Modeling kohn interaction maps with beta-binders: an example

Authors:
Federica Ciocchetta;Corrado Priami;Paola Quaglia
Affiliations:
Dipartimento di Informatica e Telecomunicazioni, Università di Trento, Italy;Dipartimento di Informatica e Telecomunicazioni, Università di Trento, Italy;Dipartimento di Informatica e Telecomunicazioni, Università di Trento, Italy
Venue:
Transactions on Computational Systems Biology III
Year:
2005

Citing 7
Cited 5

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
PI-Calculus: A Theory of Mobile Processes

PI-Calculus: A Theory of Mobile Processes
BioAmbients: an abstraction for biological compartments

Theoretical Computer Science - Special issue: Computational systems biology
Core formal molecular biology

ESOP'03 Proceedings of the 12th European conference on Programming
Beta binders for biological interactions

CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
Operational patterns in beta-binders

Transactions on Computational Systems Biology I

An Automatic Translation of SBML into Beta-Binders

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Stochastic π -Calculus Modelling of Multisite Phosphorylation Based Signaling: The PHO Pathway in Saccharomyces Cerevisiae

Transactions on Computational Systems Biology X
The BlenX Language with Biological Transactions

Transactions on Computational Systems Biology IX
Bio-PEPA: A framework for the modelling and analysis of biological systems

Theoretical Computer Science
Simulation of kohn's molecular interaction maps through translation into stochastic CLS+

PSI'09 Proceedings of the 7th international Andrei Ershov Memorial conference on Perspectives of Systems Informatics

Quantified Score

Hi-index	0.00

Visualization

Abstract

We represent a subset of the mammalian cell cycle Kohn interaction map using Beta-binders, a formalism inspired to the pi-calculus and enriched with binders that allow the description of enclosing surfaces equipped with interaction sites. Specifically, the interactions between the p53 protein and its main regulator Mdm2 is analyzed. Beta-binders comes equipped with a reduction semantics for the formal description of the evolution of the specified systems. This allows a dynamic representation of the intrinsically static Kohn maps.