From 130d3fd5e96009d3eaeb1dec77541cdf27380f63 Mon Sep 17 00:00:00 2001 From: FFroehlich Date: Tue, 12 Oct 2021 20:05:18 -0400 Subject: [PATCH 1/4] reduce condition table and fix data annotation --- ...experimentalCondition_Bachmann_MSB2011.tsv | 19 +++++++------------ 1 file changed, 7 insertions(+), 12 deletions(-) diff --git a/Benchmark-Models/Bachmann_MSB2011/experimentalCondition_Bachmann_MSB2011.tsv b/Benchmark-Models/Bachmann_MSB2011/experimentalCondition_Bachmann_MSB2011.tsv index 32f396c..a9b6eae 100644 --- a/Benchmark-Models/Bachmann_MSB2011/experimentalCondition_Bachmann_MSB2011.tsv +++ b/Benchmark-Models/Bachmann_MSB2011/experimentalCondition_Bachmann_MSB2011.tsv @@ -26,17 +26,12 @@ model1_data24 dose response 30 min 1 0 0 2.5E-08 0 0 0 0 model1_data25 dose response 30 min 1 0 0 2.5E-09 0 0 0 0 model1_data26 dose response 10 min 1 0 0 1.25E-07 0 0 0 0 model1_data27 dose response 10 min 1 0 0 1.25E-08 0 0 0 0 -model1_data28 dose response 10 min 1 0 0 1.75E-08 0 0 0 0 -model1_data29 dose response 10 min 1 0 0 1.7675E-07 0 0 0 0 model1_data30 dose response 10 min 1 0 0 2.5E-06 0 0 0 0 model1_data31 dose response 10 min 1 0 0 2.5E-07 0 0 0 0 -model1_data32 dose response 90 min 1 0 0 2.5E-08 0 0 0 0 -model1_data33 dose response 90 min 1 0 0 2.5E-09 0 0 0 0 -model1_data34 dose response 90 min 1 0 0 3.95E-08 0 0 0 0 -model1_data35 dose response 90 min 1 0 0 7.905E-07 0 0 0 0 -model1_data36 dose response 90 min 1 0 0 7.905E-09 0 0 0 0 -model1_data38 1 0 0 1.25E-07 0 0 0 0 -model1_data39 1 0 0 2.5E-06 0 0 0 0 -model1_data40 1 0 0 2.5E-07 0 0 0 0 -model1_data41 1 0 0 2.5E-08 0 0 0 0 -model1_data42 1 0 0 2.5E-09 0 0 0 0 +model1_data32 dose response 10 min 1 0 0 2.5E-08 0 0 0 0 +model1_data33 dose response 10 min 1 0 0 2.5E-09 0 0 0 0 +model1_data38 dose response 90 min 1 0 0 1.25E-07 0 0 0 0 +model1_data39 dose response 90 min 1 0 0 2.5E-06 0 0 0 0 +model1_data40 dose response 90 min 1 0 0 2.5E-07 0 0 0 0 +model1_data41 dose response 90 min 1 0 0 2.5E-08 0 0 0 0 +model1_data42 dose response 90 min 1 0 0 2.5E-09 0 0 0 0 From fba7552dd7e89c49e47f42b5ede0fa8cafa10b48 Mon Sep 17 00:00:00 2001 From: FFroehlich Date: Tue, 12 Oct 2021 21:24:31 -0400 Subject: [PATCH 2/4] add prior, fixes #135 --- .../parameters_Bachmann_MSB2011.tsv | 232 +++++++++--------- 1 file changed, 116 insertions(+), 116 deletions(-) diff --git a/Benchmark-Models/Bachmann_MSB2011/parameters_Bachmann_MSB2011.tsv b/Benchmark-Models/Bachmann_MSB2011/parameters_Bachmann_MSB2011.tsv index 6714504..e074ded 100644 --- a/Benchmark-Models/Bachmann_MSB2011/parameters_Bachmann_MSB2011.tsv +++ b/Benchmark-Models/Bachmann_MSB2011/parameters_Bachmann_MSB2011.tsv @@ -1,116 +1,116 @@ -parameterId parameterName parameterScale lowerBound upperBound nominalValue estimate -CISEqc CISEqc log10 0.001 10000 432.854027325732 1 -CISEqcOE CISEqcOE log10 0.001 1000 0.53027229006794 1 -CISInh CISInh log10 0.001 1000000000000 785221045.232906 1 -CISRNADelay CISRNADelay log10 0.001 1000 0.144777009620017 1 -CISRNAEqc CISRNAEqc log10 0.001 1000 1 0 -CISRNATurn CISRNATurn log10 0.001 1000 1000 1 -CISTurn CISTurn log10 0.001 1000 0.008398825029262 1 -EpoRActJAK2 EpoRActJAK2 log10 0.001 10000 0.267299659481333 1 -EpoRCISInh EpoRCISInh log10 0.001 1000000 1000000 1 -EpoRCISRemove EpoRCISRemove log10 0.001 1000 5.42989282766407 1 -JAK2ActEpo JAK2ActEpo log10 0.001 1000000000 633154.209632843 1 -JAK2EpoRDeaSHP1 JAK2EpoRDeaSHP1 log10 0.001 10000 142.723069412318 1 -SHP1ActEpoR SHP1ActEpoR log10 0.001 1000 0.001 1 -SHP1Dea SHP1Dea log10 0.001 1000 0.008162255244283 1 -SHP1ProOE SHP1ProOE log10 0.001 1000 2.82568032716189 1 -SOCS3Eqc SOCS3Eqc log10 0.001 1000 173.64095522801 1 -SOCS3EqcOE SOCS3EqcOE log10 0.001 1000 0.679185853534469 1 -SOCS3Inh SOCS3Inh log10 0.001 1000 10.4074255973465 1 -SOCS3RNADelay SOCS3RNADelay log10 0.001 1000 1.06454014521077 1 -SOCS3RNAEqc SOCS3RNAEqc log10 0.001 1000 1 0 -SOCS3RNATurn SOCS3RNATurn log10 0.001 1000 0.008309263619427 1 -SOCS3Turn SOCS3Turn log10 0.001 10000 10000 1 -STAT5ActEpoR STAT5ActEpoR log10 0.001 1000 38.9972748894298 1 -STAT5ActJAK2 STAT5ActJAK2 log10 0.001 1000 0.078108833252848 1 -STAT5Exp STAT5Exp log10 0.001 1000 0.074514698833232 1 -STAT5Imp STAT5Imp log10 0.001 1000 0.026887318057561 1 -init_EpoRJAK2 init_{EpoRJAK2} log10 0.001 1000 3.97622379188569 1 -init_SHP1 init_{SHP1} log10 0.001 1000 26.7251164163486 1 -init_STAT5 init_{STAT5} log10 0.001 1000 79.753639977851 1 -offset_CIS_actd offset_{CIS,actd} log10 0.001 1000 0.009388328725541 1 -offset_CIS_cisoe offset_{CIS,cisoe} log10 0.001 1000 0.030012199170223 1 -offset_CIS_long offset_{CIS,long} log10 0.001 1000 0.026460000624405 1 -offset_CIS_shp1oe offset_{CIS,shp1oe} log10 0.001 1000 0.058794513917949 1 -offset_CIS_socs3oe offset_{CIS,socs3oe} log10 0.001 1000 0.090496783983191 1 -offset_SOCS3_cisoe offset_{SOCS3,cisoe} log10 0.001 1000 0.278270301775932 1 -offset_SOCS3_long offset_{SOCS3,long} log10 0.001 1000 0.114475234936677 1 -offset_SOCS3_socs3oe offset_{SOCS3,socs3oe} log10 0.001 1000 0.025584406819207 1 -offset_pEpoR_actd offset_{pEpoR,actd} log10 0.001 1000 0.018840236081137 1 -offset_pEpoR_cisoe offset_{pEpoR,cisoe} log10 0.001 1000 0.030210854745913 1 -offset_pEpoR_cisoe_pepor offset_{pEpoR,cisoe,pepor} log10 0.001 1000 0.131027220027866 1 -offset_pEpoR_dr30 offset_{pEpoR,dr30} log10 0.001 1000 0.001 1 -offset_pEpoR_dr7 offset_{pEpoR,dr7} log10 0.001 1000 0.028405110847623 1 -offset_pEpoR_fine