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Best known solutions

The solutions are grouped after the original system that they are based on, an overview is shown in the following table with links to more detailed output files:

Model space of chemical rate equations and simulated data

Source system/model Test problem Error of source model Error Residual Time (s) (1GHz) Similarity with source model FP/FN/ME Stability between runs Output files Reference to algorithm
simpleLin simpleLin1 8 8 0 17 0/0/0 5/5 Output files 1 (footnote)
  simpleLin2 187.4 140.2 132.2 86 0/0/- 5/5 Output files 1
simpleFb simpleFb1 7 7 0 14 0/0/0 5/5 Output files 1
  simpleFb2 45.46 42.14 34.14 36 1/1/- 3/5 Output files 1
  simpleFb3 7 7 0 41 0/0/0 3/5 Output files 1
  simpleFb4 18.39 7.071 0.0713 47 0/0/- 2/5 Output files 1
osc osc1 6 6.149 0.1491 18 0/0/0 5/5 Output files 1
  osc2 122.1 87.34 57.34 24 0/0 4/5 Output files 1
metabol metabol1 30 30 0 5400 0/0/0 3/3 Output files 1
  metabol2 1214 751.6 601.6 11000 0/0/- 2/3 Output files 1
  metabol3 1442 861.1 696.1 13000 2/1/- 1/5* Output files 1
3genes 3genes1 39 39 0 35000 0/0/0 3/3 Output files 1
feedf feedf1   1.760 1.640 54   5/5 Output files 3
  feedf2   1958 1858 70   5/5 Output files 3
inhosc inhosc1   9.863 9.813 9.0   5/5 Output files 3
  inhosc2   814.4 789.4 14   4/5 Output files 3
bifeedb bifeedb1   8.463 8.313 110   5/5 Output files 3
  bifeedb2   2933 2793 140   5/5 Output files 3

S-system model space and simulated data

Source system/model Test problem Error of source model Error Residual Time (s) (1GHz) Similarity with source model FP/FN/ME Stability between runs Output files Reference to algorithm
ss_cascade ss_cascade1 14 14 0 180 0/0/0 5/5 Output files 1
  ss_cascade2 14 14 0 130 0/0/0 5/5 Output files 1
  ss_cascade3 498.9 476.7 462.7 860 1/1/- 1/5* Output files 1
ss_branch ss_branch1 17 17 0 68 0/0/0 5/5 Output files 1
  ss_branch2 17 17 0 110 0/0/0 5/5 Output files 1
  ss_branch3 17 17 0 150 0/0/0 5/5 Output files 1
  ss_branch4 17 17 0 71 0/0/0 5/5 Output files 1
  ss_branch5 211.3 142.1 122.1 300 4/1/- 3/5 Output files 1
  ss_branch6 18 18 0 90 0/0/0 5/5 Output files 1
ss_5genes ss_5genes1 23 23 0 600 0/0/0 5/5 Output files 1
  ss_5genes2 300.3 211.0 183.0 2100 5/0/- 2/5* Output files 1
  ss_5genes3 23 23 0 380 0/0/0 5/5 Output files 1
  ss_5genes4 23 23 0 640 0/0/0 5/5 Output files 1
  ss_5genes5 23 23.00 1.14E-3 400 0/0/0.02 5/5 Output files 1
  ss_5genes6 23 23 0 130 0/0/0 5/5 Output files 1
  ss_5genes7 23 23 0 190 0/0/0 5/5 Output files 1
  ss_5genes8 28 28 0 440 0/0/0 5/5 Output files 1
ss_15genes ss_15genes1 62 62 0 1500 0/0/0 5/5 Output files 1
  ss_15genes2 2010 1783 1478 18000 3/4/- 2/5* Output files 1
ss_30genes ss_30genes1 128 128 0 7900 0/0/0 5/5 Output files 1
  ss_30genes2 4098 3628 2993 94000 6/7/- 1/3* Output files 1
  ss_30genes3 128 128 0 18000 0/0/0 3/3 Output files 1
ss_feedf ss_feedf1   0.1969 0.0469 580   2/5 Output files 3
  ss_feedf2   1953 1793 1500   4/5 Output files 3
ss_inhosc ss_inhosc1   0.2105 0.1505 11   5/5 Output files 3
  ss_inhosc2   376.4 346.4 32   5/5 Output files 3
ss_bifeedb ss_bifeedb1   1.098 0.858 1100   1/5 Output files 3
  ss_bifeedb2   2488 2308 2000   5/5 Output files 3

