Rule-Based Modeling of Biochemical Systems

The use of rules to represent and simulate the interactions of molecules in biochemical regulatory networks [1] is an emerging area of systems biology that promises to change the way these networks are modeled and understood. The purpose of this proposed workshop is to bring together representatives from major research groups active in this area for the purpose of exchanging ideas, discussing applications of rule-based modeling methods, surveying existing capabilities, mapping out where the field is headed, and developing standards that will promote the exchange of models and the development of new software tools. As part of this, one pratical goal will be to discuss and (hopefully) settle on a draft proposal for representing multicomponent species and complexes within the framework of SBML.

Workshop Organization

The workshop organizers are:

• Jim Faeder (Theoretical Biology and Biophysics Group, LANL)
• Bill Hlavacek (Center for Nonlinear Studies, LANL)
• Walter Fontana (Depart. of Systems Biology, Harvard Medical School)
• Michael Hucka (Caltech)

This workshop is made possible thanks to generous support from the following organizations:

• The Santa Fe Institute
• Center for Nonlinear Studies, Los Alamos National Laboratory
• Beckman Institute BNMC at Caltech

Preliminary Workshop Schedule and Venue Information

We will begin with a reception on Wednesday June 13 (to be held at the Hotel Santa Fe), followed by two full days of meetings at the Santa Fe Institute on June 14 and 15.

A more detailed agenda is forthcoming.

Background Readings

If you have time for nothing else, we strongly at least recommend reading the following before coming to the meeting:

• A comprehensive review of rule-based modeling written by the organizers (Hlavacek WS, Faeder JR, Blinov ML, Posner RG, Hucka M, Fontana W, Rules for modeling signal-transduction systems, Science STKE, 18 July 2006 PDF).

The following are important for the discussions about extending SBML to support this class of modeling:

• Michael Blinov et al.'s 2004 proposal for SBML Level 3 extensions for multicomponent species PDF
• Andrew Finney's 2004 proposal for SBML Level 3 extensions for multicomponent species PDF
• The SBML Level 2 Version 3 public prerelease specification PDF

Additional readings for context and background:

• Faeder, Blinov, Goldstein & Hlavacek, "Combinatorial complexity and dynamical restriction of network flows in signal transduction", Systems Biology 2(1):5-15, 2005. PDF
• Lok & Brent, "Automatic generation of cellular reaction networks with Moleculizer 1.0", Nat. Biotech. 23(1):131-136, 2005. PDF
• Blinov et al., Comment on "Automatic generation of cellular reaction networks with Moleculizer 1.0", Nat. Biotech., 23(11):1344-1345, 2005. PDF
• Lok & Brent, Response to comment on "Automatic generation of cellular reaction networks with Moleculizer 1.0", Nat. Biotech., 23(11):1345, 2005. PDF
• Blinov, Faeder, Goldstein & Hlavacek, "BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains", Bioinformatics 20(17):3289--3291, 2004. PDF
• Faeder et al., "Investigation of early events in FceRI-mediated signaling using a detailed mathematical model", J. Immunology. 170(7):3769-3781, 2003. PDF

Travel Information

The Santa Fe Institute is located in Santa Fe, a small town in New Mexico, USA.

• Link to Google map showing the SFI
• GIF image of a map showing the SFI and the rest of Santa Fe
• Live weather forecast for Santa Fe

To get to the Santa Fe Institute from outside of New Mexico, you will most likely be flying into Albuquerque International Airport (code: ABQ), which is 60 miles (~100km) away from Santa Fe. It is also possible, but unlikely, that you will fly into the Santa Fe Municipal Airport (code: SAF) because so few airlines make connections there. The Santa Fe Institute provides the following useful pages of information about transportation to SFI from ABQ:

• Ground transportation options from ABQ to Santa Fe
• Driving to the Hotel Santa Fe from ABQ
• Driving to SFI from ABQ

The following are some suggestions and recommendations for international visitors:

• Distances in the western USA are deceptively long (much longer than you may expect from driving in other areas of the world) and the region is sparsely populated. If you are planning on doing any sightseeing, make sure to check your distances carefully.
• English is the dominant language in Santa Fe. Many residents also speak Spanish.
• Airport currency exchange services are usually more expensive than taking cash out of an ATM or exchanging at a bank. You may want to check the current exchange rates (e.g., at xe.com) so that you have some idea of what to expect, although of course you will not get the exact exchange rate because all services charge a percentage for doing the exchange.
• Tipping is customary in the USA and generally not precomputed on bills. 15%-20% is typical and expected for restaurants and taxis, tipping $2-$5 if someone carries your bags or parks your car is also typical, and leaving $2 for the hotel room cleaning staff every day is also appreciated by the staff.
• You may wish to obtain whatever kind of power adapter is necessary for you to use your laptop and other electrical devices before you arrive into Santa Fe. It may be possible to buy converters at shops around your hotel or elsewhere in Santa Fe, but it is not guaranteed, nor is it assured they will have the right type for your electrical needs. See [2] for information about electric standards in the USA.