Bench- mark | Input file (.bngl) | Reference(s) | RuleMonkey | DYNSTOC | Problem specific code | BioNetGen |
|---|
1 | testcase1 | [14] | 1.3 × 10-5 | 1.6 × 10-2 | N/A | 3.4 × 10-5 |
2 | testcase2b | [14, 19] | 2.4 × 10-5 | 1.2 × 10-4 | 2.2 × 10-5 | -- |
3 | stiff | This study | 4.6 × 10-6 | 2.6 × 10-4 | N/A | 5.0 × 10-7 |
4 | pltr | [20] | 1.1 | 1.1 | 4.1 × 10-5 | -- |
5 | egfr net | [45] | 1.1 × 10-5 | 1.8 × 10-4 | N/A | 3.7 × 10-6 |
6 | fceri | [46, 47] | 1.9 × 10-5 | 1.9 × 10-3 | N/A | 6.7 × 10-6 |
7 | lat | [44] | 9.9 × 10-3 | 1.3 × 10-2 | 1.8 × 10-5 | -- |
- The performance of RuleMonkey for seven benchmark problems is compared against that of DYNSTOC [14], problem-specific codes implementing network-free procedures [20, 44], and the simulate-ssa procedure of BioNetGen [21, 25, 29]. The problem-specific codes for benchmark problems 2, 4 and 7 were provided by M. I. Monine; these codes have been described by Yang et al. [19], Monine et al. [28], and Nag et al. [44]. Each table entry indicates seconds of CPU time per reaction event. For benchmark problems 2, 4, and 7, BioNetGen is unable to exhaustively generate the reaction network needed for generate-first simulation (without network truncation), as these problems involve simulating polymerization-like reactions. For BioNetGen simulations, the cost of network generation is not included in the table entries. All simulations were performed on a Macintosh desktop computer, equipped with a single G5 processor. Simulations were performed as specified in the indicated BioNetGen input files, which are available as Additional files 1 and 3-8 and at the RuleMonkey web site [40]. The benchmark problems are described in more detail in the text and in the references cited.
