Bergmann Frank T, Keating Sarah M, Gauges Ralph, Sahle Sven, Wengler Katja
BioQuant/COS, Heidelberg University, Heidelberg, Germany.
Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA.
J Integr Bioinform. 2018 Apr 2;15(1):20170078. doi: 10.1515/jib-2017-0078.
Many software tools provide facilities for depicting reaction network diagrams in a visual form. Two aspects of such a visual diagram can be distinguished: the layout (i.e.: the positioning and connections) of the elements in the diagram, and the graphical form of the elements (for example, the glyphs used for symbols, the properties of the lines connecting them, and so on). This document describes the SBML Level 3 Render package that complements the SBML Level 3 Layout package and provides a means of capturing the precise rendering of the elements in a diagram. The SBML Level 3 Render package provides a flexible approach to rendering that is independent of both the underlying SBML model and the Layout information. There can be one block of render information that applies to all layouts or an additional block for each layout. Many of the elements used in the current render specification are based on corresponding elements from the SVG specification. This allows us to easily convert a combination of layout information and render information into a SVG drawing.
许多软件工具提供了以可视化形式描绘反应网络图的功能。这样的可视化图表可以区分两个方面:图表中元素的布局(即:定位和连接),以及元素的图形形式(例如,用于符号的字形、连接它们的线条的属性等)。本文档描述了SBML Level 3渲染包,它补充了SBML Level 3布局包,并提供了一种捕获图表中元素精确渲染的方法。SBML Level 3渲染包提供了一种灵活的渲染方法,该方法独立于基础的SBML模型和布局信息。可以有一个适用于所有布局的渲染信息块,或者为每个布局提供一个额外的块。当前渲染规范中使用的许多元素都基于SVG规范中的相应元素。这使我们能够轻松地将布局信息和渲染信息的组合转换为SVG绘图。