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Reduction of dynamical biochemical reactions networks in computational biology
Biochemical networks are used in computational biology, to model mechanistic details of
systems involved in cell signaling, metabolism, and regulation of gene expression …
systems involved in cell signaling, metabolism, and regulation of gene expression …
ERODE: a tool for the evaluation and reduction of ordinary differential equations
We present ERODE, a multi-platform tool for the solution and exact reduction of systems of
ordinary differential equations (ODEs). ERODE supports two recently introduced …
ordinary differential equations (ODEs). ERODE supports two recently introduced …
Forward and backward bisimulations for chemical reaction networks
L Cardelli, M Tribastone, M Tschaikowski… - ar**
Motivation Stochastic reaction networks are a widespread model to describe biological
systems where the presence of noise is relevant, such as in cell regulatory processes …
systems where the presence of noise is relevant, such as in cell regulatory processes …
Comparing chemical reaction networks: A categorical and algorithmic perspective
We study chemical reaction networks (CRNs) as a kernel language for concurrency models
with semantics based on ordinary differential equations. We investigate the problem of …
with semantics based on ordinary differential equations. We investigate the problem of …
Compositionality of rewriting rules with conditions
We extend the notion of compositional associative rewriting as recently studied in the rule
algebra framework literature to the setting of rewriting rules with conditions. Our …
algebra framework literature to the setting of rewriting rules with conditions. Our …
Syntactic Markovian bisimulation for chemical reaction networks
In chemical reaction networks (CRNs) with stochastic semantics based on continuous-time
Markov chains (CTMCs), the typically large populations of species cause combinatorially …
Markov chains (CTMCs), the typically large populations of species cause combinatorially …
[HTML][HTML] Symbolic computation of differential equivalences
Ordinary differential equations (ODEs) are widespread in many natural sciences including
chemistry, ecology, and systems biology, and in disciplines such as control theory and …
chemistry, ecology, and systems biology, and in disciplines such as control theory and …