Kolker on a Systems Biology Encyclopedia and Sansone on ISA Infrastructure at GSC8

submitted by: JGI

Eugene Kolker from Seattle Children's Hospital briefly discusses "The Encyclopedia of Systems Biology and OMICS," followed by Susanna Sansone from the EBI on "The ISA Infrastructure for multi-omics data" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 11, 2009.

Tatiana Tatusova on "Annotations in Refseq" at GSC8

submitted by: JGI

Tatiana Tatusova of NCBI discusses "Annotations in Refseq" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 10, 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.

Yilmaz on MIENS specification and Kolker on GSC's non-for-profit

submitted by: JGI

Pelin Yilmaz of the Max Planck Institute-Bremen talks about the MIENS specification and Eugene Kolker of Seattle Children's Hospital discusses the GSC's non-for-profit at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

Field on RCN4GSC and Sterk on MIGS-compliant data curation at GSC8

submitted by: JGI

Dawn Field of the NERC Centre for Ecology & Hydrology briefly describes RCN4GSC and Peter Sterk of the NERC Centre for Ecology & Hydrology follows with a talk on curation of MIGS-compliant data at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

Challenges in Ecological Metagenomics

submitted by: dougramsey
Since the first metagenomics study was published 17 years ago, the ability to make ecological inferences has been limited by sequencing throughput and the ability to analyze the data. Yet, if the potential of metagenomics to help us decipher the structure and function of microbial ecosystems is to be realized, it is essential that our bioinformatics tools motivate our sequencing efforts. This is analogous to the bioinformatics advances that were made to accelerating the sequencing of the...

The Importance of Context for the Design and Interpretation of Comparative Metagenomics Studies: The MINIMESS Proposal

submitted by: dougramsey
Jeroen Raes, European Molecular Biology Laboratory Comparative metagenomics is a powerful tool to detect environment-specific adaptation of the communities that inhabit them. However, a wide range of technical and biological interfering factors hamper the correct interpretation of comparative metagenomics results. Here, I will describe some of these factors and pitfalls and propose a minimal metagenome sequence analysis standard (MINIMESS) to cope with these issues. This suggested...

Analyzing the Mobile Metagenome

submitted by: dougramsey
Metagenomic approaches are being use to investigate many diverse ecosystems and reveal many novel functions therein. However these methods can frequently pass over the DNA which we find in the mobile metagenome or mobilome. Much of this DNA is not easily cloned into fosmids or BACs for functional analysis and DNA based metagenomics projects do not always provide sufficient information to determine from where the sequence arose, genome or mobilome. Couple these limitations to the fact that...

Implementing MIGS/MIMS: The Genomic Contextual

submitted by: dougramsey
The MIGS/MIMS checklist developed by the Genomic Standards Consortium (GSC) aims to enrich our ever growing data collection of genomic and metagenomic sequences. Therefore, the checklist defines what minimal list of contextual data attributes has to be added to the sequences in order to conform to the MIGS/MIMS specification. However, MIGS/MIMS itself does not specify how the contextual data should be documented; thus the GSC is developing the Genomic Contextual Data Markup Language (GCDML),...