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sbml-diff: A Tool for Visually Comparing SBML Models in Synthetic Biology

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journal contribution
posted on 30.12.2016 by James Scott-Brown, Antonis Papachristodoulou
We present sbml-diff, a tool that is able to read a model of a biochemical reaction network in SBML format and produce a range of diagrams showing different levels of detail. Each diagram type can be used to visualize a single model or to visually compare two or more models. The default view depicts species as ellipses, reactions as rectangles, rules as parallelograms, and events as diamonds. A cartoon view replaces the symbols used for reactions on the basis of the associated Systems Biology Ontology terms. An abstract view represents species as ellipses and draws edges between them to indicate whether a species increases or decreases the production or degradation of another species. sbml-diff is freely licensed under the three-clause BSD license and can be downloaded from and used as a python package called from other software, as a free-standing command-line application, or online using the form at