Executable cell biology
J Fisher, TA Henzinger - Nature biotechnology, 2007 - nature.com
Computational modeling of biological systems is becoming increasingly important in efforts
to better understand complex biological behaviors. In this review, we distinguish between …
to better understand complex biological behaviors. In this review, we distinguish between …
Bio-PEPA: A framework for the modelling and analysis of biological systems
F Ciocchetta, J Hillston - Theoretical Computer Science, 2009 - Elsevier
In this work we present Bio-PEPA, a process algebra for the modelling and the analysis of
biochemical networks. It is a modification of PEPA, originally defined for the performance …
biochemical networks. It is a modification of PEPA, originally defined for the performance …
Petri nets for systems and synthetic biology
We give a description of a Petri net-based framework for modelling and analysing
biochemical pathways, which unifies the qualitative, stochastic and continuous paradigms …
biochemical pathways, which unifies the qualitative, stochastic and continuous paradigms …
A unifying framework for modelling and analysing biochemical pathways using Petri nets
We give a description of a Petri net-based framework for modelling and analysing
biochemical pathways, which unifies the qualitative, stochastic and continuous paradigms …
biochemical pathways, which unifies the qualitative, stochastic and continuous paradigms …
Bio-PEPA: an extension of the process algebra PEPA for biochemical networks
F Ciocchetta, J Hillston - Electronic Notes in Theoretical Computer Science, 2008 - Elsevier
In this work we introduce Bio-PEPA, a process algebra for the modelling and the analysis of
biochemical networks. It is a modification of PEPA to deal with some features of biological …
biochemical networks. It is a modification of PEPA to deal with some features of biological …
Verifiable biology
S Konur, M Gheorghe… - Journal of the Royal …, 2023 - royalsocietypublishing.org
The formalization of biological systems using computational modelling approaches as an
alternative to mathematical-based methods has recently received much interest because …
alternative to mathematical-based methods has recently received much interest because …
The attributed pi calculus
M John, C Lhoussaine, J Niehren… - … Computational Methods in …, 2008 - Springer
The attributed pi calculus (ϕ(\mathcalL)) forms an extension of the pi calculus with attributed
processes and attribute dependent synchronization. To ensure flexibility, the calculus is …
processes and attribute dependent synchronization. To ensure flexibility, the calculus is …
The Continuous π-Calculus: A Process Algebra for Biochemical Modelling
M Kwiatkowski, I Stark - … on Computational Methods in Systems Biology, 2008 - Springer
We introduce the continuous π-calculus, a process algebra for modelling behaviour and
variation in molecular systems. Key features of the language are: its expressive …
variation in molecular systems. Key features of the language are: its expressive …
Process algebras in systems biology
F Ciocchetta, J Hillston - International school on formal methods for the …, 2008 - Springer
In this chapter we introduce process algebras, a class of formal modelling techniques
developed in theoretical computer science, and discuss their use within systems biology …
developed in theoretical computer science, and discuss their use within systems biology …
The Bio-PEPA tool suite
F Ciocchetta, A Duguid, S Gilmore… - … Conference on the …, 2009 - ieeexplore.ieee.org
Bio-PEPA is a timed process algebra designed specifically for the description of biological
phenomena and their analysis through quantitative methods such as stochastic simulation …
phenomena and their analysis through quantitative methods such as stochastic simulation …