CoRC: the COPASI R Connector

Jonas Förster; Frank T Bergmann; Jürgen Pahle

doi:10.1093/bioinformatics/btab033

CoRC: the COPASI R Connector

Bioinformatics. 2021 Sep 9;37(17):2778-2779. doi: 10.1093/bioinformatics/btab033.

Authors

Jonas Förster¹, Frank T Bergmann², Jürgen Pahle³

Affiliations

¹ Immunotherapy and Immunoprevention, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany.
² Modelling of Biological Processes, BioQuant/COS, Heidelberg University, INF267, 69120 Heidelberg, Germany.
³ Biological Information Processing Group, BioQuant, Heidelberg University, INF267, 69120 Heidelberg, Germany.

PMID: 33470404
DOI: 10.1093/bioinformatics/btab033

Abstract

Motivation: COPASI is a biochemical simulator and model analyzer which has found widespread use in academic research, teaching and beyond. One of COPASI's strengths is its graphical user interface, and this is what most users work with. COPASI also provides a command-line tool. So far, an intuitive scripting interface that allows the creation and documentation of systems biology workflows was missing though.

Results: We have developed CoRC, the COPASI R Connector, an R package which provides a high-level scripting interface for COPASI. It closely mirrors the thought process of a (graphical interface) user and should therefore be very easy to use. This allows for complex workflows to be reproducibly scripted, utilizing COPASI's powerful analytic toolset in combination with R's extensive analysis and package ecosystem.

Availability and implementation: CoRC is a free and open-source R package, available via GitHub at https://jpahle.github.io/CoRC/ under the Artistic-2.0 license.

Supplementary information: We provide tutorial articles as well as several example scripts on the project's website.

Abstract

Grants and funding