MathSBML

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Supplementary Information for the paper

MATHSBML: A PACKAGE FOR MANIPULATING SBML BASED BIOLOGICAL MODELS

An Application Note Submitted to the Journal Bioinformatics

Bruce E. Shapiro1,  Michael Hucka2,  Andrew Finney3, and John Doyle2
1Jet Propulsion Laboratory and 2Control and Dynamical Systems, California Institute of Technology, Pasadena CA, USA
3Science and Technology Research Center, University of Hertfordshire, Hatfield, United Kingdom

Copyright laws prohibit us from providing a copy of the manuscript online. If the paper is accepted for publication, when it becomes available a link to the paper on the publisher's web site will be placed here.

MathSBML Examples

1. Repressilator

Based on: Elowitz,M.B., and Leibler,S. (2000) A synthetic oscillatory network of transcriptional regulators. Nature, 403:335-338

2. MAP-Kinase

Based on: Kholodenko, B. M. (2000) Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades. Eur. J. Biochem. 267: 1583-1588.

This model also illustrates parametric plotting.

3. Mitotic Oscillator with Event

Based on: Tyson, J.J. (1991) Modeling the cell division cycle: cdc2 and cyclin interactions. Proc. Natl. Acad. Sci., USA, 88:7328-7332.

This model also illustrates analytic solution for the eigenvalues of the Jacobian at the fixed point.