From 23ea3cfbc4e19f3e40d5978dc3651fd46e119538 Mon Sep 17 00:00:00 2001 From: Maren Philipps Date: Tue, 8 Oct 2024 16:34:14 +0200 Subject: [PATCH 01/17] fix Fiedler_BMCSystBiol2016 ID --- Benchmark-Models/Fiedler_BMC2016/Fiedler_BMC2016.yaml | 11 ----------- .../Fiedler_BMCSystBiol2016.yaml | 11 +++++++++++ ...experimentalCondition_Fiedler_BMCSystBiol2016.tsv} | 0 .../measurementData_Fiedler_BMCSystBiol2016.tsv} | 0 .../model_Fiedler_BMCSystBiol2016.xml} | 2 +- .../observables_Fiedler_BMCSystBiol2016.tsv} | 0 .../parameters_Fiedler_BMCSystBiol2016.tsv} | 0 .../simulatedData_Fiedler_BMCSystBiol2016.tsv} | 0 README.md | 2 +- 9 files changed, 13 insertions(+), 13 deletions(-) delete mode 100644 Benchmark-Models/Fiedler_BMC2016/Fiedler_BMC2016.yaml create mode 100644 Benchmark-Models/Fiedler_BMCSystBiol2016/Fiedler_BMCSystBiol2016.yaml rename Benchmark-Models/{Fiedler_BMC2016/experimentalCondition_Fiedler_BMC2016.tsv => Fiedler_BMCSystBiol2016/experimentalCondition_Fiedler_BMCSystBiol2016.tsv} (100%) rename Benchmark-Models/{Fiedler_BMC2016/measurementData_Fiedler_BMC2016.tsv => Fiedler_BMCSystBiol2016/measurementData_Fiedler_BMCSystBiol2016.tsv} (100%) rename Benchmark-Models/{Fiedler_BMC2016/model_Fiedler_BMC2016.xml => Fiedler_BMCSystBiol2016/model_Fiedler_BMCSystBiol2016.xml} (99%) rename Benchmark-Models/{Fiedler_BMC2016/observables_Fiedler_BMC2016.tsv => Fiedler_BMCSystBiol2016/observables_Fiedler_BMCSystBiol2016.tsv} (100%) rename Benchmark-Models/{Fiedler_BMC2016/parameters_Fiedler_BMC2016.tsv => Fiedler_BMCSystBiol2016/parameters_Fiedler_BMCSystBiol2016.tsv} (100%) rename Benchmark-Models/{Fiedler_BMC2016/simulatedData_Fiedler_BMC2016.tsv => Fiedler_BMCSystBiol2016/simulatedData_Fiedler_BMCSystBiol2016.tsv} (100%) diff --git a/Benchmark-Models/Fiedler_BMC2016/Fiedler_BMC2016.yaml b/Benchmark-Models/Fiedler_BMC2016/Fiedler_BMC2016.yaml deleted file mode 100644 index ee19ef0..0000000 --- a/Benchmark-Models/Fiedler_BMC2016/Fiedler_BMC2016.yaml +++ /dev/null @@ -1,11 +0,0 @@ -format_version: 1 -parameter_file: parameters_Fiedler_BMC2016.tsv -problems: -- condition_files: - - experimentalCondition_Fiedler_BMC2016.tsv - measurement_files: - - measurementData_Fiedler_BMC2016.tsv - observable_files: - - observables_Fiedler_BMC2016.tsv - sbml_files: - - model_Fiedler_BMC2016.xml diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/Fiedler_BMCSystBiol2016.yaml b/Benchmark-Models/Fiedler_BMCSystBiol2016/Fiedler_BMCSystBiol2016.yaml new file mode 100644 index 0000000..9561aa9 --- /dev/null +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/Fiedler_BMCSystBiol2016.yaml @@ -0,0 +1,11 @@ +format_version: 1 +parameter_file: parameters_Fiedler_BMCSystBiol2016.tsv +problems: +- condition_files: + - experimentalCondition_Fiedler_BMCSystBiol2016.tsv + measurement_files: + - measurementData_Fiedler_BMCSystBiol2016.tsv + observable_files: + - observables_Fiedler_BMCSystBiol2016.tsv + sbml_files: + - model_Fiedler_BMCSystBiol2016.xml diff --git a/Benchmark-Models/Fiedler_BMC2016/experimentalCondition_Fiedler_BMC2016.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/experimentalCondition_Fiedler_BMCSystBiol2016.tsv similarity index 100% rename from Benchmark-Models/Fiedler_BMC2016/experimentalCondition_Fiedler_BMC2016.tsv rename to Benchmark-Models/Fiedler_BMCSystBiol2016/experimentalCondition_Fiedler_BMCSystBiol2016.tsv diff --git a/Benchmark-Models/Fiedler_BMC2016/measurementData_Fiedler_BMC2016.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/measurementData_Fiedler_BMCSystBiol2016.tsv similarity index 100% rename from Benchmark-Models/Fiedler_BMC2016/measurementData_Fiedler_BMC2016.tsv rename to Benchmark-Models/Fiedler_BMCSystBiol2016/measurementData_Fiedler_BMCSystBiol2016.tsv diff --git a/Benchmark-Models/Fiedler_BMC2016/model_Fiedler_BMC2016.xml b/Benchmark-Models/Fiedler_BMCSystBiol2016/model_Fiedler_BMCSystBiol2016.xml similarity index 99% rename from Benchmark-Models/Fiedler_BMC2016/model_Fiedler_BMC2016.xml rename to Benchmark-Models/Fiedler_BMCSystBiol2016/model_Fiedler_BMCSystBiol2016.xml index bef7143..e1abbe2 100644 --- a/Benchmark-Models/Fiedler_BMC2016/model_Fiedler_BMC2016.xml +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/model_Fiedler_BMCSystBiol2016.xml @@ -1,6 +1,6 @@ - + 
PEtab implementation of the model from Fiedler et al. (2016), BMC Systems Biology volume 10, Article number: 80
diff --git a/Benchmark-Models/Fiedler_BMC2016/observables_Fiedler_BMC2016.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/observables_Fiedler_BMCSystBiol2016.tsv similarity index 100% rename from Benchmark-Models/Fiedler_BMC2016/observables_Fiedler_BMC2016.tsv rename to Benchmark-Models/Fiedler_BMCSystBiol2016/observables_Fiedler_BMCSystBiol2016.tsv diff --git a/Benchmark-Models/Fiedler_BMC2016/parameters_Fiedler_BMC2016.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/parameters_Fiedler_BMCSystBiol2016.tsv similarity index 100% rename from Benchmark-Models/Fiedler_BMC2016/parameters_Fiedler_BMC2016.tsv rename to Benchmark-Models/Fiedler_BMCSystBiol2016/parameters_Fiedler_BMCSystBiol2016.tsv diff --git a/Benchmark-Models/Fiedler_BMC2016/simulatedData_Fiedler_BMC2016.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/simulatedData_Fiedler_BMCSystBiol2016.tsv similarity index 100% rename from Benchmark-Models/Fiedler_BMC2016/simulatedData_Fiedler_BMC2016.tsv rename to Benchmark-Models/Fiedler_BMCSystBiol2016/simulatedData_Fiedler_BMCSystBiol2016.tsv diff --git a/README.md b/README.md index 8676397..9dcaae2 100644 --- a/README.md +++ b/README.md @@ -20,7 +20,7 @@ Contributions to the collection are very welcome. Please see [CONTRIBUTING.md](C | [Chen_MSB2009](Benchmark-Models/Chen_MSB2009/) | 4 | 155 | 0 | 0 | 0 | 120 | 3 | normal | | 500 | [\[1\]](http://identifiers.org/doi/10.1038/msb.2008.74) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Chen_MSB2009/model_Chen_MSB2009.xml) | | [Crauste_CellSystems2017](Benchmark-Models/Crauste_CellSystems2017/) | 1 | 12 | 0 | 0 | 0 | 21 | 4 | normal | | 5 | [\[1\]](http://identifiers.org/doi/10.1016/j.cels.2017.01.014) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Crauste_CellSystems2017/model_Crauste_CellSystems2017.xml) | | [Elowitz_Nature2000](Benchmark-Models/Elowitz_Nature2000/) | 1 | 21 | 0 | 0 | 0 | 58 | 1 | log10-normal | | 8 | [\[1\]](http://identifiers.org/doi/10.1038/35002125) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Elowitz_Nature2000/model_Elowitz_Nature2000.xml) | -| [Fiedler_BMC2016](Benchmark-Models/Fiedler_BMC2016/) | 3 | 22 | 0 | 0 | 0 | 72 | 2 | normal | | 6 | [\[1\]](http://identifiers.org/doi/10.1186/s12918-016-0319-7) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Fiedler_BMC2016/model_Fiedler_BMC2016.xml) | +| [Fiedler_BMCSystBiol2016](Benchmark-Models/Fiedler_BMCSystBiol2016/) | 3 | 22 | 0 | 0 | 0 | 72 | 2 | normal | | 6 | [\[1\]](http://identifiers.org/doi/10.1186/s12918-016-0319-7) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Fiedler_BMCSystBiol2016/model_Fiedler_BMCSystBiol2016.xml) | | [Froehlich_CellSystems2018](Benchmark-Models/Froehlich_CellSystems2018/) | 9169 | 4231 | 0 | 0 | 9169 | 9169 | 1 | normal | | 1396 | [\[1\]](http://identifiers.org/doi/10.1016/j.cels.2018.10.013) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Froehlich_CellSystems2018/model_Froehlich_CellSystems2018.xml) | | [Fujita_SciSignal2010](Benchmark-Models/Fujita_SciSignal2010/) | 6 | 19 | 0 | 0 | 0 | 144 | 3 | normal | | 9 | [\[1\]](http://identifiers.org/doi/10.1126/scisignal.2000810) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Fujita_SciSignal2010/model_Fujita_SciSignal2010.xml) | | [Giordano_Nature2020](Benchmark-Models/Giordano_Nature2020/) | 1 | 50 | 0 | 0 | 0 | 313 | 7 | normal | | 13 | [\[1\]](http://identifiers.org/pubmed/32322102) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Giordano_Nature2020/Giordano_Nature2020_model.xml) | From 60bf58a6d0ecadce7d0ab720785e47dad0f95242 Mon Sep 17 00:00:00 2001 From: Maren Philipps Date: Tue, 8 Oct 2024 16:52:31 +0200 Subject: [PATCH 02/17] run bmp-create-overview --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 9dcaae2..4994bfd 100644 --- a/README.md +++ b/README.md @@ -20,7 +20,7 @@ Contributions to the collection are very welcome. Please see [CONTRIBUTING.md](C | [Chen_MSB2009](Benchmark-Models/Chen_MSB2009/) | 4 | 155 | 0 | 0 | 0 | 120 | 3 | normal | | 500 | [\[1\]](http://identifiers.org/doi/10.1038/msb.2008.74) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Chen_MSB2009/model_Chen_MSB2009.xml) | | [Crauste_CellSystems2017](Benchmark-Models/Crauste_CellSystems2017/) | 