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update dev packages; add README for Isensee; remove default values fr…
…om model selection parameters in SBML
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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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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 | ||
| xi_pAC \xi_{pAC} log10 0.001 1 1 0 parameterScaleNormal 0;3 H2: AC inhibition | ||
| kp_AC kp_{AC} log10 1E-5 1E3 0 0 H2: AC inhibition | ||
| kdp_AC kdp_{AC} log10 1E-5 1E3 0 0 H2: AC inhibition | ||
| xi_i_Rp8_Br_cAMPS_pAB \xi_{i,Rp8,Br,cAMPS,pAB} log10 1E-05 1 1 0 parameterScaleNormal 0;3 H3: incomplete import | ||
| xi_i_Rp8_pCPT_cAMPS_pAB \xi_{i,Rp8,pCPT,cAMPS,pAB} log10 1E-05 1 1 0 parameterScaleNormal 0;3 H3: incomplete import | ||
| xi_i_Rp_cAMPS_pAB \xi_{i,Rp,cAMPS,pAB} log10 1E-05 1 1 0 parameterScaleNormal 0;3 H3: incomplete import | ||
| xi_i_Sp8_Br_cAMPS_AM \xi_{i,Sp8,Br,cAMPS,AM} log10 1E-05 1 1 0 parameterScaleNormal 0;3 H3: incomplete import | ||
| xi_pPDE \xi_{pPDE} log10 1 1000 1 0 parameterScaleNormal 0.397940008672038;3 H4: PDE_inhibition | ||
| kf_PDE_Csub kf_{PDE,Csub} log10 1E-5 1E3 0 0 H4: PDE_inhibition | ||
| KD_PDE_Csub KD_{PDE,Csub} log10 1E-5 1E3 0 0 H4: PDE_inhibition | ||
| 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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