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Table 6 Sample experiment output with constitutively active Ras.

From: ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists

   Average Inputs Average Outputs
Global Output Count ECM EGF ExtPump alpha_q Ligand alpha_i Ligand alpha_s Ligand alpha_12_13 Ligand IL1_TNF Stress Akt Erk Cdc42 Rac
2200 229 39 62 37 51 50 49 51 2 2 49 79 4 3
2211 172 83 46 42 46 48 45 52 2 2 42 75 18 15
2210 153 55 69 53 51 52 51 49 2 2 48 82 15 5
1000 142 19 23 64 51 46 47 45 2 2 19 3 1 1
2000 75 11 62 44 54 54 50 56 1 2 42 3 0 0
1211 45 87 24 71 48 46 53 54 2 2 23 63 16 19
2100 32 13 78 61 49 51 48 51 3 2 49 15 1 0
2201 28 83 46 22 46 56 51 57 2 2 46 76 6 14
1200 25 41 27 77 48 50 43 47 2 2 22 61 5 4
1201 21 75 9 65 57 48 46 47 2 2 21 58 5 17
1210 16 54 37 83 48 61 38 50 2 2 23 64 14 6
2221 13 89 68 57 43 35 53 49 2 1 46 79 32 15
1001 6 58 11 49 43 26 52 53 1 3 16 1 5 11
2220 5 79 92 86 39 82 33 45 3 2 57 88 32 8
1100 5 32 12 46 45 65 44 57 2 2 22 18 6 4
1011 4 66 13 71 24 33 60 45 2 2 14 2 19 14
1010 4 50 14 88 63 66 46 62 1 2 15 1 16 7
2110 3 36 35 29 31 64 55 55 3 1 34 18 11 5
1212 2 95 4 50 40 65 68 91 2 1 23 56 12 31
1110 2 60 39 84 71 61 26 81 5 3 23 19 19 8
0011 2 67 1 91 54 5 46 74 2 4 8 2 10 17
1202 2 90 5 61 68 53 41 51 2 4 19 57 9 30
1111 2 67 16 100 55 89 80 20 2 3 13 16 24 15
0001 1 71 0 64 68 4 97 69 5 1 8 5 6 17
0100 1 47 16 100 31 13 1 85 3 5 9 15 4 6
0201 1 92 3 100 73 92 85 82 2 5 5 53 6 29
2212 1 99 15 47 59 24 32 17 4 0 34 64 23 30
0010 1 29 20 98 73 7 71 63 1 5 7 1 11 3
1002 1 98 3 58 43 5 59 70 5 3 13 5 9 33
1221 1 100 38 87 95 40 79 51 0 1 23 69 33 26
1021 1 81 23 88 73 10 78 22 1 0 15 1 34 21
0212 1 100 9 99 62 54 19 3 5 1 9 57 17 34
2111 1 50 14 24 41 90 22 32 3 0 31 27 18 10
0202 1 100 4 90 41 49 39 48 5 5 9 55 2 33
0211 1 75 9 96 80 91 95 21 1 3 8 57 11 17
  1. Similarly to Table 5, results summarized in this table were generated during an experiment consisting of 1,000 simulation with the same paremeters (e.g., all dosages were selected randomly in a stress limited environment, discretization, etc.). Contrary to the simulation from Table 5 however, in this example, cells were simulated with constitutively active Ras. Results of this experiment show a marked increase in Erk activity (as has been suggested by laboratory research, [24, 25]), simulating a growth-factor independent activation of Erk. This phenomena can be easily seen either in the Global Output and Count columns where 229 of the 1,000 simulations produced the '2200' pattern (global output) and over 500 simulations resulted in '22XX' or the Average Output column which shows that the majority of external-input combinations resulted in Erk average activity of 75–82%.