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Table 1 Performance comparisons

From: Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms

 

Code

Run time per output [s]

Memory use [kB]

Size of input S [n × m]

FindPath

3.1 × 10-2 - 1.1 × 10-9x

4.2 × 10+1 + 1.5 × 10-2x

 

efmtool

1.6 × 10-1 + 6.7 × 10-9x

2.0 × 10+5 + 9.6 × 10-2x

 

ExPA

4.2 × 10-1 + 1.6 × 10-7x

3.3 × 10+3 + 1.1 × 10-5x

Size of output [no. of pathways]

FindPath

3.2 × 10-2 - 4.0 × 10-5x

-1.6 × 10+1 + 5.4 × 10+1x

 

efmtool

1.5 × 10-1 + 2.3 × 10-4x

1.0 × 10+5 + 3.3 × 10+4x

 

ExPA

2.5 × 10-1 + 5.7 × 10-3x

3.2 × 10+3 + 3.9 × 10+0x

  1. Performance of the codes FindPath, efmtool and Expa in terms of run time per output and memory use in function of size of input stoichiometric matrix S and size of output (number of pathways).
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BMC Systems Biology

ISSN: 1752-0509

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