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February 11-12, 2006, at AIST in Tokyo, Japan.

Introduction

The first international workshop on the Systems Biology Graphical Notation (SBGN-1) took place February 11-12, 2006, at the National Institute of Advanced Industrial Science and Technology (AIST), in Tokyo, Japan. This first workshop was aimed at intensive discussions about the formation of a standard for the graphical display for biological network diagrams. Diagrams may cover a wide range of biological processes and express various levels of abstraction. The limitations of current graphical notations has been widely recognized, and several efforts has been made to rectify the situation.

Workshop co-organizers:

  • Ken Ichirou Fukuda (AIST)
  • Hiroaki Kitano (SBI & Sony CSL)
  • Mike Hucka (Caltech)
  • Nicolas Le Novère (EBI)
  • Yukiko Matsuoka (SBI & JST)
  • Akira Funahashi (SBI & JST)

This workshop was made possible by support from the NEDO METI International Grant (Japan), the JST SORST program (Japan), the Genome Network Project (MEXT, Japan), the Swedish-Japanese Strategic Research Program (JST), and AIST CBRC (METI).

Agenda: Presentations, Discussions and Notes

image: sbgn1-discussion2.jpg

Click here for a photo album from the event

Day 1 (Saturday, 11 February 2006)

Time Topic Speaker Files
09:30–09:45 Introduction Hiroaki Kitano
09:45-10:00 Meeting agenda and Notes Michael Hucka PDF
10:00-10:45 Molecular Interaction Maps Mirit Aladjem PDF
10:45-11:30 Process Diagram notation Hiroaki Kitano PDF
11:30-11:45 Break
11:45-12:05 Cytoscape Nerius Landys PDF
12:05-12:25 INOH Ken Fukuda PDF
12:25-12:45 Panther Pathway Huaiyu Mi PDF
12:45-14:30 Lunch
14:30-14:50 VLX Design Suite Zheng Li PDF
14:50-15:10 JDesigner Frank Bergmann PDF
15:10-15:40 Patika Ugur Dogrusoz PDF
15:40-16:00 Break
16:00-16:20 EPE Anatoly Sorokin PDF
16:20-16:40 SBML layout & render extension proposals Ralph Gauges PDF
16:40-18:00 Discussion: view from modelers and first pass at definining SBGN goals. Discussion notes

Day 2 (Sunday, 12 February 2006)

Time Topic Speaker Files
09:00-09:15 Introduction Michael Hucka
09:15-09:40 Edinburgh notation proposals Stuart Moodie PDF
09:40-10:15 Review of PDN notation Hiroaki Kitano PDF
10:15-10:40 Review of MIMs notation Mirit Aladjem PDF
10:40-11:00 Break
11:00-12:15 Discussion: tradeoffs between notations & requirements for SBGN Discussion notes
12:15-13:15 Lunch
13:15-13:35 CellML efforts Sarala Dissanayake PDF
13:35-14:00 Discussion: resolution to morning's unanswered questions Discussion notes
14:00-14:35 Discussion: 2nd pass at developing list of SBGN requirements
14:35-15:00 break
15:00-15:20 Discussion: issues in interfacing SBGN with machine readable formats Discussion notes
15:20-16:15 Discussion: 3rd pass at developing list of SBGN requirements
16:15-16:30 Discussion: moving towards a standard & planning the next steps Discussion notes
16:30-16:35 Final closing

Workshop Participants

Name Affliation Group
Mirit I. Aladjem NIH, NCI (USA) MIMs
Frank Bergmann Keck Graduate Inst. (USA) JDesigner
Emek Demir MSKCC (USA) BioPAX
Sarala Dissanayake Univ. of Auckland (New Zealand) CellML
Ugur Dogrusoz Bilkent University (Turkey) Patika
Ken Fukuda AIST (Japan) INOH, BioPAX
Akira Funahashi SBI (Japan) CellDesigner, SBML
Ralph Gauges EML (Germany) COPASI
Peter Ghazal Univ. Edinburgh (UK) DBsolve, EPE
Igor Goryanin Univ. Edinburgh (UK) DBsolve, EPE
Noriko Hiroi SBI (Japan)
Michael Hucka Caltech (USA) SBML, SBGN
Hiroaki Kitano SBI and Sony CSL (Japan) SBGN, SBML
Edda Klipp Max Planck Institute for Mol. Genetics (Germany) Kinetics Modeling Group
Marcus Krantz SBI YSBN
Nerius Landys UCSD (USA) Cytoscape
Nicolas Le Novère EBI (UK) BioModels Database
Lu Li EBI (UK) BioModels Database
Zheng Li TERANODE Corp. (USA) Design Suite
Yukiko Matsuoka SBI (Japan) SBGN, CellDesigner
Huaiyu Mi Applied Biosystems Inc. (USA) Panther Pathway
Stuart Moodie Univ. Edinburgh (UK) DBsolve, EPE
Mineo Morohashi Human Metabolome Technologies Inc.
Poul Nielsen Univ. of Auckland (New Zeland) CellML
Yasunori Osana SBI (Japan) CellDesigner
Sven Sahle EML (Germany) COPASI
Anatoly Sorokin Univ. Edinburgh (UK) DBsolve, EPE
Jörg Stelling ETH (Switzerland) YSBN
Carl Tiger Göteborg Univ. (Sweden) YSBN

Workshop Location

The workshop was held at the AIST Tokyo Waterfront Bio-IT Research Building, 11th floor. The venue was made available thanks to Ken Fukuda of AIST.

The page of detailed directions to the AIST building provide a guide for getting from the hotel to the AIST.

For those of you already familiar with the area from past visits, it may help to know that the AIST building is very near the MeSci building (Miraikan), site of past SBML and other meetings. You simply need to walk a little farther out past MeSci.

Accommodations

Reservations for SBGN-1 participants were made at the Hotel Villa Fontaine Shiodome. The hotel is located right outside a major train and subway exchange point. Getting from the hotel to the SBGN-1 venue is a simple matter of taking the Yurikamome line from the station right next to the hotel to the AIST building. Detailed directions are available on a separate page.

Pre-Meeting Background Materials

The development of graphical diagrammatic notations for biological networks is an active area of work. The following papers are valuable readings on topics that figured prominently at SBGN-2.

Kitano process diagram notation

Kohn Molecular Interaction Maps (MIM) notation

Edinburgh Pathway Notation

Patika

INOH

SBML Layout and Rendering Extensions proposals

Travel Information

Please print and take with you our pre-travel information page. This will help you find your way upon arrival at Narita airport.

Notice about visa requirements: All overseas visitors wishing to enter Japan require a valid Passport. A visa is also required for participants coming from countries without visa exemption agreements with Japan. Please visit http://www.mofa.go.jp/j_info/visit/visa/index.html for more information.

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