An algorithm to detect and communicate the differences in computational models describing biological systems
Open accessAbstract
Motivation: Repositories support the reuse of models and ensure transparency about results in publications linked to those models. With thousands of models available in repositories, such as the BioModels database or the Physiome Model Repository, a framework to track the differences between models and their versions is essential to compare and combine models. Difference detection not only allows users to study the history of models but also helps in the detection of errors and inconsistencies. Existing repositories lack algorithms to track a model’s development over time. Results: Focusing on SBML and CellML, we present an algorithm to accurately detect and describe differences between coexisting versions of a model with respect to (i) the models’ encoding, (ii) the structure of biological networks and (iii) mathematical expressions. This algorithm is implemented in a comprehensive and open source library called BiVeS. BiVeS helps to identify and characterize changes in computational models and thereby contributes to the documentation of a model’s history. Our work facilitates the reuse and extension of existing models and supports collaborative modelling. Finally, it contributes to better reproducibility of modelling results and to the challenge of model provenance. Availability and implementation: The workflow described in this article is implemented in BiVeS. BiVeS is freely available as source code and binary from sems.uni-rostock.de. The web interface BudHat demonstrates the capabilities of BiVeS at budhat.sems.uni-rostock.de. Contact: martin.scharm@uni-rostock.de Supplementary information: Supplementary data are available at Bioinformatics online.
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Tools such as BiVeS are helpful to compare different versions of one particular simulation model, but comparing different models-even of the same system-is a difficult task because the syntax of these models, as well as their reactions, might be completely different.
“Tools such as BiVeS [15] are helpful to compare different versions of one particular simulation model, but comparing different models—even of the same system—is a difficult task because the syntax of these models (e.g., the names of the species), as well as their reactions, might be completely different.”
From Relating simulation studies by provenance—Developing a family of Wnt signaling models (2021) · cites this paper as [15]
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- Authors
- Scharm, M., Wolkenhauer, O., & Waltemath, D.
- Affiliations
- University of Rostock (DE)
- 1 Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany and
- Corresponding author
- Scharm, Martin
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-10-21
- Volume
- 32
- Issue
- 4
- Pages
- 563-570
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC4743622
- OpenAlex
- W2179501783
- Cited by
- 24
- References
- 35
- Citations by year
- 2026: 2 · 2024: 1 · 2023: 1 · 2022: 4 · 2021: 1 · 2020: 2 · 2019: 2 · 2018: 3 · 2016: 7
- FWCI
- 1.59
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Bioinformatics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- Bundesministerium für Bildung und Forschung (FKZ 031, FKZ 0316194, 0316194)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- model version comparison, SBML, CellML, model provenance, model repository, model reuse, reproducibility
- MeSH terms
- Algorithms, Computer Simulation, Humans, Models, Biological, Reproducibility of Results, Databases, Factual, Systems Biology, Workflow
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