Action-based analysis of discrete regulatory networks with short-term stimuli

C. Krause; E.P. Vink, de

doi:10.1145/1839764.1839773

Action-based analysis of discrete regulatory networks with short-term stimuli

C. Krause, E.P. Vink, de

Formal System Analysis

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

1 Citation (Scopus)

Abstract

To incorporate instant effects and different timescales within a single biological system, an extension of discrete regulatory networks with short-term stimuli is proposed. By maintaining a vector of recent changes, activities initiated by a steep increase or decrease can be captured in a qualitative setting. In order to compensate for the blow-up due to enhanced states, we focus on observable behavior. Identification of bisimilar states yields a compact system representation truthfully expressing the information relevant for deciding logical properties. The approach is implemented by means of a front-end to the mCRL2 tool set and illustrated for the switching of bacteriophage lambda and a bio-medical case study related to TGFß driven fibrotic conditions.

Original language	English
Title of host publication	Proceedings of the 8th Conference on Computational Methods in Systems Biology (CMSB 2010, Trento, Italy, September 29-October 1, 2010)
Editors	P. Quaglia
Place of Publication	New York NY
Publisher	Association for Computing Machinery, Inc
Pages	65-75
ISBN (Print)	978-1-4503-0068-1
DOIs	https://doi.org/10.1145/1839764.1839773
Publication status	Published - 2010
Event	conference; The 8th Conference on Computational Methods in Systems Biology (CMSB 2010); 2010-09-29; 2010-10-01 - Duration: 29 Sept 2010 → 1 Oct 2010

Conference

Conference	conference; The 8th Conference on Computational Methods in Systems Biology (CMSB 2010); 2010-09-29; 2010-10-01
Period	29/09/10 → 1/10/10
Other	The 8th Conference on Computational Methods in Systems Biology (CMSB 2010)

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10.1145/1839764.1839773

Cite this

@inproceedings{6512f81063724202a886d778c3f077b4,

title = "Action-based analysis of discrete regulatory networks with short-term stimuli",

abstract = "To incorporate instant effects and different timescales within a single biological system, an extension of discrete regulatory networks with short-term stimuli is proposed. By maintaining a vector of recent changes, activities initiated by a steep increase or decrease can be captured in a qualitative setting. In order to compensate for the blow-up due to enhanced states, we focus on observable behavior. Identification of bisimilar states yields a compact system representation truthfully expressing the information relevant for deciding logical properties. The approach is implemented by means of a front-end to the mCRL2 tool set and illustrated for the switching of bacteriophage lambda and a bio-medical case study related to TGF{\ss} driven fibrotic conditions.",

author = "C. Krause and {Vink, de}, E.P.",

year = "2010",

doi = "10.1145/1839764.1839773",

language = "English",

isbn = "978-1-4503-0068-1",

pages = "65--75",

editor = "P. Quaglia",

booktitle = "Proceedings of the 8th Conference on Computational Methods in Systems Biology (CMSB 2010, Trento, Italy, September 29-October 1, 2010)",

publisher = "Association for Computing Machinery, Inc",

address = "United States",

note = "conference; The 8th Conference on Computational Methods in Systems Biology (CMSB 2010); 2010-09-29; 2010-10-01 ; Conference date: 29-09-2010 Through 01-10-2010",

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Krause, C & Vink, de, EP 2010, Action-based analysis of discrete regulatory networks with short-term stimuli. in P Quaglia (ed.), Proceedings of the 8th Conference on Computational Methods in Systems Biology (CMSB 2010, Trento, Italy, September 29-October 1, 2010). Association for Computing Machinery, Inc, New York NY, pp. 65-75, conference; The 8th Conference on Computational Methods in Systems Biology (CMSB 2010); 2010-09-29; 2010-10-01, 29/09/10. https://doi.org/10.1145/1839764.1839773

Action-based analysis of discrete regulatory networks with short-term stimuli. / Krause, C.; Vink, de, E.P.
Proceedings of the 8th Conference on Computational Methods in Systems Biology (CMSB 2010, Trento, Italy, September 29-October 1, 2010). ed. / P. Quaglia. New York NY: Association for Computing Machinery, Inc, 2010. p. 65-75.

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

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T1 - Action-based analysis of discrete regulatory networks with short-term stimuli

AU - Krause, C.

AU - Vink, de, E.P.

PY - 2010

Y1 - 2010

N2 - To incorporate instant effects and different timescales within a single biological system, an extension of discrete regulatory networks with short-term stimuli is proposed. By maintaining a vector of recent changes, activities initiated by a steep increase or decrease can be captured in a qualitative setting. In order to compensate for the blow-up due to enhanced states, we focus on observable behavior. Identification of bisimilar states yields a compact system representation truthfully expressing the information relevant for deciding logical properties. The approach is implemented by means of a front-end to the mCRL2 tool set and illustrated for the switching of bacteriophage lambda and a bio-medical case study related to TGFß driven fibrotic conditions.

AB - To incorporate instant effects and different timescales within a single biological system, an extension of discrete regulatory networks with short-term stimuli is proposed. By maintaining a vector of recent changes, activities initiated by a steep increase or decrease can be captured in a qualitative setting. In order to compensate for the blow-up due to enhanced states, we focus on observable behavior. Identification of bisimilar states yields a compact system representation truthfully expressing the information relevant for deciding logical properties. The approach is implemented by means of a front-end to the mCRL2 tool set and illustrated for the switching of bacteriophage lambda and a bio-medical case study related to TGFß driven fibrotic conditions.

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DO - 10.1145/1839764.1839773

M3 - Conference contribution

SN - 978-1-4503-0068-1

SP - 65

EP - 75

BT - Proceedings of the 8th Conference on Computational Methods in Systems Biology (CMSB 2010, Trento, Italy, September 29-October 1, 2010)

A2 - Quaglia, P.

PB - Association for Computing Machinery, Inc

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T2 - conference; The 8th Conference on Computational Methods in Systems Biology (CMSB 2010); 2010-09-29; 2010-10-01

Y2 - 29 September 2010 through 1 October 2010

ER -

Action-based analysis of discrete regulatory networks with short-term stimuli

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