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Cell Signaling
This series of lectures, which is offered at the Santa Fe campus, will be focused on modeling cell signaling. We will begin with a brief overview of the hallmark features of cell signaling systems. We will then discuss how these features complicate efforts to develop predictive mechanistic models of cell signaling systems. We then introduce the rule-based modeling approach. We will cover methods for specifying, visualizing and annotating a model, methods for simulating models, and methods for analyzing models, including sensitivity analysis and parameter identification. We will make extensive use of software tools that are compatible with the BioNetGen language (BNGL). An example of such a tool is BioNetGen (http://bionetgen.org). For additional information, contact Bill Hlavacek.
Contents
Lecturers (tenative)
- Steve Andrews (student symposium speaker)
- James R. Faeder, PhD, University of Pittsburgh School of Medicine
- Leonard Harris
- William S. Hlavacek, PhD, Los Alamos National Laboratory and University of New Mexico
- Tomasz Lipniacki
- Xuedong Liu, University of Colorado
- Gerry Ostheimer
- Bridget S. Wilson, PhD, University of New Mexico School of Medicine
Program
- See schedule
Topics
- Features of cell signaling systems
- Combinatorial complexity
- Limitations of traditional approaches for modeling chemical kinetics
- The rule-based modeling approach (a link to a course that covers rule-based modeling at Pittsburgh is here)
- BioNetGen language (BNGL)
- Visualizing and annotating a rule-based model
- Simulation methods
- Software tools
- Fitting
Student projects
Individual students or teams of students will work on projects. Journal clubs and faculty-recommended team projects will be announced at the start of the school. See recommended reading.
Software
- RuleBender
- BioNetGen
- NFsim
- MCell & CellBlender For further info see MCell at q-bio Summer School 2014.
- PySB
