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Isensee_JCB2018: fix bounds and scales for some parameters (#132)
* see README to use other models from the model selection problem * update dev packages
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‎Benchmark-Models/Isensee_JCB2018/README.md‎

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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.
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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.
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```python
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import pandas as pd
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import petab
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petab_problem = petab.Problem.from_yaml("Isensee_JCB2018.yaml")
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model_selection_parameter_df = petab.get_parameter_df("parameters_Isensee_JCB2018_model_selection.tsv")
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petab_problem.parameter_df = petab.get_parameter_df(pd.concat([
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# Remove the H1 parameters
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petab_problem.parameter_df.query("model_selection_group != 'H1: different KD'"),
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# Add the H2 and H3 parameters
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model_selection_parameter_df.query("model_selection_group in ['H2: AC inhibition', 'H3: incomplete import']")
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]))
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```

‎Benchmark-Models/Isensee_JCB2018/model_Isensee_JCB2018.xml‎

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<parameter metaid="KD_Fsk" id="KD_Fsk" value="14.2656743301721"/>
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<parameter metaid="KD_H89" id="KD_H89" value="0.0480736009761681"/>
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<parameter metaid="KD_IBMX" id="KD_IBMX" value="11.9768989891142"/>
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<parameter metaid="KD_PDE_Csub" id="KD_PDE_Csub" value="0"/>
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<parameter metaid="KD_cAMP" id="KD_cAMP" value="2.84986906175302"/>
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<parameter metaid="PDE_total" id="PDE_total" value="1"/>
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<parameter metaid="RII2_total" id="RII2_total" value="1"/>
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<parameter metaid="kdeg_cAMP" id="kdeg_cAMP" value="1.00032978441703e-05"/>
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<parameter metaid="kdeg_cAMP_free" id="kdeg_cAMP_free" value="7.35892283451732"/>
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<parameter metaid="kdp_AC" id="kdp_AC" value="0"/>
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<parameter metaid="kf_Fsk" id="kf_Fsk" value="999.991987450139"/>
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<parameter metaid="kf_H89" id="kf_H89" value="0.000741493422675392"/>
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<parameter metaid="kf_PDE_Csub" id="kf_PDE_Csub" value="0"/>
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<parameter metaid="kf_RII_2__RII_C_2" id="kf_RII_2__RII_C_2" value="1.26077939273477"/>
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<parameter metaid="kf_RII_C_2__RII_2" id="kf_RII_C_2__RII_2" value="0.0187262534054505"/>
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<parameter metaid="kf_RII_C_2__RIIp_C_2" id="kf_RII_C_2__RIIp_C_2" value="0.0227841500487899"/>
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<parameter metaid="ki_Rp8_pCPT_cAMPS_pAB" id="ki_Rp8_pCPT_cAMPS_pAB" value="9.24294887100985"/>
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<parameter metaid="ki_Rp_cAMPS_pAB" id="ki_Rp_cAMPS_pAB" value="0.0163472838984393"/>
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<parameter metaid="ki_Sp8_Br_cAMPS_AM" id="ki_Sp8_Br_cAMPS_AM" value="0.131083036712545"/>
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<parameter metaid="kp_AC" id="kp_AC" value="0"/>
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<parameter metaid="ks_AC_cAMP" id="ks_AC_cAMP" value="0.423299046028554"/>
