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Context Dependent Analysis of BioAmbients

Authors: Henrik Pilegaard, Hanne Riis-Nielson, and Flemming Nielson

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

Abstract

BioAmbients is a derivative of mobile ambients that has shown promise of describing interesting features of the behaviour of biological systems. The technical contribution of this paper is to extend the Flow Logic approach to static analysis with a couple of new techniques in order to give precise information about the behaviour of systems written in BioAmbients. Applying the development to a simple model of a cell releasing nutrients from food compunds we illustrate how the proposed analysis does indeed improve on previous efforts.

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Henrik Pilegaard, Hanne Riis-Nielson, and Flemming Nielson. Context Dependent Analysis of BioAmbients. In Simulation and Verification of Dynamic Systems. Dagstuhl Seminar Proceedings, Volume 6161, pp. 1-18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)

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@InProceedings{pilegaard_et_al:DagSemProc.06161.6,
  author =	{Pilegaard, Henrik and Riis-Nielson, Hanne and Nielson, Flemming},
  title =	{{Context Dependent Analysis of BioAmbients}},
  booktitle =	{Simulation and Verification of Dynamic Systems},
  pages =	{1--18},
  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.06161.6},
  URN =		{urn:nbn:de:0030-drops-7093},
  doi =		{10.4230/DagSemProc.06161.6},
  annote =	{Keywords: Static analysis, abstract interpretation, BioAmbients}
}

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DOI: 10.4230/DagSemProc.06161.9

Static Analysis of a Model of the LDL Degradation Pathway

Authors: Henrik Pilegaard, Hanne Riis-Nielson, and Flemming Nielson

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

Abstract

BioAmbients is a derivative of mobile ambients that has shown promise of describing interesting features of the behaviour of biological systems. As for other ambient calculi static program analysis can be used to compute safe approximations of the behaviour of system models. We use these tools to model and analyse the production of cholesterol in living cells and show that we are able to pinpoint the difference in behaviour between models of healthy systems and models of mutated systems giving rise to known diseases.

Cite as

Henrik Pilegaard, Hanne Riis-Nielson, and Flemming Nielson. Static Analysis of a Model of the LDL Degradation Pathway. In Simulation and Verification of Dynamic Systems. Dagstuhl Seminar Proceedings, Volume 6161, pp. 1-13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)

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@InProceedings{pilegaard_et_al:DagSemProc.06161.9,
  author =	{Pilegaard, Henrik and Riis-Nielson, Hanne and Nielson, Flemming},
  title =	{{Static Analysis of a Model of the LDL Degradation Pathway}},
  booktitle =	{Simulation and Verification of Dynamic Systems},
  pages =	{1--13},
  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.06161.9},
  URN =		{urn:nbn:de:0030-drops-7230},
  doi =		{10.4230/DagSemProc.06161.9},
  annote =	{Keywords: Static analysis, Systems Biology, BioAmbients, LDL Degradation Pathway}
}

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Documents authored by Pilegaard, Henrik

Context Dependent Analysis of BioAmbients

Abstract

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Static Analysis of a Model of the LDL Degradation Pathway

Abstract

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