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August 2009 GMOD Meeting
| August 2009 GMOD Meeting 6-7 August, 2009 Oxford UK
|
GMOD Europe 2009 | GMOD Europe 2009}} |
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The next GMOD Community Meeting will be held 6-7 August, 2009, in Oxford UK. The meeting is a part of GMOD Europe 2009, a week long event that also includes a GMOD Summer School. This is the first time a GMOD meeting has been held in Europe.
Registration is now open, and space is available on a first come, first served basis. There is room for 50 attendees, and the meeting cost is £50.
As with previous GMOD meetings, this meeting will have a mixture of project talks, component talks, and user talks. The agenda is driven by attendee suggestions, and you are encouraged to add your suggestions now. For examples of what happens at a GMOD meeting, see the writeups of the January 2009, July 2008, or any other previous meeting. GMOD meetings are an excellent way to meet GMOD developers and users, and to learn (and affect) what's coming in the project.
Please join us in Oxford this August.
Cost and Registration
The cost is £50, which includes a catered lunch on Friday. Payment can be made with a credit card. After registering you will receive a confirmation email from Oxford, listing amount paid and your order number.
Space is limited to the first 50 people to register and is available on a first come, first served basis.
Note: We cannot provide invoices. However, we can provide a signed letter on NESCent letterhead stating that payment was received, and listing your order number, and who to contact at Oxford to confirm this. If you want such a letter, please contact Dave Clements.
Schedule
Dr Heng Li of the Sanger Institute will be the meetings special guest speaker. Heng will discuss his recent work with SAMtools, a set of file formats and scripts for efficiently storing and accessing next generation sequence data. A SAMtools adaptor for GBrowse is currently being developed by Lincoln Stein. Heng is one of the chief developers of several projects focused on next generation sequencing, including SAMtools, BWA, and MAQ, as well as the TreeSoft and TreeFam phylogenetic resources.
Scott is actively working on this agenda. If you'd like to leave a comment, add it below in the suggestions section.
Please save your presentations in PDF and then upload the PDF to the wiki by either clicking on the red "PDF" link by your talk (if you have a wiki login), or by sending it to Dave C (if you don't). For reasons that we don't understand, uploading most PowerPoint files currently does not work. Please email your presentations in their original format to Dave C and he will upload them when this works.
| Date | Time | Session | Link(s) |
|---|---|---|---|
| Thursday 6 August |
8:30-12:00 | Last half day of 2009 GMOD Summer School - Europe | |
| 13:30-14:30 | Scott Cain - Introductions and the State of GMOD | Prezi, PDF | |
| 14:30-15:00 | Dave Clements - GMOD Help Desk Stuff | PPT, PDF | |
| 15:00-15:30 | Jun Zhao - Linked Data for GMOD Databases | PPT, PDF | |
| 15:30-15:45 | Coffee Break | ||
| 15:45-16:15 | Steve Taylor - GMOD from the Trenches | PPT, PDF | |
| 16:15-16:30 | Scott Cain (for Robert Buels) - A DBIx::Class layer for Chado | S5 Slides | |
| 16:30-17:00 | Ed Lee - GMOD Biological Object Layer | PPT, PDF | |
| 17:00-17:30 | Josh Goodman - A Restful interface for MODs | PPT, PDF | |
| 17:30 | Dinner (on your own) | ||
| Friday 7 August |
8:45-9:15 | Heng Li - SAMtools for NextGen Sequence Data | PPT, PDF |
| 9:15-9:45 | Dave Clements - GBrowse 2, NextGen, PopGen | PPT, PDF | |
| 9:45-10:15 | Erick Antezana/Frederic Potier - GBrowse 2, Lessons Learned and Statement of Interest. | ||
| 10:15-11:45 | Ian Holmes - JBrowse | ||
| 10:45-11:00 | Coffee Break | ||
| 11:00-11:30 | Sheldon McKay - GBrowse_syn | ||
| 11:30-12:30 | Discussion: NextGen data and GMOD: What do we do (and not do)? | ||
| 12:30-13:30 | Catered Lunch | ||
| 13:30-14:00 | Alessandra Bilardi - GBrowse.org | PPT, PDF | |
| 14:00-14:30 | Jonathan Warren - DAS update | PPT, PDF | |
| 14:30-15:00 | Julie Sullivan - InterMine update | PPT, PDF | |
| 15:00-18:00 | Show and Tell, Discussion | ||
Agenda Suggestions
If you have items that you would like to discuss (or be discussed) at this meeting, please add them here.