offset_{pEpoR,fine} log10 0.001 1000 0.064550876993068 1 -offset_pEpoR_long offset_{pEpoR,long} log10 0.001 1000 0.004391399791279 1 -offset_pEpoR_shp1oe offset_{pEpoR,shp1oe} log10 0.001 1000 0.031327226759826 1 -offset_pEpoR_socs3oe offset_{pEpoR,socs3oe} log10 0.001 1000 0.056711915845858 1 -offset_pJAK2_actd offset_{pJAK2,actd} log10 0.001 1000 0.017059890602388 1 -offset_pJAK2_cisoe offset_{pJAK2,cisoe} log10 0.001 1000 0.021928076840931 1 -offset_pJAK2_dr30 offset_{pJAK2,dr30} log10 0.001 1000 0.029944254724382 1 -offset_pJAK2_dr7 offset_{pJAK2,dr7} log10 0.001 1000 0.04733977489635 1 -offset_pJAK2_fine offset_{pJAK2,fine} log10 0.001 1000 0.021658276199496 1 -offset_pJAK2_long offset_{pJAK2,long} log10 0.001 1000 0.009473351822798 1 -offset_pJAK2_shp1oe offset_{pJAK2,shp1oe} log10 0.001 1000 0.026667365128327 1 -offset_pJAK2_socs3oe offset_{pJAK2,socs3oe} log10 0.001 1000 0.059752453075581 1 -offset_pSTAT5_actd offset_{pSTAT5,actd} log10 0.001 1000 0.001868785567417 1 -offset_pSTAT5_cisoe offset_{pSTAT5,cisoe} log10 0.001 1000 0.070791697579138 1 -offset_pSTAT5_conc offset_{pSTAT5,conc} log10 0.001 1000 0.236827475949589 1 -offset_pSTAT5_long offset_{pSTAT5,long} log10 0.001 1000 0.001093070638337 1 -offset_pSTAT5_shp1oe offset_{pSTAT5,shp1oe} log10 0.001 1000 0.054941495350482 1 -offset_pSTAT5_socs3oe offset_{pSTAT5,socs3oe} log10 0.001 1000 0.005613364786273 1 -scale1_CIS_dr90 scale1_{CIS,dr90} log10 0.001 1000 17.5631450183542 1 -scale2_CIS_dr90 scale2_{CIS,dr90} log10 0.001 1000 16.1205634424041 1 -scale_CISRNA_foldA scale_{CISRNA,foldA} log10 0.001 1000 33.2822368277369 1 -scale_CISRNA_foldB scale_{CISRNA,foldB} log10 0.001 1000 31.0176342778512 1 -scale_CISRNA_foldC scale_{CISRNA,foldC} log10 0.001 1000 19.6194113406379 1 -scale_CIS_actd scale_{CIS,actd} log10 0.001 1000 14.5490143154214 1 -scale_CIS_cisoe scale_{CIS,cisoe} log10 0.001 1000 1.37088201048354 1 -scale_CIS_long scale_{CIS,long} log10 0.001 1000 16.4036102124066 1 -scale_CIS_shp1oe scale_{CIS,shp1oe} log10 0.001 1000 51.7115711834136 1 -scale_CIS_socs3oe scale_{CIS,socs3oe} log10 0.001 1000 21.1493834462165 1 -scale_SHP1_shp1oe scale_{SHP1,shp1oe} log10 0.001 1000 0.225547534442942 1 -scale_SOCS3RNA_foldA scale_{SOCS3RNA,foldA} log10 0.001 1000 56.9631412510002 1 -scale_SOCS3RNA_foldB scale_{SOCS3RNA,foldB} log10 0.001 1000 49.074989211721 1 -scale_SOCS3RNA_foldC scale_{SOCS3RNA,foldC} log10 0.001 1000 80.7316820439984 1 -scale_SOCS3_cisoe scale_{SOCS3,cisoe} log10 0.001 1000 11.5682149955845 1 -scale_SOCS3_long scale_{SOCS3,long} log10 0.001 1000 15.485524391452 1 -scale_SOCS3_socs3oe scale_{SOCS3,socs3oe} log10 0.001 1000 1.20457246908681 1 -scale_pEpoR_actd scale_{pEpoR,actd} log10 0.001 1000 0.215657294488182 1 -scale_pEpoR_cisoe scale_{pEpoR,cisoe} log10 0.001 1000 0.273625536372832 1 -scale_pEpoR_cisoe_pepor scale_{pEpoR,cisoe_pepor} log10 0.001 1000 0.156616708581292 1 -scale_pEpoR_dr30 scale_{pEpoR,dr30} log10 0.001 1000 0.537385100441811 1 -scale_pEpoR_dr7 scale_{pEpoR,dr7} log10 0.001 1000 0.101429038197386 1 -scale_pEpoR_fine scale_{pEpoR,fine} log10 0.001 1000 0.080269467995686 1 -scale_pEpoR_long scale_{pEpoR,long} log10 0.001 1000 0.256529988627087 1 -scale_pEpoR_shp1oe scale_{pEpoR,shp1oe} log10 0.001 1000 0.241283495329875 1 -scale_pEpoR_socs3oe scale_{pEpoR,socs3oe} log10 0.001 1000 0.637275573973593 1 -scale_pJAK2_actd scale_{pJAK2,actd} log10 0.001 1000 0.809491692283694 1 -scale_pJAK2_cisoe scale_{pJAK2,cisoe} log10 0.001 1000 1.85429884799069 1 -scale_pJAK2_dr30 scale_{pJAK2,dr30} log10 0.001 1000 1.77561150477407 1 -scale_pJAK2_dr7 scale_{pJAK2,dr7} log10 0.001 1000 0.506322186585869 1 -scale_pJAK2_fine scale_{pJAK2,fine} log10 0.001 1000 0.400770707451671 1 -scale_pJAK2_long scale_{pJAK2,long} log10 0.001 1000 0.882775356861714 1 -scale_pJAK2_shp1oe scale_{pJAK2,shp1oe} log10 0.001 1000 2.31011130113927 1 -scale_pJAK2_socs3oe scale_{pJAK2,socs3oe} log10 0.001 1000 1.266550022901 1 -scale_pSTAT5_actd scale_{pSTAT5,actd} log10 0.001 1000 1.09743435047828 1 -scale_pSTAT5_cisoe scale_{pSTAT5,cisoe} log10 0.001 1000 2.41904111907135 1 -scale_pSTAT5_dr10 scale_{pSTAT5,dr10} log10 0.001 1000 1.00950903665707 1 -scale_pSTAT5_long scale_{pSTAT5,long} log10 0.001 1000 1.47372211945355 1 -scale_pSTAT5_shp1oe scale_{pSTAT5,shp1oe} log10 0.001 1000 1.15158552971751 1 -scale_pSTAT5_socs3oe scale_{pSTAT5,socs3oe} log10 0.001 1000 1.76032560825919 1 -scale_tSTAT5_actd scale_{tSTAT5,actd} log10 0.001 1000 0.815207201779241 1 -scale_tSTAT5_long scale_{tSTAT5,long} log10 0.001 1000 0.762143611844065 1 -scale_tSTAT5_shp1oe scale_{tSTAT5,shp1oe} log10 0.001 1000 0.681101374792296 1 -sd_CIS_abs sd_{CIS,abs} log10 0.001 1000 0.071666890399901 1 -sd_CIS_au sd_{CIS,au} log10 0.001 1000 0.134037028009804 1 -sd_JAK2EpoR_au sd_{JAK2EpoR,au} log10 0.001 1000 0.191838137085675 1 -sd_RNA_fold sd_{RNA,fold} log10 0.001 1000 0.103074376969697 1 -sd_SHP1_abs sd_{SHP1,abs} log10 0.001 1000 0.064904672549311 1 -sd_SHP1_au sd_{SHP1,au} log10 0.001 1000 0.077438644411215 1 -sd_SOCS3_abs sd_{SOCS3,abs} log10 0.001 1000 0.10271619027042 1 -sd_SOCS3_au sd_{SOCS3,au} log10 0.001 1000 0.076348614779106 1 -sd_STAT5_abs sd_{STAT5,abs} log10 0.001 1000 0.119518171917816 1 -sd_STAT5_au sd_{STAT5,au} log10 0.001 1000 0.123518909217589 1 -sd_pSTAT5_rel sd_{pSTAT5,rel} log10 0.001 1000 2.56704055700378 1 -sd_pSTAT5_socs3oe sd_{pSTAT5,socs3oe} log10 0.001 1000 0.573852497761907 1 +parameterId parameterName parameterScale lowerBound upperBound nominalValue estimate objectivePrior objectivePriorParameters +CISEqc CISEqc log10 0.001 10000 432.854027325732 1 parameterScaleUniform -3;3 +CISEqcOE CISEqcOE log10 0.001 1000 0.53027229006794 1 parameterScaleUniform -3;3 +CISInh CISInh log10 0.001 1000000000000 785221045.232906 1 parameterScaleUniform -3;12 +CISRNADelay CISRNADelay log10 0.001 1000 0.144777009620017 1 parameterScaleUniform -3;3 +CISRNAEqc CISRNAEqc log10 0.001 1000 1 0 parameterScaleUniform -3;3 +CISRNATurn CISRNATurn log10 0.001 1000 1000 1 parameterScaleUniform -3;3 +CISTurn CISTurn log10 0.001 1000 0.008398825029262 1 parameterScaleUniform -3;3 +EpoRActJAK2 EpoRActJAK2 log10 0.001 10000 0.267299659481333 1 parameterScaleUniform -3;4 +EpoRCISInh EpoRCISInh log10 0.001 1000000 1000000 1 parameterScaleUniform -3;6 +EpoRCISRemove EpoRCISRemove log10 0.001 1000 5.42989282766407 1 parameterScaleUniform -3;3 +JAK2ActEpo JAK2ActEpo log10 0.001 1000000000 633154.209632843 1 parameterScaleUniform -3;9 +JAK2EpoRDeaSHP1 JAK2EpoRDeaSHP1 log10 0.001 10000 142.723069412318 1 parameterScaleUniform -3;4 +SHP1ActEpoR SHP1ActEpoR log10 0.001 1000 0.001 1 parameterScaleUniform -3;3 +SHP1Dea SHP1Dea log10 0.001 1000 0.008162255244283 1 parameterScaleUniform -3;3 +SHP1ProOE SHP1ProOE log10 0.001 1000 2.82568032716189 1 parameterScaleUniform -3;3 +SOCS3Eqc SOCS3Eqc log10 0.001 1000 173.64095522801 1 parameterScaleUniform -3;3 +SOCS3EqcOE SOCS3EqcOE log10 0.001 1000 0.679185853534469 1 parameterScaleUniform -3;3 +SOCS3Inh SOCS3Inh log10 0.001 1000 10.4074255973465 1 parameterScaleUniform -3;3 +SOCS3RNADelay SOCS3RNADelay log10 0.001 1000 1.06454014521077 1 parameterScaleUniform -3;3 +SOCS3RNAEqc SOCS3RNAEqc log10 0.001 1000 1 0 parameterScaleUniform -3;3 +SOCS3RNATurn SOCS3RNATurn log10 0.001 1000 0.008309263619427 1 parameterScaleUniform -3;3 +SOCS3Turn SOCS3Turn log10 0.001 10000 10000 1 parameterScaleUniform -3;4 +STAT5ActEpoR STAT5ActEpoR log10 0.001 1000 38.9972748894298 1 parameterScaleUniform -3;3 +STAT5ActJAK2 STAT5ActJAK2 log10 0.001 1000 0.078108833252848 1 parameterScaleUniform -3;3 +STAT5Exp STAT5Exp log10 0.001 1000 0.074514698833232 1 parameterScaleUniform -3;3 +STAT5Imp STAT5Imp log10 0.001 1000 0.026887318057561 1 parameterScaleUniform -3;3 +init_EpoRJAK2 init_{EpoRJAK2} log10 0.001 1000 3.97622379188569 1 parameterScaleNormal 0.599471;0.193459 +init_SHP1 init_{SHP1} log10 0.001 1000 26.7251164163486 1 parameterScaleUniform -3;3 +init_STAT5 init_{STAT5} log10 0.001 1000 79.753639977851 1 parameterScaleUniform -3;3 +offset_CIS_actd offset_{CIS,actd} log10 0.001 1000 0.009388328725541 1 parameterScaleUniform -3;3 +offset_CIS_cisoe offset_{CIS,cisoe} log10 0.001 1000 0.030012199170223 1 parameterScaleUniform -3;3 +offset_CIS_long offset_{CIS,long} log10 0.001 1000 0.026460000624405 1 parameterScaleUniform -3;3 +offset_CIS_shp1oe offset_{CIS,shp1oe} log10 0.001 1000 0.058794513917949 1 parameterScaleUniform -3;3 +offset_CIS_socs3oe offset_{CIS,socs3oe} log10 0.001 1000 0.090496783983191 1 parameterScaleUniform -3;3 +offset_SOCS3_cisoe offset_{SOCS3,cisoe} log10 0.001 1000 0.278270301775932 1 parameterScaleUniform -3;3 +offset_SOCS3_long offset_{SOCS3,long} log10 0.001 1000 0.114475234936677 1 parameterScaleUniform -3;3 +offset_SOCS3_socs3oe offset_{SOCS3,socs3oe} log10 0.001 1000 0.025584406819207 1 parameterScaleUniform -3;3 +offset_pEpoR_actd offset_{pEpoR,actd} log10 0.001 1000 0.018840236081137 1 parameterScaleUniform -3;3 +offset_pEpoR_cisoe offset_{pEpoR,cisoe} log10 0.001 1000 0.030210854745913 1 parameterScaleUniform -3;3 +offset_pEpoR_cisoe_pepor offset_{pEpoR,cisoe,pepor} log10 0.001 1000 0.131027220027866 1 parameterScaleUniform -3;3 +offset_pEpoR_dr30 offset_{pEpoR,dr30} log10 0.001 1000 0.001 1 parameterScaleUniform -3;3 +offset_pEpoR_dr7 offset_{pEpoR,dr7} log10 0.001 1000 0.028405110847623 1 parameterScaleUniform -3;3 +offset_pEpoR_fine offset_{pEpoR,fine} log10 0.001 1000 0.064550876993068 1 parameterScaleUniform -3;3 +offset_pEpoR_long offset_{pEpoR,long} log10 0.001 1000 0.004391399791279 1 parameterScaleUniform -3;3 +offset_pEpoR_shp1oe offset_{pEpoR,shp1oe} log10 0.001 1000 0.031327226759826 1 parameterScaleUniform -3;3 +offset_pEpoR_socs3oe offset_{pEpoR,socs3oe} log10 0.001 1000 0.056711915845858 1 parameterScaleUniform -3;3 +offset_pJAK2_actd offset_{pJAK2,actd} log10 0.001 1000 0.017059890602388 1 parameterScaleUniform -3;3 +offset_pJAK2_cisoe offset_{pJAK2,cisoe} log10 0.001 1000 0.021928076840931 1 parameterScaleUniform -3;3 +offset_pJAK2_dr30 offset_{pJAK2,dr30} log10 0.001 1000 0.029944254724382 1 parameterScaleUniform -3;3 +offset_pJAK2_dr7 offset_{pJAK2,dr7} log10 0.001 1000 0.04733977489635 1 parameterScaleUniform -3;3 +offset_pJAK2_fine offset_{pJAK2,fine} log10 0.001 1000 0.021658276199496 1 parameterScaleUniform -3;3 +offset_pJAK2_long offset_{pJAK2,long} log10 0.001 1000 0.009473351822798 1 parameterScaleUniform -3;3 +offset_pJAK2_shp1oe offset_{pJAK2,shp1oe} log10 0.001 1000 0.026667365128327 1 parameterScaleUniform -3;3 +offset_pJAK2_socs3oe offset_{pJAK2,socs3oe} log10 0.001 1000 0.059752453075581 1 parameterScaleUniform -3;3 +offset_pSTAT5_actd offset_{pSTAT5,actd} log10 0.001 1000 0.001868785567417 1 parameterScaleUniform -3;3 +offset_pSTAT5_cisoe offset_{pSTAT5,cisoe} log10 0.001 1000 0.070791697579138 1 parameterScaleUniform -3;3 +offset_pSTAT5_conc offset_{pSTAT5,conc} log10 