A compositional approach to performance modelling
A compositional approach to performance modelling
Theoretical Computer Science - Special issue: Computational systems biology
The Definitive ANTLR Reference: Building Domain-Specific Languages
The Definitive ANTLR Reference: Building Domain-Specific Languages
The pathway editor: a tool for managing complex biological networks
IBM Journal of Research and Development - Systems biology
Integrated Simulation and Model-Checking for the Analysis of Biochemical Systems
Electronic Notes in Theoretical Computer Science (ENTCS)
Bio-PEPA: A framework for the modelling and analysis of biological systems
Theoretical Computer Science
Process Algebra Modelling Styles for Biomolecular Processes
Transactions on Computational Systems Biology XI
The BlenX language: a tutorial
SFM'08 Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology
Bioinformatics
Design and development of software tools for Bio-PEPA
Winter Simulation Conference
CMSB'06 Proceedings of the 2006 international conference on Computational Methods in Systems Biology
Rule-based modelling of cellular signalling
CONCUR'07 Proceedings of the 18th international conference on Concurrency Theory
Hi-index | 0.00 |
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 (PFA) that can also be 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.