# HG changeset patch
# User iuc
# Date 1754333868 0
# Node ID c78f852b1a458753e2f1f5308179ea516d5c4b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
diff -r 000000000000 -r c78f852b1a45 README.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.txt Mon Aug 04 18:57:48 2025 +0000
@@ -0,0 +1,23 @@
+pcdl
+====
+
+Galaxy wrapper for the pcdl PhysiCell Data Loader command line commands.
+Pcdl is paramount for downstream analysis from PhysiCell output.
+As such, the pcdl Galaxy tools are useful if you work with the interactive
+PhysiCell Studio Galaxy tool.
++ https://usegalaxy.eu/?tool_id=interactive_tool_pcstudio&version=latest
+
+You will have to unzip the PhysiCell output folder before you can run
+pcdl Galaxy tools on it.
++ https://usegalaxy.eu/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimgteam%2Funzip%2Funzip%2F6.0%2Bgalaxy0&version=latest
++ https://usegalaxy.org/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frheiland%2Fphysicell_studio%2Finteractive_tool_pcstudio%2F0.3&version=latest
+
+More information about PhysiCell, PhysiCell Studio, and PhysiCell Data Loader
+can be found here:
++ https://physicell.org/index.html
++ https://physicell-studio.readthedocs.io/en/latest/index.html
++ https://github.com/elmbeech/physicelldataloader
+
+Date: 2025-06-06
+License: BSD-3-Clause
+Author: Elmar Bucher
diff -r 000000000000 -r c78f852b1a45 pcdl_get_anndata.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/pcdl_get_anndata.xml Mon Aug 04 18:57:48 2025 +0000
@@ -0,0 +1,128 @@
+
+
+ pcdl_macros.xml
+
+
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diff -r 000000000000 -r c78f852b1a45 pcdl_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/pcdl_macros.xml Mon Aug 04 18:57:48 2025 +0000
@@ -0,0 +1,444 @@
+
+
+
+ pcdl
+
+
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+
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+ ^[enoENO0-9-. ]*$
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+
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+ ^[enoENO0-9-. ]*$
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+
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+ ^[enoENO0-9-. ]*$
+
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+
+
+ @misc{githubphysicelldataloader,
+ author = {Bucher, Elmar},
+ year = {2025},
+ title = {physicelldataloader},
+ publisher = {GitHub},
+ journal = {GitHub repository},
+ url = {https://github.com/elmbeech/physicelldataloader},
+ }
+
+
diff -r 000000000000 -r c78f852b1a45 test-data/PhysiCell_settings.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/PhysiCell_settings.xml Mon Aug 04 18:57:48 2025 +0000
@@ -0,0 +1,405 @@
+
+
+
+ -30
+ 300
+ -20
+ 200
+ -10
+ 100
+ 30
+ 20
+ 10
+ false
+
+
+
+ 1440.0
+ min
+ micron
+ 0.01
+ 0.1
+ 6
+
+
+
+ 1
+
+
+
+ output
+
+ 60
+ true
+
+
+
+ false
+
+
+
+
+ false
+ true
+ false
+ 0
+
+
+
+
+
+ 1e3
+ 1
+
+ 1e3
+ 0.0
+
+
+
+
+
+
+
+
+
+
+
+ 1e6
+ 0.001
+
+ 1e3
+ 1e3
+
+ 1e3
+ 1e3
+ 1e3
+ 1e3
+ 1e3
+ 1e3
+
+
+
+ true
+ true
+
+ ./config/initial.mat
+
+
+ ./config/dirichlet.mat
+
+
+
+
+
+
+
+
+
+ 0.003333
+ 0.002083
+ 0.004167
+ 0.016667
+
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+
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+ 5.31667e-05
+
+ 516
+
+
+ 0.05
+ 0
+ 1.66667e-02
+ 5.83333e-03
+ 0
+ 2.0
+
+
+
+ 0.0
+
+ 0
+ 86400
