Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology

Author:

Niarakis Anna12ORCID,Waltemath Dagmar3ORCID,Glazier James4,Schreiber Falk56,Keating Sarah M7,Nickerson David8,Chaouiya Claudine9ORCID,Siegel Anne10ORCID,Noël Vincent111213,Hermjakob Henning14ORCID,Helikar Tomáš15ORCID,Soliman Sylvain2ORCID,Calzone Laurence111213ORCID

Affiliation:

1. Université Paris-Saclay, Laboratoire Européen de Recherche pour la Polyarthrite rhumatoïde - Genhotel , Univ Evry, Evry, France

2. Lifeware Group, Inria, Saclay-île de France , 91120 Palaiseau, France

3. Department of Medical Informatics, University Medicine Greifswald , Greifswald, Germany

4. Biocomplexity Institute and Department of Intelligent Systems Engineering, Indiana University , Bloomington, IN, USA

5. Department of Computer and Information Science, University of Konstanz , Konstanz, Germany

6. Faculty of Information Technology, Monash University , Clayton, Australia

7. University College London , London, United Kingdom

8. Auckland Bioengineering Institute, University of Auckland , Auckland, New Zealand

9. Aix Marseille Univ, CNRS , I2M, Marseille, France

10. Univ Rennes, CNRS, Inria - IRISA lab. Rennes

11. Institut Curie, PSL Research University , Paris, France

12. INSERM , U900, Paris, France

13. MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology , Paris, France

14. EMBL-European Bioinformatics Institute, Wellcome Genome Campus , Cambridge, UK

15. Department of Biochemistry, University of Nebraska-Lincoln , Lincoln, NE, 68588, USA

Abstract

Abstract Computational models are often employed in systems biology to study the dynamic behaviours of complex systems. With the rise in the number of computational models, finding ways to improve the reusability of these models and their ability to reproduce virtual experiments becomes critical. Correct and effective model annotation in community-supported and standardised formats is necessary for this improvement. Here, we present recent efforts toward a common framework for annotated, accessible, reproducible and interoperable computational models in biology, and discuss key challenges of the field.

Funder

sanofi-aventis

National Institutes of Health

Inserm Cancer

Deutsche Forschungsgemeinschaft

Innovative Medicines Initiative

National Institute for Biomedical Imaging and Bioengineering

Publisher

Oxford University Press (OUP)

Subject

Molecular Biology,Information Systems

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