Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

add new model Liu_IFACPapersOnLine2025 #260

Draft
wants to merge 9 commits into
base: master
Choose a base branch
from
Draft

add new model Liu_IFACPapersOnLine2025 #260

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
5b900e0
add the petab files for Liu_IFACPapersOnLine2025
EchoRLiu Dec 4, 2024
48eebcc
replace the baseline model with age-of-infection model
EchoRLiu Dec 19, 2024
a4d97f4
add individual based age of infection model in the subfolder
EchoRLiu Dec 19, 2024
53334ce
rename files, add visualization spec
m-philipps Jan 4, 2025
532f5e9
add estimated parameters
m-philipps Jan 5, 2025
be8b2c3
add simulated data
m-philipps Jan 5, 2025
2e61708
update PEtab ID
m-philipps Jan 6, 2025
721ceca
fix PEtab subproblem
m-philipps Jan 6, 2025
ede623d
add visualization matching manuscript Figures
m-philipps Jan 6, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
13 changes: 13 additions & 0 deletions Benchmark-Models/Liu_IFACPapersOnLine2025/Liu_IFACPapersOnLine2025.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
format_version: 1
parameter_file: parameters.tsv
problems:
- condition_files:
- conditions.tsv
measurement_files:
- measurements.tsv
observable_files:
- observables.tsv
sbml_files:
- model.xml
visualization_files:
- visualization.tsv
3 changes: 3 additions & 0 deletions Benchmark-Models/Liu_IFACPapersOnLine2025/conditions.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
conditionId conditionName u_2
vvDD vvDD 1000000000.0
ctrl ctrl 0.0
13 changes: 13 additions & 0 deletions ...Models/Liu_IFACPapersOnLine2025/individual-based/Liu_IFACPapersOnLine2025_individual.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
format_version: 1
parameter_file: parameters.tsv
problems:
- condition_files:
- conditions.tsv
measurement_files:
- measurements.tsv
observable_files:
- observables.tsv
sbml_files:
- model_individual.xml
visualization_files:
- visualization.tsv
21 changes: 21 additions & 0 deletions Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/conditions.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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
101 changes: 101 additions & 0 deletions Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/measurements.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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
Loading
Loading