkingdoms of life. We used a carefully constructed structural alignment of selected kinases as the basis for a study of the structural evolution of the protein kinase–like superfamily. The comparison of structures revealed a “universal core” domain consisting only of...
Authors: Eric d Scheeff, Philip e Bourne