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add new model Liu_IFACPapersOnLine2025 (#260)
* add the petab files for Liu_IFACPapersOnLine2025 * add individual based age of infection model in the subfolder * update readme --------- Co-authored-by: Yuhong Echo Liu <yliu49@uw.edu>
1 parent 99ab31b commit e276369

17 files changed

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‎Benchmark-Models/Liu_IFACPapersOnLine2025/Liu_IFACPapersOnLine2025.yaml‎

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format_version: 1
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parameter_file: parameters.tsv
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problems:
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- condition_files:
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- conditions.tsv
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measurement_files:
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- measurements.tsv
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observable_files:
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- observables.tsv
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sbml_files:
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- model.xml
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visualization_files:
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- visualization.tsv

‎Benchmark-Models/Liu_IFACPapersOnLine2025/conditions.tsv‎

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conditionId conditionName u_2
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vvDD vvDD 1000000000.0
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ctrl ctrl 0.0

‎Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/Liu_IFACPapersOnLine2025_individual.yaml‎

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format_version: 1
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parameter_file: parameters.tsv
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problems:
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- condition_files:
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- conditions.tsv
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measurement_files:
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- measurements.tsv
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observable_files:
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- observables.tsv
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sbml_files:
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- model_individual.xml
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visualization_files:
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- visualization.tsv

‎Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/conditions.tsv‎

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conditionId conditionName u_2 xi_i_k
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vvDD_1 vvDD_1 1000000000.0 xi_v_1
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vvDD_2 vvDD_2 1000000000.0 xi_v_2
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vvDD_3 vvDD_3 1000000000.0 xi_v_3
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vvDD_4 vvDD_4 1000000000.0 xi_v_4
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vvDD_5 vvDD_5 1000000000.0 xi_v_5
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vvDD_6 vvDD_6 1000000000.0 xi_v_6
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vvDD_7 vvDD_7 1000000000.0 xi_v_7
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vvDD_8 vvDD_8 1000000000.0 xi_v_8
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vvDD_9 vvDD_9 1000000000.0 xi_v_9
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vvDD_10 vvDD_10 1000000000.0 xi_v_10
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ctrl_1 ctrl_1 0.0 xi_c_1
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ctrl_2 ctrl_2 0.0 xi_c_2
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ctrl_3 ctrl_3 0.0 xi_c_3
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ctrl_4 ctrl_4 0.0 xi_c_4
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ctrl_5 ctrl_5 0.0 xi_c_5
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ctrl_6 ctrl_6 0.0 xi_c_6
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ctrl_7 ctrl_7 0.0 xi_c_7
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ctrl_8 ctrl_8 0.0 xi_c_8
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ctrl_9 ctrl_9 0.0 xi_c_9
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ctrl_10 ctrl_10 0.0 xi_c_10

