Skip to content

Fix bounds and scales for some parameters in Isensee_JCB2018 #132

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

Merged
dilpath merged 7 commits into from
Nov 11, 2024
Merged

Fix bounds and scales for some parameters in Isensee_JCB2018 #132

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
edbb78a
fix parameter scales
dilpath Aug 17, 2021
9ecffc9
Merge branch 'master' into fix_isensee
dilpath Sep 30, 2021
12beb32
Merge branch 'master' into fix_isensee
dilpath Oct 5, 2021
8b2f364
Merge branch 'master' into fix_isensee
dilpath Nov 7, 2024
a65c02e
newline
dilpath Nov 7, 2024
e4e8325
group parameters by model selection hypothesis
dilpath Nov 7, 2024
1645810
update dev packages; add README for Isensee; remove default values fr…
dilpath Nov 8, 2024
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
17 changes: 17 additions & 0 deletions Benchmark-Models/Isensee_JCB2018/README.md
View file
Open in desktop
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']")
]))
```
32 changes: 18 additions & 14 deletions Benchmark-Models/Isensee_JCB2018/model_Isensee_JCB2018.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -97,16 +97,13 @@
<parameter metaid="KD_Fsk" id="KD_Fsk" value="14.2656743301721"/>
<parameter metaid="KD_H89" id="KD_H89" value="0.0480736009761681"/>
<parameter metaid="KD_IBMX" id="KD_IBMX" value="11.9768989891142"/>
<parameter metaid="KD_PDE_Csub" id="KD_PDE_Csub" value="0"/>
<parameter metaid="KD_cAMP" id="KD_cAMP" value="2.84986906175302"/>
<parameter metaid="PDE_total" id="PDE_total" value="1"/>
<parameter metaid="RII2_total" id="RII2_total" value="1"/>
<parameter metaid="kdeg_cAMP" id="kdeg_cAMP" value="1.00032978441703e-05"/>
<parameter metaid="kdeg_cAMP_free" id="kdeg_cAMP_free" value="7.35892283451732"/>
<parameter metaid="kdp_AC" id="kdp_AC" value="0"/>
<parameter metaid="kf_Fsk" id="kf_Fsk" value="999.991987450139"/>
<parameter metaid="kf_H89" id="kf_H89" value="0.000741493422675392"/>
<parameter metaid="kf_PDE_Csub" id="kf_PDE_Csub" value="0"/>
<parameter metaid="kf_RII_2__RII_C_2" id="kf_RII_2__RII_C_2" value="1.26077939273477"/>
<parameter metaid="kf_RII_C_2__RII_2" id="kf_RII_C_2__RII_2" value="0.0187262534054505"/>
<parameter metaid="kf_RII_C_2__RIIp_C_2" id="kf_RII_C_2__RIIp_C_2" value="0.0227841500487899"/>
Expand All @@ -119,25 +116,14 @@
<parameter metaid="ki_Rp8_pCPT_cAMPS_pAB" id="ki_Rp8_pCPT_cAMPS_pAB" value="9.24294887100985"/>
<parameter metaid="ki_Rp_cAMPS_pAB" id="ki_Rp_cAMPS_pAB" value="0.0163472838984393"/>
<parameter metaid="ki_Sp8_Br_cAMPS_AM" id="ki_Sp8_Br_cAMPS_AM" value="0.131083036712545"/>
<parameter metaid="kp_AC" id="kp_AC" value="0"/>
<parameter metaid="ks_AC_cAMP" id="ks_AC_cAMP" value="0.423299046028554"/>
<parameter metaid="xi_AC_cAMP_Fsk" id="xi_AC_cAMP_Fsk" value="640.551657640036"/>
