• The CoLoMoTo Interactive Noteb...

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

Title:
The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks
Authors:
Naldi, Aurélien, Hernandez, Céline, Levy, Nicolas, Stoll, Gautier, Monteiro, Pedro, Chaouiya, Claudine, Helikar, Tomáš, Zinovyev, Andrei, Calzone, Laurence, Cohen-Boulakia, Sarah, Thieffry, Denis, Paulevé, Loïc
Contributors:
Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS-PSL (IBENS), École normale supérieure - Paris (ENS-PSL), Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Bioinformatique (LRI) (BioInfo - LRI), Laboratoire de Recherche en Informatique (LRI), Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), École normale supérieure de Lyon (ENS de Lyon), Université de Lyon, Université Paris Descartes - Paris 5 (UPD5), Centre de Recherche des Cordeliers (CRC), Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Santé et de la Recherche Médicale (INSERM), Université Pierre et Marie Curie - Paris 6 - UFR de Médecine Pierre et Marie Curie (UPMC), Université Pierre et Marie Curie - Paris 6 (UPMC), Plateforme de métabolomique, Analyse moléculaire, modélisation et imagerie de la maladie cancéreuse (AMMICa), Institut Gustave Roussy (IGR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut Gustave Roussy (IGR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa (INESC-ID), Instituto Superior Técnico (Universidade de Lisboa) [Lisboa] (IST / Técnico Lisboa), Universidade de Lisboa = University of Lisbon = Université de Lisbonne [Lisboa] (ULISBOA)-Universidade de Lisboa = University of Lisbon = Université de Lisbonne [Lisboa] (ULISBOA)-Instituto de Engenharia de Sistemas e Computadores (INESC), Instituto Gulbenkian de Ciência [Oeiras] (IGC), Fundação Calouste Gulbenkian = Fondation Calouste Gulbenkian = Calouste Gulbenkian Foundation [Lisbonne], University of Nebraska–Lincoln, University of Nebraska System, Institut Curie [Paris], Cancer et génome: Bioinformatique, biostatistiques et épidémiologie d'un système complexe, Mines Paris - PSL (École nationale supérieure des mines de Paris), Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Sciences et Lettres (PSL), Lobachevsky State University [Nizhni Novgorod], Centre Inria de Saclay, Institut National de Recherche en Informatique et en Automatique (Inria), ANR-16-CE12-0034,AlgoReCell,Modèles informatiques et algorithmes pour la prédiction de cibles de reprogrammation cellulaire avec haute fidélité et haute efficacité(2016), ANR-11-LABX-0045,DIGICOSME,Mondes numériques: Données, programmes et architectures distribués(2011), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011)
Source:
Frontiers in Physiology. 9:n-n
Publisher Information:
CCSD; Frontiers, 2018.
Publication Year:
2018
Collection:
collection:ENS-LYON
collection:UNIV-PARIS5
collection:UNIV-PARIS7
collection:ENSMP
collection:ENS-PARIS
collection:EPHE
collection:CNRS
collection:INRIA
collection:UNIV-PSUD
collection:INRIA-SACLAY
collection:ENSMP_CBIO
collection:PARISTECH
collection:INRIA_TEST
collection:FNCLCC
collection:IGR
collection:CURIE
collection:TESTALAIN1
collection:CORDELIERS
collection:UMR8623
collection:CENTRALESUPELEC
collection:INRIA2
collection:LRI-BIOINFO
collection:PSL
collection:USPC
collection:INSERM-SACLAY2
collection:UNIV-PARIS-SACLAY
collection:UNIV-PSUD-SACLAY
collection:INRIA-SACLAY-2015
collection:CENTRALESUPELEC-SACLAY
collection:IGR-SACLAY
collection:ENSMP_DEP_MS
collection:INRIA-300009
collection:SORBONNE-UNIVERSITE
collection:SORBONNE-UNIV
collection:SU-SCIENCES
collection:TEST-DEV
collection:UDL
collection:UNIV-LYON
collection:UNIV-PARIS
collection:UP-SANTE
collection:TEST-HALCNRS
collection:ENSMP-PSL
collection:ENS-PSL
collection:EPHE-PSL
collection:INSTITUT-CURIE-PSL
collection:SU-TI
collection:ANR
collection:LISN
collection:GS-ENGINEERING
collection:GS-COMPUTER-SCIENCE
collection:LISN-BIOINFO
collection:ALLIANCE-SU
collection:INRIAARTDOI
collection:INRIA-ETATSUNIS
collection:AMMICA
collection:SUPRA_BIOLOGIE
Subject Terms:
Python programming language, model analysis, computational systems biology, reproducibility, Boolean networks, [INFO.INFO-BI]Computer Science [cs], Bioinformatics [q-bio.QM]
Original Identifier:
HAL: hal-01794294
Document Type:
Zeitschrift article<br />Journal articles
Language:
English
ISSN:
1664-042X
Relation:
info:eu-repo/semantics/altIdentifier/doi/10.3389/fphys.2018.00680
DOI:
10.3389/fphys.2018.00680
Access URL:
https://hal.science/hal-01794294
https://hal.science/hal-01794294v2/document
https://hal.science/hal-01794294v2/file/fphys-09-00680.pdf
Rights:
info:eu-repo/semantics/OpenAccess
Accession Number:
edshal.hal.01794294v2
Database:
HAL

Weitere Informationen

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 visualisation 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 software tools including GINsim, BioLQM, Pint, MaBoSS, and Cell Collective for the modelling 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.