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Agenda: 1pm Welcome and introductions 1:15 Summary of Wageningen meeting

Agenda: 1pm Welcome and introductions 1:15 Summary of Wageningen meeting 1:30 Reports from chromsome sequencing projects: 1, 10, 11 (USA): Lukas Mueller 2 (Korea): Cheol-Goo Hur 3 (China): not attending? 4 (UK): Christine Nicholson 5 (India): Arun Sharma

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Agenda: 1pm Welcome and introductions 1:15 Summary of Wageningen meeting

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  1. Agenda: • 1pm Welcome and introductions • 1:15 Summary of Wageningen meeting • 1:30 Reports from chromsome sequencing projects: • 1, 10, 11 (USA): Lukas Mueller • 2 (Korea): Cheol-Goo Hur • 3 (China): not attending? • 4 (UK): Christine Nicholson • 5 (India): Arun Sharma • 6 (Netherlands): Rene Klein Lankhorst • 7 (France): Farid Regad • 8 (Japan): Satoshi Tabata • 9 (Spain): (funding in progress) • 12 (Italy): Maria Luisa Chiusano • 3:00 Coffee Break • 3:30 seed BAC selection, verification and shipment overview (Eileen Wang) and discussion • 4:00 Data standards, data transfer, BAC registry • 4:30 Annotation issues and standards (other issues as requested) • 5:30 Planning of next meeting at the SOL meeting in Ischia, Italy.

  2. Attendees • USA: SGN: Beth Skwarecky, Nick Taylor, Robert Buels, John Binns, Cornell: Eileen Wang • Korea: Doil Choi, Cheol-Goo Hur • China: - • UK:Christine Nicholson • India: Arun Sharma • Netherlands: Rene Klein Lankhosrt, Mark van Haaren, Roeland van Ham • France: Mathilde Causse, Farid Regad • Japan: Satoshi Tabata, Daisuke Shibata • Spain: - • Italy: Maria Luisa Chuisano, Mara Ercolano, Giorgio Valle • Canada: David DeKoeyer • Belgium: Stephane Rombauts • Germany: Heiko Schoof

  3. Summary of Wageningen Mtg • Use data format/methods SOL standards • All data attributed to data generators and processors • All centers involved in annotation • Annotation pipeline distributed

  4. BACs • BAC sequences submitted un-altered • Archive original data (chromatograms, assembly files, annotation basis) • No annotations submitted to Genbank clone record • BAC-based annotations

  5. Publications • Publication policy • Every country has priority for their chromosome • Full genome publication by consortium

  6. Central Data Repository • All original data archived in one project archive • Chromatograms, assembly files (.ace), blast reports, etc. • Use standard formats for data • Archive at SGN, other locations

  7. US sequencing project progress

  8. BAC end sequences • Total of 400,000 reads (200,000 BACs from both ends) selected from the 3 BAC libraries • Batch of 75,000 BACs in process (HindIII library) • ~45,000 BAC end sequences already obtained (ftp://ftp.sgn.cornell.edu/tomato_genome/bac_ends/) • SeqWright Inc, Houston, TX • Sheared library reads uploaded to SGN servers

  9. Overgo Anchoring Results Overgo Analysis is complete (all data on SGN) Eileen Wang will talk more about Overgo results

  10. BAC Registry • Keep Track of BACs and their statuses • Not sequenced • In progress • Sequenced • Genbank HTGS status • Comments/problems • Web interface • Demo

  11. SOL Annotation Pipeline • High-quality, timely, homogeneous Annotation among chromosomes • Distributed Pipeline • Moby Services • Standardized MOBY objects for annotation calls • BAC seq obj ------> GAME XML object

  12. Meeting in Ischia, Sept 2005 • Focus annotation • 2 day bioinfo/annotation meeting

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