SBGN-3.5
Super-hackathon "standards and ontologies for Systems Biology"
The Okinawa super hackathon aims to gather developers of the various standard formats and ontologies used in the field of Systems Biology, in order to improve their interfacing. The event will be held from January 28 through February 2 at the Okinawa Institute of Science and Technology, Japan. It combines both the fifth SBGN meeting and the 3rd annual BioModels.net meeting.
The fifth SBGN meeting will be a “Spec-a-thon” devoted to finalise SBGN Level 1, and a hackathon, where we will develop software support for the language. The third annual BioModels.net meeting should feature presentations about progresses of the core projects and related efforts. We will also work on the interactions of SBGN and BioModels.net efforts with other formats such as BioPAX and SBML.
The workshop co-organizers are:
- Hiroaki Kitano (SBI & Sony CSL)
- Nicolas Le Novère (EMBL-EBI)
- Mike Hucka (Caltech CDS)
- Akira Funahashi (SBI & Keio University)
We gratefully acknowledge generous funding from the following agencies:
- Okinawa Institute of Science and Technology
- New Energy and Industrial Technology Development Organization (NEDO)
- The Systems Biology Institute
Contents |
Photo Album
Agenda, Presentations & Video Recordings
For the first time, we are video-recording talks and discussions and will post files online as each session progresses. The files are included in the table below. Beware that they are quite large (150 MB–1 GB each). They are QuickTime movie files. Free players are available for Mac and Windows.
Suggested approach for using the recordings: for talks that involved slide presentations, open both the video and the copy of the slides at the same time on your computer, so that you can follow along in the presentation during the talk. (Note: The volume and quality are low on the first day's recordings but is improved on the subsequent days. Thankfully, voices are generally clear, but you may need to really turn up the volume on your speakers or use earphones.)
Day 1 (Monday, 28 January 2008)
| Time | Topic | Speaker | Video | Files |
|---|---|---|---|---|
| 09:00–09:07 | General intro to OIST and the meeting | Hiroaki | MOV | (none) |
| 09:15–09:20 | Intro to the week and today | Mike | MOV | (none) |
| 09:20–09:45 | Summary of SBGN so far | Nicolas | MOV | Slides |
| 09:45–10:15 | Break | |||
| 10:15–11:45 | Edinburgh group issues & discussions | Anatoly + everyone | MOV | Freeman et al. comments |
| 11:45–13:00 | Lunch | |||
| 13:00–14:45 | Discussion: remaining SBGN issues | Moderator: Emek | MOV | (none) |
| 14:45–15:20 | Break | |||
| 15:20–16:30 | Discussion: remaining SBGN issues (cont.) | Moderator: Emek | MOV | (none) |
| 16:30–18:00 | Breakout discussion about tags | Moderators: Emek & Anatoly | MOV | (none) |
| 18:00–18:30 | Shuttle back to hotel + break | |||
| 18:30–21:00 | Reception + dinner at Rizzan Sea-park hotel "Koushou Room" | |||
Day 2 (Tuesday, 29 January 2008)
| Time | Topic | Speaker | Video | Files |
|---|---|---|---|---|
| 09:00-09:15 | Introduction to the day | Mike, Nicolas | (none) | (none) |
| 09:15–09:30 | BioModels.net, MIRIAM & SBO | Nicolas | recording corrupted & unavailable | Slides |
| 09:30–10:30 | SBO, MIRIAM, & URI scheme proposal | Camille | MOV | SBO primer |
| 10:30–11:00 | Break | |||
| 11:00–11:30 | MIASE and KiSAO | Dagmar | MOV | KiSAO slides |
| 11:30–11:45 | TEDDY | Christian | MOV | Slides |
| 11:45–12:00 | MIRIAM 2 | Nicolas | MOV | Slides |
| 12:00-13:20 | Lunch | |||
| 13:20–13:40 | SABIO-RK, SBO, MIRIAM | Martin | MOV | Slides |
| 13:45–14:00 | Forthcoming resources | Nicolas Rodriguez | MOV | Slides |
| 14:00–14:40 | BioPAX Level 3 | Emek | MOV | Slides |
| 15:15–18:00 | SBGN break-out discussion | Moderator: Stuart | MOV | (none) |
| 18:30-20:00 | Dinner in 3rd floor cafeteria at OIST | |||