0.001 1000 0.236827475949589 1 parameterScaleUniform -3;3 +offset_pSTAT5_long offset_{pSTAT5,long} log10 0.001 1000 0.001093070638337 1 parameterScaleUniform -3;3 +offset_pSTAT5_shp1oe offset_{pSTAT5,shp1oe} log10 0.001 1000 0.054941495350482 1 parameterScaleUniform -3;3 +offset_pSTAT5_socs3oe offset_{pSTAT5,socs3oe} log10 0.001 1000 0.005613364786273 1 parameterScaleUniform -3;3 +scale1_CIS_dr90 scale1_{CIS,dr90} log10 0.001 1000 17.5631450183542 1 parameterScaleUniform -3;3 +scale2_CIS_dr90 scale2_{CIS,dr90} log10 0.001 1000 16.1205634424041 1 parameterScaleUniform -3;3 +scale_CISRNA_foldA scale_{CISRNA,foldA} log10 0.001 1000 33.2822368277369 1 parameterScaleUniform -3;3 +scale_CISRNA_foldB scale_{CISRNA,foldB} log10 0.001 1000 31.0176342778512 1 parameterScaleUniform -3;3 +scale_CISRNA_foldC scale_{CISRNA,foldC} log10 0.001 1000 19.6194113406379 1 parameterScaleUniform -3;3 +scale_CIS_actd scale_{CIS,actd} log10 0.001 1000 14.5490143154214 1 parameterScaleUniform -3;3 +scale_CIS_cisoe scale_{CIS,cisoe} log10 0.001 1000 1.37088201048354 1 parameterScaleUniform -3;3 +scale_CIS_long scale_{CIS,long} log10 0.001 1000 16.4036102124066 1 parameterScaleUniform -3;3 +scale_CIS_shp1oe scale_{CIS,shp1oe} log10 0.001 1000 51.7115711834136 1 parameterScaleUniform -3;3 +scale_CIS_socs3oe scale_{CIS,socs3oe} log10 0.001 1000 21.1493834462165 1 parameterScaleUniform -3;3 +scale_SHP1_shp1oe scale_{SHP1,shp1oe} log10 0.001 1000 0.225547534442942 1 parameterScaleUniform -3;3 +scale_SOCS3RNA_foldA scale_{SOCS3RNA,foldA} log10 0.001 1000 56.9631412510002 1 parameterScaleUniform -3;3 +scale_SOCS3RNA_foldB scale_{SOCS3RNA,foldB} log10 0.001 1000 49.074989211721 1 parameterScaleUniform -3;3 +scale_SOCS3RNA_foldC scale_{SOCS3RNA,foldC} log10 0.001 1000 80.7316820439984 1 parameterScaleUniform -3;3 +scale_SOCS3_cisoe scale_{SOCS3,cisoe} log10 0.001 1000 11.5682149955845 1 parameterScaleUniform -3;3 +scale_SOCS3_long scale_{SOCS3,long} log10 0.001 1000 15.485524391452 1 parameterScaleUniform -3;3 +scale_SOCS3_socs3oe scale_{SOCS3,socs3oe} log10 0.001 1000 1.20457246908681 1 parameterScaleUniform -3;3 +scale_pEpoR_actd scale_{pEpoR,actd} log10 0.001 1000 0.215657294488182 1 parameterScaleUniform -3;3 +scale_pEpoR_cisoe scale_{pEpoR,cisoe} log10 0.001 1000 0.273625536372832 1 parameterScaleUniform -3;3 +scale_pEpoR_cisoe_pepor scale_{pEpoR,cisoe_pepor} log10 0.001 1000 0.156616708581292 1 parameterScaleUniform -3;3 +scale_pEpoR_dr30 scale_{pEpoR,dr30} log10 0.001 1000 0.537385100441811 1 parameterScaleUniform -3;3 +scale_pEpoR_dr7 scale_{pEpoR,dr7} log10 0.001 1000 0.101429038197386 1 parameterScaleUniform -3;3 +scale_pEpoR_fine scale_{pEpoR,fine} log10 0.001 1000 0.080269467995686 1 parameterScaleUniform -3;3 +scale_pEpoR_long scale_{pEpoR,long} log10 0.001 1000 0.256529988627087 1 parameterScaleUniform -3;3 +scale_pEpoR_shp1oe scale_{pEpoR,shp1oe} log10 0.001 1000 0.241283495329875 1 parameterScaleUniform -3;3 +scale_pEpoR_socs3oe scale_{pEpoR,socs3oe} log10 0.001 1000 0.637275573973593 1 parameterScaleUniform -3;3 +scale_pJAK2_actd scale_{pJAK2,actd} log10 0.001 1000 0.809491692283694 1 parameterScaleUniform -3;3 +scale_pJAK2_cisoe scale_{pJAK2,cisoe} log10 0.001 1000 1.85429884799069 1 parameterScaleUniform -3;3 +scale_pJAK2_dr30 scale_{pJAK2,dr30} log10 0.001 1000 1.77561150477407 1 parameterScaleUniform -3;3 +scale_pJAK2_dr7 scale_{pJAK2,dr7} log10 0.001 1000 0.506322186585869 1 parameterScaleUniform -3;3 +scale_pJAK2_fine scale_{pJAK2,fine} log10 0.001 1000 0.400770707451671 1 parameterScaleUniform -3;3 +scale_pJAK2_long scale_{pJAK2,long} log10 0.001 1000 0.882775356861714 1 parameterScaleUniform -3;3 +scale_pJAK2_shp1oe scale_{pJAK2,shp1oe} log10 0.001 1000 2.31011130113927 1 parameterScaleUniform -3;3 +scale_pJAK2_socs3oe scale_{pJAK2,socs3oe} log10 0.001 1000 1.266550022901 1 parameterScaleUniform -3;3 +scale_pSTAT5_actd scale_{pSTAT5,actd} log10 0.001 1000 1.09743435047828 1 parameterScaleUniform -3;3 +scale_pSTAT5_cisoe scale_{pSTAT5,cisoe} log10 0.001 1000 2.41904111907135 1 parameterScaleUniform -3;3 +scale_pSTAT5_dr10 scale_{pSTAT5,dr10} log10 0.001 1000 1.00950903665707 1 parameterScaleUniform -3;3 +scale_pSTAT5_long scale_{pSTAT5,long} log10 0.001 1000 1.47372211945355 1 parameterScaleUniform -3;3 +scale_pSTAT5_shp1oe scale_{pSTAT5,shp1oe} log10 0.001 1000 1.15158552971751 1 parameterScaleUniform -3;3 +scale_pSTAT5_socs3oe scale_{pSTAT5,socs3oe} log10 0.001 1000 1.76032560825919 1 parameterScaleUniform -3;3 +scale_tSTAT5_actd scale_{tSTAT5,actd} log10 0.001 1000 0.815207201779241 1 parameterScaleUniform -3;3 +scale_tSTAT5_long scale_{tSTAT5,long} log10 0.001 1000 0.762143611844065 1 parameterScaleUniform -3;3 +scale_tSTAT5_shp1oe scale_{tSTAT5,shp1oe} log10 0.001 1000 0.681101374792296 1 parameterScaleUniform -3;3 +sd_CIS_abs sd_{CIS,abs} log10 0.001 1000 0.071666890399901 1 parameterScaleUniform -3;3 +sd_CIS_au sd_{CIS,au} log10 0.001 1000 0.134037028009804 1 parameterScaleUniform -3;3 +sd_JAK2EpoR_au sd_{JAK2EpoR,au} log10 0.001 1000 0.191838137085675 1 parameterScaleUniform -3;3 +sd_RNA_fold sd_{RNA,fold} log10 0.001 1000 0.103074376969697 1 parameterScaleUniform -3;3 +sd_SHP1_abs sd_{SHP1,abs} log10 0.001 1000 0.064904672549311 1 parameterScaleUniform -3;3 +sd_SHP1_au sd_{SHP1,au} log10 0.001 1000 0.077438644411215 1 parameterScaleUniform -3;3 +sd_SOCS3_abs sd_{SOCS3,abs} log10 0.001 1000 0.10271619027042 1 parameterScaleUniform -3;3 +sd_SOCS3_au sd_{SOCS3,au} log10 0.001 1000 0.076348614779106 1 parameterScaleUniform -3;3 +sd_STAT5_abs sd_{STAT5,abs} log10 0.001 1000 0.119518171917816 1 parameterScaleUniform -3;3 +sd_STAT5_au sd_{STAT5,au} log10 0.001 1000 0.123518909217589 1 parameterScaleUniform -3;3 +sd_pSTAT5_rel sd_{pSTAT5,rel} log10 0.001 1000 2.56704055700378 1 parameterScaleUniform -3;3 +sd_pSTAT5_socs3oe sd_{pSTAT5,socs3oe} log10 0.001 1000 0.573852497761907 1 parameterScaleUniform -3;3 From f65847ae70af06d7e601e31e7be460b6308b95f9 Mon Sep 17 00:00:00 2001 From: FFroehlich Date: Wed, 13 Oct 2021 11:30:12 -0400 Subject: [PATCH 3/4] remove uninformative priors --- .../parameters_Bachmann_MSB2011.tsv | 228 +++++++++--------- 1 file changed, 114 insertions(+), 114 deletions(-) diff --git a/Benchmark-Models/Bachmann_MSB2011/parameters_Bachmann_MSB2011.tsv b/Benchmark-Models/Bachmann_MSB2011/parameters_Bachmann_MSB2011.tsv index e074ded..584cc18 100644 --- a/Benchmark-Models/Bachmann_MSB2011/parameters_Bachmann_MSB2011.tsv +++ b/Benchmark-Models/Bachmann_MSB2011/parameters_Bachmann_MSB2011.tsv @@ -1,116 +1,116 @@ parameterId parameterName parameterScale lowerBound upperBound nominalValue estimate objectivePrior objectivePriorParameters -CISEqc CISEqc log10 0.001 10000 432.854027325732 1 parameterScaleUniform -3;3 -CISEqcOE CISEqcOE log10 0.001 1000 0.53027229006794 1 parameterScaleUniform -3;3 -CISInh CISInh log10 0.001 1000000000000 785221045.232906 1 parameterScaleUniform -3;12 -CISRNADelay CISRNADelay log10 0.001 1000 0.144777009620017 1 parameterScaleUniform -3;3 -CISRNAEqc CISRNAEqc log10 0.001 1000 1 0 parameterScaleUniform -3;3 -CISRNATurn CISRNATurn log10 0.001 1000 1000 1 parameterScaleUniform -3;3 -CISTurn CISTurn log10 0.001 1000 0.008398825029262 1 parameterScaleUniform -3;3 -EpoRActJAK2 EpoRActJAK2 log10 0.001 10000 0.267299659481333 1 parameterScaleUniform -3;4 -EpoRCISInh EpoRCISInh log10 0.001 1000000 1000000 1 parameterScaleUniform -3;6 -EpoRCISRemove EpoRCISRemove log10 0.001 1000 5.42989282766407 1 parameterScaleUniform -3;3 -JAK2ActEpo JAK2ActEpo log10 0.001 1000000000 633154.209632843 1 parameterScaleUniform -3;9 -JAK2EpoRDeaSHP1 JAK2EpoRDeaSHP1 log10 0.001 10000 142.723069412318 1 parameterScaleUniform -3;4 -SHP1ActEpoR SHP1ActEpoR log10 0.001 1000 0.001 1 parameterScaleUniform -3;3 -SHP1Dea SHP1Dea log10 0.001 1000 0.008162255244283 1 parameterScaleUniform -3;3 -SHP1ProOE SHP1ProOE log10 0.001 1000 2.82568032716189 1 parameterScaleUniform -3;3 -SOCS3Eqc SOCS3Eqc log10 0.001 1000 173.64095522801 1 parameterScaleUniform -3;3 -SOCS3EqcOE SOCS3EqcOE log10 0.001 1000 0.679185853534469 1 parameterScaleUniform -3;3 -SOCS3Inh SOCS3Inh log10 0.001 1000 10.4074255973465 1 parameterScaleUniform -3;3 -SOCS3RNADelay SOCS3RNADelay log10 0.001 1000 1.06454014521077 1 parameterScaleUniform -3;3 -SOCS3RNAEqc SOCS3RNAEqc log10 0.001 1000 1 0 parameterScaleUniform -3;3 -SOCS3RNATurn SOCS3RNATurn log10 0.001 1000 0.008309263619427 1 parameterScaleUniform -3;3 -SOCS3Turn SOCS3Turn log10 0.001 10000 10000 1 parameterScaleUniform -3;4 -STAT5ActEpoR STAT5ActEpoR log10 0.001 1000 38.9972748894298 1 parameterScaleUniform -3;3 -STAT5ActJAK2 STAT5ActJAK2 log10 0.001 1000 0.078108833252848 1 parameterScaleUniform -3;3 -STAT5Exp STAT5Exp log10 0.001 1000 0.074514698833232 1 parameterScaleUniform -3;3 -STAT5Imp STAT5Imp log10 0.001 1000 0.026887318057561 1 parameterScaleUniform -3;3 +CISEqc CISEqc log10 0.001 10000 432.854027325732 1 +CISEqcOE CISEqcOE log10 0.001 1000 0.53027229006794 1 +CISInh CISInh log10 0.001 1000000000000 785221045.232906 1 +CISRNADelay CISRNADelay log10 0.001 1000 0.144777009620017 1 +CISRNAEqc CISRNAEqc log10 0.001 1000 1 0 +CISRNATurn CISRNATurn log10 0.001 1000 1000 1 +CISTurn CISTurn log10 0.001 1000 0.008398825029262 1 +EpoRActJAK2 EpoRActJAK2 log10 0.001 10000 0.267299659481333 1 +EpoRCISInh EpoRCISInh log10 0.001 1000000 1000000 1 +EpoRCISRemove EpoRCISRemove log10 0.001 1000 5.42989282766407 1 +JAK2ActEpo JAK2ActEpo log10 0.001 1000000000 633154.209632843 1 +JAK2EpoRDeaSHP1 JAK2EpoRDeaSHP1 log10 0.001 10000 142.723069412318 1 +SHP1ActEpoR SHP1ActEpoR log10 0.001 1000 0.001 1 +SHP1Dea SHP1Dea log10 0.001 1000 0.008162255244283 1 +SHP1ProOE SHP1ProOE log10 0.001 1000 2.82568032716189 1 +SOCS3Eqc SOCS3Eqc log10 0.001 1000 173.64095522801 1 +SOCS3EqcOE SOCS3EqcOE log10 0.001 1000 0.679185853534469 1 +SOCS3Inh SOCS3Inh log10 0.001 1000 10.4074255973465 1 +SOCS3RNADelay SOCS3RNADelay log10 0.001 1000 1.06454014521077 1 +SOCS3RNAEqc SOCS3RNAEqc log10 0.001 1000 1 0 +SOCS3RNATurn SOCS3RNATurn log10 0.001 1000 0.008309263619427 1 +SOCS3Turn SOCS3Turn log10 0.001 10000 10000 1 +STAT5ActEpoR STAT5ActEpoR log10 0.001 1000 38.9972748894298 1 +STAT5ActJAK2 STAT5ActJAK2 log10 0.001 1000 0.078108833252848 1 +STAT5Exp STAT5Exp log10 0.001 1000 0.074514698833232 1 +STAT5Imp STAT5Imp log10 0.001 1000 0.026887318057561 1 init_EpoRJAK2 init_{EpoRJAK2} log10 0.001 1000 3.97622379188569 1 parameterScaleNormal 0.599471;0.193459 -init_SHP1 init_{SHP1} log10 0.001 1000 26.7251164163486 1 parameterScaleUniform -3;3 -init_STAT5 init_{STAT5} log10 0.001 1000 79.753639977851 1 parameterScaleUniform -3;3 -offset_CIS_actd offset_{CIS,actd} log10 0.001 1000 0.009388328725541 1 parameterScaleUniform -3;3 -offset_CIS_cisoe offset_{CIS,cisoe} log10 0.001 1000 0.030012199170223 1 parameterScaleUniform -3;3 -offset_CIS_long offset_{CIS,long} log10 0.001 1000 0.026460000624405 