SBGN-3
The third SBGN meeting will be held on September 30, 2007, in Long Beach, California, at the Hyatt hotel in Long Beach in room “Seaview C”. The meeting is being funded by Japan’s New Energy and Industrial Technology Development Organization. The workshop co-organizers are:
- Hiroaki Kitano (SBI & Sony CSL)
- Mike Hucka (Caltech)
- Nicolas Le Novère (EBI)
- Akira Funahashi (SBI & JST)
Contents |
Registration
Agenda
The SBGN community has so far developed a still-incomplete draft specification for SBGN Level 1. In this workshop, our aim will be to discuss and settle the remaining issues. In particular, we need to discuss and polish the notation for state-transition diagrams, and discuss entity relationship diagrams.
| Time | Topic | Who | Files |
|---|---|---|---|
| 8:30 AM - 8:45 AM | Welcome and introduction | H. Kitano & N. Le Novère | Draft of 2007-09-27 (PDF) |
| 8:45 AM – 10:20 AM | Summary of currently agreed-upon symbols and remaining controversies | N. Le Novère | (PDF) |
| 10:50 AM – 12:00 AM | Continuing discussion of problematic and controversial symbols | N. Le Novère | |
| 12:00 AM – 1:30 PM | Lunch | Everyone | California Pizza Kitchen |
| 1:30 PM – 2:30 PM | Continuation of discussion of the reduced notation | ||
| 2:30 PM – 4:00 PM | Discussion of entity-relationship diagrams | ||
| 4:00 PM – 5:30 PM | To be determined | ||
| 5:30 PM – 6:00 PM | Discussion of future plans |
We will make arrangements for coffee/tea/soda/water breaks (one in the morning, one in the afternoon) and a lunch for everyone at the meeting. It is likely there will be a self-paid group dinner arranged as well; we will announce the details when they have been worked out.
Workshop Participants
| Name | Affiliation | Group/Project |
|---|---|---|
| Frank Bergmann | University of Washington (USA) | SBW |
| Michael Blinov | University of Connecticut Health Center (USA) | BioNetGen & BioNetGen@VCell |
| Octavian Bucur | Harvard Medical School (USA) | Apoptosis in cancer |
| Akira Funahashi | Keio University | CellDesigner, SBGN |
| Martin Golebiewski | EML Research GmbH (Germany) | SABIO-RK |
| Igor Goryanin | University of Edinburgh (UK) | EPE & EPN |
| Naoki Honda | Nara Institute of Science and Technology (Japan) | Signal transduction in chemotaxis |
| Michael Hucka | Caltech (USA) | SBML, SBGN, BioModels.net |
| Sohyoung Kim | National Institute of Health (USA) | MIM |
| Hiroaki Kitano | The Systems Biology Institute (Japan) | all things SB |
| Fedor Kolpakov | Institute of Systems Biology (Russia) | BioUML |
| Nicolas Le Novère | EMBL-EBI (UK) | BioModels Database, SBGN, SBML |
| Yukiko Matsuoka | Systems Biology Institute (Japan) | CellDesigner, SBGN |
| Huaiyu Mi | SRI International (USA) | PANTHER Pathway |
| Stuart Moodie | University of Edinburgh (UK) | EPE & EPN |
| Ion Moraru | University of Connecticut Health Center | VCell |
| Michael D Pedersen | University of Edinburgh (UK) | A language of biological systems |
| Robert Phair | Integrative Bioinformatics, Inc. (USA) | ProcessDB |
| Rune Saetre | University of Tokyo (Japan) | Genia |
| Sven Sahle | University of Heidelberg (Germany) | COPASI |
| Herbert Sauro | University of Washington (USA) | JDesigner & SBVD |
| Jim Schaff | University of Connecticut Health Center (USA | VCell |
| Bruce Shapiro | Caltech | MathSBML, SBML, Cellerator |
| Anatoly Sorokin | University of Edinburgh (UK) | EPE & EPN |
| Alice Villeger | University of Manchester | |
| Katja Wegner | University of Hertfordshire (UK) | NetBuilder |
Venue
The meeting will be held at the Long Beach Hyatt hotel in Long Beach, California.
The meeting room is called “Seaview C” on the 1st floor. Click here for a map of the Hyatt meeting rooms.
You can use the ICSB group code discount for booking a room at the hotel if you wish to stay overnight there. (Of course, if you were planning on staying in another nearby hotel for ICSB, then you may as well stay an extra night at that same hotel.)
Hotels
Travel Information
The ICSB travel information page is reasonably complete and hopefully provides enough details about travel to and from the Long Beach area.