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LeonardSchmiester / Benchmark-Models

This repository is not maintained anymore. Please use: https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab
BSD 3-Clause "New" or "Revised" License
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PEtab status of current models #53

Closed dweindl closed 5 years ago

dweindl commented 5 years ago

To re-test, after having installed https://github.com/ICB-DCM/PEtab/, run for MODEL in $(ls -1d */); do (cd $MODEL && petablint.py -v -n $(basename $MODEL)); printf '=%.0s' {1..100};echo; done on BASH in hackathon_contributions_new_data_format.

Note that some issues might not be in the model, but in the validator. Please report those cases.

Update

[20:03:19]☺︎dweindl@dweindl:~/src/Benchmark-Models-Caro/hackathon_contributions_new_data_format>./checkBenchmarkModels.py 
Looking for...
        SBML model: model_Bachmann_MSB2011.xml
        Condition table: experimentalCondition_Bachmann_MSB2011.tsv
        Measurement table: measurementData_Bachmann_MSB2011.tsv
        Parameter table: parameters_Bachmann_MSB2011.tsv
Checking SBML model...
Checking measurement table...
Whitespace around observableParameters[364] = 'offset_CIS_actd;scale_CIS_actd '.
Checking condition table...
Checking parameter table...
Whitespace around parameterName[1] = 'CISEqcOE  '.
Not OK
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Looking for...
        SBML model: model_Becker_Science2010.xml
        Condition table: experimentalCondition_Becker_Science2010.tsv
        Measurement table: measurementData_Becker_Science2010.tsv
        Parameter table: parameters_Becker_Science2010.tsv
File b'experimentalCondition_Becker_Science2010.tsv' does not exist
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Looking for...
        SBML model: model_Beer_MolBioSystems2014.xml
        Condition table: experimentalCondition_Beer_MolBioSystems2014.tsv
        Measurement table: measurementData_Beer_MolBioSystems2014.tsv
        Parameter table: parameters_Beer_MolBioSystems2014.tsv
Checking SBML model...
Checking measurement table...
Checking condition table...
Checking parameter table...
OK
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Looking for...
        SBML model: model_Boehm_JProteomeRes2014.xml
        Condition table: experimentalCondition_Boehm_JProteomeRes2014.tsv
        Measurement table: measurementData_Boehm_JProteomeRes2014.tsv
        Parameter table: parameters_Boehm_JProteomeRes2014.tsv
Checking SBML model...
Checking measurement table...
Checking condition table...
Checking parameter table...
OK
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Looking for...
        SBML model: model_Borghans_BiophysChem1997.xml
        Condition table: experimentalCondition_Borghans_BiophysChem1997.tsv
        Measurement table: measurementData_Borghans_BiophysChem1997.tsv
        Parameter table: parameters_Borghans_BiophysChem1997.tsv
Checking SBML model...
Checking measurement table...
Checking condition table...
Checking parameter table...
OK
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Looking for...
        SBML model: model_Brannmark_JBC2010.xml
        Condition table: experimentalCondition_Brannmark_JBC2010.tsv
        Measurement table: measurementData_Brannmark_JBC2010.tsv
        Parameter table: parameters_Brannmark_JBC2010.tsv
Checking SBML model...
Checking measurement table...
Checking condition table...
Checking parameter table...
OK
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Looking for...
        SBML model: model_Bruno_JExpBio2016.xml
        Condition table: experimentalCondition_Bruno_JExpBio2016.tsv
        Measurement table: measurementData_Bruno_JExpBio2016.tsv
        Parameter table: parameters_Bruno_JExpBio2016.tsv
Checking SBML model...
Checking measurement table...
Checking condition table...
Checking parameter table...
OK
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Looking for...
        SBML model: model_Chen_MSB2009.xml
        Condition table: experimentalCondition_Chen_MSB2009.tsv
        Measurement table: measurementData_Chen_MSB2009.tsv
        Parameter table: parameters_Chen_MSB2009.tsv
Checking SBML model...
Checking measurement table...
Checking condition table...
Checking parameter table...
OK
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Looking for...
        SBML model: model_Crauste_CellSystems2017.xml
        Condition table: experimentalCondition_Crauste_CellSystems2017.tsv
        Measurement table: measurementData_Crauste_CellSystems2017.tsv
        Parameter table: parameters_Crauste_CellSystems2017.tsv
Checking SBML model...
Checking measurement table...
Checking condition table...
Checking parameter table...
OK
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Looking for...
        SBML model: model_Elowitz_Nature2000.xml
        Condition table: experimentalCondition_Elowitz_Nature2000.tsv
        Measurement table: measurementData_Elowitz_Nature2000.tsv
        Parameter table: parameters_Elowitz_Nature2000.tsv
