The second Systems Biology Graphical Notation workshop was held on October 7, the day before ICSB 2006, in Yokohama, Japan. The meeting venue was the Yokohama World Porters in Yokohama.
The SBGN 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 workshop co-organizers were:
- Hiroaki Kitano (SBI & Sony CSL)
- Yukiko Matsuoka (SBI & JST)
- Akira Funahashi (SBI & JST)
- Mike Hucka (Caltech)
- Nicolas Le Novère (EBI)
This workshop was made possible by support from:
| Time | Topic | Speaker | Files |
|---|---|---|---|
| 09:30–10:00 | The goals of SBGN | Hiroaki Kitano | |
| 10:00–10:10 | Visualization in ProMoT | Sebastian Mirschel | |
| 10:10–10:20 | BioUML | Fedor Kolpakov | |
| 10:20–10:40 | Narrator | Johannes Mandel | |
| 10:40–11:00 | EPE | Stuart Moodie | |
| 11:00–11:20 | Break | ||
| 11:20–11:30 | Pathway Visualization of TDS Biological Modeler | Zheng Li | |
| 11:30–11:40 | BioPAX visualization in Cytoscape | Emek Demir | |
| 11:40–12:00 | Adding render information to the SBML Layout Extension | Ralph Gauges | |
| 12:00–12:10 | Systems Biology Workbench:JDesigner | Frank Bergmann | |
| 12:10–12:20 | Set of Rules useful for SBGN specification | Anatoly Sorokin | |
| 12:30 – 14:00 | Lunch | ||
| 14:00–14:20 | Systems Biology at the Manchester Center | Douglas Kell and Peter Li | |
| 14:20–14:40 | Molecular Interaction Maps | Sohyoung Kim | |
| 14:40–15:10 | Case study comparing MIMs to PDN using PANTHER Pathways | Huaiyu Mi | |
| 15:10–15:25 | Visualization of CellML models | Sarala Dissanayake | |
| 15:25–15:45 | Break | ||
| 15:45–16:50 | Towards a specification for SBGN | Nicolas Le Novère | |
| Name | Affiliation | Group |
|---|---|---|
| Matteo Barberis | University of Milano-Bicocca (Italy) | |
| Frank Bergmann | Keck Graduate Inst. (USA) | JDesigner |
| Eric Billings | NHLBI, NIH (USA) | QBT |
| Emek Demir | MSKCC (USA) | BioPAX |
| Sarala Dissanayake | Univ. of Auckland (New Zealand) | CellML |
| Akira Funahashi | Kitano Symbiotic Systems Project (Japan) | SBML, SBGN, CellDesigner |
| Ralph Gauges | EML (Germany) | COPASI |
| Peter Ghazal | University of Edinburgh (UK) | |
| Igor Goryanin | University of Edinburgh (UK) | DBsolve, EPE |
| Juergen Haas | University of Munich (Germany) | |
| Stefan Hohmann | Goeteborg University (Sweden) | |
| Michael Hucka | Caltech (USA) | SBML, SBGN |
| Akiya Jouraku | Kitano Symbiotic Systems Project (Japan) | SBML, SBGN, CellDesigner |
| Douglas Kell | University of Manchester (UK) | |
| Sohyoung Kim | National Institutes of Health (USA) | |
| Taeyong Kim | GIST, Gwanagju (Republic of Korea) | |
| Hiroaki Kitano | Kitano Symbiotic Systems Project (Japan) | SBML, SBGN, CellDesigner |
| Fedor Kolpakov | Institute of Systems Biology (Russia) | BioUML |
| Pradeep Kumar | GIST, Gwangju (Republic of Korea) | |
| Peter Li | University of Manchester (UK) | |
| Zheng Li | TERANODE Corp. (USA) | Design Suite |
| Chung-Yen Lin | Institute of Information Science (Taiwan, ROC) | |
| Shushi Lin | Tsing-Hua University (Taiwan, ROC) | |
| Nicolas Le Novère | EBI (UK) | BioModels Database |
| Johannes Julius Mandel | University of Ulster, Northern Ireland (UK) | Narrator |
| Yukiko Matsuoka | Kitano Symbiotic Systems Project (Japan) | SBML, SBGN, CellDesigner |
| Pedro Mendes | Virginia Bioinformatics Institute (USA) | |
| Huaiyu Mi | SRI International | |
| Sebastian Mirschel | Max Planck Institute (Germany) | ProMoT |
| Stuart Moodie | University of Edinburgh (UK) | EPN, EPE |
| Ion I. Moraru | UCHC (USA) | Virtual Cell |
| Dylan Morris | Caltech (USA) | |
| Roberta Mustacchi | Danish Technical University (Denmark) | |
| Mikkel Zahle Oestergaard | Cambridge University (UK) | |
| Hye Young Oh | Korea Food and Drug Administration (Republic of Korea) | |
| Sven Sahle | EML Research Heidelberg (Germany) | |
| Bruce Shapiro | Caltech (USA) | SBML |
| Anatoly Sorokin | University of Edinburgh (UK) | EPN, EPE |
| Yu-Tai Wang | National Yang-Ming University (Taiwan, ROC) | |
| Steven Watterson | University of Edinburgh (UK) | |
The workshop was held at the Yokohama World Porters building 6F, room 3. Yokohama World Porters is a 5 minute walk from the Pacifico Yokohama (ICSB2006 venue).
