Abstract
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.deSupplementary information: Supplementary data are available at Bioinformatics online.
Highlights
Modelling and simulation is a standard approach to investigate complex biological processes
A steadily increasing number of computational models are available from open repositories such as the BioModels database (Li et al, 2010) or the Physiome Model Repository (PMR2; Yu et al, 2011)
We present a novel algorithm for difference detection in models of biological systems
Summary
Modelling and simulation is a standard approach to investigate complex biological processes. A steadily increasing number of computational models are available from open repositories such as the BioModels database (Li et al, 2010) or the Physiome Model Repository (PMR2; Yu et al, 2011). These repositories provide the infrastructure necessary to maintain model code and associated metadata. Tracking the evolution of a model, that is providing information about changes in the model and its encoding, plays an important role in supporting the user (Waltemath et al, 2013a). The need of model version control has been emphasized repeatedly on several occasions (Li et al, 2010; Miller et al, 2011; Saffrey and Orton, 2009; Waltemath et al, 2013a)
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