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<parameter metaid="xi_AC_cAMP_Fsk" id="xi_AC_cAMP_Fsk" value="640.551657640036"/>
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<parameter metaid="xi_KD_Rp8_Br_cAMPS" id="xi_KD_Rp8_Br_cAMPS" value="0.040150612333366"/>
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<parameter metaid="xi_KD_Rp8_pCPT_cAMPS" id="xi_KD_Rp8_pCPT_cAMPS" value="0.194630402579553"/>
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<parameter metaid="xi_KD_Rp_cAMPS" id="xi_KD_Rp_cAMPS" value="0.163369645426461"/>
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<parameter metaid="xi_KD_Sp8_Br_cAMPS" id="xi_KD_Sp8_Br_cAMPS" value="0.222276461349335"/>
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<parameter metaid="xi_b_Rp8_Br_cAMPS" id="xi_b_Rp8_Br_cAMPS" value="0.0408695544562406"/>
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<parameter metaid="xi_b_Rp8_pCPT_cAMPS" id="xi_b_Rp8_pCPT_cAMPS" value="0.0268897774883765"/>
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<parameter metaid="xi_b_Rp_cAMPS" id="xi_b_Rp_cAMPS" value="0.607960299288444"/>
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<parameter metaid="xi_b_Sp8_Br_cAMPS" id="xi_b_Sp8_Br_cAMPS" value="21.7551956731725"/>
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<parameter metaid="xi_i_Rp8_Br_cAMPS_pAB" id="xi_i_Rp8_Br_cAMPS_pAB" value="1"/>
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<parameter metaid="xi_i_Rp8_pCPT_cAMPS_pAB" id="xi_i_Rp8_pCPT_cAMPS_pAB" value="1"/>
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<parameter metaid="xi_i_Rp_cAMPS_pAB" id="xi_i_Rp_cAMPS_pAB" value="1"/>
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<parameter metaid="xi_i_Sp8_Br_cAMPS_AM" id="xi_i_Sp8_Br_cAMPS_AM" value="1"/>
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<parameter metaid="xi_kf_RII_2__RII_C_2" id="xi_kf_RII_2__RII_C_2" value="0.0189295042137343"/>
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<parameter metaid="xi_kf_RII_C_2__RII_2" id="xi_kf_RII_C_2__RII_2" value="0.811223214879921"/>
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<parameter metaid="xi_pAC" id="xi_pAC" value="1"/>
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<parameter metaid="xi_pPDE" id="xi_pPDE" value="1"/>
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<parameter metaid="Fsk" id="Fsk" value="10" units="time" constant="false"/>
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<parameter metaid="IBMXex" id="IBMXex" value="0" constant="false"/>
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<parameter metaid="H89" id="H89" value="0" constant="false"/>
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<parameter metaid="Sp8_Br_cAMPS_AM_time" id="Sp8_Br_cAMPS_AM_time" value="0" units="time"/>
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<parameter metaid="fourABnOH_level" id="fourABnOH_level" value="0" units="substance"/>
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<parameter metaid="fourABnOH_time" id="fourABnOH_incubation_time" value="0" units="time"/>
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<!-- H1: different KD -->
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<parameter metaid="xi_KD_Rp8_Br_cAMPS" id="xi_KD_Rp8_Br_cAMPS" value="0"/>
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<parameter metaid="xi_KD_Rp8_pCPT_cAMPS" id="xi_KD_Rp8_pCPT_cAMPS" value="0"/>
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<parameter metaid="xi_KD_Rp_cAMPS" id="xi_KD_Rp_cAMPS" value="0"/>
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<parameter metaid="xi_KD_Sp8_Br_cAMPS" id="xi_KD_Sp8_Br_cAMPS" value="0"/>
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<!-- H2: AC inhibition -->
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<parameter metaid="xi_pAC" id="xi_pAC" value="0"/>
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<parameter metaid="kp_AC" id="kp_AC" value="0"/>
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<parameter metaid="kdp_AC" id="kdp_AC" value="0"/>
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<!-- H3: incomplete import -->
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<parameter metaid="xi_i_Rp8_Br_cAMPS_pAB" id="xi_i_Rp8_Br_cAMPS_pAB" value="0"/>
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<parameter metaid="xi_i_Rp8_pCPT_cAMPS_pAB" id="xi_i_Rp8_pCPT_cAMPS_pAB" value="0"/>
