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

Content Provider	IEEE Xplore Digital Library
Author	Bayat, M.F. Ghaznavi-Ghoushchi, M.B.
Copyright Year	2010
Description	Author affiliation: School of Engineering, Shahed University, Tehran, Iran (Bayat, M.F.; Ghaznavi-Ghoushchi, M.B.)
Abstract	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).
Starting Page	176
Ending Page	179
File Size	361003
Page Count	4
File Format	PDF
ISBN	9781424467754
e-ISBN	9781424467754
DOI	10.1109/ICBBT.2010.5478985
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2010-04-16
Publisher Place	China
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Hardware Implementation Biological system modeling Circuit simulation Petri nets Biochemistry Power system modeling Modeling Bio-pathway Concurrent computing Proteins Time Concurrency Petri-Net Hybrid power systems Chemical elements Hardware design languages SystemC
Content Type	Text
Resource Type	Article

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