| 20:00-20:30 | Shuttle back to the hotel | |||
Day 3 (Wednesday, 30 January 2008)
| Time | Topic | Speaker | Video | Files |
|---|---|---|---|---|
| 09:15–09:45 | EPE | Stuart & Anatoly | MOV | Slides |
| 09:45–10:00 | Apostrophe | Katja | MOV | Slides |
| 10:00–10:20 | Arcadia | Alice | MOV | Slides |
| 10:20-11:00 | Break | |||
| 11:00–11:15 | FANTOM4 case study | Hideya | MOV | Slides |
| 11:15–11:30 | CellDesigner 4.0beta | Akira & Yukiko | MOV | Slides |
| 11:30–11:45 | PANTHER Pathway | Huaiyu | MOV | Slides |
| 11:45-12:00 | BioUML | Fedor (virtually) | Slides | |
| 12:00-13:00 | Lunch | |||
| 13:05–13:20 | Vanted | Falk | MOV | Slides |
| 13:20–13:35 | Payao | Hiroaki | MOV | Slides |
| 13:35–13:50 | Experiences implementing SBGN | Frank | MOV | Slides |
| 13:50–14:20 | Discussion about an SBGN file format | (Everyone) | MOV | (none) |
| 14:20-15:00 | Break | |||
| 15:00–15:45 | ER & MIM & discussions | Mirit | MOV | Slides |
| 15:45-16:40 | Break | |||
| 16:40–16:40 | Activity Flow | Hiroaki | MOV | Slides |
| 16:15–17:15 | SBGN issues review pt.1 | Stuart | MOV | Issues list |
| 17:15-17:30 | Break | |||
| 17:30–18:30 | SBGN issues review pt.2 | Stuart | MOV | Issues list |
| 18:30-19:30 | Dinner in 3rd floor cafeteria at OIST | |||
| 19:40–21:00 | SBGN issues discussion pt.3 | Stuart | MOV | (none) |
| 20:30-21:00 | Shuttle back to the hotel | |||
Day 4 (Thursday, 31 January 2008)
| Time | Topic | Speaker | Video | Files |
|---|---|---|---|---|
| 09:10–09:20 | Intro | Mike | MOV | (none) |
| 09:20–09:35 | MetaCrop | Falk | MOV | Slides |
| 09:35–10:05 | COPASI progress | Sven | MOV | Slides |
| 10:05–10:35 | BioModels Database progress | Nicolas | MOV | Slides |
| 10:35-11:00 | Break | |||
| 11:00–11:15 | Using BioModels Database to test simulators | Frank | MOV | Slides |
| 11:15–11:30 | Multistate & multicomponent proposal progress | Anika | MOV | Slides |
| 11:40–12:10 | VCell progress | Ion | MOV | Slides |
| 13:10–13:25 | SBToolbox2 | Henning | MOV | Slides |
| 13:25-14:40 | Lunch | |||
| 14:40–14:50 | MIASE/simulation format pt.1 | Nicolas | ||
| 14:50–16:15 | MIASE/simulation format pt.2 | Nicolas | ||
| 16:40–18:20 | SBML Test Suite breakout discussion | Mike | MOV | (none) |
| 18:30-19:30 | Dinner in 3rd floor cafeteria at OIST | |||
| 19:30–19:55 | More SBGN issues | Nicolas | ||
| 20:00-20:30 | Shuttle back to the hotel | |||
Day 5 (Friday, 1 February 2008)
| Time | Topic | Speaker | Video | Files |
|---|---|---|---|---|
| 09:00-9:15 | Introduction to the day | Mike, Nicolas | (none) | |
| 09:15–09:45 | PSI-MI | Samuel | MOV | |
| 09:50–10:15 | MIASE-ML first draft XML format proposal | Ion | XML example | |
| 10:40–12:10 | SBGN breakout discussion 1 | Emek & Nicolas | MOV | |
| 12:10-13:15 | Lunch | |||
| 13:15–14:45 | SBGN breakout discussion 2 | Stuart | MOV | |
| 17:30-18:00 | Shuttle from OIST to restaurant | |||
| 18:00-19:45 | Dinner at Orchid restaurant at Manza Beach Hotel. Drinks self-pay (all-you-can-drink 1800JPY). | |||
| 19:45- | Shuttle back to the hotel | |||
Day 6 (Saturday, 2 February 2008)
| Time | Event |
|---|---|
| Morning | Hacking |
| 12:00 | Lunch |
| Afternoon | Hacking |
| 18:30 | Shuttle to restaurant |
| 19:00 | Dinner: Japanese restaurant "Utaki" at Manza Beach Hotel 1F |
| 21:30 | Return shuttle service |
Supplementary Materials
- SBGN Level 1 specification draft (PDF) of 2008-01-25
- Comments by Tom Freeman (Edinburgh group) submitted to sbgn-discuss list some time ago and reexamined during the workshop
- Source/Sink notation proposal from Hiroaki Kitano (from day 1 morning discussion about SBGN notation)
- Example of real-life video memory module with many connections from Hiroaki, apropos discussions about tags on modules
- Activity flow diagrams proposed by Hiroaki
