Dräger Andreas, Planatscher Hannes, Motsou Wouamba Dieudonné, Schröder Adrian, Hucka Michael, Endler Lukas, Golebiewski Martin, Müller Wolfgang, Zell Andreas
Center for Bioinformatics Tübingen (ZBIT), University of Tübingen, Tübingen, Germany.
Bioinformatics. 2009 Jun 1;25(11):1455-6. doi: 10.1093/bioinformatics/btp170. Epub 2009 Mar 23.
The XML-based Systems Biology Markup Language (SBML) has emerged as a standard for storage, communication and interchange of models in systems biology. As a machine-readable format XML is difficult for humans to read and understand. Many tools are available that visualize the reaction pathways stored in SBML files, but many components, e.g. unit declarations, complex kinetic equations or links to MIRIAM resources, are often not made visible in these diagrams. For a broader understanding of the models, support in scientific writing and error detection, a human-readable report of the complete model is needed. We present SBML2L(A)T(E)X, a Java-based stand-alone program to fill this gap. A convenient web service allows users to directly convert SBML to various formats, including DVI, L(A)T(E)X and PDF, and provides many settings for customization.
Source code, documentation and a web service are freely available at (http://www.ra.cs.uni-tuebingen.de/software/SBML2LaTeX).
基于XML的系统生物学标记语言（SBML）已成为系统生物学中模型存储、通信和交换的标准。作为一种机器可读格式，XML对于人类来说难以阅读和理解。有许多工具可用于可视化存储在SBML文件中的反应途径，但许多组件，例如单位声明、复杂动力学方程或与MIRIAM资源的链接，在这些图表中通常不可见。为了更全面地理解模型、支持科学写作和错误检测，需要一份完整模型的人类可读报告。我们展示了SBML2L(A)T(E)X，这是一个基于Java的独立程序来填补这一空白。一个便捷的网络服务允许用户直接将SBML转换为各种格式，包括DVI、L(A)T(E)X和PDF，并提供许多定制设置。
源代码、文档和网络服务可在（http://www.ra.cs.uni-tuebingen.de/software/SBML2LaTeX）免费获取。
