Abstract
Using elementary Petri nets, it is difficult to mixturely model the discrete, continuous and other complicated events, for example, DNA, RNA and amino acid sequence events. Therefore, Hybrid Functional Petri Net with extension (HFPNe) was introduced to overcome this difficulty and also to allow representation of pathway models without loss of biological details. First, this book chapter explains how modeling with Petri net is done. After which, a full definition of HFPNe is given, along with its relation to hybrid Petri net and other related Petri net extension. Finally, to demonstrate the elegance of HFPNe architecture in handling complex pathway modeling, we chose a biological pathway that involves discrete, continuous and sequence events (gene regulatory network of the cell fate determination in C. elegans). We provide the biological mechanisms of this network and show how intuitively it could be modeled on HFPNe architecture using a software tool, Cell Illustrator.
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Acknowledgement
We would like to thank André Fujita and Koh Chuan Hock for their helpful comments and critiques.
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Saito, A., Nagasaki, M., Matsuno, H., Miyano, S. (2011). Hybrid Functional Petri Net with Extension for Dynamic Pathway Modeling. In: Koch, I., Reisig, W., Schreiber, F. (eds) Modeling in Systems Biology. Computational Biology, vol 16. Springer, London. https://doi.org/10.1007/978-1-84996-474-6_6
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DOI: https://doi.org/10.1007/978-1-84996-474-6_6
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