From 5b900e0340a7d4dcedd06f63fcaf4223fe2d2193 Mon Sep 17 00:00:00 2001 From: Yuhong Echo Liu Date: Wed, 4 Dec 2024 12:54:45 +0100 Subject: [PATCH 01/13] add the petab files for Liu_IFACPapersOnLine2025 --- .../baseline_model.xml | 183 ++++++++++++++++++ .../baseline_model.yaml | 13 ++ .../Liu_IFACPapersOnLine2025/conditions.tsv | 3 + .../measurements_scaled.tsv | 101 ++++++++++ .../Liu_IFACPapersOnLine2025/observables.tsv | 2 + .../Liu_IFACPapersOnLine2025/parameters.tsv | 9 + .../visualizations.tsv | 2 + 7 files changed, 313 insertions(+) create mode 100644 Benchmark-Models/Liu_IFACPapersOnLine2025/baseline_model.xml create mode 100644 Benchmark-Models/Liu_IFACPapersOnLine2025/baseline_model.yaml create mode 100644 Benchmark-Models/Liu_IFACPapersOnLine2025/conditions.tsv create mode 100644 Benchmark-Models/Liu_IFACPapersOnLine2025/measurements_scaled.tsv create mode 100644 Benchmark-Models/Liu_IFACPapersOnLine2025/observables.tsv create mode 100644 Benchmark-Models/Liu_IFACPapersOnLine2025/parameters.tsv create mode 100644 Benchmark-Models/Liu_IFACPapersOnLine2025/visualizations.tsv diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/baseline_model.xml b/Benchmark-Models/Liu_IFACPapersOnLine2025/baseline_model.xml new file mode 100644 index 0000000..c1697fd --- /dev/null +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/baseline_model.xml @@ -0,0 +1,183 @@ + + + + + + + + + + + + + + + + + + + + + kappa + + + 1 + + + + + + + kappa + 400 + + 1 + + + + + + rho + + + + + + + + + + u_2 + + + + + + + 1 + 1000000000 + + + + + + + + + + + + rho + U + + + 1 + + + + + U + I + + kappa + + + + + + psi + V + U + + + + + + + + + + + + + rho + I + + + 1 + + + + + U + I + + kappa + + + + + + psi + V + U + + + + + alpha + I + + + + + + + + + + + + + alpha + beta + I + + + + psi + V + U + + + + + delta + V + + + + + + + + + + + + U + 1 -8 + + + + + + + 0 + + + + + + + diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/baseline_model.yaml b/Benchmark-Models/Liu_IFACPapersOnLine2025/baseline_model.yaml new file mode 100644 index 0000000..6e3a81a --- /dev/null +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/baseline_model.yaml @@ -0,0 +1,13 @@ +format_version: 1 +parameter_file: parameters.tsv +problems: + - condition_files: + - conditions.tsv + measurement_files: + - measurements_scaled.tsv + observable_files: + - observables.tsv + sbml_files: + - baseline_model.xml + visualization_files: + - visualizations.tsv \ No newline at end of file diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/conditions.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/conditions.tsv new file mode 100644 index 0000000..05f8ba2 --- /dev/null +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/conditions.tsv @@ -0,0 +1,3 @@ +conditionId conditionName u_2 +vvDD vvDD 1000000000.0 +ctrl ctrl 0.0 diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/measurements_scaled.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/measurements_scaled.tsv new file mode 100644 index 0000000..2fa1f20 --- /dev/null +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/measurements_scaled.tsv @@ -0,0 +1,101 @@ +observableId simulationConditionId measurement time +tumor_num vvDD 451.73401707247393 0 +tumor_num vvDD 477.41006706423315 0 +tumor_num vvDD 509.5051295539299 0 +tumor_num vvDD 554.4382170395085 0 +tumor_num vvDD 852.9222981937005 0 +tumor_num vvDD 1016.607116891161 0 +tumor_num vvDD 1058.3306981277697 0 +tumor_num vvDD 1084.006748119529 0 +tumor_num vvDD 1241.2725543190497 0 +tumor_num vvDD 1263.7390980618388 0 +tumor_num vvDD 679.6089607493324 1 +tumor_num vvDD 817.6177294550338 1 +tumor_num vvDD 535.1811795456891 1 +tumor_num vvDD 824.0367419529714 1 +tumor_num vvDD 1055.1211918788 1 +tumor_num vvDD 926.740941920006 1 +tumor_num vvDD 1571.8516979629405 1 +tumor_num vvDD 1331.1387292902025 1 +tumor_num vvDD 1481.9855229917855 1 +tumor_num vvDD 968.4645231566146 1 +tumor_num vvDD 406.80092958689744 2 +tumor_num vvDD 483.82907956217286 2 +tumor_num vvDD 294.4682108729532 2 +tumor_num vvDD 885.0173606833995 2 +tumor_num vvDD 291.25870462398325 2 +tumor_num vvDD 814.4082232060639 2 +tumor_num vvDD 958.836004409705 2 +tumor_num vvDD 1119.3113168581956 2 +tumor_num vvDD 1132.1493418540751 2 +tumor_num vvDD 1000.5595856463136 2 +tumor_num vvDD 355.4488296033791 3 +tumor_num vvDD 349.0298171054393 3 +tumor_num vvDD 220.64956714664766 3 +tumor_num vvDD 194.97351715488847 3 +tumor_num vvDD 252.74462963634662 3 +tumor_num vvDD 422.84846083174693 3 +tumor_num vvDD 772.6846419694551 3 +tumor_num vvDD 464.5720420683534 3 +tumor_num vvDD 785.5226669653348 3 +tumor_num vvDD 339.40129835853173 3 +tumor_num vvDD 50.545735951247316 4 +tumor_num vvDD 101.89783593476568 4 +tumor_num vvDD 76.2217859430065 4 +tumor_num vvDD 53.75524220021722 4 +tumor_num vvDD 191.76401090591855 4 +tumor_num vvDD 262.3731483832563 4 +tumor_num vvDD 589.7427857781752 4 +tumor_num vvDD 345.8203108564694 4 +tumor_num vvDD 631.4663670147839 4 +tumor_num vvDD 374.7058670971985 4 +tumor_num ctrl 349.1039275702164 0 +tumor_num ctrl 370.50979635893606 0 +tumor_num ctrl 407.93829872021803 0 +tumor_num ctrl 552.3499369974998 0 +tumor_num ctrl 632.5786249293225 0 +tumor_num ctrl 657.550182543784 0 +tumor_num ctrl 945.4762838668787 0 +tumor_num ctrl 985.5848518293386 0 +tumor_num ctrl 1244.9967188123485 0 +tumor_num ctrl 1343.9454339282627 0 +tumor_num ctrl 508.3483427091911 1 +tumor_num ctrl 323.8108084590962 1 +tumor_num ctrl 516.3654354989194 1 +tumor_num ctrl 917.5146511614834 1 +tumor_num ctrl 965.6460879171242 1 +tumor_num ctrl 830.874501593137 1 +tumor_num ctrl 1345.400986797869 1 +tumor_num ctrl 1404.2411339513233 1 +tumor_num ctrl 1086.00067182176 1 +tumor_num ctrl 1372.138106771691 1 +tumor_num ctrl 648.8611786571674 2 +tumor_num ctrl 343.986388512792 2 +tumor_num ctrl 480.36360598998806 2 +tumor_num ctrl 1250.5821141492872 2 +tumor_num ctrl 1140.9304646390121 2 +tumor_num ctrl 771.4696645965797 2 +tumor_num ctrl 1400.3481076254745 2 +tumor_num ctrl 1357.553698058382 2 +tumor_num ctrl 1400.3423316220221 2 +tumor_num ctrl 1592.8854066549445 2 +tumor_num ctrl 612.8651251516885 3 +tumor_num ctrl 441.73369491093814 3 +tumor_num ctrl 449.7392356937657 3 +tumor_num ctrl 1091.5802911552485 3 +tumor_num ctrl 1265.4091150075299 3 +tumor_num ctrl 959.3493729329441 3 +tumor_num ctrl 1669.2210682609186 3 +tumor_num ctrl 1441.9064524540886 3 +tumor_num ctrl 1262.7232734028994 3 +tumor_num ctrl 1749.461308199642 3 +tumor_num ctrl 705.2811803647304 4 +tumor_num ctrl 416.469455817074 4 +tumor_num ctrl 496.70391975234486 4 +tumor_num ctrl 1499.550966893223 4 +tumor_num ctrl 1357.8136182136711 4 +tumor_num ctrl 1026.0423760760882 4 +tumor_num ctrl 1531.6539940728533 4 +tumor_num ctrl 1700.1226867227788 4 +tumor_num ctrl 1470.1280053147707 4 +tumor_num ctrl 1876.6258001727879 4 diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/observables.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/observables.tsv new file mode 100644 index 0000000..c6495a2 --- /dev/null +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/observables.tsv @@ -0,0 +1,2 @@ +observableId observableName observableFormula noiseFormula noiseDistribution observableTransformation +tumor_num tumor_number U + I sqrt(sigma_a^2 + (sigma_b * (U + I))^2) normal lin diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/parameters.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/parameters.tsv new file mode 100644 index 0000000..46cc17f --- /dev/null +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/parameters.tsv @@ -0,0 +1,9 @@ +parameterId parameterName parameterScale lowerBound upperBound nominalValue estimate parameterType +rho rho log10 0.42 1.66 1 1 +kappa kappa log10 100.0 100000.0 1 1 +psi psi log10 1e-10 0.01 1 1 +beta beta log10 1.0 10000.0 1 1 +alpha alpha log10 0.0001 1000.0 1 1 +delta delta log10 0.01 100.0 1 1 +sigma_a sigma_a log10 10.0 100000.0 1 1 +sigma_b sigma_b log10 0.0001 100.0 1 1 diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/visualizations.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/visualizations.tsv new file mode 100644 index 0000000..137103f --- /dev/null +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/visualizations.tsv @@ -0,0 +1,2 @@ +plotId plotTypeData plotTypeSimulation xValues xLabel yValues yLabel legendEntry +plot1 MeanAndSD ScatterPlot condition Condition tumor_num Tumor Number Model From 48eebccbf297dafa5b7e5dca5e048ef4942dc9d0 Mon Sep 17 00:00:00 2001 From: Yuhong Echo Liu Date: Thu, 19 Dec 2024 16:33:52 +0100 Subject: [PATCH 02/13] replace the baseline model with age-of-infection model --- .../age_of_infection_model.xml | 364 ++++++++++++++++++ ...model.yaml => age_of_infection_model.yaml} | 2 +- .../baseline_model.xml | 183 --------- .../Liu_IFACPapersOnLine2025/observables.tsv | 2 +- .../Liu_IFACPapersOnLine2025/parameters.tsv | 1 + 5 files changed, 367 insertions(+), 185 deletions(-) create mode 100644 Benchmark-Models/Liu_IFACPapersOnLine2025/age_of_infection_model.xml rename Benchmark-Models/Liu_IFACPapersOnLine2025/{baseline_model.yaml => age_of_infection_model.yaml} (88%) delete mode 100644 Benchmark-Models/Liu_IFACPapersOnLine2025/baseline_model.xml diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/age_of_infection_model.xml b/Benchmark-Models/Liu_IFACPapersOnLine2025/age_of_infection_model.xml new file mode 100644 index 0000000..edd595e --- /dev/null +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/age_of_infection_model.xml @@ -0,0 +1,364 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + kappa + + + 1 + + + + + + + kappa + 400 + + 1 + + + + + + rho + + + + + + + + + + u_2 + + + + + + + 1 + 1000000000 + + + + + + + + + + + + rho + U + + + 1 + + + + + U + I_1 + I_2 + I_3 + I_4 + I_5 + + kappa + + + + + + psi + V + U + + + + + + + + + + + + + rho + I_1 + + + 1 + + + + + U + I_1 + I_2 + I_3 + I_4 + I_5 + + kappa + + + + + + psi + V + U + + + + + phi + I_1 + + + + + + + + + + + + + rho + I_2 + + + 1 + + + + + U + I_1 + I_2 + I_3 + I_4 + I_5 + + kappa + + + + + + phi + I_1 + + + + + phi + I_2 + + + + + + + + + + + + + rho + I_3 + + + 1 + + + + + U + I_1 + I_2 + I_3 + I_4 + I_5 + + kappa + + + + + + phi + I_2 + + + + + phi + I_3 + + + + + + + + + + + + + rho + I_4 + + + 1 + + + + + U + I_1 + I_2 + I_3 + I_4 + I_5 + + kappa + + + + + + phi + I_3 + + + + + phi + I_4 + + + + + + + + + + + + + rho + I_5 + + + 1 + + + + + U + I_1 + I_2 + I_3 + I_4 + I_5 + + kappa + + + + + + phi + I_4 + + + + + alpha + I_5 + + + + + + + + + + + + + beta + alpha + I_5 + + + + psi + V + U + + + + + delta + V + + + + + + + + + + + + U + 1 -8 + + + + + + + 0 + + + + + + + diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/baseline_model.yaml b/Benchmark-Models/Liu_IFACPapersOnLine2025/age_of_infection_model.yaml similarity index 88% rename from Benchmark-Models/Liu_IFACPapersOnLine2025/baseline_model.yaml rename to Benchmark-Models/Liu_IFACPapersOnLine2025/age_of_infection_model.yaml index 6e3a81a..08d74bc 100644 --- a/Benchmark-Models/Liu_IFACPapersOnLine2025/baseline_model.yaml +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/age_of_infection_model.yaml @@ -8,6 +8,6 @@ problems: observable_files: - observables.tsv sbml_files: - - baseline_model.xml + - age_of_infection_model.xml visualization_files: - visualizations.tsv \ No newline at end of file diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/baseline_model.xml b/Benchmark-Models/Liu_IFACPapersOnLine2025/baseline_model.xml deleted file mode 100644 index c1697fd..0000000 --- a/Benchmark-Models/Liu_IFACPapersOnLine2025/baseline_model.xml +++ /dev/null @@ -1,183 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - kappa - - - 1 - - - - - - - kappa - 400 - - 1 - - - - - - rho - - - - - - - - - - u_2 - - - - - - - 1 - 1000000000 - - - - - - - - - - - - rho - U - - - 1 - - - - - U - I - - kappa - - - - - - psi - V - U - - - - - - - - - - - - - rho - I - - - 1 - - - - - U - I - - kappa - - - - - - psi - V - U - - - - - alpha - I - - - - - - - - - - - - - alpha - beta - I - - - - psi - V - U - - - - - delta - V - - - - - - - - - - - - U - 1 -8 - - - - - - - 0 - - - - - - - diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/observables.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/observables.tsv index c6495a2..4eb16b2 100644 --- a/Benchmark-Models/Liu_IFACPapersOnLine2025/observables.tsv +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/observables.tsv @@ -1,2 +1,2 @@ observableId observableName observableFormula noiseFormula noiseDistribution observableTransformation -tumor_num tumor_number U + I sqrt(sigma_a^2 + (sigma_b * (U + I))^2) normal lin +tumor_num tumor_number U + I_1 + I_2 + I_3 + I_4 + I_5 sqrt(sigma_a^2 + (sigma_b * (U + I_1 + I_2 + I_3 + I_4 + I_5))^2) normal lin diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/parameters.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/parameters.tsv index 46cc17f..7cefe16 100644 --- a/Benchmark-Models/Liu_IFACPapersOnLine2025/parameters.tsv +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/parameters.tsv @@ -2,6 +2,7 @@ parameterId parameterName parameterScale lowerBound upperBound nominalValue esti rho rho log10 0.42 1.66 1 1 kappa kappa log10 100.0 100000.0 1 1 psi psi log10 1e-10 0.01 1 1 +phi phi log10 1e-08 100000000.0 1 1 beta beta log10 1.0 10000.0 1 1 alpha alpha log10 0.0001 1000.0 1 1 delta delta log10 0.01 100.0 1 1 From a4d97f4f17cfe2cf329a3f4bed8cc3f3a4a0213c Mon Sep 17 00:00:00 2001 From: Yuhong Echo Liu Date: Thu, 19 Dec 2024 16:37:57 +0100 Subject: [PATCH 03/13] add individual based age of infection model in the subfolder --- .../individual-based/conditions.tsv | 21 + ...ndividual_based_age_of_infection_model.xml | 369 ++++++++++++++++++ ...dividual_based_age_of_infection_model.yaml | 13 + .../individual-based/measurements_scaled.tsv | 101 +++++ .../individual-based/observables.tsv | 2 + .../individual-based/parameters.tsv | 30 ++ .../individual-based/visualizations.tsv | 2 + 7 files changed, 538 insertions(+) create mode 100644 Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/conditions.tsv create mode 100644 Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/individual_based_age_of_infection_model.xml create mode 100644 Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/individual_based_age_of_infection_model.yaml create mode 100644 Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/measurements_scaled.tsv create mode 100644 Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/observables.tsv create mode 100644 Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/parameters.tsv create mode 100644 Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/visualizations.tsv diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/conditions.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/conditions.tsv new file mode 100644 index 0000000..08ab2f6 --- /dev/null +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/conditions.tsv @@ -0,0 +1,21 @@ +conditionId conditionName u_2 xi_i_k +vvDD_1 vvDD_1 1000000000.0 xi_v_1 +vvDD_2 vvDD_2 1000000000.0 xi_v_2 +vvDD_3 vvDD_3 1000000000.0 xi_v_3 +vvDD_4 vvDD_4 1000000000.0 xi_v_4 +vvDD_5 vvDD_5 1000000000.0 xi_v_5 +vvDD_6 vvDD_6 1000000000.0 xi_v_6 +vvDD_7 vvDD_7 1000000000.0 xi_v_7 +vvDD_8 vvDD_8 1000000000.0 xi_v_8 +vvDD_9 vvDD_9 1000000000.0 xi_v_9 +vvDD_10 vvDD_10 1000000000.0 xi_v_10 +ctrl_1 ctrl_1 0.0 xi_c_1 +ctrl_2 ctrl_2 0.0 xi_c_2 +ctrl_3 ctrl_3 0.0 xi_c_3 +ctrl_4 ctrl_4 0.0 xi_c_4 +ctrl_5 ctrl_5 0.0 xi_c_5 +ctrl_6 ctrl_6 0.0 xi_c_6 +ctrl_7 ctrl_7 0.0 xi_c_7 +ctrl_8 ctrl_8 0.0 xi_c_8 +ctrl_9 ctrl_9 0.0 xi_c_9 +ctrl_10 ctrl_10 0.0 xi_c_10 diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/individual_based_age_of_infection_model.xml b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/individual_based_age_of_infection_model.xml new file mode 100644 index 0000000..8b5f557 --- /dev/null +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/individual_based_age_of_infection_model.xml @@ -0,0 +1,369 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + kappa + + + 1 + + + + + + + kappa + + + 400 + xi_i_k + + + 1 + + + + + + rho + + + + + + + + + + u_2 + + + + + + + 1 + 1000000000 + + + + + + + + + + + + rho + U + + + 1 + + + + + U + I_1 + I_2 + I_3 + I_4 + I_5 + + kappa + + + + + + psi + V + U + + + + + + + + + + + + + rho + I_1 + + + 1 + + + + + U + I_1 + I_2 + I_3 + I_4 + I_5 + + kappa + + + + + + psi + V + U + + + + + phi + I_1 + + + + + + + + + + + + + rho + I_2 + + + 1 + + + + + U + I_1 + I_2 + I_3 + I_4 + I_5 + + kappa + + + + + + phi + I_1 + + + + + phi + I_2 + + + + + + + + + + + + + rho + I_3 + + + 1 + + + + + U + I_1 + I_2 + I_3 + I_4 + I_5 + + kappa + + + + + + phi + I_2 + + + + + phi + I_3 + + + + + + + + + + + + + rho + I_4 + + + 1 + + + + + U + I_1 + I_2 + I_3 + I_4 + I_5 + + kappa + + + + + + phi + I_3 + + + + + phi + I_4 + + + + + + + + + + + + + rho + I_5 + + + 1 + + + + + U + I_1 + I_2 + I_3 + I_4 + I_5 + + kappa + + + + + + phi + I_4 + + + + + alpha + I_5 + + + + + + + + + + + + + beta + alpha + I_5 + + + + psi + V + U + + + + + delta + V + + + + + + + + + + + + U + 1 -8 + + + + + + + 0 + + + + + + + diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/individual_based_age_of_infection_model.yaml b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/individual_based_age_of_infection_model.yaml new file mode 100644 index 0000000..ee5c0b4 --- /dev/null +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/individual_based_age_of_infection_model.yaml @@ -0,0 +1,13 @@ +format_version: 1 +parameter_file: parameters.tsv +problems: + - condition_files: + - conditions.tsv + measurement_files: + - measurements_scaled.tsv + observable_files: + - observables.tsv + sbml_files: + - individual_based_age_of_infection_model.xml + visualization_files: + - visualizations.tsv \ No newline at end of file diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/measurements_scaled.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/measurements_scaled.tsv new file mode 100644 index 0000000..0d16e90 --- /dev/null +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/measurements_scaled.tsv @@ -0,0 +1,101 @@ +observableId simulationConditionId measurement time +tumor_num vvDD_1 451.73401707247393 0 +tumor_num vvDD_2 477.41006706423315 0 +tumor_num vvDD_3 509.5051295539299 0 +tumor_num vvDD_4 554.4382170395085 0 +tumor_num vvDD_5 852.9222981937005 0 +tumor_num vvDD_6 1016.607116891161 0 +tumor_num vvDD_7 1058.3306981277697 0 +tumor_num vvDD_8 1084.006748119529 0 +tumor_num vvDD_9 1241.2725543190497 0 +tumor_num vvDD_10 1263.7390980618388 0 +tumor_num vvDD_1 679.6089607493324 1 +tumor_num vvDD_2 817.6177294550338 1 +tumor_num vvDD_3 535.1811795456891 1 +tumor_num vvDD_4 824.0367419529714 1 +tumor_num vvDD_5 1055.1211918788 1 +tumor_num vvDD_6 926.740941920006 1 +tumor_num vvDD_7 1571.8516979629405 1 +tumor_num vvDD_8 1331.1387292902025 1 +tumor_num vvDD_9 1481.9855229917855 1 +tumor_num vvDD_10 968.4645231566146 1 +tumor_num vvDD_1 406.80092958689744 2 +tumor_num vvDD_2 483.82907956217286 2 +tumor_num vvDD_3 294.4682108729532 2 +tumor_num vvDD_4 885.0173606833995 2 +tumor_num vvDD_5 291.25870462398325 2 +tumor_num vvDD_6 814.4082232060639 2 +tumor_num vvDD_7 958.836004409705 2 +tumor_num vvDD_8 1119.3113168581956 2 +tumor_num vvDD_9 1132.1493418540751 2 +tumor_num vvDD_10 1000.5595856463136 2 +tumor_num vvDD_1 355.4488296033791 3 +tumor_num vvDD_2 349.0298171054393 3 +tumor_num vvDD_3 220.64956714664766 3 +tumor_num vvDD_4 194.97351715488847 3 +tumor_num vvDD_5 252.74462963634662 3 +tumor_num vvDD_6 422.84846083174693 3 +tumor_num vvDD_7 772.6846419694551 3 +tumor_num vvDD_8 464.5720420683534 3 +tumor_num vvDD_9 785.5226669653348 3 +tumor_num vvDD_10 339.40129835853173 3 +tumor_num vvDD_1 50.545735951247316 4 +tumor_num vvDD_2 101.89783593476568 4 +tumor_num vvDD_3 76.2217859430065 4 +tumor_num vvDD_4 53.75524220021722 4 +tumor_num vvDD_5 191.76401090591855 4 +tumor_num vvDD_6 262.3731483832563 4 +tumor_num vvDD_7 589.7427857781752 4 +tumor_num vvDD_8 345.8203108564694 4 +tumor_num vvDD_9 631.4663670147839 4 +tumor_num vvDD_10 374.7058670971985 4 +tumor_num ctrl_1 349.1039275702164 0 +tumor_num ctrl_2 370.50979635893606 0 +tumor_num ctrl_3 407.93829872021803 0 +tumor_num ctrl_4 552.3499369974998 0 +tumor_num ctrl_5 632.5786249293225 0 +tumor_num ctrl_6 657.550182543784 0 +tumor_num ctrl_7 945.4762838668787 0 +tumor_num ctrl_8 985.5848518293386 0 +tumor_num ctrl_9 1244.9967188123485 0 +tumor_num ctrl_10 1343.9454339282627 0 +tumor_num ctrl_1 508.3483427091911 1 +tumor_num ctrl_2 323.8108084590962 1 +tumor_num ctrl_3 516.3654354989194 1 +tumor_num ctrl_4 917.5146511614834 1 +tumor_num ctrl_5 965.6460879171242 1 +tumor_num ctrl_6 830.874501593137 1 +tumor_num ctrl_7 1345.400986797869 1 +tumor_num ctrl_8 1404.2411339513233 1 +tumor_num ctrl_9 1086.00067182176 1 +tumor_num ctrl_10 1372.138106771691 1 +tumor_num ctrl_1 648.8611786571674 2 +tumor_num ctrl_2 343.986388512792 2 +tumor_num ctrl_3 480.36360598998806 2 +tumor_num ctrl_4 1250.5821141492872 2 +tumor_num ctrl_5 1140.9304646390121 2 +tumor_num ctrl_6 771.4696645965797 2 +tumor_num ctrl_7 1400.3481076254745 2 +tumor_num ctrl_8 1357.553698058382 2 +tumor_num ctrl_9 1400.3423316220221 2 +tumor_num ctrl_10 1592.8854066549445 2 +tumor_num ctrl_1 612.8651251516885 3 +tumor_num ctrl_2 441.73369491093814 3 +tumor_num ctrl_3 449.7392356937657 3 +tumor_num ctrl_4 1091.5802911552485 3 +tumor_num ctrl_5 1265.4091150075299 3 +tumor_num ctrl_6 959.3493729329441 3 +tumor_num ctrl_7 1669.2210682609186 3 +tumor_num ctrl_8 1441.9064524540886 3 +tumor_num ctrl_9 1262.7232734028994 3 +tumor_num ctrl_10 1749.461308199642 3 +tumor_num ctrl_1 705.2811803647304 4 +tumor_num ctrl_2 416.469455817074 4 +tumor_num ctrl_3 496.70391975234486 4 +tumor_num ctrl_4 1499.550966893223 4 +tumor_num ctrl_5 1357.8136182136711 4 +tumor_num ctrl_6 1026.0423760760882 4 +tumor_num ctrl_7 1531.6539940728533 4 +tumor_num ctrl_8 1700.1226867227788 4 +tumor_num ctrl_9 1470.1280053147707 4 +tumor_num ctrl_10 1876.6258001727879 4 diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/observables.