Modelling Signalling Networks with Incomplete Information about Protein Activation States: A P System Framework of the KaiABC Oscillator

Hinze, Thomas; Lenser, Thorsten; Escuela, Gabi; Heiland, Ines; Schuster, Stefan

doi:10.1007/978-3-642-11467-0_23

Cited by 5 publications

(3 citation statements)

References 23 publications

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“…It is difficult to compare the expressiveness of the modelling languages used by these tools, as although they all use the same P systems paradigm, they implement different features -some use deterministic execution style [11], whereas many rely on probabilistic or stochastic behaviour [7,28,14,23,68]; SRSim uses strings as opposed to all the others employing multisets; some use explicitly geometric elements [68,14] or a topology of the environment [28], but the others make use only of the membrane structure.…”

Section: Discussionmentioning

confidence: 99%

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Infobiotics Workbench: A P Systems Based Tool for Systems and Synthetic Biology

Blakes

Twycross

Konur

et al. 2013

Emergence, Complexity and Computation

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Section: Discussionmentioning

confidence: 99%

“…• Extension of P systems with string objects for modelling protein binding domains with ligands have been considered for specifying oscillatory phenomena; a software environment, called SRSim, which incorporates spatial rules and a strong visualisation engine is available [68].…”

Section: Executable Modeling Formalismsmentioning

confidence: 99%

Infobiotics Workbench: A P Systems Based Tool for Systems and Synthetic Biology

Blakes

Twycross

Konur

et al. 2013

Emergence, Complexity and Computation

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“…Example 6.2. We take as motivating example the model of the chemical reaction regulating the circadian clock of Synechococcus Elongatus [29] that is composed of two successive phosphorylations and two successive dephosphorilations (which are the transitions labelled with phos. and dephos.…”

Section: Kleene Dialectica L =mentioning

confidence: 99%

Dialectica Petri nets

Elena¹,

Leal²,

Paiva³

2021

Preprint

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The categorical modeling of Petri nets has received much attention recently. The Dialectica construction has also had its fair share of attention. We revisit the use of the Dialectica construction as a categorical model for Petri nets generalizing the original application to suggest that Petri nets with different kinds of transitions can be modeled in the same categorical framework. Transitions representing truth-values, probabilities, rates or multiplicities, evaluated in different algebraic structures called lineales are useful and are modeled here in the same category. We investigate (categorical instances of) this generalized model and its connections to more recent models of categorical nets.

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