Projects per year
Abstract
In this work we present a Bio-PEPA model describing the Nuclear Factor κB (NF-κB) signalling pathway. In particular our model focuses on the dynamic response of NF-κB to an external stimulus. Each biochemical species in the pathway is represented by a specific Bio-PEPA component and the external stimulus is abstracted by time-dependent Bio-PEPA events describing the start and the end of the signal.
The Bio-PEPA model is a formal intermediate representation of the pathway on which various kinds of analysis can be performed. Both stochastic and deterministic simulations are carried out to validate our model against the experimental data and in-silico experiments in the literature and to verify some properties, such as, the impact of the duration of the external stimulus and of the total NF-κB initial amount on the behaviour of some species of interest. Furthermore we use stochastic simulation to compare the behaviour of the single cell against the average behaviour of a population of cells. Finally, sensitivity analysis is considered to investigate the most influential parameters of the model. Importantly, the approach taken suggests that the sensitivity of some parameters alters with the time evolution of the pathway.
The Bio-PEPA model is a formal intermediate representation of the pathway on which various kinds of analysis can be performed. Both stochastic and deterministic simulations are carried out to validate our model against the experimental data and in-silico experiments in the literature and to verify some properties, such as, the impact of the duration of the external stimulus and of the total NF-κB initial amount on the behaviour of some species of interest. Furthermore we use stochastic simulation to compare the behaviour of the single cell against the average behaviour of a population of cells. Finally, sensitivity analysis is considered to investigate the most influential parameters of the model. Importantly, the approach taken suggests that the sensitivity of some parameters alters with the time evolution of the pathway.
Original language | English |
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Title of host publication | Transactions on Computational Systems Biology XII |
Subtitle of host publication | Special Issue on Modeling Methodologies |
Publisher | Springer |
Pages | 229-262 |
Number of pages | 34 |
Volume | XII |
ISBN (Print) | 978-3-642-11711-4 |
DOIs | |
Publication status | Published - 2010 |
Publication series
Name | Lecture Notes in Computer Science |
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Publisher | Springer Berlin / Heidelberg |
Volume | 5945 |
ISSN (Print) | 0302-9743 |
ISSN (Electronic) | 1611-3349 |
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Dive into the research topics of 'Modelling and analysis of the NF-κB pathway in Bio-PEPA'. Together they form a unique fingerprint.Projects
- 3 Finished
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SIGNAL: SIGNAL -Stochastic process algebra for biochemical signaling pathway analysis
1/09/07 → 31/01/11
Project: Research
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SynthSys; formerly CSBE: Centre for Systems Biology at Edinburgh
Millar, A., Beggs, J., Ghazal, P., Goryanin, I., Hillston, J., Plotkin, G., Tollervey, D., Walton, A. & Robertson, K.
8/01/07 → 31/12/12
Project: Research
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