1 | 12 | 0 | 0 | 0 | 21 | 4 | normal | | 5 | [\[1\]](http://identifiers.org/doi/10.1016/j.cels.2017.01.014) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Crauste_CellSystems2017/model_Crauste_CellSystems2017.xml) | | [Elowitz_Nature2000](Benchmark-Models/Elowitz_Nature2000/) | 1 | 21 | 0 | 0 | 0 | 58 | 1 | log10-normal | | 8 | [\[1\]](http://identifiers.org/doi/10.1038/35002125) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Elowitz_Nature2000/model_Elowitz_Nature2000.xml) | -| [Fiedler_BMCSystBiol2016](Benchmark-Models/Fiedler_BMCSystBiol2016/) | 3 | 22 | 0 | 0 | 0 | 72 | 2 | normal | | 6 | [\[1\]](http://identifiers.org/doi/10.1186/s12918-016-0319-7) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Fiedler_BMCSystBiol2016/model_Fiedler_BMCSystBiol2016.xml) | +| [Fiedler_BMCSystBiol2016](Benchmark-Models/Fiedler_BMCSystBiol2016/) | 3 | 22 | 0 | 0 | 0 | 72 | 2 | normal | | 6 | [\[1\]](http://identifiers.org/doi/10.1186/s12918-016-0319-7) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Fiedler_BMCSystBiol2016/model_Fiedler_BMCSystBiol2016.xml) | | [Froehlich_CellSystems2018](Benchmark-Models/Froehlich_CellSystems2018/) | 9169 | 4231 | 0 | 0 | 9169 | 9169 | 1 | normal | | 1396 | [\[1\]](http://identifiers.org/doi/10.1016/j.cels.2018.10.013) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Froehlich_CellSystems2018/model_Froehlich_CellSystems2018.xml) | | [Fujita_SciSignal2010](Benchmark-Models/Fujita_SciSignal2010/) | 6 | 19 | 0 | 0 | 0 | 144 | 3 | normal | | 9 | [\[1\]](http://identifiers.org/doi/10.1126/scisignal.2000810) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Fujita_SciSignal2010/model_Fujita_SciSignal2010.xml) | | [Giordano_Nature2020](Benchmark-Models/Giordano_Nature2020/) | 1 | 50 | 0 | 0 | 0 | 313 | 7 | normal | | 13 | [\[1\]](http://identifiers.org/pubmed/32322102) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Giordano_Nature2020/Giordano_Nature2020_model.xml) | From 463333c70140c0495a0d863445aab780b37c8e19 Mon Sep 17 00:00:00 2001 From: Maren Philipps Date: Tue, 8 Oct 2024 17:18:44 +0200 Subject: [PATCH 03/17] add reformulated Fiedler model --- .../reformulated/model.xml | 1646 +++++++++++++++++ 1 file changed, 1646 insertions(+) create mode 100644 Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/model.xml diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/model.xml b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/model.xml new file mode 100644 index 0000000..6bec097 --- /dev/null +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/model.xml @@ -0,0 +1,1646 @@ + + + + + + + + + + 2024-10-06T10:20:09Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + K1_ERK0 + k10 + + + + + + + + + + K1_ERK0 + 2 + + + + k10 + 2 + + + + + + + 2 + + + K1_ERK0 + 2 + + k6 + + + k10 + 2 + + + k5_MEK0 + + + + + + + + K1_ERK0 + 2 + + + + k6 + 2 + + + + k10 + 2 + + + + + k5_MEK0 + 2 + + + + + + + + + K1_ERK0 + 2 + + + + k4 + 2 + + + + k6 + 2 + + + + + + k10 + k2 + + 2 + + + + + + + k3_Raf0 + k5_MEK0 + + 2 + + + + + + + 2 + + + K1_ERK0 + 2 + + k4 + + + k6 + 2 + + k10 + + + k10 + k2 + + + + + k3_Raf0 + + + k5_MEK0 + 2 + + + + + + + + 2 + + + K1_ERK0 + 2 + + k4 + k6 + k10 + + + k10 + k2 + + + + + k3_Raf0 + k5_MEK0 + + + + + + + 4 + K1_ERK0 + k2 + k4 + k6 + k10 + + + + k3_Raf0 + k5_MEK0 + + + + 0.5 + + + + + + K1_ERK0 + k6 + k10 + + k5_MEK0 + + + + + + + K1_ERK0 + k4 + k6 + + + k10 + k2 + + + + + k3_Raf0 + k5_MEK0 + + + + + + 2 + + + k2 + + + K1_ERK0 + k10 + + + + K1_ERK0 + k2 + + + + + + K1_ERK0 + k2 + k6 + + k5_MEK0 + + + + + + K1_ERK0 + k6 + k10 + + k5_MEK0 + + + + + + + + + + + + + + + + + + + + + + + + + K1_ERK0 + 2 + + + + k10 + 2 + + + + + + + 2 + + + K1_ERK0 + 2 + + k6 + + + k10 + 2 + + + k5_MEK0 + + + + + + + + K1_ERK0 + 2 + + + + k6 + 2 + + + + k10 + 2 + + + + + k5_MEK0 + 2 + + + + + + + + + K1_ERK0 + 2 + + + + k4 + 2 + + + + k6 + 2 + + + + + + k10 + k2 + + 2 + + + + + + + k3_Raf0 + k5_MEK0 + + 2 + + + + + + + 2 + + + K1_ERK0 + 2 + + k4 + + + k6 + 2 + + k10 + + + k10 + k2 + + + + + k3_Raf0 + + + k5_MEK0 + 2 + + + + + + + + 2 + + + K1_ERK0 + 2 + + k4 + k6 + k10 + + + k10 + k2 + + + + + k3_Raf0 + k5_MEK0 + + + + + + + 4 + K1_ERK0 + k2 + k4 + k6 + k10 + + + + k3_Raf0 + k5_MEK0 + + + + 0.5 + + + + K1_ERK0 + k10 + + + + + + K1_ERK0 + k6 + k10 + + k5_MEK0 + + + + + + + K1_ERK0 + k2 + k4 + k6 + + + + k3_Raf0 + k5_MEK0 + + + + + + + + K1_ERK0 + k4 + k6 + k10 + + + + k3_Raf0 + k5_MEK0 + + + + + + + + + + + + + + K1_ERK0 + 2 + + + + k10 + 2 + + + + + + + 2 + + + K1_ERK0 + 2 + + k6 + + + k10 + 2 + + + k5_MEK0 + + + + + + + + K1_ERK0 + 2 + + + + k6 + 2 + + + + k10 + 2 + + + + + k5_MEK0 + 2 + + + + + + + + + K1_ERK0 + 2 + + + + k4 + 2 + + + + k6 + 2 + + + + + + k10 + k2 + + 2 + + + + + + + k3_Raf0 + k5_MEK0 + + 2 + + + + + + + 2 + + + K1_ERK0 + 2 + + k4 + + + k6 + 2 + + k10 + + + k10 + k2 + + + + + k3_Raf0 + + + k5_MEK0 + 2 + + + + + + + + 2 + + + K1_ERK0 + 2 + + k4 + k6 + k10 + + + k10 + k2 + + + + + k3_Raf0 + k5_MEK0 + + + + + + + 4 + K1_ERK0 + k2 + k4 + k6 + k10 + + + + k3_Raf0 + k5_MEK0 + + + + 0.5 + + + + K1_ERK0 + k10 + + + + + + K1_ERK0 + k6 + k10 + + k5_MEK0 + + + + + + + + k2 + k4 + + k3_Raf0 + + + + + + 2 + K1_ERK0 + + + + + + K1_ERK0 + k6 + + k5_MEK0 + + 2 + + + + + + + + + K1_ERK0 + k4 + k10 + + k3_Raf0 + + + + + + k6 + k5_MEK0 + + 2 + + + + + + + + + + + + + + + + + + + + + + + + + K1_ERK0 + 2 + + + + k10 + 2 + + + + + + + 2 + + + K1_ERK0 + 2 + + k6 + + + k10 + 2 + + + k5_MEK0 + + + + + + + + K1_ERK0 + 2 + + + + k6 + 2 + + + + k10 + 2 + + + + + k5_MEK0 + 2 + + + + + + + + + K1_ERK0 + 2 + + + + k4 + 2 + + + + k6 + 2 + + + + + + k10 + k2 + + 2 + + + + + + + k3_Raf0 + k5_MEK0 + + 2 + + + + + + + 2 + + + K1_ERK0 + 2 + + k4 + + + k6 + 2 + + k10 + + + k10 + k2 + + + + + k3_Raf0 + + + k5_MEK0 + 2 + + + + + + + + 2 + + + K1_ERK0 + 2 + + k4 + k6 + k10 + + + k10 + k2 + + + + + k3_Raf0 + k5_MEK0 + + + + + + + 4 + K1_ERK0 + k2 + k4 + k6 + k10 + + + + k3_Raf0 + k5_MEK0 + + + + 0.5 + + + + K1_ERK0 + k10 + + + + + + K1_ERK0 + k6 + k10 + + k5_MEK0 + + + + + + + K1_ERK0 + k2 + k4 + k6 + + + + k3_Raf0 + k5_MEK0 + + + + + + + + K1_ERK0 + k4 + k6 + k10 + + + + k3_Raf0 + k5_MEK0 + + + + + + + + + + + + k6 + k5_MEK0 + + 1 + + + + + + + + + + K1_ERK0 + 2 + + + + k10 + 2 + + + + + + + 2 + + + K1_ERK0 + 2 + + k6 + + + k10 + 2 + + + k5_MEK0 + + + + + + + + K1_ERK0 + 2 + + + + k6 + 2 + + + + k10 + 2 + + + + + k5_MEK0 + 2 + + + + + + + + + K1_ERK0 + 2 + + + + k4 + 2 + + + + k6 + 2 + + + + + + k10 + k2 + + 2 + + + + + + + k3_Raf0 + k5_MEK0 + + 2 + + + + + + + 2 + + + K1_ERK0 + 2 + + k4 + + + k6 + 2 + + k10 + + + k10 + k2 + + + + + k3_Raf0 + + + k5_MEK0 + 2 + + + + + + + + 2 + + + K1_ERK0 + 2 + + k4 + k6 + k10 + + + k10 + k2 + + + + + k3_Raf0 + k5_MEK0 + + + + + + + 4 + K1_ERK0 + k2 + k4 + k6 + k10 + + + + k3_Raf0 + k5_MEK0 + + + + 0.5 + + + + + K1_ERK0 + k10 + + + + + + + k6 + k5_MEK0 + + 1 + + 2 + + + + + + + + + k2 + k4 + k6 + + + + k3_Raf0 + k5_MEK0 + + + + + K1_ERK0 + + + + + K1_ERK0 + k6 + + k5_MEK0 + + 2 + + + + + + + + + K1_ERK0 + + + k6 + 2 + + k10 + + + + k3_Raf0 + k5_MEK0 + + + + + + + k6 + k5_MEK0 + + 1 + + + + + + + + + + + + + K1_ERK0 + + + K1_ERK0 + x3 + + + + + + + + + k11 + k11_k10 + + + + + + + + k10 + + + k11 + + + 1 + + + + + + + time + tau1 + + + + + + + + + + + time + tau2 + + + + + + + + + + + + + + k1max + xi + + + 1 + x1 + + + + + k2 + x1 + + + + + + + + + + + + + + + k3_Raf0 + K2 + x1 + + + + K2 + sora + + + + + 1 + x2 + + + + + k4 + x2 + + + + + + + + + + + + + + + k5_MEK0 + K3 + x2 + + + + K3 + UO126 + + + + + 1 + x3 + + + + + k6 + x3 + + + + + + + From d988b8b93b6891f6feab997edd4a9b432b195702 Mon Sep 17 00:00:00 2001 From: Maren Philipps Date: Fri, 25 Oct 2024 16:18:54 +0200 Subject: [PATCH 04/17] add PEtab model for reformulated Fiedler_BMCSystBiol2016 --- .../reformulated/Fiedler_BMCSystBiol2016.yaml | 13 ++++ ...entalCondition_Fiedler_BMCSystBiol2016.tsv | 4 + ...easurementData_Fiedler_BMCSystBiol2016.tsv | 73 +++++++++++++++++++ ....xml => model_Fiedler_BMCSystBiol2016.xml} | 4 +- .../observables_Fiedler_BMCSystBiol2016.tsv | 3 + .../parameters_Fiedler_BMCSystBiol2016.tsv | 23 ++++++ ...nSpecification_Fiedler_BMCSystBiol2016.tsv | 7 ++ 7 files changed, 125 insertions(+), 2 deletions(-) create mode 100644 Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/Fiedler_BMCSystBiol2016.yaml create mode 100644 Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/experimentalCondition_Fiedler_BMCSystBiol2016.tsv create mode 