A versatile petri net based architecture for modeling and simulation of complex biological processes. Export

@article{citeulike:3066912, abstract = {The research on modeling and simulation of complex biological systems is getting more important in Systems Biology. In this respect, we have developed Hybrid Function Petri net (HFPN) that was newly developed from existing Petri net because of their intuitive graphical representation and their capabilities for mathematical analyses. However, in the process of modeling metabolic, gene regulatory or signal transduction pathways with the architecture, we have realized three extensions of HFPN, (i) an entity should be extended to contain more than one value, (ii) an entity should be extended to handle other primitive types, e.g. boolean, string, (iii) an entity should be extended to handle more advanced type called object that consists of variables and methods, are necessary for modeling biological systems with Petri net based architecture. To deal with it, we define a new enhanced Petri net called hybrid functional Petri net with extension (HFPNe). To demonstrate the effectiveness of the enhancements, we model and simulate with HFPNe four biological processes that are diffcult to represent with the previous architecture HFPN.}, address = {Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan. masao@ims.u-tokyo.ac.jp}, author = {Nagasaki, M. and Doi, A. and Matsuno, H. and Miyano, S.}, citeulike-article-id = {3066912}, citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/15712121}, citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=15712121}, issn = {0919-9454}, journal = {Genome informatics. International Conference on Genome Informatics}, keywords = {nets, petri}, number = {1}, pages = {180--197}, posted-at = {2009-03-05 12:41:17}, priority = {2}, title = {A versatile petri net based architecture for modeling and simulation of complex biological processes.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/15712121}, volume = {15}, year = {2004} }

TY - JOUR ID - citeulike:3066912 L3 - citeulike-article-id:3066912 N2 - The research on modeling and simulation of complex biological systems is getting more important in Systems Biology. In this respect, we have developed Hybrid Function Petri net (HFPN) that was newly developed from existing Petri net because of their intuitive graphical representation and their capabilities for mathematical analyses. However, in the process of modeling metabolic, gene regulatory or signal transduction pathways with the architecture, we have realized three extensions of HFPN, (i) an entity should be extended to contain more than one value, (ii) an entity should be extended to handle other primitive types, e.g. boolean, string, (iii) an entity should be extended to handle more advanced type called object that consists of variables and methods, are necessary for modeling biological systems with Petri net based architecture. To deal with it, we define a new enhanced Petri net called hybrid functional Petri net with extension (HFPNe). To demonstrate the effectiveness of the enhancements, we model and simulate with HFPNe four biological processes that are diffcult to represent with the previous architecture HFPN. IS - 1 JF - Genome informatics. International Conference on Genome Informatics SN - 0919-9454 AD - Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan. masao@ims.u-tokyo.ac.jp EP - 197 TI - A versatile petri net based architecture for modeling and simulation of complex biological processes. VL - 15 SP - 180 KW - nets KW - petri AU - Nagasaki, M AU - Doi, A AU - Matsuno, H AU - Miyano, S PY - 2004/// UR - http://view.ncbi.nlm.nih.gov/pubmed/15712121 ER -