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Archive for December, 2007

Dawn Field and Susanna-Assunta Sansone guest edited a special issue of the journal OMICS on data standards as an output of the 2nd GSC workshop. There were 22 invited papers including 5 in the area of standardization of genomic data (See: Special_Issue_of_OMICS).
An overview of the issue and its goals is captured in the foreword: http://www.liebertonline.com/doi/pdfplus/10.1089/omi.2006.10.84
The entire issue was open source and many of the papers in the issue continue to be at the top of the most downloaded list: http://www.liebertonline.com/action/showMostReadArticles?journalCode=omi

Special issue of OMICS from the 5th GSC Workshop

Dawn Field and George Garrity have been asked by the OMICS Editor and Chief Eugene Kolker to produce a special issue of OMICS based on the 5th GSC Workshop. After guaging interest in this prior to the workshop, and in response to developments at the workshop, we are going to accept this invitation.We are now considering proposals from the participants of the 5th GSC workshop (and their colleagues) for contributions on several key topics of special interest to the GSC.

Further information:

GSC web site: http://gensc.org

Dawn Field : contact info

George Garrity : contact info

Susanna-Assunta Sansone : contact info

Eugene Kolker : contact info

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The latest release of GenCat is available to download from the project SourceForge SVN repository:

gencat release-1.1

GenCat uses the latest technology including Orbeon Forms, eXist, AJAX, XForms and XML Pipeline Language (XPL/XPROC), and provides a generic XML data catalogue with input forms generated on-the-fly from XML schema files, to capture schema-compliant XML instances.

GenCat has been implemented as the Genome Catalogue, an online repository from the Genomic Standards Consortium (GSC) containing MIGS/MIMS-compliant reports.

For further information:

GSC web site: http://gensc.org

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Further to the 5th Genomic Standards Consortium (GSC) workshop, slides are available to download from the GSC wiki:

agenda and presentations

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At the 5th Genomic Standards Consortium (GSC) workshop held at the EBI on 12-14th December 2007, discussions led to a proposal to standardise the description of 16S sequences using the GSC community-led standard called Minimum Information about a Genome Sequence/ Metagenome Sample (MIGS/MIMS).

MIGS/MIMS defines descriptors that can assist in the capture of a rich set of information about 16S sequences using a community-led standard.

Further information is available on the GSC wiki:

http://gensc.org/gc_wiki/index.php/MIGS/MIMS_for_16S

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The 5th GSC Workshop is underway. The workshop will run from 12-14th December, and is hosted at the EBI in Hinxton. The GSC wiki will be updated during the workshop. For further information visit

http://gensc.org/gc_wiki/index.php/5th_GSC_Workshop

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