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eGenomics: Cataloguing our complete genome collection7-9 September 2005 |
Our complete genome collection, the result of a significant investment of public funds, is one of our most valuable biological resources and also one of the most complex. The value of these data lies in the ability to view, compare and contrast the entire genetic complement of a wide range of organisms. The complexity of these data stems not only in the vast number of biological features within these genomes (i.e. genes, promoters, binding sites etc) but also in the complexity of the evolutionary relationships and ecological lifestyles - factors that play a major role in shaping genome features and content - of the organisms to whom these genomes belong. The scientific community would benefit significantly from the establishment of a data standard to capture more of this complexity. This standard could provide electronic, machine-readable reports for submission to a public database at the time of publication of each genome (analogous to the submission of genome annotation files). In this way, the experts on each organism would be directly responsible for providing data to the wider community about the detailed features of the organism. Currently the difficulty of obtaining such metadata in a high quality and easily accessible format is a common bottleneck in large-scale computational studies and a significant source of difficulties in the process of scientific discovery. Likewise, merging ecological and environmental data with complete genome sequences opens up a new area of research possibilities. The creation of this genome catalogue would provide an extensive amount of novel data and a powerful new research tool.
This workshop is being organised by Dawn Field of the Centre for Ecology and Hydrology, Oxford and Tatiana Tatusov of the National Centre for Biotechnology Information.
The aims of this workshop are to:
Wednesday 7th September | |
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10:00 |
Registration/coffee |
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10:30 |
Welcome, background and goals of workshop (Dawn Field and Tatiana Tatusov, Oxford Centre for Ecology and Hydrology and the NCBI) |
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10:45 |
Introduction to The National Institute for Environmental E-Science (Stuart Ballard, NIEeS) |
Session I: Overview of our current and future genome collection | |
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11:00 |
GBMF Marine Microbial Genome Sequencing Project: Status Report for Phase One (Lita Procter, Moore Foundation) |
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11:20 |
Overview of Sanger Genome sequencing projects (Julian Parkhill, Sanger Centre) |
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11:40 |
The promise of Metagenomics (Robert Feldman, SymBio Corporation) |
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12:00 |
Open Discussion on "Diversity and commonalities among genome sequencing projects and the need for improved metadata capture" |
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13:00 |
Lunch |
Session II: Databases and Metadata capture efforts | |
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14:00 |
NCBI’s Genome Projects Database, (Tatiana Tatusov, NBCI) |
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14:20 |
The Integrated Microbial Community Genome (IMcG) Data Management Project (Victor Markowitz, Lawrence Berkeley National Lab) |
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14:40 |
The Genome Properties project (Jeremy Selengut, TIGR) |
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15:00 |
FIG and the SEED project (Robert Edwards, Burnham Institute) |
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15:20 |
Coffee |
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16:00 |
From genomes to Phenotypes: PUMA2 a system for high-throughput evolutionary analysis of Metabolism (Natalia Maltsev, Argonne National Laboratory) |
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16:20 |
The GenomeMine: The need for improved genomic metadata capture and exchange (Dawn Field, Oxford Centre for Ecology and Hydrology) |
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16:40 |
The GenomeAtlas: 20 Methods for Comparison of Bacterial Genomes (Dave Ussery, The Technical University of Denmark) |
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17:00 |
Open Discussion on "Data Capture and Exchange: Harmonization of Efforts" |
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17:30 |
Close |
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Thursday 8th September | |
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9:00 |
GO and MODs (Michael Ashburner, EBI) |
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9:20 |
SO and MODs (Suzi Lewis, UC Berkeley) |
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9:40 |
Face to Face Knowledge elicitation to Bootstrap Ontology building (Robert Stevens, University of Manchester) |
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10:00 |
The Taxonomic Concept (Jessie Kennedy, Napier University) |
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10:20 |
MIAME / Env (Norman Morrison, University of Manchester) |
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10:40 |
TBA (George Garrity, Michigan State University) |
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11:00 |
Coffee |
Session IV Demonstration Genomes | |
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11:30 |
Features of Bacterial pathogens (Nick Thomson, Sanger Centre) |
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11:50 |
Features of environmental viruses and plasmids (Sarah Turner, Oxford Centre for Ecology and Hydrology) |
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12:10 |
Planning for Data Management Infrastructure Needs in Genome-Enabled Environmental Microbiology Research (Matt Kane, National Science Foundation) |
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12:30 |
Open Discussion on "Issues and Challenges" |
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13:00 |
Lunch |
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14:00 |
Small group discussions at NIEeS or external visits |
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15:00 |
Coffee |
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15:30 |
Small group discussions at NIEeS or external visits |
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17:30 |
Close |
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Friday 9th September | |
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9:00 |
Evaluation of draft standard |
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10:30 |
Coffee |
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11:00 |
Evaluation of proposals for a metadata exchange format |
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13:00 |
Lunch |
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14:00 |
Membership and scope of GSWG; The Genomic Standards Working Group: A road map |
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15:00 |
Formal close of workshop and Coffee |
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15:30 |
Close |
The workshop will take place in the Centre for Mathematical Sciences, Cambridge. Details of the location, including travel plans, can be obtained here.
Overnight accommodation will be provided in Churchill College Cambridge (accommodation and breakfast & evening meals). The workshop dinner on the evening of 8th September will also be held in Churchill College.
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Centre for Mathematical Sciences, main entrance. |
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Churchill College from the junction with the main road. The entrance is on the right hand side of this photograph. |
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There is no registration charge for this workshop. Accommodation in Churchill College and meals (including the conference dinner) for UK academic participants will be provided with no charge. Registration is essential and must be done using our on-line form. In order to facilitate productive discussion, it may be necessary to limit participation numbers. You are therefore advised to book early. The NIEeS will refund reasonable travel expenses. In the event of any difficulty in booking, including not receiving an email confirmation within 24 hours, please email the NIEeS office. |
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For information about registration, and all other types of queries, please contact the NIEeS office in the first instance.
