Titre :

Constructing and Visualizing Chemical Reaction Networks from Pi-Calculus Models

Auteur(s) :

John, Mathias [Auteur correspondant]
Programming Languages for Biological Modeling and Simulation [BioComputing]
Schulz, Hans-Jörg [Auteur]
Computer Science and Electrical Engineering
Schumann, Heidrun [Auteur]
Computer Science and Electrical Engineering
Uhrmacher, Adelinde [Auteur]
Computer Science and Electrical Engineering
Unger, Andrea [Auteur]
German Research Centre for Geosciences - Helmholtz-Centre Potsdam [GFZ]

Titre de la revue :

Formal Aspects of Computing

Éditeur :

Springer Verlag

Date de publication :

2012-01-02

ISSN :

0934-5043

Mot(s)-clé(s) en anglais :

pi-calculus
stochastic modeling
reaction networks
graph visualization

Discipline(s) HAL :

Informatique [cs]/Modélisation et simulation
Informatique [cs]/Bio-informatique [q-bio.QM]
Sciences du Vivant [q-bio]/Bio-Informatique, Biologie Systémique [q-bio.QM]

Résumé en anglais : [en]

The pi-calculus, in particular its stochastic version the stochastic pi-calculus, is a common modeling formalism to concisely describe the chemical reactions occurring in biochemical systems. However, it remains largely ...
Lire la suite >The pi-calculus, in particular its stochastic version the stochastic pi-calculus, is a common modeling formalism to concisely describe the chemical reactions occurring in biochemical systems. However, it remains largely unexplored how to transform a biochemical model expressed in the stochastic pi-calculus back into a set of meaningful reactions. To this end, we present a two step approach of first translating model states to reaction sets and then visualizing sequences of reaction sets, which are obtained from state trajectories, in terms of reaction networks. Our translation from model states to reaction sets is formally defined and shown to be correct, in the sense that it reflects the states and transitions as they are derived from the continuous time Markov chain-semantics of the stochastic pi-calculus. Our visualization concept combines high level measures of network complexity with interactive, table-based network visualizations. It directly reflects the structures introduced in the first step and allows modelers to explore the resulting simulation traces by providing both: an overview of a network's evolution and a detail inspection on demand.Lire moins >

Langue :

Anglais

Comité de lecture :

Oui

Audience :

Internationale

Vulgarisation :

Non

Collections :

• Centre de Recherche en Informatique, Signal et Automatique de Lille (CRIStAL) - UMR 9189

Source :

Harvested from HAL