We propose MPath2PN, a tool which automatically translates metabolic pathways, as described in the major biological databases, into corresponding Petri net representations. The aim is to allow for a systematic reuse, in the setting of metabolic pathways, of the variety of tools existing for Petri net analysis and simulation. The current prototype implementation of MPath2PN inputs the KEGG description of a metabolic pathway and produces two Petri nets, mainly differing for the treatment of ubiquitous substances. Such Petri nets are represented using PNML, a standard format for many Petri net tools. We are extending the tool by considering further formats for metabolic pathways in input and for Petri nets in output. MPath2PN is part of a more general project aimed at developing an integrated framework which should offer the possibility of automatically querying databases for metabolic pathways, producing corresponding Petri net models and performing analysis and simulation on them by means of various tools.

MPath2PN - Translating Metabolic Pathways into Petri Nets

BALDAN, Paolo;COCCO, Nicoletta;MARIN, Andrea;SIMEONI, Marta
2011-01-01

Abstract

We propose MPath2PN, a tool which automatically translates metabolic pathways, as described in the major biological databases, into corresponding Petri net representations. The aim is to allow for a systematic reuse, in the setting of metabolic pathways, of the variety of tools existing for Petri net analysis and simulation. The current prototype implementation of MPath2PN inputs the KEGG description of a metabolic pathway and produces two Petri nets, mainly differing for the treatment of ubiquitous substances. Such Petri nets are represented using PNML, a standard format for many Petri net tools. We are extending the tool by considering further formats for metabolic pathways in input and for Petri nets in output. MPath2PN is part of a more general project aimed at developing an integrated framework which should offer the possibility of automatically querying databases for metabolic pathways, producing corresponding Petri net models and performing analysis and simulation on them by means of various tools.
2011
BIOPPN-2011 International Workshop on Biological Processes & Petri Nets
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10278/23620
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