Dataset supporting the paper: "A Case Study on the Parametric Occurrence of Multiple Steady States"

  • Russell Bradford (Contributor)
  • Charles Hoyt (Contributor)
  • Ovidiu Radulescu (Contributor)
  • Andreas Weber (Contributor)
  • Thomas Sturm (Contributor)
  • Vladimir Gerdt (Contributor)
  • James H. Davenport (Contributor)
  • Dima Grigoriev (Contributor)
  • Marek Košta (Contributor)
  • Hassan Errami (Contributor)
  • Matthew England (Contributor)

    Dataset

    Description

    Dataset supporting the paper:

    Russell Bradford, James H. Davenport, Matthew England, Hassan Errami, Vladimir Gerdt, Dima Grigoriev, Charles Hoyt, Marek Košta, Ovidiu Radulescu, Thomas Sturm, and Andreas Weber. A Case Study on the Parametric Occurrence of Multiple Steady States. In Proceedings of ISSAC ’17, Kaiserslautern, Germany, July 25-28, 2017, 8 pages. ACM, 2017.
    https://doi.org/http://dx.doi.org/10.1145/3087604.3087622
    Preprint: https://arxiv.org/abs/1704.08997

    We provide all the accompanying material for the main symbolic computations in Section 2.1

    ###############
    Section 2.1.1
    ###############

    The computations were carried out within the following setting:

    1. Compiled and functional Reduce system r3606 is available and the
    environment variable $trunk points to the trunk of Reduce source tree
    (e.g. ~/reduce-algebra/trunk). To compile and install Reduce see:
    http://redlog.eu/reduce-wiki/index.php/Installation

    2. Compiled and functional QEPCAD B v1.69 is installed and it is
    possible to call QEPCAD from Reduce (via rlqepcad). To compile and
    install QEPCAD see: https://www.usna.edu/CS/qepcadweb/B/QEPCAD.html

    To reproduce the experiments reported in the paper go:

    ./generate-problems-onevar.py

    ./compute-all.sh --csl ~/reduce-algebra/trunk ./problems-onevar 4

    ./einsetzen.sh

    A few notes BEFORE YOU RUN:

    1. To try a different value of k19, edit the file solbiomod26.red.
    Currently we set k19 = 500.

    2. It is advised to run these test on a multicore machine, e.g., we
    used 32 cores (the last argument of ./compute-all.sh script) for
    trying the 3^11 candidates (einsetzen.sh script).

    3. The script generate-problems-assignmnets.py (called from
    einsetzen.sh) creates 3^11 test files!

    4. The potential values to be tried using interval refinement are
    described as real algebraic numbers, i.e., pairs of polynomial and
    isolating interval. These numbers are stored in assignment files
    (assignment-<var>-<possibility#>) produced by ./gml-to-red.py (called
    from einsetzen.sh)

    ###############
    Section 2.1.2
    ###############

    These computation were conducted in commercial Computer Algebra System, Maple 2016.  We have included the Maple Worksheet file which is annotated to describe the calulations in detail.  We also include a pdf printout of the worksheet which those without access to Maple can read.
    Date made available25 May 2017
    PublisherZenodo
    • A Case Study on the Parametric Occurrence of Multiple Steady States

      Bradford, R., Davenport, J. H., England, M., Errami, H., Gerdt, V., Grigoriev, D., Hoyt, C., Kosta, M., Radulescu, O., Sturm, T. & Weber, A., 25 Jul 2017, Proceedings of the 42nd International Symposium on Symbolic and Algebraic Computation: ISSAC '17. Association for Computing Machinery, p. 45-52 8 p.

      Research output: Chapter in Book/Report/Conference proceedingConference proceedingpeer-review

      Open Access
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      23 Citations (Scopus)
      118 Downloads (Pure)

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