From 7a92c44e4a36345637d35a87a1c3d4d9408803f6 Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Fri, 25 Sep 2026 10:56:53 +0200 Subject: [PATCH] Fix and validate TSV file formatting for GitHub preview (#233) GitHub's TSV file preview breaks when a row has a different number of columns than the header. Mixed line endings were also present in several files. Root cause: the top-level `files: src/python` restriction in .pre-commit-config.yaml scoped every hook in the file - including trailing-whitespace, mixed-line-ending, and end-of-file-fixer - to src/python/ only, so the actual PEtab data files under Benchmark-Models/ were never checked or normalized. - Add bmp-check-tsv-format (benchmark_models_petab/check_tsv_format.py), which checks every *.tsv file for: consistent field count vs. the header, consistent line endings, no stray leading/trailing whitespace in a field, and exactly one trailing newline. Wire it into tests.yml alongside bmp-petablint. - Fix the 19 files it flagged: normalize CRLF/mixed line endings to LF and add missing final newlines (via the broadened pre-commit hooks below), pad short rows in Bachmann_MSB2011/parameters_Bachmann_MSB2011.tsv (114 rows were missing their two optional prior columns entirely), and trim stray whitespace from a handful of field values. - Extend .pre-commit-config.yaml's end-of-file-fixer and mixed-line-ending hooks to also cover *.tsv anywhere in the repo, and restore the previous src/python-only scope explicitly on every other hook (check-yaml, check-added-large-files, check-merge-conflict, check-symlinks, check-executables-have-shebangs, detect-private-key, ruff, ruff-format). trailing-whitespace is deliberately NOT extended to *.tsv, since it strips trailing tabs that PEtab TSVs use to encode a legitimately empty last column - doing so would recreate the very column-mismatch bug this fixes. - Add unit tests for check_tsv_file in src/python/test/. Co-Authored-By: Claude Sonnet 5 --- .github/workflows/tests.yml | 3 + .pre-commit-config.yaml | 17 +- ...ationSpecification_Alkan_SciSignal2018.tsv | 42 +-- ...lConditions_Armistead_CellDeathDis2024.tsv | 6 +- ...observables_Armistead_CellDeathDis2024.tsv | 10 +- .../parameters_Bachmann_MSB2011.tsv | 232 ++++++++-------- ...mentalCondition_Beer_MolBioSystems2014.tsv | 40 +-- ...measurementData_Boehm_JProteomeRes2014.tsv | 98 +++---- ...izationSpecification_Bruno_JExpBot2016.tsv | 10 +- .../simulatedData_Elowitz_Nature2000.tsv | 116 ++++---- .../observables_Fiedler_BMCSystBiol2016.tsv | 2 +- ...bservables_Fiedler_BMCSystBiol2016_rel.tsv | 2 +- ...erimentalCondition_Giordano_Nature2020.tsv | 13 +- .../experimentalCondition_Isensee_JCB2018.tsv | 248 +++++++++--------- ...entalCondition_Lang_PLOSComputBiol2024.tsv | 2 +- .../observables_Lang_PLOSComputBiol2024.tsv | 2 +- .../Liu_IFACPapersOnLine2025/measurements.tsv | 2 +- ...talCondition_Lucarelli_CellSystems2018.tsv | 34 +-- .../observables_Lucarelli_CellSystems2018.tsv | 132 +++++----- .../observables_SalazarCavazos_MBoC2020.tsv | 2 +- .../check_tsv_format.py | 94 +++++++ src/python/pyproject.toml | 1 + src/python/test/test_check_tsv_format.py | 144 ++++++++++ 23 files changed, 754 insertions(+), 498 deletions(-) create mode 100644 src/python/benchmark_models_petab/check_tsv_format.py create mode 100644 src/python/test/test_check_tsv_format.py diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index c55629c1..069e36cc 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -28,6 +28,9 @@ jobs: - name: Check with petablint run: bmp-petablint + - name: Check TSV format + run: bmp-check-tsv-format + - name: Show overview run: bmp-create-overview diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index bc7c9c23..9985a95e 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,26 +1,39 @@ -files: src/python repos: - repo: https://github.com/pre-commit/pre-commit-hooks rev: v4.6.0 hooks: - id: check-yaml description: Check yaml files for parseable syntax + files: ^src/python/ - id: check-added-large-files description: Prevent large files from being committed + files: ^src/python/ - id: check-merge-conflict description: Check for files that contain merge conflict strings + files: ^src/python/ - id: check-symlinks description: Check for symlinks which do not point to anything + files: ^src/python/ - id: check-executables-have-shebangs description: Check that (non-binary) executables have shebangs + files: ^src/python/ - id: detect-private-key description: Detects the presence of private keys + files: ^src/python/ - id: end-of-file-fixer description: Fix empty lines at ends of files + # also cover the PEtab TSV data files, not just src/python + files: (^src/python/|\.tsv$) - id: mixed-line-ending description: Replace or check mixed line endings + args: [--fix=lf] + files: (^src/python/|\.tsv$) - id: trailing-whitespace description: Trim trailing whitespaces + # not extended to *.tsv: a trailing tab there is a legitimate empty + # last field, not whitespace to strip (checked by bmp-check-tsv-format + # instead, which is field-aware) + files: ^src/python/ - repo: https://github.com/astral-sh/ruff-pre-commit # Ruff version. @@ -28,6 +41,7 @@ repos: hooks: # Run the linter. - id: ruff + files: ^src/python/ args: - --fix - --config @@ -35,6 +49,7 @@ repos: # Run the formatter. - id: ruff-format + files: ^src/python/ args: - --config - src/python/pyproject.toml diff --git a/Benchmark-Models/Alkan_SciSignal2018/visualizationSpecification_Alkan_SciSignal2018.tsv b/Benchmark-Models/Alkan_SciSignal2018/visualizationSpecification_Alkan_SciSignal2018.tsv index 5b6035e2..cca4207e 100644 --- a/Benchmark-Models/Alkan_SciSignal2018/visualizationSpecification_Alkan_SciSignal2018.tsv +++ b/Benchmark-Models/Alkan_SciSignal2018/visualizationSpecification_Alkan_SciSignal2018.tsv @@ -1,25 +1,25 @@ plotId plotName plotTypeSimulation plotTypeData datasetId xValues xOffset xLabel yValues yOffset yLabel legendEntry xScale yScale -plot1 SN38 – pATM LinePlot MeanAndSD model1_data24_SN38_pATM time 0 Time [hours] pATM_au 0 Signal (au) SN38 0.01µm lin lin -plot1 SN38 – pATM LinePlot MeanAndSD model1_data25_pATM time 0 Time [hours] pATM_au 0 Signal (au) SN38 0.05µm lin lin -plot1 SN38 – pATM LinePlot MeanAndSD model1_data26_pATM time 0 Time [hours] pATM_au 0 Signal (au) SN38 0.1µm lin lin -plot2 SN38 – pDNAPK LinePlot MeanAndSD model1_data24_SN38_pDNAPK time 0 Time [hours] pDNAPK_au 0 Signal (au) SN38 0.01µm lin lin -plot2 SN38 – pDNAPK LinePlot MeanAndSD model1_data25_pDNAPK time 0 Time [hours] pDNAPK_au 0 Signal (au) SN38 0.05µm lin lin -plot2 SN38 – pDNAPK LinePlot MeanAndSD model1_data26_pDNAPK time 0 Time [hours] pDNAPK_au 0 Signal (au) SN38 0.1µm lin lin -plot3 SN38 – pChk1_au LinePlot MeanAndSD model1_data24_SN38_pChk1 time 0 Time [hours] pChk1_au 0 Signal (au) SN38 0.01µm lin lin -plot3 SN38 – pChk1_au LinePlot MeanAndSD model1_data25_pChk1 time 0 Time [hours] pChk1_au 0 Signal (au) SN38 0.05µm lin lin -plot3 SN38 – pChk1_au LinePlot MeanAndSD model1_data26_pChk1 time 0 Time [hours] pChk1_au 0 Signal (au) SN38 0.1µm lin lin -plot4 SN38 – pChk2_au LinePlot MeanAndSD model1_data24_SN38_pChk2 time 0 Time [hours] pChk2_au 0 Signal (au) SN38 0.01µm lin lin -plot4 SN38 – pChk2_au LinePlot MeanAndSD model1_data25_pChk2 time 0 Time [hours] pChk2_au 0 Signal (au) SN38 0.05µm lin lin -plot4 SN38 – pChk2_au LinePlot MeanAndSD model1_data26_pChk2 time 0 Time [hours] pChk2_au 0 Signal (au) SN38 0.1µm lin lin -plot5 SN38 – tp53_au LinePlot MeanAndSD model1_data24_SN38_tp53 time 0 Time [hours] tp53_au 0 Signal (au) SN38 0.01µm lin lin -plot5 SN38 – tp53_au LinePlot MeanAndSD model1_data25_tp53 time 0 Time [hours] tp53_au 0 Signal (au) SN38 0.05µm lin lin -plot5 SN38 – tp53_au LinePlot MeanAndSD model1_data26_tp53 time 0 Time [hours] tp53_au 0 Signal (au) SN38 0.1µm lin lin -plot6 SN38 – pp53_au LinePlot MeanAndSD model1_data24_SN38_pp53 time 0 Time [hours] pp53_au 0 Signal (au) SN38 0.01µm lin lin -plot6 SN38 – pp53_au LinePlot MeanAndSD model1_data25_pp53 time 0 Time [hours] pp53_au 0 Signal (au) SN38 0.05µm lin lin -plot6 SN38 – pp53_au LinePlot MeanAndSD model1_data26_pp53 time 0 Time [hours] pp53_au 0 Signal (au) SN38 0.1µm lin lin -plot7 SN38 – tp21_au LinePlot MeanAndSD model1_data24_SN38_tp21 time 0 Time [hours] tp21_au 0 Signal (au) SN38 0.01µm lin lin -plot7 SN38 – tp21_au LinePlot MeanAndSD model1_data25_tp21 time 0 Time [hours] tp21_au 0 Signal (au) SN38 0.05µm lin lin -plot7 SN38 – tp21_au LinePlot MeanAndSD model1_data26_tp21 time 0 Time [hours] tp21_au 0 Signal (au) SN38 0.1µm lin lin +plot1 SN38 – pATM LinePlot MeanAndSD model1_data24_SN38_pATM time 0 Time [hours] pATM_au 0 Signal (au) SN38 0.01µm lin lin +plot1 SN38 – pATM LinePlot MeanAndSD model1_data25_pATM time 0 Time [hours] pATM_au 0 Signal (au) SN38 0.05µm lin lin +plot1 SN38 – pATM LinePlot MeanAndSD model1_data26_pATM time 0 Time [hours] pATM_au 0 Signal (au) SN38 0.1µm lin lin +plot2 SN38 – pDNAPK LinePlot MeanAndSD model1_data24_SN38_pDNAPK time 0 Time [hours] pDNAPK_au 0 Signal (au) SN38 0.01µm lin lin +plot2 SN38 – pDNAPK LinePlot MeanAndSD model1_data25_pDNAPK time 0 Time [hours] pDNAPK_au 0 Signal (au) SN38 0.05µm lin lin +plot2 SN38 – pDNAPK LinePlot MeanAndSD model1_data26_pDNAPK time 0 Time [hours] pDNAPK_au 0 Signal (au) SN38 0.1µm lin lin +plot3 SN38 – pChk1_au LinePlot MeanAndSD model1_data24_SN38_pChk1 time 0 Time [hours] pChk1_au 0 Signal (au) SN38 0.01µm lin lin +plot3 SN38 – pChk1_au LinePlot MeanAndSD model1_data25_pChk1 time 0 Time [hours] pChk1_au 0 Signal (au) SN38 0.05µm lin lin +plot3 SN38 – pChk1_au LinePlot MeanAndSD model1_data26_pChk1 time 0 Time [hours] pChk1_au 0 Signal (au) SN38 0.1µm lin lin +plot4 SN38 – pChk2_au LinePlot MeanAndSD model1_data24_SN38_pChk2 time 0 Time [hours] pChk2_au 0 Signal (au) SN38 0.01µm lin lin +plot4 SN38 – pChk2_au LinePlot MeanAndSD model1_data25_pChk2 time 0 Time [hours] pChk2_au 0 Signal (au) SN38 0.05µm lin lin +plot4 SN38 – pChk2_au LinePlot MeanAndSD model1_data26_pChk2 time 0 Time [hours] pChk2_au 0 Signal (au) SN38 0.1µm lin lin +plot5 SN38 – tp53_au LinePlot MeanAndSD model1_data24_SN38_tp53 time 0 Time [hours] tp53_au 0 Signal (au) SN38 0.01µm lin lin +plot5 SN38 – tp53_au LinePlot MeanAndSD model1_data25_tp53 time 0 Time [hours] tp53_au 0 Signal (au) SN38 0.05µm lin lin +plot5 SN38 – tp53_au LinePlot MeanAndSD model1_data26_tp53 time 0 Time [hours] tp53_au 0 Signal (au) SN38 0.1µm lin lin +plot6 SN38 – pp53_au LinePlot MeanAndSD model1_data24_SN38_pp53 time 0 Time [hours] pp53_au 0 Signal (au) SN38 0.01µm lin lin +plot6 SN38 – pp53_au LinePlot MeanAndSD model1_data25_pp53 time 0 Time [hours] pp53_au 0 Signal (au) SN38 0.05µm lin lin +plot6 SN38 – pp53_au LinePlot MeanAndSD model1_data26_pp53 time 0 Time [hours] pp53_au 0 Signal (au) SN38 0.1µm lin lin +plot7 SN38 – tp21_au LinePlot MeanAndSD model1_data24_SN38_tp21 time 0 Time [hours] tp21_au 0 Signal (au) SN38 0.01µm lin lin +plot7 SN38 – tp21_au LinePlot MeanAndSD model1_data25_tp21 time 0 Time [hours] tp21_au 0 Signal (au) SN38 0.05µm lin lin +plot7 SN38 – tp21_au LinePlot MeanAndSD model1_data26_tp21 time 0 Time [hours] tp21_au 0 Signal (au) SN38 0.1µm lin lin plot8 Dox – pATM_au LinePlot MeanAndSD model1_data20_patm_au time 0 Time [hours] pATM_au 0 Signal (au) Dox 0.01µm lin lin plot8 Dox – pATM_au LinePlot MeanAndSD model1_data21_patm_au time 0 Time [hours] pATM_au 0 Signal (au) Dox 0.05µm lin lin plot8 Dox – pATM_au LinePlot MeanAndSD model1_data22_patm_au time 0 Time [hours] pATM_au 0 Signal (au) Dox 0.1µm lin lin diff --git a/Benchmark-Models/Armistead_CellDeathDis2024/experimentalConditions_Armistead_CellDeathDis2024.tsv b/Benchmark-Models/Armistead_CellDeathDis2024/experimentalConditions_Armistead_CellDeathDis2024.tsv index 4b893889..ef870459 100644 --- a/Benchmark-Models/Armistead_CellDeathDis2024/experimentalConditions_Armistead_CellDeathDis2024.tsv +++ b/Benchmark-Models/Armistead_CellDeathDis2024/experimentalConditions_Armistead_CellDeathDis2024.tsv @@ -1,3 +1,3 @@ -conditionId conditionName S_on Cer Sphinga Sphingo S1P -wild_type wild-type 1 0.988 0.000732 0.000395 1.551 -mutant Hai1a deletion mutant 0 0.822 0.000795 0.000364 2.07 \ No newline at end of file +conditionId conditionName S_on Cer Sphinga Sphingo S1P +wild_type wild-type 1 0.988 0.000732 0.000395 1.551 +mutant Hai1a deletion mutant 0 0.822 0.000795 0.000364 2.07 diff --git