Dataset Supporting The Paper: "A Case Study On The Parametric Occurrence Of Multiple Steady States"
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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.<br> https://doi.org/http://dx.doi.org/10.1145/3087604.3087622<br> Preprint: https://arxiv.org/abs/1704.08997 We provide all the accompanying material for the main symbolic computations in Section 2.1 ###############<br> Section 2.1.1<br> ############### The computations were carried out within the following setting: 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 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 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.<br> Currently we set k19 = 500. 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). 3. The script generate-problems-assignmnets.py (called from<br> einsetzen.sh) creates 3^11 test files! 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-<var>-<possibility#>) produced by ./gml-to-red.py (called<br> from einsetzen.sh) ###############<br> Section 2.1.2<br> ############### 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.
本数据集支撑以下论文： Russell Bradford、James H. Davenport、Matthew England、Hassan Errami、Vladimir Gerdt、Dima Grigoriev、Charles Hoyt、Marek Košta、Ovidiu Radulescu、Thomas Sturm 与 Andreas Weber。《关于多稳态参数化出现的案例研究》，发表于2017年7月25日至28日于德国凯泽斯劳滕举办的ISSAC ’17会议论文集，共8页，ACM出版社，2017年。 DOI：https://doi.org/http://dx.doi.org/10.1145/3087604.3087622 预印本链接：https://arxiv.org/abs/1704.08997 我们提供了第2.1节中核心符号计算的全部配套材料。 ############### 2.1.1 小节 ############### 本次计算基于以下环境配置： 1. 已编译且可正常运行的Reduce系统（Reduce）r3606版本可用，且环境变量$trunk指向Reduce源代码树的主干目录（例如~/reduce-algebra/trunk）。如需编译安装Reduce，请参考：http://redlog.eu/reduce-wiki/index.php/Installation 2. 已编译且可正常运行的QEPCAD B v1.69版本已安装，且可通过Reduce（借助rlqepcad工具）调用QEPCAD。如需编译安装QEPCAD，请参考：https://www.usna.edu/CS/qepcadweb/B/QEPCAD.html 如需复现论文中报道的实验，请执行以下命令： ./generate-problems-onevar.py ./compute-all.sh --csl ~/reduce-algebra/trunk ./problems-onevar 4 ./einsetzen.sh 运行前请注意以下事项： 1. 若需修改k19的取值，请编辑solbiomod26.red文件。当前默认设置为k19 = 500。 2. 建议在多核机器上运行本次测试，例如我们在复现3^11个候选任务时使用了32核（对应./compute-all.sh脚本的最后一个参数）运行einsetzen.sh脚本。 3. 脚本generate-problems-assignmnets.py（由einsetzen.sh调用）将生成3^11个测试文件！ 4. 可通过区间细化尝试的候选取值以实代数数形式描述，即多项式与隔离区间的二元组。这些数值存储于由./gml-to-red.py（由einsetzen.sh调用）生成的赋值文件（assignment-<var>-<possibility#>）中。 ############### 2.1.2 小节 ############### 本次计算使用商业计算机代数系统（Computer Algebra System）Maple 2016完成。我们已上传带详细计算说明注释的Maple工作表文件，同时一并提供该工作表的PDF打印版本，供无法访问Maple的读者查阅。
