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

本研究介绍sbml-diff，一款可读取SBML（Systems Biology Markup Language）格式生化反应网络模型，并生成多组不同细节层级可视化图表的工具。每一类图表均可用于单模型可视化，或对两个及以上模型开展可视化对比分析。默认视图将生化物种表示为椭圆形，反应为矩形，规则为平行四边形，事件为菱形。卡通视图可根据关联的系统生物学本体（Systems Biology Ontology）术语，替换反应的默认符号。抽象视图将生化物种以椭圆形呈现，并通过物种间的连线，标注某一物种对另一物种的生成或降解过程起到促进还是抑制作用。sbml-diff采用三条款BSD许可证进行免费授权，可从https://github.com/jamesscottbrown/sbml-diff下载，支持以Python包形式嵌入其他软件、作为独立命令行应用程序运行，或通过http://sysos.eng.ox.ac.uk/tebio/upload处的表单在线使用。