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Abstract: For a long time biologists have used visual representations of biochemicalnetworks to gain a quick overview of important structural properties. RecentlySBGN, the Systems Biology Graphical Notation, has been developed to standardisethe way in which such graphical maps are drawn in order to facilitate theexchange of information. Its qualitative Process Diagrams SBGN-PD are basedon an implicit Process Flow Abstraction PFA that can also be used toconstruct quantitative representations, which can be used for automatedanalyses of the system. Here we explicitly describe the PFA that underpinsSBGN-PD and define attributes for SBGN-PD glyphs that make it possible tocapture the quantitative details of a biochemical reaction network. Weimplemented SBGNtext2BioPEPA, a tool that demonstrates how such quantitativedetails can be used to automatically generate working Bio-PEPA code from atextual representation of SBGN-PD that we developed. Bio-PEPA is a processalgebra that was designed for implementing quantitative models of concurrentbiochemical reaction systems. We use this approach to compute the expecteddelay between input and output using deterministic and stochastic simulationsof the MAPK signal transduction cascade. The scheme developed here is generaland can be easily adapted to other output formalisms.



Author: Laurence Loewe, Stuart Moodie, Jane Hillston

Source: https://arxiv.org/



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