a/Benchmark-Models/Armistead_CellDeathDis2024/observables_Armistead_CellDeathDis2024.tsv b/Benchmark-Models/Armistead_CellDeathDis2024/observables_Armistead_CellDeathDis2024.tsv index 4cb243a1..230a337e 100644 --- a/Benchmark-Models/Armistead_CellDeathDis2024/observables_Armistead_CellDeathDis2024.tsv +++ b/Benchmark-Models/Armistead_CellDeathDis2024/observables_Armistead_CellDeathDis2024.tsv @@ -1,5 +1,5 @@ -observableId observableName observableFormula noiseFormula noiseDistribution -Sphinga_obs Sphinganine concentration [area ratio/Protein] - indication of Cer de novo production Sphinga noiseParameter1_Sphinga_obs*Sphinga normal -Cer_obs Ceramide concentration [area ratio/Protein] Cer noiseParameter1_Cer_obs*Cer normal -Sphingo_obs Sphingosine concentration [area ratio/Protein] Sphingo noiseParameter1_Sphingo_obs*Sphingo normal -S1P_obs Sphingosine-1-phosphate indirect measurement S1P noiseParameter1_S1P_obs*S1P normal +observableId observableName observableFormula noiseFormula noiseDistribution +Sphinga_obs Sphinganine concentration [area ratio/Protein] - indication of Cer de novo production Sphinga noiseParameter1_Sphinga_obs*Sphinga normal +Cer_obs Ceramide concentration [area ratio/Protein] Cer noiseParameter1_Cer_obs*Cer normal +Sphingo_obs Sphingosine concentration [area ratio/Protein] Sphingo noiseParameter1_Sphingo_obs*Sphingo normal +S1P_obs Sphingosine-1-phosphate indirect measurement S1P noiseParameter1_S1P_obs*S1P normal diff --git a/Benchmark-Models/Bachmann_MSB2011/parameters_Bachmann_MSB2011.tsv b/Benchmark-Models/Bachmann_MSB2011/parameters_Bachmann_MSB2011.tsv index 3c2ea41b..57a272ff 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 objectivePriorType objectivePriorParameters -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 0.599470870492697;0.193459292722329 -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 objectivePriorType objectivePriorParameters +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 0.599470870492697;0.193459292722329 +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 diff --git a/Benchmark-Models/Beer_MolBioSystems2014/experimentalCondition_Beer_MolBioSystems2014.tsv b/Benchmark-Models/Beer_MolBioSystems2014/experimentalCondition_Beer_MolBioSystems2014.tsv index 621e9e39..cd50fbae 100644 --- a/Benchmark-Models/Beer_MolBioSystems2014/experimentalCondition_Beer_MolBioSystems2014.tsv +++ b/Benchmark-Models/Beer_MolBioSystems2014/experimentalCondition_Beer_MolBioSystems2014.tsv @@ -1,20 +1,20 @@ -conditionId conditionName Bacmax beta kdegi kdim ksyn tau -typeIDwt_ExpID4 typeID=wt,ExpID=4 Bacmax_typeIDwt_ExpID4 beta_typeIDwt_ExpID4 kdegi_typeIDwt kdim_typeIDwt ksyn_typeIDwt tau_typeIDwt_ExpID4 -typeIDT1_ExpID1 typeID=T1,ExpID=1 Bacmax_typeIDT1_ExpID1 beta_typeIDT1_ExpID1 kdegi_typeIDT1 kdim_typeIDT1 ksyn_typeIDT1 tau_typeIDT1_ExpID1 -typeIDT1_ExpID2 typeID=T1,ExpID=2 Bacmax_typeIDT1_ExpID2 beta_typeIDT1_ExpID2 kdegi_typeIDT1 kdim_typeIDT1 ksyn_typeIDT1 tau_typeIDT1_ExpID2 -typeIDT1_ExpID3 typeID=T1,ExpID=3 Bacmax_typeIDT1_ExpID3 beta_typeIDT1_ExpID3 kdegi_typeIDT1 kdim_typeIDT1 ksyn_typeIDT1 tau_typeIDT1_ExpID3 -typeIDT1_ExpID4 typeID=T1,ExpID=4 Bacmax_typeIDT1_ExpID4 beta_typeIDT1_ExpID4 kdegi_typeIDT1 kdim_typeIDT1 ksyn_typeIDT1 tau_typeIDT1_ExpID4 -typeIDT1_ExpID5 typeID=T1,ExpID=5 Bacmax_typeIDT1_ExpID5 beta_typeIDT1_ExpID5 kdegi_typeIDT1 kdim_typeIDT1 ksyn_typeIDT1 tau_typeIDT1_ExpID5 -typeIDT1_ExpID6 typeID=T1,ExpID=6 Bacmax_typeIDT1_ExpID6 beta_typeIDT1_ExpID6 kdegi_typeIDT1 kdim_typeIDT1 ksyn_typeIDT1 tau_typeIDT1_ExpID6 -typeIDT3_ExpID1 typeID=T3,ExpID=1 Bacmax_typeIDT3_ExpID1 beta_typeIDT3_ExpID1 kdegi_typeIDT3 kdim_typeIDT3 ksyn_typeIDT3 tau_typeIDT3_ExpID1 -typeIDT3_ExpID2 typeID=T3,ExpID=2 Bacmax_typeIDT3_ExpID2 beta_typeIDT3_ExpID2 kdegi_typeIDT3 kdim_typeIDT3 ksyn_typeIDT3 tau_typeIDT3_ExpID2 -typeIDT3_ExpID3 typeID=T3,ExpID=3 Bacmax_typeIDT3_ExpID3 beta_typeIDT3_ExpID3 kdegi_typeIDT3 kdim_typeIDT3 ksyn_typeIDT3 tau_typeIDT3_ExpID3 -typeIDT3_ExpID4 typeID=T3,ExpID=4 Bacmax_typeIDT3_ExpID4 beta_typeIDT3_ExpID4 kdegi_typeIDT3 kdim_typeIDT3 ksyn_typeIDT3 tau_typeIDT3_ExpID4 -typeIDT3_ExpID5 typeID=T3,ExpID=5 Bacmax_typeIDT3_ExpID5 beta_typeIDT3_ExpID5 kdegi_typeIDT3 kdim_typeIDT3 ksyn_typeIDT3 tau_typeIDT3_ExpID5 -typeIDT3_ExpID6 typeID=T3,ExpID=6 Bacmax_typeIDT3_ExpID6 beta_typeIDT3_ExpID6 kdegi_typeIDT3 kdim_typeIDT3 ksyn_typeIDT3 tau_typeIDT3_ExpID6 -typeIDT5_ExpID1 typeID=T5,ExpID=1 Bacmax_typeIDT5_ExpID1 beta_typeIDT5_ExpID1 kdegi_typeIDT5 kdim_typeIDT5 ksyn_typeIDT5 tau_typeIDT5_ExpID1 -typeIDT5_ExpID2 typeID=T5,ExpID=2 Bacmax_typeIDT5_ExpID2 beta_typeIDT5_ExpID2 kdegi_typeIDT5 kdim_typeIDT5 ksyn_typeIDT5 tau_typeIDT5_ExpID2 -typeIDT5_ExpID3 typeID=T5,ExpID=3 Bacmax_typeIDT5_ExpID3 beta_typeIDT5_ExpID3 kdegi_typeIDT5 kdim_typeIDT5 ksyn_typeIDT5 tau_typeIDT5_ExpID3 -typeIDT5_ExpID4 typeID=T5,ExpID=4 Bacmax_typeIDT5_ExpID4 beta_typeIDT5_ExpID4 kdegi_typeIDT5 kdim_typeIDT5 ksyn_typeIDT5 tau_typeIDT5_ExpID4 -typeIDT5_ExpID5 typeID=T5,ExpID=5 Bacmax_typeIDT5_ExpID5 beta_typeIDT5_ExpID5 kdegi_typeIDT5 kdim_typeIDT5 ksyn_typeIDT5 tau_typeIDT5_ExpID5 -typeIDT5_ExpID6 typeID=T5,ExpID=6 Bacmax_typeIDT5_ExpID6 beta_typeIDT5_ExpID6 kdegi_typeIDT5 kdim_typeIDT5 ksyn_typeIDT5 tau_typeIDT5_ExpID6 +conditionId conditionName Bacmax beta kdegi kdim ksyn tau +typeIDwt_ExpID4 typeID=wt,ExpID=4 Bacmax_typeIDwt_ExpID4 beta_typeIDwt_ExpID4 kdegi_typeIDwt kdim_typeIDwt ksyn_typeIDwt tau_typeIDwt_ExpID4 +typeIDT1_ExpID1 typeID=T1,ExpID=1 Bacmax_typeIDT1_ExpID1 beta_typeIDT1_ExpID1 kdegi_typeIDT1 kdim_typeIDT1 ksyn_typeIDT1 tau_typeIDT1_ExpID1 +typeIDT1_ExpID2 typeID=T1,ExpID=2 Bacmax_typeIDT1_ExpID2 beta_typeIDT1_ExpID2 kdegi_typeIDT1 kdim_typeIDT1 ksyn_typeIDT1 tau_typeIDT1_ExpID2 +typeIDT1_ExpID3 typeID=T1,ExpID=3 Bacmax_typeIDT1_ExpID3 beta_typeIDT1_ExpID3 kdegi_typeIDT1 kdim_typeIDT1 ksyn_typeIDT1 tau_typeIDT1_ExpID3 +typeIDT1_ExpID4 typeID=T1,ExpID=4 Bacmax_typeIDT1_ExpID4 beta_typeIDT1_ExpID4 kdegi_typeIDT1 kdim_typeIDT1 ksyn_typeIDT1 tau_typeIDT1_ExpID4 +typeIDT1_ExpID5 typeID=T1,ExpID=5 Bacmax_typeIDT1_ExpID5 beta_typeIDT1_ExpID5 kdegi_typeIDT1 kdim_typeIDT1 ksyn_typeIDT1 tau_typeIDT1_ExpID5 +typeIDT1_ExpID6 typeID=T1,ExpID=6 Bacmax_typeIDT1_ExpID6 beta_typeIDT1_ExpID6 kdegi_typeIDT1 kdim_typeIDT1 ksyn_typeIDT1 tau_typeIDT1_ExpID6 +typeIDT3_ExpID1 typeID=T3,ExpID=1 Bacmax_typeIDT3_ExpID1 beta_typeIDT3_ExpID1 kdegi_typeIDT3 kdim_typeIDT3 ksyn_typeIDT3 tau_typeIDT3_ExpID1 +typeIDT3_ExpID2 typeID=T3,ExpID=2 Bacmax_typeIDT3_ExpID2 beta_typeIDT3_ExpID2 kdegi_typeIDT3 kdim_typeIDT3 ksyn_typeIDT3 tau_typeIDT3_ExpID2 +typeIDT3_ExpID3 typeID=T3,ExpID=3 Bacmax_typeIDT3_ExpID3 beta_typeIDT3_ExpID3 kdegi_typeIDT3 kdim_typeIDT3 ksyn_typeIDT3 tau_typeIDT3_ExpID3 +typeIDT3_ExpID4 typeID=T3,ExpID=4 Bacmax_typeIDT3_ExpID4 beta_typeIDT3_ExpID4 kdegi_typeIDT3 kdim_typeIDT3 ksyn_typeIDT3 tau_typeIDT3_ExpID4 +typeIDT3_ExpID5 typeID=T3,ExpID=5 Bacmax_typeIDT3_ExpID5 beta_typeIDT3_ExpID5 kdegi_typeIDT3 kdim_typeIDT3 ksyn_typeIDT3 tau_typeIDT3_ExpID5 +typeIDT3_ExpID6 typeID=T3,ExpID=6 Bacmax_typeIDT3_ExpID6 beta_typeIDT3_ExpID6 kdegi_typeIDT3 kdim_typeIDT3 ksyn_typeIDT3 tau_typeIDT3_ExpID6 +typeIDT5_ExpID1 typeID=T5,ExpID=1 Bacmax_typeIDT5_ExpID1 beta_typeIDT5_ExpID1 kdegi_typeIDT5 kdim_typeIDT5 ksyn_typeIDT5 tau_typeIDT5_ExpID1 +typeIDT5_ExpID2 typeID=T5,ExpID=2 Bacmax_typeIDT5_ExpID2 beta_typeIDT5_ExpID2 kdegi_typeIDT5 kdim_typeIDT5 ksyn_typeIDT5 tau_typeIDT5_ExpID2 +typeIDT5_ExpID3 typeID=T5,ExpID=3 Bacmax_typeIDT5_ExpID3 beta_typeIDT5_ExpID3 kdegi_typeIDT5 kdim_typeIDT5 ksyn_typeIDT5 tau_typeIDT5_ExpID3 +typeIDT5_ExpID4 typeID=T5,ExpID=4 Bacmax_typeIDT5_ExpID4 beta_typeIDT5_ExpID4 kdegi_typeIDT5 kdim_typeIDT5 ksyn_typeIDT5 tau_typeIDT5_ExpID4 +typeIDT5_ExpID5 typeID=T5,ExpID=5 Bacmax_typeIDT5_ExpID5 beta_typeIDT5_ExpID5 kdegi_typeIDT5 kdim_typeIDT5 ksyn_typeIDT5 tau_typeIDT5_ExpID5 +typeIDT5_ExpID6 typeID=T5,ExpID=6 Bacmax_typeIDT5_ExpID6 beta_typeIDT5_ExpID6 kdegi_typeIDT5 kdim_typeIDT5 ksyn_typeIDT5 tau_typeIDT5_ExpID6 diff --git a/Benchmark-Models/Boehm_JProteomeRes2014/measurementData_Boehm_JProteomeRes2014.tsv b/Benchmark-Models/Boehm_JProteomeRes2014/measurementData_Boehm_JProteomeRes2014.tsv index 179ec28f..814cdb18 100644 --- a/Benchmark-Models/Boehm_JProteomeRes2014/measurementData_Boehm_JProteomeRes2014.tsv +++ b/Benchmark-Models/Boehm_JProteomeRes2014/measurementData_Boehm_JProteomeRes2014.tsv @@ -1,49 +1,49 @@ -observableId preequilibrationConditionId simulationConditionId measurement time observableParameters noiseParameters datasetId -pSTAT5A_rel model1_data1 7.90107299873911 0.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel -pSTAT5A_rel model1_data1 66.3634939682528 2.5 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel -pSTAT5A_rel model1_data1 81.1713239165337 5.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel -pSTAT5A_rel model1_data1 94.7303080627876 10.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel -pSTAT5A_rel model1_data1 95.1164830493244 15.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel -pSTAT5A_rel model1_data1 91.44171655392 20.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel -pSTAT5A_rel model1_data1 91.2570992263545 30.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel -pSTAT5A_rel model1_data1 93.672297840992 40.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel -pSTAT5A_rel model1_data1 88.754232823019 50.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel -pSTAT5A_rel model1_data1 85.2697032178279 60.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel -pSTAT5A_rel model1_data1 81.1323953369608 80.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel -pSTAT5A_rel model1_data1 76.135928475796 100.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel -pSTAT5A_rel model1_data1 65.2480591250229 120.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel -pSTAT5A_rel model1_data1 42.5996587097166 160.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel -pSTAT5A_rel model1_data1 25.1577975445976 200.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel -pSTAT5A_rel model1_data1 15.4301823994994 240.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel -pSTAT5B_rel model1_data1 4.59653334288927 0.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel -pSTAT5B_rel model1_data1 29.6345459874189 2.5 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel -pSTAT5B_rel model1_data1 46.0438064695701 5.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel -pSTAT5B_rel model1_data1 81.9747336191685 10.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel -pSTAT5B_rel model1_data1 80.5716092952489 15.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel -pSTAT5B_rel model1_data1 79.0357196371442 20.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel -pSTAT5B_rel model1_data1 75.6723803658298 30.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel -pSTAT5B_rel model1_data1 71.6247198618303 40.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel -pSTAT5B_rel model1_data1 69.0628632755742 50.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel -pSTAT5B_rel model1_data1 67.1473843168934 60.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel -pSTAT5B_rel model1_data1 60.8994762938824 80.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel -pSTAT5B_rel model1_data1 54.8092577721492 100.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel -pSTAT5B_rel model1_data1 43.9812899778025 120.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel -pSTAT5B_rel model1_data1 29.7714581636675 160.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel -pSTAT5B_rel model1_data1 20.089016562771 200.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel -pSTAT5B_rel model1_data1 10.961845166698 240.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel -rSTAT5A_rel model1_data1 14.7231682180584 0.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel -rSTAT5A_rel model1_data1 33.762342293107 2.5 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel -rSTAT5A_rel model1_data1 36.7998512942493 5.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel -rSTAT5A_rel model1_data1 49.7176022859654 10.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel -rSTAT5A_rel model1_data1 46.9281200952955 15.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel -rSTAT5A_rel model1_data1 47.8365745550135 20.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel -rSTAT5A_rel model1_data1 46.9287272497385 30.