Cooperative development of logical modelling standards and tools with CoLoMoTo

Aurélien Naldi, Pedro T. Monteiro, Christoph Müssel, Hans A. Kestler, Denis Thieffry, Ioannis Xenarios, Julio Saez-Rodriguez, Tomas Helikar, Claudine Chaouiya, Reka Albert, Matteo Barberis, Laurence Calzone, Anastasia Chasapi, Thomas Cokelaer, Isaac Crespo, Julien Dorier, Andreas Dräger, Céline Hernandez, Michael Hucka, Hidde De JongSarah M. Keating, Steffen Klamt, Hannes Klarner, Reinhard Laubenbacher, Nicolas Le Novère, Anne Niknejad, Nicolas Rodriguez, Heike Siebert, Gautier Stoll, Jorge G.T. Zañudo.

Research output: Contribution to journalArticle

30 Citations (Scopus)

Abstract

The identification of large regulatory and signalling networks involved in the control of crucial cellular processes calls for proper modelling approaches. Indeed, models can help elucidate properties of these networks, understand their behaviour and provide (testable) predictions by performing in silico experiments. In this context, qualitative, logical frameworks have emerged as relevant approaches, as demonstrated by a growing number of published models, along with new methodologies and software tools. This productive activity now requires a concerted effort to ensure model reusability and interoperability between tools. Following an outline of the logical modelling framework, we present the most important achievements of the Consortium for Logical Models and Tools, along with future objectives. Our aim is to advertise this open community, which welcomes contributions from all researchers interested in logical modelling or in related mathematical and computational developments.

Original languageEnglish (US)
Pages (from-to)1154-1159
Number of pages6
JournalBioinformatics
Volume31
Issue number7
DOIs
StatePublished - Apr 1 2015

Fingerprint

Computer Simulation
Software
Research Personnel
Modeling
Reusability
Software Tools
Interoperability
Model
Standards
Methodology
Prediction
Experiment
Experiments
Framework

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

Naldi, A., Monteiro, P. T., Müssel, C., Kestler, H. A., Thieffry, D., Xenarios, I., ... Zañudo., J. G. T. (2015). Cooperative development of logical modelling standards and tools with CoLoMoTo. Bioinformatics, 31(7), 1154-1159. https://doi.org/10.1093/bioinformatics/btv013
Naldi, Aurélien ; Monteiro, Pedro T. ; Müssel, Christoph ; Kestler, Hans A. ; Thieffry, Denis ; Xenarios, Ioannis ; Saez-Rodriguez, Julio ; Helikar, Tomas ; Chaouiya, Claudine ; Albert, Reka ; Barberis, Matteo ; Calzone, Laurence ; Chasapi, Anastasia ; Cokelaer, Thomas ; Crespo, Isaac ; Dorier, Julien ; Dräger, Andreas ; Hernandez, Céline ; Hucka, Michael ; De Jong, Hidde ; Keating, Sarah M. ; Klamt, Steffen ; Klarner, Hannes ; Laubenbacher, Reinhard ; Le Novère, Nicolas ; Niknejad, Anne ; Rodriguez, Nicolas ; Siebert, Heike ; Stoll, Gautier ; Zañudo., Jorge G.T. / Cooperative development of logical modelling standards and tools with CoLoMoTo. In: Bioinformatics. 2015 ; Vol. 31, No. 7. pp. 1154-1159.
@article{e5a14510ec734f7a8ddeff207d3aeea4,
title = "Cooperative development of logical modelling standards and tools with CoLoMoTo",
abstract = "The identification of large regulatory and signalling networks involved in the control of crucial cellular processes calls for proper modelling approaches. Indeed, models can help elucidate properties of these networks, understand their behaviour and provide (testable) predictions by performing in silico experiments. In this context, qualitative, logical frameworks have emerged as relevant approaches, as demonstrated by a growing number of published models, along with new methodologies and software tools. This productive activity now requires a concerted effort to ensure model reusability and interoperability between tools. Following an outline of the logical modelling framework, we present the most important achievements of the Consortium for Logical Models and Tools, along with future objectives. Our aim is to advertise this open community, which welcomes contributions from all researchers interested in logical modelling or in related mathematical and computational developments.",
author = "Aur{\'e}lien Naldi and Monteiro, {Pedro T.} and Christoph M{\"u}ssel and Kestler, {Hans A.} and Denis Thieffry and Ioannis Xenarios and Julio Saez-Rodriguez and Tomas Helikar and Claudine Chaouiya and Reka Albert and Matteo Barberis and Laurence Calzone and Anastasia Chasapi and Thomas Cokelaer and Isaac Crespo and Julien Dorier and Andreas Dr{\"a}ger and C{\'e}line Hernandez and Michael Hucka and {De Jong}, Hidde and Keating, {Sarah M.} and Steffen Klamt and Hannes Klarner and Reinhard Laubenbacher and {Le Nov{\`e}re}, Nicolas and Anne Niknejad and Nicolas Rodriguez and Heike Siebert and Gautier Stoll and Za{\~n}udo., {Jorge G.T.}",
year = "2015",
month = "4",
day = "1",
doi = "10.1093/bioinformatics/btv013",
language = "English (US)",
volume = "31",
pages = "1154--1159",
journal = "Bioinformatics",
issn = "1367-4803",
publisher = "Oxford University Press",
number = "7",

