-
Notifications
You must be signed in to change notification settings - Fork 18
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge branch 'master' into fiedler_reparam
- Loading branch information
Showing
9 changed files
with
175 additions
and
149 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| src/python/.git_archival.txt export-subst |
144 changes: 72 additions & 72 deletions
144
Benchmark-Models/Fiedler_BMCSystBiol2016/simulatedData_Fiedler_BMCSystBiol2016.tsv
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,73 +1,73 @@ | ||
| observableId preequilibrationConditionId simulationConditionId simulation time observableParameters noiseParameters | ||
| pErk_20140430 model1_data1 0.033616432711445 0 s_pErk_20140430_gel1 pErk_20140430_gel1_sigma | ||
| pErk_20140430 model1_data1 0.083846008711945 0.25 s_pErk_20140430_gel1 pErk_20140430_gel1_sigma | ||
| pErk_20140430 model1_data1 0.14529413431672 1 s_pErk_20140430_gel1 pErk_20140430_gel1_sigma | ||
| pErk_20140430 model1_data1 0.033738884381949 5.5 s_pErk_20140430_gel1 pErk_20140430_gel1_sigma | ||
| pErk_20140430 model1_data1 0.033616607163819 7 s_pErk_20140430_gel1 pErk_20140430_gel1_sigma | ||
| pErk_20140430 model1_data1 0.033614607619822 8.5 s_pErk_20140430_gel1 pErk_20140430_gel1_sigma | ||
| pErk_20140430 model1_data1 0.033616822455964 10 s_pErk_20140430_gel1 pErk_20140430_gel1_sigma | ||
| pErk_20140505 model1_data1 0.812606025266457 0 s_pErk_20140505_gel1 pErk_20140505_gel1_sigma | ||
| pErk_20140505 model1_data1 2.0267995851527 0.25 s_pErk_20140505_gel1 pErk_20140505_gel1_sigma | ||
| pErk_20140505 model1_data1 3.51217780884416 1 s_pErk_20140505_gel1 pErk_20140505_gel1_sigma | ||
| pErk_20140505 model1_data1 0.815566034917377 5.5 s_pErk_20140505_gel1 pErk_20140505_gel1_sigma | ||
| pErk_20140505 model1_data1 0.812610242282909 7 s_pErk_20140505_gel1 pErk_20140505_gel1_sigma | ||
| pErk_20140505 model1_data1 0.812561907543952 8.5 s_pErk_20140505_gel1 pErk_20140505_gel1_sigma | ||
| pErk_20140505 model1_data1 0.812615446514296 10 s_pErk_20140505_gel1 pErk_20140505_gel1_sigma | ||
| pMek_20140430 model1_data1 0.048635005501051 0 s_pMek_20140430_gel1 pMek_20140430_gel1_sigma | ||
| pMek_20140430 model1_data1 0.285796206683923 0.25 s_pMek_20140430_gel1 pMek_20140430_gel1_sigma | ||
| pMek_20140430 model1_data1 0.28761271518216 1 s_pMek_20140430_gel1 pMek_20140430_gel1_sigma | ||
| pMek_20140430 model1_data1 0.048924437483009 5.5 s_pMek_20140430_gel1 pMek_20140430_gel1_sigma | ||
| pMek_20140430 model1_data1 0.048612688191705 7 s_pMek_20140430_gel1 pMek_20140430_gel1_sigma | ||
| pMek_20140430 model1_data1 0.048635537743825 8.5 s_pMek_20140430_gel1 pMek_20140430_gel1_sigma | ||
| pMek_20140430 model1_data1 0.048635221061588 10 s_pMek_20140430_gel1 pMek_20140430_gel1_sigma | ||
| pMek20140505 model1_data1 0.245523765476953 0 s_pMek_20140505_gel1 pMek_20140505_gel1_sigma | ||
| pMek20140505 model1_data1 1.44278303458916 0.25 s_pMek_20140505_gel1 pMek_20140505_gel1_sigma | ||
| pMek20140505 model1_data1 1.45195330201102 1 s_pMek_20140505_gel1 pMek_20140505_gel1_sigma | ||
| pMek20140505 model1_data1 0.246984902970983 5.5 s_pMek_20140505_gel1 pMek_20140505_gel1_sigma | ||
| pMek20140505 model1_data1 0.245411101156896 7 s_pMek_20140505_gel1 pMek_20140505_gel1_sigma | ||
| pMek20140505 model1_data1 0.245526452394512 8.5 s_pMek_20140505_gel1 pMek_20140505_gel1_sigma | ||
| pMek20140505 model1_data1 0.245524853689738 10 s_pMek_20140505_gel1 pMek_20140505_gel1_sigma | ||
| pErk_20140430 model1_data2 0.022771734786134 0 s_pErk_20140430_gel2 pErk_20140430_gel2_sigma | ||
| pErk_20140430 model1_data2 0.036318706974534 1 s_pErk_20140430_gel2 pErk_20140430_gel2_sigma | ||
| pErk_20140430 model1_data2 0.011295410041568 5.5 s_pErk_20140430_gel2 pErk_20140430_gel2_sigma | ||
| pErk_20140430 model1_data2 0.011240689927803 7 s_pErk_20140430_gel2 pErk_20140430_gel2_sigma | ||
| pErk_20140430 model1_data2 0.011246908536762 8.5 s_pErk_20140430_gel2 pErk_20140430_gel2_sigma | ||
| pErk_20140430 model1_data2 0.011246374750324 10 s_pErk_20140430_gel2 pErk_20140430_gel2_sigma | ||
| pErk_20140505 model1_data2 0.260038488973387 0 s_pErk_20140505_gel2 pErk_20140505_gel2_sigma | ||
