Second Workshop on Rule-based Modeling of Biochemical Systems

The purpose of this workshop is to advance rule-based modeling methodology and applications.

Rule-based modeling is increasingly being applied to model cell signaling systems and other biochemical systems. It can be viewed as a type of agent-based modeling in which the agents are taken to represent proteins and their component parts and the rules are such that agent behavior is consistent with chemical reaction kinetics.

Program

Sunday, August 14, 2011

07:30-09:30 Breakfast

Dining Hall is open 7:30-9:30

09:30-12:20 Session I - James R. Faeder (chair)

09:30-09:55 Eric J. Deeds, University of Kansas, Optimizing ring assembly: the strength of weak bonds

09:55-10:20 Dennis Bray, University of Cambridge, Diffusive wave and gradients in cell signaling

10:20-10:45 Carlos F. Lopez, Harvard Medical School, Implementation of novel rules-based and numerical methods to understand Bcl-2 pro- and anti-apoptotic protein family interactions

10:45-11:10 Katrin Kolczyk, Max Planck Institute, Magdeburg, A common representation of rule-based and Boolean models

11:10-11:30 Coffee Break

11:30-11:55 David J. Klinke II, West Virginia University, Simplifying rule-based reaction networks using timescale analysis

11:55-12:20 S. Gnanakaran, Los Alamos National Laboratory, Molecular modeling to quantify intramolecular binding in multivalent interactions

12:20-13:30 Lunch

Dining Hall is open 11:30-13:30

13:30-16:45 Session II - S. Gnanakaran (chair)

13:30-13:55 Jayajit Das, The Research Institute at Nationwide Children's Hospital, Can we extract mechanistic insights from large biochemical networks using pair correlations?

13:55-14:20 Justin S. Hogg, Pittsburgh University, Towards whole cell modeling: reducing the cost of large-scale simulations with hybrid methods

14:20-14:45 Bin Hu, Los Alamos National Laboratory, Data formats for rule-based models

14:45-15:10 Lily A. Chylek, Cornell University, Visualizing and annotating rule-based models

15:10-15:30 Coffee Break

15:30-15:55 Edward C. Stites, Translational Genomics Research Institute, Rule-based models for cancer cell signaling

15:55-16:20 Dipak Barua, Los Alamos National Laboratory, A rule-based model for membrane-proximal B cell antigen receptor signaling

16:20-16:45 William S. Hlavacek, Los Alamos National Laboratory, Large models

Organizers

• Michael L. Blinov, University of Connecticut Health Center
• Vincent Danos, University of Edinburgh
• James R. Faeder, University of Pittsburgh School of Medicine
• S. Gnanakaran, Los Alamos National Laboratory
• William S. Hlavacek, Los Alamos National Laboratory

Links

• First Workshop on Rule-based Modeling of Biochemical Systems, Santa Fe Institute, Santa Fe, NM, June 14 and 15, 2007