2014 Workshop: Student Exercises and Projects
Teams
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:
- Math Discussion: A get-acquainted-while-learning exercise posed the question "Is math a reality or is it just a human construct?" The general consensus, after much discussion and debate, was that the question was badly posed and should have been "Math is a construct that we use to explain reality."
- Using RuleBender: Toy Model for a tyrosine kinase pathway
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
- The Ras Pathway: Two papers that we will depend on for the Ras pathway models. I found these very difficult with my limited biology/chemistry background! You're welcome to get started on them at any time.
Potential projects
Base models
Mutations references
Wittinghofer videos
Initial Investigations of Models
Nancy Griffeth
nancy.griffeth@lehman.cuny.edu