Using the Hornberg 2005 MAPK signal transduction pathway model a Genetic Algorithm was implemented in Matlab for moving the peak (i.e. global maximum) of the ERK-PP time series as late as possible i.e. as further away in time as possible. The algorithm starts with a population of randomly initialized individuals and runs for a given number of iterations. In the end, all the individuals for which the peak of the time series of ERK-PP is reached later than a given threshold value are printed in a file “output.txt”. The source code is open source and can be adapted for other projects. You can access it from the github repository behaviour-driver. Thank you to Qian Gao for providing the set of ODEs already implemented in Matlab. They are the result of her own work and only a modified version of the model was used here. For more details regarding the original model, please contact the author.
During the process of familiarizing myself with the concepts of Petri nets and continuous simulations of bio-chemical networks, I wanted to discover the mechanism of deriving the set of ordinary differential equations (ODEs) corresponding to a given set of chemical reactions or the graphical representation of a Petri net. I have summarized my findings in the following guide and published it here such that other people facing the same question can get a quicker answer. Therefore, this guide is intended to be read by “beginners” and not professionals or experts.