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/observables.tsv new file mode 100644 index 0000000..4eb16b2 --- /dev/null +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/observables.tsv @@ -0,0 +1,2 @@ +observableId observableName observableFormula noiseFormula noiseDistribution observableTransformation +tumor_num tumor_number U + I_1 + I_2 + I_3 + I_4 + I_5 sqrt(sigma_a^2 + (sigma_b * (U + I_1 + I_2 + I_3 + I_4 + I_5))^2) normal lin diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/parameters.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/parameters.tsv new file mode 100644 index 0000000..79a7a3b --- /dev/null +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/parameters.tsv @@ -0,0 +1,30 @@ +parameterId parameterName parameterScale lowerBound upperBound nominalValue estimate parameterType +rho rho log10 0.42 1.66 1 1 +kappa kappa log10 100.0 100000.0 1 1 +psi psi log10 1e-10 0.01 1 1 +phi phi log10 1e-08 100000000.0 1 1 +beta beta log10 1.0 10000.0 1 1 +alpha alpha log10 0.0001 1000.0 1 1 +delta delta log10 0.01 100.0 1 1 +xi_c_1 xi_c_1 log10 1e-07 1.0 1 1 +xi_c_2 xi_c_2 log10 1e-07 1.0 1 1 +xi_c_3 xi_c_3 log10 1e-07 1.0 1 1 +xi_c_4 xi_c_4 log10 1e-07 1.0 1 1 +xi_c_5 xi_c_5 log10 1e-07 1.0 1 1 +xi_c_6 xi_c_6 log10 1e-07 1.0 1 1 +xi_c_7 xi_c_7 log10 1e-07 1.0 1 1 +xi_c_8 xi_c_8 log10 1e-07 1.0 1 1 +xi_c_9 xi_c_9 log10 1e-07 1.0 1 1 +xi_c_10 xi_c_10 log10 1e-07 1.0 1 1 +xi_v_1 xi_v_1 log10 1e-07 1.0 1 1 +xi_v_2 xi_v_2 log10 1e-07 1.0 1 1 +xi_v_3 xi_v_3 log10 1e-07 1.0 1 1 +xi_v_4 xi_v_4 log10 1e-07 1.0 1 1 +xi_v_5 xi_v_5 log10 1e-07 1.0 1 1 +xi_v_6 xi_v_6 log10 1e-07 1.0 1 1 +xi_v_7 xi_v_7 log10 1e-07 1.0 1 1 +xi_v_8 xi_v_8 log10 1e-07 1.0 1 1 +xi_v_9 xi_v_9 log10 1e-07 1.0 1 1 +xi_v_10 xi_v_10 log10 1e-07 1.0 1 1 +sigma_a sigma_a log10 10.0 100000.0 1 1 +sigma_b sigma_b log10 0.0001 100.0 1 1 diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/visualizations.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/visualizations.tsv new file mode 100644 index 0000000..137103f --- /dev/null +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/visualizations.tsv @@ -0,0 +1,2 @@ +plotId plotTypeData plotTypeSimulation xValues xLabel yValues yLabel legendEntry +plot1 MeanAndSD ScatterPlot condition Condition tumor_num Tumor Number Model From 53334ce2c869152717307c300d542998f4971ba8 Mon Sep 17 00:00:00 2001 From: Maren Philipps Date: Sat, 4 Jan 2025 22:14:13 +0100 Subject: [PATCH 04/13] rename files, add visualization spec --- ...el.yaml => Liu_IFAC-PapersOnLine2025.yaml} | 6 +- .../Liu_IFACPapersOnLine2025/measurements.tsv | 101 ++++++++++++++++++ .../measurements_scaled.tsv | 101 ------------------ .../{age_of_infection_model.xml => model.xml} | 2 +- .../visualization.tsv | 3 + .../visualizations.tsv | 2 - 6 files changed, 108 insertions(+), 107 deletions(-) rename Benchmark-Models/Liu_IFACPapersOnLine2025/{age_of_infection_model.yaml => Liu_IFAC-PapersOnLine2025.yaml} (70%) create mode 100644 Benchmark-Models/Liu_IFACPapersOnLine2025/measurements.tsv delete mode 100644 Benchmark-Models/Liu_IFACPapersOnLine2025/measurements_scaled.tsv rename Benchmark-Models/Liu_IFACPapersOnLine2025/{age_of_infection_model.xml => model.xml} (99%) create mode 100644 Benchmark-Models/Liu_IFACPapersOnLine2025/visualization.tsv delete mode 100644 Benchmark-Models/Liu_IFACPapersOnLine2025/visualizations.tsv diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/age_of_infection_model.yaml b/Benchmark-Models/Liu_IFACPapersOnLine2025/Liu_IFAC-PapersOnLine2025.yaml similarity index 70% rename from Benchmark-Models/Liu_IFACPapersOnLine2025/age_of_infection_model.yaml rename to Benchmark-Models/Liu_IFACPapersOnLine2025/Liu_IFAC-PapersOnLine2025.yaml index 08d74bc..4a2c774 100644 --- a/Benchmark-Models/Liu_IFACPapersOnLine2025/age_of_infection_model.yaml +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/Liu_IFAC-PapersOnLine2025.yaml @@ -4,10 +4,10 @@ problems: - condition_files: - conditions.tsv measurement_files: - - measurements_scaled.tsv + - measurements.tsv observable_files: - observables.tsv sbml_files: - - age_of_infection_model.xml + - model.xml visualization_files: - - visualizations.tsv \ No newline at end of file + - visualization.tsv \ No newline at end of file diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/measurements.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/measurements.tsv new file mode 100644 index 0000000..051a99e --- /dev/null +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/measurements.tsv @@ -0,0 +1,101 @@ +observableId simulationConditionId measurement time datasetId +tumor_num vvDD 451.73401707247393 0 virus +tumor_num vvDD 477.41006706423315 0 virus +tumor_num vvDD 509.5051295539299 0 virus +tumor_num vvDD 554.4382170395085 0 virus +tumor_num vvDD 852.9222981937005 0 virus +tumor_num vvDD 1016.607116891161 0 virus +tumor_num vvDD 1058.3306981277697 0 virus +tumor_num vvDD 1084.006748119529 0 virus +tumor_num vvDD 1241.2725543190497 0 virus +tumor_num vvDD 1263.7390980618388 0 virus +tumor_num vvDD 679.6089607493324 1 virus +tumor_num vvDD 817.6177294550338 1 virus +tumor_num vvDD 535.1811795456891 1 virus +tumor_num vvDD 824.0367419529714 1 virus +tumor_num vvDD 1055.1211918788 1 virus +tumor_num vvDD 926.740941920006 1 virus +tumor_num vvDD 1571.8516979629405 1 virus +tumor_num vvDD 1331.1387292902025 1 virus +tumor_num vvDD 1481.9855229917855 1 virus +tumor_num vvDD 968.4645231566146 1 virus +tumor_num vvDD 406.80092958689744 2 virus +tumor_num vvDD 483.82907956217286 2 virus +tumor_num vvDD 294.4682108729532 2 virus +tumor_num vvDD 885.0173606833995 2 virus +tumor_num vvDD 291.25870462398325 2 virus +tumor_num vvDD 814.4082232060639 2 virus +tumor_num vvDD 958.836004409705 2 virus +tumor_num vvDD 1119.3113168581956 2 virus +tumor_num vvDD 1132.1493418540751 2 virus +tumor_num vvDD 1000.5595856463136 2 virus +tumor_num vvDD 355.4488296033791 3 virus +tumor_num vvDD 349.0298171054393 3 virus +tumor_num vvDD 220.64956714664766 3 virus +tumor_num vvDD 194.97351715488847 3 virus +tumor_num vvDD 252.74462963634662 3 virus +tumor_num vvDD 422.84846083174693 3 virus +tumor_num vvDD 772.6846419694551 3 virus +tumor_num vvDD 464.5720420683534 3 virus +tumor_num vvDD 785.5226669653348 3 virus +tumor_num vvDD 339.40129835853173 3 virus +tumor_num vvDD 50.545735951247316 4 virus +tumor_num vvDD 101.89783593476568 4 virus +tumor_num vvDD 76.2217859430065 4 virus +tumor_num vvDD 53.75524220021722 4 virus +tumor_num vvDD 191.76401090591855 4 virus +tumor_num vvDD 262.3731483832563 4 virus +tumor_num vvDD 589.7427857781752 4 virus +tumor_num vvDD 345.8203108564694 4 virus +tumor_num vvDD 631.4663670147839 4 virus +tumor_num vvDD 374.7058670971985 4 virus +tumor_num ctrl 349.1039275702164 0 control +tumor_num ctrl 370.50979635893606 0 control +tumor_num ctrl 407.93829872021803 0 control +tumor_num ctrl 552.3499369974998 0 control +tumor_num ctrl 632.5786249293225 0 control +tumor_num ctrl 657.550182543784 0 control +tumor_num ctrl 945.4762838668787 0 control +tumor_num ctrl 985.5848518293386 0 control +tumor_num ctrl 1244.9967188123485 0 control +tumor_num ctrl 1343.9454339282627 0 control +tumor_num ctrl 508.3483427091911 1 control +tumor_num ctrl 323.8108084590962 1 control +tumor_num ctrl 516.3654354989194 1 control +tumor_num ctrl 917.5146511614834 1 control +tumor_num ctrl 965.6460879171242 1 control +tumor_num ctrl 830.874501593137 1 control +tumor_num ctrl 1345.400986797869 1 control +tumor_num ctrl 1404.2411339513233 1 control +tumor_num ctrl 1086.00067182176 1 control +tumor_num ctrl 1372.138106771691 1 control +tumor_num ctrl 648.8611786571674 2 control +tumor_num ctrl 343.986388512792 2 control +tumor_num ctrl 480.36360598998806 2 control +tumor_num ctrl 1250.5821141492872 2 control +tumor_num ctrl 1140.9304646390121 2 control +tumor_num ctrl 771.4696645965797 2 control +tumor_num ctrl 1400.3481076254745 2 control +tumor_num ctrl 1357.553698058382 2 control +tumor_num ctrl 1400.3423316220221 2 control +tumor_num ctrl 1592.8854066549445 2 control +tumor_num ctrl 612.8651251516885 3 control +tumor_num ctrl 441.73369491093814 3 control +tumor_num ctrl 449.7392356937657 3 control +tumor_num ctrl 1091.5802911552485 3 control +tumor_num ctrl 1265.4091150075299 3 control +tumor_num ctrl 959.3493729329441 3 control +tumor_num ctrl 1669.2210682609186 3 control +tumor_num ctrl 1441.9064524540886 3 control +tumor_num ctrl 1262.7232734028994 3 control +tumor_num ctrl 1749.461308199642 3 control +tumor_num ctrl 705.2811803647304 4 control +tumor_num ctrl 416.469455817074 4 control +tumor_num ctrl 496.70391975234486 4 control +tumor_num ctrl 1499.550966893223 4 control +tumor_num ctrl 1357.8136182136711 4 control +tumor_num ctrl 1026.0423760760882 4 control +tumor_num ctrl 1531.6539940728533 4 control +tumor_num ctrl 1700.1226867227788 4 control +tumor_num ctrl 1470.1280053147707 4 control +tumor_num ctrl 1876.6258001727879 4 control \ No newline at end of file diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/measurements_scaled.