Fabian Fröhlich
Fabian Fröhlich
As with #924, I think transiently adding anything to a model that could also be done in SBML is a bad idea.
I don't see any issues with defining observables with parameter assignments.
@dweindl is this fixed by PEtab?
Sounds good to me!
> Might be helpful to add an option to pass assumptions on parameters and states during model import that might allow for better symbolic simplifications. (E.g. helpful for #1151) >...
> Yes, that's pretty much what I meant. I think otherwise it will be too easy to shoot yourself in the foot. Great! > Also, once such assumptions are supported,...
Assuming strict positivity based on log-transformsof parameters probably has the biggest effect, not sure whether ranges are that important.
> * An explanation of how sbml-import/pySB and ode-export are linked and intertwined. These routines are some thousand lines of code, which is really tricky and has functions/classes with really...
Regarding directly implementing pickling in python, I think its feasible to implement this by automatically identifying getter/setter methods by text parsing and store the respective values. This approach would ensure...
sbml/pysb import is probably parallelizable. Not so sure about ode_export. Most of the time is probably spent in `_writeFunctionFile` which probably isnt so easily paralellizable given the nonlinearity of `ODEExporter.eq(...)`.