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel -rSTAT5A_rel model1_data1 40.5977529351181 40.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel -rSTAT5A_rel model1_data1 43.783663885071 50.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel -rSTAT5A_rel model1_data1 44.4573876523855 60.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel -rSTAT5A_rel model1_data1 41.3271592618297 80.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel -rSTAT5A_rel model1_data1 41.0627332148332 100.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel -rSTAT5A_rel model1_data1 39.2358300289377 120.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel -rSTAT5A_rel model1_data1 36.6194605442418 160.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel -rSTAT5A_rel model1_data1 34.8937144010561 200.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel -rSTAT5A_rel model1_data1 32.2110771608676 240.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel \ No newline at end of file +observableId preequilibrationConditionId simulationConditionId measurement time observableParameters noiseParameters datasetId +pSTAT5A_rel model1_data1 7.90107299873911 0.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel +pSTAT5A_rel model1_data1 66.3634939682528 2.5 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel +pSTAT5A_rel model1_data1 81.1713239165337 5.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel +pSTAT5A_rel model1_data1 94.7303080627876 10.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel +pSTAT5A_rel model1_data1 95.1164830493244 15.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel +pSTAT5A_rel model1_data1 91.44171655392 20.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel +pSTAT5A_rel model1_data1 91.2570992263545 30.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel +pSTAT5A_rel model1_data1 93.672297840992 40.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel +pSTAT5A_rel model1_data1 88.754232823019 50.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel +pSTAT5A_rel model1_data1 85.2697032178279 60.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel +pSTAT5A_rel model1_data1 81.1323953369608 80.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel +pSTAT5A_rel model1_data1 76.135928475796 100.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel +pSTAT5A_rel model1_data1 65.2480591250229 120.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel +pSTAT5A_rel model1_data1 42.5996587097166 160.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel +pSTAT5A_rel model1_data1 25.1577975445976 200.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel +pSTAT5A_rel model1_data1 15.4301823994994 240.0 sd_pSTAT5A_rel model1_data1_pSTAT5A_rel +pSTAT5B_rel model1_data1 4.59653334288927 0.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel +pSTAT5B_rel model1_data1 29.6345459874189 2.5 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel +pSTAT5B_rel model1_data1 46.0438064695701 5.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel +pSTAT5B_rel model1_data1 81.9747336191685 10.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel +pSTAT5B_rel model1_data1 80.5716092952489 15.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel +pSTAT5B_rel model1_data1 79.0357196371442 20.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel +pSTAT5B_rel model1_data1 75.6723803658298 30.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel +pSTAT5B_rel model1_data1 71.6247198618303 40.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel +pSTAT5B_rel model1_data1 69.0628632755742 50.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel +pSTAT5B_rel model1_data1 67.1473843168934 60.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel +pSTAT5B_rel model1_data1 60.8994762938824 80.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel +pSTAT5B_rel model1_data1 54.8092577721492 100.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel +pSTAT5B_rel model1_data1 43.9812899778025 120.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel +pSTAT5B_rel model1_data1 29.7714581636675 160.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel +pSTAT5B_rel model1_data1 20.089016562771 200.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel +pSTAT5B_rel model1_data1 10.961845166698 240.0 sd_pSTAT5B_rel model1_data1_pSTAT5B_rel +rSTAT5A_rel model1_data1 14.7231682180584 0.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel +rSTAT5A_rel model1_data1 33.762342293107 2.5 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel +rSTAT5A_rel model1_data1 36.7998512942493 5.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel +rSTAT5A_rel model1_data1 49.7176022859654 10.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel +rSTAT5A_rel model1_data1 46.9281200952955 15.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel +rSTAT5A_rel model1_data1 47.8365745550135 20.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel +rSTAT5A_rel model1_data1 46.9287272497385 30.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel +rSTAT5A_rel model1_data1 40.5977529351181 40.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel +rSTAT5A_rel model1_data1 43.783663885071 50.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel +rSTAT5A_rel model1_data1 44.4573876523855 60.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel +rSTAT5A_rel model1_data1 41.3271592618297 80.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel +rSTAT5A_rel model1_data1 41.0627332148332 100.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel +rSTAT5A_rel model1_data1 39.2358300289377 120.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel +rSTAT5A_rel model1_data1 36.6194605442418 160.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel +rSTAT5A_rel model1_data1 34.8937144010561 200.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel +rSTAT5A_rel model1_data1 32.2110771608676 240.0 sd_rSTAT5A_rel model1_data1_rSTAT5A_rel diff --git a/Benchmark-Models/Bruno_JExpBot2016/visualizationSpecification_Bruno_JExpBot2016.tsv b/Benchmark-Models/Bruno_JExpBot2016/visualizationSpecification_Bruno_JExpBot2016.tsv index ae01734a..2671c4b8 100644 --- a/Benchmark-Models/Bruno_JExpBot2016/visualizationSpecification_Bruno_JExpBot2016.tsv +++ b/Benchmark-Models/Bruno_JExpBot2016/visualizationSpecification_Bruno_JExpBot2016.tsv @@ -7,13 +7,13 @@ plot3 model1_data3 LinePlot MeanAndSD model1_data3_ob10 time 0 Time [min] ob10 0 plot5 model1_data5 LinePlot MeanAndSD model1_data5_oohb10 time 0 Time [min] oohb10 0 amount [nmol] 3-OH-$\beta$-apo-10-carotenal lin lin plot6 model1_data6 LinePlot MeanAndSD model1_data6_oohb10 time 0 Time [min] oohb10 0 amount [nmol] 3-OH-$\beta$-apo-10-carotenal lin log10 plot6 model1_data6 LinePlot MeanAndSD model1_data6_ozea time 0 Time [min] ozea 0 amount [nmol] zeaxanthin lin log10 -plot7 $\beta$-apo-10-carotenal LinePlot MeanAndSD model1_data1_ob10 time 0 Time [min] ob10 0 amount [nmol] model1_data1 lin lin -plot7 $\beta$-apo-10-carotenal LinePlot MeanAndSD model1_data2_ob10 time 0 Time [min] ob10 0 amount [nmol] model1_data2 lin lin -plot7 $\beta$-apo-10-carotenal LinePlot MeanAndSD model1_data3_ob10 time 0 Time [min] ob10 0 amount [nmol] model1_data3 lin lin -plot7 $\beta$-apo-10-carotenal LinePlot MeanAndSD model1_data4_ob10 time 0 Time [min] ob10 0 amount [nmol] model1_data4 lin lin +plot7 $\beta$-apo-10-carotenal LinePlot MeanAndSD model1_data1_ob10 time 0 Time [min] ob10 0 amount [nmol] model1_data1 lin lin +plot7 $\beta$-apo-10-carotenal LinePlot MeanAndSD model1_data2_ob10 time 0 Time [min] ob10 0 amount [nmol] model1_data2 lin lin +plot7 $\beta$-apo-10-carotenal LinePlot MeanAndSD model1_data3_ob10 time 0 Time [min] ob10 0 amount [nmol] model1_data3 lin lin +plot7 $\beta$-apo-10-carotenal LinePlot MeanAndSD model1_data4_ob10 time 0 Time [min] ob10 0 amount [nmol] model1_data4 lin lin plot8 $\beta$-carotene LinePlot MeanAndSD model1_data2_obcar time 0 Time [min] obcar 0 amount [nmol] model1_data2 lin lin plot8 $\beta$-carotene LinePlot MeanAndSD model1_data3_obcar time 0 Time [min] obcar 0 amount [nmol] model1_data3 lin lin plot9 3-OH-$\beta$-apo-10-carotenal LinePlot MeanAndSD model1_data4_oohb10 time 0 Time [min] oohb10 0 amount [nmol] model1_data4 lin lin plot9 3-OH-$\beta$-apo-10-carotenal LinePlot MeanAndSD model1_data5_oohb10 time 0 Time [min] oohb10 0 amount [nmol] model1_data5 lin lin plot9 3-OH-$\beta$-apo-10-carotenal LinePlot MeanAndSD model1_data6_oohb10 time 0 Time [min] oohb10 0 amount [nmol] model1_data6 lin lin -plot10 zeaxanthin LinePlot MeanAndSD model1_data6_ozea time 0 Time [min] ozea 0 amount [nmol] model1_data6 lin log10 +plot10 zeaxanthin LinePlot MeanAndSD model1_data6_ozea time 0 Time [min] ozea 0 amount [nmol] model1_data6 lin log10 diff --git a/Benchmark-Models/Elowitz_Nature2000/simulatedData_Elowitz_Nature2000.tsv b/Benchmark-Models/Elowitz_Nature2000/simulatedData_Elowitz_Nature2000.tsv index 629fbc15..3e015f0d 100644 --- a/Benchmark-Models/Elowitz_Nature2000/simulatedData_Elowitz_Nature2000.tsv +++ b/Benchmark-Models/Elowitz_Nature2000/simulatedData_Elowitz_Nature2000.tsv @@ -1,59 +1,59 @@ observableId preequilibrationConditionId simulationConditionId simulation time observableParameters noiseParameters -fluorescence model1_data1 0.17985510790355 10 -4.98107438218408;-0.279017032524776 -1.14362512938604 -fluorescence model1_data1 0.154075279670803 30 -4.98107438218408;-0.279017032524776 -1.14362512938604 -fluorescence model1_data1 0.133013932596571 50 -4.98107438218408;-0.279017032524776 -1.14362512938604 -fluorescence model1_data1 0.124925789264688 60 -4.98107438218408;-0.279017032524776 -1.14362512938604 -fluorescence model1_data1 0.122632345769039 70 -4.98107438218408;-0.279017032524776 -1.14362512938604 -fluorescence model1_data1 0.142076536313219 80 -4.98107438218408;-0.279017032524776 -1.14362512938604 -fluorescence model1_data1 0.22571784377453 90 -4.98107438218408;-0.279017032524776 -1.14362512938604 -fluorescence model1_data1 0.422552020849143 100 -4.98107438218408;-0.279017032524776 -1.14362512938604 -fluorescence model1_data1 0.638934172948195 110 -4.98107438218408;-0.279017032524776 -1.14362512938604 -fluorescence model1_data1 0.705442006015758 120 -4.98107438218408;-0.279017032524776 -1.14362512938604 -fluorescence model1_data1 0.678865646865378 130 -4.98107438218408;-0.279017032524776 -1.14362512938604 -fluorescence model1_data1 0.629642448692058 140 -4.98107438218408;-0.279017032524776 -1.14362512938604 -fluorescence model1_data1 0.578382618178207 150 -4.98107438218408;-0.279017032524776 -1.14362512938604 -fluorescence model1_data1 0.529904079110556 160 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-4.98107438218408;-0.279017032524776 -1.14362512938604 +fluorescence model1_data1 0.510746501720169 540 -4.98107438218408;-0.279017032524776 -1.14362512938604 +fluorescence model1_data1 0.488833432013139 550 -4.98107438218408;-0.279017032524776 -1.14362512938604 +fluorescence model1_data1 0.483791447278071 560 -4.98107438218408;-0.279017032524776 -1.14362512938604 +fluorescence model1_data1 0.50319917222794 570 -4.98107438218408;-0.279017032524776 -1.14362512938604 +fluorescence model1_data1 0.552755027484643 580 -4.98107438218408;-0.279017032524776 -1.14362512938604 +fluorescence model1_data1 0.625869019664127 590 -4.98107438218408;-0.279017032524776 -1.14362512938604 +fluorescence model1_data1 0.69596759290456 600 -4.98107438218408;-0.279017032524776 -1.14362512938604 diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/observables_Fiedler_BMCSystBiol2016.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/observables_Fiedler_BMCSystBiol2016.tsv index 48b2bbbb..2d872971 100644 --- a/Benchmark-Models/Fiedler_BMCSystBiol2016/observables_Fiedler_BMCSystBiol2016.tsv +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/observables_Fiedler_BMCSystBiol2016.tsv @@ -1,3 +1,3 @@ observableId observableName observableFormula noiseFormula observableTransformation noiseDistribution pErk pERK * observableParameter1_pErk noiseParameter1_pErk*noiseParameter2_pErk lin normal -pMek pMEK * observableParameter1_pMek noiseParameter1_pMek*noiseParameter2_pMek lin normal \ No newline at end of file +pMek pMEK * observableParameter1_pMek noiseParameter1_pMek*noiseParameter2_pMek lin normal diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/observables_Fiedler_BMCSystBiol2016_rel.