1 parameterScaleUniform -3;3 -offset_CIS_shp1oe offset_{CIS,shp1oe} log10 0.001 1000 0.058794513917949 1 parameterScaleUniform -3;3 -offset_CIS_socs3oe offset_{CIS,socs3oe} log10 0.001 1000 0.090496783983191 1 parameterScaleUniform -3;3 -offset_SOCS3_cisoe offset_{SOCS3,cisoe} log10 0.001 1000 0.278270301775932 1 parameterScaleUniform -3;3 -offset_SOCS3_long offset_{SOCS3,long} log10 0.001 1000 0.114475234936677 1 parameterScaleUniform -3;3 -offset_SOCS3_socs3oe offset_{SOCS3,socs3oe} log10 0.001 1000 0.025584406819207 1 parameterScaleUniform -3;3 -offset_pEpoR_actd offset_{pEpoR,actd} log10 0.001 1000 0.018840236081137 1 parameterScaleUniform -3;3 -offset_pEpoR_cisoe offset_{pEpoR,cisoe} log10 0.001 1000 0.030210854745913 1 parameterScaleUniform -3;3 -offset_pEpoR_cisoe_pepor offset_{pEpoR,cisoe,pepor} log10 0.001 1000 0.131027220027866 1 parameterScaleUniform -3;3 -offset_pEpoR_dr30 offset_{pEpoR,dr30} log10 0.001 1000 0.001 1 parameterScaleUniform -3;3 -offset_pEpoR_dr7 offset_{pEpoR,dr7} log10 0.001 1000 0.028405110847623 1 parameterScaleUniform -3;3 -offset_pEpoR_fine offset_{pEpoR,fine} log10 0.001 1000 0.064550876993068 1 parameterScaleUniform -3;3 -offset_pEpoR_long offset_{pEpoR,long} log10 0.001 1000 0.004391399791279 1 parameterScaleUniform -3;3 -offset_pEpoR_shp1oe offset_{pEpoR,shp1oe} log10 0.001 1000 0.031327226759826 1 parameterScaleUniform -3;3 -offset_pEpoR_socs3oe offset_{pEpoR,socs3oe} log10 0.001 1000 0.056711915845858 1 parameterScaleUniform -3;3 -offset_pJAK2_actd offset_{pJAK2,actd} log10 0.001 1000 0.017059890602388 1 parameterScaleUniform -3;3 -offset_pJAK2_cisoe offset_{pJAK2,cisoe} log10 0.001 1000 0.021928076840931 1 parameterScaleUniform -3;3 -offset_pJAK2_dr30 offset_{pJAK2,dr30} log10 0.001 1000 0.029944254724382 1 parameterScaleUniform -3;3 -offset_pJAK2_dr7 offset_{pJAK2,dr7} log10 0.001 1000 0.04733977489635 1 parameterScaleUniform -3;3 -offset_pJAK2_fine offset_{pJAK2,fine} log10 0.001 1000 0.021658276199496 1 parameterScaleUniform -3;3 -offset_pJAK2_long offset_{pJAK2,long} log10 0.001 1000 0.009473351822798 1 parameterScaleUniform -3;3 -offset_pJAK2_shp1oe offset_{pJAK2,shp1oe} log10 0.001 1000 0.026667365128327 1 parameterScaleUniform -3;3 -offset_pJAK2_socs3oe offset_{pJAK2,socs3oe} log10 0.001 1000 0.059752453075581 1 parameterScaleUniform -3;3 -offset_pSTAT5_actd offset_{pSTAT5,actd} log10 0.001 1000 0.001868785567417 1 parameterScaleUniform -3;3 -offset_pSTAT5_cisoe offset_{pSTAT5,cisoe} log10 0.001 1000 0.070791697579138 1 parameterScaleUniform -3;3 -offset_pSTAT5_conc offset_{pSTAT5,conc} log10 0.001 1000 0.236827475949589 1 parameterScaleUniform -3;3 -offset_pSTAT5_long offset_{pSTAT5,long} log10 0.001 1000 0.001093070638337 1 parameterScaleUniform -3;3 -offset_pSTAT5_shp1oe offset_{pSTAT5,shp1oe} log10 0.001 1000 0.054941495350482 1 parameterScaleUniform -3;3 -offset_pSTAT5_socs3oe offset_{pSTAT5,socs3oe} log10 0.001 1000 0.005613364786273 1 parameterScaleUniform -3;3 -scale1_CIS_dr90 scale1_{CIS,dr90} log10 0.001 1000 17.5631450183542 1 parameterScaleUniform -3;3 -scale2_CIS_dr90 scale2_{CIS,dr90} log10 0.001 1000 16.1205634424041 1 parameterScaleUniform -3;3 -scale_CISRNA_foldA scale_{CISRNA,foldA} log10 0.001 1000 33.2822368277369 1 parameterScaleUniform -3;3 -scale_CISRNA_foldB scale_{CISRNA,foldB} log10 0.001 1000 31.0176342778512 1 parameterScaleUniform -3;3 -scale_CISRNA_foldC scale_{CISRNA,foldC} log10 0.001 1000 19.6194113406379 1 parameterScaleUniform -3;3 -scale_CIS_actd scale_{CIS,actd} log10 0.001 1000 14.5490143154214 1 parameterScaleUniform -3;3 -scale_CIS_cisoe scale_{CIS,cisoe} log10 0.001 1000 1.37088201048354 1 parameterScaleUniform -3;3 -scale_CIS_long scale_{CIS,long} log10 0.001 1000 16.4036102124066 1 parameterScaleUniform -3;3 -scale_CIS_shp1oe scale_{CIS,shp1oe} log10 0.001 1000 51.7115711834136 1 parameterScaleUniform -3;3 -scale_CIS_socs3oe scale_{CIS,socs3oe} log10 0.001 1000 21.1493834462165 1 parameterScaleUniform -3;3 -scale_SHP1_shp1oe scale_{SHP1,shp1oe} log10 0.001 1000 0.225547534442942 1 parameterScaleUniform -3;3 -scale_SOCS3RNA_foldA scale_{SOCS3RNA,foldA} log10 0.001 1000 56.9631412510002 1 parameterScaleUniform -3;3 -scale_SOCS3RNA_foldB scale_{SOCS3RNA,foldB} log10 0.001 1000 49.074989211721 1 parameterScaleUniform -3;3 -scale_SOCS3RNA_foldC scale_{SOCS3RNA,foldC} log10 0.001 1000 80.7316820439984 1 parameterScaleUniform -3;3 -scale_SOCS3_cisoe scale_{SOCS3,cisoe} log10 0.001 1000 11.5682149955845 1 parameterScaleUniform -3;3 -scale_SOCS3_long scale_{SOCS3,long} log10 0.001 1000 15.485524391452 1 parameterScaleUniform -3;3 -scale_SOCS3_socs3oe scale_{SOCS3,socs3oe} log10 0.001 1000 1.20457246908681 1 parameterScaleUniform -3;3 -scale_pEpoR_actd scale_{pEpoR,actd} log10 0.001 1000 0.215657294488182 1 parameterScaleUniform -3;3 -scale_pEpoR_cisoe scale_{pEpoR,cisoe} log10 0.001 1000 0.273625536372832 1 parameterScaleUniform -3;3 -scale_pEpoR_cisoe_pepor scale_{pEpoR,cisoe_pepor} log10 0.001 1000 0.156616708581292 1 parameterScaleUniform -3;3 -scale_pEpoR_dr30 scale_{pEpoR,dr30} log10 0.001 1000 0.537385100441811 1 parameterScaleUniform -3;3 -scale_pEpoR_dr7 scale_{pEpoR,dr7} log10 0.001 1000 0.101429038197386 1 parameterScaleUniform -3;3 -scale_pEpoR_fine scale_{pEpoR,fine} log10 0.001 1000 0.080269467995686 1 parameterScaleUniform -3;3 -scale_pEpoR_long scale_{pEpoR,long} log10 0.001 1000 0.256529988627087 1 parameterScaleUniform -3;3 -scale_pEpoR_shp1oe