Symbolic Versus Numerical Computation and Visualization of Parameter Regions for Multistationarity of Biological Networks

Matthew England; Hassan Errami; Dima Grigoriev; Ovidiu Radulescu; Thomas Sturm; Andreas Weber

doi:10.1007/978-3-319-66320-3

Symbolic Versus Numerical Computation and Visualization of Parameter Regions for Multistationarity of Biological Networks

Matthew England, Hassan Errami, Dima Grigoriev, Ovidiu Radulescu, Thomas Sturm, Andreas Weber

Research output: Chapter in Book/Report/Conference proceeding › Conference proceeding › peer-review

14 Citations (Scopus)

55 Downloads (Pure)

Abstract

We investigate models of the mitogenactivated protein kinases (MAPK) network, with the aim of determining where in parameter space there exist multiple positive steady states. We build on recent progress which combines various symbolic computation methods for mixed systems of equalities and inequalities. We demonstrate that those techniques benefit tremendously from a newly implemented graph theoretical symbolic preprocessing method. We compare computation times and quality of results of numerical continuation methods with our symbolic approach before and after the application of our preprocessing.

Original language	English
Title of host publication	Proceedings of the the 19th International Workshop on Computer Algebra in Scientific Computing
Subtitle of host publication	CASC '17
Editors	Vladimir P. Gerdt, Wolfram Koepf, Werner M. Seiler, Evgenii V. Vorozhtsov
Publisher	Springer
Pages	93-108
Number of pages	16
Edition	1
ISBN (Electronic)	978-3-319-66320-3
ISBN (Print)	978-3-319-66319-7
DOIs	https://doi.org/10.1007/978-3-319-66320-3
Publication status	Published - 2017
Event	19th International Workshop on Computer Algebra in Scientific Computing - Beijing, China Duration: 18 Sept 2017 → 22 Sept 2017 http://www.casc.cs.uni-bonn.de/2017/

Workshop

Workshop	19th International Workshop on Computer Algebra in Scientific Computing
Abbreviated title	CASC '17
Country/Territory	China
City	Beijing
Period	18/09/17 → 22/09/17
Internet address	http://www.casc.cs.uni-bonn.de/2017/

Bibliographical note

The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-319-66320-3

Copyright © and Moral Rights are retained by the author(s) and/ or other copyright owners. A copy can be downloaded for personal non-commercial research or study, without prior permission or charge. This item cannot be reproduced or quoted extensively from without first obtaining permission in writing from the copyright holder(s). The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the copyright holders.

Access to Document

10.1007/978-3-319-66320-3

Post-PrintAccepted author manuscript, 1.94 MBLicence: CC BY-NC

Dataset supporting the paper: Symbolic Versus Numerical Computation and Visualization of Parameter Regions for Multistationarity of Biological Networks
England, M. (Creator), Errami, H. (Creator), Grigoriev, D. (Creator), Radulescu, O. (Creator), Sturm, T. (Creator) & Weber, A. (Creator), Zenodo, 2017
DOI: 10.5281/zenodo.807678, https://zenodo.org/record/807678
Dataset

Cite this

England, M., Errami, H., Grigoriev, D., Radulescu, O., Sturm, T., & Weber, A. (2017). Symbolic Versus Numerical Computation and Visualization of Parameter Regions for Multistationarity of Biological Networks. In V. P. Gerdt, W. Koepf, W. M. Seiler, & E. V. Vorozhtsov (Eds.), Proceedings of the the 19th International Workshop on Computer Algebra in Scientific Computing: CASC '17 (1 ed., pp. 93-108). Springer. https://doi.org/10.1007/978-3-319-66320-3

Symbolic Versus Numerical Computation and Visualization of Parameter Regions for Multistationarity of Biological Networks. / England, Matthew; Errami, Hassan; Grigoriev, Dima et al.
Proceedings of the the 19th International Workshop on Computer Algebra in Scientific Computing: CASC '17. ed. / Vladimir P. Gerdt; Wolfram Koepf; Werner M. Seiler; Evgenii V. Vorozhtsov. 1. ed. Springer, 2017. p. 93-108.

Research output: Chapter in Book/Report/Conference proceeding › Conference proceeding › peer-review

England, M, Errami, H, Grigoriev, D, Radulescu, O, Sturm, T & Weber, A 2017, Symbolic Versus Numerical Computation and Visualization of Parameter Regions for Multistationarity of Biological Networks. in VP Gerdt, W Koepf, WM Seiler & EV Vorozhtsov (eds), Proceedings of the the 19th International Workshop on Computer Algebra in Scientific Computing: CASC '17. 1 edn, Springer, pp. 93-108, 19th International Workshop on Computer Algebra in Scientific Computing, Beijing, China, 18/09/17. https://doi.org/10.1007/978-3-319-66320-3

England M, Errami H, Grigoriev D, Radulescu O, Sturm T, Weber A. Symbolic Versus Numerical Computation and Visualization of Parameter Regions for Multistationarity of Biological Networks. In Gerdt VP, Koepf W, Seiler WM, Vorozhtsov EV, editors, Proceedings of the the 19th International Workshop on Computer Algebra in Scientific Computing: CASC '17. 1 ed. Springer. 2017. p. 93-108 doi: 10.1007/978-3-319-66320-3

England, Matthew ; Errami, Hassan ; Grigoriev, Dima et al. / Symbolic Versus Numerical Computation and Visualization of Parameter Regions for Multistationarity of Biological Networks. Proceedings of the the 19th International Workshop on Computer Algebra in Scientific Computing: CASC '17. editor / Vladimir P. Gerdt ; Wolfram Koepf ; Werner M. Seiler ; Evgenii V. Vorozhtsov. 1. ed. Springer, 2017. pp. 93-108

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author = "Matthew England and Hassan Errami and Dima Grigoriev and Ovidiu Radulescu and Thomas Sturm and Andreas Weber",

note = "The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-319-66320-3 Copyright {\textcopyright} and Moral Rights are retained by the author(s) and/ or other copyright owners. A copy can be downloaded for personal non-commercial research or study, without prior permission or charge. This item cannot be reproduced or quoted extensively from without first obtaining permission in writing from the copyright holder(s). The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the copyright holders. ; 19th International Workshop on Computer Algebra in Scientific Computing, CASC '17 ; Conference date: 18-09-2017 Through 22-09-2017",

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Symbolic Versus Numerical Computation and Visualization of Parameter Regions for Multistationarity of Biological Networks

Abstract

Workshop

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Dataset supporting the paper: Symbolic Versus Numerical Computation and Visualization of Parameter Regions for Multistationarity of Biological Networks

Cite this