Xs-systems: Extended S-systems and algebraic differential automata for modeling cellular behavior

Marco Antoniotti, Alberto Policriti, Nadia Ugel, Bhubaneswar Mishra

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Several biological and biochemical mechanisms can be modeled with relativelysimp le sets of differential algebraic equations (DAE). The numerical solution to these differential equations provide the main investigative tool for biologists and biochemists. However, the set of numerical traces of verycomp lex systems become unwieldyt o wade through when several variables are involved. To address this problem, we propose a novel wayto querylarge sets of numerical traces bycom bining in a new wayw ell known tools from numerical analysis, temporal logic and verification, and visualization. In this paper we describe XS-systems: computational models whose aim is to provide the users of S-systems with the extra tool of an automaton modeling the temporal evolution of complex biochemical reactions. The automaton construction is described starting from both numerical and analytic solutions of the differential equations involved, and parameter determination and tuning are also considered. A temporal logic language for expressing and verifying properties of XS-systems is introduced and a prototype implementation is presented.

Original languageEnglish (US)
Title of host publicationHigh Performance Computing - HiPC 2002 - 9th International Conference, Proceedings
PublisherSpringer Verlag
Pages431-442
Number of pages12
Volume2552
ISBN (Print)3540003037, 9783540003038
StatePublished - 2002
Event9th International Conference on High Performance Computing, HiPC 2002 - Bangalore, India
Duration: Dec 18 2002Dec 21 2002

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume2552
ISSN (Print)03029743
ISSN (Electronic)16113349

Other

Other9th International Conference on High Performance Computing, HiPC 2002
CountryIndia
CityBangalore
Period12/18/0212/21/02

Fingerprint

S-system
Extended Systems
Automata
Differential equations
Temporal logic
Temporal Logic
Trace
Modeling
Numerical Solution
Differential equation
Algebraic Differential Equations
Several Variables
Analytic Solution
Computational Model
Numerical analysis
Numerical Analysis
Tuning
Visualization
Prototype

ASJC Scopus subject areas

  • Computer Science(all)
  • Theoretical Computer Science

Cite this

Antoniotti, M., Policriti, A., Ugel, N., & Mishra, B. (2002). Xs-systems: Extended S-systems and algebraic differential automata for modeling cellular behavior. In High Performance Computing - HiPC 2002 - 9th International Conference, Proceedings (Vol. 2552, pp. 431-442). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 2552). Springer Verlag.

Xs-systems : Extended S-systems and algebraic differential automata for modeling cellular behavior. / Antoniotti, Marco; Policriti, Alberto; Ugel, Nadia; Mishra, Bhubaneswar.

High Performance Computing - HiPC 2002 - 9th International Conference, Proceedings. Vol. 2552 Springer Verlag, 2002. p. 431-442 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 2552).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Antoniotti, M, Policriti, A, Ugel, N & Mishra, B 2002, Xs-systems: Extended S-systems and algebraic differential automata for modeling cellular behavior. in High Performance Computing - HiPC 2002 - 9th International Conference, Proceedings. vol. 2552, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 2552, Springer Verlag, pp. 431-442, 9th International Conference on High Performance Computing, HiPC 2002, Bangalore, India, 12/18/02.
Antoniotti M, Policriti A, Ugel N, Mishra B. Xs-systems: Extended S-systems and algebraic differential automata for modeling cellular behavior. In High Performance Computing - HiPC 2002 - 9th International Conference, Proceedings. Vol. 2552. Springer Verlag. 2002. p. 431-442. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
Antoniotti, Marco ; Policriti, Alberto ; Ugel, Nadia ; Mishra, Bhubaneswar. / Xs-systems : Extended S-systems and algebraic differential automata for modeling cellular behavior. High Performance Computing - HiPC 2002 - 9th International Conference, Proceedings. Vol. 2552 Springer Verlag, 2002. pp. 431-442 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
@inproceedings{c39e04a3b6b4477a8116279cf88dbb27,
title = "Xs-systems: Extended S-systems and algebraic differential automata for modeling cellular behavior",
abstract = "Several biological and biochemical mechanisms can be modeled with relativelysimp le sets of differential algebraic equations (DAE). The numerical solution to these differential equations provide the main investigative tool for biologists and biochemists. However, the set of numerical traces of verycomp lex systems become unwieldyt o wade through when several variables are involved. To address this problem, we propose a novel wayto querylarge sets of numerical traces bycom bining in a new wayw ell known tools from numerical analysis, temporal logic and verification, and visualization. In this paper we describe XS-systems: computational models whose aim is to provide the users of S-systems with the extra tool of an automaton modeling the temporal evolution of complex biochemical reactions. The automaton construction is described starting from both numerical and analytic solutions of the differential equations involved, and parameter determination and tuning are also considered. A temporal logic language for expressing and verifying properties of XS-systems is introduced and a prototype implementation is presented.",
author = "Marco Antoniotti and Alberto Policriti and Nadia Ugel and Bhubaneswar Mishra",
year = "2002",
language = "English (US)",
isbn = "3540003037",
volume = "2552",
series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",
publisher = "Springer Verlag",
pages = "431--442",
booktitle = "High Performance Computing - HiPC 2002 - 9th International Conference, Proceedings",

}

TY - GEN

T1 - Xs-systems

T2 - Extended S-systems and algebraic differential automata for modeling cellular behavior

AU - Antoniotti, Marco

AU - Policriti, Alberto

AU - Ugel, Nadia

AU - Mishra, Bhubaneswar

PY - 2002

Y1 - 2002

N2 - Several biological and biochemical mechanisms can be modeled with relativelysimp le sets of differential algebraic equations (DAE). The numerical solution to these differential equations provide the main investigative tool for biologists and biochemists. However, the set of numerical traces of verycomp lex systems become unwieldyt o wade through when several variables are involved. To address this problem, we propose a novel wayto querylarge sets of numerical traces bycom bining in a new wayw ell known tools from numerical analysis, temporal logic and verification, and visualization. In this paper we describe XS-systems: computational models whose aim is to provide the users of S-systems with the extra tool of an automaton modeling the temporal evolution of complex biochemical reactions. The automaton construction is described starting from both numerical and analytic solutions of the differential equations involved, and parameter determination and tuning are also considered. A temporal logic language for expressing and verifying properties of XS-systems is introduced and a prototype implementation is presented.

AB - Several biological and biochemical mechanisms can be modeled with relativelysimp le sets of differential algebraic equations (DAE). The numerical solution to these differential equations provide the main investigative tool for biologists and biochemists. However, the set of numerical traces of verycomp lex systems become unwieldyt o wade through when several variables are involved. To address this problem, we propose a novel wayto querylarge sets of numerical traces bycom bining in a new wayw ell known tools from numerical analysis, temporal logic and verification, and visualization. In this paper we describe XS-systems: computational models whose aim is to provide the users of S-systems with the extra tool of an automaton modeling the temporal evolution of complex biochemical reactions. The automaton construction is described starting from both numerical and analytic solutions of the differential equations involved, and parameter determination and tuning are also considered. A temporal logic language for expressing and verifying properties of XS-systems is introduced and a prototype implementation is presented.

UR - http://www.scopus.com/inward/record.url?scp=67349162798&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=67349162798&partnerID=8YFLogxK

M3 - Conference contribution

AN - SCOPUS:67349162798

SN - 3540003037

SN - 9783540003038

VL - 2552

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 431

EP - 442

BT - High Performance Computing - HiPC 2002 - 9th International Conference, Proceedings

PB - Springer Verlag

ER -