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FFroehlichFFroehlich
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Fix Isensee prior (#144)
* fix column name and increase mean accuracy * remove nan measurements from Blasi
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Lines changed: 7 additions & 43 deletions

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‎Benchmark-Models/Blasi_CellSystems2016/measurementData_Blasi_CellSystems2016.tsv‎

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@@ -108,73 +108,37 @@ observable_k5k8 control 0.006899493 inf sigma
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observable_k5k8 control 0.0038748389 inf sigma
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observable_k5k8 control 0.0037448182 inf sigma
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observable_k5k12 control 0.0434158865 inf sigma
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observable_k5k12 control NaN inf sigma
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observable_k5k12 control 0.0443789052 inf sigma
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observable_k5k12 control NaN inf sigma
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observable_k5k12 control 0.0470881206 inf sigma
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observable_k5k12 control NaN inf sigma
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observable_k5k12 control NaN inf sigma
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observable_k5k12 control 0.0477700658 inf sigma
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observable_k5k12 control 0.0600586224 inf sigma
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observable_k5k12 control NaN inf sigma
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observable_k5k12 control 0.0578341883 inf sigma
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observable_k5k12 control 0.0571466513 inf sigma
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observable_k5k12 control 0.0540117162 inf sigma
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observable_k5k12 control NaN inf sigma
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observable_k5k12 control 0.0511675275 inf sigma
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observable_k5k12 control 0.0440053677 inf sigma
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observable_k5k12 control 0.0307945134 inf sigma
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observable_k5k12 control 0.0388013075 inf sigma
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observable_k5k16 control NaN inf sigma
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observable_k5k16 control NaN inf sigma
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observable_k5k16 control NaN inf sigma
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observable_k5k16 control NaN inf sigma
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observable_k5k16 control NaN inf sigma
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observable_k5k16 control NaN inf sigma
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observable_k5k16 control NaN inf sigma
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observable_k5k16 control NaN inf sigma
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observable_k5k16 control NaN inf sigma
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observable_k5k16 control NaN inf sigma
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observable_k5k16 control NaN inf sigma
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observable_k5k16 control NaN inf sigma
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observable_k5k16 control NaN inf sigma
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observable_k5k16 control NaN inf sigma
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observable_k5k16 control NaN inf sigma
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observable_k5k16 control NaN inf sigma
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observable_k5k16 control NaN inf sigma
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observable_k5k16 control NaN inf sigma
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observable_k8k12 control 0.0080967193 inf sigma
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observable_k8k12 control NaN inf sigma
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observable_k8k12 control 0.0065363759 inf sigma
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observable_k8k12 control NaN inf sigma
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observable_k8k12 control 0.0065426513 inf sigma
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observable_k8k12 control NaN inf sigma
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observable_k8k12 control NaN inf sigma
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observable_k8k12 control 0.0133786749 inf sigma
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observable_k8k12 control 0.0121658868 inf sigma
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observable_k8k12 control NaN inf sigma
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observable_k8k12 control 0.0079245333 inf sigma
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observable_k8k12 control 0.0054277999 inf sigma
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observable_k8k12 control 0.0053220896 inf sigma
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observable_k8k12 control NaN inf sigma
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observable_k8k12 control 0.0054696133 inf sigma
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observable_k8k12 control 0.0101090455 inf sigma
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observable_k8k12 control 0.0094183962 inf sigma
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observable_k8k12 control 0.0060419851 inf sigma
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observable_k8k16 control 0.0038262075 inf sigma
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observable_k8k16 control NaN inf sigma
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observable_k8k16 control 0.0067116281 inf sigma
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observable_k8k16 control NaN inf sigma
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observable_k8k16 control 0.0055278515 inf sigma
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observable_k8k16 control NaN inf sigma
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observable_k8k16 control NaN inf sigma
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observable_k8k16 control 0.0039600068 inf sigma
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observable_k8k16 control 0.0013848019 inf sigma
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observable_k8k16 control NaN inf sigma
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observable_k8k16 control 0.0052229185 inf sigma
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observable_k8k16 control 0.0066441942 inf sigma
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observable_k8k16 control 0.0067009986 inf sigma
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observable_k8k16 control NaN inf sigma
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observable_k8k16 control 0.0076181629 inf sigma
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observable_k8k16 control 0.0040375288 inf sigma
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observable_k8k16 control 0.0012796644 inf sigma

‎Benchmark-Models/Isensee_JCB2018/parameters_Isensee_JCB2018.tsv‎

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parameterId parameterName parameterScale lowerBound upperBound nominalValue estimate objectivePrior objectivePriorParameters
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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 0.845098;0.2
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KD_H89 KD_{H89} log10 1E-05 1000 0.048074027232332 1 parameterScaleNormal -1.31876;0.2
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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 0.462398;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
@@ -54,8 +54,8 @@ xi_i_Rp8_Br_cAMPS_pAB \xi_{i,Rp8,Br,cAMPS,pAB} log10 1E-05 1 1 0 parameterScaleN
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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 -1.74244;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 -0.0621479;0.1
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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 0.39794;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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