Directly input ODE systems #654
Description
The idea is to replace reaction networks by ODE systems so that one can easily run parameter estimation on ODE systems that are not motivated by reaction networks. I want to run parameter estimation on ODE systems with pyPESTO so this would be the core extension necessary for that, I think the scenario appears often. I talked to @paulstapor about this and he suggested this rough guideline of what would have to be done:
This files takes SBML-files as input https://github.com/ICB-DCM/AMICI/blob/master/python/amici/sbml_import.py, there would need to be an an alternative standardised format that directly corresponds to ODE systems which would be accepted in a similar file. The output format (refer to the class ODEModel) has to be consistent with the above mentionend file and is documented here https://github.com/ICB-DCM/AMICI/blob/master/python/amici/ode_export.py.