- Abstract:
-
Biologists have used visual representations of biochemical networks for a long time 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. However, SBGN at this stage includes neither an explicit textual representation nor a defined way of including the quantitative details that are needed for computing quantitative properties of the underlying network. Here we define a possible mapping of SBGN Process Diagrams to a textual representation to facilitate the automatic parsing of SBGN-PD maps. We then define attributes for SBGN-PD glyphs to allow the specification of the quantitative information that is needed for quantitative analyses. We implemented SBGNtext2BioPEPA, a tool that demonstrates how such quantitative details can be used to automatically generate working Bio-PEPA code from our textual representation. Bio-PEPA is a process algebra that was designed for implementing quantitative models of concurrent biochemical reaction systems. We use this approach to compute the expected delay between input and output in deterministic and stochastic simulations of the MAPK signal transduction cascade. The scheme developed here is general and can be easily adapted to other output formalisms.
- Copyright:
- 2009 by The University of Edinburgh. All Rights Reserved
- Links To Paper
- No links available
- Bibtex format
- @Misc{EDI-INF-RR-1334,
- author = {
Laurence Loewe
and Stuart Moodie
and Jane Hillston
},
- title = {Technical Report: Defining a textual representation for SBGN Process Diagrams and translating it to Bio-PEPA for quantitative analysis of the MAPK signal transduction cascade},
- publisher = {School for Informatics, University of Edinburgh},
- year = 2009,
- month = {Jul},
- howpublished={Internet Publication},
- }
|