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<parameter metaid="xi_i_Rp_cAMPS_pAB" id="xi_i_Rp_cAMPS_pAB" value="0"/>
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<parameter metaid="xi_i_Sp8_Br_cAMPS_AM" id="xi_i_Sp8_Br_cAMPS_AM" value="0"/>
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<!-- H4: PDE inhibition -->
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<parameter metaid="xi_pPDE" id="xi_pPDE" value="0"/>
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<parameter metaid="kf_PDE_Csub" id="kf_PDE_Csub" value="0"/>
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<parameter metaid="KD_PDE_Csub" id="KD_PDE_Csub" value="0"/>
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</listOfParameters>
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<listOfRules>
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<assignmentRule metaid="CDMT00167" variable="Fsk">

‎Benchmark-Models/Isensee_JCB2018/parameters_Isensee_JCB2018.tsv‎

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parameterId parameterName parameterScale lowerBound upperBound nominalValue estimate objectivePriorType objectivePriorParameters
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AC_total AC_{total} log10 1E-05 1000 1 0
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KD_Fsk KD_{Fsk} log10 1E-05 1000 14.2805171742694 1 parameterScaleNormal 0.845098040014257;0.2
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KD_H89 KD_{H89} log10 1E-05 1000 0.048074027232332 1 parameterScaleNormal -1.318758762624413;0.2
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KD_IBMX KD_{IBMX} log10 1E-05 1000 11.960772655864 1 parameterScaleNormal 1.0;0.2
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KD_PDE_Csub KD_{PDE,Csub} lin -5 3 0 0
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KD_cAMP KD_{cAMP} log10 1E-05 1000 2.85002019924967 1 parameterScaleNormal 0.462397997898956;0.2
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PDE_total PDE_{total} log10 1E-05 1000 1 0
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RII2_total RII2_{total} log10 1E-05 1000 1 0
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b_Calpha_global b_{Calpha,global} log10 0.001 1000 101.662732662228 1 parameterScaleNormal 2;0.1
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b_pRII_global b_{pRII,global} log10 0.001 1000 99.7184671220999 1 parameterScaleNormal 2;0.1
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kdeg_cAMP kdeg_{cAMP} log10 1E-05 1000 1.00000660182181E-05 1
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kdeg_cAMP_free kdeg_{cAMP,free} log10 1E-05 1000 7.38363782272545 1
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kdp_AC kdp_{AC} lin -5 3 0 0
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kf_Fsk kf_{Fsk} log10 1E-05 1000 999.999958296064 1
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kf_H89 kf_{H89} log10 1E-05 1000 0.000742716621349 1
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kf_PDE_Csub kf_{PDE,Csub} lin -5 3 0 0
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kf_RII_2__RII_C_2 kf_{RII_2,RII_C_2} log10 1E-05 100000 1.26446106685121 1
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kf_RII_C_2__RII_2 kf_{RII_C_2,RII_2} log10 1E-05 1000 0.018746739843535 1
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kf_RII_C_2__RIIp_C_2 kf_{RII_C_2,RIIp_C_2} log10 1E-05 1000 0.022767932816744 1
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kf_RIIp_2__RII_2 kf_{RIIp_2,RII_2} log10 1E-05 1000 0.03230162532087 1
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kf_RIIp_C_2__RII_C_2 kf_{RIIp_C_2,RII_C_2} log10 1E-05 1000 0.025703919542656 1
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kf_RIIp_cAMP_C_2__RIIp_2 kf_{RIIp_cAMP_C_2,RIIp_2} log10 1E-05 1000 0.105283748414996 1
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kf_cAMP kf_{cAMP} log10 1E-05 1000 0.501542412469253 1
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ki_IBMX ki_{IBMX} log10 1E-05 1000 999.99999999947 1
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ki_Rp8_Br_cAMPS_pAB ki_{Rp8,Br,cAMPS,pAB} log10 1E-05 1000 6.44560005260773 1
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ki_Rp8_pCPT_cAMPS_pAB ki_{Rp8,pCPT,cAMPS,pAB} log10 1E-05 1000 9.3898794585472 1
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ki_Rp_cAMPS_pAB ki_{Rp,cAMPS,pAB} log10 1E-05 1000 0.016320587381729 1
