The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

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 anal...

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Vydáno v:Frontiers in physiology Ročník 9; s. 680 - 13
Hlavní autoři: Naldi, Aurélien, Hernandez, Céline, Levy, Nicolas, Stoll, Gautier, Monteiro, Pedro T., Chaouiya, Claudine, Helikar, Tomáš, Zinovyev, Andrei, Calzone, Laurence, Cohen-Boulakia, Sarah, Thieffry, Denis, Paulevé, Loïc
Médium: Journal Article
Jazyk:angličtina
Vydáno: Switzerland Frontiers 19.06.2018
Frontiers Media S.A
Témata:
Bioinformatics
Boolean networks
computational systems biology
Computer Science
model analysis
Physiology
Python programming language
reproducibility
computational systems biology
model analysis
Python programming language
reproducibility
Boolean networks
ISSN:1664-042X, 1664-042X
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Shrnutí: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.
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Reviewed by: Oksana Sorokina, University of Edinburgh, United Kingdom; Kyle B. Gustafson, Naval Surface Warfare Center Carderock Division (NSWCCD), United States
This article was submitted to Systems Biology, a section of the journal Frontiers in Physiology
Edited by: Pierre De Meyts, de Duve Institute, Belgium
ISSN:1664-042X
1664-042X
DOI:10.3389/fphys.2018.00680