Abstract
The paper proposes a new software design method of biopathway’s modeling and simulation application. In order for the software tool can be used by biologists easily and intuitively, we use Petri net and Stochastic Petri net to model biopathway, combining corresponding algorithms then can do deterministic and stochastic simulation, add the function that Petri net handle string, thus users can model biopathway such as transcription and translation more effectively. We introduce how to model and simulate biopathway with it in detail, it will be accepted by biologist quickly and used widely.
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References
Gillespie, D.T.: Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81, 2340–2361 (1977)
Gibson, A., Bruck, M.: Efficient exact stochastic simulation of chemical systems with many species and many channels. J. Phys. Chem.A 104, 1876–1889 (2000)
Nagasaki, M., Doi, A., Matsuno, H., Miyano, S.: Genomic object net: I.a platform for modeling and simulating biopathways. Applied Bioinformatics 3, 181–184 (2004)
Kanehisa, M., Goto, S.: Kegg: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 1, 27–30 (2000)
Mendes, P.: Gepasi: A software package for modelling the dynamics, steady states and control of biochemical and other systems. Comput. Appl. Biosci. 5, 563–571 (1993)
Tomita, M., Hashimoto, K., Takahashi, K., Shimizu, T., Matsuzaki, Y., Miyoshi, F., Saito, K., Tanida, S., Yugi, K.: E-cell: Software environment for whole cell simulation. Bioinformatics 1, 72–84 (1999)
Sanders, W., Obal, W., Qureshi, M., Widjanarko, F.: The ultrasan modeling environment. Performance Evaluation 115, 1–2 (1995)
Hucka, M., Finney, A., Sauro, H.M., Bolouri, H., Doyle, J.C., Kitano, H., Arkin, A.P., et al.: The systems biology markup language (sbml): a medium for representation and exchange of biochemical network models. Bioinformatics 4, 524–531 (2003)
Chuang, L. (ed.): Stochastic Petri net and System Performance evaluation. Tsing Hua Press, Beijing (2005)
Reisig, W., Rozenberg, G.: Lecture on petri nets i: Basic models lecture notes in computer science. In: Reisig, W., Rozenberg, G. (eds.) APN 1998. LNCS, vol. 1491, Springer, Heidelberg (1998)
Meng, T.C., Somani, S., Dhar, P.: Modeling and simulation of biological systems with stochasticity. Silico Biology 4, 293–309 (2004)
Goss, P., Peccoud, J.: Quantitative modeling of stochastic systems in molecular biology using stochastic petri nets. Proc. Natl. Acad. Sci 95, 6750–6755 (1998)
Schulz-Trieglaff, O.: Modelling randomness in biological systems. M.Sc. thesis. University of Edinburgh (2005)
Nagasaki, M.: A Platform For Biopathway Modeling/Simulation And Recreating biopathway Databases Towards Simulation. PhD thesis.University of Tokyo (2003)
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Ji, C., Lv, X., Li, S. (2006). The Design of Biopathway’s Modelling and Simulation System Based on Petri Net. In: Wang, GY., Peters, J.F., Skowron, A., Yao, Y. (eds) Rough Sets and Knowledge Technology. RSKT 2006. Lecture Notes in Computer Science(), vol 4062. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11795131_105
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DOI: https://doi.org/10.1007/11795131_105
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-36297-5
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