Cargando…

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

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Niarakis, Anna, Waltemath, Dagmar, Glazier, James, Schreiber, Falk, Keating, Sarah M, Nickerson, David, Chaouiya, Claudine, Siegel, Anne, Noël, Vincent, Hermjakob, Henning, Helikar, Tomáš, Soliman, Sylvain, Calzone, Laurence
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9294410/
https://www.ncbi.nlm.nih.gov/pubmed/35671510
http://dx.doi.org/10.1093/bib/bbac212
_version_ 1784749847997317120
author Niarakis, Anna
Waltemath, Dagmar
Glazier, James
Schreiber, Falk
Keating, Sarah M
Nickerson, David
Chaouiya, Claudine
Siegel, Anne
Noël, Vincent
Hermjakob, Henning
Helikar, Tomáš
Soliman, Sylvain
Calzone, Laurence
author_facet Niarakis, Anna
Waltemath, Dagmar
Glazier, James
Schreiber, Falk
Keating, Sarah M
Nickerson, David
Chaouiya, Claudine
Siegel, Anne
Noël, Vincent
Hermjakob, Henning
Helikar, Tomáš
Soliman, Sylvain
Calzone, Laurence
author_sort Niarakis, Anna
collection PubMed
description 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.
format Online
Article
Text
id pubmed-9294410
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-92944102022-07-20 Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology Niarakis, Anna Waltemath, Dagmar Glazier, James Schreiber, Falk Keating, Sarah M Nickerson, David Chaouiya, Claudine Siegel, Anne Noël, Vincent Hermjakob, Henning Helikar, Tomáš Soliman, Sylvain Calzone, Laurence Brief Bioinform Review 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. Oxford University Press 2022-06-08 /pmc/articles/PMC9294410/ /pubmed/35671510 http://dx.doi.org/10.1093/bib/bbac212 Text en © The Author(s) 2022. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Review
Niarakis, Anna
Waltemath, Dagmar
Glazier, James
Schreiber, Falk
Keating, Sarah M
Nickerson, David
Chaouiya, Claudine
Siegel, Anne
Noël, Vincent
Hermjakob, Henning
Helikar, Tomáš
Soliman, Sylvain
Calzone, Laurence
Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology
title Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology
title_full Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology
title_fullStr Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology
title_full_unstemmed Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology
title_short Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology
title_sort addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9294410/
https://www.ncbi.nlm.nih.gov/pubmed/35671510
http://dx.doi.org/10.1093/bib/bbac212
work_keys_str_mv AT niarakisanna addressingbarriersincomprehensivenessaccessibilityreusabilityinteroperabilityandreproducibilityofcomputationalmodelsinsystemsbiology
AT waltemathdagmar addressingbarriersincomprehensivenessaccessibilityreusabilityinteroperabilityandreproducibilityofcomputationalmodelsinsystemsbiology
AT glazierjames addressingbarriersincomprehensivenessaccessibilityreusabilityinteroperabilityandreproducibilityofcomputationalmodelsinsystemsbiology
AT schreiberfalk addressingbarriersincomprehensivenessaccessibilityreusabilityinteroperabilityandreproducibilityofcomputationalmodelsinsystemsbiology
AT keatingsarahm addressingbarriersincomprehensivenessaccessibilityreusabilityinteroperabilityandreproducibilityofcomputationalmodelsinsystemsbiology
AT nickersondavid addressingbarriersincomprehensivenessaccessibilityreusabilityinteroperabilityandreproducibilityofcomputationalmodelsinsystemsbiology
AT chaouiyaclaudine addressingbarriersincomprehensivenessaccessibilityreusabilityinteroperabilityandreproducibilityofcomputationalmodelsinsystemsbiology
AT siegelanne addressingbarriersincomprehensivenessaccessibilityreusabilityinteroperabilityandreproducibilityofcomputationalmodelsinsystemsbiology
AT noelvincent addressingbarriersincomprehensivenessaccessibilityreusabilityinteroperabilityandreproducibilityofcomputationalmodelsinsystemsbiology
AT hermjakobhenning addressingbarriersincomprehensivenessaccessibilityreusabilityinteroperabilityandreproducibilityofcomputationalmodelsinsystemsbiology
AT helikartomas addressingbarriersincomprehensivenessaccessibilityreusabilityinteroperabilityandreproducibilityofcomputationalmodelsinsystemsbiology
AT solimansylvain addressingbarriersincomprehensivenessaccessibilityreusabilityinteroperabilityandreproducibilityofcomputationalmodelsinsystemsbiology
AT calzonelaurence addressingbarriersincomprehensivenessaccessibilityreusabilityinteroperabilityandreproducibilityofcomputationalmodelsinsystemsbiology