scale_{pEpoR,shp1oe} log10 0.001 1000 0.241283495329875 1 parameterScaleUniform -3;3 -scale_pEpoR_socs3oe scale_{pEpoR,socs3oe} log10 0.001 1000 0.637275573973593 1 parameterScaleUniform -3;3 -scale_pJAK2_actd scale_{pJAK2,actd} log10 0.001 1000 0.809491692283694 1 parameterScaleUniform -3;3 -scale_pJAK2_cisoe scale_{pJAK2,cisoe} log10 0.001 1000 1.85429884799069 1 parameterScaleUniform -3;3 -scale_pJAK2_dr30 scale_{pJAK2,dr30} log10 0.001 1000 1.77561150477407 1 parameterScaleUniform -3;3 -scale_pJAK2_dr7 scale_{pJAK2,dr7} log10 0.001 1000 0.506322186585869 1 parameterScaleUniform -3;3 -scale_pJAK2_fine scale_{pJAK2,fine} log10 0.001 1000 0.400770707451671 1 parameterScaleUniform -3;3 -scale_pJAK2_long scale_{pJAK2,long} log10 0.001 1000 0.882775356861714 1 parameterScaleUniform -3;3 -scale_pJAK2_shp1oe scale_{pJAK2,shp1oe} log10 0.001 1000 2.31011130113927 1 parameterScaleUniform -3;3 -scale_pJAK2_socs3oe scale_{pJAK2,socs3oe} log10 0.001 1000 1.266550022901 1 parameterScaleUniform -3;3 -scale_pSTAT5_actd scale_{pSTAT5,actd} log10 0.001 1000 1.09743435047828 1 parameterScaleUniform -3;3 -scale_pSTAT5_cisoe scale_{pSTAT5,cisoe} log10 0.001 1000 2.41904111907135 1 parameterScaleUniform -3;3 -scale_pSTAT5_dr10 scale_{pSTAT5,dr10} log10 0.001 1000 1.00950903665707 1 parameterScaleUniform -3;3 -scale_pSTAT5_long scale_{pSTAT5,long} log10 0.001 1000 1.47372211945355 1 parameterScaleUniform -3;3 -scale_pSTAT5_shp1oe scale_{pSTAT5,shp1oe} log10 0.001 1000 1.15158552971751 1 parameterScaleUniform -3;3 -scale_pSTAT5_socs3oe scale_{pSTAT5,socs3oe} log10 0.001 1000 1.76032560825919 1 parameterScaleUniform -3;3 -scale_tSTAT5_actd scale_{tSTAT5,actd} log10 0.001 1000 0.815207201779241 1 parameterScaleUniform -3;3 -scale_tSTAT5_long scale_{tSTAT5,long} log10 0.001 1000 0.762143611844065 1 parameterScaleUniform -3;3 -scale_tSTAT5_shp1oe scale_{tSTAT5,shp1oe} log10 0.001 1000 0.681101374792296 1 parameterScaleUniform -3;3 -sd_CIS_abs sd_{CIS,abs} log10 0.001 1000 0.071666890399901 1 parameterScaleUniform -3;3 -sd_CIS_au sd_{CIS,au} log10 0.001 1000 0.134037028009804 1 parameterScaleUniform -3;3 -sd_JAK2EpoR_au sd_{JAK2EpoR,au} log10 0.001 1000 0.191838137085675 1 parameterScaleUniform -3;3 -sd_RNA_fold sd_{RNA,fold} log10 0.001 1000 0.103074376969697 1 parameterScaleUniform -3;3 -sd_SHP1_abs sd_{SHP1,abs} log10 0.001 1000 0.064904672549311 1 parameterScaleUniform -3;3 -sd_SHP1_au sd_{SHP1,au} log10 0.001 1000 0.077438644411215 1 parameterScaleUniform -3;3 -sd_SOCS3_abs sd_{SOCS3,abs} log10 0.001 1000 0.10271619027042 1 parameterScaleUniform -3;3 -sd_SOCS3_au sd_{SOCS3,au} log10 0.001 1000 0.076348614779106 1 parameterScaleUniform -3;3 -sd_STAT5_abs sd_{STAT5,abs} log10 0.001 1000 0.119518171917816 1 parameterScaleUniform -3;3 -sd_STAT5_au sd_{STAT5,au} log10 0.001 1000 0.123518909217589 1 parameterScaleUniform -3;3 -sd_pSTAT5_rel sd_{pSTAT5,rel} log10 0.001 1000 2.56704055700378 1 parameterScaleUniform -3;3 -sd_pSTAT5_socs3oe sd_{pSTAT5,socs3oe} log10 0.001 1000 0.573852497761907 1 parameterScaleUniform -3;3 +init_SHP1 init_{SHP1} log10 0.001 1000 26.7251164163486 1 +init_STAT5 init_{STAT5} log10 0.001 1000 79.753639977851 1 +offset_CIS_actd offset_{CIS,actd} log10 0.001 1000 0.009388328725541 1 +offset_CIS_cisoe offset_{CIS,cisoe} log10 0.001 1000 0.030012199170223 1 +offset_CIS_long offset_{CIS,long} log10 0.001 1000 0.026460000624405 1 +offset_CIS_shp1oe offset_{CIS,shp1oe} log10 0.001 1000 0.058794513917949 1 +offset_CIS_socs3oe offset_{CIS,socs3oe} log10 0.001 1000 0.090496783983191 1 +offset_SOCS3_cisoe offset_{SOCS3,cisoe} log10 0.001 1000 0.278270301775932 1 +offset_SOCS3_long offset_{SOCS3,long} log10 0.001 1000 0.114475234936677 1 +offset_SOCS3_socs3oe offset_{SOCS3,socs3oe} log10 0.001 1000 0.025584406819207 1 +offset_pEpoR_actd offset_{pEpoR,actd} log10 0.001 1000 0.018840236081137 1 +offset_pEpoR_cisoe offset_{pEpoR,cisoe} log10 0.001 1000 0.030210854745913 1 +offset_pEpoR_cisoe_pepor offset_{pEpoR,cisoe,pepor} log10 0.001 1000 0.131027220027866 1 +offset_pEpoR_dr30 offset_{pEpoR,dr30} log10 0.001 1000 0.001 1 +offset_pEpoR_dr7 offset_{pEpoR,dr7} log10 0.001 1000 0.028405110847623 1 +offset_pEpoR_fine offset_{pEpoR,fine} log10 0.001 1000 0.064550876993068 1 +offset_pEpoR_long offset_{pEpoR,long} log10 0.001 1000 0.004391399791279 1 +offset_pEpoR_shp1oe offset_{pEpoR,shp1oe} log10 0.001 1000 0.031327226759826 1 +offset_pEpoR_socs3oe offset_{pEpoR,socs3oe} log10 0.001 1000 0.056711915845858 1 +offset_pJAK2_actd offset_{pJAK2,actd} log10 0.001 1000 0.017059890602388 1 +offset_pJAK2_cisoe offset_{pJAK2,cisoe} log10 0.001 1000 0.021928076840931 1 +offset_pJAK2_dr30 offset_{pJAK2,dr30} log10 0.001 1000 0.029944254724382 1 +offset_pJAK2_dr7 offset_{pJAK2,dr7} log10 0.001 1000 0.04733977489635 1 +offset_pJAK2_fine offset_{pJAK2,fine} log10 0.001 1000 0.021658276199496 1 +offset_pJAK2_long offset_{pJAK2,long} log10 0.001 1000 0.009473351822798 1 +offset_pJAK2_shp1oe offset_{pJAK2,shp1oe} log10 0.001 1000 0.026667365128327 1 +offset_pJAK2_socs3oe offset_{pJAK2,socs3oe} log10 0.001 1000 0.059752453075581 1 +offset_pSTAT5_actd offset_{pSTAT5,actd} log10 0.001 1000 0.001868785567417 1 +offset_pSTAT5_cisoe offset_{pSTAT5,cisoe} log10 0.001 1000 0.070791697579138 1 +offset_pSTAT5_conc offset_{pSTAT5,conc} log10 0.001 1000 0.236827475949589 1 +offset_pSTAT5_long offset_{pSTAT5,long} log10 0.001 1000 0.001093070638337 1 +offset_pSTAT5_shp1oe