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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...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2022
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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 |
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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 |
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