diff --git a/data/KEIO_test_data/KEIO_ROBOT6_1/KEIO_ROBOT6_1_res/Ace.svg b/data/KEIO_test_data/KEIO_ROBOT6_1/KEIO_ROBOT6_1_res/Ace.svg index d721ca0..062a27f 100644 --- a/data/KEIO_test_data/KEIO_ROBOT6_1/KEIO_ROBOT6_1_res/Ace.svg +++ b/data/KEIO_test_data/KEIO_ROBOT6_1/KEIO_ROBOT6_1_res/Ace.svg @@ -6,7 +6,7 @@ - 2022-08-17T16:42:12.561843 + 2022-09-23T14:39:08.801431 image/svg+xml @@ -39,7 +39,7 @@ z - - - - - - - - - + + + + + + + + - - - + + - - + @@ -149,7 +149,7 @@ z - + @@ -178,7 +178,7 @@ z - + @@ -217,7 +217,7 @@ z - + @@ -264,7 +264,7 @@ z - + @@ -298,7 +298,7 @@ z - + @@ -430,12 +430,12 @@ z - - + @@ -448,12 +448,12 @@ L -3.5 0 - + - + @@ -461,12 +461,12 @@ L -3.5 0 - + - + @@ -474,12 +474,12 @@ L -3.5 0 - + - + @@ -659,23 +659,23 @@ z - + - + @@ -868,7 +868,7 @@ z - + diff --git a/data/KEIO_test_data/KEIO_ROBOT6_1/KEIO_ROBOT6_1_res/Glc.svg b/data/KEIO_test_data/KEIO_ROBOT6_1/KEIO_ROBOT6_1_res/Glc.svg index 7eb9d49..8c512ec 100644 --- a/data/KEIO_test_data/KEIO_ROBOT6_1/KEIO_ROBOT6_1_res/Glc.svg +++ b/data/KEIO_test_data/KEIO_ROBOT6_1/KEIO_ROBOT6_1_res/Glc.svg @@ -6,7 +6,7 @@ - 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+ @@ -266,7 +266,7 @@ z - + @@ -300,7 +300,7 @@ z - + @@ -432,12 +432,12 @@ z - - + @@ -461,12 +461,12 @@ z - + - + @@ -476,12 +476,12 @@ z - + - + @@ -491,12 +491,12 @@ z - + - + - + - + @@ -912,7 +912,7 @@ z - + diff --git a/data/KEIO_test_data/KEIO_ROBOT6_1/KEIO_ROBOT6_1_res/flux_results.tsv b/data/KEIO_test_data/KEIO_ROBOT6_1/KEIO_ROBOT6_1_res/flux_results.tsv index c510fc3..d36c68b 100644 --- a/data/KEIO_test_data/KEIO_ROBOT6_1/KEIO_ROBOT6_1_res/flux_results.tsv +++ b/data/KEIO_test_data/KEIO_ROBOT6_1/KEIO_ROBOT6_1_res/flux_results.tsv @@ -1,7 +1,7 @@ optimal mean sd median CI_2.5 CI_97.5 -X_0 0.019821278664450825 0.020332545347466105 0.00211123465873886 0.020378235694819596 0.016321464548485286 0.024437800055734038 -mu 0.6449976976644697 0.6406649026476466 0.02033523167989749 0.6399508326282166 0.6031347778699248 0.6846435132149311 -Glc_q -6.793948932419026 -6.8321294103613335 0.3489094577765364 -6.859033131047301 -7.442967159633212 -6.110613522828935 -Glc_M0 13.886578100388485 13.93276345152388 0.17384325719225396 13.939277389925664 13.61732394026051 14.287087737348251 -Ace_q 2.610283987995981 2.670598774505059 0.38445692342237625 2.7155168269501626 1.777659707622841 3.3619017252234316 -Ace_M0 0.26517422559369924 0.24970823093407465 0.20219988426679378 0.21935635885588045 1e-06 0.7223533432213737 +X_0 0.019837910042084236 0.020055047719088507 0.001936242015519126 0.020181433524903817 0.016385933648857588 0.023991705722000656 +mu 0.6448503161617235 0.6442401851491355 0.019838552319737378 0.6422759597671867 0.6055123753172559 0.6830180317435467 +Glc_q -6.7962941185743135 -6.774793454329362 0.39318776265927613 -6.801632529773193 -7.486259488979566 -6.0294828984301505 +Glc_M0 13.890941548678349 13.881503136428412 0.2268604387133866 13.89390411710686 13.42167220505119 14.364675598831429 +Ace_q 2.574083305172119 2.5516892907444007 0.34218910204223774 2.5706434692350855 1.8525815217489552 3.109731754802952 +Ace_M0 0.28632420734796105 0.28673563941751923 0.17207412150016024 0.2778487391600317 1e-06 0.6251737133158014 