I am supposed to model EGFR trafficking. I will use matlab, maybe simbiology. But I don't know where to start. I did not do something like that before. I was good at differential equations years ago, I regurgitated the lecture and solved hundreds of equations again but I am still not able to understand models in articles. They look so different from the lecture. EGFR trafficking was looking like enzyme kinetics and as an exercise I've modelled some reaction chains, but that's all. I need to improve myself. If you have any advice, I would be really happy.
Hi,
You can find some ideas and skills in:
http://www.amazon.com/Principles-Computational-Biology-Volkhard-Helms/dp/3527315551
Moreover, you'll probably need to learn SBML (http://sbml.org/Main_Page) which is now the standard exchange file for biological models. This is used in simbiology, copasI, etc...
Hi Cansu,
You may need to look at the paper entitled "An Integrated Model of Epidermal Growth Factor Receptor Trafficking and Signal Transduction" by Haluk Resat, Jonathan A. Ewald, David A. Dixon, and H. Steven Wiley, Biophysical Journal
Volume 85 August 2003, 730-743.
and the related references to be properly familiar with the EGFR pathway and the biology related. Then you can decide on which modelling perspective, whether deterministic, stochastic, etc to take on.
In addition, you may find some helpful principles from the Book " Computational Cell Biology " edited by Christopher P. Fall Eric S. Marland John M. Wagner
John J. Tyson.
Should you not have access to those two documents, you are welcome to let me know and I provide them to you.
Useful modelling starts with well defined questions that need to be answered or assumptions that you want to validate in search of insight - in this case about EGFR trafficking. You may start with a published kinetics based model of EGFR trafficking as a learning step using matlab/simbiology or you might try StochSS ( http://www.stochss.org) .
- Badges
- Science topic