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SOL Bioinformatics Resources

Documents 
  • [Google doc] SOL Bioinformatics Standards and Guidelines
  • [Wiki] ITAG Wiki
  • [ppt] Detailed IL-BAC mapping protocol.
Meeting Records 
[odt]/[odp] – indicates OpenDocument format, see http://www.openoffice.org
[sxi] – indicates OpenOffice 1.x format, see http://www.openoffice.org
[ppt] – indicates Microsoft Powerpoint format
[txt] – indicates plain text format
[pdf] – indicates PDF format

SOL 2010 Sequencing MeetingTuesday, Sep 7, 2010 
Location
Apex Hotel, Dundee, UK
Notes
meeting minutes by Joyce van Eck [txt]
PAG 2010 Sequencing MeetingTuesday, Jan 12, 2010 
Location
Town and Country Hotel, San Diego, CA, USA
Progress Reports
Assembly Progress: Sandra Smit [pdf]
Notes
Meeting Summary [doc]
EU-SOL Next Gen Assembly WorkshopWednesday, July 15, 2009 12am-5pm 
Location
Schiphol Airport, The Netherlands
Progress Reports
USA: Lukas Mueller [ppt]
UK: Gerard Bishop [ppt]
France: Mondher Bouzayen [ppt]
Italy: Giorgio Valle [ppt]
Other Presentations
Roeland van Ham – General Outline of the Proposed Assembly Strategy [ppt]
Antoine Janssen – The Tomato Whole Genome Profiling Map [ppt]
Notes
Meeting Agenda [pdf]
PAG 2009 Sequencing MeetingSunday, Jan 11, 2009 10am-3:30pm 
Location
Town and Country Hotel, San Diego, CA, USA
Progress Reports
Chr 1 (USA): Joyce Van Eck [ppt]
Chr 2 (Korea): Doil Choi [ppt]
Chr 3 (China): Ying Wang [ppt]
Chr 4 (UK): Gerard Bishop [ppt]
Chr 7 (France): Mondher Bouzayen [ppt]
Chr 12 (Italy): Giovanni Giuliano [ppt]
Other Presentations
Todd Vision – Mimulus guttatus sequencing progress [ppt]
Steven Stack – Role of FISH in tomato sequencing [ppt]
Roeland van Hamm – Whole-genome shotgun sequencing for tomato[ppt]
Notes
Meeting Agenda (Joyce Van Eck) [pdf]
meeting notes by Robert Buels [txt]
SOL 2008 Sequencing MeetingWednesday, Oct 15, 2008 7pm-11pm 
Location
Holiday Inn Cologne am Stadtwald, Cologne, NRW, Germany
Progress Reports
Chr 1 (USA): Jim Giovannoni [ppt]
Chr 2 (Korea): Doil Choi [ppt]
Chr 3 (China): Chuanyou Li [ppt]
Chr 4 (UK): Gerard Bishop [ppt]
Chr 5 (India): Akhilesh Tyagi [ppt]
Chr 6 (Netherlands): Sander Peters [ppt]
Chr 7 (France): Mondher Bouzayen [ppt]
Chr 8 (Japan): Shusei Sato [ppt]
Chr 9 (Spain): Joyce Van Eck for A. Granell [ppt]
Chr 11 (China): not present
Chr 12 (Italy): Giovanni Giuliano [ppt]
Other Presentations
Roeland van Hamm – Whole-genome shotgun sequencing proposal[ppt]
Notes
meeting notes by Robert Buels [txt]
Supplementary Material
Titanium-series 454 sequencing overview (from Roche) [pdf]
Wageningen Finishing meeting 2008Thu, Apr 24 - Fri Apr 25, 2008, 9:00am-5pm 
Location
Wageningen Conference Center (WICC), Netherlands
Presentions
Chromosome 2 update H. Jo
Chromosome 3 update Y. Wang
Chromosome 4 update H. Beasley
Chromosome 5 update T.R. Sharma
Chromosome 6 update S. Peters
Chromosome 7 update M. Philippot
Chromosome 8 update S. Sato
Chromosome 9 updat S. Zuniga
Chromosome 11 update Z. Zhang
Chromosome 12 update J. Falcone
Presentations about discussion topics
Sanger Finishing Tools
Solexa Issues
Discussion slides (K. McLaren)

This meeting was organized by the EU-SOL project.
 
