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Commit e059aedb authored by gsaxena's avatar gsaxena
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A very small commit, moved the unwanted files outisde top level directory and... 

A very small commit, moved the unwanted files outisde top level directory and into PhysiCell_X_Extra_Files - most probably they will not be needed but still keeping them. It was part of clean-up. Changed the vrsion to 1.9.0 in VERSION.txt, have not changed CITATATION.txt
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GS_functions.txt deleted 100644 → 0
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GS_valgrind_TNF_1K_cells_1_Process.txt deleted 100644 → 0
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cell_variables.tsv deleted 100644 → 0
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time total_volume cell_type cycle_model current_phase elapsed_time_in_phase nuclear_volume cytoplasmic_volume fluid_fraction calcified_fraction x_orientation x_orientation y_orientation x_orientation x_orientation polarity migration_speed x_motility_vector x_motility_vector y_motility_vector x_motility_vector x_motility_vector migration_bias x_motility_bias_direction x_motility_bias_direction y_motility_bias_direction x_motility_bias_direction x_motility_bias_direction persistence_time motility_reserved next_physiboss_run TNFR_binding_rate TNFR_endocytosis_rate TNFR_recycling_rate TNFR_activation_threshold TNFR_receptors_per_cell TNF_net_production_rate tnf_node fadd_node nfkb_node external_tnf divide cycle_rate unbound_external_TNFR bound_external_TNFR bound_internal_TNFR TFN_net_production_rate
0 0 2494.0 0.0 5.0 14.0 0.529296214796025 540.0 1954.0 0.75 0.0 0.03251581560544081 0.0078713255500673 0.024315722535253468 0.03251581560544081 0.0078713255500673 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.24299999999999636 0.12799999999999837 0.29300000000000503 0.5 1.0 0.0 0.0 0.5254833040421792 0.0 0.0 0.0 0.000750000000000004 1.0 0.0 0.0 0.0
1 10 2480.967185009814 0.0 5.0 14.0 10.44910515801023 537.1803041779519 1943.786880831861 0.7499727202489069 0.0 0.03149577946030294 0.0062306614200278495 0.023957907567582412 0.03149577946030294 0.0062306614200278495 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.24299999999999633 0.1279999999999983 0.29300000000000503 0.5 1.0 0.0 0.0 0.5262237762237763 0.0 0.0 0.0 0.0007500000000000041 1.0 0.0 0.0 0.0
2 20 2463.992348481299 0.0 5.0 14.0 20.224971373758816 533.5249287943712 1930.4674196869291 0.7498436599353079 0.0 0.03161975348469197 0.006692989288766963 0.02157097210647273 0.03161975348469197 0.006692989288766963 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.24299999999999633 0.12799999999999823 0.29300000000000503 0.5 1.0 0.0 0.0 0.527367506516073 0.0 0.0 0.0 0.0007500000000000044 1.0 0.0 0.0 0.0
3 30 2430.773895734274 0.0 5.0 14.0 29.482951454798922 526.3757325938988 1904.3981631403756 0.7496010638214239 0.0 0.02854691931465831 0.003948386878375839 0.01907264776487619 0.02854691931465831 0.003948386878375839 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.2429999999999963 0.12799999999999806 0.29300000000000503 0.5 1.0 0.0 0.0 0.5274442538593482 0.0 0.0 0.0 0.0007500000000000046 1.0 0.0 0.0 0.0
4 40 2421.4983139263923 0.0 5.0 14.0 39.17576824242522 524.4458890409182 1897.0524248854754 0.74923606219575 0.0 0.027409410763966576 0.0029534284291068374 0.021494682279429703 0.027409410763966576 0.0029534284291068374 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.2429999999999963 0.127999999999998 0.29300000000000503 0.5 1.0 0.0 0.0 0.5286080273270709 0.0 0.0 0.0 0.0007500000000000047 1.0 0.0 0.0 0.0
