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The Ninth q-bio Summer School - Albuquerque: Cell signaling
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Back to The Ninth q-bio Summer School - Albuquerque
Contents
About the Cell Signaling focus area
Lead scientific organizer: Bill Hlavacek (E-mail)
Faculty
- Ludmil B. Alexandrov, Los Alamos National Laboratory
- James R. Faeder, University of Pittsburgh School of Medicine
- Ryan N. Gutenkunst, University of Arizona
- William S. Hlavacek, Los Alamos National Laboratory
- Brian Munsky, Colorado State University
- Danny Perez, Los Alamos National Laboratory
- Gerard Ostheimer, United Nations Sustainable Energy for All Initiative
- Nikolai A. Sinitsyn, Los Alamos National Laboratory
Topics
- Kinetic Monte Carlo (KMC) and other methods for modeling stochastic (biological) processes
- Non-negative matrix factorization (NMF) and (biological) applications
- Parameter estimation, sensitivity analysis and sloppiness of systems biology models
- Partial least squares regression (PLSR) and (biological) applications
- Rule-based modeling of biomolecular site dynamics in cellular regulatory systems
- Spatial modeling via Brownian dynamics (BD)
Projects
- Using MCell to model anomalous diffusion and its potential effects on nuclear localization of activated ERK
- Using BioNetGen and NFsim to model positive and negative feedback mechanisms targeting SOS downstream of activated EGFR
Software
Please install the following software to prepare for scheduled computer labs:
- 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.
- R
- R is a framework for statistical computing.
- RuleBender
- 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.
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)
- Network analysis of oncogenic Ras activation in cancer (paper for project focused on positive feedback to Ras)
- Fast rebinding increases dwell time of Src homology 2 (SH2)-containing proteins near the plasma membrane (paper for project focused on how receptor clustering influences recruitment of binding partners)
