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CMSB
2008
Springer
13 years 6 months ago
Stochastic Analysis of Amino Acid Substitution in Protein Synthesis
Abstract. We present a formal analysis of amino acid replacement during mRNA translation. Building on an abstract stochastic model of arrival of tRNAs and their processing at the r...
Dragan Bosnacki, Huub M. M. ten Eikelder, M. N. St...
CMSB
2008
Springer
13 years 6 months ago
A Language for Biochemical Systems
Abstract. CBS is a Calculus of Biochemical Systems intended to allow the modelling of metabolic, signalling and regulatory networks in a natural and modular manner. In this paper w...
Michael Pedersen, Gordon D. Plotkin
CMSB
2008
Springer
13 years 6 months ago
Formal Analysis of Abnormal Excitation in Cardiac Tissue
We present the Piecewise Linear Approximation Model of Ion Channel contribution (PLAMIC) to cardiac excitation. We use the PLAMIC model to conduct formal analysis of cardiac arrhyt...
Pei Ye, Radu Grosu, Scott A. Smolka, Emilia Entche...
CMSB
2008
Springer
13 years 6 months ago
A Model Checking Approach to the Parameter Estimation of Biochemical Pathways
Model checking has historically been an important tool to verify models of a wide variety of systems. Typically a model has to exhibit certain properties to be classed `acceptable&...
Robin Donaldson, David Gilbert
CMSB
2008
Springer
13 years 6 months ago
Compositional Definitions of Minimal Flows in Petri Nets
Abstract. This paper gives algebraic definitions for obtaining the minimal transition and place flows of a modular Petri net from the minimal transition and place flows of its comp...
Michael Pedersen
CMSB
2008
Springer
13 years 6 months ago
Analyzing a Discrete Model of Aplysia Central Pattern Generator
We present a discrete formal model of the central pattern generator (CPG) located in the buccal ganglia of Aplysia that is responsible for mediating the rhythmic movements of its f...
Ashish Tiwari, Carolyn L. Talcott
CMSB
2008
Springer
13 years 6 months ago
Integrated Analysis from Abstract Stochastic Process Algebra Models
Stochastic Process Algebra Models Jane Hillston. University of Edinburgh.
Jane Hillston, Federica Ciocchetta, Adam Duguid, S...
CMSB
2008
Springer
13 years 6 months ago
Automatic Complexity Analysis and Model Reduction of Nonlinear Biochemical Systems
Kinetic models for biochemical systems often comprise a large amount of coupled differential equations with species concentrations varying on different time scales. In this paper w...
Dirk Lebiedz, Dominik Skanda, Marc Fein