100644 Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/measurementData_Fiedler_BMCSystBiol2016.tsv rename Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/{model.xml => model_Fiedler_BMCSystBiol2016.xml} (99%) create mode 100644 Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/observables_Fiedler_BMCSystBiol2016.tsv create mode 100644 Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/parameters_Fiedler_BMCSystBiol2016.tsv create mode 100644 Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/visualizationSpecification_Fiedler_BMCSystBiol2016.tsv diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/Fiedler_BMCSystBiol2016.yaml b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/Fiedler_BMCSystBiol2016.yaml new file mode 100644 index 0000000..67687dd --- /dev/null +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/Fiedler_BMCSystBiol2016.yaml @@ -0,0 +1,13 @@ +format_version: 1 +parameter_file: parameters_Fiedler_BMCSystBiol2016.tsv +problems: +- condition_files: + - experimentalCondition_Fiedler_BMCSystBiol2016.tsv + measurement_files: + - measurementData_Fiedler_BMCSystBiol2016.tsv + observable_files: + - observables_Fiedler_BMCSystBiol2016.tsv + sbml_files: + - model_Fiedler_BMCSystBiol2016.xml + visualization_files: + - visualizationSpecification_Fiedler_BMCSystBiol2016.tsv diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/experimentalCondition_Fiedler_BMCSystBiol2016.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/experimentalCondition_Fiedler_BMCSystBiol2016.tsv new file mode 100644 index 0000000..2d18519 --- /dev/null +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/experimentalCondition_Fiedler_BMCSystBiol2016.tsv @@ -0,0 +1,4 @@ +conditionId conditionName Sorafenib UO126 +model1_data1 0 0 +model1_data2 5 0 +model1_data3 0 30 diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/measurementData_Fiedler_BMCSystBiol2016.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/measurementData_Fiedler_BMCSystBiol2016.tsv new file mode 100644 index 0000000..c2a1473 --- /dev/null +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/measurementData_Fiedler_BMCSystBiol2016.tsv @@ -0,0 +1,73 @@ +observableId preequilibrationConditionId simulationConditionId measurement time observableParameters noiseParameters datasetId +pMek_rel model1_data1 0.116721 0 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.232984 0.25 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.305171 1 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.125647 5.5 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.073706 7 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.058253 8.5 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.066667 10 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.22033 0 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data1 1.683107 0.25 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data1 1.441176 1 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.225572 5.5 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.278346 7 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.137178 8.5 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.196426 10 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data2 0.121231 0 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.086929466 1 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.054910478 5.5 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.048881617 7 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.052341248 8.5 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.052595374 10 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.155276 0 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.24 1 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.12 5.5 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.12 7 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.07 8.5 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.07 10 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data3 1.724493879 1 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 1.683168571 5.5 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 1.470175735 7 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 1.557371739 8.5 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 1.559108205 10 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 5.857600733 1 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 2.857976654 5.5 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 4.607660706 7 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 2.789397964 8.5 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 1.623004546 10 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel UO126 +pErk_rel model1_data1 0.037959 0 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.042262 0.25 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.162628 1 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.052124 5.5 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.023196 7 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.037687 8.5 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.028724 10 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.297881 0 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data1 3.043549 0.25 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data1 3.098459 1 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.224662 5.5 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.38254 7 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.123338 8.5 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.229486 10 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data2 0.039731 0 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.03303482 1 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.019296634 5.5 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.017683446 7 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.020209467 8.5 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.02141076 10 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.301624 0 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.54 1 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.27 5.5 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.25 7 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.18 8.5 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.15 10 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data3 0.004107653 1 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.011631788 5.5 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.012694322 7 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.003687738 8.5 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.002426131 10 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.176167582 1 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.069008927 5.5 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.074311261 7 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.073151837 8.5 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.048102336 10 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel UO126 diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/model.xml b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/model_Fiedler_BMCSystBiol2016.xml similarity index 99% rename from Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/model.xml rename to Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/model_Fiedler_BMCSystBiol2016.xml index 6bec097..e5e1d64 100644 --- a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/model.xml +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/model_Fiedler_BMCSystBiol2016.xml @@ -196,7 +196,7 @@ - + @@ -1590,7 +1590,7 @@ K2 - sora + Sorafenib diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/observables_Fiedler_BMCSystBiol2016.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/observables_Fiedler_BMCSystBiol2016.tsv new file mode 100644 index 0000000..da0359b --- /dev/null +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/observables_Fiedler_BMCSystBiol2016.tsv @@ -0,0 +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 diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/parameters_Fiedler_BMCSystBiol2016.