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 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 meeting should feature presentations about progresses of the core projects and related efforts. We will also work on the interactions of SBGN and efforts with other formats such as BioPAX and SBML.

The workshop co-organizers are:

We gratefully acknowledge generous funding from the following agencies:


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

Proposed additions

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, MIRIAM & SBO Nicolas recording
09:30–10:30 SBO, MIRIAM, & URI scheme proposal Camille MOV SBO primer

MIRIAM slides
URI slides
URI scheme

10:30–11:00 Break
11:00–11:30 MIASE and KiSAO Dagmar MOV KiSAO slides

MIASE 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

Additional materials

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

  • 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


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)
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,
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
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


The meeting will be held at the seaside house of the Okinawa Institute of Science and Technology.


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)

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

Click for Naha City, Japan Forecast

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

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