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# Textbooks and simulations

edited June 2020

Note this one though, from the Petri net web page:

• Darren J. Wilkinson, Stochastic Modelling for Systems Biology, Taylor & Francis, New York, 2006. Good introduction to stochastic Petri nets, with applications to gene expression and the Lotka-Volterra equations for predator-prey interactions.

This has a short chapter called case studies, with the following applications and simulation challenges:

• Dimerisation kinetics
• Michaelis-Menten enzyme kinetics
• An auto-regulatory genetic network
• The lac operon

I was hoping for a more basic text to start with, and one that covered a wider range of applications, but for the time being we can use it as a working text. We can discuss some of the simulation challenges on a new thread, and who ever is up for it can try their hand at coding them up and sharing their results.

These are small, homework level simulations, which can be done on any laptop in anyone's language of choice.

@DanielGeisler if you are interested in digging into this subject, I recommend getting this textbook. Although oriented to biology, it gives a broader theoretical foundation.

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@DavidTanzer thanks for the info on Stochastic modelling for systems biology. I purchased a copy and would be happy to be in a study group if anyone is interested.

Comment Source:@DavidTanzer thanks for the info on ***Stochastic modelling for systems biology***. I purchased a copy and would be happy to be in a study group if anyone is interested.
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edited May 2020

Sure thing, thanks.

Comment Source:Sure thing, thanks.
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edited May 2020

When it arrives, one good thing that we can do is to post some reading notes to a discussion. The notes can be in whatever style one chooses, not necessarily formal or structured. Since I like to teach math, my notes go beyond notes and have a flavor of tutorials on related topics - but that's just me. Notes could be just simple quotes, or a description of the flow of topics, or questions. By posting notes we contribute to the circulation of ideas.

Comment Source:When it arrives, one good thing that we can do is to post some reading notes to a discussion. The notes can be in whatever style one chooses, not necessarily formal or structured. Since I like to teach math, my notes go beyond notes and have a flavor of tutorials on related topics - but that's just me. Notes could be just simple quotes, or a description of the flow of topics, or questions. By posting notes we contribute to the circulation of ideas.