5 50 2412.631834335452 0.0 5.0 14.0 48.78821142399595 522.6197473983075 1890.012086937147 0.7488799650486995 0.0 0.027546385867240827 0.0015431478477818067 0.02007522635652047 0.027546385867240827 0.0015431478477818067 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.2429999999999963 0.12799999999999798 0.29300000000000503 0.5 1.0 0.0 0.0 0.5280612244897959 0.0 0.0 0.0 0.0007500000000000048 1.0 0.0 0.0 0.0
6 60 2396.059532886967 0.0 5.0 14.0 57.924154379392775 519.1301131769562 1876.9294197100123 0.7485361706508131 0.0 0.02398843051055608 0.00038659927604193427 0.01900133134666345 0.02398843051055608 0.00038659927604193427 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.2429999999999963 0.12799999999999787 0.2930000000000051 0.5 1.0 0.0 0.0 0.5265822784810127 0.0 0.0 0.0 0.000750000000000005 1.0 0.0 0.0 0.0
7 70 2380.211242177048 0.0 5.0 14.0 66.97804632434926 515.8106816415916 1864.4005605354562 0.7481059947446206 0.0 0.023109040023695036 -0.0023597527261810937 0.01981375884727623 0.023109040023695036 -0.0023597527261810937 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.24299999999999627 0.12799999999999778 0.2930000000000051 0.5 1.0 0.0 0.0 0.525963149078727 0.0 0.0 0.0 0.0007500000000000052 1.0 0.0 0.0 0.0
8 80 2365.0564669546907 0.0 5.0 14.0 75.90886852357987 512.6555552905182 1852.4009116641714 0.7476612788320893 0.0 0.02357751326895822 -0.0032811493036845824 0.020374504288767106 0.02357751326895822 -0.0032811493036845824 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.24299999999999627 0.1279999999999977 0.2930000000000051 0.5 1.0 0.0 0.0 0.5245220282626767 0.0 0.0 0.0 0.0007500000000000053 1.0 0.0 0.0 0.0
9 90 2340.9495925880806 0.0 5.0 14.0 84.11664676529955 507.57054748713006 1833.3790451009509 0.7471303323958576 0.0 0.021906042789236784 -0.001517060729724737 0.017606298596850745 0.021906042789236784 -0.001517060729724737 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.24299999999999625 0.12799999999999756 0.2930000000000051 0.5 1.0 0.0 0.0 0.5283483976992605 0.0 0.0 0.0 0.0007500000000000057 1.0 0.0 0.0 0.0
10 100 2333.093910018274 0.0 5.0 14.0 93.18517515082398 506.02331473579824 1827.0705952824737 0.7465902936257853 0.0 0.022102981869337825 -0.0019630834936961617 0.018617043862767812 0.022102981869337825 -0.0019630834936961617 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.24299999999999625 0.1279999999999975 0.2930000000000051 0.5 1.0 0.0 0.0 0.5257563368765331 0.0 0.0 0.0 0.0007500000000000058 1.0 0.0 0.0 0.0
11 110 2320.1281996052176 0.0 5.0 14.0 101.70456484030747 503.37385760738533 1816.7543419978317 0.7460814544082286 0.0 0.021908151934548033 -0.003338839937010538 0.019238550540017944 0.021908151934548033 -0.003338839937010538 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.24299999999999625 0.12799999999999742 0.29300000000000515 0.5 1.0 0.0 0.0 0.5267857142857143 0.0 0.0 0.0 0.0007500000000000059 1.0 0.0 0.0 0.0
12 120 2304.135738009199 0.0 5.0 14.0 109.72222955199071 500.07306231359155 1804.0626756956071 0.7456243971889877 0.0 0.019063634155847952 -0.00451460379353415 0.017897381881376764 0.019063634155847952 -0.00451460379353415 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.24299999999999622 0.1279999999999973 0.29300000000000515 0.5 1.0 0.0 0.0 0.5237329042638778 0.0 0.0 0.0 0.0007500000000000061 1.0 0.0 0.0 0.0