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/observables_Fiedler_BMCSystBiol2016_rel.tsv index da0359bd..87e639dc 100644 --- a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/observables_Fiedler_BMCSystBiol2016_rel.tsv +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/observables_Fiedler_BMCSystBiol2016_rel.tsv @@ -1,3 +1,3 @@ observableId observableName observableFormula noiseFormula observableTransformation noiseDistribution pMek_rel [pMEK]/MEK_0 x2 * observableParameter1_pMek_rel noiseParameter1_pMek_rel*noiseParameter2_pMek_rel lin normal -pErk_rel [pERK]/ERK_0 x3 * observableParameter1_pErk_rel noiseParameter1_pErk_rel*noiseParameter2_pErk_rel lin normal \ No newline at end of file +pErk_rel [pERK]/ERK_0 x3 * observableParameter1_pErk_rel noiseParameter1_pErk_rel*noiseParameter2_pErk_rel lin normal diff --git a/Benchmark-Models/Giordano_Nature2020/experimentalCondition_Giordano_Nature2020.tsv b/Benchmark-Models/Giordano_Nature2020/experimentalCondition_Giordano_Nature2020.tsv index 556b599e..61ac1239 100644 --- a/Benchmark-Models/Giordano_Nature2020/experimentalCondition_Giordano_Nature2020.tsv +++ b/Benchmark-Models/Giordano_Nature2020/experimentalCondition_Giordano_Nature2020.tsv @@ -1,7 +1,6 @@ -conditionId conditionName alpha_50 beta_50 gamma_50 delta_50 epsilon_50 zeta_50 eta_50 kappa_50 lam_50 mu_50 nu_50 xi_50 rho_50 sigma_50 -pred1 pred_NoChanges 0.21 0.005 0.11 0.005 0.2 0.025 0.025 0.02 0.08 0.08 0.015 0.02 0.02 0.01 -pred2 pred_LessSocDist 0.252 0.005 0.11 0.005 0.2 0.025 0.025 0.02 0.08 0.08 0.015 0.02 0.02 0.01 -pred3 pred_MoreSocDist 0.105 0.005 0.11 0.005 0.2 0.025 0.025 0.02 0.08 0.08 0.015 0.02 0.02 0.01 -pred4 pred_MoreTests 0.21 0.005 0.11 0.005 0.4 0.025 0.025 0.02 0.08 0.08 0.015 0.02 0.02 0.01 -pred5 pred_MoreTestsLessSocDist 0.42 0.005 0.11 0.005 0.6 0.025 0.025 0.02 0.08 0.08 0.015 0.02 0.02 0.01 - +conditionId conditionName alpha_50 beta_50 gamma_50 delta_50 epsilon_50 zeta_50 eta_50 kappa_50 lam_50 mu_50 nu_50 xi_50 rho_50 sigma_50 +pred1 pred_NoChanges 0.21 0.005 0.11 0.005 0.2 0.025 0.025 0.02 0.08 0.08 0.015 0.02 0.02 0.01 +pred2 pred_LessSocDist 0.252 0.005 0.11 0.005 0.2 0.025 0.025 0.02 0.08 0.08 0.015 0.02 0.02 0.01 +pred3 pred_MoreSocDist 0.105 0.005 0.11 0.005 0.2 0.025 0.025 0.02 0.08 0.08 0.015 0.02 0.02 0.01 +pred4 pred_MoreTests 0.21 0.005 0.11 0.005 0.4 0.025 0.025 0.02 0.08 0.08 0.015 0.02 0.02 0.01 +pred5 pred_MoreTestsLessSocDist 0.42 0.005 0.11 0.005 0.6 0.025 0.025 0.02 0.08 0.08 0.015 0.02 0.02 0.01 diff --git a/Benchmark-Models/Isensee_JCB2018/experimentalCondition_Isensee_JCB2018.tsv b/Benchmark-Models/Isensee_JCB2018/experimentalCondition_Isensee_JCB2018.tsv index c7f0c44f..1a441b34 100644 --- a/Benchmark-Models/Isensee_JCB2018/experimentalCondition_Isensee_JCB2018.tsv +++ b/Benchmark-Models/Isensee_JCB2018/experimentalCondition_Isensee_JCB2018.tsv @@ -1,124 +1,124 @@ -conditionId conditionName Fsk_level Fsk_time H89_level H89_time IBMX_level IBMX_time Rp8_Br_cAMPS_pAB_level Rp8_Br_cAMPS_pAB_incubation_time Rp8_pCPT_cAMPS_pAB_level Rp8_pCPT_cAMPS_pAB_incubation_time Rp_cAMPS_pAB_level Rp_cAMPS_pAB_incubation_time Sp8_Br_cAMPS_AM_level Sp8_Br_cAMPS_AM_time fourABnOH_level 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JI09_150302_Drg345_343_CycNuc__4_ABnOH_and_Fsk 10 60 0 0 0 0 0 0 0 0 0 0 0 0 1 59 +model1_data30 JI09_150302_Drg345_343_CycNuc__4_ABnOH_and_Fsk 10 60 0 0 0 0 0 0 0 0 0 0 0 0 1 60 +model1_data31 JI09_150302_Drg345_343_CycNuc__Rp8_Br_cAMPS_pAB_and_Fsk 10 60 0 0 0 0 10 0 0 0 0 0 0 0 0 0 +model1_data32 JI09_150302_Drg345_343_CycNuc__Rp8_Br_cAMPS_pAB_and_Fsk 10 60 0 0 0 0 10 30 0 0 0 0 0 0 0 0 +model1_data33 JI09_150302_Drg345_343_CycNuc__Rp8_Br_cAMPS_pAB_and_Fsk 10 60 0 0 0 0 10 45 0 0 0 0 0 0 0 0 +model1_data34 JI09_150302_Drg345_343_CycNuc__Rp8_Br_cAMPS_pAB_and_Fsk 10 60 0 0 0 0 10 55 0 0 0 0 0 0 0 0 +model1_data35 JI09_150302_Drg345_343_CycNuc__Rp8_Br_cAMPS_pAB_and_Fsk 10 60 0 0 0 0 10 59 0 0 0 0 0 0 0 0 +model1_data36 JI09_150302_Drg345_343_CycNuc__Rp8_Br_cAMPS_pAB_and_Fsk 10 60 0 0 0 0 10 60 0 0 0 0 0 0 0 0 +model1_data37 JI09_150302_Drg345_343_CycNuc__Rp8_pCPT_cAMPS_pAB_and_Fsk 10 60 0 0 0 0 0 0 10 0 0 0 0 0 0 0 +model1_data38 JI09_150302_Drg345_343_CycNuc__Rp8_pCPT_cAMPS_pAB_and_Fsk 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JI09_150330_Drg353_351_CycNuc__Rp8_pCPT_cAMPS_pAB_and_ctrl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +model1_data69 JI09_150330_Drg353_351_CycNuc__Rp8_pCPT_cAMPS_pAB_and_ctrl 0 0 0 0 0 0 0 0 0.016 0 0 0 0 0 0 0 +model1_data70 JI09_150330_Drg353_351_CycNuc__Rp8_pCPT_cAMPS_pAB_and_ctrl 0 0 0 0 0 0 0 0 0.08 0 0 0 0 0 0 0 +model1_data71 JI09_150330_Drg353_351_CycNuc__Rp8_pCPT_cAMPS_pAB_and_ctrl 0 0 0 0 0 0 0 0 0.4 0 0 0 0 0 0 0 +model1_data72 JI09_150330_Drg353_351_CycNuc__Rp8_pCPT_cAMPS_pAB_and_ctrl 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 +model1_data73 JI09_150330_Drg353_351_CycNuc__Rp8_pCPT_cAMPS_pAB_and_ctrl 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 +model1_data74 JI09_150330_Drg353_351_CycNuc__Rp8_pCPT_cAMPS_pAB_and_ctrl 0 0 0 0 0 0 0 0 50 0 0 0 0 0 0 0 +model1_data75 JI09_150330_Drg353_351_CycNuc__Rp_cAMPS_pAB_and_ctrl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +model1_data76 JI09_150330_Drg353_351_CycNuc__Rp_cAMPS_pAB_and_ctrl 0 0 0 0 0 0 0 0 0 0 0.016 0 0 0 0 0 +model1_data77 JI09_150330_Drg353_351_CycNuc__Rp_cAMPS_pAB_and_ctrl 0 0 0 0 0 0 0 0 0 0 0.08 0 0 0 0 0 +model1_data78 JI09_150330_Drg353_351_CycNuc__Rp_cAMPS_pAB_and_ctrl 0 0 0 0 0 0 0 0 0 0 0.4 0 0 0 0 0 +model1_data79 JI09_150330_Drg353_351_CycNuc__Rp_cAMPS_pAB_and_ctrl 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 +model1_data80 JI09_150330_Drg353_351_CycNuc__Rp_cAMPS_pAB_and_ctrl 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 +model1_data81 JI09_150330_Drg353_351_CycNuc__Rp_cAMPS_pAB_and_ctrl 0 0 0 0 0 0 0 0 0 0 50 0 0 0 0 0 +model1_data82 JI09_150330_Drg353_351_CycNuc__4_ABnOH_and_Fsk 10 30 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +model1_data83 JI09_150330_Drg353_351_CycNuc__4_ABnOH_and_Fsk 10 30 0 0 0 0 0 0 0 0 0 0 0 0 0.016 0 +model1_data84 JI09_150330_Drg353_351_CycNuc__4_ABnOH_and_Fsk 10 30 0 0 0 0 0 0 0 0 0 0 0 0 0.08 0 +model1_data85 JI09_150330_Drg353_351_CycNuc__4_ABnOH_and_Fsk 10 30 0 0 0 0 0 0 0 0 0 0 0 0 0.4 0 +model1_data86 JI09_150330_Drg353_351_CycNuc__4_ABnOH_and_Fsk 10 30 0 0 0 0 0 0 0 0 0 0 0 0 10 0 +model1_data87 JI09_150330_Drg353_351_CycNuc__4_ABnOH_and_Fsk 10 30 0 0 0 0 0 0 0 0 0 0 0 0 2 0 +model1_data88 JI09_150330_Drg353_351_CycNuc__4_ABnOH_and_Fsk 10 30 0 0 0 0 0 0 0 0 0 0 0 0 50 0 +model1_data89 JI09_150330_Drg353_351_CycNuc__Rp8_Br_cAMPS_pAB_and_Fsk 10 30 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +model1_data90 JI09_150330_Drg353_351_CycNuc__Rp8_Br_cAMPS_pAB_and_Fsk 10 30 0 0 0 0 0.016 0 0 0 0 0 0 0 0 0 +model1_data91 JI09_150330_Drg353_351_CycNuc__Rp8_Br_cAMPS_pAB_and_Fsk 10 30 0 0 0 0 0.08 0 0 0 0 0 0 0 0 0 +model1_data92 JI09_150330_Drg353_351_CycNuc__Rp8_Br_cAMPS_pAB_and_Fsk 10 30 0 0 0 0 0.4 0 0 0 0 0 0 0 0 0 +model1_data93 JI09_150330_Drg353_351_CycNuc__Rp8_Br_cAMPS_pAB_and_Fsk 10 30 0 0 0 0 10 0 0 0 0 0 0 0 0 0 +model1_data94 JI09_150330_Drg353_351_CycNuc__Rp8_Br_cAMPS_pAB_and_Fsk 10 30 0 0 0 0 2 0 0 0 0 0 0 0 0 0 +model1_data95 JI09_150330_Drg353_351_CycNuc__Rp8_Br_cAMPS_pAB_and_Fsk 10 30 0 0 0 0 50 0 0 0 0 0 0 0 0 0 +model1_data96 JI09_150330_Drg353_351_CycNuc__Rp8_pCPT_cAMPS_pAB_and_Fsk 10 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JI09_151102_Drg421_418_Age__H8910_and_Fsk3 3 60 10 0 0 0 0 0 0 0 0 0 0 0 0 0 +model1_data117 JI09_151102_Drg421_418_Age__H8925_and_Fsk3 3 60 25 0 0 0 0 0 0 0 0 0 0 0 0 0 +model1_data118 JI09_160201_Drg453_452_CycNuc__ctrl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +model1_data119 JI09_160201_Drg453_452_CycNuc__Fsk 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +model1_data120 JI09_160201_Drg453_452_CycNuc__Sp8_Br_cAMPS_AM 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0 +model1_data121 JI09_160126_Drg449_444_CycNuc__ctrl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +model1_data122 JI09_160126_Drg449_444_CycNuc__Fsk10_and_IBMX100 10 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 +model1_data123 JI09_160126_Drg449_444_CycNuc__Sp8_Br_cAMPS_AM10 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0 diff --git a/Benchmark-Models/Lang_PLOSComputBiol2024/experimentalCondition_Lang_PLOSComputBiol2024.tsv b/Benchmark-Models/Lang_PLOSComputBiol2024/experimentalCondition_Lang_PLOSComputBiol2024.tsv index 9ea81dcd..428e41f6 100644 --- a/Benchmark-Models/Lang_PLOSComputBiol2024/experimentalCondition_Lang_PLOSComputBiol2024.tsv +++ b/Benchmark-Models/Lang_PLOSComputBiol2024/experimentalCondition_Lang_PLOSComputBiol2024.tsv @@ -1,2 +1,2 @@ conditionId _Cyt__CCND _Cyt__CCNE_CDKN1A_B_ _Cyt__E2F_DBD_RB1_Ser332u_ _Cyt__E2F_DBD_RB1_Ser332p_ _Cyt__CCNA_CDKN1A_B_ _Cyt__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_ _Cyt__E2F_DBD_RB1_1_Ser332u__RB1_E2F_1_Ser807_Ser811u_ _Cyt__E2F_DBD_RB1_1_Ser332p__RB1_E2F_1_Ser807_Ser811u_ _Cyt__RB1_E2F_Ser807_Ser811u_ _Cyt__RB1_E2F_Ser807_Ser811p_ _Cyt__PPP2R2B_ENSA_ARPP19_ _Cyt__APC_FBXO5_FZR1_CDC20_Ser355u_ _Cyt__CDC20_APC_ _Cyt__APC_FBXO5_FZR1_CDC20_1_Ser355p__CDC20_APC_1_ _Cyt__APC_FBXO5_FZR1_CDC20_Ser355p_ _Cyt__APC_FBXO5_FZR1_CDC20_1_Ser355u__FZR1_APC_1_FBXO5_nTermu_ _Cyt__FZR1_APC_FBXO5_nTermu_ _Cyt__FZR1_APC_FBXO5_nTermp_ _Cyt__APC_FBXO5_1_FZR1_CDC20_2_Ser355u__FBXO5_APC_1_FZR1_3_Ser182u__FZR1_APC_2_FBXO5_3_nTermu_ _Cyt__FBXO5_APC_FZR1_Ser182u_ _Cyt__APC_FBXO5_1_FZR1_CDC20_2_Ser355p__FBXO5_APC_1_FZR1_3_Ser182u__FZR1_APC_2_FBXO5_3_nTermu_ _Cyt__APC_FBXO5_FZR1_CDC20_1_Ser355p__FZR1_APC_1_FBXO5_nTermu_ _Cyt__FBXO5_APC_FZR1_Ser182p_ _Cyt__FOXM1_DBD_Thr600u_ _Cyt__FOXM1_DBD_Thr600p_ _Cyt__WEE1_Ser123u_ _Cyt__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_ _Cyt__WEE1_Ser123p_ _Cyt__CDC25_pSitesp_ _Cyt__CDC25_pSitesu_ _Cyt__MASTL_Thr198u_ _Cyt__MASTL_Thr198p_ _Cyt__ENSA_ARPP19_PPP2R2B_Ser62_Ser67u_ _Cyt__ENSA_ARPP19_PPP2R2B_Ser62_Ser67p_ _Cyt__ENSA_ARPP19_PPP2R2B_1_Ser62_Ser67p__PPP2R2B_ENSA_ARPP19_1_ _Cyt__SKP2 _Cyt__TP53_DBD_Ser15p_ _Cyt__FOXO_DBD_ _Num__NUP_pSitesu_ _Nuc__CCND _Nuc__CCNE_CDKN1A_B_ _Nuc__E2F_DBD_RB1_Ser332u_ _Nuc__E2F_DBD_RB1_Ser332p_ _Nuc__CCNA_CDKN1A_B_ _Nuc__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_ _Nuc__E2F_DBD_RB1_1_Ser332u__RB1_E2F_1_Ser807_Ser811u_ _Nuc__E2F_DBD_RB1_1_Ser332p__RB1_E2F_1_Ser807_Ser811u_ _Nuc__RB1_E2F_Ser807_Ser811u_ _Nuc__RB1_E2F_Ser807_Ser811p_ _Nuc__PPP2R2B_ENSA_ARPP19_ _Nuc__APC_FBXO5_FZR1_CDC20_Ser355u_ _Nuc__CDC20_APC_ _Nuc__APC_FBXO5_FZR1_CDC20_1_Ser355p__CDC20_APC_1_ _Nuc__APC_FBXO5_FZR1_CDC20_Ser355p_ _Nuc__APC_FBXO5_FZR1_CDC20_1_Ser355u__FZR1_APC_1_FBXO5_nTermu_ _Nuc__FZR1_APC_FBXO5_nTermu_ _Nuc__FZR1_APC_FBXO5_nTermp_ _Nuc__APC_FBXO5_1_FZR1_CDC20_2_Ser355u__FBXO5_APC_1_FZR1_3_Ser182u__FZR1_APC_2_FBXO5_3_nTermu_ _Nuc__FBXO5_APC_FZR1_Ser182u_ _Nuc__APC_FBXO5_1_FZR1_CDC20_2_Ser355p__FBXO5_APC_1_FZR1_3_Ser182u__FZR1_APC_2_FBXO5_3_nTermu_ _Nuc__APC_FBXO5_FZR1_CDC20_1_Ser355p__FZR1_APC_1_FBXO5_nTermu_ _Nuc__FBXO5_APC_FZR1_Ser182p_ _Nuc__FOXM1_DBD_Thr600u_ _Nuc__FOXM1_DBD_Thr600p_ _Nuc__CCNB_promoter_FOXM1_1__FOXM1_DBD_1_Thr600p_ _Nuc__CCNB_promoter_FOXM1_ _Nuc__CDC20_promoter_FOXM1_ _Nuc__CDC20_promoter_FOXM1_1__FOXM1_DBD_1_Thr600p_ _Nuc__WEE1_Ser123u_ _Nuc__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_ _Nuc__WEE1_Ser123p_ _Nuc__CDC25_pSitesp_ _Nuc__CDC25_pSitesu_ _Nuc__MASTL_Thr198u_ _Nuc__MASTL_Thr198p_ _Nuc__ENSA_ARPP19_PPP2R2B_Ser62_Ser67u_ _Nuc__ENSA_ARPP19_PPP2R2B_Ser62_Ser67p_ _Nuc__ENSA_ARPP19_PPP2R2B_1_Ser62_Ser67p__PPP2R2B_ENSA_ARPP19_1_ _Nuc__CCNE_promoter_E2F_ _Nuc__CCNA_promoter_E2F_ _Nuc__E2F_promoter_E2F_ _Nuc__FBXO5_promoter_E2F_ _Nuc__FOXM1_promoter_E2F_ _Nuc__CCNE_promoter_E2F_1__E2F_DBD_1_RB1_Ser332u_ _Nuc__CCNA_promoter_E2F_1__E2F_DBD_1_RB1_Ser332u_ _Nuc__E2F_DBD_1_RB1_Ser332u__E2F_promoter_E2F_1_ _Nuc__E2F_DBD_1_RB1_Ser332u__FBXO5_promoter_E2F_1_ _Nuc__E2F_DBD_1_RB1_Ser332u__FOXM1_promoter_E2F_1_ _Nuc__CCNE_promoter_E2F_1__E2F_DBD_1_RB1_Ser332p_ _Nuc__CCNA_promoter_E2F_1__E2F_DBD_1_RB1_Ser332p_ _Nuc__E2F_DBD_1_RB1_Ser332p__E2F_promoter_E2F_1_ _Nuc__E2F_DBD_1_RB1_Ser332p__FBXO5_promoter_E2F_1_ _Nuc__E2F_DBD_1_RB1_Ser332p__FOXM1_promoter_E2F_1_ _Nuc__SKP2 _Nuc__TP53_DBD_Ser15p_ _Nuc__CDKN1A_promoter_TP53_ _Nuc__FOXO_DBD_ _Nuc__CDKN1B_promoter_FOXO_ _Nuc__CDKN1A_promoter_TP53_1__TP53_DBD_1_Ser15p_ _Cyt__CDKN1A_CCNE_A_B_Ser130u_ _Nuc__CDKN1B_promoter_FOXO_1__FOXO_DBD_1_ _Cyt__CDKN1B_CCNE_A_Thr187u_ _Cyt__CCNA_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ _Cyt__CCNE_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ _Cyt__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ _Cyt__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ _Cyt__CDKN1A_CCNE_A_B_Ser130p_ _Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ _Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ _Cyt__CDKN1B_CCNE_A_Thr187p_ _Nuc__CDKN1A_CCNE_A_B_Ser130u_ _Nuc__CDKN1B_CCNE_A_Thr187u_ _Nuc__CCNA_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ _Nuc__CCNE_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ _Nuc__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ _Nuc__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ _Nuc__CDKN1A_CCNE_A_B_Ser130p_ _Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ _Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ _Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ _Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ _Nuc__CDKN1B_CCNE_A_Thr187p_ _Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ _Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ -wt ic_wt_Cyt__CCND ic_wt_Cyt__CCNE_CDKN1A_B_ ic_wt_Cyt__E2F_DBD_RB1_Ser332u_ ic_wt_Cyt__E2F_DBD_RB1_Ser332p_ ic_wt_Cyt__CCNA_CDKN1A_B_ ic_wt_Cyt__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_ ic_wt_Cyt__E2F_DBD_RB1_1_Ser332u__RB1_E2F_1_Ser807_Ser811u_ ic_wt_Cyt__E2F_DBD_RB1_1_Ser332p__RB1_E2F_1_Ser807_Ser811u_ ic_wt_Cyt__RB1_E2F_Ser807_Ser811u_ ic_wt_Cyt__RB1_E2F_Ser807_Ser811p_ ic_wt_Cyt__PPP2R2B_ENSA_ARPP19_ ic_wt_Cyt__APC_FBXO5_FZR1_CDC20_Ser355u_ ic_wt_Cyt__CDC20_APC_ ic_wt_Cyt__APC_FBXO5_FZR1_CDC20_1_Ser355p__CDC20_APC_1_ ic_wt_Cyt__APC_FBXO5_FZR1_CDC20_Ser355p_ ic_wt_Cyt__APC_FBXO5_FZR1_CDC20_1_Ser355u__FZR1_APC_1_FBXO5_nTermu_ ic_wt_Cyt__FZR1_APC_FBXO5_nTermu_ ic_wt_Cyt__FZR1_APC_FBXO5_nTermp_ ic_wt_Cyt__APC_FBXO5_1_FZR1_CDC20_2_Ser355u__FBXO5_APC_1_FZR1_3_Ser182u__FZR1_APC_2_FBXO5_3_nTermu_ ic_wt_Cyt__FBXO5_APC_FZR1_Ser182u_ ic_wt_Cyt__APC_FBXO5_1_FZR1_CDC20_2_Ser355p__FBXO5_APC_1_FZR1_3_Ser182u__FZR1_APC_2_FBXO5_3_nTermu_ ic_wt_Cyt__APC_FBXO5_FZR1_CDC20_1_Ser355p__FZR1_APC_1_FBXO5_nTermu_ ic_wt_Cyt__FBXO5_APC_FZR1_Ser182p_ ic_wt_Cyt__FOXM1_DBD_Thr600u_ ic_wt_Cyt__FOXM1_DBD_Thr600p_ ic_wt_Cyt__WEE1_Ser123u_ ic_wt_Cyt__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_ ic_wt_Cyt__WEE1_Ser123p_ ic_wt_Cyt__CDC25_pSitesp_ ic_wt_Cyt__CDC25_pSitesu_ ic_wt_Cyt__MASTL_Thr198u_ ic_wt_Cyt__MASTL_Thr198p_ ic_wt_Cyt__ENSA_ARPP19_PPP2R2B_Ser62_Ser67u_ ic_wt_Cyt__ENSA_ARPP19_PPP2R2B_Ser62_Ser67p_ ic_wt_Cyt__ENSA_ARPP19_PPP2R2B_1_Ser62_Ser67p__PPP2R2B_ENSA_ARPP19_1_ ic_wt_Cyt__SKP2 ic_wt_Cyt__TP53_DBD_Ser15p_ ic_wt_Cyt__FOXO_DBD_ ic_wt_Num__NUP_pSitesu_ ic_wt_Nuc__CCND ic_wt_Nuc__CCNE_CDKN1A_B_ ic_wt_Nuc__E2F_DBD_RB1_Ser332u_ ic_wt_Nuc__E2F_DBD_RB1_Ser332p_ ic_wt_Nuc__CCNA_CDKN1A_B_ ic_wt_Nuc__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_ ic_wt_Nuc__E2F_DBD_RB1_1_Ser332u__RB1_E2F_1_Ser807_Ser811u_ ic_wt_Nuc__E2F_DBD_RB1_1_Ser332p__RB1_E2F_1_Ser807_Ser811u_ ic_wt_Nuc__RB1_E2F_Ser807_Ser811u_ ic_wt_Nuc__RB1_E2F_Ser807_Ser811p_ ic_wt_Nuc__PPP2R2B_ENSA_ARPP19_ ic_wt_Nuc__APC_FBXO5_FZR1_CDC20_Ser355u_ ic_wt_Nuc__CDC20_APC_ ic_wt_Nuc__APC_FBXO5_FZR1_CDC20_1_Ser355p__CDC20_APC_1_ ic_wt_Nuc__APC_FBXO5_FZR1_CDC20_Ser355p_ ic_wt_Nuc__APC_FBXO5_FZR1_CDC20_1_Ser355u__FZR1_APC_1_FBXO5_nTermu_ ic_wt_Nuc__FZR1_APC_FBXO5_nTermu_ ic_wt_Nuc__FZR1_APC_FBXO5_nTermp_ ic_wt_Nuc__APC_FBXO5_1_FZR1_CDC20_2_Ser355u__FBXO5_APC_1_FZR1_3_Ser182u__FZR1_APC_2_FBXO5_3_nTermu_ ic_wt_Nuc__FBXO5_APC_FZR1_Ser182u_ ic_wt_Nuc__APC_FBXO5_1_FZR1_CDC20_2_Ser355p__FBXO5_APC_1_FZR1_3_Ser182u__FZR1_APC_2_FBXO5_3_nTermu_ ic_wt_Nuc__APC_FBXO5_FZR1_CDC20_1_Ser355p__FZR1_APC_1_FBXO5_nTermu_ ic_wt_Nuc__FBXO5_APC_FZR1_Ser182p_ ic_wt_Nuc__FOXM1_DBD_Thr600u_ ic_wt_Nuc__FOXM1_DBD_Thr600p_ ic_wt_Nuc__CCNB_promoter_FOXM1_1__FOXM1_DBD_1_Thr600p_ ic_wt_Nuc__CCNB_promoter_FOXM1_ ic_wt_Nuc__CDC20_promoter_FOXM1_ ic_wt_Nuc__CDC20_promoter_FOXM1_1__FOXM1_DBD_1_Thr600p_ ic_wt_Nuc__WEE1_Ser123u_ ic_wt_Nuc__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_ ic_wt_Nuc__WEE1_Ser123p_ ic_wt_Nuc__CDC25_pSitesp_ ic_wt_Nuc__CDC25_pSitesu_ ic_wt_Nuc__MASTL_Thr198u_ ic_wt_Nuc__MASTL_Thr198p_ ic_wt_Nuc__ENSA_ARPP19_PPP2R2B_Ser62_Ser67u_ ic_wt_Nuc__ENSA_ARPP19_PPP2R2B_Ser62_Ser67p_ ic_wt_Nuc__ENSA_ARPP19_PPP2R2B_1_Ser62_Ser67p__PPP2R2B_ENSA_ARPP19_1_ ic_wt_Nuc__CCNE_promoter_E2F_ ic_wt_Nuc__CCNA_promoter_E2F_ ic_wt_Nuc__E2F_promoter_E2F_ ic_wt_Nuc__FBXO5_promoter_E2F_ ic_wt_Nuc__FOXM1_promoter_E2F_ ic_wt_Nuc__CCNE_promoter_E2F_1__E2F_DBD_1_RB1_Ser332u_ ic_wt_Nuc__CCNA_promoter_E2F_1__E2F_DBD_1_RB1_Ser332u_ ic_wt_Nuc__E2F_DBD_1_RB1_Ser332u__E2F_promoter_E2F_1_ ic_wt_Nuc__E2F_DBD_1_RB1_Ser332u__FBXO5_promoter_E2F_1_ ic_wt_Nuc__E2F_DBD_1_RB1_Ser332u__FOXM1_promoter_E2F_1_ ic_wt_Nuc__CCNE_promoter_E2F_1__E2F_DBD_1_RB1_Ser332p_ ic_wt_Nuc__CCNA_promoter_E2F_1__E2F_DBD_1_RB1_Ser332p_ ic_wt_Nuc__E2F_DBD_1_RB1_Ser332p__E2F_promoter_E2F_1_ ic_wt_Nuc__E2F_DBD_1_RB1_Ser332p__FBXO5_promoter_E2F_1_ ic_wt_Nuc__E2F_DBD_1_RB1_Ser332p__FOXM1_promoter_E2F_1_ ic_wt_Nuc__SKP2 ic_wt_Nuc__TP53_DBD_Ser15p_ ic_wt_Nuc__CDKN1A_promoter_TP53_ ic_wt_Nuc__FOXO_DBD_ ic_wt_Nuc__CDKN1B_promoter_FOXO_ ic_wt_Nuc__CDKN1A_promoter_TP53_1__TP53_DBD_1_Ser15p_ ic_wt_Cyt__CDKN1A_CCNE_A_B_Ser130u_ ic_wt_Nuc__CDKN1B_promoter_FOXO_1__FOXO_DBD_1_ ic_wt_Cyt__CDKN1B_CCNE_A_Thr187u_ ic_wt_Cyt__CCNA_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ ic_wt_Cyt__CCNE_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ ic_wt_Cyt__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ ic_wt_Cyt__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ ic_wt_Cyt__CDKN1A_CCNE_A_B_Ser130p_ ic_wt_Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ ic_wt_Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ ic_wt_Cyt__CDKN1B_CCNE_A_Thr187p_ ic_wt_Nuc__CDKN1A_CCNE_A_B_Ser130u_ ic_wt_Nuc__CDKN1B_CCNE_A_Thr187u_ ic_wt_Nuc__CCNA_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ ic_wt_Nuc__CCNE_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ ic_wt_Nuc__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ ic_wt_Nuc__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ ic_wt_Nuc__CDKN1A_CCNE_A_B_Ser130p_ ic_wt_Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ ic_wt_Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ ic_wt_Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ ic_wt_Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ ic_wt_Nuc__CDKN1B_CCNE_A_Thr187p_ ic_wt_Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ ic_wt_Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ \ No newline at end of file +wt ic_wt_Cyt__CCND ic_wt_Cyt__CCNE_CDKN1A_B_ ic_wt_Cyt__E2F_DBD_RB1_Ser332u_ ic_wt_Cyt__E2F_DBD_RB1_Ser332p_ ic_wt_Cyt__CCNA_CDKN1A_B_ ic_wt_Cyt__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_ ic_wt_Cyt__E2F_DBD_RB1_1_Ser332u__RB1_E2F_1_Ser807_Ser811u_ ic_wt_Cyt__E2F_DBD_RB1_1_Ser332p__RB1_E2F_1_Ser807_Ser811u_ ic_wt_Cyt__RB1_E2F_Ser807_Ser811u_ ic_wt_Cyt__RB1_E2F_Ser807_Ser811p_ ic_wt_Cyt__PPP2R2B_ENSA_ARPP19_ ic_wt_Cyt__APC_FBXO5_FZR1_CDC20_Ser355u_ ic_wt_Cyt__CDC20_APC_ ic_wt_Cyt__APC_FBXO5_FZR1_CDC20_1_Ser355p__CDC20_APC_1_ ic_wt_Cyt__APC_FBXO5_FZR1_CDC20_Ser355p_ ic_wt_Cyt__APC_FBXO5_FZR1_CDC20_1_Ser355u__FZR1_APC_1_FBXO5_nTermu_ ic_wt_Cyt__FZR1_APC_FBXO5_nTermu_ ic_wt_Cyt__FZR1_APC_FBXO5_nTermp_ ic_wt_Cyt__APC_FBXO5_1_FZR1_CDC20_2_Ser355u__FBXO5_APC_1_FZR1_3_Ser182u__FZR1_APC_2_FBXO5_3_nTermu_ ic_wt_Cyt__FBXO5_APC_FZR1_Ser182u_ ic_wt_Cyt__APC_FBXO5_1_FZR1_CDC20_2_Ser355p__FBXO5_APC_1_FZR1_3_Ser182u__FZR1_APC_2_FBXO5_3_nTermu_ ic_wt_Cyt__APC_FBXO5_FZR1_CDC20_1_Ser355p__FZR1_APC_1_FBXO5_nTermu_ ic_wt_Cyt__FBXO5_APC_FZR1_Ser182p_ ic_wt_Cyt__FOXM1_DBD_Thr600u_ ic_wt_Cyt__FOXM1_DBD_Thr600p_ ic_wt_Cyt__WEE1_Ser123u_ ic_wt_Cyt__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_ ic_wt_Cyt__WEE1_Ser123p_ ic_wt_Cyt__CDC25_pSitesp_ ic_wt_Cyt__CDC25_pSitesu_ ic_wt_Cyt__MASTL_Thr198u_ ic_wt_Cyt__MASTL_Thr198p_ ic_wt_Cyt__ENSA_ARPP19_PPP2R2B_Ser62_Ser67u_ ic_wt_Cyt__ENSA_ARPP19_PPP2R2B_Ser62_Ser67p_ ic_wt_Cyt__ENSA_ARPP19_PPP2R2B_1_Ser62_Ser67p__PPP2R2B_ENSA_ARPP19_1_ ic_wt_Cyt__SKP2 ic_wt_Cyt__TP53_DBD_Ser15p_ ic_wt_Cyt__FOXO_DBD_ ic_wt_Num__NUP_pSitesu_ ic_wt_Nuc__CCND ic_wt_Nuc__CCNE_CDKN1A_B_ ic_wt_Nuc__E2F_DBD_RB1_Ser332u_ ic_wt_Nuc__E2F_DBD_RB1_Ser332p_ ic_wt_Nuc__CCNA_CDKN1A_B_ ic_wt_Nuc__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_ ic_wt_Nuc__E2F_DBD_RB1_1_Ser332u__RB1_E2F_1_Ser807_Ser811u_ ic_wt_Nuc__E2F_DBD_RB1_1_Ser332p__RB1_E2F_1_Ser807_Ser811u_ ic_wt_Nuc__RB1_E2F_Ser807_Ser811u_ ic_wt_Nuc__RB1_E2F_Ser807_Ser811p_ ic_wt_Nuc__PPP2R2B_ENSA_ARPP19_ ic_wt_Nuc__APC_FBXO5_FZR1_CDC20_Ser355u_ ic_wt_Nuc__CDC20_APC_ ic_wt_Nuc__APC_FBXO5_FZR1_CDC20_1_Ser355p__CDC20_APC_1_ ic_wt_Nuc__APC_FBXO5_FZR1_CDC20_Ser355p_ ic_wt_Nuc__APC_FBXO5_FZR1_CDC20_1_Ser355u__FZR1_APC_1_FBXO5_nTermu_ ic_wt_Nuc__FZR1_APC_FBXO5_nTermu_ ic_wt_Nuc__FZR1_APC_FBXO5_nTermp_ ic_wt_Nuc__APC_FBXO5_1_FZR1_CDC20_2_Ser355u__FBXO5_APC_1_FZR1_3_Ser182u__FZR1_APC_2_FBXO5_3_nTermu_ ic_wt_Nuc__FBXO5_APC_FZR1_Ser182u_ ic_wt_Nuc__APC_FBXO5_1_FZR1_CDC20_2_Ser355p__FBXO5_APC_1_FZR1_3_Ser182u__FZR1_APC_2_FBXO5_3_nTermu_ ic_wt_Nuc__APC_FBXO5_FZR1_CDC20_1_Ser355p__FZR1_APC_1_FBXO5_nTermu_ ic_wt_Nuc__FBXO5_APC_FZR1_Ser182p_ ic_wt_Nuc__FOXM1_DBD_Thr600u_ ic_wt_Nuc__FOXM1_DBD_Thr600p_ ic_wt_Nuc__CCNB_promoter_FOXM1_1__FOXM1_DBD_1_Thr600p_ ic_wt_Nuc__CCNB_promoter_FOXM1_ ic_wt_Nuc__CDC20_promoter_FOXM1_ ic_wt_Nuc__CDC20_promoter_FOXM1_1__FOXM1_DBD_1_Thr600p_ ic_wt_Nuc__WEE1_Ser123u_ ic_wt_Nuc__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_ ic_wt_Nuc__WEE1_Ser123p_ ic_wt_Nuc__CDC25_pSitesp_ ic_wt_Nuc__CDC25_pSitesu_ ic_wt_Nuc__MASTL_Thr198u_ ic_wt_Nuc__MASTL_Thr198p_ ic_wt_Nuc__ENSA_ARPP19_PPP2R2B_Ser62_Ser67u_ ic_wt_Nuc__ENSA_ARPP19_PPP2R2B_Ser62_Ser67p_ ic_wt_Nuc__ENSA_ARPP19_PPP2R2B_1_Ser62_Ser67p__PPP2R2B_ENSA_ARPP19_1_ ic_wt_Nuc__CCNE_promoter_E2F_ ic_wt_Nuc__CCNA_promoter_E2F_ ic_wt_Nuc__E2F_promoter_E2F_ ic_wt_Nuc__FBXO5_promoter_E2F_ ic_wt_Nuc__FOXM1_promoter_E2F_ ic_wt_Nuc__CCNE_promoter_E2F_1__E2F_DBD_1_RB1_Ser332u_ ic_wt_Nuc__CCNA_promoter_E2F_1__E2F_DBD_1_RB1_Ser332u_ ic_wt_Nuc__E2F_DBD_1_RB1_Ser332u__E2F_promoter_E2F_1_ ic_wt_Nuc__E2F_DBD_1_RB1_Ser332u__FBXO5_promoter_E2F_1_ ic_wt_Nuc__E2F_DBD_1_RB1_Ser332u__FOXM1_promoter_E2F_1_ ic_wt_Nuc__CCNE_promoter_E2F_1__E2F_DBD_1_RB1_Ser332p_ ic_wt_Nuc__CCNA_promoter_E2F_1__E2F_DBD_1_RB1_Ser332p_ ic_wt_Nuc__E2F_DBD_1_RB1_Ser332p__E2F_promoter_E2F_1_ ic_wt_Nuc__E2F_DBD_1_RB1_Ser332p__FBXO5_promoter_E2F_1_ ic_wt_Nuc__E2F_DBD_1_RB1_Ser332p__FOXM1_promoter_E2F_1_ ic_wt_Nuc__SKP2 ic_wt_Nuc__TP53_DBD_Ser15p_ ic_wt_Nuc__CDKN1A_promoter_TP53_ ic_wt_Nuc__FOXO_DBD_ ic_wt_Nuc__CDKN1B_promoter_FOXO_ ic_wt_Nuc__CDKN1A_promoter_TP53_1__TP53_DBD_1_Ser15p_ ic_wt_Cyt__CDKN1A_CCNE_A_B_Ser130u_ ic_wt_Nuc__CDKN1B_promoter_FOXO_1__FOXO_DBD_1_ ic_wt_Cyt__CDKN1B_CCNE_A_Thr187u_ ic_wt_Cyt__CCNA_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ ic_wt_Cyt__CCNE_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ ic_wt_Cyt__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ ic_wt_Cyt__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ ic_wt_Cyt__CDKN1A_CCNE_A_B_Ser130p_ ic_wt_Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ ic_wt_Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ ic_wt_Cyt__CDKN1B_CCNE_A_Thr187p_ ic_wt_Nuc__CDKN1A_CCNE_A_B_Ser130u_ ic_wt_Nuc__CDKN1B_CCNE_A_Thr187u_ ic_wt_Nuc__CCNA_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ ic_wt_Nuc__CCNE_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ ic_wt_Nuc__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ ic_wt_Nuc__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ ic_wt_Nuc__CDKN1A_CCNE_A_B_Ser130p_ ic_wt_Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ ic_wt_Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ ic_wt_Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ ic_wt_Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ ic_wt_Nuc__CDKN1B_CCNE_A_Thr187p_ ic_wt_Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ ic_wt_Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ diff --git a/Benchmark-Models/Lang_PLOSComputBiol2024/observables_Lang_PLOSComputBiol2024.tsv