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ki_Sp8_Br_cAMPS_AM ki_{Sp8,Br,cAMPS,AM} log10 1E-05 1000 0.131657936881857 1
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kp_AC kp_{AC} lin -5 3 0 0
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ks_AC_cAMP ks_{AC,cAMP} log10 1E-05 1000 0.423150583624568 1
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rel_open rel_{open} log10 1E-05 1 0.232684484588385 1
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s_Calpha_JI09_160201_Drg453_452_CycNuc s_{Calpha,JI09,160201,Drg453,452,CycNuc} log10 1E-5 1000 1 0
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s_Calpha_global s_{Calpha,global} log10 1000 3162.27766016838 1758.15501421399 1
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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
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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
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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
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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
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s_pRII_Western s_{pRII,Western} log10 0.1 100000 1.14849828435972 1
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s_pRII_global s_{pRII,global} log10 1000 3162.27766016838 2206.77137565008 1
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rho_Calpha_Microscopy \rho_{Calpha,Microscopy} log10 1E-05 1000 0.049753182233122 1
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rho_pRII_Microscopy \rho_{pRII,Microscopy} log10 1E-05 1000 0.040685236621013 1
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rho_pRII_Western \rho_{pRII,Western} log10 1E-05 1000 0.099334983213923 1
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xi_AC_cAMP_Fsk \xi_{AC_{cAMP,Fsk} log10 1E-05 1000 642.370332155571 1
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xi_KD_Rp8_Br_cAMPS \xi_{KD,Rp8,Br,cAMPS} log10 1E-05 100000 0.039962383560766 1 parameterScaleNormal 0;3
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xi_KD_Rp8_pCPT_cAMPS \xi_{KD,Rp8,pCPT,cAMPS} log10 1E-05 100000 0.194212924719718 1 parameterScaleNormal 0;3
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xi_KD_Rp_cAMPS \xi_{KD,Rp,cAMPS} log10 1E-05 100000 0.163047074866588 1 parameterScaleNormal 0;3
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xi_KD_Sp8_Br_cAMPS \xi_{KD,Sp8,Br,cAMPS} log10 1E-05 100000 0.22324026500667 1 parameterScaleNormal 0;3
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xi_b_Rp8_Br_cAMPS \xi_{b,Rp8,Br,cAMPS} log10 1E-05 100000 0.040559301141753 1 parameterScaleNormal 0;3
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xi_b_Rp8_pCPT_cAMPS \xi_{b,Rp8,pCPT,cAMPS} log10 1E-05 100000 0.026684466293791 1 parameterScaleNormal 0;3
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xi_b_Rp_cAMPS \xi_{b,Rp,cAMPS} log10 1E-05 100000 0.603928050380137 1 parameterScaleNormal 0;3
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xi_b_Sp8_Br_cAMPS \xi_{b,Sp8,Br,cAMPS} log10 1E-05 100000 21.6150210996832 1 parameterScaleNormal 0;3
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xi_i_Rp8_Br_cAMPS_pAB \xi_{i,Rp8,Br,cAMPS,pAB} log10 1E-05 1 1 0 parameterScaleNormal 0;3
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xi_i_Rp8_pCPT_cAMPS_pAB \xi_{i,Rp8,pCPT,cAMPS,pAB} log10 1E-05 1 1 0 parameterScaleNormal 0;3
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xi_i_Rp_cAMPS_pAB \xi_{i,Rp,cAMPS,pAB} log10 1E-05 1 1 0 parameterScaleNormal 0;3
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xi_i_Sp8_Br_cAMPS_AM \xi_{i,Sp8,Br,cAMPS,AM} log10 1E-05 1 1 0 parameterScaleNormal 0;3
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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
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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
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xi_pAC \xi_{pAC} log10 0.001 1 1 0 parameterScaleNormal 0;3
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xi_pPDE \xi_{pPDE} log10 1 1000 1 0 parameterScaleNormal 0.397940008672038;3
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xi_rel_open \xi_{rel,open} log10 1E-05 1 0.749424660751357 1