- Examples from PANTHER Pathway by Huaiyu Mi, to illustrate the problems discussed on 2008-01-27. Example 1: Synaptic_vesicle_trafficking.png and Example 2: p38_MAPK_pathway.png
- Examples of PANTHER diagrams relevant to gene regulation, by Huaiyu Mi:
- Example by Christian Knuepfer about why non-overlapping rules for labels don't really solve the problem: label-problem.pdf
Fun Quotes
Overheard at this meeting: ;-)
- ”I have a very good understanding of the misunderstanding.” – Emek Demir
- ”I don't like dangling things.” – Nicolas Le Novère
- ”You are obsessed by dots!” – Nicolas Le Novère
- ”My semantic alarms are going off at the moment.” – Emek Demir
- ”I'm not sure if it's apathy, tardiness or conversion.” – Stuart Moodie
- ”It hardly seems credible, but I think we are actually in agreement.” – Stuart Moodie
- ”Can I raise a concern that will never happen but I will raise it anyway?” – Emek Demir
- ”If you don’t care, you don’t care, here we are talking about the case you care.” – Nicolas Le Novère
- ”I think that was a remarkable amount of agreement.” – Mike Hucka
Participants
| Name | Affiliation | Group/Project |
|---|---|---|
| Mirit Aladjem | National Cancer Institute (USA) | MIM |
| Kimberly Begley | Griffiths University (Australia) | SBML Test Suite |
| Frank Bergmann | University of Washington (USA) | http://www.sys-bio.org/ |
| Emek Demir | MSKCC (USA) | BioPax |
| Akira Funahashi | Keio University (Japan) | CellDesigner, SBGN |
| Ralph Gauges | University of Heidelberg (Germany) | COPASI |
| Martin Golebiewski | EML Research GmbH (Germany) | SABIO-RK |
| Igor Goryanin | University of Edinburgh (UK) | EPE & EPN |
| Samik Ghosh | ||
| Michael Hucka | Caltech (USA) | SBML, SBGN, BioModels.net |
| Akiya Jouraku | Keio University (Japan) | CellDesigner, SBML |
| Hideya Kawaji | Riken (Japan) | FANTOM |
| Brian Kemper | University of Tokyo (Japan) | |
| Samuel Kerrien | EMBL-EBI | IntAct, PSI-MI |
| Norihiko Kikuchi | MKI | CellDesigner |
| Hiroaki Kitano | The Systems Biology Institute (Japan) | all things SB |
| Dagmar Koehn | Univ Rostock | MIASE |
| Fedor Kolpakov | Institute of Systems Biology (Russia) | BioUML |
| Christian Knuepfer | Univ Jena (Germany) | TEDDY |
| Camille Laibe | EMBL-EBI (UK) | MIRIAM, SBO |
| Nicolas Le Novère | EMBL-EBI (UK) | BioModels Database, SBGN, SBML |
| Yukiko Matsuoka | EMBL-EBI (UK) | CellDesigner, SBGN |
| Huaiyu Mi | SRI International (USA) | PANTHER Pathway |
| Stuart Moodie | University of Edinburgh (UK) | EPE & EPN |
| Ion Moraru | University of Connecticut Health Center (USA) | VCell |
| Anika Oellrich | EMBL-EBI (UK) | StochSim |
| Nicolas Rodriguez | EMBL-EBI (UK) | SBMLeditor, SBO |
| Sven Sahle | University of Heidelberg (Germany) | COPASI |
| Henning Schmidt | Univ Rostock (Germany) | SBToolbox2 |
| Falk Schreiber | IPK (Germany) | Vanted, MetaCrop |
| Anatoly Sorokin | University of Edinburgh (UK) | EPE & EPN |
| Alice Villeger | University of Manchester (UK) | Utopia |
| Katja Wegner | University of Hertfordshire (UK) | NetBuilder |
Logistical Information
Venue
The meeting will be held at the seaside house of the Okinawa Institute of Science and Technology.
Accommodations
Accommodation will be arranged by OIST/local organiser for all the participants. We are planning to stay in the following hotel (not confirmed yet as of Dec 15)
- Rizzan Sea-Park Hotel at Tancha-bay http://www.rizzan.co.jp tel:+81-(0)98-964-6611
- Seaside house Tel:+81-(0)98-966-8711
Transportation between the hotel and the venue: Shuttle service will be available during the following period: 8:30-8:45 and 19:30-20:30
Travel Information
Transportation between Naha airport and your hotels will be arranged. (About an hour drive to the hotel/venue from the airport.) On your arrival at the airport, look for the person with “OIST Super Hackathon Workshop” sign.
General Info on Okinawa: Okinawa Tourist Information