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/parameters_Fiedler_BMCSystBiol2016.tsv new file mode 100644 index 0000000..ede65e5 --- /dev/null +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/parameters_Fiedler_BMCSystBiol2016.tsv @@ -0,0 +1,23 @@ +parameterId parameterName parameterScale lowerBound upperBound nominalValue estimate +k11_k10 k_{1,1}/k{1,0} log10 1E-04 1E02 1 1 +tau1 \tau_{1} log10 1E-04 1E02 0.242822010781068 1 +tau2 \tau_{2} log10 1E-04 1E02 0.021140927521636 1 +K1_ERK0 K_1/[ERK]_0 log10 1E-04 1E02 1 1 +k11 k_{1,1} log10 1E-04 1E02 1 1 +k2 k_2 log10 1E-04 1E02 1 1 +K2 K_2 log10 1E-04 1E02 1 1 +k3_Raf0 k_3[Raf]_0 log10 1E-04 1E02 1 1 +k4 k_4 log10 1E-04 1E02 1 1 +K3 K_3 log10 1E-04 1E02 1 1 +k5_MEK0 k_5[MEK]_0 log10 1E-04 1E02 1 1 +k6 k_6 log10 1E-04 1E02 1 1 +s_pMek_rel_20140430_gel1 s_{pMek_rel,20140430,gel1} log10 1E-04 1E02 77.7404398920619 1 +s_pMek_rel_20140430_gel2 s_{pMek_rel,20140430,gel2} log10 1E-04 1E02 404.217160578548 1 +s_pMek_rel_20140505_gel1 s_{pMek_rel,20140505,gel1} log10 1E-04 1E02 392.45653075379 1 +s_pMek_rel_20140505_gel2 s_{pMek_rel,20140505,gel2} log10 1E-04 1E02 999.992845715073 1 +s_pErk_rel_20140430_gel1 s_{pErk_rel,20140430,gel1} log10 1E-04 1E02 0.369256805232789 1 +s_pErk_rel_20140430_gel2 s_{pErk_rel,20140430,gel2} log10 1E-04 1E02 0.250134156378628 1 +s_pErk_rel_20140505_gel1 s_{pErk_rel,20140505,gel1} log10 1E-04 1E02 8.92600078593847 1 +s_pErk_rel_20140505_gel2 s_{pErk_rel,20140505,gel2} log10 1E-04 1E02 2.85637035018243 1 +sigma_pMek_rel \sigma_{pMek_rel} log10 1E-10 1E02 0.000580451138215 1 +sigma_pErk_rel \sigma_{pErk_rel} log10 1E-10 1E02 0.045270131337451 1 diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/visualizationSpecification_Fiedler_BMCSystBiol2016.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/visualizationSpecification_Fiedler_BMCSystBiol2016.tsv new file mode 100644 index 0000000..7d7378c --- /dev/null +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/visualizationSpecification_Fiedler_BMCSystBiol2016.tsv @@ -0,0 +1,7 @@ +plotId plotName plotTypeSimulation plotTypeData xLabel yValues yLabel datasetId +Fig8c_pMek_control relative pMek - control LinePlot replicate time [h] pMek_rel relative pMek [UI] control +Fig8c_pMek_Sorafenib relative pMek - 5 muM Sorafenib LinePlot replicate time [h] pMek_rel relative pMek [UI] Sorafenib +Fig8c_pMek_UO126 relative pMek - 30 muM UO126 LinePlot replicate time [h] pMek_rel relative pMek [UI] UO126 +Fig8c_pErk_control relative pErk - control LinePlot replicate time [h] pErk_rel relative pErk [UI] control +Fig8c_pErk_Sorafenib relative pMrk - 5 muM Sorafenib LinePlot replicate time [h] pErk_rel relative pErk [UI] Sorafenib +Fig8c_pErk_UO126 relative pMrk - 30 muM UO126 LinePlot replicate time [h] pErk_rel relative pErk [UI] UO126 From 21e903f91f2f9eeeaab5c6b16565fb77d82f2005 Mon Sep 17 00:00:00 2001 From: Maren Philipps Date: Fri, 25 Oct 2024 17:24:11 +0200 Subject: [PATCH 05/17] try optimisation --- .../reformulated/opt/calibrate.py | 68 +++++++++++++++++++ .../reformulated/opt/sbatch.sh | 13 ++++ 2 files changed, 81 insertions(+) create mode 100644 Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/opt/calibrate.py create mode 100644 Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/opt/sbatch.sh diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/opt/calibrate.py b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/opt/calibrate.py new file mode 100644 index 0000000..7568fbc --- /dev/null +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/opt/calibrate.py @@ -0,0 +1,68 @@ +import petab +import amici +import pypesto +import pypesto.petab +import pypesto.optimize +import pypesto.store +from pathlib import Path + +model_name = "Fiedler_BMCSystBiol2016" +petab_problem = petab.Problem.from_yaml(f"../{model_name}.yaml") +petab_problem_flat = petab.Problem.from_yaml(f"../{model_name}.yaml") +petab.flatten_timepoint_specific_output_overrides(petab_problem_flat) +petab_problem_flat.visualization_df = None + +pypesto_importer = pypesto.petab.PetabImporter(petab_problem_flat) +pypesto_problem = pypesto_importer.create_problem() + +result = pypesto.optimize.minimize( + pypesto_problem, + optimizer=pypesto.optimize.FidesOptimizer(), + n_starts=1000, +) + +# Save result object in hdf5 file +pypesto.store.save_to_hdf5.write_result(result, 'result.hdf5', overwrite= True) + +# Visualization +import pypesto.visualize as vis +import matplotlib.pyplot as plt + +vis.waterfall(result, size=(8, 4)) +plt.savefig('waterfall.png') +plt.close() + +from pypesto.visualize.model_fit import visualize_optimized_model_fit +visualize_optimized_model_fit( + petab_problem=petab_problem_flat, + result=result, + pypesto_problem=pypesto_problem, + return_dict=False, + start_index=n, + unflattened_petab_problem=petab_problem, +) +plt.savefig("fit.png") +plt.close() + +FITS_PATH = Path(__file__).resolve().parent / "fits" +FITS_PATH.mkdir(exist_ok=True) +for n in range(1, 20): + visualize_optimized_model_fit( + petab_problem=petab_problem_flat, + result=result, + pypesto_problem=pypesto_problem, + return_dict=False, + start_index=n, + unflattened_petab_problem=petab_problem, + ) + plt.savefig(FITS_PATH / f"fit_{str(n).rjust(2, '0')}.png") + plt.close() + + +vis.parameters( + result, + legends="optimizer", + start_indices=[0, 1, 2, 3], +) +plt.savefig('parameters.png') +plt.close() \ No newline at end of file diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/opt/sbatch.sh b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/opt/sbatch.sh new file mode 100644 index 0000000..844e732 --- /dev/null +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/opt/sbatch.sh @@ -0,0 +1,13 @@ +#!/bin/bash +#SBATCH --job-name fied +#SBATCH --output log/%j.log +#SBATCH --nodes 1 +#SBATCH --ntasks 1 +#SBATCH --cpus-per-task 48 +#SBATCH --time 07-00:00:00 +#SBATCH --mail-type=BEGIN,END,FAIL +#SBATCH --mail-user=maren.philipps@uni-bonn.de + +source home/maren/prerequisites.sh +source /home/maren/devenv/bin/activate +python calibrate.py From 3abfb1de36f065123c84c3d56fb8594e4a751d98 Mon Sep 17 00:00:00 2001 From: Maren Philipps Date: Wed, 4 Dec 2024 14:59:47 +0100 Subject: [PATCH 06/17] remove PREEEQUILIBRATION column --- ...easurementData_Fiedler_BMCSystBiol2016.tsv | 146 +++++++++--------- 1 file changed, 73 insertions(+), 73 deletions(-) diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/measurementData_Fiedler_BMCSystBiol2016.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/measurementData_Fiedler_BMCSystBiol2016.tsv index df0578f..dd1d84f 100644 --- a/Benchmark-Models/Fiedler_BMCSystBiol2016/measurementData_Fiedler_BMCSystBiol2016.tsv +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/measurementData_Fiedler_BMCSystBiol2016.tsv @@ -1,73 +1,73 @@ -observableId preequilibrationConditionId simulationConditionId measurement time observableParameters noiseParameters -pErk model1_data1 0.037959 0 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk -pErk model1_data1 0.042262 0.25 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk -pErk model1_data1 0.162628 1 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk -pErk model1_data1 0.052124 5.5 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk -pErk model1_data1 0.023196 7 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk -pErk model1_data1 0.037687 8.5 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk -pErk model1_data1 0.028724 10 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk -pErk model1_data1 0.297881 0 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk -pErk model1_data1 3.043549 0.25 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk -pErk model1_data1 3.098459 1 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk -pErk model1_data1 0.224662 5.5 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk -pErk model1_data1 0.38254 7 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk -pErk model1_data1 0.123338 8.5 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk -pErk model1_data1 0.229486 10 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk -pErk model1_data2 0.039731 0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data2 0.03303482 1 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data2 0.019296634 5.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data2 0.017683446 7 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data2 0.020209467 8.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data2 0.02141076 10 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data2 0.301624 0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data2 0.54 1 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data2 0.27 5.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data2 0.25 7 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data2 0.18 8.