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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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| 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. | ||
| ```python | ||
| import pandas as pd | ||
| import petab | ||
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| petab_problem = petab.Problem.from_yaml("Isensee_JCB2018.yaml") | ||
| 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([ | ||
| # 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']") | ||
| ])) | ||
| ``` |
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112 changes: 51 additions & 61 deletions
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Benchmark-Models/Isensee_JCB2018/parameters_Isensee_JCB2018.tsv
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| Original file line number | Diff line number | Diff line change |
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| @@ -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 |
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Benchmark-Models/Isensee_JCB2018/parameters_Isensee_JCB2018_model_selection.tsv
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| Original file line number | Diff line number | Diff line change |
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| 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 |
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