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The Tenth q-bio Summer School - New Mexico: Cell Signaling
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Back to The Tenth q-bio Summer School - New Mexico
Contents
About the Cell Signaling focus area
Lead organizer: Bill Hlavacek (E-mail)
Faculty
- Brian J. Drawert, University of California, Santa Barbara
- James R. Faeder, University of Pittsburgh School of Medicine
- Ryan N. Gutenkunst, University of Arizona
- William S. Hlavacek, Los Alamos National Laboratory
- Martin Lopez Garcia, University of Leeds
- Martin Meier-Schellersheim, National Institute of Allergy and Infectious Disease
- Whelton A. Miller III, Lincoln University
- Danny Perez, Los Alamos National Laboratory
- Emanuel Salazar Cavazos, University of New Mexico
- Ryan Suderman, Los Alamos National Laboratory
Topics
- Annotation, visualization, and reuse of mathematical models
- Kinetic Monte Carlo (KMC) and other methods for modeling stochastic (biological) processes
- Molecular docking
- Parameter estimation, sensitivity analysis and sloppiness of systems biology models
- Rule-based modeling of biomolecular site dynamics in cellular regulatory systems
- Spatial modeling via Brownian dynamics (BD) and partial differential equation (PDE) modeling
Projects
- A mentored project will be organized that involves using MCell and/or Simmune
- A mentored project will be organized that involves using RuleBender, BioNetGen and NFsim
Software
Please install the following software to prepare for scheduled computer labs:
- AutoDock
- BioNetFit
- ML-Rules and SESSL
- COPASI
- MATLAB (MathWorks, Natick, MA) - license available courtesy of MathWorks if required (contact organizers for details)
- MCell and CellBlender
- MCell is a spatial simulator based on Brownian dynamics and CellBlender is a Blendor-based interface to MCell.
- BioNetGen
- RuleBender is an Eclipse-based IDE for BioNetGen and NFsim, which provide deterministic and stochastic simulation capabilities appropriate in the well-mixed limit.
- These tools are freely available and easy to install on most platforms (Mac OS, Windows, Linux). They enable rule-based modeling of cellular regulatory systems.
- Download all the rule-based modeling software at http://bionetgen.org/index.php/Download
- Simmune
- StochSS
Please also familiarize yourself with BioModels Database.
Recommended Reading
- Modeling for (physical) biologists: an introduction to the rule-based approach (Preprint)
- Multi-state modeling of biomolecules (The most informative Wikipedia page about rule-based modeling)
