2014 Workshop: Student Exercises and Projects



Random: Rui Yan, Alina, Kamil

Presentation: The Activation and Deactivation of Ras


DAN: Neno, Dylan, Alessandro

Presentation: Extending The Network Analysis of Oncogenic Ras Activation In Cancer (Stites, et.al.) Model With Positive Feedback From The Allosteric Binding Of Ras To The SOS GEF Complex.


Rulebenders: Piotr, Gianluca, Lyle

Presentation: Modeling the Effects of Mutants and Drugs on the Ras Signaling Pathway


KScience: Eitan, Jen, Stephanie

Presentation: Comparing GEF-Induced GTP binding between the Hlavacek and Faeder Models


Modelers: Faiza, Nick, Rav

Presentation: RAS & Its Effect on Cancer

Week 1:

Week 2:

  • The Model Sort: A discussion of models produced the following conclusions as to the most/least important properties of models. Surprisingly, all groups agreed on the most important property, the the model is an accurate reflection of the system.


  • The Frog Cell Cycle: The goal is to use BioNetGen/RuleBender to solve a significant problem with known answers, to get you accustomed to debugging BNG models.
    There are three documents below, a class module discussing the frog cell cycle, a class exercise to simulate it with ode's, and a research paper. I suggest that if you have time, you might read at least the module and exercise and try to model it using the BioNetGen language. Hint: the most useful parts are the beautiful diagram in Figure 3 of the Class Module and the differential equations in Figure 2 of the research paper. To run the model, you also need the rate parameters from Table 1 in the paper.
    If your experience is anything like mine, you'll need more time to get it done, so just be happy with anything you're able to do. Working on making a BNG model of this system can help you start thinking in BNG terms, and we'll go over the details early this coming week.

Week 3

Potential projects

Base models

Mutations references

Wittinghofer videos


Initial Investigations of Models

Nancy Griffeth

Last modified: Feb 1, 2014