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
[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 Meeting | Tuesday, Sep 7, 2010 |
- Location
- Apex Hotel, Dundee, UK
- Notes
-
meeting minutes by Joyce van Eck [txt]
| PAG 2010 Sequencing Meeting | Tuesday, Jan 12, 2010 |
| EU-SOL Next Gen Assembly Workshop | Wednesday, 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 Meeting | Sunday, 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 Meeting | Wednesday, 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 2008 | Thu, 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 meeting | Sun, 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 meeting | Fri, 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 Meeting | Mon, Apr 16 - Tues, Apr 17, 2007 |
| PAG 2007 meeting | Sun, 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 meeting | Mon, 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 meeting | Wed, 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 meeting | Sun, 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 meeting | Wed, 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.
- 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.
| PAG meeting 2005 | Sat, January 15, 2005, 1pm-6pm |
- Location
- Dover Room, Town and Country Hotel, San Diego, California, USA
- Agenda
- 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 Netherlands | Sat, 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]
Working