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/measurements_scaled.tsv deleted file mode 100644 index 2fa1f20..0000000 --- a/Benchmark-Models/Liu_IFACPapersOnLine2025/measurements_scaled.tsv +++ /dev/null @@ -1,101 +0,0 @@ -observableId simulationConditionId measurement time -tumor_num vvDD 451.73401707247393 0 -tumor_num vvDD 477.41006706423315 0 -tumor_num vvDD 509.5051295539299 0 -tumor_num vvDD 554.4382170395085 0 -tumor_num vvDD 852.9222981937005 0 -tumor_num vvDD 1016.607116891161 0 -tumor_num vvDD 1058.3306981277697 0 -tumor_num vvDD 1084.006748119529 0 -tumor_num vvDD 1241.2725543190497 0 -tumor_num vvDD 1263.7390980618388 0 -tumor_num vvDD 679.6089607493324 1 -tumor_num vvDD 817.6177294550338 1 -tumor_num vvDD 535.1811795456891 1 -tumor_num vvDD 824.0367419529714 1 -tumor_num vvDD 1055.1211918788 1 -tumor_num vvDD 926.740941920006 1 -tumor_num vvDD 1571.8516979629405 1 -tumor_num vvDD 1331.1387292902025 1 -tumor_num vvDD 1481.9855229917855 1 -tumor_num vvDD 968.4645231566146 1 -tumor_num vvDD 406.80092958689744 2 -tumor_num vvDD 483.82907956217286 2 -tumor_num vvDD 294.4682108729532 2 -tumor_num vvDD 885.0173606833995 2 -tumor_num vvDD 291.25870462398325 2 -tumor_num vvDD 814.4082232060639 2 -tumor_num vvDD 958.836004409705 2 -tumor_num vvDD 1119.3113168581956 2 -tumor_num vvDD 1132.1493418540751 2 -tumor_num vvDD 1000.5595856463136 2 -tumor_num vvDD 355.4488296033791 3 -tumor_num vvDD 349.0298171054393 3 -tumor_num vvDD 220.64956714664766 3 -tumor_num vvDD 194.97351715488847 3 -tumor_num vvDD 252.74462963634662 3 -tumor_num vvDD 422.84846083174693 3 -tumor_num vvDD 772.6846419694551 3 -tumor_num vvDD 464.5720420683534 3 -tumor_num vvDD 785.5226669653348 3 -tumor_num vvDD 339.40129835853173 3 -tumor_num vvDD 50.545735951247316 4 -tumor_num vvDD 101.89783593476568 4 -tumor_num vvDD 76.2217859430065 4 -tumor_num vvDD 53.75524220021722 4 -tumor_num vvDD 191.76401090591855 4 -tumor_num vvDD 262.3731483832563 4 -tumor_num vvDD 589.7427857781752 4 -tumor_num vvDD 345.8203108564694 4 -tumor_num vvDD 631.4663670147839 4 -tumor_num vvDD 374.7058670971985 4 -tumor_num ctrl 349.1039275702164 0 -tumor_num ctrl 370.50979635893606 0 -tumor_num ctrl 407.93829872021803 0 -tumor_num ctrl 552.3499369974998 0 -tumor_num ctrl 632.5786249293225 0 -tumor_num ctrl 657.550182543784 0 -tumor_num ctrl 945.4762838668787 0 -tumor_num ctrl 985.5848518293386 0 -tumor_num ctrl 1244.9967188123485 0 -tumor_num ctrl 1343.9454339282627 0 -tumor_num ctrl 508.3483427091911 1 -tumor_num ctrl 323.8108084590962 1 -tumor_num ctrl 516.3654354989194 1 -tumor_num ctrl 917.5146511614834 1 -tumor_num ctrl 965.6460879171242 1 -tumor_num ctrl 830.874501593137 1 -tumor_num ctrl 1345.400986797869 1 -tumor_num ctrl 1404.2411339513233 1 -tumor_num ctrl 1086.00067182176 1 -tumor_num ctrl 1372.138106771691 1 -tumor_num ctrl 648.8611786571674 2 -tumor_num ctrl 343.986388512792 2 -tumor_num ctrl 480.36360598998806 2 -tumor_num ctrl 1250.5821141492872 2 -tumor_num ctrl 1140.9304646390121 2 -tumor_num ctrl 771.4696645965797 2 -tumor_num ctrl 1400.3481076254745 2 -tumor_num ctrl 1357.553698058382 2 -tumor_num ctrl 1400.3423316220221 2 -tumor_num ctrl 1592.8854066549445 2 -tumor_num ctrl 612.8651251516885 3 -tumor_num ctrl 441.73369491093814 3 -tumor_num ctrl 449.7392356937657 3 -tumor_num ctrl 1091.5802911552485 3 -tumor_num ctrl 1265.4091150075299 3 -tumor_num ctrl 959.3493729329441 3 -tumor_num ctrl 1669.2210682609186 3 -tumor_num ctrl 1441.9064524540886 3 -tumor_num ctrl 1262.7232734028994 3 -tumor_num ctrl 1749.461308199642 3 -tumor_num ctrl 705.2811803647304 4 -tumor_num ctrl 416.469455817074 4 -tumor_num ctrl 496.70391975234486 4 -tumor_num ctrl 1499.550966893223 4 -tumor_num ctrl 1357.8136182136711 4 -tumor_num ctrl 1026.0423760760882 4 -tumor_num ctrl 1531.6539940728533 4 -tumor_num ctrl 1700.1226867227788 4 -tumor_num ctrl 1470.1280053147707 4 -tumor_num ctrl 1876.6258001727879 4 diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/age_of_infection_model.xml b/Benchmark-Models/Liu_IFACPapersOnLine2025/model.xml similarity index 99% rename from Benchmark-Models/Liu_IFACPapersOnLine2025/age_of_infection_model.xml rename to Benchmark-Models/Liu_IFACPapersOnLine2025/model.xml index edd595e..d07b90a 100644 --- a/Benchmark-Models/Liu_IFACPapersOnLine2025/age_of_infection_model.xml +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/model.xml @@ -1,6 +1,6 @@ - + diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/visualization.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/visualization.tsv new file mode 100644 index 0000000..e6a0993 --- /dev/null +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/visualization.tsv @@ -0,0 +1,3 @@ +plotId plotTypeData plotTypeSimulation xValues xLabel yValues yLabel datasetId legendEntry +plot1 MeanAndSD ScatterPlot time Time [Days] tumor_num Tumor [#] control Control +plot1 MeanAndSD ScatterPlot time Time [Days] tumor_num Tumor [#] virus OncVirus diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/visualizations.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/visualizations.tsv deleted file mode 100644 index 137103f..0000000 --- a/Benchmark-Models/Liu_IFACPapersOnLine2025/visualizations.tsv +++ /dev/null @@ -1,2 +0,0 @@ -plotId plotTypeData plotTypeSimulation xValues xLabel yValues yLabel legendEntry -plot1 MeanAndSD ScatterPlot condition Condition tumor_num Tumor Number Model From 532f5e9cc4ac3eaef914e75d550e3d6e8d1fd351 Mon Sep 17 00:00:00 2001 From: Maren Philipps Date: Sun, 5 Jan 2025 18:29:43 +0100 Subject: [PATCH 05/13] add estimated parameters --- .../individual-based/parameters.tsv | 58 +++++++++---------- .../Liu_IFACPapersOnLine2025/parameters.tsv | 20 +++---- 2 files changed, 39 insertions(+), 39 deletions(-) diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/parameters.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/parameters.tsv index 79a7a3b..9d54b45 100644 --- a/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/parameters.tsv +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/parameters.tsv @@ -1,30 +1,30 @@ parameterId parameterName parameterScale lowerBound upperBound nominalValue estimate parameterType -rho rho log10 0.42 1.66 1 1 -kappa kappa log10 100.0 100000.0 1 1 -psi psi log10 1e-10 0.01 1 1 -phi phi log10 1e-08 100000000.0 1 1 -beta beta log10 1.0 10000.0 1 1 -alpha alpha log10 0.0001 1000.0 1 1 -delta delta log10 0.01 100.0 1 1 -xi_c_1 xi_c_1 log10 1e-07 1.0 1 1 -xi_c_2 xi_c_2 log10 1e-07 1.0 1 1 -xi_c_3 xi_c_3 log10 1e-07 1.0 1 1 -xi_c_4 xi_c_4 log10 1e-07 1.0 1 1 -xi_c_5 xi_c_5 log10 1e-07 1.0 1 1 -xi_c_6 xi_c_6 log10 1e-07 1.0 1 1 -xi_c_7 xi_c_7 log10 1e-07 1.0 1 1 -xi_c_8 xi_c_8 log10 1e-07 1.0 1 1 -xi_c_9 xi_c_9 log10 1e-07 1.0 1 1 -xi_c_10 xi_c_10 log10 1e-07 1.0 1 1 -xi_v_1 xi_v_1 log10 1e-07 1.0 1 1 -xi_v_2 xi_v_2 log10 1e-07 1.0 1 1 -xi_v_3 xi_v_3 log10 1e-07 1.0 1 1 -xi_v_4 xi_v_4 log10 1e-07 1.0 1 1 -xi_v_5 xi_v_5 log10 1e-07 1.0 1 1 -xi_v_6 xi_v_6 log10 1e-07 1.0 1 1 -xi_v_7 xi_v_7 log10 1e-07 1.0 1 1 -xi_v_8 xi_v_8 log10 1e-07 1.0 1 1 -xi_v_9 xi_v_9 log10 1e-07 1.0 1 1 -xi_v_10 xi_v_10 log10 1e-07 1.0 1 1 -sigma_a sigma_a log10 10.0 100000.0 1 1 -sigma_b sigma_b log10 0.0001 100.0 1 1 +rho rho log10 0.42 1.66 1.2829082108573162 1 +kappa kappa log10 100.0 100000.0 1517.725395396992 1 +psi psi log10 1e-10 0.01 3.5025564678683694e-09 1 +phi phi log10 1e-08 100000000.0 3.0858194820075244 1 +beta beta log10 1.0 10000.0 1.0650312622041425 1 +alpha alpha log10 0.0001 1000.0 3.0921432963756565 1 +delta delta log10 0.01 100.0 0.549521198465029 1 +xi_c_1 xi_c_1 log10 1e-07 1.0 0.015593530549184092 1 +xi_c_2 xi_c_2 log10 1e-07 1.0 0.004108874191488457 1 +xi_c_3 xi_c_3 log10 1e-07 1.0 0.005715438594388586 1 +xi_c_4 xi_c_4 log10 1e-07 1.0 0.40012115137012616 1 +xi_c_5 xi_c_5 log10 1e-07 1.0 0.4519816372520485 1 +xi_c_6 xi_c_6 log10 1e-07 1.0 0.17643679894199796 1 +xi_c_7 xi_c_7 log10 1e-07 1.0 1.0 1 +xi_c_8 xi_c_8 log10 1e-07 1.0 1.0 1 +xi_c_9 xi_c_9 log10 1e-07 1.0 1.0 1 +xi_c_10 xi_c_10 log10 1e-07 1.0 1.0 1 +xi_v_1 xi_v_1 log10 1e-07 1.0 0.23681777196970688 1 +xi_v_2 xi_v_2 log10 1e-07 1.0 0.33385887248811597 1 +xi_v_3 xi_v_3 log10 1e-07 1.0 0.15154611096080445 1 +xi_v_4 xi_v_4 log10 1e-07 1.0 0.45642545748851887 1 +xi_v_5 xi_v_5 log10 1e-07 1.0 0.751351262427366 1 +xi_v_6 xi_v_6 log10 1e-07 1.0 1.0 1 +xi_v_7 xi_v_7 log10 1e-07 1.0 1.0 1 +xi_v_8 xi_v_8 log10 1e-07 1.0 1.0 1 +xi_v_9 xi_v_9 log10 1e-07 1.0 1.0 1 +xi_v_10 xi_v_10 log10 1e-07 1.0 1.0 1 +sigma_a sigma_a log10 10.0 100000.0 238.8595871521549 1 +sigma_b sigma_b log10 0.0001 100.0 0.00010397840341525495 1 diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/parameters.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/parameters.tsv index 7cefe16..6ea78c0 100644 --- a/Benchmark-Models/Liu_IFACPapersOnLine2025/parameters.tsv +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/parameters.tsv @@ -1,10 +1,10 @@ -parameterId parameterName parameterScale lowerBound upperBound nominalValue estimate parameterType -rho rho log10 0.42 1.66 1 1 -kappa kappa log10 100.0 100000.0 1 1 -psi psi log10 1e-10 0.01 1 1 -phi phi log10 1e-08 100000000.0 1 1 -beta beta log10 1.0 10000.0 1 1 -alpha alpha log10 0.0001 1000.0 1 1 -delta delta log10 0.01 100.0 1 1 -sigma_a sigma_a log10 10.0 100000.0 1 1 -sigma_b sigma_b log10 0.0001 100.0 1 1 +parameterId parameterName parameterScale lowerBound upperBound nominalValue estimate +rho rho log10 0.42 1.66 1.3719998890173604 1 +kappa kappa log10 100.0 100000.0 1138.1028737412514 1 +psi psi log10 1e-10 0.01 3.0451973420634607e-09 1 +phi phi log10 1e-08 100000000.0 2.9021941106845426 1 +beta beta log10 1.0 10000.0 1.0541567420359819 1 +alpha alpha log10 0.0001 1000.0 2.9016154167675983 1 +delta delta log10 0.01 100.0 0.37236432467696445 1 +sigma_a sigma_a log10 10.0 100000.0 166.4831321759065 1 +sigma_b sigma_b log10 0.0001 100.0 0.35929982754367545 1 From be8b2c3270f282958218e1ed113c5605841a0800 Mon Sep 17 00:00:00 2001 From: Maren Philipps Date: Sun, 5 Jan 2025 19:03:52 +0100 Subject: [PATCH 06/13] add simulated data --- ...imulatedData_Liu_IFAC-PapersOnLine2025.tsv | 101 ++++++++++++++++++ 1 file changed, 101 insertions(+) create mode 100644 Benchmark-Models/Liu_IFACPapersOnLine2025/simulatedData_Liu_IFAC-PapersOnLine2025.tsv diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/simulatedData_Liu_IFAC-PapersOnLine2025.