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.
%0 Journal Article
%1 Niarakis2022-07-18Addre-57769
%A Niarakis, Anna
%A Waltemath, Dagmar
%A Glazier, James
%A Schreiber, Falk
%A Keating, Sarah M.
%A Nickerson, David
%A Chaouiya, Claudine
%A Siegel, Anne
%A Noël, Vincent
%A Hermjakob, Henning
%D 2022
%J Briefings in bioinformatics
%K inf sfbtrr161 from:christinawarren 2022
%N 4
%R 10.1093/bib/bbac212
%T Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology
%V 23
%X 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.
@article{Niarakis2022-07-18Addre-57769,
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.},
added-at = {2022-12-09T11:09:58.000+0100},
author = {Niarakis, Anna and Waltemath, Dagmar and Glazier, James and Schreiber, Falk and Keating, Sarah M. and Nickerson, David and Chaouiya, Claudine and Siegel, Anne and Noël, Vincent and Hermjakob, Henning},
biburl = {https://puma.ub.uni-stuttgart.de/bibtex/2efec3a4ab7df076f7cc74b7106eda17c/sfbtrr161},
doi = {10.1093/bib/bbac212},
interhash = {454ae80cceec47dd58ba34433441529c},
intrahash = {efec3a4ab7df076f7cc74b7106eda17c},
issn = {1467-5463},
journal = {Briefings in bioinformatics},
keywords = {inf sfbtrr161 from:christinawarren 2022},
note = {Article Number: bbac212},
number = 4,
timestamp = {2022-12-09T10:09:58.000+0100},
title = {Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology},
volume = 23,
year = 2022
}