‎Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/measurements.tsv‎

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observableId simulationConditionId measurement time datasetId
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tumor_num vvDD_1 451.73401707247393 0 virus_1
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tumor_num vvDD_2 477.41006706423315 0 virus_2
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tumor_num vvDD_3 509.5051295539299 0 virus_3
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tumor_num vvDD_4 554.4382170395085 0 virus_4
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tumor_num vvDD_5 852.9222981937005 0 virus_5
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tumor_num vvDD_6 1016.607116891161 0 virus_6
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tumor_num vvDD_7 1058.3306981277697 0 virus_7
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tumor_num vvDD_8 1084.006748119529 0 virus_8
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tumor_num vvDD_9 1241.2725543190497 0 virus_9
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tumor_num vvDD_10 1263.7390980618388 0 virus_10
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tumor_num vvDD_1 679.6089607493324 1 virus_1
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tumor_num vvDD_2 817.6177294550338 1 virus_2
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tumor_num vvDD_3 535.1811795456891 1 virus_3
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tumor_num vvDD_4 824.0367419529714 1 virus_4
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tumor_num vvDD_5 1055.1211918788 1 virus_5
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tumor_num vvDD_6 926.740941920006 1 virus_6
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tumor_num vvDD_7 1571.8516979629405 1 virus_7
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tumor_num vvDD_8 1331.1387292902025 1 virus_8
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tumor_num vvDD_9 1481.9855229917855 1 virus_9
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tumor_num vvDD_10 968.4645231566146 1 virus_10
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tumor_num vvDD_1 406.80092958689744 2 virus_1
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tumor_num vvDD_2 483.82907956217286 2 virus_2
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tumor_num vvDD_3 294.4682108729532 2 virus_3
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tumor_num vvDD_4 885.0173606833995 2 virus_4
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tumor_num vvDD_5 291.25870462398325 2 virus_5
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tumor_num vvDD_6 814.4082232060639 2 virus_6
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tumor_num vvDD_7 958.836004409705 2 virus_7
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tumor_num vvDD_8 1119.3113168581956 2 virus_8
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tumor_num vvDD_9 1132.1493418540751 2 virus_9
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tumor_num vvDD_10 1000.5595856463136 2 virus_10
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tumor_num vvDD_1 355.4488296033791 3 virus_1
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tumor_num vvDD_2 349.0298171054393 3 virus_2
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tumor_num vvDD_3 220.64956714664766 3 virus_3
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tumor_num vvDD_4 194.97351715488847 3 virus_4
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tumor_num vvDD_5 252.74462963634662 3 virus_5
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tumor_num vvDD_6 422.84846083174693 3 virus_6
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tumor_num vvDD_7 772.6846419694551 3 virus_7
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tumor_num vvDD_8 464.5720420683534 3 virus_8
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tumor_num vvDD_9 785.5226669653348 3 virus_9
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tumor_num vvDD_10 339.40129835853173 3 virus_10
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tumor_num vvDD_1 50.545735951247316 4 virus_1
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tumor_num vvDD_2 101.89783593476568 4 virus_2
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tumor_num vvDD_3 76.2217859430065 4 virus_3
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tumor_num vvDD_4 53.75524220021722 4 virus_4
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tumor_num vvDD_5 191.76401090591855 4 virus_5
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tumor_num vvDD_6 262.3731483832563 4 virus_6
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tumor_num vvDD_7 589.7427857781752 4 virus_7
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tumor_num vvDD_8 345.8203108564694 4 virus_8
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tumor_num vvDD_9 631.4663670147839 4 virus_9
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tumor_num vvDD_10 374.7058670971985 4 virus_10
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tumor_num ctrl_1 349.1039275702164 0 control_1
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tumor_num ctrl_2 370.50979635893606 0 control_2
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tumor_num ctrl_3 407.93829872021803 0 control_3
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tumor_num ctrl_4 552.3499369974998 0 control_4
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tumor_num ctrl_5 632.5786249293225 0 control_5
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tumor_num ctrl_6 657.550182543784 0 control_6
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tumor_num ctrl_7 945.4762838668787 0 control_7
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tumor_num ctrl_8 985.5848518293386 0 control_8
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tumor_num ctrl_9 1244.9967188123485 0 control_9
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tumor_num ctrl_10 1343.9454339282627 0 control_10
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tumor_num ctrl_1 508.3483427091911 1 control_1
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tumor_num ctrl_2 323.8108084590962 1 control_2
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tumor_num ctrl_3 516.3654354989194 1 control_3
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tumor_num ctrl_4 917.5146511614834 1 control_4
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tumor_num ctrl_5 965.6460879171242 1 control_5
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tumor_num ctrl_6 830.874501593137 1 control_6
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tumor_num ctrl_7 1345.400986797869 1 control_7
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tumor_num ctrl_8 1404.2411339513233 1 control_8
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tumor_num ctrl_9 1086.00067182176 1 control_9
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tumor_num ctrl_10 1372.138106771691 1 control_10
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tumor_num ctrl_1 648.8611786571674 2 control_1
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tumor_num ctrl_2 343.986388512792 2 control_2
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tumor_num ctrl_3 480.36360598998806 2 control_3
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tumor_num ctrl_4 1250.5821141492872 2 control_4
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tumor_num ctrl_5 1140.9304646390121 2 control_5
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tumor_num ctrl_6 771.4696645965797 2 control_6
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tumor_num ctrl_7 1400.3481076254745 2 control_7
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tumor_num ctrl_8 1357.553698058382 2 control_8
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tumor_num ctrl_9 1400.3423316220221 2 control_9
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tumor_num ctrl_10 1592.8854066549445 2 control_10
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tumor_num ctrl_1 612.8651251516885 3 control_1
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tumor_num ctrl_2 441.73369491093814 3 control_2
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tumor_num ctrl_3 449.7392356937657 3 control_3
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tumor_num ctrl_4 1091.5802911552485 3 control_4
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tumor_num ctrl_5 1265.4091150075299 3 control_5
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tumor_num ctrl_6 959.3493729329441 3 control_6
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tumor_num ctrl_7 1669.2210682609186 3 control_7
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tumor_num ctrl_8 1441.9064524540886 3 control_8
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tumor_num ctrl_9 1262.7232734028994 3 control_9
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tumor_num ctrl_10 1749.461308199642 3 control_10
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tumor_num ctrl_1 705.2811803647304 4 control_1
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tumor_num ctrl_2 416.469455817074 4 control_2
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tumor_num ctrl_3 496.70391975234486 4 control_3
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tumor_num ctrl_4 1499.550966893223 4 control_4
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tumor_num ctrl_5 1357.8136182136711 4 control_5
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tumor_num ctrl_6 1026.0423760760882 4 control_6
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tumor_num ctrl_7 1531.6539940728533 4 control_7
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tumor_num ctrl_8 1700.1226867227788 4 control_8
100+
tumor_num ctrl_9 1470.1280053147707 4 control_9
101+
tumor_num ctrl_10 1876.6258001727879 4 control_10

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