Time Concurrent Hybrid Functional Petri Nets (TCHFPN), a new approach for modeling and evaluation of biological pathways

Biological pathways consisted of different elements (actions and reactors) which interact together simultaneously. Because of being closer to the nature of such processes, Concurrent Simulation will result in a much more precise simulation. In this paper, we came up with a new method for parallel processing of biological networks which is based on IEEE STD 1666-2005 standard and uses SystemC for concurrent simulation. Despite of more accurate outcomes, simulating based on SystemC, as one the standard hardware description languages, will result in models that are highly compatible with electronic hardware. We also designed an algorithm which is capable of creating “Time Concurrent Hybrid Functional Petri Network (TCHFPN) model” from “Hybrid Functional Petri Network (HFPN) model”, automatically. HFPN is one the most perfect recent models based on Petri-Net for modeling biological networks. For showing the authenticity of the offered method, we used it for simulating the P53 Transcriptional Activity. Comparing the results from this method with a similar simulation by Cell-Illustrator shows less than 0.4% of RMS error. Biological network models based on SystamC could be used both as an intellectual Property (IP) in hardware accelerators and as a System On Chip (SOC).