+
+
+ 1.11667e-2
+ 8.33333e-4
+ 5.33333e-5
+ 2.16667e-3
+ 0
+ 2.0
+
+
+
+
+ 2494
+ 0.75
+ 540
+ 0.05
+ 0.0045
+ 0.0055
+ 0
+ 0
+ 2.0
+
+
+ 0.4
+ 10.0
+ 1.25
+
+ 1.0
+ 1
+
+
+ 1.8
+ 15.12
+
+ 0.01
+ 0.05
+ 0.03
+ 12
+
+
+ 1
+ 1
+ .2
+
+ true
+ true
+
+ true
+ oxygen
+ 1
+
+
+ false
+ false
+
+ 0.0
+ 0.0
+
+
+
+
+
+
+ 0
+ 0
+ 10
+ 0.0
+
+
+ 5
+ 15
+ 0
+ 0
+
+
+
+ 0.0
+ 0.0
+ 0.0
+
+ 0.001
+ 0.0
+
+
+ 0.0025
+ 0.0
+
+ 1.0
+ 0.1
+
+ 0.0
+ 0.005
+
+
+
+
+ 0.0
+ 0.0
+
+
+
+ 0.0
+ 0.0
+
+
+
+ 1.0
+
+
+
+
+
+
+
+
+ 1388.888889
+
+
+
+
+ 5.31667e-05
+
+ 0.001938
+
+
+ 0.05
+ 0
+ 1.66667e-02
+ 5.83333e-03
+ 0
+ 2.0
+
+
+
+ 0.0
+
+ 9000000000.0
+ 1.15741e-05
+
+
+ 1.11667e-02
+ 8.33333e-4
+ 5.33333e-05
+ 2.16667e-4
+ 7e-05
+ 2.0
+
+
+
+
+ 2494
+ 0.75
+ 540
+ 0.05
+ 0.0045
+ 0.0055
+ 0.0
+ 0.0
+ 2
+
+
+ 0.4
+ 10.0
+ 1.25
+
+ 1.0
+ 1.0
+
+
+ 1.8
+ 15.12
+
+ 0.01
+ 0.0
+ 0.0
+ 12
+
+
+ 2.5
+ 1.0
+ .5
+
+ true
+ true
+
+ true
+ water
+ 1
+
+
+ false
+ false
+
+ 0.0
+ 0.0
+
+
+
+
+
+
+ 1000
+ 50000
+ 0
+ 0.0
+
+
+ 0
+ 1.0
+ 10
+ 0.0
+
+
+
+ 0.0
+ 0.0
+ 0.0
+
+ 0.0
+ 0.0005
+
+
+ 0
+ 0.006
+
+ 1.0
+ 0.1
+
+ 0.0
+ 0.0
+
+
+
+
+ 0.0
+ 0.0
+
+
+
+ 0.0
+ 0.0
+
+
+
+ 0.0
+
+
+
+
+
+
+
+
+ ./config
+ cells.csv
+
+
+
+
+
+
+ ./config
+ cell_rules.csv
+
+
+
+
+
+
+ 0
+ 64
+
+
diff -r 000000000000 -r c78f852b1a45 test-data/final.svg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/final.svg Mon Aug 04 18:57:48 2025 +0000
@@ -0,0 +1,153 @@
+
+
+
diff -r 000000000000 -r c78f852b1a45 test-data/final.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/final.xml Mon Aug 04 18:57:48 2025 +0000
@@ -0,0 +1,168 @@
+
+
+
+
+ PhysiCell
+ 1.14.1
+ http://physicell.org
+
+
+ 0000-0002-9925-0151
+ Paul
+ Macklin
+ macklinp@iu.edu
+ http://MathCancer.org
+ Indiana University & PhysiCell Project
+ Intelligent Systems Engineering
+
+
+
+ A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin. PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellular Systems, PLoS Comput. Biol. 14(2): e1005991, 2018. DOI: 10.1371/journal.pcbi.1005991
+ 10.1371/journal.pcbi.1005991
+ https://dx.doi.org/PMC5841829
+ 29474446
+ PMC5841829
+
+
+
+
+ 1440.010000
+ 10.548248
+ 2025-01-05T08:14:42Z
+ 2025-01-05T08:14:42Z
+
+
+
+
+ -30.000000 -20.000000 -10.000000 300.000000 200.000000 100.000000
+ -15 15 45 75 105 135 165 195 225 255 285
+ -10 10 30 50 70 90 110 130 150 170 190
+ -5 5 15 25 35 45 55 65 75 85 95
+
+ initial_mesh0.mat
+
+
+
+
+
+
+ 1000.000000
+ 1.000000
+
+
+
+
+
+ 1000000.000000
+ 0.001000
+
+
+
+
+ final_microenvironment0.mat
+
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+ default
+ blood_cells
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+ final_cells.mat
+
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+ final_cell_neighbor_graph.txt
+
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+ final_attached_cells_graph.txt
+
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+ final_spring_attached_cells_graph.txt
+
+
+
+
+
+
diff -r 000000000000 -r c78f852b1a45 test-data/final_attached_cells_graph.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/final_attached_cells_graph.txt Mon Aug 04 18:57:48 2025 +0000
@@ -0,0 +1,153 @@
+210:
+1:
+221:
+225:
+211:
+206:
+108:
+230:
+164:
+152:
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+185:
+159:
+229:
+242:
+17:
+102:
+161:
+217:
+115:
+135:
+160:
+239:
+244:
+106:
+181:
+120:
+112:
+188:
+116:
+125:
+158:
+136:
+186:
+139:
+190:
+124:
+226:
+132:
+238:
+142:
+228:
+148:
+153:
+145:
+123:
+48:
+154:
+131:
+51:
+215:
+127:
+216:
+144:
+130:
+57:
+214:
+121:
+180:
+61:
+163:
+227:
+64:
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+67:
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+69:
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+114:
+75:
+76:
+241:
+78:
+79:
+150:
+81:
+82:
+83:
+84:
+151:
+119:
+87:
+88:
+89:
+90:
+91:
+92:
+93:
+94:
+95:
+96:
+97:
+98:
+149:
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+147:
+156:
+157:
+165:
+166:
+167:
+168:
+169:
+170:
+171:
+172:
+173:
+174:
+175:
+177:
+182:
+183:
+184:
+187:
+218:
+245:
+194:
+195:
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+243:
+199:
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+202:
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+204:
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+207:
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+219:
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+231:
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+234:
+235:
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+246:
+247:
+248:
+249:
+250:
+251:
+252:
\ No newline at end of file
diff -r 000000000000 -r c78f852b1a45 test-data/final_cell_neighbor_graph.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/final_cell_neighbor_graph.txt Mon Aug 04 18:57:48 2025 +0000
@@ -0,0 +1,153 @@
+210:
+1:
+221:
+225: 195
+211:
+206: 158,217
+108: 17
+230: 180,96,188
+164: 48
+152:
+213:
+137: 218,51
+143: 102
+185:
+159:
+229: 250,139
+242: 204
+17: 243,108
+102: 143
+161: 214,94
+217: 206
+115: 195,226
+135:
+160: 97
+239: 124
+244: 170
+106:
+181: 57
+120: 168,240
+112:
+188: 230
+116:
+125: 158,182
+158: 206,125
+136: 87
+186: 134
+139: 151,229
+190:
+124: 239
+226: 115,90
+132:
+238:
+142:
+228: 72
+148:
+153: 95
+145:
+123: 169
+48: 164
+154:
+131:
+51: 137,236,247
+215:
+127: 207,157
+216:
+144: 173
+130:
+57: 181,98
+214: 161,94,202,165
+121: 209
+180: 230
+61:
+163:
+227: 150
+64: 252,194
+65:
+138: 204
+67:
+134: 186
+69: 209
+70:
+71:
+72: 228
+73: 183,96
+114:
+75:
+76:
+241:
+78: 249,194
+79:
+150: 227
+81: 209
+82:
+83:
+84: 243
+151: 139
+119:
+87: 136
+88:
+89:
+90: 226
+91: 165
+92:
+93:
+94: 161,235,214
+95: 153
+96: 230,73
+97: 160
+98: 183,57
+149:
+146:
+147: 170,171
+156: 197
+157: 248,127
+165: 91,214
+166: 251,209
+167: 184
+168: 120
+169: 123
+170: 147,244
+171: 147
+172:
+173: 177,144
+174:
+175:
+177: 173
+182: 125
+183: 98,73
+184: 167
+187:
+218: 137
+245:
+194: 78,249,64,224
+195: 115,225
+197: 156
+243: 17,84
+199:
+200:
+201:
+202: 214
+212:
+204: 138,242
+205:
+207: 127
+208:
+209: 166,251,81,69,121
+219:
+224: 249,194
+231:
+232:
+233:
+234:
+235: 94
+236: 51,247
+237:
+240: 120
+246:
+247: 236,51
+248: 157
+249: 78,194,224
+250: 229
+251: 166,209
+252: 64
\ No newline at end of file
diff -r 000000000000 -r c78f852b1a45 test-data/final_cells.mat
Binary file test-data/final_cells.mat has changed
diff -r 000000000000 -r c78f852b1a45 test-data/final_microenvironment0.mat
Binary file test-data/final_microenvironment0.mat has changed
