Cell ML

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Cell ML is a markup language for mathematical models of cell biology. See http://www.cellml.org/ for a fuller description.

Notes on trying to get Cell ML working on a linux box

  • Trying to get Cell ML working, first using CESE (Ian Holmes, 3/30/2005)
    • First downloaded from here, then tried checking it out via CVS
    • typically, much-vaunted java portability is a sham. For example, InstallAnywhere doesn't (see Why Dart Is Not In Java)
    • did apt-get install ant to install ant
      • ...ant, of course, doesn't work either; is missing sun.tools.native2ascii.Main
      • Remember, comrades, Java Will Solve All Portability Problems (pukes)
      • tried downloading latest ant from ant.apache.org
      • ...and lo, the java API used by CESE appears to be out of date
      • did I mention Why Dart Is Not In Java?
  • Next trying mozCell
  • Back to CESE: Yuri Bendana pointed out I should be using JDK 1.4.2. (grumbles: I thought Java was supposed to be all version-independent... and clearly ant is not as good at detecting dependencies as autoconf.... grumble...) anyway it now seems to work.
    • CESE users' guide is very helpful
    • See also page on using CellML models in CESE
    • After copying in the Perelson model I had to add it to the bin/models/build.xml file as described here
    • However this turned out to be premature as the java code for the model (autogenerated from the Cell ML XML) did not even compile. Is all this effort worth it, given that the equations are actually quite simple? Can we do better with (ulp) Matlab, or C or (even) Perl? I think so. Taking the papers home to pore over them....