Exploring the evolution of biochemical models at the network level.
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2022
2022
Historique:
received:
25
06
2021
accepted:
07
03
2022
entrez:
21
3
2022
pubmed:
22
3
2022
medline:
6
5
2022
Statut:
epublish
Résumé
The evolution of biochemical models is difficult to track. At present, it is not possible to inspect the differences between model versions at the network level. Biochemical models are often constructed in a distributed, non-linear process: collaborators create model versions on different branches from novel information, model extensions, during curation and adaption. To discuss and align the versions, it is helpful to abstract the changes to the network level. The differences between two model versions can be detected by the software tool BiVeS. However, it cannot show the structural changes resulting from the differences. Here, we present a method to visualise the differences between model versions effectively. We developed a JSON schema to communicate the differences at the network level and extended BiVeS accordingly. Additionally, we developed DiVil, a web-based tool to represent the model and the differences as a standardised network using D3. It combines an automatic layout with an interactive user interface to improve the visualisation and to inspect the model. The network can be exported in standardised formats as images or markup language. Our method communicates the structural differences between model versions. It facilitates the discussion of changes and thus supports the collaborative and non-linear nature of model development. Availability and implementation: DiVil prototype: https://divil.bio.informatik.uni-rostock.de, Code on GitHub: https://github.com/Gebbi8/DiVil, licensed under Apache License 2.0. Contact: url="tom.gebhardt@uni-rostock.de.
Identifiants
pubmed: 35312734
doi: 10.1371/journal.pone.0265735
pii: PONE-D-21-20866
pmc: PMC8936491
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0265735Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
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