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data2 0.15 10 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data3 0.004107653 1 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data3 0.011631788 5.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data3 0.012694322 7 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data3 0.003687738 8.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data3 0.002426131 10 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data3 0.176167582 1 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data3 0.069008927 5.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data3 0.074311261 7 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data3 0.073151837 8.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data3 0.048102336 10 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pMek model1_data1 0.116721 0 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek -pMek model1_data1 0.232984 0.25 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek -pMek model1_data1 0.305171 1 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek -pMek model1_data1 0.125647 5.5 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek -pMek model1_data1 0.073706 7 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek -pMek model1_data1 0.058253 8.5 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek -pMek model1_data1 0.066667 10 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek -pMek model1_data1 0.22033 0 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek -pMek model1_data1 1.683107 0.25 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek -pMek model1_data1 1.441176 1 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek -pMek model1_data1 0.225572 5.5 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek -pMek model1_data1 0.278346 7 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek -pMek model1_data1 0.137178 8.5 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek -pMek model1_data1 0.196426 10 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek -pMek model1_data2 0.121231 0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data2 0.086929466 1 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data2 0.054910478 5.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data2 0.048881617 7 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data2 0.052341248 8.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data2 0.052595374 10 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data2 0.155276 0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data2 0.24 1 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data2 0.12 5.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data2 0.12 7 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data2 0.07 8.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data2 0.07 10 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data3 1.724493879 1 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data3 1.683168571 5.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data3 1.470175735 7 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data3 1.557371739 8.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data3 1.559108205 10 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data3 5.857600733 1 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data3 2.857976654 5.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data3 4.607660706 7 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data3 2.789397964 8.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data3 1.623004546 10 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek +observableId simulationConditionId measurement time observableParameters noiseParameters +pErk model1_data1 0.037959 0 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk +pErk model1_data1 0.042262 0.25 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk +pErk model1_data1 0.162628 1 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk +pErk model1_data1 0.052124 5.5 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk +pErk model1_data1 0.023196 7 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk +pErk model1_data1 0.037687 8.5 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk +pErk model1_data1 0.028724 10 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk +pErk model1_data1 0.297881 0 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk +pErk model1_data1 3.043549 0.25 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk +pErk model1_data1 3.098459 1 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk +pErk model1_data1 0.224662 5.5 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk +pErk model1_data1 0.38254 7 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk +pErk model1_data1 0.123338 8.5 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk +pErk model1_data1 0.229486 10 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk +pErk model1_data2 0.039731 0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk +pErk model1_data2 0.03303482 1 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk +pErk model1_data2 0.019296634 5.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk +pErk model1_data2 0.017683446 7 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk +pErk model1_data2 0.020209467 8.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk +pErk model1_data2 0.02141076 10 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk +pErk model1_data2 0.301624 0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk +pErk model1_data2 0.54 1 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk +pErk model1_data2 0.27 5.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk +pErk model1_data2 0.25 7 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk +pErk model1_data2 0.18 8.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk +pErk model1_data2 0.15 10 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk +pErk model1_data3 0.004107653 1 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk +pErk model1_data3 0.011631788 5.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk +pErk model1_data3 0.012694322 7 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk +pErk model1_data3 0.003687738 8.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk +pErk model1_data3 0.002426131 10 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk +pErk model1_data3 0.176167582 1 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk +pErk model1_data3 0.069008927 5.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk +pErk model1_data3 0.074311261 7 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk +pErk model1_data3 0.073151837 8.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk +pErk model1_data3 0.048102336 10 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk +pMek model1_data1 0.116721 0 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek +pMek model1_data1 0.232984 0.25 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek +pMek model1_data1 0.305171 1 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek +pMek model1_data1 0.125647 5.5 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek +pMek model1_data1 0.073706 7 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek +pMek model1_data1 0.058253 8.5 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek +pMek model1_data1 0.066667 10 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek +pMek model1_data1 0.22033 0 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek +pMek model1_data1 1.683107 0.25 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek +pMek model1_data1 1.441176 1 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek +pMek model1_data1 0.225572 5.5 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek +pMek model1_data1 0.278346 7 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek +pMek model1_data1 0.137178 8.5 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek +pMek model1_data1 0.196426 10 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek +pMek model1_data2 0.121231 0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek +pMek model1_data2 0.086929466 1 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek +pMek model1_data2 0.054910478 5.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek +pMek model1_data2 0.048881617 7 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek +pMek model1_data2 0.052341248 8.