}

Naldi, A, Monteiro, PT, Müssel, C, Kestler, HA, Thieffry, D, Xenarios, I, Saez-Rodriguez, J, Helikar, T, Chaouiya, C, Albert, R, Barberis, M, Calzone, L, Chasapi, A, Cokelaer, T, Crespo, I, Dorier, J, Dräger, A, Hernandez, C, Hucka, M, De Jong, H, Keating, SM, Klamt, S, Klarner, H, Laubenbacher, R, Le Novère, N, Niknejad, A, Rodriguez, N, Siebert, H, Stoll, G & Zañudo., JGT 2015, 'Cooperative development of logical modelling standards and tools with CoLoMoTo', Bioinformatics, vol. 31, no. 7, pp. 1154-1159. https://doi.org/10.1093/bioinformatics/btv013

Cooperative development of logical modelling standards and tools with CoLoMoTo. / Naldi, Aurélien; Monteiro, Pedro T.; Müssel, Christoph; Kestler, Hans A.; Thieffry, Denis; Xenarios, Ioannis; Saez-Rodriguez, Julio; Helikar, Tomas; Chaouiya, Claudine; Albert, Reka; Barberis, Matteo; Calzone, Laurence; Chasapi, Anastasia; Cokelaer, Thomas; Crespo, Isaac; Dorier, Julien; Dräger, Andreas; Hernandez, Céline; Hucka, Michael; De Jong, Hidde; Keating, Sarah M.; Klamt, Steffen; Klarner, Hannes; Laubenbacher, Reinhard; Le Novère, Nicolas; Niknejad, Anne; Rodriguez, Nicolas; Siebert, Heike; Stoll, Gautier; Zañudo., Jorge G.T.

In: Bioinformatics, Vol. 31, No. 7, 01.04.2015, p. 1154-1159.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Cooperative development of logical modelling standards and tools with CoLoMoTo

AU - Naldi, Aurélien

AU - Monteiro, Pedro T.

AU - Müssel, Christoph

AU - Kestler, Hans A.

AU - Thieffry, Denis

AU - Xenarios, Ioannis

AU - Saez-Rodriguez, Julio

AU - Helikar, Tomas

AU - Chaouiya, Claudine

AU - Albert, Reka

AU - Barberis, Matteo

AU - Calzone, Laurence

AU - Chasapi, Anastasia

AU - Cokelaer, Thomas

AU - Crespo, Isaac

AU - Dorier, Julien

AU - Dräger, Andreas

AU - Hernandez, Céline

AU - Hucka, Michael

AU - De Jong, Hidde

AU - Keating, Sarah M.

AU - Klamt, Steffen

AU - Klarner, Hannes

AU - Laubenbacher, Reinhard

AU - Le Novère, Nicolas

AU - Niknejad, Anne

AU - Rodriguez, Nicolas

AU - Siebert, Heike

AU - Stoll, Gautier

AU - Zañudo., Jorge G.T.

PY - 2015/4/1

Y1 - 2015/4/1

N2 - The identification of large regulatory and signalling networks involved in the control of crucial cellular processes calls for proper modelling approaches. Indeed, models can help elucidate properties of these networks, understand their behaviour and provide (testable) predictions by performing in silico experiments. In this context, qualitative, logical frameworks have emerged as relevant approaches, as demonstrated by a growing number of published models, along with new methodologies and software tools. This productive activity now requires a concerted effort to ensure model reusability and interoperability between tools. Following an outline of the logical modelling framework, we present the most important achievements of the Consortium for Logical Models and Tools, along with future objectives. Our aim is to advertise this open community, which welcomes contributions from all researchers interested in logical modelling or in related mathematical and computational developments.

AB - The identification of large regulatory and signalling networks involved in the control of crucial cellular processes calls for proper modelling approaches. Indeed, models can help elucidate properties of these networks, understand their behaviour and provide (testable) predictions by performing in silico experiments. In this context, qualitative, logical frameworks have emerged as relevant approaches, as demonstrated by a growing number of published models, along with new methodologies and software tools. This productive activity now requires a concerted effort to ensure model reusability and interoperability between tools. Following an outline of the logical modelling framework, we present the most important achievements of the Consortium for Logical Models and Tools, along with future objectives. Our aim is to advertise this open community, which welcomes contributions from all researchers interested in logical modelling or in related mathematical and computational developments.

UR - http://www.scopus.com/inward/record.url?scp=84929144070&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84929144070&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btv013

DO - 10.1093/bioinformatics/btv013

M3 - Article

C2 - 25619997

AN - SCOPUS:84929144070

VL - 31

SP - 1154

EP - 1159

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 7

ER -

Naldi A, Monteiro PT, Müssel C, Kestler HA, Thieffry D, Xenarios I et al. Cooperative development of logical modelling standards and tools with CoLoMoTo. Bioinformatics. 2015 Apr 1;31(7):1154-1159. https://doi.org/10.1093/bioinformatics/btv013