Model Repository
1. Example model files
A collection of XPPAUT .ode model files is provided in the folder ode model.
These models are taken from the following works:
1. Li, C., & Wang, J. (2015). Quantifying the landscape for development and cancer from a core cancer stem cell circuit. Cancer research,
75(13), 2607-2618.
2. Wang, J., Zhang, K., Xu, L., & Wang, E. (2011). Quantifying the Waddington landscape and biological paths for development and
differentiation. Proceedings of the National Academy of Sciences, 108(20), 8257-8262.
3. Huang, S., Guo, Y. P., May, G., & Enver, T. (2007). Bifurcation dynamics in lineage-commitment in bipotent progenitor cells. Developmental
biology, 305(2), 695-713.
4. Gardner, T. S., Cantor, C. R., & Collins, J. J. (2000). Construction of a genetic toggle switch in Escherichia coli. Nature, 403(6767), 339.
5. Zhou, J. X., Aliyu, M. D. S., Aurell, E., & Huang, S. (2012). Quasi-potential landscape in complex multi-stable systems. Journal of the Royal
Society Interface, 9(77), 3539-3553.
Two SBML model files are provided in the folder SBML model
These models are taken from the following works:
1. Gardner, T. S., Cantor, C. R., & Collins, J. J. (2000). Construction of a genetic toggle switch in Escherichia coli. Nature, 403(6767), 339.
2. Li, C., & Wang, J. (2015). Quantifying the landscape for development and cancer from a core cancer stem cell circuit. Cancer research,
75(13), 2607-2618.
The SBML model files were created using SBML Editor from this paper by Rodriguez et al. (2007).
Rodriguez, N., Donizelli, M., & Le Novère, N. (2007). SBMLeditor: effective creation of models in the Systems Biology Markup Language (SBML). BMC bioinformatics, 8(1), 79.
If you have any questions, suggestions or feedback, please email to: zhengjie@shanghaitech.edu.cn, kething.chong@lincolnuni.ac.nz