13 130 2279.687590714928 0.0 5.0 14.0 116.80520917944402 494.9456367732905 1784.7419539416367 0.74510511942423 0.0 0.022194099852511858 -0.0029433249130945754 0.021613296235600148 0.022194099852511858 -0.0029433249130945754 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.24299999999999622 0.12799999999999717 0.29300000000000515 0.5 1.0 0.0 0.0 0.5246422893481717 0.0 0.0 0.0 0.0007500000000000064 1.0 0.0 0.0 0.0
14 140 2267.3212202465425 0.0 5.0 14.0 124.75615825338528 492.45429084268477 1774.8669294038602 0.7445484847559241 0.0 0.0205744123671973 -0.0024989566483684706 0.02089310033958461 0.0205744123671973 -0.0024989566483684706 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.24299999999999622 0.1279999999999971 0.29300000000000515 0.5 1.0 0.0 0.0 0.5228706624605678 0.0 0.0 0.0 0.0007500000000000065 1.0 0.0 0.0 0.0
15 150 2234.838143636916 0.0 5.0 14.0 130.08469335695688 485.6071691351264 1749.2309745017872 0.7440195754631687 0.0 0.024015156496236187 0.0009608872870142146 0.020688382360485046 0.024015156496236187 0.0009608872870142146 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.2429999999999962 0.1279999999999969 0.2930000000000052 0.5 1.0 0.0 0.0 0.5217054263565891 0.0 0.0 0.0 0.000750000000000007 1.0 0.0 0.0 0.0
16 160 2226.2171018264535 0.0 5.0 14.0 138.14731792320916 483.9638205925239 1742.2532812339305 0.743359975100339 0.0 0.024507011787779292 0.0017760072266962594 0.019700845705087098 0.024507011787779292 0.0017760072266962594 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.2429999999999962 0.1279999999999968 0.2930000000000052 0.5 1.0 0.0 0.0 0.5204003079291762 0.0 0.0 0.0 0.0007500000000000071 1.0 0.0 0.0 0.0
17 170 2224.9677112071263 0.0 5.0 14.0 147.00437716101686 483.91955568151184 1741.048155525611 0.7428320334140069 0.0 0.02303700615362476 0.0010889624531146573 0.018645801611503195 0.02303700615362476 0.0010889624531146573 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.24299999999999616 0.12799999999999678 0.2930000000000052 0.5 1.0 0.0 0.0 0.5207055214723927 0.0 0.0 0.0 0.0007500000000000072 1.0 0.0 0.0 0.0
18 180 2220.580998407029 0.0 5.0 14.0 155.32186196575907 483.1840149091201 1737.3969834979075 0.7423953134152993 0.0 0.021753644614599135 -0.0012551966389882884 0.017998009816068514 0.021753644614599135 -0.0012551966389882884 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.24299999999999616 0.12799999999999673 0.2930000000000052 0.5 1.0 0.0 0.0 0.5198473282442748 0.0 0.0 0.0 0.0007500000000000073 1.0 0.0 0.0 0.0
19 190 2220.186896339118 0.0 5.0 14.0 164.05584177090216 483.30486865972017 1736.8820276793974 0.7420207867229845 0.0 0.02272439258824381 -0.0013744914822790334 0.01726589931217209 0.02272439258824381 -0.0013744914822790334 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.24299999999999616 0.1279999999999967 0.2930000000000052 0.5 1.0 0.0 0.0 0.5193916349809886 0.0 0.0 0.0 0.0007500000000000073 1.0 0.0 0.0 0.0
20 200 2203.5177348214224 0.0 5.0 14.0 170.20429171692214 479.87415148228445 1723.6435833391376 0.7416859631414765 0.0 0.022956047147005647 -0.002881517306432352 0.01756097709843449 0.022956047147005647 -0.002881517306432352 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.24299999999999616 0.12799999999999656 0.2930000000000052 0.5 1.0 0.0 0.0 0.5165413533834586 0.0 0.0 0.0 0.0007500000000000076 1.0 0.0 0.0 0.0
21 210 2190.5155278512348 0.0 5.0 14.0 176.86924127359686 477.24910712935923 1713.2664207218832 0.7412655383834714 0.0 0.021482448952045173 -0.0012059319263642222 0.017931674757684046 0.021482448952045173 -0.0012059319263642222 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.24299999999999614 0.12799999999999648 0.2930000000000052 0.5 1.0 0.0 0.0 0.517524235645041 0.0 0.0 0.0 0.0007500000000000077 1.0 0.0 0.0 0.0
