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

James Scott-Brown,Antonis Papachristodoulou

doi:10.1021/acssynbio.6b00273

Abstract

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 https://github.com/jamesscottbrown/sbml-diff and used as a python package called from other software, as a free-standing command-line application, or online using the form at http://sysos.eng.ox.ac.uk/tebio/upload.

Highlights

We present sbml-diff, a tool that is able to read a model of a biochemical reaction network in Systems Biology Markup Language (SBML) format and produce a range of diagrams showing different levels of detail
I n order to predict how synthetic biological circuits will function or to determine how parameters should be tuned, it is necessary to use mathematical models. These models would be expressed in a standardized data format that provides interoperability between software packages, so that models can be constructed and simulated using different software, the results of simulating the same model using different simulation packages can be compared, and researchers can use their preferred tools to reproduce or extend previous work that used different tools. One such standardized format is the Systems Biology Markup Language (SBML),[1] a free and open interchange format for computer models of biological processes based on the Extensible Markup Language (XML)
An SBML model consists of species that participate in reactions

Summary

Introduction

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. This is often accompanied by the use of file differencing (diff) tools to directly compare different versions and identify what changes were made. We present smbl-diff, a tool that reads SBML models of biochemical networks and produces a range of diagrams showing different levels of detail.

Results

Conclusion