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sbmlteam / libsbml

LibSBML is a native library for reading, writing and manipulating files and data streams containing the Systems Biology Markup Language (SBML). It offers language bindings for C, C++, C#, Java, JavaScript, MATLAB, Perl, PHP, Python, R and Ruby.
https://sbml.org/software/libsbml
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Add piecewise-to-events translators #363

Open luciansmith opened 8 months ago

luciansmith commented 8 months ago

We found a model that didn't work correctly on roadrunner, since there was a piecewise equation that only changed for a window of time that wasn't checked by the CVODE algorithm. Translating the logic to events worked fine, however. It might be nice to have a translator in libsbml that would convert piecewise equations to events, something like (in Antimony)

...piecewise(x, cond1, y, cond2, z)...

changes to:

...piecewise_var1...

piecewise_var1 = z at cond1, t0=false: piecewise_var1 = x at cond2 && !cond1, t0=false: piecewise_var1 = y at !cond2 && !cond1, t0=false: piecewise_var1 = z

fbergmann commented 8 months ago

good idea, that is also what COPASI does.