22 220 2173.8907522137447 0.0 5.0 14.0 182.91771813233228 473.83455814304136 1700.0561940707016 0.7407109986202515 0.0 0.01817676542098395 -0.0025535090112689452 0.019185335734235004 0.01817676542098395 -0.0025535090112689452 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.24299999999999614 0.12799999999999637 0.29300000000000526 0.5 1.0 0.0 0.0 0.5187914517317612 0.0 0.0 0.0 0.0007500000000000079 1.0 0.0 0.0 0.0
23 230 2175.2917013153196 0.0 5.0 14.0 191.53616671162305 474.35176592523936 1700.9399353900785 0.7402769329065295 0.0 0.019492010797647206 -0.0020825302328922614 0.018416160040886073 0.019492010797647206 -0.0020825302328922614 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.24299999999999614 0.1279999999999963 0.29300000000000526 0.5 1.0 0.0 0.0 0.5172667156502572 0.0 0.0 0.0 0.000750000000000008 1.0 0.0 0.0 0.0
24 240 2169.3648265761603 0.0 5.0 14.0 198.80226389005287 473.26080241040466 1696.1040241657563 0.7398733036439293 0.0 0.019171051007040942 -0.001926053174445983 0.016431672849251965 0.019171051007040942 -0.001926053174445983 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.2429999999999961 0.12799999999999626 0.29300000000000526 0.5 1.0 0.0 0.0 0.5193289569657185 0.0 0.0 0.0 0.0007500000000000081 1.0 0.0 0.0 0.0
25 250 2155.34883889305 0.0 5.0 14.0 204.34551489146887 470.4068599028958 1684.9419789901565 0.7394641940927844 0.0 0.01716357756313239 -0.002829685664465698 0.015047273817149341 0.01716357756313239 -0.002829685664465698 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.2429999999999961 0.12799999999999614 0.29300000000000526 0.5 1.0 0.0 0.0 0.5184381778741866 0.0 0.0 0.0 0.0007500000000000084 1.0 0.0 0.0 0.0
26 260 2159.1121096407114 0.0 5.0 14.0 212.85766148617685 471.41561872337024 1687.6964909173373 0.7392105202592649 0.0 0.014455973537112162 -0.0029699294435071187 0.014381648154525875 0.014455973537112162 -0.0029699294435071187 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.2429999999999961 0.12799999999999612 0.29300000000000526 0.5 1.0 0.0 0.0 0.5191059841384282 0.0 0.0 0.0 0.0007500000000000084 1.0 0.0 0.0 0.0
27 270 2157.2205793802354 0.0 5.0 14.0 220.2473436637959 471.1876455153647 1686.0329338648726 0.739022174191735 0.0 0.015967994562032538 -0.004698677458820418 0.014040140318542735 0.015967994562032538 -0.004698677458820418 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.2429999999999961 0.1279999999999961 0.29300000000000526 0.5 1.0 0.0 0.0 0.5186513629842181 0.0 0.0 0.0 0.0007500000000000085 1.0 0.0 0.0 0.0
28 280 2155.853017331245 0.0 5.0 14.0 227.46209339522596 471.06143923353187 1684.7915780977114 0.738907515017797 0.0 0.015710331660398202 -0.006050347125014229 0.011997692192558742 0.015710331660398202 -0.006050347125014229 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.24299999999999608 0.127999999999996 0.29300000000000526 0.5 1.0 0.0 0.0 0.5178316690442225 0.0 0.0 0.0 0.0007500000000000086 1.0 0.0 0.0 0.0
29 290 2146.9063789216157 0.0 5.0 14.0 233.31222283570744 469.27519967551774 1677.6311792460997 0.7387502171040394 0.0 0.01726509247823571 -0.003893612293510723 0.012168900413075872 0.01726509247823571 -0.003893612293510723 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.24299999999999608 0.12799999999999592 0.29300000000000526 0.5 1.0 0.0 0.0 0.5183875530410184 0.0 0.0 0.0 0.0007500000000000088 1.0 0.0 0.0 0.0
