Coloured Petri nets for multilevel, multiscale and multidimensional modelling of biological systems
Owing to the availability of data of one biological phenomenon at different levels/scales,
modelling of biological systems is moving from single level/scale to multiple levels/scales …
modelling of biological systems is moving from single level/scale to multiple levels/scales …
[HTML][HTML] Snoopy's hybrid simulator: a tool to construct and simulate hybrid biological models
Background Hybrid simulation of (computational) biochemical reaction networks, which
combines stochastic and deterministic dynamics, is an important direction to tackle future …
combines stochastic and deterministic dynamics, is an important direction to tackle future …
Biomodel engineering with Petri nets
We present a unifying Petri net framework comprising the qualitative, stochastic, continuous,
and hybrid paradigm for modeling and analyzing biological reaction networks. By means of …
and hybrid paradigm for modeling and analyzing biological reaction networks. By means of …
Coloured Hybrid Petri Nets: An adaptable modelling approach for multi-scale biological networks
Coloured Petri nets are an excellent choice for exploring large biological models,
particularly when there are repetitions of components. Such models can be easily adapted …
particularly when there are repetitions of components. Such models can be easily adapted …
Efficient modelling of yeast cell cycles based on multisite phosphorylation using coloured hybrid Petri nets with marking-dependent arc weights
With the increasing interest in systems biology to investigate the dynamics and behaviour of
biological reaction networks, the scales as well as the complexities of the models under …
biological reaction networks, the scales as well as the complexities of the models under …
Adaptive and bio-semantics of continuous Petri nets: choosing the appropriate interpretation
Continuous Petri nets (CPN) provide a graphical tool to model and analyse the deterministic
dynamic behaviour of biological reaction networks. They can be considered as an …
dynamic behaviour of biological reaction networks. They can be considered as an …
Accelerated simulation of hybrid biological models with quasi-disjoint deterministic and stochastic subnets
Computational biological models are indispensable tools for in silico hypothesis testing. But
with the increasing complexity of biological systems, traditional simulators become inefficient …
with the increasing complexity of biological systems, traditional simulators become inefficient …
[HTML][HTML] Modelling and simulation of biochemical processes using Petri nets
Systems composed of many components which interact with each other and lead to
unpredictable global behaviour, are considered as complex systems. In a biological context …
unpredictable global behaviour, are considered as complex systems. In a biological context …
[PDF][PDF] Simulative analysis of coloured extended stochastic Petri nets
C Rohr - 2017 - pure.mpg.de
Stochastic modelling of biochemical reaction networks is getting more and more popular.
Throughout the past decades typical biological models increased in their size and …
Throughout the past decades typical biological models increased in their size and …
A graphical approach for hybrid modelling of intracellular calcium dynamics based on coloured hybrid Petri nets
Intracellular calcium dynamics plays an important role in influencing the outcome of many
cellular processes. Constructing and simulating computational models to investigate this …
cellular processes. Constructing and simulating computational models to investigate this …