I am a biologist who is trying to become more quantitative as well as more model savvy. One excellent tool I have stumbled upon is the SimBiology toolbox for MatLab where you can graphically layout your model. This has been very useful but I have come up against a problem: I cannot use a conditional statement.
My goal is to make a bacterial growth model such that when there is sugar present, the bacterial population increases while if there is no sugar present, the cells start to die. Does anyone have experience with this kind of "if-then" statement in this program?
I am also open to any reccomendations on modeling in general or other EASY programs that can be used to make models.
Here are a few tools that you might want to consider: ModelBuilder (http://model-builder.sourceforge.net/), Cain (http://cain.sourceforge.net), and xppaut (http://www.pitt.edu/~phase/). I am not sure how hard or easy they are to use. I don't know what sort of modeling approach you use (ode? stochastic?), so I am not sure how relevant these tools might be to what you wish to do. All are open-source, and the first two are available in Ubuntu repositories. Since you talk about bacteria in a sugar(free) environment, are you aware of http://www.ncbi.nlm.nih.gov/pubmed/19186128 ? netlogo (ccl.northwestern.edu/netlogo/) might offer similar capabilities; in any case, netlogo is fun to play with.
Mihir,
Thank you for the useful information.
I may not try the tools because someone from MatLab contacted me with an answer for using SimBiology but I will keep them in mind.
That paper is an excellent resource.
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