Compile models from a manually defined set of equations to AMICI, this applies to any ODE system Perform identification analysis and optimal experimental design (i.e. obtain a series of time dependent inupts for you model which improve parameter estimations)
Beta version 1.0 (march 24 2022)
This is a beta version of the ODE compilation and experimental design program we will prepare a pip version in the near future (August 2022).
More function will be added over time.
You can download the code folder to your desktop, this contains 2 subfolders
-Dependencies
-Main
within the dependencies script you will find the write up of Modelobject/model builder and compilation with AMICI (you can make use of subfunctions in the Measurementobject and experiment generation ModelSolver where model object with conditions is simulated ParameterOptimization (fitting data) ExperimentalOptization (optimizing control inputs)
In the demonstration folder are 2:
-A model folder, where we define a model or a set of models -A main folder where we call the different optimization and analysis scripts
The user will need to install the following packages
-Tellurium https://pypi.org/project/python-libsbml/](https://pypi.org/project/tellurium/
-Roadrunner https://pypi.org/project/libroadrunner/
-Libsbml https://pypi.org/project/python-libsbml/
-AMICI https://amici.readthedocs.io/en/latest/about.html
-pyDOE https://pythonhosted.org/pyDOE/
-sobolseq https://pypi.org/project/sobol-seq/
-importlib https://pypi.org/project/importlib/
The next version of this script will include a pip install for all dependencies excluding AMICI
for the AMICI installation we refer the user to the AMICI website https://amici.readthedocs.io/en/latest/about.html
Note that the windows install requires path changes, similarly amici requires specific compilers to be present. Note that for the compilation of the model to AMICI we reload the script, when we create the SBML file from the model the user defines we use tellurium and libsbml, to our knowlegde these have conflicting packages with AMICI thus we reload the system (with packages ordered differently) to compile the model after the SBML file has been created.