diff --git a/data/KEIO_test_data/KEIO_ROBOT6_1/KEIO_ROBOT6_1_res/log.txt b/data/KEIO_test_data/KEIO_ROBOT6_1/KEIO_ROBOT6_1_res/log.txt index dc39309..bcb4983 100644 --- a/data/KEIO_test_data/KEIO_ROBOT6_1/KEIO_ROBOT6_1_res/log.txt +++ b/data/KEIO_test_data/KEIO_ROBOT6_1/KEIO_ROBOT6_1_res/log.txt @@ -1,6 +1,6 @@ -2022-08-17 16:42:04,190 - INFO - Initializing Weight matrix... +2022-09-23 14:39:00,763 - INFO - Initializing Weight matrix... -2022-08-17 16:42:04,191 - INFO - Weight Matrix: +2022-09-23 14:39:00,763 - INFO - Weight Matrix: [[0.02 0.5 0.5 ] [0.02 0.5 0.5 ] [0.02 0.5 0.5 ] @@ -18,117 +18,117 @@ [0.02 0.5 0.5 ] [0.02 0.5 0.5 ]] -2022-08-17 16:42:04,191 - INFO - Initializing bounds... +2022-09-23 14:39:00,763 - INFO - Initializing bounds... -2022-08-17 16:42:04,191 - INFO - Bounds: ((0.001, 10), (0.001, 3), (-50, 50), (1e-06, 50), (-50, 50), (1e-06, 50)) +2022-09-23 14:39:00,763 - INFO - Bounds: ((0.001, 10), (0.001, 3), (-50, 50), (1e-06, 50), (-50, 50), (1e-06, 50)) -2022-08-17 16:42:04,210 - INFO - -Configuration file saved in: C:\Users\legregam\Documents\Projets\PhysioFit4Galaxy\data\KEIO_test_data\KEIO_ROBOT6_1\KEIO_ROBOT6_1_res\config_file.json -2022-08-17 16:42:04,210 - INFO - +2022-09-23 14:39:00,779 - INFO - +Configuration file saved at: C:\Users\legregam\Documents\Projets\PhysioFit4Galaxy\data\KEIO_test_data\KEIO_ROBOT6_1\KEIO_ROBOT6_1_res\config_file.json +2022-09-23 14:39:00,795 - INFO - Running optimization... -2022-08-17 16:42:05,834 - INFO - Optimization results: - fun: 10.461094284993804 - jac: array([-0.03579377, -0.00545857, -0.11797994, -0.02868034, -0.00388756, - -0.10945254]) +2022-09-23 14:39:01,882 - INFO - Optimization results: + fun: 10.465071032170075 + jac: array([ 0.39989114, 0.04606715, -0.08850023, 0.0993948 , -0.16591688, + 0.1575204 ]) message: 'Optimization terminated successfully.' - nfev: 7458 - nit: 80 + nfev: 6620 + nit: 71 success: True - x: array([ 0.01982128, 0.6449977 , -6.79394893, 13.8865781 , 2.61028399, - 0.26517423]) + x: array([ 0.01983791, 0.64485032, -6.79629412, 13.89094155, 2.57408331, + 0.28632421]) -2022-08-17 16:42:05,834 - INFO - -X_0 = 0.019821278664450825 +2022-09-23 14:39:01,882 - INFO - +X_0 = 0.019837910042084236 -2022-08-17 16:42:05,834 - INFO - -mu = 0.6449976976644697 +2022-09-23 14:39:01,882 - INFO - +mu = 0.6448503161617235 -2022-08-17 16:42:05,835 - INFO - -Glc_q = -6.793948932419026 +2022-09-23 14:39:01,898 - INFO - +Glc_q = -6.7962941185743135 -2022-08-17 16:42:05,835 - INFO - -Glc_M0 = 13.886578100388485 +2022-09-23 14:39:01,898 - INFO - +Glc_M0 = 13.890941548678349 -2022-08-17 16:42:05,835 - INFO - -Ace_q = 2.610283987995981 +2022-09-23 14:39:01,898 - INFO - +Ace_q = 2.574083305172119 -2022-08-17 16:42:05,835 - INFO - -Ace_M0 = 0.26517422559369924 +2022-09-23 14:39:01,898 - INFO - +Ace_M0 = 0.28632420734796105 -2022-08-17 16:42:05,841 - INFO - Final Simulated Data: +2022-09-23 14:39:01,898 - INFO - Final Simulated Data: X Glc Ace Time -1.350000 NaN 13.596642 0.376570 -1.694722 0.059136 NaN NaN -1.916667 NaN 13.376591 0.461115 -2.300278 0.087394 NaN NaN -2.698333 0.112976 NaN NaN -2.866667 NaN 12.768873 0.694604 -3.436111 0.181824 NaN NaN -3.821111 0.233076 NaN NaN -4.000000 NaN 