XS-systems: eXtended S-Systems and Algebraic Differential Automata for Modeling Cellular Behavior

  • Marco Antoniotti
  • Alberto Policriti
  • Nadia Ugel
  • Bud Mishra
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2552)


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.


Temporal Logic Differential Algebraic Equation Genetic Regulatory Network Algebraic Constraint Qualitative Simulation 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2002

Authors and Affiliations

  • Marco Antoniotti
    • 1
  • Alberto Policriti
    • 2
  • Nadia Ugel
    • 1
  • Bud Mishra
    • 3
  1. 1.Courant Institute of Mathematical SciencesNYU New YorkUSA
  2. 2.Università di UdineUdineItaly
  3. 3.Watson School of Biological Sciences Cold Spring HarborUSA

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