diff -r 000000000000 -r c78f852b1a45 test-data/final_spring_attached_cells_graph.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/final_spring_attached_cells_graph.txt Mon Aug 04 18:57:48 2025 +0000
@@ -0,0 +1,153 @@
+210:
+1:
+221:
+225:
+211:
+206:
+108: 17
+230: 96,160
+164: 48
+152:
+213:
+137: 51
+143:
+185:
+159:
+229:
+242:
+17: 108,243
+102:
+161:
+217:
+115:
+135:
+160: 230
+239: 184
+244:
+106:
+181:
+120:
+112:
+188:
+116:
+125:
+158:
+136:
+186:
+139:
+190:
+124:
+226:
+132:
+238:
+142:
+228:
+148:
+153:
+145:
+123:
+48: 164
+154:
+131:
+51: 247,137
+215:
+127:
+216:
+144:
+130:
+57: 98
+214: 165,94
+121: 209
+180:
+61:
+163:
+227: 150
+64:
+65:
+138:
+67:
+134:
+69:
+70:
+71:
+72:
+73: 183
+114:
+75:
+76:
+241:
+78: 194
+79:
+150: 227
+81: 209
+82:
+83:
+84:
+151:
+119:
+87:
+88:
+89:
+90:
+91:
+92:
+93:
+94: 214
+95:
+96: 230
+97:
+98: 57
+149:
+146:
+147:
+156:
+157:
+165: 214
+166:
+167: 184
+168:
+169:
+170:
+171:
+172:
+173:
+174:
+175:
+177:
+182:
+183: 73
+184: 167,239
+187:
+218:
+245:
+194: 78
+195:
+197:
+243: 17
+199:
+200:
+201:
+202:
+212:
+204:
+205:
+207:
+208:
+209: 121,251,81
+219:
+224:
+231:
+232:
+233:
+234:
+235:
+236:
+237:
+240:
+246:
+247: 51
+248:
+249:
+250:
+251: 209
+252:
\ No newline at end of file
diff -r 000000000000 -r c78f852b1a45 test-data/initial.svg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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+ http://MathCancer.org
+ Indiana University & PhysiCell Project
+ Intelligent Systems Engineering
+
+
+
+ A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin. PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellular Systems, PLoS Comput. Biol. 14(2): e1005991, 2018. DOI: 10.1371/journal.pcbi.1005991
+ 10.1371/journal.pcbi.1005991
+ https://dx.doi.org/PMC5841829
+ 29474446
+ PMC5841829
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diff -r 000000000000 -r c78f852b1a45 test-data/initial_attached_cells_graph.txt
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diff -r 000000000000 -r c78f852b1a45 test-data/output00000000.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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+ http://MathCancer.org
+ Indiana University & PhysiCell Project
+ Intelligent Systems Engineering
+
+
+
+ A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin. PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellular Systems, PLoS Comput. Biol. 14(2): e1005991, 2018. DOI: 10.1371/journal.pcbi.1005991
+ 10.1371/journal.pcbi.1005991
+ https://dx.doi.org/PMC5841829
+ 29474446
+ PMC5841829
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diff -r 000000000000 -r c78f852b1a45 test-data/output00000000_attached_cells_graph.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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\ No newline at end of file
diff -r 000000000000 -r c78f852b1a45 test-data/output00000000_cell_neighbor_graph.txt
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diff -r 000000000000 -r c78f852b1a45 test-data/output00000000_cells.mat
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diff -r 000000000000 -r c78f852b1a45 test-data/output00000001.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output00000001.xml Mon Aug 04 18:57:48 2025 +0000
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+ macklinp@iu.edu
+ http://MathCancer.org
