Evolution of computational models in BioModels Database and the Physiome Model Repository
Date
2018-04-12
Journal Title
Journal ISSN
Volume Title
Publisher
BioMed Central
Abstract
ENGLISH SUMMARY : Background: A useful model is one that is being (re)used. The development of a successful model does not finish with its publication. During reuse, models are being modified, i.e. expanded, corrected, and refined. Even small
changes in the encoding of a model can, however, significantly affect its interpretation. Our motivation for the present
study is to identify changes in models and make them transparent and traceable.
Methods: We analysed 13734 models from BioModels Database and the Physiome Model Repository. For each
model, we studied the frequencies and types of updates between its first and latest release. To demonstrate the
impact of changes, we explored the history of a Repressilator model in BioModels Database.
Results: We observed continuous updates in the majority of models. Surprisingly, even the early models are still
being modified. We furthermore detected that many updates target annotations, which improves the information
one can gain from models. To support the analysis of changes in model repositories we developed MoSt, an online
tool for visualisations of changes in models. The scripts used to generate the data and figures for this study are
available from GitHub github.com/binfalse/BiVeS-StatsGenerator and as a Docker image at
hub.docker.com/r/binfalse/bives-statsgenerator. The website most.bio.informatik.uni-rostock.de provides interactive
access to model versions and their evolutionary statistics.
Conclusion: The reuse of models is still impeded by a lack of trust and documentation. A detailed and transparent
documentation of all aspects of the model, including its provenance, will improve this situation. Knowledge about a
model’s provenance can avoid the repetition of mistakes that others already faced. More insights are gained into how
the system evolves from initial findings to a profound understanding. We argue that it is the responsibility of the
maintainers of model repositories to offer transparent model provenance to their users.
Description
CITATION: Scharm, M., et al. 2018. Evolution of computational models in BioModels Database and the Physiome Model Repository. BMC Systems Biology, 12:53, doi:10.1186/s12918-018-0553-2.
The original publication is available at https://bmcsystbiol.biomedcentral.com
The original publication is available at https://bmcsystbiol.biomedcentral.com
Keywords
BioModels Database, Computer simulation, Physiome Model Repository, Biological models
Citation
Scharm, M., et al. 2018. Evolution of computational models in BioModels Database and the Physiome Model Repository. BMC Systems Biology, 12:53, doi:10.1186/s12918-018-0553-2.