The CoLoMoTo interactive notebook: Accessible and reproducible computational analyses for qualitative biological networks

Aurélien Naldi, Céline Hernandez, Nicolas Levy, Gautier Stoll, Pedro T. Monteiro, Claudine Chaouiya, Tomáš Helikar, Andrei Zinovyev, Laurence Calzone, Sarah Cohen-Boulakia, Denis Thieffry, Loïc Paulevé

Research output: Contribution to journalArticle

6 Scopus citations

Abstract

Analysing models of biological networks typically relies on workflows in which different software tools with sensitive parameters are chained together, many times with additional manual steps. The accessibility and reproducibility of such workflows is challenging, as publications often overlook analysis details, and because some of these tools may be difficult to install, and/or have a steep learning curve. The CoLoMoTo Interactive Notebook provides a unified environment to edit, execute, share, and reproduce analyses of qualitative models of biological networks. This framework combines the power of different technologies to ensure repeatability and to reduce users' learning curve of these technologies. The framework is distributed as a Docker image with the tools ready to be run without any installation step besides Docker, and is available on Linux, macOS, and Microsoft Windows. The embedded computational workflows are edited with a Jupyter web interface, enabling the inclusion of textual annotations, along with the explicit code to execute, as well as the visualization of the results. The resulting notebook files can then be shared and re-executed in the same environment. To date, the CoLoMoTo Interactive Notebook provides access to the software tools GINsim, BioLQM, Pint, MaBoSS, and Cell Collective, for the modeling and analysis of Boolean and multi-valued networks. More tools will be included in the future. We developed a Python interface for each of these tools to offer a seamless integration in the Jupyter web interface and ease the chaining of complementary analyses.

Original languageEnglish (US)
Article number680
JournalFrontiers in Physiology
Volume9
Issue numberJUN
DOIs
StatePublished - Jun 19 2018

Keywords

  • Boolean networks
  • Computational systems biology
  • Model analysis
  • Python programming language
  • Reproducibility

ASJC Scopus subject areas

  • Physiology
  • Physiology (medical)

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    Naldi, A., Hernandez, C., Levy, N., Stoll, G., Monteiro, P. T., Chaouiya, C., Helikar, T., Zinovyev, A., Calzone, L., Cohen-Boulakia, S., Thieffry, D., & Paulevé, L. (2018). The CoLoMoTo interactive notebook: Accessible and reproducible computational analyses for qualitative biological networks. Frontiers in Physiology, 9(JUN), [680]. https://doi.org/10.3389/fphys.2018.00680