PAG 2008 meetingSun, Jan 13, 2008, 9:00am-4pm 
Location
The Boardroom, Town and Country Hotel, San Diego, California, USA
Progress Reports
Chr 1 (USA): Joyce Van Eck [ppt]
Chr 2 (Korea): Doil Choi [ppt]
Chr 3 (China): Mingsheng Chen [ppt]
Chr 4 (UK): Clare Riddle [ppt]
Chr 5 (India): Nagendra Singh [ppt]
Chr 6 (Netherlands): Rene Klein-Lankhorst [ppt]
Chr 7 (France): Mondher Bouzayen [ppt]
Chr 9 (Spain): not present
Chr 11 (China): Sanwen Huang [ppt]
Chr 12 (Italy): Alessandro Vezzi [ppt]
Other Presentations
Hans de Jong – BAC FISH and repeat bar-coding technology for tomato and potato [ppt]
Giovanni Giuliano – Finishing Criteria [ppt]
Mingsheng Chen – Towards an Integrated Physical Map of the Tomato Genome [ppt]
Steven Stack – Role of FISH in Tomato Genome Sequencing [ppt]
Notes
Meeting Agenda (Joyce Van Eck) [doc]
a few notes by Robert Buels [txt]
SOL 2007 meetingFri, Sept 14, 2007, 8:30am-4pm 
Location
Ramada Plaza Jeju, Jeju City, Korea
Progress Reports
Chr 1 (USA): Jim Giovannoni [ppt]
Chr 2 (Korea): Sunghwan Jo [ppt]
Chr 3 (China): not present
Chr 4 (UK): Gerard Bishop [ppt]
Chr 5 (India): J.P. Khurana [ppt]
Chr 6 (Netherlands): Sander Peters [ppt]
Chr 7 (France): Mondher Bouzayen [ppt]
Chr 8 (Japan): Erika Asamizu (presented earlier in main conference session)[ppt]
Chr 9 (Spain): Antonio Granell
Chr 12 (Italy): Mara Ercolano [ppt]
Other Presentations
Rene Klein-Lankhorst – Using FISH to determine euchromatin/heterochromatin boundaries [ppt]
Mondher Bouzayen – Alternative methods for BAC anchoring [ppt]
Gerard Bishop – Sequencing standards update [ppt]
Stephane Rombauts – ITAG Pipeline [pdf]
Notes
Meeting Summary (Giovannoni, Mueller, Van Eck) [doc]
a few notes by Daniel Buchan [doc]
a few notes by Robert Buels [txt]
1st International Tomato Finishing MeetingMon, Apr 16 - Tues, Apr 17, 2007 
Location
Sanger Centre, Hinxton, UK
Talk Slides
Mapping presentation by Christine Nicholson [ppt]
Finishing presentation by Helen Beasley [ppt]
Meeting Report [Karen McLaren] [pdf]
PAG 2007 meetingSun, Jan 14, 2007 
Location
Terrace Salon 3, Town and Country Hotel, San Diego, California, USA
Progress Reports
Chr 1 (USA): Jim Giovannoni [ppt]
Chr 2 (Korea): Doil Choi [ppt]
Chr 3 (China): not present
Chr 4 (UK): Christine Nicholson [ppt]
Chr 5 (India): Paramjit Khurana [ppt]
Chr 6 (Netherlands): Rene Klein-Lankhorst [ppt]
Chr 7 (France): not present
Chr 8 (Japan): not present
Chr 9 (Spain): Antonio Granell [ppt]
Chr 12 (Italy): Mara Ercolano [ppt]
Other Presentations
Rene Klein-Lankhorst – Using FISH to determine euchromatin/heterochromatin boundaries [ppt]
Jim Giovannoni – Discussion on BAC extension protocols [ppt]
Jim Giovannoni – US Contribution to Sequencing [ppt]
Robert Buels – BAC submission and annotation protocols and tools [odp] [ppt]
Giovanni Giuliano – Tomato Affy chip [ppt]
Nevin Young – Medicago truncatula sequencing update[ppt]
Matthew Lorence – Tomato Affy chip [ppt]
Christian Bachem – Potato Genome Initiative [ppt]
Syngenta – Contribution of BAC mapping to sequencing effort [ppt]
Agenda
by Joyce Van Eck [doc]
Minutes
Notes by Joyce van Eck [pdf].
A few notes by Robert Buels [txt].
Ghent 2006 Tomato Annotation meetingMon, Oct 23-25, 2006 
Location
LEAF Conference Room, Flanders Interuniversity Institute for Biotechnology, Ghent, Belgium
Meeting Summary
by Lukas Mueller and Robert Buels [html] [odt]
Presentations
New Developments at SGN: Lukas Mueller [odp]
Cyrille2 Tomato Annotation: Mark Fiers and Erwin Datema [ppt]
Training GeneID: Francisco Camara [ppt]
India Sequencing Progress: Saloni Mathur [ppt]
SOL 2006 meetingWed, Aug 26, 2006, 8:30am-11:45am 
Location
Hall of Ideas Room E, Monona Terrace Convention Center, Madison, Wisconsin, USA
Progress Reports
Chr 1 (USA): Jim Giovannoni [ppt]
Chr 2 (Korea): Sung-Hwan Cho [ppt]
Chr 3 (China): Eileen Wang [ppt]
Chr 4 (UK): Christine Nicholson and Karen McLaren [ppt]
Chr 5 (India): Jitendra Khurana [ppt]
Chr 6 (Netherlands): Roeland van Hamm [ppt]
Chr 7 (France): Farid Regad [ppt]
Chr 8 (Japan): Erika Asamizu [ppt]
Chr 9 (Spain): Antonio Granell [ppt]
Chr 12 (Italy): Silvana Grandillo [ppt]
Minutes
notes by Robert Buels and Marty Kreuter [txt]
notes by Lukas Mueller (includes potato session and afternoon bioinformatics session) [txt]
PAG 2006 meetingSun, Jan 16, 2006, 1pm-6pm 
Location
Dover Room, Town and Country Hotel, San Diego, California, USA
Progress Reports
Chr 1 (USA): Lukas Mueller
Chr 2 (Korea): not present
Chr 3 (China): Eileen Wang [ppt]
Chr 4 (UK): Christine Nicholson
Chr 5 (India): not present
Chr 6 (Netherlands): Rene Klein-Lankhorst [ppt]
Chr 7 (France): not present
Chr 8 (Japan): not present
Chr 9 (Spain): not present
Chr 12 (Italy): Giovanni Giuliano [ppt] and Giorgio Valle [ppt]
Other Presentations
Remy Bruggman – Training Gene Finders for Tomato [ppt]
Robert Buels – Submitting BACs to SGN [sxi] [ppt]
Stephen Stack – Tomato FISH [ppt]
Naama Menda – Ontologies for Describing Solanaceae Phenotypes ppt
Minutes
a few notes by Robert Buels [txt].
Dutch BAC extension protocol
The complete protocol as presented by Rene Klein Lankhorst, kindly provided by Sander Peters [doc | pdf]
SOL 2005 meetingWed, Sep 28, 2005 
Location
Ischia, Italy
Agenda
Link
Progress Reports
Intro: Lukas Mueller [sxi]
Chromosome 1: Lukas Mueller [sxi]
Chromosome 2: [ppt]
Chromosome 3: Eileen Wang [ppt]
Chromosome 4: Christine Nicholson [ppt]
Chromosome 5: Jiten Khurana [ppt]
Chromosome 6: Rene Klein-Lankhorst [ppt-part1] | [ppt-part2]
Chromosome 7: Farid Regad
Chromosome 8: Satoshi Tabata
Chromosome 9: No presentation (only recently funded)
Chromosome 12: Mara Ercolano [ppt]
Key conclusions
  • Evidence presented indicates that a number of gene prediction programs tested with different matrices don't work reliably on tomato genomic sequence. It is therefore necessary to calibrate them for use with tomato. A training/test set will be developed for this purpose by MIPS/Ghent/U Naples.

