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

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

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Section 2.1.1
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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)

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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.