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Table 4 Performance of iNA's steady state parameter scan

From: How reliable is the linear noise approximation of gene regulatory networks?

method

REs

LNA

IOS

SSA per sample (overall)

GiNaC

0.61s

1.48s

39.93s

--

BCI

0.19s

0.19s

0.39s

11ms (16h)

JIT

0.17s

0.17s

0.28s

7ms (10h)

  1. Execution times of iNA's parameter scan for the gene autoregulation network reproducing Additional file 2 (a) and (b), respectively. The table compares the REs, LNA, IOS and SSA method using the bytecode interpreter or iNA's JIT feature. For comparison we also show the execution time using the computer algebra system GiNaC which is limited by its arbitrary precision arithmetic. The SSA value denotes the average time per sample per parameter while the values in the brackets denote the extrapolated value for a sample size of 50, 000 and 100 sets of parameter values as has been used in Additional file 2. Benchmarks were performed on Ubuntu (64bit), Dell OptiPlex 9010 SF, Core i7-3770 @ 3.4GHz using a single core.