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

Marco Antoniotti, Alberto Policriti, Nadia Ugel, Bud 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
EditorsSartaj Sahni, Viktor K. Prasanna, Uday Shukla
PublisherSpringer Verlag
Pages431-442
Number of pages12
ISBN (Print)3540003037, 9783540003038
DOIs
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)0302-9743
ISSN (Electronic)1611-3349

Other

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

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

Fingerprint Dive into the research topics of 'Xs-systems: Extended S-systems and algebraic differential automata for modeling cellular behavior'. Together they form a unique fingerprint.

Cite this