b/Benchmark-Models/Lang_PLOSComputBiol2024/observables_Lang_PLOSComputBiol2024.tsv index 6f1c7cb9..fe88a2f9 100644 --- a/Benchmark-Models/Lang_PLOSComputBiol2024/observables_Lang_PLOSComputBiol2024.tsv +++ b/Benchmark-Models/Lang_PLOSComputBiol2024/observables_Lang_PLOSComputBiol2024.tsv @@ -14,4 +14,4 @@ obs_E2F1__cyt_median oE2F + sE2F * (_Cyt__E2F_DBD_RB1_Ser332u_ + _Cyt__E2F_DBD_ obs_pRB__cyt_median oRB1_pSer807Ser811 + sRB1_pSer807Ser811 * (_Cyt__RB1_E2F_Ser807_Ser811p_) noiseParameter1 + noiseParameter2_pRB_cyt * (oRB1_pSer807Ser811 + sRB1_pSer807Ser811 * (_Cyt__RB1_E2F_Ser807_Ser811p_)) lin normal obs_Skp2__cyt_median oSKP2 + sSKP2 * _Cyt__SKP2 noiseParameter1 + noiseParameter2_Skp2_cyt * (oSKP2 + sSKP2 * _Cyt__SKP2) lin normal obs_p21__cyt_median oCDKN1A + sCDKN1A * (_Cyt__CDKN1A_CCNE_A_B_Ser130u_ + _Cyt__CCNA_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Cyt__CCNE_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Cyt__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Cyt__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Cyt__CDKN1A_CCNE_A_B_Ser130p_) noiseParameter1 + noiseParameter2_p21_cyt * (oCDKN1A + sCDKN1A * (_Cyt__CDKN1A_CCNE_A_B_Ser130u_ + _Cyt__CCNA_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Cyt__CCNE_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Cyt__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Cyt__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ + _Cyt__CDKN1A_CCNE_A_B_Ser130p_)) lin normal -obs_p27__cyt_median oCDKN1B + sCDKN1B * (_Cyt__CDKN1B_CCNE_A_Thr187u_ + _Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ + _Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ + _Cyt__CDKN1B_CCNE_A_Thr187p_ + _Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ + _Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_) noiseParameter1 + noiseParameter2_p27_cyt * (oCDKN1B + sCDKN1B * (_Cyt__CDKN1B_CCNE_A_Thr187u_ + _Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ + _Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ + _Cyt__CDKN1B_CCNE_A_Thr187p_ + _Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ + _Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_)) lin normal \ No newline at end of file +obs_p27__cyt_median oCDKN1B + sCDKN1B * (_Cyt__CDKN1B_CCNE_A_Thr187u_ + _Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ + _Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ + _Cyt__CDKN1B_CCNE_A_Thr187p_ + _Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ + _Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_) noiseParameter1 + noiseParameter2_p27_cyt * (oCDKN1B + sCDKN1B * (_Cyt__CDKN1B_CCNE_A_Thr187u_ + _Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ + _Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ + _Cyt__CDKN1B_CCNE_A_Thr187p_ + _Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ + _Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_)) lin normal diff --git a/Benchmark-Models/Liu_IFACPapersOnLine2025/measurements.tsv b/Benchmark-Models/Liu_IFACPapersOnLine2025/measurements.tsv index 051a99ea..01c379d0 100644 --- a/Benchmark-Models/Liu_IFACPapersOnLine2025/measurements.tsv +++ b/Benchmark-Models/Liu_IFACPapersOnLine2025/measurements.tsv @@ -98,4 +98,4 @@ tumor_num ctrl 1026.0423760760882 4 control tumor_num ctrl 1531.6539940728533 4 control tumor_num ctrl 1700.1226867227788 4 control tumor_num ctrl 1470.1280053147707 4 control -tumor_num ctrl 1876.6258001727879 4 control \ No newline at end of file +tumor_num ctrl 1876.6258001727879 4 control diff --git a/Benchmark-Models/Lucarelli_CellSystems2018/experimentalCondition_Lucarelli_CellSystems2018.tsv b/Benchmark-Models/Lucarelli_CellSystems2018/experimentalCondition_Lucarelli_CellSystems2018.tsv index edd92ef3..cd583f0c 100644 --- a/Benchmark-Models/Lucarelli_CellSystems2018/experimentalCondition_Lucarelli_CellSystems2018.tsv +++ b/Benchmark-Models/Lucarelli_CellSystems2018/experimentalCondition_Lucarelli_CellSystems2018.tsv @@ -1,17 +1,17 @@ -conditionId conditionName init_S2 init_S3 init_S4 init_TGFb -model1_data1 S2tot S3tot S4tot 0 -model1_data2 S2tot S3tot S4tot 0.1 -model1_data3 S2tot S3tot S4tot 1 -model1_data4 S2tot S3tot S4tot 1 -model1_data5 S2tot S3tot S4tot 0 -model1_data6 S2tot S3tot S4tot 1 -model1_data7 S2tot S3tot S4tot 0 -model1_data8 142.34 14.234 208.41 0 -model1_data9 142.34 14.234 69.47 0 -model1_data10 142.34 227.744 69.47 0 -model1_data11 284.68 14.234 69.47 0 -model1_data12 142.34 14.234 208.41 1 -model1_data13 142.34 14.234 69.47 1 -model1_data14 142.34 227.744 69.47 1 -model1_data15 284.68 14.234 69.47 1 -model1_data16 142.34 S3tot 69.47 1 +conditionId conditionName init_S2 init_S3 init_S4 init_TGFb +model1_data1 S2tot S3tot S4tot 0 +model1_data2 S2tot S3tot S4tot 0.1 +model1_data3 S2tot S3tot S4tot 1 +model1_data4 S2tot S3tot S4tot 1 +model1_data5 S2tot S3tot S4tot 0 +model1_data6 S2tot S3tot S4tot 1 +model1_data7 S2tot S3tot S4tot 0 +model1_data8 142.34 14.234 208.41 0 +model1_data9 142.34 14.234 69.47 0 +model1_data10 142.34 227.744 69.47 0 +model1_data11 284.68 14.234 69.47 0 +model1_data12 142.34 14.234 208.41 1 +model1_data13 142.34 14.234 69.47 1 +model1_data14 142.34 227.744 69.47 1 +model1_data15 284.68 14.234 69.47 1 +model1_data16 142.34 S3tot 69.47 1 diff --git a/Benchmark-Models/Lucarelli_CellSystems2018/observables_Lucarelli_CellSystems2018.tsv b/Benchmark-Models/Lucarelli_CellSystems2018/observables_Lucarelli_CellSystems2018.tsv index affc759d..e1683e35 100644 --- a/Benchmark-Models/Lucarelli_CellSystems2018/observables_Lucarelli_CellSystems2018.tsv +++ b/Benchmark-Models/Lucarelli_CellSystems2018/observables_Lucarelli_CellSystems2018.tsv @@ -1,66 +1,66 @@ -observableId observableName observableFormula observableTransformation noiseFormula -Bmp4_gene_expression_OE_nExpID100 Bmp4 geneH + 0.000001 log10 sd_Bmp4_nExpID100 -Cxcl15_gene_expression_OE_nExpID100 Cxcl15 geneI + 0.000001 log10 sd_Cxcl15_nExpID100 -Dnmt3a_gene_expression_OE_nExpID100 Dnmt3a geneC + 0.000001 log10 sd_Dnmt3a_nExpID100 -Dusp5_gene_expression_OE_nExpID100 Dusp5 geneJ + 0.000001 log10 sd_Dusp5_nExpID100 -Jun_gene_expression_OE_nExpID100 Jun geneE + 0.000001 log10 sd_Jun_nExpID100 -Klf10_gene_expression_OE_nExpID100 Klf10 geneG + 0.000001 log10 sd_Klf10_nExpID100 -Pdk4_gene_expression_OE_nExpID100 Pdk4 geneL + 0.000001 log10 sd_Pdk4_nExpID100 -S23IP_S2_MSPL2_PL_hepa16_pS2_pS3_time_course_nExpID5 S23IP_S2 (100*(S2 + S2_S4_S4))/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) lin 5 -S23IP_S2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S23IP_S2 (100*(S2 + S2_S4_S4))/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) lin 5 -S23IP_S3_MSPL2_PL_hepa16_pS2_pS3_time_course_nExpID5 S23IP_S3 (100*S3)/(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 -S23IP_S3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S23IP_S3 (100*S3)/(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 -S23IP_pS2_MSPL2_PL_hepa16_pS2_pS3_time_course_nExpID5 S23IP_pS2 (100*pS2)/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) lin 5 -S23IP_pS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S23IP_pS2 (100*pS2)/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) lin 5 -S23IP_pS3_MSPL2_PL_hepa16_pS2_pS3_time_course_nExpID5 S23IP_pS3 (100*pS3)/(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 -S23IP_pS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S23IP_pS3 (100*pS3)/(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 -S23IP_ppS2_MSPL2_PL_hepa16_pS2_pS3_time_course_nExpID5 S23IP_ppS2 (100*(ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3))/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) lin 5 -S23IP_ppS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S23IP_ppS2 (100*(ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3))/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) lin 5 -S23IP_ppS3_MSPL2_PL_hepa16_pS2_pS3_time_course_nExpID5 S23IP_ppS3 (100*(ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3))/(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 -S23IP_ppS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S23IP_ppS3 (100*(ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3))/(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 -S23IP_tS2_MSPL2_PL_PN_molecules_per_cell_hepa16_nExpID1 S23IP_tS2 S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3 lin 15 -S23IP_tS2_MSPL2_PL_PN_molecules_per_cell_hepa16_ratios_nExpID10 S23IP_tS2 (100*(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3))/(S2 + S3 + S2_S4_S4 + pS2 + pS3 + ppS2 + ppS3 + ppS2_S4_S4 + ppS3_S4_S4 + 2*ppS2_ppS2_S4 + 2*ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 1 -S23IP_tS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S23IP_tS2 (100*(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3))/(S2 + S3 + 3*S2_S4_S4 + pS2 + pS3 + ppS2 + ppS3 + 3*ppS2_S4_S4 + 3*ppS3_S4_S4 + 3*ppS2_ppS2_S4 + 4*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 -S23IP_tS3_MSPL2_PL_PN_molecules_per_cell_hepa16_ratios_nExpID10 S23IP_tS3 (100*(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3))/(S2 + S3 + S2_S4_S4 + pS2 + pS3 + ppS2 + ppS3 + ppS2_S4_S4 + ppS3_S4_S4 + 2*ppS2_ppS2_S4 + 2*ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 1 -S23IP_tS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S23IP_tS3 (100*(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3))/(S2 + S3 + 3*S2_S4_S4 + pS2 + pS3 + ppS2 + ppS3 + 3*ppS2_S4_S4 + 3*ppS3_S4_S4 + 3*ppS2_ppS2_S4 + 4*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 -S23IP_tS4_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S23IP_tS4 (100*(2*S2_S4_S4 + 2*ppS2_S4_S4 + 2*ppS3_S4_S4 + ppS2_ppS2_S4 + 2*ppS2_ppS3_S4 + ppS3_ppS3_S4))/(S2 + S3 + 3*S2_S4_S4 + pS2 + pS3 + ppS2 + ppS3 + 3*ppS2_S4_S4 + 3*ppS3_S4_S4 + 3*ppS2_ppS2_S4 + 4*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 -S2IP_S2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S2IP_S2 (100*(S2 + S2_S4_S4))/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) lin 5 -S2IP_S2_MSPL2_complexes_all_hepa16_time_course_nExpID6 S2IP_S2 (100*(S2 + S2_S4_S4))/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) lin 5 -S2IP_S3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S2IP_S3 0 lin 5 -S2IP_pS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S2IP_pS2 (100*pS2)/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) lin 5 -S2IP_pS2_MSPL2_complexes_all_hepa16_time_course_nExpID6 S2IP_pS2 (100*pS2)/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) lin 5 -S2IP_pS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S2IP_pS3 0 lin 5 -S2IP_ppS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S2IP_ppS2 (100*(ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3))/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) lin 5 -S2IP_ppS2_MSPL2_complexes_all_hepa16_time_course_nExpID6 S2IP_ppS2 (100*(ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3))/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) lin 5 -S2IP_ppS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S2IP_ppS3 100 lin 5 -S2IP_tS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S2IP_tS2 (100*(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3))/(S2 + 3*S2_S4_S4 + pS2 + ppS2 + 3*ppS2_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3) lin 5 -S2IP_tS2_MSPL2_complexes_all_hepa16_time_course_nExpID6 S2IP_tS2 (100*(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3))/(S2 + 3*S2_S4_S4 + pS2 + ppS2 + 3*ppS2_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3) lin 5 -S2IP_tS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S2IP_tS3 (100*(ppS2_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3))/(S2 + 3*S2_S4_S4 + pS2 + ppS2 + 3*ppS2_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3) lin 5 -S2IP_tS3_MSPL2_complexes_all_hepa16_time_course_nExpID6 S2IP_tS3 (100*(ppS2_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3))/(S2 + 3*S2_S4_S4 + pS2 + ppS2 + 3*ppS2_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3) lin 5 -S2IP_tS4_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S2IP_tS4 (100*(2*ppS2_S4_S4 + ppS2_ppS2_S4 + ppS2_ppS3_S4))/(S2 + 3*S2_S4_S4 + pS2 + ppS2 + 3*ppS2_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3) lin 5 -S2IP_tS4_MSPL2_complexes_all_hepa16_time_course_nExpID6 S2IP_tS4 (100*(2*ppS2_S4_S4 + ppS2_ppS2_S4 + ppS2_ppS3_S4))/(S2 + 3*S2_S4_S4 + pS2 + ppS2 + 3*ppS2_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3) lin 5 -S3IP_S2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S3IP_S2 