Algebraic Methods: Discrete Models in Systems Biology Workshop - December 3-5, 2008
Workshop Information
December 3, 2008 - December 5, 2008
General Information
The workshop focused on the use of discrete models in systems biology. Discrete modeling approaches have been applied to a wide variety of biological contexts, including gene regulatory networks, epidemiology, and ecosystem dynamics. Examples of topics of interest in the workshop are
- Discrete dynamical systems: multi-state models such as Boolean networks, logical models, and finite dynamical systems; random networks; and analytic tools including statistical-mechanical approaches
- Bayesian networks, including dynamic Bayesian networks and graphical models
- Static networks: interaction networks and graph-theoretic approaches
- Biochemical reaction networks
- Simulation: finite-state machines, agent-based networks, process algebras
A chief goal was to stimulate discussion focused on key challenges in discrete modeling in computational systems biology, particularly the establishment of unifying themes and principles.
Organizing Committee: Elena Dimitrova (Clemson University), Ilya Shmulevich (Institute for Systems Biology), Brandilyn Stigler (Southern Methodist University)
Schedule
Wednesday, December 3, 2008
| 8:15-8:45 | Registration and Continental Breakfast |
| 8:45-9:00 | Welcome |
| 9:00-10:00 | Lloyd Demetrius, Harvard University Statistical Mechanics and Evolutionary Theory |
| 10:00-10:30 | Break |
| 10:30-11:15 | Abdul Jarrah, Virginia Tech Discrete Algebraic Models in Systems Biology |
| 11:15-11:30 | Break |
| 11:30-12:30 | Discussion: Goals and wishes (of the workshop) |
| 12:30-2:30 | Lunch |
| 2:30-3:15 | Anne Shiu, Univ. of California - Berkeley Siphons, Primary Decomposition and the Global Attractor Conjecture |
| 3:15-3:30 | Break |
| 3:30-4:15 | David Anderson, University of Wisconsin Persistence and Stationary Distributions of Biochemical Reaction Networks |
| 4:15-4:30 | Break |
| 4:30-5:00 | Poster Advertisements (2 minute ads each) |
| 5:00-7:00 | Poster Session and Reception SAMSI will provide poster presentation boards and tape. The board dimensions are 4 ft. wide by 3 ft. high. They are tri-fold with each side being 1 ft. wide and the center 2 ft. wide. Please make sure your poster fits the board. The boards can accommodate up to 16 pages of paper measuring 8.5 inches by 11 inches. |
Thursday, December 4, 2008
| 8:30-9:00 | Registration and Continental Breakfast |
| 9:00-10:00 | Joshua Socolar, Duke University Continuous Dynamics and Boolean Approximations in Complex Networks |
| 10:00-10:30 | Break |
| 10:30-11:15 | Juilee Thakar, Pennsylvania State University |
| 11:15-11:30 | Break |
| 11:30-12:30 | Discussion: Open problems |
| 12:30-2:30 | Lunch |
| 2:30-3:15 | Duygu Ucar, Ohio State University |
| 3:15-3:30 | Break |
| 3:30-4:15 | Ovidiu Lipan, University of Richmond A stochastic model for stress response in CHO mammalian cells |
| 4:15-4:30 | Break |
| 4:30-5:15 | Jim Smith, University of Warwick |
| 5:15-6:30 | Discussion: Second chance (to ask the "dumb" questions) |
Friday, December 5, 2008
| 8:00-8:30 | Registration and Continental Breakfast |
| 8:30-9:30 | Carla Piazza, University of Udine Model Checking, Hybrid Automata, and Systems Biology |
| 9:30-9:45 | Break |
| 9:45-10:30 | Henning Mortveit, Virginia Tech Graph Dynamical Systems - A Mathematical Framework for Interaction-Based Systems, Their Analysis and Simulations |
| 10:30-10:45 | Break |
| 10:45-11:30 | Greg Rempala, Medical College of Georgia Algebraic Methods for Inferring Genetic Networks |
| 11:30-12:30 | Discussion: Building bridges and closing |
| 12:30-1:30 | Lunch |