The 14th SBML Forum Meeting
Stanford University
September 3–4, 2009
The annual SBML Forum meeting is an opportunity for the SBML community to meet face-to-face and discuss developments in SBML as well as software systems for systems biology. The SBML Forum Meeting will include technical presentations by software developers, modelers and researchers on topics relevant to software for systems biology, as well as focused discussions about SBML itself. (Attendees are cautioned, however, not to expect any tutorials about SBML itself, and are referred to the documents at http://sbml.org/Documents and the sbml-discuss mailing list for questions of a more basic nature about SBML.)
There will be times available during the meeting for people to give short presentations on the following topics: SBML-enabled applications, the use of SBML to integrate different applications, proposals for SBML extensions, proposals for standards that compliment SBML, announcements of software or standards or events of interest to SBML users, and general experiences of using SBML "in the field".
We are grateful for support from the following organizations for this year's SBML Forum:
- The National Institute of General Medical Sciences
(Grant #GM070923) USA - The Beckman Institute BNMC
California Institute of Technology
Pasadena, California, USA
Agenda
The meeting room is room 380-Y in building Jordan Hall #380.
Thursday, September 3
| Time | Topic | Speaker/Leader | Files | Audio (MP3) |
|---|---|---|---|---|
| 13:55–14:05 | Introductions | Mike Hucka | Slides | Audio |
| 14:05–14:20 | Brief summary of SBML news for 2009 | Mike Hucka | Slides | Audio |
| 14:20–14:30 | libSBML update | Sarah Keating | Slides | Audio |
| 14:30–14:50 | Antimony 1.2 | Lucian Smith | Slides | Audio |
| 14:50–15:00 | SBW 2.7.10 | Frank Bergmann | Slides | Audio |
| 15:00–15:10 | CaliBayes | Darren Wilkinson | Slides | Audio |
| 15:10–15:20 | iBioSim 1.2 | Chris Myers | Slides | Audio |
| 15:20–15:30 | CellDesigner 4.1 beta | Akira Funahashi | Slides | Audio |
| 15:30–15:40 | ProcessDB | Robert Phair | Slides | Audio |
| 15:40–16:20 | — break — | |||
| 16:20–16:30 | Cellucidate | Ty Thomson | Slides | Audio |
| 16:30–16:40 | E-Cell IDE | Takeshi Sakurada | Slides | Audio |
| 16:40–16:50 | BioNetGen rule-based modeling | Bin Hu | Slides | Audio |
| 16:50–18:00 | SBML Level 3 Core draft specification | Mike Hucka | Slides | Audio |
| 18:00–19:30 | — Break and go to restaurant — | |||
| 19:30–22:00 | — Dinner at California Cafe — |
The California Cafe is on
the Stanford campus within walking distance of the meeting room. You can
also take the A-line Marguerite bus.
Friday, September 4
| Time | Topic | Speaker/Leader | Files | Audio (MP3) |
|---|---|---|---|---|
| 09:15–09:30 | L3 conversions proposal status | Lucian Smith | Slides | Audio |
| 09:30–10:10 | L3 FBA package discussion | Brett Olivier | Slides | Audio |
| 10:10–10:25 | L3 Groups package discussion | Mike Hucka | Slides | Audio |
| 10:25–11:00 | — Break — | |||
| 11:00–11:50 | L3 multicomponent/multistate species proposal status | Anika Oellrich & Nicolas Le Novère | Slides | Audio |
| 12:00–13:00 | — Lunch provided on-site — | |||
| 13:00–15:05 | L3 spatial geometries proposal | Jim Schaff | Slides | Audio |
| 15:05–15:45 | — Break — | |||
| 15:45–16:25 | L3 hierarchical composition review | Stefan Hoops | Web | Audio |
| 16:25–17:45 | Revisiting Level 3 Core unsettled issues | Mike Hucka | Slides | Audio |
| 17:45–18:00 | Wrap-up & discussion of future meetings | Mike Hucka | Slides | Audio |
Fees
The 2009 SBML Forum will take place as a workshop of ICSB 2009. You are not required to attend ICSB 2009; however, if you do not, you must stillĀ register with ICSB 2009 and indicate you are attending a workshop. A small fee of US $45 is charged by ICSB for workshop attendance to cover the costs of facilities and breaks.
Location
The 14th SBML Forum is being held as a satellite workshop of ICSB 2009 at Stanford University. The meeting room is expected to be in Jordan Hall (building #420) on the Stanford campus. Jordan Hall is located at the top of the main loop. The full address of the building is Jordan Hall, Building 420, Stanford, CA 94305.
Stanford provides the following maps that may be helpful in finding your way:
Stanford University was founded in 1885 and is consistently ranked as one of the top institutions in the USA and in the world. Locals and members of the university community are known to refer to the school as The Farm, a nod to the fact that the university is located on the former site of founder Leland Stanford's horse farm. The Wikipedia page for Stanford provides more information about the university and its history, and debunks some famous myths about its origins.
Travel, Accommodations, and Transportation
As mentioned above, the SBML Forum is being held as a workshop at the International Conference on Systems Biology (ICSB 2009), at Stanford University. A detailed travel information page is available on the ICSB 2009 website; please refer to that page for information about airports, transportation, accommodations, and other useful information.
We regret that we have no travel support available for this meeting, and hope that potential attendees can extend their ICSB 2009 stay in order to attend the SBML Forum.
Other notes
A warning about distances
Looking at maps and seeing shops and restaurants located near Stanford's campus, you may think that they're all a quick walk away. For people used to European distances or tight urban areas, beware: this is California, and distances may be farther than they appear.
Weather
The weather in the Stanford during August and September is usually very warm, with temperatures ranging from 75 °F – 100 ° (24 – 38 C). There is sometimes a chance of light rain, so make sure to bring a small umbrella and some light clothes for wet weather.
Restaurants & pubs
There are cafes and snack at various places on campus, but they generally close at 6pm. For dinner, you are better off going slightly north of Stanford's campus to downtown Palo Alto, where, off of University Ave., you will find dozens of restaurants and bars. A more selective and somewhat wider-ranging guide to area restaurants is the one from the Stanford business school, which usefully categorizes choices by types of foods. There is also an upscale shopping mall right on campus, and it features a number of cafes and restaurants.
Keep in mind that Stanford is a prestigious institution, so while there are many outstanding restaurants around Stanford, the prices are sometimes on the higher end of the spectrum. On the other hand, there are plenty of student hang-outs, so it's certainly not impossible to find fun and reasonably priced eateries.
Internet access
We don't have specific information yet, but we expect that all of Stanford is blanketed by wireless networking.
Electrical supply
If you are traveling from outside of the USA, be sure to bring an appropriate power plug converter for your laptop and all other electrical devices you're bringing. Electric current in the USA is 60 Hz, 120 V. The plug types are depicted below. You may be able to find an appropriate converter once you get to Stanford, but it's best not to count on it, and to bring your own before you leave your home country.
| Type A Plug |
|
|---|
| Type B Plug |
|
|---|
Contacts
| Linda Taddeo | Michael Hucka |
|---|---|
| ltaddeo at caltech.edu | mhucka at caltech.edu |
| Tel: +1 626 395 3375 Fax: +1 636 395 3336 | Tel: +1 626 395 8128 |
| Biological Network Modeling Center The Beckman Institute at Caltech MC 139-74 Pasadena, California 91125 USA | Biological Network Modeling Center The Beckman Institute at Caltech MC 139-74 Pasadena, California 91125 USA |



