The Sixth q-bio Summer School: Cell Signaling

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This series of lectures, which is offered at the Santa Fe campus, will be focused on modeling cell signaling. We will begin with an overview of the inherent features of cell signaling systems, including the modularity of proteins, the importance of post-translational modifications (e.g., multisite phosphorylation), and an overview of cell signaling motifs, such as kinetic proofreading, serial engagement, and regulated recruitment (co-localization of enzymes and substrates). We will then discuss how these features complicate efforts to develop predictive mechanistic models of cell signaling systems and possible solutions, in particular the rule-based modeling approach. We will cover methods for simulating a model, visualizing and annotating a model, and fitting procedures. We will make extensive use of software tools that are compatible with the BioNetGen language (BNGL) or the closely related Kappa language ( An example of such a tool is BioNetGen ( For additional information, contact Bill Hlavacek.




A detailed program for the Santa Fe campus is available here. An overview of the school is available here.


  • Inherent features of cell signaling systems
  • Combinatorial complexity
  • 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) and Kappa
  • Visualizing and annotating a rule-based model
  • Generate-first simulation
  • On-the-fly simulation
  • Network-free simulation
  • Software tools
  • Fitting
  • Sensitivity analysis
  • Sloppiness
  • Fragmentation
  • Multiscale simulation algorithms

Student projects

Individual students or teams of students will develop computational models for Ras/RAF/MEK/ERK signaling. All students participating in this track are expected to read two modeling papers before arriving in Santa Fe: PMID:17947584 and PMID:19167334. Additional reading about Ras/RAF/MEK/ERK signaling is encouraged. Journal club discussions will be led by a student selected by the organizers; this student will receive a special scholarship.


Recommended reading

In addition to the required reading (noted above), which is needed to prepare for journal club discussions, students are encouraged to read the following papers before the summer school:

Course credit

You may receive course credit from the University of New Mexico (3 credit hours) for participating in the Cell Signaling section of the 2012 q-bio Summer School. To learn more, contact Bill Hlavacek.

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