30 300 2144.6676836036227 0.0 5.0 14.0 239.89491220591276 468.94948369460366 1675.7181999090174 0.7386628587840253 0.0 0.017092127247959076 -0.00648747162156472 0.012698421083020061 0.017092127247959076 -0.00648747162156472 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.24299999999999608 0.12799999999999587 0.2930000000000053 0.5 1.0 0.0 0.0 0.5179198875614898 0.0 0.0 0.0 0.0007500000000000089 1.0 0.0 0.0 0.0
31 310 2126.4361198822985 0.0 5.0 14.0 242.97436909755146 465.1256003667841 1661.3105195155126 0.7384946645849986 0.0 0.01481121333157772 -0.006943070486882393 0.011720789449983246 0.01481121333157772 -0.006943070486882393 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.24299999999999605 0.12799999999999573 0.2930000000000053 0.5 1.0 0.0 0.0 0.5190575190575191 0.0 0.0 0.0 0.0007500000000000092 1.0 0.0 0.0 0.0
32 320 2126.5366341042186 0.0 5.0 14.0 250.34055461541152 465.318120668688 1661.218513435532 0.7382118187360811 0.0 0.01410637666347532 -0.005514189763653184 0.012511637344719793 0.01410637666347532 -0.005514189763653184 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.24299999999999605 0.12799999999999567 0.2930000000000053 0.5 1.0 0.0 0.0 0.5155065472088215 0.0 0.0 0.0 0.0007500000000000093 1.0 0.0 0.0 0.0
33 330 2119.6735442581275 0.0 5.0 14.0 255.55290443086594 463.9823799093134 1655.691164348816 0.7380060012972245 0.0 0.01694692983236693 -0.004616678604293777 0.012619718945900714 0.01694692983236693 -0.004616678604293777 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.24299999999999605 0.1279999999999956 0.2930000000000053 0.5 1.0 0.0 0.0 0.5157103825136612 0.0 0.0 0.0 0.0007500000000000094 1.0 0.0 0.0 0.0
34 340 2117.5175380222868 0.0 5.0 14.0 261.7916612553309 463.6720526754736 1653.8454853468138 0.7378473246241571 0.0 0.015087167779087585 -0.007603552726348875 0.012264380652807686 0.015087167779087585 -0.007603552726348875 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.24299999999999605 0.12799999999999553 0.2930000000000053 0.5 1.0 0.0 0.0 0.5169606512890095 0.0 0.0 0.0 0.0007500000000000096 1.0 0.0 0.0 0.0
35 350 2117.1298565495154 0.0 5.0 14.0 268.2858142041286 463.73347140437244 1653.3963851451472 0.7377670058369168 0.0 0.011985096890743167 -0.006849457330594265 0.012562689829325839 0.011985096890743167 -0.006849457330594265 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.24299999999999602 0.12799999999999548 0.2930000000000053 0.5 1.0 0.0 0.0 0.5138419986495611 0.0 0.0 0.0 0.0007500000000000097 1.0 0.0 0.0 0.0
36 360 2117.2029967570625 0.0 5.0 14.0 274.8066235920904 463.8833860283618 1653.3196107287033 0.737683767649573 0.0 0.010510275387794909 -0.008021215532070166 0.012127469361923313 0.010510275387794909 -0.008021215532070166 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.24299999999999602 0.12799999999999542 0.2930000000000053 0.5 1.0 0.0 0.0 0.5134408602150538 0.0 0.0 0.0 0.0007500000000000098 1.0 0.0 0.0 0.0
37 370 2119.9619547869993 0.0 5.0 14.0 282.06235970782086 464.621366367821 1655.340588419183 0.7376067807693153 0.0 0.010147973770513586 -0.008494070636350387 0.01381532088063958 0.010147973770513586 -0.008494070636350387 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.24299999999999602 0.1279999999999954 0.2930000000000053 0.5 1.0 0.0 0.0 0.5140562248995983 0.0 0.0 0.0 0.0007500000000000099 1.0 0.0 0.0 0.0
38 380 2119.7186256739456 0.0 5.0 14.0 288.2732060903204 464.7000827351337 1655.0185429388075 0.7375975750498128 0.0 0.011812883847591762 -0.007907454983161368 0.016322335310028767 0.011812883847591762 -0.007907454983161368 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.24299999999999602 0.12799999999999534 0.29300000000000537 0.5 1.0 0.0 0.0 0.5126498002663116 0.0 0.0 0.0 0.00075000000000001 1.0 0.0 0.0 0.0