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parameterId parameterName parameterScale lowerBound upperBound nominalValue estimate objectivePriorType objectivePriorParameters model_selection_group
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AC_total AC_{total} log10 1E-05 1000 1 0
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KD_Fsk KD_{Fsk} log10 1E-05 1000 14.2805171742694 1 parameterScaleNormal 0.845098040014257;0.2
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KD_H89 KD_{H89} log10 1E-05 1000 0.048074027232332 1 parameterScaleNormal -1.318758762624413;0.2
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KD_IBMX KD_{IBMX} log10 1E-05 1000 11.960772655864 1 parameterScaleNormal 1.0;0.2
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KD_cAMP KD_{cAMP} log10 1E-05 1000 2.85002019924967 1 parameterScaleNormal 0.462397997898956;0.2
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PDE_total PDE_{total} log10 1E-05 1000 1 0
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RII2_total RII2_{total} log10 1E-05 1000 1 0
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b_Calpha_global b_{Calpha,global} log10 0.001 1000 101.662732662228 1 parameterScaleNormal 2;0.1
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b_pRII_global b_{pRII,global} log10 0.001 1000 99.7184671220999 1 parameterScaleNormal 2;0.1
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kdeg_cAMP kdeg_{cAMP} log10 1E-05 1000 1.00000660182181E-05 1
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kdeg_cAMP_free kdeg_{cAMP,free} log10 1E-05 1000 7.38363782272545 1
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kf_Fsk kf_{Fsk} log10 1E-05 1000 999.999958296064 1
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kf_H89 kf_{H89} log10 1E-05 1000 0.000742716621349 1
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kf_RII_2__RII_C_2 kf_{RII_2,RII_C_2} log10 1E-05 100000 1.26446106685121 1
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kf_RII_C_2__RII_2 kf_{RII_C_2,RII_2} log10 1E-05 1000 0.018746739843535 1
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kf_RII_C_2__RIIp_C_2 kf_{RII_C_2,RIIp_C_2} log10 1E-05 1000 0.022767932816744 1
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kf_RIIp_2__RII_2 kf_{RIIp_2,RII_2} log10 1E-05 1000 0.03230162532087 1
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kf_RIIp_C_2__RII_C_2 kf_{RIIp_C_2,RII_C_2} log10 1E-05 1000 0.025703919542656 1
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kf_RIIp_cAMP_C_2__RIIp_2 kf_{RIIp_cAMP_C_2,RIIp_2} log10 1E-05 1000 0.105283748414996 1
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kf_cAMP kf_{cAMP} log10 1E-05 1000 0.501542412469253 1
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ki_IBMX ki_{IBMX} log10 1E-05 1000 999.99999999947 1
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ki_Rp8_Br_cAMPS_pAB ki_{Rp8,Br,cAMPS,pAB} log10 1E-05 1000 6.44560005260773 1
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ki_Rp8_pCPT_cAMPS_pAB ki_{Rp8,pCPT,cAMPS,pAB} log10 1E-05 1000 9.3898794585472 1
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ki_Rp_cAMPS_pAB ki_{Rp,cAMPS,pAB} log10 1E-05 1000 0.016320587381729 1
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ki_Sp8_Br_cAMPS_AM ki_{Sp8,Br,cAMPS,AM} log10 1E-05 1000 0.131657936881857 1
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ks_AC_cAMP ks_{AC,cAMP} log10 1E-05 1000 0.423150583624568 1
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rel_open rel_{open} log10 1E-05 1 0.232684484588385 1
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s_Calpha_JI09_160201_Drg453_452_CycNuc s_{Calpha,JI09,160201,Drg453,452,CycNuc} log10 1E-5 1000 1 0
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s_Calpha_global s_{Calpha,global} log10 1000 3162.27766016838 1758.15501421399 1
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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
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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
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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
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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
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s_pRII_Western s_{pRII,Western} log10 0.1 100000 1.14849828435972 1
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s_pRII_global s_{pRII,global} log10 1000 3162.27766016838 2206.77137565008 1
