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

<p>Dataset supporting the paper:</p> <p>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.<br> https://doi.org/http://dx.doi.org/10.1145/3087604.3087622<br> Preprint: https://arxiv.org/abs/1704.08997</p> <p>We provide all the accompanying material for the main symbolic computations in Section 2.1</p> <p>###############<br> Section 2.1.1<br> ###############</p> <p>The computations were carried out within the following setting:</p> <p>1. Compiled and functional Reduce system r3606 is available and the<br> environment variable $trunk points to the trunk of Reduce source tree<br> (e.g. ~/reduce-algebra/trunk). To compile and install Reduce see:<br> http://redlog.eu/reduce-wiki/index.php/Installation</p> <p>2. Compiled and functional QEPCAD B v1.69 is installed and it is<br> possible to call QEPCAD from Reduce (via rlqepcad). To compile and<br> install QEPCAD see: https://www.usna.edu/CS/qepcadweb/B/QEPCAD.html</p> <p>To reproduce the experiments reported in the paper go:</p> <p>./generate-problems-onevar.py</p> <p>./compute-all.sh --csl ~/reduce-algebra/trunk ./problems-onevar 4</p> <p>./einsetzen.sh</p> <p>A few notes BEFORE YOU RUN:</p> <p>1. To try a different value of k19, edit the file solbiomod26.red.<br> Currently we set k19 = 500.</p> <p>2. It is advised to run these test on a multicore machine, e.g., we<br> used 32 cores (the last argument of ./compute-all.sh script) for<br> trying the 3^11 candidates (einsetzen.sh script).</p> <p>3. The script generate-problems-assignmnets.py (called from<br> einsetzen.sh) creates 3^11 test files!</p> <p>4. The potential values to be tried using interval refinement are<br> described as real algebraic numbers, i.e., pairs of polynomial and<br> isolating interval. These numbers are stored in assignment files<br> (assignment-&lt;var&gt;-&lt;possibility#&gt;) produced by ./gml-to-red.py (called<br> from einsetzen.sh)</p> <p>###############<br> Section 2.1.2<br> ###############</p> <p>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.</p>