| pErk_20140505 model1_data2 0.414736153034584 1 s_pErk_20140505_gel2 pErk_20140505_gel2_sigma | ||
| pErk_20140505 model1_data2 0.128986280014672 5.5 s_pErk_20140505_gel2 pErk_20140505_gel2_sigma | ||
| pErk_20140505 model1_data2 0.128361411692886 7 s_pErk_20140505_gel2 pErk_20140505_gel2_sigma | ||
| pErk_20140505 model1_data2 0.128432424186774 8.5 s_pErk_20140505_gel2 pErk_20140505_gel2_sigma | ||
| pErk_20140505 model1_data2 0.128426328690751 10 s_pErk_20140505_gel2 pErk_20140505_gel2_sigma | ||
| pMek_20140430 model1_data2 0.252881304191901 0 s_pMek_20140430_gel2 pMek_20140430_gel2_sigma | ||
| pMek_20140430 model1_data2 0.380893878854849 1 s_pMek_20140430_gel2 pMek_20140430_gel2_sigma | ||
| pMek_20140430 model1_data2 0.119215863446706 5.5 s_pMek_20140430_gel2 pMek_20140430_gel2_sigma | ||
| pMek_20140430 model1_data2 0.118810984399152 7 s_pMek_20140430_gel2 pMek_20140430_gel2_sigma | ||
| pMek_20140430 model1_data2 0.118873391352447 8.5 s_pMek_20140430_gel2 pMek_20140430_gel2_sigma | ||
| pMek_20140430 model1_data2 0.118865602961338 10 s_pMek_20140430_gel2 pMek_20140430_gel2_sigma | ||
| pMek20140505 model1_data2 0.625603066047608 0 s_pMek_20140505_gel2 pMek_20140505_gel2_sigma | ||
| pMek20140505 model1_data2 0.942293378357194 1 s_pMek_20140505_gel2 pMek_20140505_gel2_sigma | ||
| pMek20140505 model1_data2 0.2949281281671 5.5 s_pMek_20140505_gel2 pMek_20140505_gel2_sigma | ||
| pMek20140505 model1_data2 0.293926497879176 7 s_pMek_20140505_gel2 pMek_20140505_gel2_sigma | ||
| pMek20140505 model1_data2 0.294080886442809 8.5 s_pMek_20140505_gel2 pMek_20140505_gel2_sigma | ||
| pMek20140505 model1_data2 0.294061618741811 10 s_pMek_20140505_gel2 pMek_20140505_gel2_sigma | ||
| pErk_20140430 model1_data3 0.006788283169659 1 s_pErk_20140430_gel2 pErk_20140430_gel2_sigma | ||
| pErk_20140430 model1_data3 0.004167647682283 5.5 s_pErk_20140430_gel2 pErk_20140430_gel2_sigma | ||
| pErk_20140430 model1_data3 0.004164243853991 7 s_pErk_20140430_gel2 pErk_20140430_gel2_sigma | ||
| pErk_20140430 model1_data3 0.004164954335285 8.5 s_pErk_20140430_gel2 pErk_20140430_gel2_sigma | ||
| pErk_20140430 model1_data3 0.00416484168866 10 s_pErk_20140430_gel2 pErk_20140430_gel2_sigma | ||
| pErk_20140505 model1_data3 0.077517805065801 1 s_pErk_20140505_gel2 pErk_20140505_gel2_sigma | ||
| pErk_20140505 model1_data3 0.047591842081971 5.5 s_pErk_20140505_gel2 pErk_20140505_gel2_sigma | ||
| pErk_20140505 model1_data3 0.04755297256351 7 s_pErk_20140505_gel2 pErk_20140505_gel2_sigma | ||
| pErk_20140505 model1_data3 0.047561085800548 8.5 s_pErk_20140505_gel2 pErk_20140505_gel2_sigma | ||
| pErk_20140505 model1_data3 0.047559799448914 10 s_pErk_20140505_gel2 pErk_20140505_gel2_sigma | ||
| pMek_20140430 model1_data3 2.04308413890321 1 s_pMek_20140430_gel2 pMek_20140430_gel2_sigma | ||
| pMek_20140430 model1_data3 1.3779161198805 5.5 s_pMek_20140430_gel2 pMek_20140430_gel2_sigma | ||
| pMek_20140430 model1_data3 1.37805049573013 7 s_pMek_20140430_gel2 pMek_20140430_gel2_sigma | ||
| pMek_20140430 model1_data3 1.37812830229416 8.5 s_pMek_20140430_gel2 pMek_20140430_gel2_sigma | ||
| pMek_20140430 model1_data3 1.37810668857163 10 s_pMek_20140430_gel2 pMek_20140430_gel2_sigma | ||
| pMek20140505 model1_data3 5.05438591269344 1 s_pMek_20140505_gel2 pMek_20140505_gel2_sigma | ||
| pMek20140505 model1_data3 3.40882673042334 5.5 s_pMek_20140505_gel2 pMek_20140505_gel2_sigma | ||
| pMek20140505 model1_data3 3.40915916284176 7 s_pMek_20140505_gel2 pMek_20140505_gel2_sigma | ||
| pMek20140505 model1_data3 3.40935164850287 8.5 s_pMek_20140505_gel2 pMek_20140505_gel2_sigma | ||
| pMek20140505 model1_data3 3.40929817831406 10 s_pMek_20140505_gel2 pMek_20140505_gel2_sigma | ||
| pErk model1_data1 0.03361643271144515 0.0 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk | ||
| pErk model1_data1 0.08384600871194502 0.25 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk | ||
| pErk model1_data1 0.14529413431664095 1.0 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk | ||
| pErk model1_data1 0.03373888438216745 5.5 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk | ||