<parameter metaid="xi_KD_Rp8_Br_cAMPS" id="xi_KD_Rp8_Br_cAMPS" value="0.040150612333366"/>
<parameter metaid="xi_KD_Rp8_pCPT_cAMPS" id="xi_KD_Rp8_pCPT_cAMPS" value="0.194630402579553"/>
<parameter metaid="xi_KD_Rp_cAMPS" id="xi_KD_Rp_cAMPS" value="0.163369645426461"/>
<parameter metaid="xi_KD_Sp8_Br_cAMPS" id="xi_KD_Sp8_Br_cAMPS" value="0.222276461349335"/>
<parameter metaid="xi_b_Rp8_Br_cAMPS" id="xi_b_Rp8_Br_cAMPS" value="0.0408695544562406"/>
<parameter metaid="xi_b_Rp8_pCPT_cAMPS" id="xi_b_Rp8_pCPT_cAMPS" value="0.0268897774883765"/>
<parameter metaid="xi_b_Rp_cAMPS" id="xi_b_Rp_cAMPS" value="0.607960299288444"/>
<parameter metaid="xi_b_Sp8_Br_cAMPS" id="xi_b_Sp8_Br_cAMPS" value="21.7551956731725"/>
<parameter metaid="xi_i_Rp8_Br_cAMPS_pAB" id="xi_i_Rp8_Br_cAMPS_pAB" value="1"/>
<parameter metaid="xi_i_Rp8_pCPT_cAMPS_pAB" id="xi_i_Rp8_pCPT_cAMPS_pAB" value="1"/>
<parameter metaid="xi_i_Rp_cAMPS_pAB" id="xi_i_Rp_cAMPS_pAB" value="1"/>
<parameter metaid="xi_i_Sp8_Br_cAMPS_AM" id="xi_i_Sp8_Br_cAMPS_AM" value="1"/>
<parameter metaid="xi_kf_RII_2__RII_C_2" id="xi_kf_RII_2__RII_C_2" value="0.0189295042137343"/>
<parameter metaid="xi_kf_RII_C_2__RII_2" id="xi_kf_RII_C_2__RII_2" value="0.811223214879921"/>
<parameter metaid="xi_pAC" id="xi_pAC" value="1"/>
<parameter metaid="xi_pPDE" id="xi_pPDE" value="1"/>
<parameter metaid="Fsk" id="Fsk" value="10" units="time" constant="false"/>
<parameter metaid="IBMXex" id="IBMXex" value="0" constant="false"/>
<parameter metaid="H89" id="H89" value="0" constant="false"/>
Expand All @@ -162,6 +148,24 @@
<parameter metaid="Sp8_Br_cAMPS_AM_time" id="Sp8_Br_cAMPS_AM_time" value="0" units="time"/>
<parameter metaid="fourABnOH_level" id="fourABnOH_level" value="0" units="substance"/>
<parameter metaid="fourABnOH_time" id="fourABnOH_incubation_time" value="0" units="time"/>
<!-- H1: different KD -->
<parameter metaid="xi_KD_Rp8_Br_cAMPS" id="xi_KD_Rp8_Br_cAMPS" value="0"/>
<parameter metaid="xi_KD_Rp8_pCPT_cAMPS" id="xi_KD_Rp8_pCPT_cAMPS" value="0"/>
<parameter metaid="xi_KD_Rp_cAMPS" id="xi_KD_Rp_cAMPS" value="0"/>
<parameter metaid="xi_KD_Sp8_Br_cAMPS" id="xi_KD_Sp8_Br_cAMPS" value="0"/>
<!-- H2: AC inhibition -->
<parameter metaid="xi_pAC" id="xi_pAC" value="0"/>
<parameter metaid="kp_AC" id="kp_AC" value="0"/>
<parameter metaid="kdp_AC" id="kdp_AC" value="0"/>
<!-- H3: incomplete import -->
<parameter metaid="xi_i_Rp8_Br_cAMPS_pAB" id="xi_i_Rp8_Br_cAMPS_pAB" value="0"/>
<parameter metaid="xi_i_Rp8_pCPT_cAMPS_pAB" id="xi_i_Rp8_pCPT_cAMPS_pAB" value="0"/>
<parameter metaid="xi_i_Rp_cAMPS_pAB" id="xi_i_Rp_cAMPS_pAB" value="0"/>
<parameter metaid="xi_i_Sp8_Br_cAMPS_AM" id="xi_i_Sp8_Br_cAMPS_AM" value="0"/>
<!-- H4: PDE inhibition -->
<parameter metaid="xi_pPDE" id="xi_pPDE" value="0"/>
<parameter metaid="kf_PDE_Csub" id="kf_PDE_Csub" value="0"/>
