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

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Niarakis_2-glgemut7d62v3.pdf
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2022
Autor:innen
Niarakis, Anna
Waltemath, Dagmar
Glazier, James
Keating, Sarah M.
Nickerson, David
Chaouiya, Claudine
Siegel, Anne
Noël, Vincent
Hermjakob, Henning
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Zusammenfassung

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.

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computational modelling, model annotations, reproducibility, systems biology, community standards
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ISO 690NIARAKIS, Anna, Dagmar WALTEMATH, James GLAZIER, Falk SCHREIBER, Sarah M. KEATING, David NICKERSON, Claudine CHAOUIYA, Anne SIEGEL, Vincent NOËL, Henning HERMJAKOB, 2022. Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology. In: Briefings in bioinformatics. Oxford University Press. 2022, 23(4), bbac212. ISSN 1467-5463. eISSN 1477-4054. Available under: doi: 10.1093/bib/bbac212
BibTex
@article{Niarakis2022-07-18Addre-57769,
  year={2022},
  doi={10.1093/bib/bbac212},
  title={Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology},
  number={4},
  volume={23},
  issn={1467-5463},
  journal={Briefings in bioinformatics},
  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},
  note={Article Number: bbac212}
}
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