I would like to investigate a model of AMPK-mediated survival signalling during transient neuronal excitotoxicity (pathway hypothesised by Weisova et al (2009), J. Neurosci. http://www.jneurosci.org/content/29/9/2997.long). I have previously implemented a version of this model in MATLAB, with manual parameter optimisation. I managed to fit the model to experimental data for two of the state variables (ATP and AMPK), but have not been able to fit a third state variable (glucose).
For this project, I will implement the model in VCell, and perform parameter optimisation using the inbuilt functions. I will also perform parameter optimisation in COPASI (and maybe MATLAB SimBio). I would like to be confident that the model in its current state is unable to adequately represent the entire dataset, and investigate what additional reactions may be required.
* This project proposal was written using British English spelling…….!