<parameter metaid="KD_PDE_Csub" id="KD_PDE_Csub" value="0"/>
</listOfParameters>
<listOfRules>
<assignmentRule metaid="CDMT00167" variable="Fsk">
Expand Down
112 changes: 51 additions & 61 deletions Benchmark-Models/Isensee_JCB2018/parameters_Isensee_JCB2018.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,61 +1,51 @@
parameterId parameterName parameterScale lowerBound upperBound nominalValue estimate objectivePriorType objectivePriorParameters
AC_total AC_{total} log10 1E-05 1000 1 0
KD_Fsk KD_{Fsk} log10 1E-05 1000 14.2805171742694 1 parameterScaleNormal 0.845098040014257;0.2
KD_H89 KD_{H89} log10 1E-05 1000 0.048074027232332 1 parameterScaleNormal -1.318758762624413;0.2
KD_IBMX KD_{IBMX} log10 1E-05 1000 11.960772655864 1 parameterScaleNormal 1.0;0.2
KD_PDE_Csub KD_{PDE,Csub} lin -5 3 0 0
KD_cAMP KD_{cAMP} log10 1E-05 1000 2.85002019924967 1 parameterScaleNormal 0.462397997898956;0.2
PDE_total PDE_{total} log10 1E-05 1000 1 0
RII2_total RII2_{total} log10 1E-05 1000 1 0
b_Calpha_global b_{Calpha,global} log10 0.001 1000 101.662732662228 1 parameterScaleNormal 2;0.1
b_pRII_global b_{pRII,global} log10 0.001 1000 99.7184671220999 1 parameterScaleNormal 2;0.1
kdeg_cAMP kdeg_{cAMP} log10 1E-05 1000 1.00000660182181E-05 1
kdeg_cAMP_free kdeg_{cAMP,free} log10 1E-05 1000 7.38363782272545 1
kdp_AC kdp_{AC} lin -5 3 0 0
kf_Fsk kf_{Fsk} log10 1E-05 1000 999.999958296064 1
kf_H89 kf_{H89} log10 1E-05 1000 0.000742716621349 1
kf_PDE_Csub kf_{PDE,Csub} lin -5 3 0 0
kf_RII_2__RII_C_2 kf_{RII_2,RII_C_2} log10 1E-05 100000 1.26446106685121 1
kf_RII_C_2__RII_2 kf_{RII_C_2,RII_2} log10 1E-05 1000 0.018746739843535 1
kf_RII_C_2__RIIp_C_2 kf_{RII_C_2,RIIp_C_2} log10 1E-05 1000 0.022767932816744 1
kf_RIIp_2__RII_2 kf_{RIIp_2,RII_2} log10 1E-05 1000 0.03230162532087 1
kf_RIIp_C_2__RII_C_2 kf_{RIIp_C_2,RII_C_2} log10 1E-05 1000 0.025703919542656 1
kf_RIIp_cAMP_C_2__RIIp_2 kf_{RIIp_cAMP_C_2,RIIp_2} log10 1E-05 1000 0.105283748414996 1
kf_cAMP kf_{cAMP} log10 1E-05 1000 0.501542412469253 1
ki_IBMX ki_{IBMX} log10 1E-05 1000 999.99999999947 1
ki_Rp8_Br_cAMPS_pAB ki_{Rp8,Br,cAMPS,pAB} log10 1E-05 1000 6.44560005260773 1
ki_Rp8_pCPT_cAMPS_pAB ki_{Rp8,pCPT,cAMPS,pAB} log10 1E-05 1000 9.3898794585472 1
ki_Rp_cAMPS_pAB ki_{Rp,cAMPS,pAB} log10 1E-05 1000 0.016320587381729 1
ki_Sp8_Br_cAMPS_AM ki_{Sp8,Br,cAMPS,AM} log10 1E-05 1000 0.131657936881857 1
kp_AC kp_{AC} lin -5 3 0 0
ks_AC_cAMP ks_{AC,cAMP} log10 1E-05 1000 0.423150583624568 1
rel_open rel_{open} log10 1E-05 1 0.232684484588385 1
s_Calpha_JI09_160201_Drg453_452_CycNuc s_{Calpha,JI09,160201,Drg453,452,CycNuc} log10 1E-5 1000 1 0
s_Calpha_global s_{Calpha,global} log10 1000 3162.27766016838 1758.15501421399 1
s_pRII_JI09_150302_Drg345_343_CycNuc s_{pRII,JI09,150302,Drg345,343,CycNuc} log10 0.001 1000 1.1029976101468 1 parameterScaleNormal 0;0.1
