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

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

本报告推出sbml-diff工具，该工具能够读取SBML格式的生物化学反应网络模型，并生成一系列展示不同细节层次的图表。各类图表不仅可用于单一模型的可视化呈现，亦可用于两个或多个模型之间的直观对比。默认视图以椭圆表示物种，矩形表示反应，平行四边形表示规则，菱形表示事件。卡通视图基于关联的系统生物学本体术语替换了反应所用的符号。抽象视图则以椭圆表示物种，并绘制连接它们的边以指示物种是否增加了或减少了另一种物种的生产或降解。sbml-diff工具遵循三条款BSD许可证自由许可，可从https://github.com/jamesscottbrown/sbml-diff下载，并可作为Python包从其他软件中调用，或作为独立的命令行应用程序使用，亦可通过http://sysos.eng.ox.ac.uk/tebio/upload上的表单在线使用。