Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK.
Bioinformatics. 2011 Feb 1;27(3):433-4. doi: 10.1093/bioinformatics/btq679. Epub 2010 Dec 9.
Constraint-based modeling of genome-scale metabolic networks has been successfully used in numerous applications such as prediction of gene essentiality and metabolic engineering. We present SurreyFBA, which provides constraint-based simulations and network map visualization in a free, stand-alone software. In addition to basic simulation protocols, the tool also implements the analysis of minimal substrate and product sets, which is useful for metabolic engineering and prediction of nutritional requirements in complex in vivo environments, but not available in other commonly used programs. The SurreyFBA is based on a command line interface to the GLPK solver distributed as binary and source code for the three major operating systems. The command line tool, implemented in C++, is easily executed within scripting languages used in the bioinformatics community and provides efficient implementation of tasks requiring iterative calls to the linear programming solver. SurreyFBA includes JyMet, a graphics user interface allowing spreadsheet-based model presentation, visualization of numerical results on metabolic networks represented in the Petri net convention, as well as in charts and plots.
SurreyFBA is distributed under GNU GPL license and available from http://sysbio3.fhms.surrey.ac.uk/SurreyFBA.zip.
基于约束的基因组规模代谢网络建模已成功应用于许多领域，如基因必需性预测和代谢工程。我们提出了 SurreyFBA，它提供了免费的、独立的软件中的约束模拟和网络映射可视化。除了基本的模拟协议外，该工具还实现了最小底物和产物集的分析，这对于代谢工程和预测复杂体内环境中的营养需求非常有用，但在其他常用程序中不可用。SurreyFBA 基于 GLPK 求解器的命令行接口，该求解器以二进制和源代码形式提供，适用于三个主要操作系统。用 C++实现的命令行工具可以在生物信息学社区中使用的脚本语言中轻松执行，并提供了高效的实现，需要迭代调用线性规划求解器来执行任务。SurreyFBA 包括 JyMet，这是一个图形用户界面，允许基于电子表格的模型表示，在以 Petri 网约定表示的代谢网络上对数值结果进行可视化，以及在图表和图形上进行可视化。
SurreyFBA 根据 GNU GPL 许可证分发，可从 http://sysbio3.fhms.surrey.ac.uk/SurreyFBA.zip 获得。