Checking SBML model...
Checking measurement table...
Checking condition table...
Checking parameter table...
OK
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Looking for...
        SBML model: model_Fiedler_BMC2016.xml
        Condition table: experimentalCondition_Fiedler_BMC2016.tsv
        Measurement table: measurementData_Fiedler_BMC2016.tsv
        Parameter table: parameters_Fiedler_BMC2016.tsv
Checking SBML model...
Checking measurement table...
Checking condition table...
Checking parameter table...
OK
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Looking for...
        SBML model: model_Fujita_SciSignal2010.xml
        Condition table: experimentalCondition_Fujita_SciSignal2010.tsv
        Measurement table: measurementData_Fujita_SciSignal2010.tsv
        Parameter table: parameters_Fujita_SciSignal2010.tsv
Checking SBML model...
Checking measurement table...
Checking condition table...
Checking parameter table...
OK
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Looking for...
        SBML model: model_Hass_PONE2017.xml
        Condition table: experimentalCondition_Hass_PONE2017.tsv
        Measurement table: measurementData_Hass_PONE2017.tsv
        Parameter table: parameters_Hass_PONE2017.tsv
Checking SBML model...
Checking measurement table...
Checking condition table...
Checking parameter table...
OK
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Looking for...
        SBML model: model_Isensee_JCB2018.xml
        Condition table: experimentalCondition_Isensee_JCB2018.tsv
        Measurement table: measurementData_Isensee_JCB2018.tsv
        Parameter table: parameters_Isensee_JCB2018.tsv
Checking SBML model...
Checking measurement table...
Checking condition table...
Checking parameter table...
Mismatch of observable parameter overrides for {'name': '', 'formula': 'observableParameter2_Calpha + observableParameter1_Calpha * (2 * Csub + 2 * Csub_H89 + 2 * observableParameter3_Calpha * (RIIp_C_2 + RIIp_Rp_cAMPS_C_2 + RIIp_Rp8_Br_cAMPS_C_2 + RIIp_Rp8_pCPT_cAMPS_C_2) + 2 * (RIIp_cAMP_C_2 + RIIp_Sp8_Br_cAMPS_C_2) * (observableParameter3_Calpha - observableParameter4_Calpha * (observableParameter3_Calpha - 1)))'} in:                                                                               
observableId                                            Calpha                                                                                                                                                                                                                                  
preequilibrationConditionId                            control                                                                                                                                                                                                                                  
simulationConditionId                                  control                                                                                                                                                                                                                                  
measurement                                            983.648                                                                                                                                                                                                                                  
time                                                         0                                                                                                                                                                                                                                  
observableParameters           s_Calpha_global;b_Calpha_global                                                                                                                                                                                                                                  
noiseParameters                   s_Calpha_global;sigma_Calpha                                                                                                                                                                                                                                  
observableTransformation                                   lin                                                                                                                                                                                                                                  
experimentId                     JI09_160201_Drg453_452_CycNuc                                                                                                                                                                                                                                  
replicateId                                             Drg452                                                                                                                                                                                                                                  
