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Translation from the Quantified Implicit Process Flow Abstraction in SBGN-PD Diagrams to Bio-PEPA Illustrated on the Cholesterol Pathway

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Original languageEnglish
Title of host publicationTRANSACTIONS ON COMPUTATIONAL SYSTEMS BIOLOGY XIII
EditorsC Priami, RJ Back, I Petre, E DeVink
Place of PublicationBERLIN
PublisherSpringer-Verlag GmbH
Pages13-38
Number of pages26
ISBN (Print)978-3-642-19747-5
Publication statusPublished - 2011
EventWorkshop on Computational Models for Cell Processes - Eindhoven
Duration: 2 Nov 2009 → …

Conference

ConferenceWorkshop on Computational Models for Cell Processes
CityEindhoven
Period2/11/09 → …

Abstract

For a long time biologists have used visual representations of biochemical networks to gain a quick overview of important structural properties. Recently SBGN, the Systems Biology Graphical Notation, has been developed to standardise the way in which such graphical maps are drawn in order to facilitate the exchange of information. Its qualitative Process Description (SBGN-PD) diagrams are based on an implicit Process Flow Abstraction (PEA) that can also he used to construct quantitative representations, which facilitate automated analyses of the system. Here we explicitly describe the PFA that underpins SBGN-PD and define attributes for SBGN-PD glyphs that make it possible to capture the quantitative details of a biochemical reaction network. Such quantitative details can be used to automatically generate an executable model. To facilitate this, we developed a textual representation for SBGN-PD called "SBGNtext" and implemented SBGNtext2BioPEPA. a tool that demonstrates how Bio-PEPA models can be generated automatically from SBGNtext. Bio-PEPA is a process algebra that was designed for implementing quantitative models of concurrent biochemical reaction systems. The scheme developed here is general and can be easily adapted to other output formalisms. To illustrate the intended workflow. we model the metabolic pathway of the cholesterol synthesis. We use this to compute the statin dosage response of the flux through the cholesterol pathway for different concentrations of the enzyme HMGCR that is inhibited by statin.

    Research areas

  • DENSITY-LIPOPROTEIN CHOLESTEROL, COENZYME-A REDUCTASE, STOCHASTIC SIMULATION, BIOLOGICAL NETWORKS, SYSTEMS, TOOL, REPRESENTATION, METAANALYSIS, SIMVASTATIN, NOTATION

Event

Workshop on Computational Models for Cell Processes

2/11/09 → …

Eindhoven

Event: Conference

ID: 1230959