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Archive for May, 2007

The 4th Genomic Standards Consortium Workshop will be held next week, 6-8th June, 2007 at the National Institute for Environmental e-Science (NIEeS), Cambridge.

As at previous workshops there will be a mix of talks and discussion sessions, although this year the talks will be shorter and more focused on progress made towards GSC goals. There will be 6 sessions covering key topics of interest to the GSC.

There will be a special focus on progress to date, the development of MIMS, future implementation of MIGS/MIMS, CVs and ontologies for describing genomes and metagenomes, the need for a single, global list of genomes and metagenomes and the role of the GSC’s proposed Genomic Rosetta Stone.

The latest agenda is available on the GSC wiki. Workshop homepage on NIEeSweb site

Date: 6-8 June, 2007

Venue: National Institute for Environmental e-Science, Cambridge, UK

Organizers: Dawn Field, Tatiana Tatusova, Tanya Gray, George Garrity, and Frank Oliver Glöckner

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Minimum Information about a Genome Sequence/ Minimum Information about a Metagenomic Sequence/Sample

Some pointers to resources to retrieve, visualize and explore the MIGS/MIMS specification:

Introduction to MIGS/MIMS

GSC Wiki page describing MIGS/MIMS

MIGS/MIMS XML Schema web service

The MIGS/MIMS XML schema can be downloaded via a URL-based web service. The web service API is described in the GSC wiki.

MIGS/MIMS XML Schema CSV file

The same web service allows the XML schema to be downloaded as a comma separated text file (csv) that can be imported into a spreadsheet application, including Google Docs.

GSC Wiki page describing web service to download MIGS XML schema and CSV file

MIGS XML schema download

The following link also allows the XML schema file to be downloaded:

Download latest MIGS XML schema file

 

MIGS/MIMS graph visualization

Graph visualization of latest MIGS schema (Java applet)


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From a news release (April 30, 2007) describing research by an international team of scientists led by Scripps Institution of Oceanography at UC San Diego and the Department of Energy’s Joint Genome Institute:

The international team’s work, published in the online edition of Proceedings of the National Academy of Sciences, is the first comparison of the genetic makeup of two closely related eukaryotic phytoplankton and the mechanisms that make them biologically similar and distinct.

“Through our research we’ve been trying to understand Ostreococcus’ role in marine ecosystems,” said Palenik, who indicated Ostreococcus cells contain nearly five times the DNA of comparably sized organisms such as cyanobacteria. Genomics has taught us that you can learn much more when you can do a comparison. The first genome is exciting but the second genome is even more exciting because you can suddenly compare organisms and see what each is doing differently and what they are doing the same.”

The researchers comparison of Ostreococcus lucimarinus (recently sequenced by the Department Of Energy’s Joint Genome Institute) and Ostreococcus tauri yielded several surprising results, including the documentation of a “new” chromosome differing between the species. Another chromosome appeared somewhat different between the species and the researchers believe it may serve as a gene transfer “trash can” where foreign DNA is integrated. Yet another difference was the identification of a chromosome featuring the same—albeit rearranged—genes in the two species. The researchers hypothesize that this chromosome may be related to sexual functions because the rearrangements are enough to prevent sex between the species.

Genome report for Ostreococcus tauri:

http://darwin.nox.ac.uk/gsc/gcat/report-file/000191_GCAT.xml/html

Genome report for Ostreococcus lucimarinus:

http://darwin.nox.ac.uk/gsc/gcat/report-file/BA93C73D-0D9E-90E5-FC3C-27F61FF8D162.xml/html

Genome wiki page for Ostreococcus tauri:

http://darwin.nerc-oxford.ac.uk/gc_wiki/index.php//gcat/report-file/000191_GCAT.xml/html

News release:

http://ucsdnews.ucsd.edu/newsrel/science/04-07GenomeMA-.asp

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