Name: 645, dtype: object                                                                                                                                                                                                                                                                        
Expected 0 or 4 but got 2                                                                                                                                                                                                                                                                       
Not OK
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Looking for...
        SBML model: model_Lucarelli_CellSystems2018.xml
        Condition table: experimentalCondition_Lucarelli_CellSystems2018.tsv
        Measurement table: measurementData_Lucarelli_CellSystems2018.tsv
        Parameter table: parameters_Lucarelli_CellSystems2018.tsv
Checking SBML model...
Checking measurement table...
Checking condition table...
Checking parameter table...
OK
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Looking for...
        SBML model: model_Merkle_PCB2016.xml
        Condition table: experimentalCondition_Merkle_PCB2016.tsv
        Measurement table: measurementData_Merkle_PCB2016.tsv
        Parameter table: parameters_Merkle_PCB2016.tsv
SBML model not available. Skipping.
Checking measurement table...
Checking condition table...
Checking parameter table...
Not all files of the PEtab problem definition could be checked.
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Looking for...
        SBML model: model_Raia_CancerResearch2011.xml
        Condition table: experimentalCondition_Raia_CancerResearch2011.tsv
        Measurement table: measurementData_Raia_CancerResearch2011.tsv
        Parameter table: parameters_Raia_CancerResearch2011.tsv
Checking SBML model...
Checking measurement table...
Checking condition table...
Checking parameter table...
OK
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Looking for...
        SBML model: model_Schwen_PONE2014.xml
        Condition table: experimentalCondition_Schwen_PONE2014.tsv
        Measurement table: measurementData_Schwen_PONE2014.tsv
        Parameter table: parameters_Schwen_PONE2014.tsv
Checking SBML model...
Checking measurement table...
Checking condition table...
Checking parameter table...
OK
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Looking for...
        SBML model: model_Sneyd_PNAS2002.xml
        Condition table: experimentalCondition_Sneyd_PNAS2002.tsv
        Measurement table: measurementData_Sneyd_PNAS2002.tsv
        Parameter table: parameters_Sneyd_PNAS2002.tsv
Checking SBML model...
Checking measurement table...
Checking condition table...
Checking parameter table...
OK
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Looking for...
        SBML model: model_Sobotta_Frontiers2017.xml
        Condition table: experimentalCondition_Sobotta_Frontiers2017.tsv
        Measurement table: measurementData_Sobotta_Frontiers2017.tsv
        Parameter table: parameters_Sobotta_Frontiers2017.tsv
Checking SBML model...
Checking measurement table...
Whitespace around observableParameters[0] = 'offset_pjak1_wb_bohl_hep_2005_02_03_Cont40ng_T90min;scale_pjak1_wb_bohl_hep_2005_02_03_Cont40ng_T90min '.
Checking condition table...
Checking parameter table...
Not OK
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Looking for...
        SBML model: model_Swameye_PNAS2003.xml
        Condition table: experimentalCondition_Swameye_PNAS2003.tsv
        Measurement table: measurementData_Swameye_PNAS2003.tsv
        Parameter table: parameters_Swameye_PNAS2003.tsv
Checking SBML model...
Checking measurement table...
Checking condition table...
Checking parameter table...
OK
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Looking for...
        SBML model: model_Weber_BMC2015.xml
        Condition table: experimentalCondition_Weber_BMC2015.tsv
        Measurement table: measurementData_Weber_BMC2015.tsv
        Parameter table: parameters_Weber_BMC2015.tsv
Checking SBML model...
Checking measurement table...
Checking condition table...
Checking parameter table...
OK
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Looking for...
        SBML model: model_Zheng_PNAS2012.xml
        Condition table: experimentalCondition_Zheng_PNAS2012.tsv
        Measurement table: measurementData_Zheng_PNAS2012.tsv
        Parameter table: parameters_Zheng_PNAS2012.tsv
Checking SBML model...
Checking measurement table...
Checking condition table...
Checking parameter table...
OK
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[20:05:31]☺︎dweindl@dweindl:~/src/Benchmark-Models-Caro/hackathon_contributions_new_data_format>
elbaraim commented 5 years ago

It can be easily done by just: ./checkBenchmarkModels.py

the script has been updated to the latest PEtab version

dweindl commented 5 years ago

Now running automatically, see https://travis-ci.com/LoosC/Benchmark-Models