39 390 2121.282499710806 0.0 5.0 14.0 295.34217349012096 465.1623773863697 1656.120122324439 0.737539165065179 0.0 0.012694917065521578 -0.005572742729490956 0.017579139060698253 0.012694917065521578 -0.005572742729490956 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.24299999999999602 0.12799999999999528 0.29300000000000537 0.5 1.0 0.0 0.0 0.5132450331125827 0.0 0.0 0.0 0.00075000000000001 1.0 0.0 0.0 0.0
40 400 2121.481323840121 0.0 5.0 14.0 301.8444412433197 465.3140721467163 1656.167251693402 0.7375601939637682 0.0 0.011971992408403876 -0.00503514687560739 0.018353367762623383 0.011971992408403876 -0.00503514687560739 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 10.0 0.242999999999996 0.12799999999999523 0.29300000000000537 0.5 1.0 0.0 0.0 0.5128373930217248 0.0 0.0 0.0 0.0007500000000000101 1.0 0.0 0.0 0.0
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summarize_simulation.py deleted 100755 → 0
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#!/usr/bin/env python
# coding: utf-8
import re
import os
import sys
import numpy as np
import pandas as pd
import xml.dom.minidom
import matplotlib.pyplot as plt
from multicellds import MultiCellDS
pd.options.mode.chained_assignment = None
def get_timeserie_mean(mcds, filter_alive=True):
time = []
values = []
filter_alive = True
for t, df in mcds.cells_as_frames_iterator():
time.append(t)
df = df.iloc[:,3:]
if filter_alive:
mask = df['current_phase'] <= 14
df = df[mask]
values.append(df.mean(axis=0).values)
cell_columns = df.columns.tolist()
df = pd.DataFrame(values, columns=cell_columns)
df['time'] = time
return df[['time'] + cell_columns]
def get_timeserie_density(mcds):
data = []
for t,m in mcds.microenvironment_as_matrix_iterator():
data.append((t, m[5,:].sum()))
df = pd.DataFrame(data=data, columns=['time', 'tnf'])
return df
def plot_molecular_model(df_cell_variables, list_of_variables, ax1):
threshold = 0.5
for label in list_of_variables:
y = df_cell_variables[label]
time = df_cell_variables["time"]
ax1.plot(time, y, label="% X " + label)
ax1.set_ylabel("% X")
ax1.yaxis.grid(True)
ax1.set_xlim((0,time.values[-1]))
ax1.set_ylim((0,1.1))
# ax1.set_xlabel("time (min)")
def plot_cells(df_time_course, color_dict, ax):
# Alive/Apoptotic/Necrotic vs Time
for k in color_dict:
ax.plot(df_time_course.time, df_time_course[k], "-", c=color_dict[k], label=k)
# setting axes labels
# ax.set_xlabel("time (min)")
ax.set_ylabel("Nº of cells")
# Showing legend
ax.legend()
ax.yaxis.grid(True)
def main():
color_dict = {"alive": "g", "apoptotic": "r", "necrotic":"k"}
setting_file= sys.argv[1]
instance_folder = "./"
doc = xml.dom.minidom.parse(setting_file)
custom_data = doc.getElementsByTagName("TNFR_binding_rate")
k1 = custom_data[0].firstChild.nodeValue
custom_data = doc.getElementsByTagName("TNFR_endocytosis_rate")
k2 = custom_data[0].firstChild.nodeValue
custom_data = doc.getElementsByTagName("TNFR_recycling_rate")
k3 = custom_data[0].firstChild.nodeValue
output_data = instance_folder + 'output/'
mcds = MultiCellDS(output_folder=output_data)
df_time_course = mcds.get_cells_summary_frame()
df_cell_variables = get_timeserie_mean(mcds)
df_time_tnf = get_timeserie_density(mcds)
df_time_course.to_csv(instance_folder + "time_course.tsv", sep="\t")
df_cell_variables.to_csv(instance_folder + "cell_variables.tsv", sep="\t")
df_time_tnf.to_csv(instance_folder + "tnf_time.tsv", sep="\t")
fig, axes = plt.subplots(3, 1, figsize=(12,12), dpi=150, sharex=True)
