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

Authors

Anna Niarakis, Univ Evry, University of Paris-SaclayFollow
Dagmar Waltemath, University of Medicine, Greifswald
James Glazier, Indiana University
Falk Schreiber, University of Konstanz
Sarah M. Keating, University College London
David Nickerson, Auckland Bioengineering Institute
Claudine Chaouiya, I2M, Aix-Marseille University
Anne Siegel, Centre National de la Recherche Scientifique
Vincent Noël, Institut Curie
Henning Hermjakob, European Molecular Biology Laboratory -European Bioinformatics Institute
Tomáš Helikar, University of Nebraska‐LincolnFollow
Sylvain Soliman, Inria, Saclay
Laurence Calzone, Institut Curie

Document Type

Article

Date of this Version

2022

Citation

Briefings in Bioinformatics, 2022, 23(4), 1–11

doi:10.1093/bib/bbac212

Comments

This is an Open Access article distributed under the terms of the Creative Commons Attribution License

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.

Scientists from different systems biology fields have long been developing community-driven guidelines and best practices for annotation, interoperability and reusability of computational models in biology. However, the parallel work, grounded on shared needs and similar aims, of separate communities creates a need for exchange and alignment of the different efforts to harmonise best practices. Hence, members of the Consortium for Logical Models and Tools (CoLoMoTo, http://colomoto.org) and the Computational Modelling of Biological Systems community of the International Society for Computational Biology (SysMod, https:// sysmod.info/) organised aworkshop to discusscommunitydriven guidelines and efforts for the curation and annotation of computational models during [BC]2 2021. The workshop grew from a previous edition organised during [BC]2 2019 focused on logical modelling [1]. The second edition brought together scientists with various research backgrounds and from different working groups such as BioModels [2], a central repository of mathematical models of biological/biomedical processes; the Computational Modelling in Biology Network initiative (COMBINE) [3]; CoLoMoTo, [4]; SysMod, [5]; the Systems Biology Graphical Notation (SBGN) project [6]; the systems biology markup language (SBML) [7] and simulation experiment description markup language (SED-ML) [8], to exchange and expand on several key topics of common interest (Figure 1). While the modelling approaches across these communities differ, several critical points are shared, such as (i) the importance of annotations for reproducibility, (ii) the use of community standards for exchange and annotation encoding, (iii) the need to implement standards in tools and platforms to boost reusability and interoperability, (iv) the importance of transparency of modelling frameworks in publications and (v) the use of shared repositories to enhance model accessibility (Figure 2). We use the term annotation to describe ‘a computeraccessible metadata item that captures, entirely or in part, the meaning of a model, model component or data element’. We borrow this definition from [9] which is in accordance with its use in [1]. We discuss the identified needs in the following sections.