| pErk model1_data1 0.03361660721448361 7.0 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk | ||
| pErk model1_data1 0.033614606544540175 8.5 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk | ||
| pErk model1_data1 0.03361682359235068 10.0 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk | ||
| pErk model1_data1 0.8126060252664574 0.0 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk | ||
| pErk model1_data1 2.0267995851526917 0.25 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk | ||
| pErk model1_data1 3.5121778088422517 1.0 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk | ||
| pErk model1_data1 0.8155660349226578 5.5 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk | ||
| pErk model1_data1 0.8126102435076284 7.0 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk | ||
| pErk model1_data1 0.812561881551303 8.5 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk | ||
| pErk model1_data1 0.8126154739840452 10.0 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk | ||
| pMek model1_data1 0.04863500550105047 0.0 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek | ||
| pMek model1_data1 0.28579620668392197 0.25 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek | ||
| pMek model1_data1 0.28761271518189074 1.0 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek | ||
| pMek model1_data1 0.04892443748331804 5.5 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek | ||
| pMek model1_data1 0.04861268829425418 7.0 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek | ||
| pMek model1_data1 0.048635535764149945 8.5 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek | ||
| pMek model1_data1 0.04863522217188459 10.0 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek | ||
| pMek model1_data1 0.24552376547695293 0.0 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek | ||
| pMek model1_data1 1.4427830345891586 0.25 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek | ||
| pMek model1_data1 1.45195330200966 1.0 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek | ||
| pMek model1_data1 0.24698490297254252 5.5 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek | ||
| pMek model1_data1 0.24541110167459282 7.0 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek | ||
| pMek model1_data1 0.2455264424005296 8.5 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek | ||
| pMek model1_data1 0.2455248592948422 10.0 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek | ||
| pErk model1_data2 0.022771734786134104 0.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk | ||
| pErk model1_data2 0.03631870697453655 1.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk | ||
| pErk model1_data2 0.011295410041568654 5.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk | ||
| pErk model1_data2 0.011240689927851936 7.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk | ||
| pErk model1_data2 0.01124690853273153 8.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk | ||
| pErk model1_data2 0.011246374775472459 10.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk | ||
| pErk model1_data2 0.2600384889733869 0.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk | ||
| pErk model1_data2 0.41473615303461114 1.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk | ||
| pErk model1_data2 0.12898628001468046 5.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk | ||
| pErk model1_data2 0.1283614116934487 7.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk | ||
| pErk model1_data2 0.12843242414074793 8.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk | ||
| pErk model1_data2 0.12842632897793177 10.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk | ||
| pMek model1_data2 0.25288130419190086 0.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek | ||
| pMek model1_data2 0.38089387885488346 1.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek | ||
| pMek model1_data2 0.11921586344671047 5.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek | ||
| pMek model1_data2 0.11881098439949271 7.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek | ||