s_pRII_JI09_150330_Drg350_348_CycNuc s_{pRII,JI09,150330,Drg350,348,CycNuc} log10 0.001 1000 0.9067516915655 1 parameterScaleNormal 0;0.1
s_pRII_JI09_150330_Drg353_351_CycNuc s_{pRII,JI09,150330,Drg353,351,CycNuc} log10 0.001 1000 0.934506349283962 1 parameterScaleNormal 0;0.1
s_pRII_JI09_151102_Drg421_418_Age s_{pRII,JI09,151102,Drg421,418,Age} log10 0.001 1000 1.06693094665605 1 parameterScaleNormal 0;0.1
s_pRII_Western s_{pRII,Western} log10 0.1 100000 1.14849828435972 1
s_pRII_global s_{pRII,global} log10 1000 3162.27766016838 2206.77137565008 1
rho_Calpha_Microscopy \rho_{Calpha,Microscopy} log10 1E-05 1000 0.049753182233122 1
rho_pRII_Microscopy \rho_{pRII,Microscopy} log10 1E-05 1000 0.040685236621013 1
rho_pRII_Western \rho_{pRII,Western} log10 1E-05 1000 0.099334983213923 1
xi_AC_cAMP_Fsk \xi_{AC_{cAMP,Fsk} log10 1E-05 1000 642.370332155571 1
xi_KD_Rp8_Br_cAMPS \xi_{KD,Rp8,Br,cAMPS} log10 1E-05 100000 0.039962383560766 1 parameterScaleNormal 0;3
xi_KD_Rp8_pCPT_cAMPS \xi_{KD,Rp8,pCPT,cAMPS} log10 1E-05 100000 0.194212924719718 1 parameterScaleNormal 0;3
xi_KD_Rp_cAMPS \xi_{KD,Rp,cAMPS} log10 1E-05 100000 0.163047074866588 1 parameterScaleNormal 0;3
xi_KD_Sp8_Br_cAMPS \xi_{KD,Sp8,Br,cAMPS} log10 1E-05 100000 0.22324026500667 1 parameterScaleNormal 0;3
xi_b_Rp8_Br_cAMPS \xi_{b,Rp8,Br,cAMPS} log10 1E-05 100000 0.040559301141753 1 parameterScaleNormal 0;3
xi_b_Rp8_pCPT_cAMPS \xi_{b,Rp8,pCPT,cAMPS} log10 1E-05 100000 0.026684466293791 1 parameterScaleNormal 0;3
xi_b_Rp_cAMPS \xi_{b,Rp,cAMPS} log10 1E-05 100000 0.603928050380137 1 parameterScaleNormal 0;3
xi_b_Sp8_Br_cAMPS \xi_{b,Sp8,Br,cAMPS} log10 1E-05 100000 21.6150210996832 1 parameterScaleNormal 0;3
xi_i_Rp8_Br_cAMPS_pAB \xi_{i,Rp8,Br,cAMPS,pAB} log10 1E-05 1 1 0 parameterScaleNormal 0;3
xi_i_Rp8_pCPT_cAMPS_pAB \xi_{i,Rp8,pCPT,cAMPS,pAB} log10 1E-05 1 1 0 parameterScaleNormal 0;3
xi_i_Rp_cAMPS_pAB \xi_{i,Rp,cAMPS,pAB} log10 1E-05 1 1 0 parameterScaleNormal 0;3
xi_i_Sp8_Br_cAMPS_AM \xi_{i,Sp8,Br,cAMPS,AM} log10 1E-05 1 1 0 parameterScaleNormal 0;3
xi_kf_RII_2__RII_C_2 \xi_{kf_RII_2,RII_C_2} log10 1E-05 1 0.01893099823943 1 parameterScaleNormal -1.742435698117109;0.1
xi_kf_RII_C_2__RII_2 \xi_{kf_RII_C_2,RII_2} log10 1E-05 100000 0.810991675177056 1 parameterScaleNormal -0.062147906748844;0.1
xi_pAC \xi_{pAC} log10 0.001 1 1 0 parameterScaleNormal 0;3
xi_pPDE \xi_{pPDE} log10 1 1000 1 0 parameterScaleNormal 0.397940008672038;3
xi_rel_open \xi_{rel,open} log10 1E-05 1 0.749424660751357 1
parameterId parameterName parameterScale lowerBound upperBound nominalValue estimate objectivePriorType objectivePriorParameters model_selection_group
AC_total AC_{total} log10 1E-05 1000 1 0
KD_Fsk KD_{Fsk} log10 1E-05 1000 14.2805171742694 1 parameterScaleNormal 0.845098040014257;0.2