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/simulatedData_Liu_IFAC-PapersOnLine2025.tsv new file mode 100644 index 0000000..45c9c6f --- /dev/null +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/simulatedData_Liu_IFAC-PapersOnLine2025.tsv @@ -0,0 +1,101 @@ +observableId simulationConditionId simulation time datasetId +tumor_num ctrl 775.2977296644885 0 control +tumor_num ctrl 775.2977296644885 0 control +tumor_num ctrl 775.2977296644885 0 control +tumor_num ctrl 775.2977296644885 0 control +tumor_num ctrl 775.2977296644885 0 control +tumor_num ctrl 775.2977296644885 0 control +tumor_num ctrl 775.2977296644885 0 control +tumor_num ctrl 775.2977296644885 0 control +tumor_num ctrl 775.2977296644885 0 control +tumor_num ctrl 775.2977296644885 0 control +tumor_num ctrl 1017.3684154380732 1 control +tumor_num ctrl 1017.3684154380732 1 control +tumor_num ctrl 1017.3684154380732 1 control +tumor_num ctrl 1017.3684154380732 1 control +tumor_num ctrl 1017.3684154380732 1 control +tumor_num ctrl 1017.3684154380732 1 control +tumor_num ctrl 1017.3684154380732 1 control +tumor_num ctrl 1017.3684154380732 1 control +tumor_num ctrl 1017.3684154380732 1 control +tumor_num ctrl 1017.3684154380732 1 control +tumor_num ctrl 1104.8519276179647 2 control +tumor_num ctrl 1104.8519276179647 2 control +tumor_num ctrl 1104.8519276179647 2 control +tumor_num ctrl 1104.8519276179647 2 control +tumor_num ctrl 1104.8519276179647 2 control +tumor_num ctrl 1104.8519276179647 2 control +tumor_num ctrl 1104.8519276179647 2 control +tumor_num ctrl 1104.8519276179647 2 control +tumor_num ctrl 1104.8519276179647 2 control +tumor_num ctrl 1104.8519276179647 2 control +tumor_num ctrl 1129.4824924755844 3 control +tumor_num ctrl 1129.4824924755844 3 control +tumor_num ctrl 1129.4824924755844 3 control +tumor_num ctrl 1129.4824924755844 3 control +tumor_num ctrl 1129.4824924755844 3 control +tumor_num ctrl 1129.4824924755844 3 control +tumor_num ctrl 1129.4824924755844 3 control +tumor_num ctrl 1129.4824924755844 3 control +tumor_num ctrl 1129.4824924755844 3 control +tumor_num ctrl 1129.4824924755844 3 control +tumor_num ctrl 1135.9041895344703 4 control +tumor_num ctrl 1135.9041895344703 4 control +tumor_num ctrl 1135.9041895344703 4 control +tumor_num ctrl 1135.9041895344703 4 control +tumor_num ctrl 1135.9041895344703 4 control +tumor_num ctrl 1135.9041895344703 4 control +tumor_num ctrl 1135.9041895344703 4 control +tumor_num ctrl 1135.9041895344703 4 control +tumor_num ctrl 1135.9041895344703 4 control +tumor_num ctrl 1135.9041895344703 4 control +tumor_num vvDD 775.2977296644885 0 virus +tumor_num vvDD 775.2977296644885 0 virus +tumor_num vvDD 775.2977296644885 0 virus +tumor_num vvDD 775.2977296644885 0 virus +tumor_num vvDD 775.2977296644885 0 virus +tumor_num vvDD 775.2977296644885 0 virus +tumor_num vvDD 775.2977296644885 0 virus +tumor_num vvDD 775.2977296644885 0 virus +tumor_num vvDD 775.2977296644885 0 virus +tumor_num vvDD 775.2977296644885 0 virus +tumor_num vvDD 956.1071181150951 1 virus +tumor_num vvDD 956.1071181150951 1 virus +tumor_num vvDD 956.1071181150951 1 virus +tumor_num vvDD 956.1071181150951 1 virus +tumor_num vvDD 956.1071181150951 1 virus +tumor_num vvDD 956.1071181150951 1 virus +tumor_num vvDD 956.1071181150951 1 virus +tumor_num vvDD 956.1071181150951 1 virus +tumor_num vvDD 956.1071181150951 1 virus +tumor_num vvDD 956.1071181150951 1 virus +tumor_num vvDD 709.9529215779593 2 virus +tumor_num vvDD 709.9529215779593 2 virus +tumor_num vvDD 709.9529215779593 2 virus +tumor_num vvDD 709.9529215779593 2 virus +tumor_num vvDD 709.9529215779593 2 virus +tumor_num vvDD 709.9529215779593 2 virus +tumor_num vvDD 709.9529215779593 2 virus +tumor_num vvDD 709.9529215779593 2 virus +tumor_num vvDD 709.9529215779593 2 virus +tumor_num vvDD 709.9529215779593 2 virus +tumor_num vvDD 433.3851417515748 3 virus +tumor_num vvDD 433.3851417515748 3 virus +tumor_num vvDD 433.3851417515748 3 virus +tumor_num vvDD 433.3851417515748 3 virus +tumor_num vvDD 433.3851417515748 3 virus +tumor_num vvDD 433.3851417515748 3 virus +tumor_num vvDD 433.3851417515748 3 virus +tumor_num vvDD 433.3851417515748 3 virus +tumor_num vvDD 433.3851417515748 3 virus +tumor_num vvDD 433.3851417515748 3 virus +tumor_num vvDD 264.52757975472423 4 virus +tumor_num vvDD 264.52757975472423 4 virus +tumor_num vvDD 264.52757975472423 4 virus +tumor_num vvDD 264.52757975472423 4 virus +tumor_num vvDD 264.52757975472423 4 virus +tumor_num vvDD 264.52757975472423 4 virus +tumor_num vvDD 264.52757975472423 4 virus +tumor_num vvDD 264.52757975472423 4 virus +tumor_num vvDD 264.52757975472423 4 virus +tumor_num vvDD 264.52757975472423 4 virus From 2e61708dca958b866392b8670b4e8033a09b3638 Mon Sep 17 00:00:00 2001 From: Maren Philipps Date: Mon, 6 Jan 2025 16:38:53 +0100 Subject: [PATCH 07/13] update PEtab ID --- ...-PapersOnLine2025.yaml => Liu_IFACPapersOnLine2025.yaml} | 0 ..._model.yaml => Liu_IFACPapersOnLine2025_individual.yaml} | 6 +++--- ...ased_age_of_infection_model.xml => model_individual.xml} | 2 +- ...e2025.tsv => simulatedData_Liu_IFACPapersOnLine2025.tsv} | 0 4 files changed, 4 insertions(+), 4 deletions(-) rename Benchmark-Models/Liu_IFACPapersOnLine2025/{Liu_IFAC-PapersOnLine2025.yaml => Liu_IFACPapersOnLine2025.yaml} (100%) rename Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/{individual_based_age_of_infection_model.yaml => Liu_IFACPapersOnLine2025_individual.yaml} (66%) rename Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/{individual_based_age_of_infection_model.xml => model_individual.xml} (99%) rename Benchmark-Models/Liu_IFACPapersOnLine2025/{simulatedData_Liu_IFAC-PapersOnLine2025.tsv => simulatedData_Liu_IFACPapersOnLine2025.tsv} (100%) diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/Liu_IFAC-PapersOnLine2025.yaml b/Benchmark-Models/Liu_IFACPapersOnLine2025/Liu_IFACPapersOnLine2025.yaml similarity index 100% rename from Benchmark-Models/Liu_IFACPapersOnLine2025/Liu_IFAC-PapersOnLine2025.yaml rename to Benchmark-Models/Liu_IFACPapersOnLine2025/Liu_IFACPapersOnLine2025.yaml diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/individual_based_age_of_infection_model.yaml b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/Liu_IFACPapersOnLine2025_individual.yaml similarity index 66% rename from Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/individual_based_age_of_infection_model.yaml rename to Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/Liu_IFACPapersOnLine2025_individual.yaml index ee5c0b4..1f5b62c 100644 --- a/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/individual_based_age_of_infection_model.yaml +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/Liu_IFACPapersOnLine2025_individual.yaml @@ -4,10 +4,10 @@ problems: - condition_files: - conditions.tsv measurement_files: - - measurements_scaled.tsv + - measurements.tsv observable_files: - observables.tsv sbml_files: - - individual_based_age_of_infection_model.xml + - model_individual.xml visualization_files: - - visualizations.tsv \ No newline at end of file + - visualization.tsv \ No newline at end of file diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/individual_based_age_of_infection_model.xml b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/model_individual.xml similarity index 99% rename from Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/individual_based_age_of_infection_model.xml rename to Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/model_individual.xml index 8b5f557..3b26f7c 100644 --- a/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/individual_based_age_of_infection_model.xml +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/model_individual.xml @@ -1,6 +1,6 @@ - + diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/simulatedData_Liu_IFAC-PapersOnLine2025.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/simulatedData_Liu_IFACPapersOnLine2025.tsv similarity index 100% rename from Benchmark-Models/Liu_IFACPapersOnLine2025/simulatedData_Liu_IFAC-PapersOnLine2025.tsv rename to Benchmark-Models/Liu_IFACPapersOnLine2025/simulatedData_Liu_IFACPapersOnLine2025.tsv From 721ceca06528a666c5391b860e7181f4c3b0d211 Mon Sep 17 00:00:00 2001 From: Maren Philipps Date: Mon, 6 Jan 2025 16:39:47 +0100 Subject: [PATCH 08/13] fix PEtab subproblem --- .../individual-based/measurements.tsv | 101 ++++++++++++++++++ .../individual-based/measurements_scaled.tsv | 101 ------------------ .../individual-based/parameters.tsv | 60 +++++------ ...ta_Liu_IFACPapersOnLine2025_individual.tsv | 101 ++++++++++++++++++ 4 files changed, 232 insertions(+), 131 deletions(-) create mode 100644 Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/measurements.tsv delete mode 100644 Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/measurements_scaled.tsv create mode 100644 Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/simulatedData_Liu_IFACPapersOnLine2025_individual.tsv diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/measurements.