## 2014 Workshop: Student Exercises and Projects

### Participants

## Teams

**Random**: Rui Yan, Alina, Kamil

**Presentation**: The Activation and Deactivation of Ras

**DAN**: Neno, Dylan, Alessandro

**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."

- A related blog, that appeared on the WGBH site a week later: http://www.pbs.org/wgbh/nova/physics/blog/2014/01/why-weve-underestimated-not-only-the-size-of-our-cosmos-but-also-our-ability-to-understand-it/. The thesis: "our universe isn't just
*described*by math, but ... it*is*math in the sense that we're all parts of a giant mathematical object." - Hamming lecture on math: This doesn't seem to work. On the other hand, if you go to youtube and search for "Hamming mathematics" you get the same link and the same video, and it works. Go figure.

- A related blog, that appeared on the WGBH site a week later: http://www.pbs.org/wgbh/nova/physics/blog/2014/01/why-weve-underestimated-not-only-the-size-of-our-cosmos-but-also-our-ability-to-understand-it/. The thesis: "our universe isn't just
**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.

Base models

- Based on Science paper, no feedback loop, now containing the adjustment for membrane localization
- Faeder model with feedback loop: minimal model with feedback
- Hlavacek mass-action model: complex model

Mutations references

Wittinghofer videos

Initial Investigations of Models

Nancy Griffeth

nancy.griffeth@lehman.cuny.edu

Last modified: Feb 1, 2014