plot_cells(df_time_course, color_dict, axes[0])
list_of_variables = ['bound_external_TNFR', 'unbound_external_TNFR', 'bound_internal_TNFR']
plot_molecular_model(df_cell_variables, list_of_variables, axes[1])
threshold = 0.5
axes[1].hlines(threshold, 0, df_time_course.time.iloc[-1], label="Activation threshold")
ax2 = axes[1].twinx()
ax2.plot(df_time_tnf.time, df_time_tnf['tnf'], 'r', label="[TNF]")
ax2.set_ylabel("[TNF]")
#ax2.set_ylim([0, 1000])
axes[1].legend(loc="upper left")
ax2.legend(loc="upper right")
list_of_variables = ['tnf_node', 'nfkb_node', 'fadd_node']
plot_molecular_model(df_cell_variables, list_of_variables, axes[2])
axes[2].set_xlabel("time (min)")
ax2 = axes[2].twinx()
ax2.plot(df_time_tnf.time, df_time_tnf['tnf'], 'r', label="[TNF]")
ax2.set_ylabel("[TNF]")
#ax2.set_ylim([0, 1000])
axes[2].legend(loc="upper left")
ax2.legend(loc="upper right")
fig.suptitle('k_1:{}, k_2:{}, k_3:{}'.format(k1,k2,k3))#, fontsize=16)
fig.tight_layout()
fig.savefig(instance_folder + 'variables_vs_time.png')
s = instance_folder.split('/')
dirname = os.path.dirname(__file__)
persistpath = os.path.join(instance_folder, '..','figures')
if not os.path.exists(persistpath):
os.makedirs(persistpath)
fig.savefig(os.path.join(persistpath, s[-2]+'variables_vs_time.png'))
df_time_course.to_csv(os.path.join(persistpath, s[-2]+"time_course.tsv"), sep="\t")
df_cell_variables.to_csv(os.path.join(persistpath, s[-2]+"cell_variables.tsv"), sep="\t")
df_time_tnf.to_csv(os.path.join(persistpath, s[-2]+"tnf_time.tsv"), sep="\t")
k_df = pd.DataFrame([[k1, k2, k3]], columns = ['k1', 'k2', 'k3'])
k_df.to_csv(os.path.join(persistpath, s[-2]+"ki_values.tsv"), sep="\t")
main()
time_course.tsv deleted 100644 → 0
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time alive necrotic apoptotic
0 0 1138 0 0
1 10 1144 0 0
2 20 1151 0 1
3 30 1166 0 2
4 40 1171 0 2
5 50 1176 0 2
6 60 1185 0 2
7 70 1194 0 2
8 80 1203 0 2
9 90 1217 0 2
10 100 1223 0 2
11 110 1232 0 2
12 120 1243 0 2
13 130 1258 0 3
14 140 1268 0 3
15 150 1290 0 3
16 160 1299 0 3
17 170 1304 0 3
18 180 1310 0 4
19 190 1315 0 4
20 200 1330 0 4
21 210 1341 0 6
22 220 1357 0 6
23 230 1361 0 7
24 240 1371 0 7
25 250 1383 0 10
26 260 1387 0 11
27 270 1394 0 12
28 280 1402 0 12
29 290 1414 0 13
30 300 1423 0 13
31 310 1443 0 13
32 320 1451 0 13
33 330 1464 0 13
34 340 1474 0 13
35 350 1481 0 15
36 360 1488 0 17
37 370 1494 0 18
38 380 1502 0 19
39 390 1510 0 19
40 400 1519 0 19
tnf_time.tsv deleted 100644 → 0
View file @ 479ed9f1
time tnf
0 0 0.0
1 10 15.959563453806751
2 20 12.129413783667768
3 30 9.21339680420142
4 40 6.998415767295248
5 50 5.315935511384067
6 60 15.959563454763396
7 70 12.122745052078132
8 80 9.208331293912803
9 90 6.994568049908638
10 100 5.313012818852876
11 110 15.959563454683625
12 120 12.136086185070273
13 130 9.218465102047844
14 140 7.002265602086429
15 150 5.3188598122772826
16 160 15.959563454763924
17 170 12.122745052078532
18 180 9.208331293913107
19 190 6.994568049908869
20 200 5.31301281885305
21 210 15.95956345476287
22 220 12.122745052077732
23 230 9.2083312939125
24 240 6.994568049908407
25 250 5.3130128188527
26 260 15.95956345476287
27 270 12.129413784365287
28 280 9.213396804731246
29 290 6.9984157676977
30 300 5.315935511689764
31 310 15.959563454763396
32 320 12.12941378436567
33 330 9.213396804731538
34 340 6.998415767697921
35 350 5.315935511689933
36 360 15.959563454684172
37 370 12.136086185070656
38 380 9.218465102048137
39 390 7.00226560208665
40 400 5.31885981227745
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