SBpipe

SBpipe allows mathematical modellers to automatically repeat the tasks of model simulation and parameter estimation, and extract robustness information from these repeat sequences in a solid and consistent manner, facilitating model development and analysis. SBpipe can run models implemented in COPASI, Python or coded in any other programming language using Python as a wrapper module. Pipelines can run on multicore computers, Sun Grid Engine (SGE), Load Sharing Facility (LSF) clusters, or via Snakemake.

Project info

Copyright © 2015-2018, Piero Dalle Pezze

Affiliation: The Babraham Institute, Cambridge, CB22 3AT, UK

License: MIT License (https://opensource.org/licenses/MIT)

Home Page: http://sbpipe.readthedocs.io

Anaconda Cloud: https://anaconda.org/bioconda/sbpipe

PyPI: https://pypi.org/project/sbpipe

sbpiper (R dependency for data analysis): https://cran.r-project.org/package=sbpiper

sbpipe_snake (Snakemake workflows for SBpipe): https://github.com/pdp10/sbpipe_snake

Mailing list: sbpipe@googlegroups.com

Forum: https://groups.google.com/forum/#!forum/sbpipe

GitHub (dev): https://github.com/pdp10/sbpipe

Travis-CI (dev): https://travis-ci.org/pdp10/sbpipe

Issues / Feature requests (dev): https://github.com/pdp10/sbpipe/issues

Citation: Dalle Pezze P, Le Novère N. SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks. BMC Systems Biology. 2017 Apr;11:46. https://doi.org/10.1186/s12918-017-0423-3