offset_{pSTAT5,shp1oe} log10 0.001 1000 0.054941495350482 1 +offset_pSTAT5_socs3oe offset_{pSTAT5,socs3oe} log10 0.001 1000 0.005613364786273 1 +scale1_CIS_dr90 scale1_{CIS,dr90} log10 0.001 1000 17.5631450183542 1 +scale2_CIS_dr90 scale2_{CIS,dr90} log10 0.001 1000 16.1205634424041 1 +scale_CISRNA_foldA scale_{CISRNA,foldA} log10 0.001 1000 33.2822368277369 1 +scale_CISRNA_foldB scale_{CISRNA,foldB} log10 0.001 1000 31.0176342778512 1 +scale_CISRNA_foldC scale_{CISRNA,foldC} log10 0.001 1000 19.6194113406379 1 +scale_CIS_actd scale_{CIS,actd} log10 0.001 1000 14.5490143154214 1 +scale_CIS_cisoe scale_{CIS,cisoe} log10 0.001 1000 1.37088201048354 1 +scale_CIS_long scale_{CIS,long} log10 0.001 1000 16.4036102124066 1 +scale_CIS_shp1oe scale_{CIS,shp1oe} log10 0.001 1000 51.7115711834136 1 +scale_CIS_socs3oe scale_{CIS,socs3oe} log10 0.001 1000 21.1493834462165 1 +scale_SHP1_shp1oe scale_{SHP1,shp1oe} log10 0.001 1000 0.225547534442942 1 +scale_SOCS3RNA_foldA scale_{SOCS3RNA,foldA} log10 0.001 1000 56.9631412510002 1 +scale_SOCS3RNA_foldB scale_{SOCS3RNA,foldB} log10 0.001 1000 49.074989211721 1 +scale_SOCS3RNA_foldC scale_{SOCS3RNA,foldC} log10 0.001 1000 80.7316820439984 1 +scale_SOCS3_cisoe scale_{SOCS3,cisoe} log10 0.001 1000 11.5682149955845 1 +scale_SOCS3_long scale_{SOCS3,long} log10 0.001 1000 15.485524391452 1 +scale_SOCS3_socs3oe scale_{SOCS3,socs3oe} log10 0.001 1000 1.20457246908681 1 +scale_pEpoR_actd scale_{pEpoR,actd} log10 0.001 1000 0.215657294488182 1 +scale_pEpoR_cisoe scale_{pEpoR,cisoe} log10 0.001 1000 0.273625536372832 1 +scale_pEpoR_cisoe_pepor scale_{pEpoR,cisoe_pepor} log10 0.001 1000 0.156616708581292 1 +scale_pEpoR_dr30 scale_{pEpoR,dr30} log10 0.001 1000 0.537385100441811 1 +scale_pEpoR_dr7 scale_{pEpoR,dr7} log10 0.001 1000 0.101429038197386 1 +scale_pEpoR_fine scale_{pEpoR,fine} log10 0.001 1000 0.080269467995686 1 +scale_pEpoR_long scale_{pEpoR,long} log10 0.001 1000 0.256529988627087 1 +scale_pEpoR_shp1oe scale_{pEpoR,shp1oe} log10 0.001 1000 0.241283495329875 1 +scale_pEpoR_socs3oe scale_{pEpoR,socs3oe} log10 0.001 1000 0.637275573973593 1 +scale_pJAK2_actd scale_{pJAK2,actd} log10 0.001 1000 0.809491692283694 1 +scale_pJAK2_cisoe scale_{pJAK2,cisoe} log10 0.001 1000 1.85429884799069 1 +scale_pJAK2_dr30 scale_{pJAK2,dr30} log10 0.001 1000 1.77561150477407 1 +scale_pJAK2_dr7 scale_{pJAK2,dr7} log10 0.001 1000 0.506322186585869 1 +scale_pJAK2_fine scale_{pJAK2,fine} log10 0.001 1000 0.400770707451671 1 +scale_pJAK2_long scale_{pJAK2,long} log10 0.001 1000 0.882775356861714 1 +scale_pJAK2_shp1oe scale_{pJAK2,shp1oe} log10 0.001 1000 2.31011130113927 1 +scale_pJAK2_socs3oe scale_{pJAK2,socs3oe} log10 0.001 1000 1.266550022901 1 +scale_pSTAT5_actd scale_{pSTAT5,actd} log10 0.001 1000 1.09743435047828 1 +scale_pSTAT5_cisoe scale_{pSTAT5,cisoe} log10 0.001 1000 2.41904111907135 1 +scale_pSTAT5_dr10 scale_{pSTAT5,dr10} log10 0.001 1000 1.00950903665707 1 +scale_pSTAT5_long scale_{pSTAT5,long} log10 0.001 1000 1.47372211945355 1 +scale_pSTAT5_shp1oe scale_{pSTAT5,shp1oe} log10 0.001 1000 1.15158552971751 1 +scale_pSTAT5_socs3oe scale_{pSTAT5,socs3oe} log10 0.001 1000 1.76032560825919 1 +scale_tSTAT5_actd scale_{tSTAT5,actd} log10 0.001 1000 0.815207201779241 1 +scale_tSTAT5_long scale_{tSTAT5,long} log10 0.001 1000 0.762143611844065 1 +scale_tSTAT5_shp1oe scale_{tSTAT5,shp1oe} log10 0.001 1000 0.681101374792296 1 +sd_CIS_abs sd_{CIS,abs} log10 0.001 1000 0.071666890399901 1 +sd_CIS_au sd_{CIS,au} log10 0.001 1000 0.134037028009804 1 +sd_JAK2EpoR_au sd_{JAK2EpoR,au} log10 0.001 1000 0.191838137085675 1 +sd_RNA_fold sd_{RNA,fold} log10 0.001 1000 0.103074376969697 1 +sd_SHP1_abs sd_{SHP1,abs} log10 0.001 1000 0.064904672549311 1 +sd_SHP1_au sd_{SHP1,au} log10 0.001 1000 0.077438644411215 1 +sd_SOCS3_abs sd_{SOCS3,abs} log10 0.001 1000 0.10271619027042 1 +sd_SOCS3_au sd_{SOCS3,au} log10 0.001 1000 0.076348614779106 1 +sd_STAT5_abs sd_{STAT5,abs} log10 0.001 1000 0.119518171917816 1 +sd_STAT5_au sd_{STAT5,au} log10 0.001 1000 0.123518909217589 1 +sd_pSTAT5_rel sd_{pSTAT5,rel} log10 0.001 1000 2.56704055700378 1 +sd_pSTAT5_socs3oe sd_{pSTAT5,socs3oe} log10 0.001 1000 0.573852497761907 1 From a4ef5eba6b5f3bd48ad3c109cf03851a173549c0 Mon Sep 17 00:00:00 2001 From: FFroehlich Date: Wed, 13 Oct 2021 12:35:22 -0400 Subject: [PATCH 4/4] fixup --- .../Bachmann_MSB2011/parameters_Bachmann_MSB2011.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Benchmark-Models/Bachmann_MSB2011/parameters_Bachmann_MSB2011.tsv b/Benchmark-Models/Bachmann_MSB2011/parameters_Bachmann_MSB2011.tsv index 584cc18..1d78d29 100644 --- a/Benchmark-Models/Bachmann_MSB2011/parameters_Bachmann_MSB2011.tsv +++ b/Benchmark-Models/Bachmann_MSB2011/parameters_Bachmann_MSB2011.tsv @@ -42,7 +42,7 @@ offset_pEpoR_cisoe_pepor offset_{pEpoR,cisoe,pepor} log10 0.001 1000 0.131027220 offset_pEpoR_dr30 offset_{pEpoR,dr30} log10 0.001 1000 0.001 1 offset_pEpoR_dr7 offset_{pEpoR,dr7} log10 0.001 1000 0.028405110847623 1 offset_pEpoR_fine offset_{pEpoR,fine} log10 0.001 1000 0.064550876993068 1 -offset_pEpoR_long offset_{pEpoR,long} log10 0.001 1000 0.004391399791279 1 +offset_pEpoR_long offset_{pEpoR,long} log10 0.001 1000 0.004391399791279 1 offset_pEpoR_shp1oe offset_{pEpoR,shp1oe} log10 0.001 1000 0.031327226759826 1 offset_pEpoR_socs3oe offset_{pEpoR,socs3oe} log10 0.001 1000 0.056711915845858 1 offset_pJAK2_actd offset_{pJAK2,actd} log10 0.001 1000 0.017059890602388 1