Shapiro Bruce E, Hucka Michael, Finney Andrew, Doyle John
Jet Propulsion Laboratory, California Institute of Technology, Mail Stop 126-347, 4800 Oak Grove Drive, Pasadena, CA 91109, USA.
Bioinformatics. 2004 Nov 1;20(16):2829-31. doi: 10.1093/bioinformatics/bth271. Epub 2004 Apr 15.
MathSBML is a Mathematica package designed for manipulating Systems Biology Markup Language (SBML) models. It converts SBML models into Mathematica data structures and provides a platform for manipulating and evaluating these models. Once a model is read by MathSBML, it is fully compatible with standard Mathematica functions such as NDSolve (a differential-algebraic equations solver). MathSBML also provides an application programming interface for viewing, manipulating, running numerical simulations; exporting SBML models; and converting SBML models in to other formats, such as XPP, HTML and FORTRAN. By accessing the full breadth of Mathematica functionality, MathSBML is fully extensible to SBML models of any size or complexity.
Open Source (LGPL) at http://www.sbml.org and http://www.sf.net/projects/sbml
MathSBML是一个用于处理系统生物学标记语言(SBML)模型的Mathematica软件包。它将SBML模型转换为Mathematica数据结构,并提供一个用于操作和评估这些模型的平台。一旦MathSBML读取了一个模型,它就与标准的Mathematica函数(如NDSolve,一个微分代数方程求解器)完全兼容。MathSBML还提供了一个应用程序编程接口,用于查看、操作、运行数值模拟;导出SBML模型;以及将SBML模型转换为其他格式,如XPP、HTML和FORTRAN。通过访问Mathematica的全部功能,MathSBML可以完全扩展到任何大小或复杂度的SBML模型。
在http://www.sbml.org和http://www.sf.net/projects/sbml上开源(LGPL)