| pMek model1_data2 0.11887339130720243 8.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek | ||
| pMek model1_data2 0.11886560414931766 10.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek | ||
| pMek model1_data2 0.6256030660476078 0.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek | ||
| pMek model1_data2 0.9422933783572799 1.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek | ||
| pMek model1_data2 0.29492812816711056 5.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek | ||
| pMek model1_data2 0.29392649788001884 7.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek | ||
| pMek model1_data2 0.29408088633087925 8.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek | ||
| pMek model1_data2 0.29406162168075384 10.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek | ||
| pErk model1_data3 0.00678828316965931 1.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk | ||
| pErk model1_data3 0.0041676476822826445 5.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk | ||
| pErk model1_data3 0.00416424385399046 7.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk | ||
| pErk model1_data3 0.004164954335288319 8.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk | ||
| pErk model1_data3 0.004164841688668539 10.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk | ||
| pErk model1_data3 0.07751780506580175 1.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk | ||
| pErk model1_data3 0.04759184208197086 5.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk | ||
| pErk model1_data3 0.04755297256350257 7.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk | ||
| pErk model1_data3 0.04756108580058681 8.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk | ||
| pErk model1_data3 0.047559799449016726 10.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk | ||
| pMek model1_data3 2.0430841389034655 1.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek | ||
| pMek model1_data3 1.377916119880504 5.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek | ||
| pMek model1_data3 1.378050495730159 7.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek | ||
| pMek model1_data3 1.3781283022947328 8.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek | ||
| pMek model1_data3 1.3781066885745035 10.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek | ||
| pMek model1_data3 5.05438591269406 1.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek | ||
| pMek model1_data3 3.408826730423337 5.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek | ||
| pMek model1_data3 3.4091591628418403 7.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek | ||
| pMek model1_data3 3.40935164850428 8.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek | ||
| pMek model1_data3 3.4092981783211544 10.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,17 @@ | ||
| The paper describes a model selection problem with four hypotheses. Each hypothesis involves adding a set of parameters to the model -- these sets of parameters are annotated in the `model_selection_group` column of the parameters table. The paper shows a result where the model with the first hypothesis alone (H1) was accepted as the best by AIC. | ||
|
|
||
| This benchmark problem is the parameter estimation problem for the H1-only model. The parameters for the other hypotheses are specified in `parameters_Isensee_JCB2018_model_selection.tsv`. For example, this Python code will create the PEtab problem for the H2+H3 model. | ||
| ```python | ||
| import pandas as pd | ||
| import petab | ||
|
|
||
| petab_problem = petab.Problem.from_yaml("Isensee_JCB2018.yaml") | ||
| model_selection_parameter_df = petab.get_parameter_df("parameters_Isensee_JCB2018_model_selection.tsv") | ||
|
|
||
| petab_problem.parameter_df = petab.get_parameter_df(pd.concat([ | ||
| # Remove the H1 parameters | ||
| petab_problem.parameter_df.query("model_selection_group != 'H1: different KD'"), | ||
| # Add the H2 and H3 parameters | ||
| model_selection_parameter_df.query("model_selection_group in ['H2: AC inhibition', 'H3: incomplete import']") | ||
| ])) | ||
| ``` |
Oops, something went wrong.