This project holds a couple of sample scripts, that show how COPASI simulations can be used in pyABC.
Checkout the project:
git clone https://github.com/fbergmann/pyabc-copasi
Install the requirments (pyabc, python-copasi, basico) in a new virtual environment:
cd pyabc-copasi
pip install -r requirements.txt
At the moment the scripts port the markov jump example from the pyabc tutorial. It is present twice, once as:
* `example_distance_gillespie.py`: this is just copy pasted from the tutorial, and uses the pure python gillespie implementation
* `example_distance_basico.py`: uses basico to simulate the models included in the `data` directory.
Running:
python example_distance_basico.py
Yields:
INFO:Sampler:Parallelizing the sampling on 8 cores.
INFO:History:Start <ABCSMC id=27, start_time=2021-03-04 10:51:38.388675>
INFO:ABC:Calibration sample t=-1.
INFO:Epsilon:initial epsilon is 5.55
INFO:ABC:t: 0, eps: 5.55.
INFO:ABC:Acceptance rate: 500 / 1039 = 4.8123e-01, ESS=5.0000e+02.
INFO:Adaptation:Change nr particles 500 -> 109
INFO:ABC:t: 1, eps: 2.8.
INFO:ABC:Acceptance rate: 109 / 305 = 3.5738e-01, ESS=1.0582e+02.
INFO:Adaptation:Change nr particles 109 -> 85
INFO:ABC:t: 2, eps: 2.2.
INFO:ABC:Acceptance rate: 85 / 222 = 3.8288e-01, ESS=4.7117e+01.
INFO:Adaptation:Change nr particles 85 -> 69
INFO:ABC:t: 3, eps: 1.95.
INFO:ABC:Acceptance rate: 69 / 215 = 3.2093e-01, ESS=4.1095e+01.
INFO:Adaptation:Change nr particles 69 -> 89
INFO:ABC:t: 4, eps: 1.6028273013884138.
INFO:ABC:Acceptance rate: 89 / 336 = 2.6488e-01, ESS=4.0208e+01.
INFO:Adaptation:Change nr particles 89 -> 95
INFO:ABC:t: 5, eps: 1.45.
INFO:ABC:Acceptance rate: 95 / 419 = 2.2673e-01, ESS=3.8843e+01.
INFO:Adaptation:Change nr particles 95 -> 87
INFO:ABC:t: 6, eps: 1.25.
INFO:ABC:Acceptance rate: 87 / 417 = 2.0863e-01, ESS=4.5705e+01.
INFO:Adaptation:Change nr particles 87 -> 93
INFO:ABC:t: 7, eps: 0.85.
INFO:ABC:Acceptance rate: 93 / 474 = 1.9620e-01, ESS=5.8819e+01.
INFO:Adaptation:Change nr particles 93 -> 57
INFO:ABC:t: 8, eps: 0.7.
INFO:ABC:Acceptance rate: 57 / 387 = 1.4729e-01, ESS=5.5188e+01.
INFO:Adaptation:Change nr particles 57 -> 48
INFO:pyabc.util:Stopping: minimum epsilon.
INFO:History:Done <ABCSMC id=27, duration=0:00:32.578834, end_time=2021-03-04 10:52:10.967509>
as well as images as these ones:
Which matches what was found in the original example. Sometimes the it doesn't work and stops with:
pyabc.transition.exceptions.NotEnoughParticles: Fitting not possible.
in that case you just run it again.
The packages available on this page are provided under the Artistic License 2.0, which is an OSI approved license. This license allows non-commercial and commercial use free of charge.