apricopt 0.0.2a3

A library for simulation-based parameter optimization

Apricopt

Apricopt is a python framework for simulation-based optimisation of dynamical systems.

It is agnostic with respect to the optimiser and to the simulator.

Apricopt supports the PEtab format for the definition of the optimisation problem. More info about PEtab here.

Currently, we support the following simulators:

• COPASI. A state-of-the-art simulator for models of biological processes. We support SBML models (any level and version).
• RoadRunner. A fast state-of-the-art simulator of biological models.

Currently, we support the following black-box optimisers:

• NOMAD. A state-of the art black-box solver that supports surrogate models. More info here.
• SciPy.optimize. A python library that implements several algorithms for multivariate optimization. More info here.
• PySwarms. A python library that implements various forms of the Particle Swarm Optimization algorithm. More info here.

Currently, we support the following white-box optimisers:

• COPASI. It supports several optimisation algorithms for biological processes. More info here

Info

WIP

• Version 0.0.2a3

Who do I talk to?

• Marco Esposito (author) - [e-mail]
• Leonardo Picchiami (author) - [e-mail]

Copyright (C) 2020-2021 Marco Esposito, Leonardo Picchiami.

Distributed under GNU General Public License v3.