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

Anna Niarakis, Dagmar Waltemath, James Glazier, Falk Schreiber, Sarah M. Keating, David Nickerson, Claudine Chaouiya, Anne Siegel, Vincent Noël, Henning Hermjakob, Tomáš Helikar, Sylvain Soliman, Laurence Calzone

Research output: Contribution to journalReview articlepeer-review

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.

Original languageEnglish (US)
Article numberbbac212
JournalBriefings in bioinformatics
Volume23
Issue number4
DOIs
StatePublished - Jul 1 2022

Keywords

  • Community standards
  • Computational modelling
  • Model annotations
  • Reproducibility
  • Systems biology

ASJC Scopus subject areas

  • Information Systems
  • Molecular Biology

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