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek +pMek model1_data2 0.052595374 10 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek +pMek model1_data2 0.155276 0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek +pMek model1_data2 0.24 1 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek +pMek model1_data2 0.12 5.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek +pMek model1_data2 0.12 7 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek +pMek model1_data2 0.07 8.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek +pMek model1_data2 0.07 10 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek +pMek model1_data3 1.724493879 1 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek +pMek model1_data3 1.683168571 5.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek +pMek model1_data3 1.470175735 7 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek +pMek model1_data3 1.557371739 8.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek +pMek model1_data3 1.559108205 10 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek +pMek model1_data3 5.857600733 1 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek +pMek model1_data3 2.857976654 5.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek +pMek model1_data3 4.607660706 7 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek +pMek model1_data3 2.789397964 8.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek +pMek model1_data3 1.623004546 10 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek From 065f414b27d5eeeb13872ba299a4a8cc891cd4b6 Mon Sep 17 00:00:00 2001 From: Maren Philipps Date: Wed, 4 Dec 2024 15:00:36 +0100 Subject: [PATCH 07/17] remove PREEQUILIBRATION column --- ...easurementData_Fiedler_BMCSystBiol2016.tsv | 146 +++++++++--------- 1 file changed, 73 insertions(+), 73 deletions(-) diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/measurementData_Fiedler_BMCSystBiol2016.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/measurementData_Fiedler_BMCSystBiol2016.tsv index c2a1473..0c8c060 100644 --- a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/measurementData_Fiedler_BMCSystBiol2016.tsv +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/measurementData_Fiedler_BMCSystBiol2016.tsv @@ -1,73 +1,73 @@ -observableId preequilibrationConditionId simulationConditionId measurement time observableParameters noiseParameters datasetId -pMek_rel model1_data1 0.116721 0 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control -pMek_rel model1_data1 0.232984 0.25 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control -pMek_rel model1_data1 0.305171 1 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control -pMek_rel model1_data1 0.125647 5.5 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control -pMek_rel model1_data1 0.073706 7 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control -pMek_rel model1_data1 0.058253 8.5 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control -pMek_rel model1_data1 0.066667 10 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control -pMek_rel model1_data1 0.22033 0 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control -pMek_rel model1_data1 1.683107 0.25 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control -pMek_rel model1_data1 1.441176 1 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control -pMek_rel model1_data1 0.225572 5.5 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control -pMek_rel model1_data1 0.278346 7 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control -pMek_rel model1_data1 0.137178 8.5 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control -pMek_rel model1_data1 0.196426 10 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control -pMek_rel model1_data2 0.121231 0 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib -pMek_rel model1_data2 0.086929466 1 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib -pMek_rel model1_data2 0.054910478 5.5 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib -pMek_rel model1_data2 0.048881617 7 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib -pMek_rel model1_data2 0.052341248 8.5 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib -pMek_rel model1_data2 0.052595374 10 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib -pMek_rel model1_data2 0.155276 0 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib -pMek_rel model1_data2 0.24 1 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib -pMek_rel model1_data2 0.12 5.5 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib -pMek_rel model1_data2 0.12 7 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib -pMek_rel model1_data2 0.07 8.5 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib -pMek_rel model1_data2 0.07 10 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib -pMek_rel model1_data3 1.724493879 1 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel UO126 -pMek_rel model1_data3 1.683168571 5.5 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel UO126 -pMek_rel model1_data3 1.470175735 7 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel UO126 -pMek_rel model1_data3 1.557371739 8.5 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel UO126 -pMek_rel model1_data3 1.559108205 10 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel UO126 -pMek_rel model1_data3 5.857600733 1 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel UO126 -pMek_rel model1_data3 2.857976654 5.5 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel UO126 -pMek_rel model1_data3 4.607660706 7 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel UO126 -pMek_rel model1_data3 2.789397964 8.5 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel UO126 -pMek_rel model1_data3 1.623004546 10 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel UO126 -pErk_rel model1_data1 0.037959 0 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control -pErk_rel model1_data1 0.042262 0.25 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control -pErk_rel model1_data1 0.162628 1 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control -pErk_rel model1_data1 0.052124 5.5 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control -pErk_rel model1_data1 0.023196 7 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control -pErk_rel model1_data1 0.037687 8.5 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control -pErk_rel model1_data1 0.028724 10 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control -pErk_rel model1_data1 0.297881 0 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control -pErk_rel model1_data1 3.043549 0.25 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control -pErk_rel model1_data1 3.098459 1 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control -pErk_rel model1_data1 0.224662 5.5 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control -pErk_rel model1_data1 0.38254 7 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control -pErk_rel model1_data1 0.123338 8.5 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control -pErk_rel model1_data1 0.229486 10 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control -pErk_rel model1_data2 0.039731 0 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib -pErk_rel model1_data2 0.03303482 1 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib -pErk_rel model1_data2 0.019296634 5.5 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib -pErk_rel model1_data2 0.017683446 7 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib -pErk_rel model1_data2 0.020209467 8.5 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib -pErk_rel model1_data2 0.02141076 10 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib -pErk_rel model1_data2 0.301624 0 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib -pErk_rel model1_data2 0.54 1 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib -pErk_rel model1_data2 0.27 5.5 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib -pErk_rel model1_data2 0.25 7 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib -pErk_rel model1_data2 0.18 8.5 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib -pErk_rel model1_data2 0.15 10 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib -pErk_rel model1_data3 0.004107653 1 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel UO126 -pErk_rel model1_data3 0.011631788 5.5 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel UO126 -pErk_rel model1_data3 0.012694322 7 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel UO126 -pErk_rel model1_data3 