Rule-Based Modeling Community

From BioNetWiki

This page serves as link to rule-based modeling efforts by multiple research groups all over the world. We think the time is right to organize our community, with our own meetings, mailing lists and other community activities.

This page is currently under construction. Please excuse the missing links and other debris.

Contents 1 Meetings devoted to rule-based modeling 2 Software tools with (at least some) rule-based modeling capabilities 3 Model-specification languages 4 Research groups 5 Applications of rule-based modeling

Meetings devoted to rule-based modeling

• Workshop on rule-based modeling of biochemical systems, Santa Fe Institute, Santa Fe, NM, May 2007
• Advanced Modeling Workshop at ICSB 2010, October 15th, 2010
• Vienna meeting?
• Satellite Workshop of the The Fifth q-bio Conference on Cellular Information Processing, Santa Fe, New Mexico, August 14, 2011.

Software tools with (at least some) rule-based modeling capabilities

• ALC (Automated Layer Construction)
• ANC (Allosteric Network Compiler)
• BioNetGen
• BioSPI
• BlenX4Bio
• CplexA
• DYNSTOC
• E-cell (in process)
• GetBonNie
• KaSim
• little b
• Meredys (Stochastic simulation of particle dynamics)
• Moleculizer
• NFsim
• PottersWheel (MatLab Toolbox)
• RuleBase
• Simmune
• Smoldyn/libMoleculizer (Stochastic simulation of particle dynamics)
• SRSim (Rule Based Modelling in Space)
• SSC (Stochastic Simulation Compiler)
• StochSim
• RuleMonkey
• URBAN
• VCell

Model-specification languages

• BioNetGen language (BNGL)
• Kappa (the same as BNGL except for a few small differences)
• little b programming language
• BlenX programming language
• Brane calculus

Research groups

• Michael Blinov group at University of Connecticut Health Center
• Vincent Danos group at University of Edinburgh
• Thierry Emonet group at Yale University
• James Faeder group at University of Pittsburgh
• Jerome Feret group at École Normale Supérieure
• Ryan Gutenkunst group at University of Arizona
• William Hlavacek group at Los Alamos National Lab/University of New Mexico
• Jean Krivine group at Université Paris 7.
• Martin Meier-Schellersheim group at NIH
• Adelinde Uhrmacher group at the University of Rostock

Applications of rule-based modeling