KD_H89 KD_{H89} log10 1E-05 1000 0.048074027232332 1 parameterScaleNormal -1.318758762624413;0.2
KD_IBMX KD_{IBMX} log10 1E-05 1000 11.960772655864 1 parameterScaleNormal 1.0;0.2
KD_cAMP KD_{cAMP} log10 1E-05 1000 2.85002019924967 1 parameterScaleNormal 0.462397997898956;0.2
PDE_total PDE_{total} log10 1E-05 1000 1 0
RII2_total RII2_{total} log10 1E-05 1000 1 0
b_Calpha_global b_{Calpha,global} log10 0.001 1000 101.662732662228 1 parameterScaleNormal 2;0.1
b_pRII_global b_{pRII,global} log10 0.001 1000 99.7184671220999 1 parameterScaleNormal 2;0.1
kdeg_cAMP kdeg_{cAMP} log10 1E-05 1000 1.00000660182181E-05 1
kdeg_cAMP_free kdeg_{cAMP,free} log10 1E-05 1000 7.38363782272545 1
kf_Fsk kf_{Fsk} log10 1E-05 1000 999.999958296064 1
kf_H89 kf_{H89} log10 1E-05 1000 0.000742716621349 1
kf_RII_2__RII_C_2 kf_{RII_2,RII_C_2} log10 1E-05 100000 1.26446106685121 1
kf_RII_C_2__RII_2 kf_{RII_C_2,RII_2} log10 1E-05 1000 0.018746739843535 1
kf_RII_C_2__RIIp_C_2 kf_{RII_C_2,RIIp_C_2} log10 1E-05 1000 0.022767932816744 1
kf_RIIp_2__RII_2 kf_{RIIp_2,RII_2} log10 1E-05 1000 0.03230162532087 1
kf_RIIp_C_2__RII_C_2 kf_{RIIp_C_2,RII_C_2} log10 1E-05 1000 0.025703919542656 1
kf_RIIp_cAMP_C_2__RIIp_2 kf_{RIIp_cAMP_C_2,RIIp_2} log10 1E-05 1000 0.105283748414996 1
kf_cAMP kf_{cAMP} log10 1E-05 1000 0.501542412469253 1
ki_IBMX ki_{IBMX} log10 1E-05 1000 999.99999999947 1
ki_Rp8_Br_cAMPS_pAB ki_{Rp8,Br,cAMPS,pAB} log10 1E-05 1000 6.44560005260773 1
ki_Rp8_pCPT_cAMPS_pAB ki_{Rp8,pCPT,cAMPS,pAB} log10 1E-05 1000 9.3898794585472 1
ki_Rp_cAMPS_pAB ki_{Rp,cAMPS,pAB} log10 1E-05 1000 0.016320587381729 1
ki_Sp8_Br_cAMPS_AM ki_{Sp8,Br,cAMPS,AM} log10 1E-05 1000 0.131657936881857 1
ks_AC_cAMP ks_{AC,cAMP} log10 1E-05 1000 0.423150583624568 1
rel_open rel_{open} log10 1E-05 1 0.232684484588385 1
s_Calpha_JI09_160201_Drg453_452_CycNuc s_{Calpha,JI09,160201,Drg453,452,CycNuc} log10 1E-5 1000 1 0
s_Calpha_global s_{Calpha,global} log10 1000 3162.27766016838 1758.15501421399 1
s_pRII_JI09_150302_Drg345_343_CycNuc s_{pRII,JI09,150302,Drg345,343,CycNuc} log10 0.001 1000 1.1029976101468 1 parameterScaleNormal 0;0.1
s_pRII_JI09_150330_Drg350_348_CycNuc s_{pRII,JI09,150330,Drg350,348,CycNuc} log10 0.001 1000 0.9067516915655 1 parameterScaleNormal 0;0.1
s_pRII_JI09_150330_Drg353_351_CycNuc s_{pRII,JI09,150330,Drg353,351,CycNuc} log10 0.001 1000 0.934506349283962 1 parameterScaleNormal 0;0.1
s_pRII_JI09_151102_Drg421_418_Age s_{pRII,JI09,151102,Drg421,418,Age} log10 0.001 1000 1.06693094665605 1 parameterScaleNormal 0;0.1
s_pRII_Western s_{pRII,Western} log10 0.1 100000 1.14849828435972 1
s_pRII_global s_{pRII,global} log10 1000 3162.27766016838 2206.77137565008 1
rho_Calpha_Microscopy \rho_{Calpha,Microscopy} log10 1E-05 1000 0.049753182233122 1
rho_pRII_Microscopy \rho_{pRII,Microscopy} log10 1E-05 1000 0.040685236621013 1
