Exercises for experimental biologists (Phair)

Some modelers find it more natural and more informative to work in the time domain rather than in phase space. When I say the time domain, I mean that we like to see plots of species, and fluxes as functions of time. For those of you who have an affinity for this approach it might be useful to get together to think about modeling from the perspective of real world applications with many, many state variables. Here are some things we could do:

  1. We could build a Diagram for one or more of YOUR biological problems. We’d talk through the decisions that a modeler makes based on what the experimental biologist says. Watching this process can be amazingly instructive even if the biological system being modeled is not your own.
  2. We could discuss the important differences between  process diagrams and connection diagrams. We’d see why one of them immediately and unambiguously translates to ODEs and the other does not. This is an exercise about my post on a general rule for biological diagrams.

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