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. 2016 Feb 15;32(4):563-70.
doi: 10.1093/bioinformatics/btv484. Epub 2015 Oct 21.

An algorithm to detect and communicate the differences in computational models describing biological systems

Martin Scharm  1 , Olaf Wolkenhauer  2 , Dagmar Waltemath  1
Affiliations

An algorithm to detect and communicate the differences in computational models describing biological systems

Martin Scharm et al. Bioinformatics. .

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.

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Figures

Fig. 1.
Fig. 1.
Sketch of a model’s temporal evolution. Changes in a single reaction of Novak and Tyson’s model with ID BIOMD0000000107 in the BioModels database. The differences between versions from June 2007 (release number 8), June 2013 (release number 25) and February 2015 (latest available version) are shown. The branch represents a modification. The boxes visualize the differences between related versions
Fig. 2.
Fig. 2.
Schematic of the mapping procedure. The procedure to communicate the differences between two versions of a model (row one) to the user (row seven) is shown. Nodes A–H represent single entities in the model documents. Dashed lines indicate mappings between the nodes. The values of σ and ω represent signatures and weights of nodes. They are calculated during pre-processing. The different colours of the nodes indicate modifications: updates are yellow, inserts are green and deletes are red. In the evaluation step, moves are blue
Fig. 3.
Fig. 3.
Outputs as generated by BiVeS and available from BudHat. All three figures show the differences between versions June 2007 and November 2013 of model BIOMD0000000107 (cf. Fig. 1). The reaction network (a) and the report (b) present the differences in a human readable format. The XML encoded delta (c) allows for further processing by computers. The modifications described in Figure 1 are highlighted in orange. In the highlighted reaction network (a), deletes are coloured in red, while inserts are blue and updates are yellow
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