  • Extension BACs were found for all seed BACs on chromosome 6 and for more than half the seed BACs on chromosome 2. This shows that the approach is sound, but the lower success rate on chromosome 2 needs to be investigated.
PAG meeting 2005Sat, January 15, 2005, 1pm-6pm 
Location
Dover Room, Town and Country Hotel, San Diego, California, USA
Agenda
pdf
Progress Reports
Chr 1 (USA): Lukas Mueller [ppt]
Chr 2 (Korea): Doil Choi [ppt]
Chr 3 (China): not able to attend
Chr 4 (UK): Christine Nicholson presentation [without slides]
Chr 5 (India): Arun Sharma [ppt]
Chr 6 (Netherlands): Rene Lank Kleinhorst
Chr 7 (France): Farid Regad presentation [without slides]
Chr 8 (Japan): Satoshi Tabata [ppt]
Chr 9 (Spain): (Funding in progress)
Chr 12 (Italy): Maria Luisa Chiusano [ppt]
Other presentations
Lukas' Solanaceae workshop presentation [ppt]
Eileen's Overgo and BAC selection presentation [ppt]
Minutes
Kindly provided by Robert Buels [txt]
SOL 2004 meeting, Wageningen, The NetherlandsSat, Sept 18, 2004, 9am-6pm 
Location
Wageningen, The Netherlands
Presentations
Sarah Butcher, GB [ppt]
Stephane Rombauts, Belgium [ppt]
David de Koeyer, Canada [ppt]
Silvana Grandillo, Italy [ppt]
Lukas Mueller, USA [ppt]
Farid Regad, France
Ralph van Berloo, NL
Key Conclusions
Data archiving, formats and access
  • Primary data needs to be archived and available to anyone
  • Procedure/method/parameters used to generate a dataset need to be documented
  • All working on a common datatype should agree on a common exchange format
Data Access
  • Central archive at SGN
  • Method, how data arrives at SGN (upload, download, SMTP) agreed between SGN and other data source
  • Data providers should implement the services required to integrate into the SOL platform/workgroup
Credit and Traceability
  • Keep original source information even if data travels through many hands
Annotation
  • Sequences--> a one-stop-shop
  • Latest BAC, transcripts available
  • FTP, maintain version and history of sequences @ SGN
Minutes
[from Sarah]
[from Heiko]