Communication of Data from the Dynamic Genome -- A UHTS Data Workshop
| Background Emerging technologies for very high-throughput DNA sequencing are being applied to many biological problems. The Microarray and Gene Expression (MGED) Society, the author of MIAME standard for microarray data, in collaboration with the Genomics Standards Consortium is organizing a workshop to develop standards for exchanging ultra-high throughput sequencing (UHTS) data. Participants will be actively working to adapt existing data exchange standards, such as MIAME, MIGS, MAGE-TAB and OBI, towards expressing key aspects of experiments exploiting ultra-high-throughput sequencing technologies, especially with respect to annotating biological annotations of samples and descriptions of experimental details. Some elements of sequencing data exchange standards have already been proposed; for instance Minimum Information about a Genome Sequence (MIGS) covers much of the annotation for a single sequencing run, though does not describe experimental factors of an investigation. The NCBI and EBI are establishing 'Short Read Archives' and are defining the respective description format. However, many of UHTS applications require a consistent format for describing all important experiment elements - sample properties and treatments (metadata), raw data, and summary data, data processing methods, etc., analogous to similar microarray experiments. Since describing biological experiments can be largely technology-independent, we can exploit previously-developed standards for microarray experiments, such as MIAME and MAGE-TAB.
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Aerial photo of LBNL
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| Location 717 Potter St, Berkeley, CA 94720 (offsite from Lawrence Berkeley National Lab) Information on the building site is here
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Transportation Parking is available in the lots at 717 Recommended hotels are approx. 1 mile from site The #19 bus runs on 7th street
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Times Monday and Tuesday, March 17th and 18th, 9am to 5pm
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Agenda
The agenda has not yet been fully determined, but the following topics will likely form part of the agenda
- A comparison of use cases in UHTS for different technologies represented and
for the common applications (e.g., ChIP Seq)
- General agreement as to what to keep and what to share (i.e. a MIAME). In
this regard, what changes if any are required to MIGS/MIMS giving the new
technology and applications?
- Use MAGE-TAB as a strawman effort to see what works and what doesn't for
capturing the results from point 2.
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The Potter St facility is the green school icon in the center of the map.
Nine hotels are shown that are in walking distance. More hotels are located near UC Berkeley Campus. For those looking for upscale accommodations the Claremont hotel in Oakland is well regarded.