11.340045 1.243571 -4.201111 0.297812 NaN NaN -4.598056 0.384711 NaN NaN -4.800000 NaN 9.479352 1.958462 -4.995000 0.496965 NaN NaN -5.183333 NaN 8.184570 2.455927 -5.375278 0.635110 NaN NaN -5.583333 NaN 6.444802 3.124358 - -2022-08-17 16:42:05,841 - INFO - Running monte carlo analysis. Number of iterations: 100 - -2022-08-17 16:42:10,396 - INFO - Optimized parameters statistics: -2022-08-17 16:42:10,397 - INFO - optimal: [ 0.01982128 0.6449977 -6.79394893 13.8865781 2.61028399 0.26517423] -2022-08-17 16:42:10,397 - INFO - mean: [ 0.02033255 0.6406649 -6.83212941 13.93276345 2.67059877 0.24970823] -2022-08-17 16:42:10,397 - INFO - sd: [0.00211123 0.02033523 0.34890946 0.17384326 0.38445692 0.20219988] -2022-08-17 16:42:10,397 - INFO - median: [ 0.02037824 0.63995083 -6.85903313 13.93927739 2.71551683 0.21935636] -2022-08-17 16:42:10,398 - INFO - CI_2.5: [ 1.63214645e-02 6.03134778e-01 -7.44296716e+00 1.36173239e+01 - 1.77765971e+00 1.00000000e-06] -2022-08-17 16:42:10,398 - INFO - CI_97.5: [ 0.0244378 0.68464351 -6.11061352 14.28708774 3.36190173 0.72235334] -2022-08-17 16:42:10,398 - INFO - Simulated matrix lower confidence interval: -[[ nan 13.34131066 0.13238488] - [ 0.0520758 nan nan] - [ nan 13.12843292 0.22137224] - [ 0.07882834 nan nan] - [ 0.10352246 nan nan] - [ nan 12.54364578 0.46282416] - [ 0.17146464 nan nan] - [ 0.22270804 nan nan] - [ nan 11.14987605 1.0363068 ] - [ 0.28748425 nan nan] - [ 0.37347244 nan nan] - [ nan 9.25763266 1.69861328] - [ 0.48523657 nan nan] - [ nan 7.88983486 2.091237 ] - [ 0.61641029 nan nan] - [ nan 6.02976993 2.64729164]] - -2022-08-17 16:42:10,399 - INFO - Simulated matrix higher confidence interval: -[[ nan 13.96972365 0.79900093] - [ 0.06791753 nan nan] - [ nan 13.73460803 0.87192934] - [ 0.09785942 nan nan] - [ 0.12441431 nan nan] - [ nan 13.08569219 1.05002608] - [ 0.19427075 nan nan] - [ 0.24600155 nan nan] - [ nan 11.60699355 1.4843221 ] - [ 0.31029406 nan nan] - [ 0.39674964 nan nan] - [ nan 9.7228962 2.27288408] - [ 0.51009565 nan nan] - [ nan 8.50021376 2.82823848] - [ 0.64911577 nan nan] - [ nan 6.88723069 3.68873384]] - -2022-08-17 16:42:10,400 - INFO - khi2 test results: -khi2 value: 10.461094284993804 +1.350000 NaN 13.600695 0.396255 +1.694722 0.059171 NaN NaN +1.916667 NaN 13.380437 0.479677 +2.300278 0.087438 NaN NaN +2.698333 0.113026 NaN NaN +2.866667 NaN 12.772218 0.710039 +3.436111 0.181885 NaN NaN +3.821111 0.233140 NaN NaN +4.000000 NaN 11.342435 1.251566 +4.201111 0.297878 NaN NaN +4.598056 0.384773 NaN NaN +4.800000 NaN 9.480755 1.956674 +4.995000 0.497016 NaN NaN +5.183333 NaN 8.185395 2.447289 +5.375278 0.635139 NaN NaN +5.583333 NaN 6.444949 3.106479 + +2022-09-23 14:39:01,898 - INFO - Running monte carlo analysis. Number of iterations: 100 + +2022-09-23 14:39:06,791 - INFO - Optimized parameters statistics: +2022-09-23 14:39:06,791 - INFO - optimal: [ 0.01983791 0.64485032 -6.79629412 13.89094155 2.57408331 0.28632421] +2022-09-23 14:39:06,791 - INFO - mean: [ 0.02005505 0.64424019 -6.77479345 13.88150314 2.55168929 0.28673564] +2022-09-23 14:39:06,791 - INFO - sd: [0.00193624 0.01983855 0.39318776 0.22686044 0.3421891 0.17207412] +2022-09-23 14:39:06,791 - INFO - median: [ 0.02018143 