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Documents authored by Sedwards, Sean

Document
DOI: 10.4230/DagSemProc.09091.3
Analyzing various models of Circadian Clock and Cell Cycle coupling

Authors: Attila Csikász-Nagy, Adrien Faure, Roberto Larcher, Paola Lecca, Ivan Mura, Ferenc Jordan, Alida Palmisano, Alessandro Romanel, Sean Sedwards, Heike Siebert, Sylvain Soliman, Denis Thieffry, Judit Zámborszky, Tommaso Mazza, and Paolo Ballarini

Published in: Dagstuhl Seminar Proceedings, Volume 9091, Formal Methods in Molecular Biology (2009)

Abstract
The daily rhythm can influence the proliferation rate of many cell types. In the mammalian system the transcription of the cell cycle regulatory protein Wee1 is controlled by the circadian clock. Zamborszky et al. (2007) present a computational model coupling the cell cycle and circadian rhythm, showing that this coupling can lead to multimodal cell cycle time distributions. Biological data points to additional couplings, including a link back from the cell cycle to the circadian clock. Proper modelling of this coupling requires a more detailed description of both parts of the model. Hence, we aim at further extending and analysing earlier models using a combination of modelling techniques and computer software, including CoSBI lab, BIOCHAM, and GINsim.
Cite as

Attila Csikász-Nagy, Adrien Faure, Roberto Larcher, Paola Lecca, Ivan Mura, Ferenc Jordan, Alida Palmisano, Alessandro Romanel, Sean Sedwards, Heike Siebert, Sylvain Soliman, Denis Thieffry, Judit Zámborszky, Tommaso Mazza, and Paolo Ballarini. Analyzing various models of Circadian Clock and Cell Cycle coupling. In Formal Methods in Molecular Biology. Dagstuhl Seminar Proceedings, Volume 9091, pp. 1-6, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2009)

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@InProceedings{csikasznagy_et_al:DagSemProc.09091.3,
  author =	{Csik\'{a}sz-Nagy, Attila and Faure, Adrien and Larcher, Roberto and Lecca, Paola and Mura, Ivan and Jordan, Ferenc and Palmisano, Alida and Romanel, Alessandro and Sedwards, Sean and Siebert, Heike and Soliman, Sylvain and Thieffry, Denis and Z\'{a}mborszky, Judit and Mazza, Tommaso and Ballarini, Paolo},
  title =	{{Analyzing various models of Circadian Clock and Cell Cycle coupling}},
  booktitle =	{Formal Methods in Molecular Biology},
  pages =	{1--6},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2009},
  volume =	{9091},
  editor =	{Rainer Breitling and David Roger Gilbert and Monika Heiner and Corrado Priami},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09091.3},
  URN =		{urn:nbn:de:0030-drops-19944},
  doi =		{10.4230/DagSemProc.09091.3},
  annote =	{Keywords: Cell cycle, circadian clock, computational modelling}
}
Document
DOI: 10.4230/DagSemProc.06161.7
Modeling and Simulating Biological Processes with Stochastic Multiset Rewriting

Authors: Matteo Cavaliere and Sean Sedwards

Published in: Dagstuhl Seminar Proceedings, Volume 6161, Simulation and Verification of Dynamic Systems (2006)

Abstract
Membrane systems were originally introduced as models of computation inspired by the structure and the functioning of living cells. More recently, membrane systems have been shown to be suitable also to model cellular processes. Inspired by brane calculi, a new model of membrane system with peripheral proteins has been recently introduced. Such model has compartments (enclosed by membranes), floating objects, and objects attached to the internal and external surfaces of the membranes. The objects can be processed/transported inside/across the compartments and the transport is regulated by opportune objects attached to the membranes surfaces. We present a stochastic simulator of this model, with a style of syntax based on chemical reactions. We show that the simulator can be particularly useful in modelling biological processes that involve compartments, surface and integral membrane proteins, transport and processing of chemical substances. As examples we present the simulation of circadian clock and the G-protein cycle in yeast.
Cite as

Matteo Cavaliere and Sean Sedwards. Modeling and Simulating Biological Processes with Stochastic Multiset Rewriting. In Simulation and Verification of Dynamic Systems. Dagstuhl Seminar Proceedings, Volume 6161, pp. 1-8, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)

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@InProceedings{cavaliere_et_al:DagSemProc.06161.7,
  author =	{Cavaliere, Matteo and Sedwards, Sean},
  title =	{{Modeling and Simulating Biological Processes with Stochastic Multiset Rewriting}},
  booktitle =	{Simulation and Verification of Dynamic Systems},
  pages =	{1--8},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{6161},
  editor =	{David M. Nicol and Corrado Priami and Hanne Riis Nielson and Adelinde M. Uhrmacher},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.06161.7},
  URN =		{urn:nbn:de:0030-drops-7061},
  doi =		{10.4230/DagSemProc.06161.7},
  annote =	{Keywords: Systems biology, membrane systems, formal language, simulation}
}
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