论文信息 - MathSBML: a package for manipulating SBML-based biological models

MathSBML: a package for manipulating SBML-based biological models

UNLABELLED 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. AVAILABILITY Open Source (LGPL) at http://www.sbml.org and http://www.sf.net/projects/sbml

[1] Hiroaki Kitano,et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..

[2] Bruce E. Shapiro,et al. Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations , 2003, Bioinform..

[3] A. Hindmarsh. LSODE and LSODI, two new initial value ordinary differential equation solvers , 1980, SGNM.

[4] J. Tyson. Modeling the cell division cycle: cdc2 and cyclin interactions. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[5] Bard Ermentrout,et al. Simulating, analyzing, and animating dynamical systems - a guide to XPPAUT for researchers and students , 2002, Software, environments, tools.

[6] A Finney,et al. Systems biology markup language: Level 2 and beyond. , 2003, Biochemical Society transactions.

[7] M. Elowitz,et al. A synthetic oscillatory network of transcriptional regulators , 2000, Nature.

[8] B. Kholodenko,et al. Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades. , 2000, European journal of biochemistry.