GMA model space and simulated data

Source system/model Test problem Error of source model Error Residual Time (s) (1GHz) Similarity with source model FP/FN/ME Stability between runs Output files Reference to algorithm
gma_feedf gma_feedf1   0.1783 0.0183 1600   5/5 Output files 3
  gma_feedf2   1917 1747 5600   5/5 Output files 3
gma_inhosc gma_inhosc1   0.2089 0.1489 50   5/5 Output files 3
  gma_inhosc2   371.4 341.4 170   1/5 Output files 3
gma_bifeedb gma_bifeedb1   0.2565 0.0065 4700   5/5 Output files 3
  gma_bifeedb2   2480 2290 7600   1/5 Output files 3

Data from real biological systems

Source system/model Test problem Error of source model Error Residual Time (s) (1GHz) Similarity with source model FP/FN/ME Stability between runs Output files Reference to algorithm
cytokine cytokine1   25.92 17.92 11   1/5 Output files 1
  cytokine2   42.17 32.17 23   1/5 Output files 1
ss_ethanolferm ss_ethanolferm1   127.4 110.4 190   1/5 Output files 1
  ss_ethanolferm2   1308 1292 360   1/5 Output files 1
ss_sosrepair ss_sosrepair1   2642 2611 510   1/5 Output files 1
  ss_sosrepair2   2823 2789 470   1/5 Output files 1
ss_cadBA ss_cadBA1   750.6 726.6 250   1/5 Output files 1
  ss_cadBA2   709.1 687.1 260   1/5 Output files 1
ss_clock ss_clock1   928.4 803.4 360   1/5 Output files 1
  ss_clock2   814.5 649.5 440   1/5 Output files 1

Parameter estimation problems (the structure is fixed)

Source system/model Test problem Error of source model Residual Time (s) (1GHz) Stability between runs Output files Reference to algorithm
3genes pe_3genes1 0.00 0.00 57 6/10 Output files 2
  pe_3genes2f   1286 90 5/10 Output files 2
  pe_3genes2   1214 140 5/10 Output files 2
  pe_3genes3f 0.00 3128 100 1/10 Output files 2
  pe_3genes3 0.00 2309 170 1/10 Output files 2
4genes pe_4genes1 0.00 0.00 610 7/10 Output files 2
5genes pe_5genes1 0.00 0.00 840 10/10 Output files 2
6genes pe_6genes1 0.00 0.00 1100 8/10 Output files 2
pinene pe_pinene   9.936 0.1 10/10 Output files 2
ss_cascade pe_ss_cascade1 0.00 0.00 13 10/10 Output files 2
ss_branch pe_ss_branch4 0.00 0.00 0.5 10/10 Output files 2
ss_30genes pe_ss_30genes2f   3240 210 10/10 Output files 2
  pe_ss_30genes2   3004 1000 10/10 Output files 2
pe_feedf pe_feedf1   1.653 1.6 5/5 Output files 3
  pe_feedf2   1856 3.1 5/5 Output files 3
pe_inhosc pe_inhosc1   9.815 0.43 5/5 Output files 3
  pe_inhosc2   799.6 1.1 5/5 Output files 3
pe_bifeedb pe_bifeedb1   8.449 2.7 5/5 Output files 3
  pe_bifeedb2   2814 6.3 5/5 Output files 3
pe_ss_feedf pe_ss_feedf1   0.1006 24 1/5 Output files 3
  pe_ss_feedf2   1825 22 5/5 Output files 3
pe_ss_inhosc pe_ss_inhosc1   0.1256 1.3 1/5 Output files 3
  pe_ss_inhosc2   339.3 1.5 5/5 Output files 3
pe_ss_bifeedb pe_ss_bifeedb1   1.767 25 5/5 Output files 3
  pe_ss_bifeedb2   2361 24 5/5 Output files 3
pe_gma_feedf pe_gma_feedf1   0.01984 70 1/5 Output files 3
  pe_gma_feedf2   1772 78 5/5 Output files 3
pe_gma_inhosc pe_gma_inhosc1   0.1229 6.7 4/5 Output files 3
  pe_gma_inhosc2   340.2 5.4 5/5 Output files 3
pe_gma_bifeedb pe_gma_bifeedb1   1.506 54 5/5 Output files 3
  pe_gma_bifeedb2   2386 100 5/5 Output files 3

#var = number of dependent variables, #exp = number of experimental conditions with different initial conditions and/or input functions, #pts = number of data-points per time-series. Noise is added from a Gaussian distribution with standard deviation given as a certain percentage (denoted Noise) of each experimental value. Problem names starting with ss_ correspond to S-systems.

1) Gennemark and Wedelin, IET Systems biology (2007).

2) Gennemark and Wedelin, LNCS 5688, 205-217 (2009).

3) Kattas, Gennemark and Wedelin, CMSB (2010).