rho_pRII_Western \rho_{pRII,Western} log10 1E-05 1000 0.099334983213923 1
xi_AC_cAMP_Fsk \xi_{AC_{cAMP,Fsk} log10 1E-05 1000 642.370332155571 1
xi_b_Rp8_Br_cAMPS \xi_{b,Rp8,Br,cAMPS} log10 1E-05 100000 0.040559301141753 1 parameterScaleNormal 0;3
xi_b_Rp8_pCPT_cAMPS \xi_{b,Rp8,pCPT,cAMPS} log10 1E-05 100000 0.026684466293791 1 parameterScaleNormal 0;3
xi_b_Rp_cAMPS \xi_{b,Rp,cAMPS} log10 1E-05 100000 0.603928050380137 1 parameterScaleNormal 0;3
xi_b_Sp8_Br_cAMPS \xi_{b,Sp8,Br,cAMPS} log10 1E-05 100000 21.6150210996832 1 parameterScaleNormal 0;3
xi_kf_RII_2__RII_C_2 \xi_{kf_RII_2,RII_C_2} log10 1E-05 1 0.01893099823943 1 parameterScaleNormal -1.742435698117109;0.1
xi_kf_RII_C_2__RII_2 \xi_{kf_RII_C_2,RII_2} log10 1E-05 100000 0.810991675177056 1 parameterScaleNormal -0.062147906748844;0.1
xi_rel_open \xi_{rel,open} log10 1E-05 1 0.749424660751357 1
xi_KD_Rp8_Br_cAMPS \xi_{KD,Rp8,Br,cAMPS} log10 1E-05 100000 0.039962383560766 1 parameterScaleNormal 0;3 H1: different KD
xi_KD_Rp8_pCPT_cAMPS \xi_{KD,Rp8,pCPT,cAMPS} log10 1E-05 100000 0.194212924719718 1 parameterScaleNormal 0;3 H1: different KD
xi_KD_Rp_cAMPS \xi_{KD,Rp,cAMPS} log10 1E-05 100000 0.163047074866588 1 parameterScaleNormal 0;3 H1: different KD
xi_KD_Sp8_Br_cAMPS \xi_{KD,Sp8,Br,cAMPS} log10 1E-05 100000 0.22324026500667 1 parameterScaleNormal 0;3 H1: different KD
11 changes: 11 additions & 0 deletions Benchmark-Models/Isensee_JCB2018/parameters_Isensee_JCB2018_model_selection.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
parameterId parameterName parameterScale lowerBound upperBound nominalValue estimate objectivePriorType objectivePriorParameters model_selection_group
xi_pAC \xi_{pAC} log10 0.001 1 1 1 parameterScaleNormal 0;3 H2: AC inhibition
kp_AC kp_{AC} log10 1E-5 1E3 0 1 H2: AC inhibition
kdp_AC kdp_{AC} log10 1E-5 1E3 0 1 H2: AC inhibition
xi_i_Rp8_Br_cAMPS_pAB \xi_{i,Rp8,Br,cAMPS,pAB} log10 1E-05 1 1 1 parameterScaleNormal 0;3 H3: incomplete import
xi_i_Rp8_pCPT_cAMPS_pAB \xi_{i,Rp8,pCPT,cAMPS,pAB} log10 1E-05 1 1 1 parameterScaleNormal 0;3 H3: incomplete import
xi_i_Rp_cAMPS_pAB \xi_{i,Rp,cAMPS,pAB} log10 1E-05 1 1 1 parameterScaleNormal 0;3 H3: incomplete import
xi_i_Sp8_Br_cAMPS_AM \xi_{i,Sp8,Br,cAMPS,AM} log10 1E-05 1 1 1 parameterScaleNormal 0;3 H3: incomplete import
xi_pPDE \xi_{pPDE} log10 1 1000 1 1 parameterScaleNormal 0.397940008672038;3 H4: PDE inhibition
kf_PDE_Csub kf_{PDE,Csub} log10 1E-5 1E3 0 1 H4: PDE inhibition
KD_PDE_Csub KD_{PDE,Csub} log10 1E-5 1E3 0 1 H4: PDE inhibition
2 changes: 1 addition & 1 deletion src/python/pyproject.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ dependencies = [
]

[project.optional-dependencies]
dev = ["ruff"]
dev = ["pre-commit", "pytest", "ruff"]

[project.scripts]
bmp-petablint = "benchmark_models_petab.check_petablint:main"
Expand Down