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rho_Calpha_Microscopy \rho_{Calpha,Microscopy} log10 1E-05 1000 0.049753182233122 1
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rho_pRII_Microscopy \rho_{pRII,Microscopy} log10 1E-05 1000 0.040685236621013 1
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rho_pRII_Western \rho_{pRII,Western} log10 1E-05 1000 0.099334983213923 1
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xi_AC_cAMP_Fsk \xi_{AC_{cAMP,Fsk} log10 1E-05 1000 642.370332155571 1
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xi_b_Rp8_Br_cAMPS \xi_{b,Rp8,Br,cAMPS} log10 1E-05 100000 0.040559301141753 1 parameterScaleNormal 0;3
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xi_b_Rp8_pCPT_cAMPS \xi_{b,Rp8,pCPT,cAMPS} log10 1E-05 100000 0.026684466293791 1 parameterScaleNormal 0;3
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xi_b_Rp_cAMPS \xi_{b,Rp,cAMPS} log10 1E-05 100000 0.603928050380137 1 parameterScaleNormal 0;3
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xi_b_Sp8_Br_cAMPS \xi_{b,Sp8,Br,cAMPS} log10 1E-05 100000 21.6150210996832 1 parameterScaleNormal 0;3
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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
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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
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xi_rel_open \xi_{rel,open} log10 1E-05 1 0.749424660751357 1
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xi_KD_Rp8_Br_cAMPS \xi_{KD,Rp8,Br,cAMPS} log10 1E-05 100000 0.039962383560766 1 parameterScaleNormal 0;3 H1: different KD
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xi_KD_Rp8_pCPT_cAMPS \xi_{KD,Rp8,pCPT,cAMPS} log10 1E-05 100000 0.194212924719718 1 parameterScaleNormal 0;3 H1: different KD
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xi_KD_Rp_cAMPS \xi_{KD,Rp,cAMPS} log10 1E-05 100000 0.163047074866588 1 parameterScaleNormal 0;3 H1: different KD
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xi_KD_Sp8_Br_cAMPS \xi_{KD,Sp8,Br,cAMPS} log10 1E-05 100000 0.22324026500667 1 parameterScaleNormal 0;3 H1: different KD

‎Benchmark-Models/Isensee_JCB2018/parameters_Isensee_JCB2018_model_selection.tsv‎

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parameterId parameterName parameterScale lowerBound upperBound nominalValue estimate objectivePriorType objectivePriorParameters model_selection_group
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xi_pAC \xi_{pAC} log10 0.001 1 1 1 parameterScaleNormal 0;3 H2: AC inhibition
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kp_AC kp_{AC} log10 1E-5 1E3 0 1 H2: AC inhibition
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kdp_AC kdp_{AC} log10 1E-5 1E3 0 1 H2: AC inhibition
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xi_i_Rp8_Br_cAMPS_pAB \xi_{i,Rp8,Br,cAMPS,pAB} log10 1E-05 1 1 1 parameterScaleNormal 0;3 H3: incomplete import
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xi_i_Rp8_pCPT_cAMPS_pAB \xi_{i,Rp8,pCPT,cAMPS,pAB} log10 1E-05 1 1 1 parameterScaleNormal 0;3 H3: incomplete import
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xi_i_Rp_cAMPS_pAB \xi_{i,Rp,cAMPS,pAB} log10 1E-05 1 1 1 parameterScaleNormal 0;3 H3: incomplete import
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xi_i_Sp8_Br_cAMPS_AM \xi_{i,Sp8,Br,cAMPS,AM} log10 1E-05 1 1 1 parameterScaleNormal 0;3 H3: incomplete import
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xi_pPDE \xi_{pPDE} log10 1 1000 1 1 parameterScaleNormal 0.397940008672038;3 H4: PDE inhibition
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kf_PDE_Csub kf_{PDE,Csub} log10 1E-5 1E3 0 1 H4: PDE inhibition
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KD_PDE_Csub KD_{PDE,Csub} log10 1E-5 1E3 0 1 H4: PDE inhibition

‎src/python/pyproject.toml‎

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]
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[project.optional-dependencies]
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dev = ["ruff"]
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dev = ["pre-commit", "pytest", "ruff"]
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[project.scripts]
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bmp-petablint = "benchmark_models_petab.check_petablint:main"

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