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/measurements.tsv new file mode 100644 index 0000000..a883dc4 --- /dev/null +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/measurements.tsv @@ -0,0 +1,101 @@ +observableId simulationConditionId measurement time datasetId +tumor_num vvDD_1 451.73401707247393 0 virus_1 +tumor_num vvDD_2 477.41006706423315 0 virus_2 +tumor_num vvDD_3 509.5051295539299 0 virus_3 +tumor_num vvDD_4 554.4382170395085 0 virus_4 +tumor_num vvDD_5 852.9222981937005 0 virus_5 +tumor_num vvDD_6 1016.607116891161 0 virus_6 +tumor_num vvDD_7 1058.3306981277697 0 virus_7 +tumor_num vvDD_8 1084.006748119529 0 virus_8 +tumor_num vvDD_9 1241.2725543190497 0 virus_9 +tumor_num vvDD_10 1263.7390980618388 0 virus_10 +tumor_num vvDD_1 679.6089607493324 1 virus_1 +tumor_num vvDD_2 817.6177294550338 1 virus_2 +tumor_num vvDD_3 535.1811795456891 1 virus_3 +tumor_num vvDD_4 824.0367419529714 1 virus_4 +tumor_num vvDD_5 1055.1211918788 1 virus_5 +tumor_num vvDD_6 926.740941920006 1 virus_6 +tumor_num vvDD_7 1571.8516979629405 1 virus_7 +tumor_num vvDD_8 1331.1387292902025 1 virus_8 +tumor_num vvDD_9 1481.9855229917855 1 virus_9 +tumor_num vvDD_10 968.4645231566146 1 virus_10 +tumor_num vvDD_1 406.80092958689744 2 virus_1 +tumor_num vvDD_2 483.82907956217286 2 virus_2 +tumor_num vvDD_3 294.4682108729532 2 virus_3 +tumor_num vvDD_4 885.0173606833995 2 virus_4 +tumor_num vvDD_5 291.25870462398325 2 virus_5 +tumor_num vvDD_6 814.4082232060639 2 virus_6 +tumor_num vvDD_7 958.836004409705 2 virus_7 +tumor_num vvDD_8 1119.3113168581956 2 virus_8 +tumor_num vvDD_9 1132.1493418540751 2 virus_9 +tumor_num vvDD_10 1000.5595856463136 2 virus_10 +tumor_num vvDD_1 355.4488296033791 3 virus_1 +tumor_num vvDD_2 349.0298171054393 3 virus_2 +tumor_num vvDD_3 220.64956714664766 3 virus_3 +tumor_num vvDD_4 194.97351715488847 3 virus_4 +tumor_num vvDD_5 252.74462963634662 3 virus_5 +tumor_num vvDD_6 422.84846083174693 3 virus_6 +tumor_num vvDD_7 772.6846419694551 3 virus_7 +tumor_num vvDD_8 464.5720420683534 3 virus_8 +tumor_num vvDD_9 785.5226669653348 3 virus_9 +tumor_num vvDD_10 339.40129835853173 3 virus_10 +tumor_num vvDD_1 50.545735951247316 4 virus_1 +tumor_num vvDD_2 101.89783593476568 4 virus_2 +tumor_num vvDD_3 76.2217859430065 4 virus_3 +tumor_num vvDD_4 53.75524220021722 4 virus_4 +tumor_num vvDD_5 191.76401090591855 4 virus_5 +tumor_num vvDD_6 262.3731483832563 4 virus_6 +tumor_num vvDD_7 589.7427857781752 4 virus_7 +tumor_num vvDD_8 345.8203108564694 4 virus_8 +tumor_num vvDD_9 631.4663670147839 4 virus_9 +tumor_num vvDD_10 374.7058670971985 4 virus_10 +tumor_num ctrl_1 349.1039275702164 0 control_1 +tumor_num ctrl_2 370.50979635893606 0 control_2 +tumor_num ctrl_3 407.93829872021803 0 control_3 +tumor_num ctrl_4 552.3499369974998 0 control_4 +tumor_num ctrl_5 632.5786249293225 0 control_5 +tumor_num ctrl_6 657.550182543784 0 control_6 +tumor_num ctrl_7 945.4762838668787 0 control_7 +tumor_num ctrl_8 985.5848518293386 0 control_8 +tumor_num ctrl_9 1244.9967188123485 0 control_9 +tumor_num ctrl_10 1343.9454339282627 0 control_10 +tumor_num ctrl_1 508.3483427091911 1 control_1 +tumor_num ctrl_2 323.8108084590962 1 control_2 +tumor_num ctrl_3 516.3654354989194 1 control_3 +tumor_num ctrl_4 917.5146511614834 1 control_4 +tumor_num ctrl_5 965.6460879171242 1 control_5 +tumor_num ctrl_6 830.874501593137 1 control_6 +tumor_num ctrl_7 1345.400986797869 1 control_7 +tumor_num ctrl_8 1404.2411339513233 1 control_8 +tumor_num ctrl_9 1086.00067182176 1 control_9 +tumor_num ctrl_10 1372.138106771691 1 control_10 +tumor_num ctrl_1 648.8611786571674 2 control_1 +tumor_num ctrl_2 343.986388512792 2 control_2 +tumor_num ctrl_3 480.36360598998806 2 control_3 +tumor_num ctrl_4 1250.5821141492872 2 control_4 +tumor_num ctrl_5 1140.9304646390121 2 control_5 +tumor_num ctrl_6 771.4696645965797 2 control_6 +tumor_num ctrl_7 1400.3481076254745 2 control_7 +tumor_num ctrl_8 1357.553698058382 2 control_8 +tumor_num ctrl_9 1400.3423316220221 2 control_9 +tumor_num ctrl_10 1592.8854066549445 2 control_10 +tumor_num ctrl_1 612.8651251516885 3 control_1 +tumor_num ctrl_2 441.73369491093814 3 control_2 +tumor_num ctrl_3 449.7392356937657 3 control_3 +tumor_num ctrl_4 1091.5802911552485 3 control_4 +tumor_num ctrl_5 1265.4091150075299 3 control_5 +tumor_num ctrl_6 959.3493729329441 3 control_6 +tumor_num ctrl_7 1669.2210682609186 3 control_7 +tumor_num ctrl_8 1441.9064524540886 3 control_8 +tumor_num ctrl_9 1262.7232734028994 3 control_9 +tumor_num ctrl_10 1749.461308199642 3 control_10 +tumor_num ctrl_1 705.2811803647304 4 control_1 +tumor_num ctrl_2 416.469455817074 4 control_2 +tumor_num ctrl_3 496.70391975234486 4 control_3 +tumor_num ctrl_4 1499.550966893223 4 control_4 +tumor_num ctrl_5 1357.8136182136711 4 control_5 +tumor_num ctrl_6 1026.0423760760882 4 control_6 +tumor_num ctrl_7 1531.6539940728533 4 control_7 +tumor_num ctrl_8 1700.1226867227788 4 control_8 +tumor_num ctrl_9 1470.1280053147707 4 control_9 +tumor_num ctrl_10 1876.6258001727879 4 control_10 diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/measurements_scaled.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/measurements_scaled.tsv deleted file mode 100644 index 0d16e90..0000000 --- a/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/measurements_scaled.tsv +++ /dev/null @@ -1,101 +0,0 @@ -observableId simulationConditionId measurement time -tumor_num vvDD_1 451.73401707247393 0 -tumor_num vvDD_2 477.41006706423315 0 -tumor_num vvDD_3 509.5051295539299 0 -tumor_num vvDD_4 554.4382170395085 0 -tumor_num vvDD_5 852.9222981937005 0 -tumor_num vvDD_6 1016.607116891161 0 -tumor_num vvDD_7 1058.3306981277697 0 -tumor_num vvDD_8 1084.006748119529 0 -tumor_num vvDD_9 1241.2725543190497 0 -tumor_num vvDD_10 1263.7390980618388 0 -tumor_num vvDD_1 679.6089607493324 1 -tumor_num vvDD_2 817.6177294550338 1 -tumor_num vvDD_3 535.1811795456891 1 -tumor_num vvDD_4 824.0367419529714 1 -tumor_num vvDD_5 1055.1211918788 1 -tumor_num vvDD_6 926.740941920006 1 -tumor_num vvDD_7 1571.8516979629405 1 -tumor_num vvDD_8 1331.1387292902025 1 -tumor_num vvDD_9 1481.9855229917855 1 -tumor_num vvDD_10 968.4645231566146 1 -tumor_num vvDD_1 406.80092958689744 2 -tumor_num vvDD_2 483.82907956217286 2 -tumor_num vvDD_3 294.4682108729532 2 -tumor_num vvDD_4 885.0173606833995 2 -tumor_num vvDD_5 291.25870462398325 2 -tumor_num vvDD_6 814.4082232060639 2 -tumor_num vvDD_7 958.836004409705 2 -tumor_num vvDD_8 1119.3113168581956 2 -tumor_num vvDD_9 1132.1493418540751 2 -tumor_num vvDD_10 1000.5595856463136 2 -tumor_num vvDD_1 355.4488296033791 3 -tumor_num vvDD_2 349.0298171054393 3 -tumor_num vvDD_3 220.64956714664766 3 -tumor_num vvDD_4 194.97351715488847 3 -tumor_num vvDD_5 252.74462963634662 3 -tumor_num vvDD_6 422.84846083174693 3 -tumor_num vvDD_7 772.6846419694551 3 -tumor_num vvDD_8 464.5720420683534 3 -tumor_num vvDD_9 785.5226669653348 3 -tumor_num vvDD_10 339.40129835853173 3 -tumor_num vvDD_1 50.545735951247316 4 -tumor_num vvDD_2 101.89783593476568 4 -tumor_num vvDD_3 76.2217859430065 4 -tumor_num vvDD_4 53.75524220021722 4 -tumor_num vvDD_5 191.76401090591855 4 -tumor_num vvDD_6 262.3731483832563 4 -tumor_num vvDD_7 589.7427857781752 4 -tumor_num vvDD_8 345.8203108564694 4 -tumor_num vvDD_9 631.4663670147839 4 -tumor_num vvDD_10 374.7058670971985 4 -tumor_num ctrl_1 349.1039275702164 0 -tumor_num ctrl_2 370.50979635893606 0 -tumor_num ctrl_3 407.93829872021803 0 -tumor_num ctrl_4 552.3499369974998 0 -tumor_num ctrl_5 632.5786249293225 0 -tumor_num ctrl_6 657.550182543784 0 -tumor_num ctrl_7 945.4762838668787 0 -tumor_num ctrl_8 985.5848518293386 0 -tumor_num ctrl_9 1244.9967188123485 0 -tumor_num ctrl_10 1343.9454339282627 0 -tumor_num ctrl_1 508.3483427091911 1 -tumor_num ctrl_2 323.8108084590962 1 -tumor_num ctrl_3 516.3654354989194 1 -tumor_num ctrl_4 917.5146511614834 1 -tumor_num ctrl_5 965.6460879171242 1 -tumor_num ctrl_6 830.874501593137 1 -tumor_num ctrl_7 1345.400986797869 1 -tumor_num ctrl_8 1404.2411339513233 1 -tumor_num ctrl_9 1086.00067182176 1 -tumor_num ctrl_10 1372.138106771691 1 -tumor_num ctrl_1 648.8611786571674 2 -tumor_num ctrl_2 343.986388512792 2 -tumor_num ctrl_3 480.36360598998806 2 -tumor_num ctrl_4 1250.5821141492872 2 -tumor_num ctrl_5 1140.9304646390121 2 -tumor_num ctrl_6 771.4696645965797 2 -tumor_num ctrl_7 1400.3481076254745 2 -tumor_num ctrl_8 1357.553698058382 2 -tumor_num ctrl_9 1400.3423316220221 2 -tumor_num ctrl_10 1592.8854066549445 2 -tumor_num ctrl_1 612.8651251516885 3 -tumor_num ctrl_2 441.73369491093814 3 -tumor_num ctrl_3 449.7392356937657 3 -tumor_num ctrl_4 1091.5802911552485 3 -tumor_num ctrl_5 1265.4091150075299 3 -tumor_num ctrl_6 959.3493729329441 3 -tumor_num ctrl_7 1669.2210682609186 3 -tumor_num ctrl_8 1441.9064524540886 3 -tumor_num ctrl_9 1262.7232734028994 3 -tumor_num ctrl_10 1749.461308199642 3 -tumor_num ctrl_1 705.2811803647304 4 -tumor_num ctrl_2 416.469455817074 4 -tumor_num ctrl_3 496.70391975234486 4 -tumor_num ctrl_4 1499.550966893223 4 -tumor_num ctrl_5 1357.8136182136711 4 -tumor_num ctrl_6 1026.0423760760882 4 -tumor_num ctrl_7 1531.6539940728533 4 -tumor_num ctrl_8 1700.1226867227788 4 -tumor_num ctrl_9 1470.1280053147707 4 -tumor_num ctrl_10 1876.6258001727879 4 diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/parameters.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/parameters.tsv index 9d54b45..52250e9 100644 --- a/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/parameters.tsv +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/parameters.tsv @@ -1,30 +1,30 @@ -parameterId parameterName parameterScale lowerBound upperBound nominalValue estimate parameterType -rho rho log10 0.42 1.66 1.2829082108573162 1 -kappa kappa log10 100.0 100000.0 1517.725395396992 1 -psi psi log10 1e-10 0.01 3.5025564678683694e-09 1 -phi phi log10 1e-08 100000000.0 3.0858194820075244 1 -beta beta log10 1.0 10000.0 1.0650312622041425 1 -alpha alpha log10 0.0001 1000.0 3.0921432963756565 1 -delta delta log10 0.01 100.0 0.549521198465029 1 -xi_c_1 xi_c_1 log10 1e-07 1.0 0.015593530549184092 1 -xi_c_2 xi_c_2 log10 1e-07 1.0 0.004108874191488457 1 -xi_c_3 xi_c_3 log10 1e-07 1.0 0.005715438594388586 1 -xi_c_4 xi_c_4 log10 1e-07 1.0 0.40012115137012616 1 -xi_c_5 xi_c_5 log10 1e-07 1.0 0.4519816372520485 1 -xi_c_6 xi_c_6 log10 1e-07 1.0 0.17643679894199796 1 -xi_c_7 xi_c_7 log10 1e-07 1.0 1.0 1 -xi_c_8 xi_c_8 log10 1e-07 1.0 1.0 1 -xi_c_9 xi_c_9 log10 1e-07 1.0 1.0 1 -xi_c_10 xi_c_10 log10 1e-07 1.0 1.0 1 -xi_v_1 xi_v_1 log10 1e-07 1.0 0.23681777196970688 1 -xi_v_2 xi_v_2 log10 1e-07 1.0 0.33385887248811597 1 -xi_v_3 xi_v_3 log10 1e-07 1.0 0.15154611096080445 1 -xi_v_4 xi_v_4 log10 1e-07 1.0 0.45642545748851887 1 -xi_v_5 xi_v_5 log10 1e-07 1.0 0.751351262427366 1 -xi_v_6 xi_v_6 log10 1e-07 1.0 1.0 1 -xi_v_7 xi_v_7 log10 1e-07 1.0 1.0 1 -xi_v_8 xi_v_8 log10 1e-07 1.0 1.0 1 -xi_v_9 xi_v_9 log10 1e-07 1.0 1.0 1 -xi_v_10 xi_v_10 log10 1e-07 1.0 1.0 1 -sigma_a sigma_a log10 10.0 100000.0 238.8595871521549 1 -sigma_b sigma_b log10 0.0001 100.0 0.00010397840341525495 1 +parameterId parameterName parameterScale lowerBound upperBound nominalValue estimate +rho rho log10 0.42 1.66 1.2829082108573162 1 +kappa kappa log10 100.0 100000.0 1517.725395396992 1 +psi psi log10 1e-10 0.01 3.5025564678683694e-09 1 +phi phi log10 1e-08 100000000.0 3.0858194820075244 1 +beta beta log10 1.0 10000.0 1.0650312622041425 1 +alpha alpha log10 0.0001 1000.0 3.0921432963756565 1 +delta delta log10 0.01 100.0 0.549521198465029 1 +xi_c_1 xi_c_1 log10 1e-07 1.0 0.015593530549184092 1 +xi_c_2 xi_c_2 log10 1e-07 1.0 0.004108874191488457 1 +xi_c_3 xi_c_3 log10 1e-07 1.0 0.005715438594388586 1 +xi_c_4 xi_c_4 log10 1e-07 1.0 0.40012115137012616 1 +xi_c_5 xi_c_5 log10 1e-07 1.0 0.4519816372520485 1 +xi_c_6 xi_c_6 log10 1e-07 1.0 0.17643679894199796 1 +xi_c_7 xi_c_7 log10 1e-07 1.0 1.0 1 +xi_c_8 xi_c_8 log10 1e-07 1.0 1.0 1 +xi_c_9 xi_c_9 log10 1e-07 1.0 1.0 1 +xi_c_10 xi_c_10 log10 1e-07 1.0 1.0 1 +xi_v_1 xi_v_1 log10 1e-07 1.0 0.23681777196970688 1 +xi_v_2 xi_v_2 log10 1e-07 1.0 0.33385887248811597 1 +xi_v_3 xi_v_3 log10 1e-07 1.0 0.15154611096080445 1 +xi_v_4 xi_v_4 log10 1e-07 1.0 0.45642545748851887 1 +xi_v_5 xi_v_5 log10 1e-07 1.0 0.751351262427366 1 +xi_v_6 xi_v_6 log10 1e-07 1.0 1.0 1 +xi_v_7 xi_v_7 log10 1e-07 1.0 1.0 1 +xi_v_8 xi_v_8 log10 1e-07 1.0 1.0 1 +xi_v_9 xi_v_9 log10 1e-07 1.0 1.0 1 +xi_v_10 xi_v_10 log10 1e-07 1.0 1.0 1 +sigma_a sigma_a log10 10.0 100000.0 238.8595871521549 1 +sigma_b sigma_b log10 0.0001 100.0 0.00010397840341525495 1 diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/simulatedData_Liu_IFACPapersOnLine2025_individual.