- Project update
- GMOD REST API - Presentation of the current draft spec and a feedback/discussion period. --Jogoodma
- DAS: Current Situation and Developments -- JWarren
- InterMine - update and new project with SGD, RGD and ZFIN -- Julie Sullivan
- Next Generation Sequencing - methods for viewing NGS data in GBrowse -- Steve Taylor
- GBrowse 1.70 and 2.0 releases
- JBrowse 1.0 release
- GBrowse_syn update
- Apollo plans for the next generation of Apollo
- Chado 1.1 release
- GMOD for Metagenomics? -- Clements
- Assembly life cycle management for beginners --DanBolser 14:04, 20 July 2009 (UTC)
- Linked Data for GMOD Databases - making GMOD databases machine-accessible to achieve better data sharing and reuse for bioinformaticians and application developers -- Jun Zhao
- GMOD Biological Object Layer framework
Location
The meeting is being held at the Medical Science Teaching Centre (MSTC) at the University of Oxford, in Oxford, United Kingdom.
The course will be held in the Lower Ground Seminar Rooms (LGa / LGb) of the MSTC.
Lodging
See the Lodging section of the GMOD Europe 2009 page for information on lodging for both the summer school and this meeting.
Mailing List
The meeting has a mailing list that all meeting related correspondence will be sent to:
Once you register for the meeting, your email address will be added to the list within 24-48 hours. Any meeting participant can send an email to the list.
Sponsors
We would like to thank the Computational Biology Research Group (CBRG) of the University of Oxford for hosting and sponsoring the week's events.
We would also welcome additional sponsors to help reduce the cost of registration. Please contact the GMOD Help Desk if you are interested.
Attendees
| First Name | Last Name | Affiliation |
|---|---|---|
| Ambrose | Andongabo | Rothamsted Research |
| ERICK | ANTEZANA | BAYER BIOSCIENCE NV |
| T. Grant | Belgard | MRC FGU |
| Alessandra | Bilardi | CRIBI - University of Padova |
| Dan | Bolser | Dundee University |
| Baptiste | Brault | INRA Versailles |
| Tim | Burgis | Imperial College- London |
| Scott | Cain | Ontario Institute for Cancer Research |
| Maria | Cartolano | University of Oxford |
| Dave | Clements | NESCent |
| Ros | Cutts | Imperial College |
| sobral | daniel | IBDML |
| Etienne P | de Villiers | ILRI |
| Phil | East | Cancer Research UK |
| Matt | Eldridge | Cancer Research UK- Cambridge Research Institute |
| Ben | Elsworth | University of Edinburgh |
| Josh | Goodman | FlyBase (Indiana University) |
| Cyprien | GUERIN | INRA |
| Zong-Pei | Han | Computational Biology Research Group, Oxford |
| Andreas | Heger | MRC FGU |
| Ian | Holmes | UC Berkeley |
| Jim | Hughes | MRC |
| Bernd | Jagla | Institut Pasteur |
| Baptiste | Laporte | IBDML |
| Ed | Lee | Lawrence Berkeley National Laboratory |
| Jacob | Lemieux | Computational Biology Research Group |
| Siu-wai | Leung | University of Macau |
| Christopher | Love | Rothamsted Research |
| Emanuele | Marchi | University of Oxford |
| Simon | McGowan | Computational Biology Research Group, Oxford |
| Sheldon | McKay | Cold Spring Harbor Laboratory |
| FREDERIC | POTIER | BAYER BIOSCIENCE NV |
| Peter | Rice | European Bioinformatics Institute |
| Kim | Rutherford | University of Cambridge |
| michelle | simon | Medical Research Council |
| Aengus | Stewart | London Research Institute CRUK |
| Julie | Sullivan | InterMine- Dept of Genetics- Cambridge |
| Steve | Taylor | Computational Biology Research Group, Oxford |
| Adrian | Tivey | Wellcome Trust Sanger Institute |
| Giles | Velarde | Welcome Trust Sanger Institute |
| Pieter Emiel | Ver Loren van Themaat | Macx Planck Institute for Plant Breeding Research |
| Jonathan | Warren | The Sanger Institue |
| Xikun | Wu | Institute for Animal Health |
| Jun | Zhao | University of Oxford |
| Pinglei | Zhou | Harvard University/FlyBase |
Evaluation
Please provide feedback on this meeting.
