Translating SBML models into the stochastic π-calculus for stochastic simulation

Authors:
Claudio Eccher;Paola Lecca
Affiliations:
Dept. of Information and Communication Technologies, University of Trento, Italy;Dept. of Information and Communication Technologies, University of Trento, Italy
Venue:
Transactions on Computational Systems Biology VII
Year:
2006

Citing 5
Cited 0

Communicating and mobile systems: the &pgr;-calculus

Communicating and mobile systems: the &pgr;-calculus
Application of a stochastic name-passing calculus to representation and simulation of molecular processes

Information Processing Letters
An Overview of the GXL Graph Exchange Language

Revised Lectures on Software Visualization, International Seminar
The Immune System as a Reactive System: Modeling T Cell Activation With Statecharts

HCC '01 Proceedings of the IEEE 2001 Symposia on Human Centric Computing Languages and Environments (HCC'01)
A multi-agent system for the quantitative simulation of biological networks

AAMAS '03 Proceedings of the second international joint conference on Autonomous agents and multiagent systems

Quantified Score

Hi-index	0.00

Visualization

Abstract

This paper addresses the translation of Systems Biology Mark-Up Language (SBML) Level 2 models of network of biochemical reactions into the Biochemical Stochastic π-calculus (SPI). SBML is XML-based formalism for systems biology, while SPI can describe the concurrency of the different interactions occurring in a network of biochemical stochastic reactions. SPI models can be used for simulation by available computer packages. We present the approach followed in designing a software tool for working biologists that parses an SBML model and performs the unsupervised translation into the process algebra model. To test the correctness of the translation process we present the results obtained by performing simulations of a translated simplified circadian clock model, comparing our results with that obtained with the original differential equation model.