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/simulatedData_Liu_IFACPapersOnLine2025_individual.tsv new file mode 100644 index 0000000..9b95bec --- /dev/null +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/simulatedData_Liu_IFACPapersOnLine2025_individual.tsv @@ -0,0 +1,101 @@ +observableId simulationConditionId simulation time datasetId +tumor_num ctrl_1 22.26055114595074 0 control_1 +tumor_num ctrl_1 77.33904551666109 1 control_1 +tumor_num ctrl_1 246.2554053460344 2 control_1 +tumor_num ctrl_1 624.2195217238929 3 control_1 +tumor_num ctrl_1 1086.5529104939178 4 control_1 +tumor_num ctrl_10 855.2169058814992 0 control_10 +tumor_num ctrl_10 1249.4024178062066 1 control_10 +tumor_num ctrl_10 1432.4405440921562 2 control_10 +tumor_num ctrl_10 1493.0811359890924 3 control_10 +tumor_num ctrl_10 1510.8124351048816 4 control_10 +tumor_num ctrl_2 5.911781803914768 0 control_2 +tumor_num ctrl_2 21.110116763465285 1 control_2 +tumor_num ctrl_2 73.48196417540083 2 control_2 +tumor_num ctrl_2 235.35048196098248 3 control_2 +tumor_num ctrl_2 604.5349678155902 4 control_2 +tumor_num ctrl_3 8.214238638512759 0 control_3 +tumor_num ctrl_3 29.217462401346623 1 control_3 +tumor_num ctrl_3 100.35404329397257 2 control_3 +tumor_num ctrl_3 308.76216747827107 3 control_3 +tumor_num ctrl_3 727.7524368282859 4 control_3 +tumor_num ctrl_4 452.8203255530103 0 control_4 +tumor_num ctrl_4 918.7389662831866 1 control_4 +tumor_num ctrl_4 1285.3968810941685 2 control_4 +tumor_num ctrl_4 1445.3044579516488 3 control_4 +tumor_num ctrl_4 1496.9312782721781 4 control_4 +tumor_num ctrl_5 497.6033635936474 0 control_5 +tumor_num ctrl_5 967.7266508534578 1 control_5 +tumor_num ctrl_5 1311.140500288747 2 control_5 +tumor_num ctrl_5 1454.205097390625 3 control_5 +tumor_num ctrl_5 1499.5664189237318 4 control_5 +tumor_num ctrl_6 227.04595023610926 0 control_6 +tumor_num ctrl_6 589.1886747791158 1 control_6 +tumor_num ctrl_6 1056.2477744139346 2 control_6 +tumor_num ctrl_6 1353.7551080904732 3 control_6 +tumor_num ctrl_6 1468.4178178570428 4 control_6 +tumor_num ctrl_7 855.2169058814992 0 control_7 +tumor_num ctrl_7 1249.4024178062066 1 control_7 +tumor_num ctrl_7 1432.4405440921562 2 control_7 +tumor_num ctrl_7 1493.0811359890924 3 control_7 +tumor_num ctrl_7 1510.8124351048816 4 control_7 +tumor_num ctrl_8 855.2169058814992 0 control_8 +tumor_num ctrl_8 1249.4024178062066 1 control_8 +tumor_num ctrl_8 1432.4405440921562 2 control_8 +tumor_num ctrl_8 1493.0811359890924 3 control_8 +tumor_num ctrl_8 1510.8124351048816 4 control_8 +tumor_num ctrl_9 855.2169058814992 0 control_9 +tumor_num ctrl_9 1249.4024178062066 1 control_9 +tumor_num ctrl_9 1432.4405440921562 2 control_9 +tumor_num ctrl_9 1493.0811359890924 3 control_9 +tumor_num ctrl_9 1510.8124351048816 4 control_9 +tumor_num vvDD_1 293.8725730462032 0 virus_1 +tumor_num vvDD_1 643.2201140149581 1 virus_1 +tumor_num vvDD_1 617.1246632994361 2 virus_1 +tumor_num vvDD_1 390.8686298897414 3 virus_1 +tumor_num vvDD_1 245.23441223674956 4 virus_1 +tumor_num vvDD_10 855.2169058814992 0 virus_10 +tumor_num vvDD_10 1149.500376575116 1 virus_10 +tumor_num vvDD_10 823.0795807548609 2 virus_10 +tumor_num vvDD_10 467.3346925002291 3 virus_10 +tumor_num vvDD_10 280.60325047783573 4 virus_10 +tumor_num vvDD_2 391.82336068697174 0 virus_2 +tumor_num vvDD_2 772.8630871451893 1 virus_2 +tumor_num vvDD_2 682.132147641495 2 virus_2 +tumor_num vvDD_2 416.84508326723596 3 virus_2 +tumor_num vvDD_2 257.6006853025773 4 virus_2 +tumor_num vvDD_3 198.03635489148448 0 virus_3 +tumor_num vvDD_3 485.5505127993499 1 virus_3 +tumor_num vvDD_3 521.0065684936792 2 virus_3 +tumor_num vvDD_3 348.79221248666715 3 virus_3 +tumor_num vvDD_3 224.38243106318626 4 virus_3 +tumor_num vvDD_4 501.32771719434317 0 virus_4 +tumor_num vvDD_4 890.4814244346633 1 virus_4 +tumor_num vvDD_4 732.7128801403255 2 virus_4 +tumor_num vvDD_4 435.8262495764218 3 virus_4 +tumor_num vvDD_4 266.4042748970078 4 virus_4 +tumor_num vvDD_5 714.971593356841 0 virus_5 +tumor_num vvDD_5 1063.5370355710932 1 virus_5 +tumor_num vvDD_5 795.80640469497 2 virus_5 +tumor_num vvDD_5 458.1311255406502 3 virus_5 +tumor_num vvDD_5 276.5079994286401 4 virus_5 +tumor_num vvDD_6 855.2169058814992 0 virus_6 +tumor_num vvDD_6 1149.500376575116 1 virus_6 +tumor_num vvDD_6 823.0795807548609 2 virus_6 +tumor_num vvDD_6 467.3346925002291 3 virus_6 +tumor_num vvDD_6 280.60325047783573 4 virus_6 +tumor_num vvDD_7 855.2169058814992 0 virus_7 +tumor_num vvDD_7 1149.500376575116 1 virus_7 +tumor_num vvDD_7 823.0795807548609 2 virus_7 +tumor_num vvDD_7 467.3346925002291 3 virus_7 +tumor_num vvDD_7 280.60325047783573 4 virus_7 +tumor_num vvDD_8 855.2169058814992 0 virus_8 +tumor_num vvDD_8 1149.500376575116 1 virus_8 +tumor_num vvDD_8 823.0795807548609 2 virus_8 +tumor_num vvDD_8 467.3346925002291 3 virus_8 +tumor_num vvDD_8 280.60325047783573 4 virus_8 +tumor_num vvDD_9 855.2169058814992 0 virus_9 +tumor_num vvDD_9 1149.500376575116 1 virus_9 +tumor_num vvDD_9 823.0795807548609 2 virus_9 +tumor_num vvDD_9 467.3346925002291 3 virus_9 +tumor_num vvDD_9 280.60325047783573 4 virus_9 From ede623d10492a8418789cba00163d9778bbe0a61 Mon Sep 17 00:00:00 2001 From: Maren Philipps Date: Mon, 6 Jan 2025 16:40:12 +0100 Subject: [PATCH 09/13] add visualization matching manuscript Figures --- .../individual-based/visualization.tsv | 5 +++++ .../individual-based/visualizations.tsv | 2 -- Benchmark-Models/Liu_IFACPapersOnLine2025/visualization.tsv | 6 +++--- 3 files changed, 8 insertions(+), 5 deletions(-) create mode 100644 Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/visualization.tsv delete mode 100644 Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/visualizations.tsv diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/visualization.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/visualization.tsv new file mode 100644 index 0000000..4e23969 --- /dev/null +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/visualization.tsv @@ -0,0 +1,5 @@ +plotId PlotTypeData xValues xOffset xLabel yValues yLabel datasetId legendEntry +Fig6 MeanAndSD time 3 Time [Days] tumor_num Tumor cells [#] control_6 control 6 +Fig6 MeanAndSD time 3 Time [Days] tumor_num Tumor cells [#] virus_1 vvDD 1 +Fig6 MeanAndSD time 3 Time [Days] tumor_num Tumor cells [#] control_7 control 7 +Fig6 MeanAndSD time 3 Time [Days] tumor_num Tumor cells [#] virus_2 vvDD 2 diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/visualizations.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/visualizations.tsv deleted file mode 100644 index 137103f..0000000 --- a/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/visualizations.tsv +++ /dev/null @@ -1,2 +0,0 @@ -plotId plotTypeData plotTypeSimulation xValues xLabel yValues yLabel legendEntry -plot1 MeanAndSD ScatterPlot condition Condition tumor_num Tumor Number Model diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/visualization.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/visualization.tsv index e6a0993..e68ee52 100644 --- a/Benchmark-Models/Liu_IFACPapersOnLine2025/visualization.tsv +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/visualization.tsv @@ -1,3 +1,3 @@ -plotId plotTypeData plotTypeSimulation xValues xLabel yValues yLabel datasetId legendEntry -plot1 MeanAndSD ScatterPlot time Time [Days] tumor_num Tumor [#] control Control -plot1 MeanAndSD ScatterPlot time Time [Days] tumor_num Tumor [#] virus OncVirus +plotId PlotTypeData xValues xOffset xLabel yValues yLabel datasetId legendEntry Color +Fig4b MeanAndSD time 3 Time [Days] tumor_num Tumor cells [#] control control red +Fig4b MeanAndSD time 3 Time [Days] tumor_num Tumor cells [#] virus vvDD blue From bd6016966f270720c4dda721f623241b77223295 Mon Sep 17 00:00:00 2001 From: Maren Philipps Date: Thu, 1 Jan 2026 15:54:37 +0100 Subject: [PATCH 10/13] add DOI --- .../individual-based/model_individual.xml | 11 +++++++++++ Benchmark-Models/Liu_IFACPapersOnLine2025/model.xml | 11 +++++++++++ 2 files changed, 22 insertions(+) diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/model_individual.xml b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/model_individual.xml index 3b26f7c..a45b444 100644 --- a/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/model_individual.xml +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/model_individual.xml @@ -1,6 +1,17 @@ + + + + + + + + + + + diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/model.xml b/Benchmark-Models/Liu_IFACPapersOnLine2025/model.xml index d07b90a..60cf206 100644 --- a/Benchmark-Models/Liu_IFACPapersOnLine2025/model.xml +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/model.xml @@ -1,6 +1,17 @@ + + + + + + + + + + + From 9a9641af83ece7098e29be581886696ebb4978c1 Mon Sep 17 00:00:00 2001 From: Maren Philipps Date: Thu, 1 Jan 2026 16:00:00 +0100 Subject: [PATCH 11/13] update readme bmp --- README.md | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index a3b6178..16ac341 100644 --- a/README.md +++ b/README.md @@ -29,12 +29,13 @@ A sortable version of the table is available | [Fiedler_BMCSystBiol2016](Benchmark-Models/Fiedler_BMCSystBiol2016/) | 3 | 22 | 0 | | 0 | 0 | 72 | 2 | normal | | 6 | [\[1\]](http://identifiers.org/doi/10.1186/s12918-016-0319-7) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Fiedler_BMCSystBiol2016/model_Fiedler_BMCSystBiol2016.xml) | | [Froehlich_CellSystems2018](Benchmark-Models/Froehlich_CellSystems2018/) | 9169 | 4231 | 0 | | 0 | 9169 | 9169 | 1 | normal | | 1396 | [\[1\]](http://identifiers.org/doi/10.1016/j.cels.2018.10.013) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Froehlich_CellSystems2018/model_Froehlich_CellSystems2018.xml) | | [Fujita_SciSignal2010](Benchmark-Models/Fujita_SciSignal2010/) | 6 | 19 | 0 | ✓ | 0 | 0 | 144 | 3 | normal | | 9 | [\[1\]](http://identifiers.org/doi/10.1126/scisignal.2000810) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Fujita_SciSignal2010/model_Fujita_SciSignal2010.xml) | -| [Giordano_Nature2020](Benchmark-Models/Giordano_Nature2020/) | 1 | 50 | 0 | ✓ | 0 | 0 | 313 | 7 | normal | | 13 | [\[1\]](http://identifiers.org/pubmed/32322102) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Giordano_Nature2020/Giordano_Nature2020_model.xml) | +| [Giordano_Nature2020](Benchmark-Models/Giordano_Nature2020/) | 1 | 50 | 0 | ✓ | 0 | 0 | 313 | 7 | normal | | 13 | [\[1\]](http://identifiers.org/pubmed/32322102) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Giordano_Nature2020/model_Giordano_Nature2020.xml) | | [Isensee_JCB2018](Benchmark-Models/Isensee_JCB2018/) | 123 | 46 | 0 | ✓ | 1 | 0 | 687 | 3 | normal | parameterScaleNormal | 25 | [\[1\]](http://identifiers.org/doi/10.1083/jcb.201708053) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Isensee_JCB2018/model_Isensee_JCB2018.xml) | | [Lang_PLOSComputBiol2024](Benchmark-Models/Lang_PLOSComputBiol2024/) | 1 | 294 | 0 | | 0 | 0 | 9600 | 16 | normal | laplace; uniform | 124 | [\[1\]](http://identifiers.org/doi/10.1371/journal.pcbi.1011151) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Lang_PLOSComputBiol2024/model_Lang_PLOSComputBiol2024.xml) | | [Laske_PLOSComputBiol2019](Benchmark-Models/Laske_PLOSComputBiol2019/) | 3 | 13 | 0 | | 0 | 0 | 42 | 13 | normal; log-normal | | 41 | [\[1\]](http://identifiers.org/biomodels.db/BIOMD0000000463) [\[2\]](http://identifiers.org/biomodels.db/MODEL1307270000) [\[3\]](http://identifiers.org/doi/10.1371/journal.pcbi.1006944) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Laske_PLOSComputBiol2019/model_Laske_PLOSComputBiol2019.xml) | +| [Liu_IFACPapersOnLine2025](Benchmark-Models/Liu_IFACPapersOnLine2025/) | 2 | 9 | 1 | ✓ | 0 | 0 | 100 | 1 | normal | | 0 | | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Liu_IFACPapersOnLine2025/model.xml) | | [Lucarelli_CellSystems2018](Benchmark-Models/Lucarelli_CellSystems2018/) | 16 | 84 | 0 | | 0 | 0 | 1755 | 65 | normal; log10-normal | | 33 | [\[1\]](http://identifiers.org/doi/10.1016/j.cels.2017.11.010) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Lucarelli_CellSystems2018/model_Lucarelli_CellSystems2018.xml) | -| [Okuonghae_ChaosSolitonsFractals2020](Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/) | 1 | 16 | 0 | | 0 | 0 | 92 | 2 | normal | | 9 | [\[1\]](http://identifiers.org/doi/10.1016/j.chaos.2020.110032) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/Okuonghae_ChaosSolitonsFractals2020_model.xml) | +| [Okuonghae_ChaosSolitonsFractals2020](Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/) | 1 | 16 | 0 | | 0 | 0 | 92 | 2 | normal | | 9 | [\[1\]](http://identifiers.org/doi/10.1016/j.chaos.2020.110032) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/model_Okuonghae_ChaosSolitonsFractals2020.xml) | | [Oliveira_NatCommun2021](Benchmark-Models/Oliveira_NatCommun2021/) | 1 | 12 | 0 | ✓ | 0 | 0 | 120 | 2 | normal | | 9 | [\[1\]](http://identifiers.org/doi/10.1038/s41467-020-19798-3) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Oliveira_NatCommun2021/Oliveira_NatCommun2021_model.xml) | | [Perelson_Science1996](Benchmark-Models/Perelson_Science1996/) | 1 | 3 | 0 | | 0 | 0 | 16 | 1 | log10-normal | | 4 | [\[1\]](http://identifiers.org/doi/10.1126/science.271.5255.1582) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Perelson_Science1996/model_Perelson_Science1996.xml) | | [Rahman_MBS2016](Benchmark-Models/Rahman_MBS2016/) | 1 | 9 | 0 | | 0 | 0 | 23 | 1 | normal | | 7 | [\[1\]](http://identifiers.org/doi/10.1016/j.mbs.2016.07.009) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Rahman_MBS2016/model_Rahman_MBS2016.xml) | @@ -45,8 +46,8 @@ A sortable version of the table is available | [Smith_BMCSystBiol2013](Benchmark-Models/Smith_BMCSystBiol2013/) | 35 | 25 | 3 | ✓ | 0 | 0 | 62 | 9 | normal | | 133 | [\[1\]](http://identifiers.org/doi/10.1186/1752-0509-7-41) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Smith_BMCSystBiol2013/model_Smith_BMCSystBiol2013.xml) | | [Sneyd_PNAS2002](Benchmark-Models/Sneyd_PNAS2002/) | 9 | 15 | 0 | | 0 | 0 | 135 | 1 | normal | | 6 | [\[1\]](http://identifiers.org/doi/10.1073/pnas.032281999) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Sneyd_PNAS2002/model_Sneyd_PNAS2002.xml) | | [Weber_BMC2015](Benchmark-Models/Weber_BMC2015/) | 2 | 36 | 0 | ✓ | 1 | 0 | 135 | 8 | normal | | 7 | [\[1\]](http://identifiers.org/doi/10.1186/s12918-015-0147-1) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Weber_BMC2015/model_Weber_BMC2015.xml) | -| [Zhao_QuantBiol2020](Benchmark-Models/Zhao_QuantBiol2020/) | 7 | 28 | 0 | | 0 | 0 | 82 | 1 | normal | | 5 | [\[1\]](http://identifiers.org/pubmed/32219006) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Zhao_QuantBiol2020/SBML_Zhao_QuantBiol2020.xml) | -| [Zheng_PNAS2012](Benchmark-Models/Zheng_PNAS2012/) | 1 | 46 | 0 | | 1 | 0 | 60 | 15 | normal | | 15 | [\[1\]](http://identifiers.org/doi/10.1073/pnas.1201240109) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Zheng_PNAS2012/model_Zheng_PNAS2012.xml) | +| [Zhao_QuantBiol2020](Benchmark-Models/Zhao_QuantBiol2020/) | 7 | 28 | 0 | | 0 | 0 | 82 | 1 | normal | | 5 | [\[1\]](http://identifiers.org/pubmed/32219006) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Zhao_QuantBiol2020/model_Zhao_QuantBiol2020.xml) | +| [Zheng_PNAS2012](Benchmark-Models/Zheng_PNAS2012/) | 1 | 46 | 0 | | 1 | 0 | 60 | 15 | normal | | 15 | [\[1\]](http://identifiers.org/doi/10.1073/pnas.1205707109) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Zheng_PNAS2012/model_Zheng_PNAS2012.xml) | ## License From a32b4353a018c74a0d1f1e519e3288bf1f22ba8c Mon Sep 17 00:00:00 2001 From: Maren Philipps Date: Thu, 1 Jan 2026 16:07:20 +0100 Subject: [PATCH 12/13] add model name --- .../individual-based/model_individual.xml | 2 +- Benchmark-Models/Liu_IFACPapersOnLine2025/model.xml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/model_individual.xml b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/model_individual.xml index a45b444..4acc8ff 100644 --- a/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/model_individual.xml +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/model_individual.xml @@ -1,6 +1,6 @@ - + diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/model.xml b/Benchmark-Models/Liu_IFACPapersOnLine2025/model.xml index 60cf206..131dd79 100644 --- a/Benchmark-Models/Liu_IFACPapersOnLine2025/model.xml +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/model.xml @@ -1,6 +1,6 @@ - + From dab9ce650c481dfc2086c13ce26a97b0ed772a94 Mon Sep 17 00:00:00 2001 From: Maren Philipps Date: Thu, 1 Jan 2026 17:01:08 +0100 Subject: [PATCH 13/13] remove metaid, fix readme --- .../individual-based/model_individual.xml | 2 +- Benchmark-Models/Liu_IFACPapersOnLine2025/model.xml | 2 +- README.md | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/model_individual.xml b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/model_individual.xml index 4acc8ff..fe7036f 100644 --- a/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/model_individual.xml +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/model_individual.xml @@ -1,6 +1,6 @@ - + diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/model.xml b/Benchmark-Models/Liu_IFACPapersOnLine2025/model.xml index 131dd79..8c0c354 100644 --- a/Benchmark-Models/Liu_IFACPapersOnLine2025/model.xml +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/model.xml @@ -1,6 +1,6 @@ - + diff --git a/README.md b/README.md index 16ac341..716ce6c 100644 --- a/README.md +++ b/README.md @@ -33,7 +33,7 @@ A sortable version of the table is available | [Isensee_JCB2018](Benchmark-Models/Isensee_JCB2018/) | 123 | 46 | 0 | ✓ | 1 | 0 | 687 | 3 | normal | parameterScaleNormal | 25 | [\[1\]](http://identifiers.org/doi/10.1083/jcb.201708053) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Isensee_JCB2018/model_Isensee_JCB2018.xml) | | [Lang_PLOSComputBiol2024](Benchmark-Models/Lang_PLOSComputBiol2024/) | 1 | 294 | 0 | | 0 | 0 | 9600 | 16 | normal | laplace; uniform | 124 | [\[1\]](http://identifiers.org/doi/10.1371/journal.pcbi.1011151) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Lang_PLOSComputBiol2024/model_Lang_PLOSComputBiol2024.xml) | | [Laske_PLOSComputBiol2019](Benchmark-Models/Laske_PLOSComputBiol2019/) | 3 | 13 | 0 | | 0 | 0 | 42 | 13 | normal; log-normal | | 41 | [\[1\]](http://identifiers.org/biomodels.db/BIOMD0000000463) [\[2\]](http://identifiers.org/biomodels.db/MODEL1307270000) [\[3\]](http://identifiers.org/doi/10.1371/journal.pcbi.1006944) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Laske_PLOSComputBiol2019/model_Laske_PLOSComputBiol2019.xml) | -| [Liu_IFACPapersOnLine2025](Benchmark-Models/Liu_IFACPapersOnLine2025/) | 2 | 9 | 1 | ✓ | 0 | 0 | 100 | 1 | normal | | 0 | | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Liu_IFACPapersOnLine2025/model.xml) | +| [Liu_IFACPapersOnLine2025](Benchmark-Models/Liu_IFACPapersOnLine2025/) | 2 | 9 | 1 | ✓ | 0 | 0 | 100 | 1 | normal | | 0 | [\[1\]](http://identifiers.org/doi/10.1016/j.ifacol.2025.07.160) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Liu_IFACPapersOnLine2025/model.xml) | | [Lucarelli_CellSystems2018](Benchmark-Models/Lucarelli_CellSystems2018/) | 16 | 84 | 0 | | 0 | 0 | 1755 | 65 | normal; log10-normal | | 33 | [\[1\]](http://identifiers.org/doi/10.1016/j.cels.2017.11.010) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Lucarelli_CellSystems2018/model_Lucarelli_CellSystems2018.xml) | | [Okuonghae_ChaosSolitonsFractals2020](Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/) | 1 | 16 | 0 | | 0 | 0 | 92 | 2 | normal | | 9 | [\[1\]](http://identifiers.org/doi/10.1016/j.chaos.2020.110032) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/model_Okuonghae_ChaosSolitonsFractals2020.xml) | | [Oliveira_NatCommun2021](Benchmark-Models/Oliveira_NatCommun2021/) | 1 | 12 | 0 | ✓ | 0 | 0 | 120 | 2 | normal | | 9 | [\[1\]](http://identifiers.org/doi/10.1038/s41467-020-19798-3) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Oliveira_NatCommun2021/Oliveira_NatCommun2021_model.xml) |