Gauges Ralph, Rost Ursula, Sahle Sven, Wegner Katja
Bioinformatics and Computational Biochemistry, EML Research Schloss-Wolfsbrunnen Weg 33, D-69118 Heidelberg, Germany.
Bioinformatics. 2006 Aug 1;22(15):1879-85. doi: 10.1093/bioinformatics/btl195. Epub 2006 May 18.
Since the knowledge about processes in living cells is increasing, modelling and simulation techniques are used to get new insights into these complex processes. During the last few years, the SBML file format has gained in popularity and support as a means of exchanging model data between the different modelling and simulation tools. In addition to specifying the model as a set of equations, many modern modelling tools allow the user to create and to interact with the model in the form of a reaction graph. Unfortunately, the SBML file format does not provide for the storage of this graph data along with the mathematical description of the model.
Therefore, we developed an extension to the SBML file format that makes it possible to store such layout information which describes position and size of objects in the graphical representation.
The complete specification can be found on (http://projects.villa-bosch.de/bcb/sbml/ (SBML Layout Extension documentation, 2005). Additionally, a complete implementation exists as part of libSBML (2006, http://www.sbml.org/software/libsbml/).
随着对活细胞内过程的了解不断增加，建模和仿真技术被用于深入探究这些复杂过程。在过去几年中，SBML文件格式作为在不同建模和仿真工具之间交换模型数据的一种方式，越来越受欢迎并得到广泛支持。除了将模型指定为一组方程外，许多现代建模工具还允许用户以反应图的形式创建模型并与之交互。不幸的是，SBML文件格式并未规定将此图数据与模型的数学描述一起存储。
因此，我们开发了SBML文件格式的一个扩展，使其能够存储此类布局信息，该信息描述了图形表示中对象的位置和大小。
完整规范可在（http://projects.villa-bosch.de/bcb/sbml/ （SBML布局扩展文档，2005年））上找到。此外，作为libSBML（2006年，http://www.sbml.org/software/libsbml/）的一部分存在完整的实现。
