Table 1

Relative efficiency of RuleMonkey for benchmark problems

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.

Colvin et al. BMC Bioinformatics 2010 11:404   doi:10.1186/1471-2105-11-404