List of software

AMICI provides a multilanguage (Python, C++, Matlab) interface for the SUNDIALS solvers CVODES (for ordinary differential equations) and IDAS (for algebraic differential equations). AMICI allows the user to read differential equation models specified as SBML and automatically compiles such models as .mex simulation files, C++ executables or python modules. Beyond forward integration, the compiled simulation file also allows for forward and adjoint sensitivity analysis.

pyABC is a python toolbox for Approximate Bayesian Computation - Sequential Monte Carlo (ABC-SMC) sampling for parameter estimation of complex stochastic models. It is very flexible, customizable and facilitates massively parallel computations. This facilitates the analysis of computationally very demanding inference problems. Applications used already up to 10^5 cores and several thousand core hours.

A repository provides a collection of SBML models and experimental data. It can be used for the benchmarking of existing and new methodologies for data-based modeling, for instance optimization and uncertainty analysis methods.

An Integrated Platform for Data-Driven Modeling of Multi-Cellular Processes. It delivers that by combining the simulation tool Morpheus and the likelihood-free inference tool pyABC.

PEtab describes a data format for specifying parameter estimation problems in systems biology, and provides a Python library for easy access and validation of PEtab files. The format is used in pyPESTO and the collection of benchmark problems.

pyPESTO is a widely applicable and highly customizable python toolbox for parameter estimation. It is based on PESTO but offers additional functionalities. Furthermore, is tightly integrated with SBML and PEtab to streamline the data-driven modelling of cellular pathways.