ABC-SysBio swMATH ID: 24739 Software Authors: Liepe, J., Barnes, C., Cule, E., Erguler, K., Kirk, P., Toni, T., Stumpf, M. P. H. Description: ABC-SysBio: Approximate Bayesian Computation in Python with GPU support. MOTIVATION: The growing field of systems biology has driven demand for flexible tools to model and simulate biological systems. Two established problems in the modeling of biological processes are model selection and the estimation of associated parameters. A number of statistical approaches, both frequentist and Bayesian, have been proposed to answer these questions. RESULTS: Here we present a Python package, ABC-SysBio, that implements parameter inference and model selection for dynamical systems in an approximate Bayesian computation (ABC) framework. ABC-SysBio combines three algorithms: ABC rejection sampler, ABC SMC for parameter inference and ABC SMC for model selection. It is designed to work with models written in Systems Biology Markup Language (SBML). Deterministic and stochastic models can be analyzed in ABC-SysBio. AVAILABILITY: http://abc-sysbio.sourceforge.net Homepage: https://www.ncbi.nlm.nih.gov/pubmed/20591907 Dependencies: Python Related Software: BioBayes; astroABC; EasyABC; SciPy; Python; BCM; Stan; DAKOTA; abc; al3c; PyTorch; ipyparallel; Dask; IPython; pyABC; ELFI; SWIG; NumPy; Apache Spark; OpenMPI Referenced in: 6 Publications all top 5 Referenced by 20 Authors 1 Arampatzis, Georgios 1 Barnes, Chris P. 1 Bonassi, Fernando V. 1 Economides, Athena E. 1 Filippi, Sarah 1 Grima, Ramon 1 Hilbers, Peter A. J. 1 Karabatsos, George 1 Karnakov, Petr 1 Koumoutsakos, Petros D. 1 Leisen, Fabrizio 1 Martin, Sergio M. 1 Sanguinetti, Guido 1 Schnoerr, David 1 Stumpf, Michael P. H. 1 Tiemann, C. A. 1 van Riel, N. A. W. 1 Vanlier, J. 1 Wälchli, Daniel 1 West, Mike all top 5 Referenced in 6 Serials 1 Computer Methods in Applied Mechanics and Engineering 1 Mathematical Biosciences 1 Journal of Physics A: Mathematical and Theoretical 1 Statistics Surveys 1 Statistics and Computing 1 Bayesian Analysis all top 5 Referenced in 7 Fields 4 Statistics (62-XX) 2 Probability theory and stochastic processes (60-XX) 2 Numerical analysis (65-XX) 2 Biology and other natural sciences (92-XX) 1 Ordinary differential equations (34-XX) 1 Computer science (68-XX) 1 Operations research, mathematical programming (90-XX) Referencing Publications by Year