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+ Intelligent Systems Engineering
+
+
+
+ A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin. PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellular Systems, PLoS Comput. Biol. 14(2): e1005991, 2018. DOI: 10.1371/journal.pcbi.1005991
+ 10.1371/journal.pcbi.1005991
+ https://dx.doi.org/PMC5841829
+ 29474446
+ PMC5841829
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\ No newline at end of file
diff -r 000000000000 -r c78f852b1a45 test-data/output00000001_cell_neighbor_graph.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output00000001_cell_neighbor_graph.txt Mon Aug 04 18:57:48 2025 +0000
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\ No newline at end of file
diff -r 000000000000 -r c78f852b1a45 test-data/output00000001_cells.mat
Binary file test-data/output00000001_cells.mat has changed
diff -r 000000000000 -r c78f852b1a45 test-data/output00000001_microenvironment0.mat
Binary file test-data/output00000001_microenvironment0.mat has changed
diff -r 000000000000 -r c78f852b1a45 test-data/output00000001_oxygen.jpeg
Binary file test-data/output00000001_oxygen.jpeg has changed
diff -r 000000000000 -r c78f852b1a45 test-data/output00000001_spring_attached_cells_graph.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output00000001_spring_attached_cells_graph.txt Mon Aug 04 18:57:48 2025 +0000
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\ No newline at end of file
diff -r 000000000000 -r c78f852b1a45 test-data/timeseries_cell_attribute_minmax.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/timeseries_cell_attribute_minmax.json Mon Aug 04 18:57:48 2025 +0000
@@ -0,0 +1,1 @@
+{"apoptotic_phagocytosis_rate": [0.0, 0.0], "asymmetric_division_probabilities_000": [0.0, 0.0], "asymmetric_division_probabilities_001": [0.0, 0.0], "attachment_elastic_constant": [0.01, 0.01], "attachment_rate": [0.0, 0.05], "attack_damage_rate": [1.0, 1.0], "attack_duration": [0.1, 0.1], "attack_target": [-1.0, -1.0], "attack_total_damage_delivered": [0.0, 0.20000000000003126], "blood_cells_attack_rates": [0.0, 0.0025], "blood_cells_cell_adhesion_affinities": [1.0, 1.0], "blood_cells_fusion_rates": [0.0, 0.0], "blood_cells_immunogenicities": [1.0, 1.0], "blood_cells_live_phagocytosis_rates": [0.0, 0.001], "blood_cells_transformation_rates": [0.0, 0.0], "calcification_rate": [0.0, 0.0], "calcified_fraction": [0.0, 0.0], "cell_BM_adhesion_strength": [4.0, 4.0], "cell_BM_repulsion_strength": [100.0, 100.0], "cell_cell_adhesion_strength": [0.4, 0.4], "cell_cell_repulsion_strength": [10.0, 10.0], "cell_count_voxel": [1, 2], "cell_density_micron3": [0.00016666666666666666, 0.0003333333333333333], "cell_type": ["blood_cells", "default"], "chemotaxis_direction": [1.0, 1.0], "chemotaxis_index": ["oxygen", "water"], "contact_with_basement_membrane": [false], "current_cycle_phase_exit_rate": [0.0007199999999424, 0.003333], "current_death_model": ["0"], "current_phase": ["G0G1_phase", "S_phase", "apoptotic", "live"], "cycle_model": ["apoptosis_death_model", "flow_cytometry_separated_cycle_model", "live_cells_cycle_model"], "cytoplasmic_biomass_change_rate": [0.0045, 0.0166667], "cytoplasmic_volume": [983.5947499999987, 5862.0], "damage": [0.0, 0.20000000000003126], "damage_rate": [0.0, 0.0], "damage_repair_rate": [0.0, 