PDF map to the Meeting room at World Porters
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/Funahashi/Matsuoka/Oda 2005 paper in Nature Biotech.
- Kitano 2003 on biochemical networks in BIOSILICO.
- The Process Diagram: Rationale and Definition unpublished manuscript
- Kohn/Aladjem/Kim/Weinstein/Pommier (forthcoming) paper in Molecular Systems Biology
- Kohn/Aladjem/Weinstein/Pommier 2006 paper in Mol. Bio. of the Cell
- Kohn/Aladjem commentary in Mol. Sys. Bio. 2006
- Kohn 2001 paper in Chaos
- Moodie/Sorokin/Goryanin/Ghazal 2006 paper in J. Integrative Bioinformatics 2006
- Demir et al. 2004 paper in Bioinformatics
- Dogrusoz et al. paper submitted, in review in ACM Trans. Graphics
- Fukuda and Takagi 2004 paper in ACM conference on Asia-Pacific bioinformatics
- Yamamoto et al. 2003 paper in Genome Informatics
- Cook/Farley/Tapscott 2001 in Genome Biology
- Gauges/Rost/Sahle/Wegner paper submitted, in-review in Bioinformatics
- Gauges/Sahle/Wegner draft render extensions proposal manuscript
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.
- You may want to check the weather forecast for Tokyo immediately prior to your departure. It often rains unpredictably in Tokyo, so at least bring a light jacket, shoes that can get wet, and an umbrella.
- It is important to become familiar with the Airport Limousine Bus service that you will take to get from Narita airport to the hotel. Here is their web site: http://www.limousinebus.co.jp/e/index_forforeign.html
- You may wish to obtain whatever kind of power adapter is necessary for you to use your laptop and other electrical devices in Japan. It may be possible to buy converters at the shops around the hotel, but the supply is not guaranteed, nor is it assured they will have the right type for everyone. Japanese electrical current is 50 Hz, 100 V. See http://kropla.com/electric2.htm or http://www.jnto.go.jp/eng/arrange/essential/electricity.html for information on power and plugs in Japan.
Restrictions on carry-on items have been increased dramatically. For current information on what is and is-not permitted on US and UK flights (Travelers flying from other countries, please check your local aviation authority for current guidelines.):
- UK Department for Transport - measures implemented at UK airports and for UK-bound flights
- US Transportation Safety Administration - measures implemented at US airports and for US-bound flights
- Information on Narita Airport
The ICSB organizers have recommended two ways to get from Narita Airport to the conference location. One is the Airport Limousine bus, and the other is the Japan Railways Narita Express. Both drop you at Yokohama Station in Yokohama, from which you take the Minato Mirai Line for a 3 minute ride to Minato Mirai Station. From that station, you can walk to the venue and most of the hotels.
For information on Japan Railways:
http://www.jreast.co.jp/e/nex/index.html
For a timetable for the Airport Limousine bus:
http://www.limousinebus.co.jp/e/timetable/index_n/yokohama_h.html