0.003687738 8.5 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel UO126 -pErk_rel model1_data3 0.002426131 10 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel UO126 -pErk_rel model1_data3 0.176167582 1 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel UO126 -pErk_rel model1_data3 0.069008927 5.5 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel UO126 -pErk_rel model1_data3 0.074311261 7 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel UO126 -pErk_rel model1_data3 0.073151837 8.5 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel UO126 -pErk_rel model1_data3 0.048102336 10 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel UO126 +observableId simulationConditionId measurement time observableParameters noiseParameters datasetId +pMek_rel model1_data1 0.116721 0 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.232984 0.25 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.305171 1 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.125647 5.5 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.073706 7 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.058253 8.5 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.066667 10 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.22033 0 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data1 1.683107 0.25 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data1 1.441176 1 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.225572 5.5 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.278346 7 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.137178 8.5 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.196426 10 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data2 0.121231 0 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.086929466 1 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.054910478 5.5 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.048881617 7 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.052341248 8.5 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.052595374 10 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.155276 0 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.24 1 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.12 5.5 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.12 7 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.07 8.5 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.07 10 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data3 1.724493879 1 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 1.683168571 5.5 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 1.470175735 7 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 1.557371739 8.5 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 1.559108205 10 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 5.857600733 1 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 2.857976654 5.5 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 4.607660706 7 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 2.789397964 8.5 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 1.623004546 10 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel UO126 +pErk_rel model1_data1 0.037959 0 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.042262 0.25 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.162628 1 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.052124 5.5 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.023196 7 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.037687 8.5 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.028724 10 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.297881 0 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data1 3.043549 0.25 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data1 3.098459 1 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.224662 5.5 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.38254 7 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.123338 8.5 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.229486 10 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data2 0.039731 0 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.03303482 1 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.019296634 5.5 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.017683446 7 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.020209467 8.5 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.02141076 10 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.301624 0 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.54 1 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.27 5.5 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.25 7 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.18 8.5 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.15 10 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data3 0.004107653 1 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.011631788 5.5 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.012694322 7 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.003687738 8.5 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.002426131 10 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.176167582 1 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.069008927 5.5 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.074311261 7 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.073151837 8.5 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.048102336 10 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel UO126 From 97be5bb09969d7b10635d8adeb4efb9af2a051f0 Mon Sep 17 00:00:00 2001 From: Maren Philipps Date: Wed, 4 Dec 2024 15:05:26 +0100 Subject: [PATCH 08/17] update calibration script --- .../reformulated/opt/calibrate.py | 11 +---------- 1 file changed, 1 insertion(+), 10 deletions(-) diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/opt/calibrate.py b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/opt/calibrate.py index 7568fbc..0b0c421 100644 --- a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/opt/calibrate.py +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/opt/calibrate.py @@ -38,7 +38,7 @@ result=result, pypesto_problem=pypesto_problem, return_dict=False, - start_index=n, + start_index=0, unflattened_petab_problem=petab_problem, ) plt.savefig("fit.png") @@ -57,12 +57,3 @@ ) plt.savefig(FITS_PATH / f"fit_{str(n).rjust(2, '0')}.png") plt.close() - - -vis.parameters( - result, - legends="optimizer", - start_indices=[0, 1, 2, 3], -) -plt.savefig('parameters.png') -plt.close() \ No newline at end of file From 2a7d38ca5c638e6a02e9ae1ac78a4769d7953868 Mon Sep 17 00:00:00 2001 From: Maren Philipps Date: Wed, 4 Dec 2024 15:11:32 +0100 Subject: [PATCH 09/17] add dataset id column for convenience --- ...easurementData_Fiedler_BMCSystBiol2016.tsv | 146 +++++++++--------- 1 file changed, 73 insertions(+), 73 deletions(-) diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/measurementData_Fiedler_BMCSystBiol2016.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/measurementData_Fiedler_BMCSystBiol2016.tsv index dd1d84f..9d1adc7 100644 --- a/Benchmark-Models/Fiedler_BMCSystBiol2016/measurementData_Fiedler_BMCSystBiol2016.tsv +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/measurementData_Fiedler_BMCSystBiol2016.tsv @@ -1,73 +1,73 @@ -observableId simulationConditionId measurement time observableParameters noiseParameters -pErk model1_data1 0.037959 0 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk -pErk model1_data1 0.042262 0.25 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk -pErk model1_data1 0.162628 1 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk -pErk model1_data1 0.052124 5.5 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk -pErk model1_data1 0.023196 7 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk -pErk model1_data1 0.037687 8.5 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk -pErk model1_data1 0.028724 10 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk -pErk model1_data1 0.297881 0 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk -pErk model1_data1 3.043549 0.25 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk -pErk model1_data1 3.098459 1 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk -pErk model1_data1 0.224662 5.5 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk -pErk model1_data1 0.38254 7 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk -pErk model1_data1 0.123338 8.5 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk -pErk model1_data1 0.229486 10 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk -pErk model1_data2 0.039731 0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data2 0.03303482 1 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data2 0.019296634 5.