0.0], "dead": [false, true], "death_rates_0": [5.31667e-05, 5.31667e-05], "death_rates_1": [0.0, 0.0], "default_attack_rates": [0.0, 0.006], "default_cell_adhesion_affinities": [1.0, 1.0], "default_fusion_rates": [0.0, 0.005], "default_immunogenicities": [1.0, 1.0], "default_live_phagocytosis_rates": [0.0, 0.0005], "default_transformation_rates": [0.0, 0.0], "detachment_rate": [0.0, 0.03], "elapsed_time_in_phase": [0.0, 59.999999999997826], "fluid_change_rate": [0.05, 0.05], "fluid_fraction": [0.6373991145328126, 0.7569238623013873], "is_motile": [false, true], "maximum_number_of_attachments": [12, 12], "migration_bias": [0.2, 0.5], "migration_bias_direction_vectorlength": [0.0, 1.0], "migration_bias_direction_x": [-1.0, 1.0], "migration_bias_direction_y": [-1.0, 1.0], "migration_bias_direction_z": [-1.0, 1.0], "migration_speed": [1.0, 2.5], "motility_vector_vectorlength": [0.0, 2.5000000000000004], "motility_vector_x": [-2.486793550458016, 2.455852993003917], "motility_vector_y": [-2.4966742471817582, 2.2730577339090874], "motility_vector_z": [-2.1068935111770823, 1.8946060981594308], "necrotic_phagocytosis_rate": [0.0, 0.0], "nuclear_biomass_change_rate": [0.0055, 0.00583333], "nuclear_radius": [4.020509832078209, 7.285770189015841], "nuclear_volume": [272.22749999999957, 1620.0], "number_of_nuclei": [1, 3], "orientation_vectorlength": [0.9999999999999999, 1.0], "orientation_x": [-0.9998198763652759, 0.9881209318256264], "orientation_y": [-0.9923765290928437, 0.9980932470125923], "orientation_z": [-0.9988291520969345, 0.9995130292635848], "other_dead_phagocytosis_rate": [0.0, 0.0], "oxygen": [680.3846029534271, 49664.8227525245], "oxygen_chemotactic_sensitivities": [0.0, 0.0], "oxygen_decay_rate": [1.0, 1.0], "oxygen_diffusion_coefficient": [1000.0, 1000.0], "oxygen_fraction_released_at_death": [0.0, 0.0], "oxygen_fraction_transferred_when_ingested": [1.0, 1.0], "oxygen_internalized_total_substrates": [-114595021520.99211, 29061231019.999565], "oxygen_net_export_rates": [0.0, 0.0], "oxygen_saturation_densities": [0.0, 50000.0], "oxygen_secretion_rates": [0.0, 1000.0], "oxygen_uptake_rates": [0.0, 10.0], "persistence_time": [1.0, 1.0], "polarity": [0.0, 0.0], "position_vectorlength": [15.702462882974425, 320.2332747956235], "pressure": [0.0, 3.477442475942624], "radius": [6.692882306092925, 12.133228172907586], "relative_maximum_adhesion_distance": [1.25, 1.25], "sample": [0.0, 1.0], "surface_area": [562.906469544556, 1849.9610886837118], "target_fluid_fraction": [0.0, 0.75], "target_solid_cytoplasmic": [0.0, 1465.5], "target_solid_nuclear": [0.0, 405.0], "total_attack_time": [0.0, 0.20000000000003126], "total_volume": [1255.8222499999983, 7482.0], "velocity_vectorlength": [0.0, 0.0], "velocity_x": [0.0, 0.0], "velocity_y": [0.0, 0.0], "velocity_z": [0.0, 0.0], "water": [937.8055019681188, 1000.0], "water_chemotactic_sensitivities": [0.0, 0.0], "water_decay_rate": [0.001, 0.001], "water_diffusion_coefficient": [1000000.0, 1000000.0], "water_fraction_released_at_death": [0.0, 0.0], "water_fraction_transferred_when_ingested": [1.0, 1.0], "water_internalized_total_substrates": [0.0, 2109883578.3197234], "water_net_export_rates": [0.0, 0.0], "water_saturation_densities": [1.0, 15.0], "water_secretion_rates": [0.0, 5.0], "water_uptake_rates": [0.0, 10.0]}
\ No newline at end of file