0 lin 5 -S3IP_S3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S3IP_S3 (100*S3)/(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 -S3IP_pS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S3IP_pS2 0 lin 5 -S3IP_pS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S3IP_pS3 (100*pS3)/(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 -S3IP_ppS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S3IP_ppS2 100 lin 5 -S3IP_ppS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S3IP_ppS3 (100*(ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3))/(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 -S3IP_tS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S3IP_tS2 (100*(ppS2_ppS3_S4 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3))/(S3 + pS3 + ppS3 + 3*ppS3_S4_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 -S3IP_tS2_MSPL2_complexes_all_hepa16_time_course_nExpID6 S3IP_tS2 (100*(ppS2_ppS3_S4 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3))/(S3 + pS3 + ppS3 + 3*ppS3_S4_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 -S3IP_tS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S3IP_tS3 (100*(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3))/(S3 + pS3 + ppS3 + 3*ppS3_S4_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 -S3IP_tS3_MSPL2_complexes_all_hepa16_time_course_nExpID6 S3IP_tS3 (100*(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3))/(S3 + pS3 + ppS3 + 3*ppS3_S4_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 -S3IP_tS4_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S3IP_tS4 (100*(2*ppS3_S4_S4 + ppS2_ppS3_S4 + ppS3_ppS3_S4))/(S3 + pS3 + ppS3 + 3*ppS3_S4_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 -S3IP_tS4_MSPL2_complexes_all_hepa16_time_course_nExpID6 S3IP_tS4 (100*(2*ppS3_S4_S4 + ppS2_ppS3_S4 + ppS3_ppS3_S4))/(S3 + pS3 + ppS3 + 3*ppS3_S4_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 -S4IP_tS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S4IP_tS2 (100*(S2_S4_S4 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4))/(S4 + 3*S2_S4_S4 + 3*S4_S4_S4 + 3*ppS2_S4_S4 + 3*ppS3_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4) lin 5 -S4IP_tS2_MSPL2_complexes_all_hepa16_time_course_nExpID6 S4IP_tS2 (100*(S2_S4_S4 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4))/(S4 + 3*S2_S4_S4 + 3*S4_S4_S4 + 3*ppS2_S4_S4 + 3*ppS3_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4) lin 5 -S4IP_tS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S4IP_tS3 (100*(ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4))/(S4 + 3*S2_S4_S4 + 3*S4_S4_S4 + 3*ppS2_S4_S4 + 3*ppS3_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4) lin 5 -S4IP_tS3_MSPL2_complexes_all_hepa16_time_course_nExpID6 S4IP_tS3 (100*(ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4))/(S4 + 3*S2_S4_S4 + 3*S4_S4_S4 + 3*ppS2_S4_S4 + 3*ppS3_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4) lin 5 -S4IP_tS4_MSPL2_PL_PN_molecules_per_cell_hepa16_nExpID1 S4IP_tS4 S4 + 2*S2_S4_S4 + 3*S4_S4_S4 + 2*ppS2_S4_S4 + 2*ppS3_S4_S4 + ppS2_ppS2_S4 + ppS2_ppS3_S4 + ppS3_ppS3_S4 lin 15 -S4IP_tS4_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S4IP_tS4 (100*(S4 + 2*S2_S4_S4 + 3*S4_S4_S4 + 2*ppS2_S4_S4 + 2*ppS3_S4_S4 + ppS2_ppS2_S4 + ppS2_ppS3_S4 + ppS3_ppS3_S4))/(S4 + 3*S2_S4_S4 + 3*S4_S4_S4 + 3*ppS2_S4_S4 + 3*ppS3_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4) lin 5 -S4IP_tS4_MSPL2_complexes_all_hepa16_time_course_nExpID6 S4IP_tS4 (100*(S4 + 2*S2_S4_S4 + 3*S4_S4_S4 + 2*ppS2_S4_S4 + 2*ppS3_S4_S4 + ppS2_ppS2_S4 + ppS2_ppS3_S4 + ppS3_ppS3_S4))/(S4 + 3*S2_S4_S4 + 3*S4_S4_S4 + 3*ppS2_S4_S4 + 3*ppS3_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4) lin 5 -Ski_gene_expression_OE_nExpID100 Ski geneA + 0.000001 log10 sd_Ski_nExpID100 -Skil_gene_expression_OE_nExpID100 Skil geneB + 0.000001 log10 sd_Skil_nExpID100 -Smad7_gene_expression_OE_nExpID100 Smad7 geneF + 0.000001 log10 sd_Smad7_nExpID100 -Sox4_gene_expression_OE_nExpID100 Sox4 geneD + 0.000001 log10 sd_Sox4_nExpID100 -TGFbR_PL_PN_TGFbR_hepa16_nExpID11 TGFbR Rec + TGFb_pRec lin 0.092 -Tgfa_gene_expression_OE_nExpID100 Tgfa geneK + 0.000001 log10 sd_Tgfa_nExpID100 \ No newline at end of file +observableId observableName observableFormula observableTransformation noiseFormula +Bmp4_gene_expression_OE_nExpID100 Bmp4 geneH + 0.000001 log10 sd_Bmp4_nExpID100 +Cxcl15_gene_expression_OE_nExpID100 Cxcl15 geneI + 0.000001 log10 sd_Cxcl15_nExpID100 +Dnmt3a_gene_expression_OE_nExpID100 Dnmt3a geneC + 0.000001 log10 sd_Dnmt3a_nExpID100 +Dusp5_gene_expression_OE_nExpID100 Dusp5 geneJ + 0.000001 log10 sd_Dusp5_nExpID100 +Jun_gene_expression_OE_nExpID100 Jun geneE + 0.000001 log10 sd_Jun_nExpID100 +Klf10_gene_expression_OE_nExpID100 Klf10 geneG + 0.000001 log10 sd_Klf10_nExpID100 +Pdk4_gene_expression_OE_nExpID100 Pdk4 geneL + 0.000001 log10 sd_Pdk4_nExpID100 +S23IP_S2_MSPL2_PL_hepa16_pS2_pS3_time_course_nExpID5 S23IP_S2 (100*(S2 + S2_S4_S4))/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) lin 5 +S23IP_S2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S23IP_S2 (100*(S2 + S2_S4_S4))/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) lin 5 +S23IP_S3_MSPL2_PL_hepa16_pS2_pS3_time_course_nExpID5 S23IP_S3 (100*S3)/(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 +S23IP_S3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S23IP_S3 (100*S3)/(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 +S23IP_pS2_MSPL2_PL_hepa16_pS2_pS3_time_course_nExpID5 S23IP_pS2 (100*pS2)/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) lin 5 +S23IP_pS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S23IP_pS2 (100*pS2)/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) lin 5 +S23IP_pS3_MSPL2_PL_hepa16_pS2_pS3_time_course_nExpID5 S23IP_pS3 (100*pS3)/(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 +S23IP_pS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S23IP_pS3 (100*pS3)/(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 +S23IP_ppS2_MSPL2_PL_hepa16_pS2_pS3_time_course_nExpID5 S23IP_ppS2 (100*(ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3))/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) lin 5 +S23IP_ppS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S23IP_ppS2 (100*(ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3))/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) lin 5 +S23IP_ppS3_MSPL2_PL_hepa16_pS2_pS3_time_course_nExpID5 S23IP_ppS3 (100*(ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3))/(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 +S23IP_ppS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S23IP_ppS3 (100*(ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3))/(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 +S23IP_tS2_MSPL2_PL_PN_molecules_per_cell_hepa16_nExpID1 S23IP_tS2 S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3 lin 15 +S23IP_tS2_MSPL2_PL_PN_molecules_per_cell_hepa16_ratios_nExpID10 S23IP_tS2 (100*(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3))/(S2 + S3 + S2_S4_S4 + pS2 + pS3 + ppS2 + ppS3 + ppS2_S4_S4 + ppS3_S4_S4 + 2*ppS2_ppS2_S4 + 2*ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 1 +S23IP_tS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S23IP_tS2 (100*(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3))/(S2 + S3 + 3*S2_S4_S4 + pS2 + pS3 + ppS2 + ppS3 + 3*ppS2_S4_S4 + 3*ppS3_S4_S4 + 3*ppS2_ppS2_S4 + 4*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 +S23IP_tS3_MSPL2_PL_PN_molecules_per_cell_hepa16_ratios_nExpID10 S23IP_tS3 (100*(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3))/(S2 + S3 + S2_S4_S4 + pS2 + pS3 + ppS2 + ppS3 + ppS2_S4_S4 + ppS3_S4_S4 + 2*ppS2_ppS2_S4 + 2*ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 1 +S23IP_tS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S23IP_tS3 (100*(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3))/(S2 + S3 + 3*S2_S4_S4 + pS2 + pS3 + ppS2 + ppS3 + 3*ppS2_S4_S4 + 3*ppS3_S4_S4 + 3*ppS2_ppS2_S4 + 4*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 +S23IP_tS4_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S23IP_tS4 (100*(2*S2_S4_S4 + 2*ppS2_S4_S4 + 2*ppS3_S4_S4 + ppS2_ppS2_S4 + 2*ppS2_ppS3_S4 + ppS3_ppS3_S4))/(S2 + S3 + 3*S2_S4_S4 + pS2 + pS3 + ppS2 + ppS3 + 3*ppS2_S4_S4 + 3*ppS3_S4_S4 + 3*ppS2_ppS2_S4 + 4*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 +S2IP_S2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S2IP_S2 (100*(S2 + S2_S4_S4))/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) lin 5 +S2IP_S2_MSPL2_complexes_all_hepa16_time_course_nExpID6 S2IP_S2 (100*(S2 + S2_S4_S4))/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) lin 5 +S2IP_S3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S2IP_S3 0 lin 5 +S2IP_pS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S2IP_pS2 (100*pS2)/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) lin 5 +S2IP_pS2_MSPL2_complexes_all_hepa16_time_course_nExpID6 S2IP_pS2 (100*pS2)/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) lin 5 +S2IP_pS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S2IP_pS3 0 lin 5 +S2IP_ppS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S2IP_ppS2 (100*(ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3))/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) lin 5 +S2IP_ppS2_MSPL2_complexes_all_hepa16_time_course_nExpID6 S2IP_ppS2 (100*(ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3))/(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3) lin 5 +S2IP_ppS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S2IP_ppS3 100 lin 5 +S2IP_tS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S2IP_tS2 (100*(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3))/(S2 + 3*S2_S4_S4 + pS2 + ppS2 + 3*ppS2_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3) lin 5 +S2IP_tS2_MSPL2_complexes_all_hepa16_time_course_nExpID6 S2IP_tS2 (100*(S2 + S2_S4_S4 + pS2 + ppS2 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3))/(S2 + 3*S2_S4_S4 + pS2 + ppS2 + 3*ppS2_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3) lin 5 +S2IP_tS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S2IP_tS3 (100*(ppS2_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3))/(S2 + 3*S2_S4_S4 + pS2 + ppS2 + 3*ppS2_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3) lin 5 +S2IP_tS3_MSPL2_complexes_all_hepa16_time_course_nExpID6 S2IP_tS3 (100*(ppS2_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3))/(S2 + 3*S2_S4_S4 + pS2 + ppS2 + 3*ppS2_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3) lin 5 +S2IP_tS4_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S2IP_tS4 (100*(2*ppS2_S4_S4 + ppS2_ppS2_S4 + ppS2_ppS3_S4))/(S2 + 3*S2_S4_S4 + pS2 + ppS2 + 3*ppS2_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3) lin 5 +S2IP_tS4_MSPL2_complexes_all_hepa16_time_course_nExpID6 S2IP_tS4 (100*(2*ppS2_S4_S4 + ppS2_ppS2_S4 + ppS2_ppS3_S4))/(S2 + 3*S2_S4_S4 + pS2 + ppS2 + 3*ppS2_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS2_ppS2_ppS2 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3) lin 5 +S3IP_S2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S3IP_S2 0 lin 5 +S3IP_S3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S3IP_S3 (100*S3)/(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 +S3IP_pS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S3IP_pS2 0 lin 5 +S3IP_pS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S3IP_pS3 (100*pS3)/(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 +S3IP_ppS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S3IP_ppS2 100 lin 5 +S3IP_ppS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S3IP_ppS3 (100*(ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3))/(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 +S3IP_tS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S3IP_tS2 (100*(ppS2_ppS3_S4 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3))/(S3 + pS3 + ppS3 + 3*ppS3_S4_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 +S3IP_tS2_MSPL2_complexes_all_hepa16_time_course_nExpID6 S3IP_tS2 (100*(ppS2_ppS3_S4 + 2*ppS2_ppS2_ppS3 + ppS2_ppS3_ppS3))/(S3 + pS3 + ppS3 + 3*ppS3_S4_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 +S3IP_tS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S3IP_tS3 (100*(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3))/(S3 + pS3 + ppS3 + 3*ppS3_S4_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 +S3IP_tS3_MSPL2_complexes_all_hepa16_time_course_nExpID6 S3IP_tS3 (100*(S3 + pS3 + ppS3 + ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4 + ppS2_ppS2_ppS3 + 2*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3))/(S3 + pS3 + ppS3 + 3*ppS3_S4_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 +S3IP_tS4_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S3IP_tS4 (100*(2*ppS3_S4_S4 + ppS2_ppS3_S4 + ppS3_ppS3_S4))/(S3 + pS3 + ppS3 + 3*ppS3_S4_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 +S3IP_tS4_MSPL2_complexes_all_hepa16_time_course_nExpID6 S3IP_tS4 (100*(2*ppS3_S4_S4 + ppS2_ppS3_S4 + ppS3_ppS3_S4))/(S3 + pS3 + ppS3 + 3*ppS3_S4_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4 + 3*ppS2_ppS2_ppS3 + 3*ppS2_ppS3_ppS3 + 3*ppS3_ppS3_ppS3) lin 5 +S4IP_tS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S4IP_tS2 (100*(S2_S4_S4 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4))/(S4 + 3*S2_S4_S4 + 3*S4_S4_S4 + 3*ppS2_S4_S4 + 3*ppS3_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4) lin 5 +S4IP_tS2_MSPL2_complexes_all_hepa16_time_course_nExpID6 S4IP_tS2 (100*(S2_S4_S4 + ppS2_S4_S4 + 2*ppS2_ppS2_S4 + ppS2_ppS3_S4))/(S4 + 3*S2_S4_S4 + 3*S4_S4_S4 + 3*ppS2_S4_S4 + 3*ppS3_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4) lin 5 +S4IP_tS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S4IP_tS3 (100*(ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4))/(S4 + 3*S2_S4_S4 + 3*S4_S4_S4 + 3*ppS2_S4_S4 + 3*ppS3_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4) lin 5 +S4IP_tS3_MSPL2_complexes_all_hepa16_time_course_nExpID6 S4IP_tS3 (100*(ppS3_S4_S4 + ppS2_ppS3_S4 + 2*ppS3_ppS3_S4))/(S4 + 3*S2_S4_S4 + 3*S4_S4_S4 + 3*ppS2_S4_S4 + 3*ppS3_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4) lin 5 +S4IP_tS4_MSPL2_PL_PN_molecules_per_cell_hepa16_nExpID1 S4IP_tS4 S4 + 2*S2_S4_S4 + 3*S4_S4_S4 + 2*ppS2_S4_S4 + 2*ppS3_S4_S4 + ppS2_ppS2_S4 + ppS2_ppS3_S4 + ppS3_ppS3_S4 lin 15 +S4IP_tS4_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 S4IP_tS4 (100*(S4 + 2*S2_S4_S4 + 3*S4_S4_S4 + 2*ppS2_S4_S4 + 2*ppS3_S4_S4 + ppS2_ppS2_S4 + ppS2_ppS3_S4 + ppS3_ppS3_S4))/(S4 + 3*S2_S4_S4 + 3*S4_S4_S4 + 3*ppS2_S4_S4 + 3*ppS3_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4) lin 5 +S4IP_tS4_MSPL2_complexes_all_hepa16_time_course_nExpID6 S4IP_tS4 (100*(S4 + 2*S2_S4_S4 + 3*S4_S4_S4 + 2*ppS2_S4_S4 + 2*ppS3_S4_S4 + ppS2_ppS2_S4 + ppS2_ppS3_S4 + ppS3_ppS3_S4))/(S4 + 3*S2_S4_S4 + 3*S4_S4_S4 + 3*ppS2_S4_S4 + 3*ppS3_S4_S4 + 3*ppS2_ppS2_S4 + 3*ppS2_ppS3_S4 + 3*ppS3_ppS3_S4) lin 5 +Ski_gene_expression_OE_nExpID100 Ski geneA + 0.000001 log10 sd_Ski_nExpID100 +Skil_gene_expression_OE_nExpID100 Skil geneB + 0.000001 log10 sd_Skil_nExpID100 +Smad7_gene_expression_OE_nExpID100 Smad7 geneF + 0.000001 log10 sd_Smad7_nExpID100 +Sox4_gene_expression_OE_nExpID100 Sox4 geneD + 0.000001 log10 sd_Sox4_nExpID100 +TGFbR_PL_PN_TGFbR_hepa16_nExpID11 TGFbR Rec + TGFb_pRec lin 0.092 +Tgfa_gene_expression_OE_nExpID100 Tgfa geneK + 0.000001 log10 sd_Tgfa_nExpID100 diff --git a/Benchmark-Models/SalazarCavazos_MBoC2020/observables_SalazarCavazos_MBoC2020.tsv b/Benchmark-Models/SalazarCavazos_MBoC2020/observables_SalazarCavazos_MBoC2020.tsv index f90e621f..b8ee70a1 100644 --- a/Benchmark-Models/SalazarCavazos_MBoC2020/observables_SalazarCavazos_MBoC2020.tsv +++ b/Benchmark-Models/SalazarCavazos_MBoC2020/observables_SalazarCavazos_MBoC2020.tsv @@ -2,4 +2,4 @@ observableId observableName observableFormula noiseFormula observableTransformat observable_pY1068_percent pY1068_percent (100*pY1068)/EGFRtot noiseParameter1_observable_pY1068_percent lin normal observable_pY1173_percent pY1173_percent (100*pY1173)/EGFRtot noiseParameter1_observable_pY1173_percent lin normal observable_unphosR_per unphosR_per (100*unphosR)/EGFRtot noiseParameter1_observable_unphosR_per lin normal -observable_phosR_per phosR_per (100*(EGFRtot-unphosR))/EGFRtot noiseParameter1_observable_phosR_per lin normal \ No newline at end of file +observable_phosR_per phosR_per (100*(EGFRtot-unphosR))/EGFRtot noiseParameter1_observable_phosR_per lin normal diff --git a/src/python/benchmark_models_petab/check_tsv_format.py b/src/python/benchmark_models_petab/check_tsv_format.py new file mode 100644 index 00000000..53f10e38 --- /dev/null +++ b/src/python/benchmark_models_petab/check_tsv_format.py @@ -0,0 +1,94 @@ +"""Check that TSV files are well-formed and render correctly in GitHub's +file preview. + +Checks, for every ``*.tsv`` file under the benchmark problem directories: + +* every row has the same number of fields as the header +* line endings are consistent (no mix of ``\\n`` and ``\\r\\n``) +* no field has stray leading/trailing whitespace +* the file ends with exactly one trailing newline +""" + +import csv +import io +import sys +from pathlib import Path + +from .C import MODELS_DIR + + +def check_tsv_file(tsv_file: Path) -> list[str]: + """Check a single TSV file for formatting issues. + + Parameters + ---------- + tsv_file: Path to the TSV file to check. + + Returns + ------- + A list of human-readable error messages. Empty if the file is fine. + """ + errors = [] + + raw = tsv_file.read_bytes() + if not raw: + return errors + + if b"\r\n" in raw and raw.replace(b"\r\n", b"").count(b"\n"): + errors.append("Mixed line endings (both '\\r\\n' and '\\n').") + elif b"\r\n" in raw: + errors.append("Uses '\\r\\n' line endings instead of '\\n'.") + + if not raw.endswith(b"\n"): + errors.append("File does not end with a newline.") + elif raw.endswith(b"\n\n") or raw.endswith(b"\r\n\r\n"): + errors.append("File ends with more than one trailing newline.") + + text = raw.decode("utf-8") + # use csv.reader (like pandas.read_csv, which petab uses under the + # hood) rather than a plain str.split("\t"), so quoted fields are + # handled the same way the actual PEtab readers would handle them + rows = list(csv.reader(io.StringIO(text), delimiter="\t")) + + if not rows: + return errors + + num_fields = len(rows[0]) + for i, fields in enumerate(rows, start=1): + # a trailing tab is a legitimate empty last field, not whitespace + # to trim, so check individual fields for stray leading/trailing + # spaces instead of checking the raw line; a field consisting + # only of whitespace is left alone, as it may be an intentional + # blank placeholder (e.g. for a visualization label) + if any(field.strip() and field != field.strip() for field in fields): + errors.append(f"Line {i}: field with leading/trailing space.") + + if i > 1 and len(fields) != num_fields: + errors.append( + f"Line {i}: expected {num_fields} fields " + f"(as in the header), got {len(fields)}." + ) + + return errors + + +def main(): + """Check the format of all TSV files in the benchmark collection.""" + num_failures = 0 + tsv_files = sorted(Path(MODELS_DIR).rglob("*.tsv")) + + for tsv_file in tsv_files: + errors = check_tsv_file(tsv_file) + if errors: + num_failures += 1 + print(tsv_file.relative_to(MODELS_DIR)) + for error in errors: + print(f"\t{error}") + + num_passed = len(tsv_files) - num_failures + print("=" * 100) + print(f"Result: {Path(__file__).stem}") + print(f"{num_passed} out of {len(tsv_files)} passed.") + print(f"{num_failures} out of {len(tsv_files)} failed.") + # Fail unless all files passed + sys.exit(1 if num_failures else 0) diff --git a/src/python/pyproject.toml b/src/python/pyproject.toml index bb87e6ab..ee53b448 100644 --- a/src/python/pyproject.toml +++ b/src/python/pyproject.toml @@ -33,6 +33,7 @@ site = ["bokeh>=3.7.3"] [project.scripts] bmp-petablint = "benchmark_models_petab.check_petablint:main" bmp-check-sbml-metadata = "benchmark_models_petab.check_sbml_metadata:main" +bmp-check-tsv-format = "benchmark_models_petab.check_tsv_format:main" bmp-create-overview = "benchmark_models_petab.overview:main" [tool.setuptools_scm] diff --git a/src/python/test/test_check_tsv_format.py b/src/python/test/test_check_tsv_format.py new file mode 100644 index 00000000..de6dbbf5 --- /dev/null +++ b/src/python/test/test_check_tsv_format.py @@ -0,0 +1,144 @@ +"""Tests for the TSV format checker.""" + +from benchmark_models_petab.check_tsv_format import check_tsv_file + + +def test_well_formed_file_passes(tmp_path): + """A clean, consistent TSV file yields no errors.""" + tsv_file = tmp_path / "ok.tsv" + tsv_file.write_bytes(b"a\tb\tc\n1\t2\t3\n4\t\t6\n") + + assert check_tsv_file(tsv_file) == [] + + +def test_empty_file_passes(tmp_path): + """An empty file is not flagged.""" + tsv_file = tmp_path / "empty.tsv" + tsv_file.write_bytes(b"") + + assert check_tsv_file(tsv_file) == [] + + +def test_missing_field_is_detected(tmp_path): + """A row with fewer fields than the header is flagged.""" + tsv_file = tmp_path / "short_row.tsv" + tsv_file.write_bytes(b"a\tb\tc\n1\t2\n") + + errors = check_tsv_file(tsv_file) + + assert len(errors) == 1 + assert "Line 2" in errors[0] + assert "expected 3 fields" in errors[0] + assert "got 2" in errors[0] + + +def test_extra_field_is_detected(tmp_path): + """A row with more fields than the header is flagged.""" + tsv_file = tmp_path / "long_row.tsv" + tsv_file.write_bytes(b"a\tb\n1\t2\t3\n") + + errors = check_tsv_file(tsv_file) + + assert len(errors) == 1 + assert "expected 2 fields" in errors[0] + assert "got 3" in errors[0] + + +def test_trailing_tab_empty_last_field_is_not_flagged(tmp_path): + """A trailing tab encoding an empty last field is valid, not + whitespace to strip, and must not be flagged.""" + tsv_file = tmp_path / "trailing_tab.tsv" + tsv_file.write_bytes(b"a\tb\n1\t\n") + + assert check_tsv_file(tsv_file) == [] + + +def test_field_with_trailing_space_is_detected(tmp_path): + """Stray trailing whitespace within a non-empty field is flagged.""" + tsv_file = tmp_path / "trailing_space.tsv" + tsv_file.write_bytes(b"a\tb\n1\t2 \n") + + errors = check_tsv_file(tsv_file) + + assert len(errors) == 1 + assert "Line 2" in errors[0] + assert "leading/trailing space" in errors[0] + + +def test_field_with_leading_space_is_detected(tmp_path): + """Stray leading whitespace within a non-empty field is flagged.""" + tsv_file = tmp_path / "leading_space.tsv" + tsv_file.write_bytes(b"a\tb\n1\t 2\n") + + errors = check_tsv_file(tsv_file) + + assert len(errors) == 1 + assert "leading/trailing space" in errors[0] + + +def test_whitespace_only_field_is_not_flagged(tmp_path): + """A field consisting solely of whitespace may be an intentional + blank placeholder (e.g. a suppressed visualization axis label) and + must not be flagged.""" + tsv_file = tmp_path / "blank_placeholder.tsv" + tsv_file.write_bytes(b"a\tb\n1\t \n") + + assert check_tsv_file(tsv_file) == [] + + +def test_crlf_line_endings_are_detected(tmp_path): + """A file using '\\r\\n' line endings throughout is flagged.""" + tsv_file = tmp_path / "crlf.tsv" + tsv_file.write_bytes(b"a\tb\r\n1\t2\r\n") + + errors = check_tsv_file(tsv_file) + + assert len(errors) == 1 + assert "\\r\\n" in errors[0] + assert "instead of" in errors[0] + + +def test_mixed_line_endings_are_detected(tmp_path): + """A file mixing '\\n' and '\\r\\n' line endings is flagged.""" + tsv_file = tmp_path / "mixed.tsv" + tsv_file.write_bytes(b"a\tb\n1\t2\r\n3\t4\n") + + errors = check_tsv_file(tsv_file) + + assert len(errors) == 1 + assert "Mixed line endings" in errors[0] + + +def test_missing_trailing_newline_is_detected(tmp_path): + """A file that does not end with a newline is flagged.""" + tsv_file = tmp_path / "no_final_newline.tsv" + tsv_file.write_bytes(b"a\tb\n1\t2") + + errors = check_tsv_file(tsv_file) + + assert len(errors) == 1 + assert "does not end with a newline" in errors[0] + + +def test_extra_trailing_newline_is_detected(tmp_path): + """A file with more than one trailing newline is flagged.""" + tsv_file = tmp_path / "extra_final_newline.tsv" + tsv_file.write_bytes(b"a\tb\n1\t2\n\n") + + errors = check_tsv_file(tsv_file) + + # the blank line also shows up as a (0-field) row, so both checks fire + assert any("more than one trailing newline" in e for e in errors) + + +def test_multiple_issues_are_all_reported(tmp_path): + """A file with several independent problems reports all of them.""" + tsv_file = tmp_path / "multiple_issues.tsv" + tsv_file.write_bytes(b"a\tb\r\n1\t2 \n3\n") + + errors = check_tsv_file(tsv_file) + + assert len(errors) == 3 + assert any("Mixed line endings" in e for e in errors) + assert any("leading/trailing space" in e for e in errors) + assert any("expected 2 fields" in e and "got 1" in e for e in errors)