0.64227596 -6.80163253 13.89390412 2.57064347 0.27784874] +2022-09-23 14:39:06,791 - INFO - CI_2.5: [ 1.63859336e-02 6.05512375e-01 -7.48625949e+00 1.34216722e+01 + 1.85258152e+00 1.00000000e-06] +2022-09-23 14:39:06,791 - INFO - CI_97.5: [ 0.02399171 0.68301803 -6.0294829 14.3646756 3.10973175 0.62517371] +2022-09-23 14:39:06,791 - INFO - Simulated matrix lower confidence interval: +[[ nan 13.17041343 0.12145073] + [ 0.05213588 nan nan] + [ nan 12.97604012 0.21352812] + [ 0.07896786 nan nan] + [ 0.10390156 nan nan] + [ nan 12.43165703 0.46493826] + [ 0.17172027 nan nan] + [ 0.2229961 nan nan] + [ nan 11.0838859 1.01555035] + [ 0.28784322 nan nan] + [ 0.37562652 nan nan] + [ nan 9.1626754 1.63070179] + [ 0.48608865 nan nan] + [ nan 7.74914218 2.02062026] + [ 0.61847299 nan nan] + [ nan 5.86844612 2.52892962]] + +2022-09-23 14:39:06,791 - INFO - Simulated matrix higher confidence interval: +[[ nan 14.00958545 0.7124087 ] + [ 0.06696923 nan nan] + [ nan 13.75168719 0.78040378] + [ 0.09663451 nan nan] + [ 0.12297537 nan nan] + [ nan 13.05285235 0.98123203] + [ 0.19224219 nan nan] + [ 0.24332781 nan nan] + [ nan 11.58118827 1.49608368] + [ 0.3078322 nan nan] + [ 0.39609947 nan nan] + [ nan 9.75396605 2.26005682] + [ 0.51322044 nan nan] + [ nan 8.53045454 2.83204401] + [ 0.6596386 nan nan] + [ nan 6.93761616 3.61650414]] + +2022-09-23 14:39:06,791 - INFO - khi2 test results: +khi2 value: 10.465071032170075 Number of measurements: 23 Number of parameters to fit: 6 Degrees of freedom: 17 -p-value = 0.11682969257810068 +p-value = 0.11701547166622563 -2022-08-17 16:42:10,400 - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.11682969257810068 -2022-08-17 16:42:13,065 - INFO - -Configuration file saved in: C:\Users\legregam\Documents\Projets\PhysioFit4Galaxy\data\KEIO_test_data\KEIO_ROBOT6_1\KEIO_ROBOT6_1_res\config_file.json +2022-09-23 14:39:06,791 - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.11701547166622563 +2022-09-23 14:39:09,055 - INFO - +Configuration file saved at: C:\Users\legregam\Documents\Projets\PhysioFit4Galaxy\data\KEIO_test_data\KEIO_ROBOT6_1\KEIO_ROBOT6_1_res\config_file.json diff --git a/data/KEIO_test_data/KEIO_ROBOT6_1/KEIO_ROBOT6_1_res/plots.pdf b/data/KEIO_test_data/KEIO_ROBOT6_1/KEIO_ROBOT6_1_res/plots.pdf index 4cef987..edead13 100644 Binary files a/data/KEIO_test_data/KEIO_ROBOT6_1/KEIO_ROBOT6_1_res/plots.pdf and b/data/KEIO_test_data/KEIO_ROBOT6_1/KEIO_ROBOT6_1_res/plots.pdf differ diff --git a/data/KEIO_test_data/KEIO_ROBOT6_1/KEIO_ROBOT6_1_res/stat_results.tsv b/data/KEIO_test_data/KEIO_ROBOT6_1/KEIO_ROBOT6_1_res/stat_results.tsv index 33d9f2a..56d2a83 100644 --- a/data/KEIO_test_data/KEIO_ROBOT6_1/KEIO_ROBOT6_1_res/stat_results.tsv +++ b/data/KEIO_test_data/KEIO_ROBOT6_1/KEIO_ROBOT6_1_res/stat_results.tsv @@ -2,10 +2,10 @@ KhiČ test results ================== -khi2_value 10.461094 +khi2_value 10.465071 number_of_measurements 23.000000 number_of_params 6.000000 Degrees_of_freedom 17.000000 -p_val 0.116830 +p_val 0.117015 -At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.11682969257810068 \ No newline at end of file +At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.11701547166622563 \ No newline at end of file