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data2 0.017683446 7 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data2 0.020209467 8.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data2 0.02141076 10 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data2 0.301624 0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data2 0.54 1 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data2 0.27 5.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data2 0.25 7 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data2 0.18 8.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data2 0.15 10 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data3 0.004107653 1 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data3 0.011631788 5.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data3 0.012694322 7 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data3 0.003687738 8.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data3 0.002426131 10 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data3 0.176167582 1 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data3 0.069008927 5.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data3 0.074311261 7 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data3 0.073151837 8.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data3 0.048102336 10 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pMek model1_data1 0.116721 0 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek -pMek model1_data1 0.232984 0.25 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek -pMek model1_data1 0.305171 1 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek -pMek model1_data1 0.125647 5.5 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek -pMek model1_data1 0.073706 7 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek -pMek model1_data1 0.058253 8.5 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek -pMek model1_data1 0.066667 10 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek -pMek model1_data1 0.22033 0 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek -pMek model1_data1 1.683107 0.25 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek -pMek model1_data1 1.441176 1 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek -pMek model1_data1 0.225572 5.5 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek -pMek model1_data1 0.278346 7 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek -pMek model1_data1 0.137178 8.5 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek -pMek model1_data1 0.196426 10 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek -pMek model1_data2 0.121231 0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data2 0.086929466 1 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data2 0.054910478 5.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data2 0.048881617 7 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data2 0.052341248 8.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data2 0.052595374 10 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data2 0.155276 0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data2 0.24 1 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data2 0.12 5.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data2 0.12 7 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data2 0.07 8.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data2 0.07 10 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data3 1.724493879 1 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data3 1.683168571 5.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data3 1.470175735 7 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data3 1.557371739 8.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data3 1.559108205 10 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data3 5.857600733 1 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data3 2.857976654 5.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data3 4.607660706 7 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data3 2.789397964 8.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data3 1.623004546 10 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek +observableId simulationConditionId measurement time observableParameters noiseParameters datasetId +pErk model1_data1 0.037959 0 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control +pErk model1_data1 0.042262 0.25 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control +pErk model1_data1 0.162628 1 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control +pErk model1_data1 0.052124 5.5 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control +pErk model1_data1 0.023196 7 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control +pErk model1_data1 0.037687 8.5 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control +pErk model1_data1 0.028724 10 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control +pErk model1_data1 0.297881 0 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk control +pErk model1_data1 3.043549 0.25 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk control +pErk model1_data1 3.098459 1 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk control +pErk model1_data1 0.224662 5.5 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk control +pErk model1_data1 0.38254 7 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk control +pErk model1_data1 0.123338 8.5 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk control +pErk model1_data1 0.229486 10 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk control +pErk model1_data2 0.039731 0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.03303482 1 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.019296634 5.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.017683446 7 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.020209467 8.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.02141076 10 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.301624 0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.54 1 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.27 5.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.25 7 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.18 8.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.15 10 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk Sorafenib +pErk model1_data3 0.004107653 1 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk UO126 +pErk model1_data3 0.011631788 5.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk UO126 +pErk model1_data3 0.012694322 7 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk UO126 +pErk model1_data3 0.003687738 8.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk UO126 +pErk model1_data3 0.002426131 10 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk UO126 +pErk model1_data3 0.176167582 1 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk UO126 +pErk model1_data3 0.069008927 5.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk UO126 +pErk model1_data3 0.074311261 7 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk UO126 +pErk model1_data3 0.073151837 8.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk UO126 +pErk model1_data3 0.048102336 10 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk UO126 +pMek model1_data1 0.116721 0 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek control +pMek model1_data1 0.232984 0.25 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek control +pMek model1_data1 0.305171 1 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek control +pMek model1_data1 0.125647 5.5 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek control +pMek model1_data1 0.073706 7 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek control +pMek model1_data1 0.058253 8.5 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek control +pMek model1_data1 0.066667 10 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek control +pMek model1_data1 0.22033 0 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek control +pMek model1_data1 1.683107 0.25 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek control +pMek model1_data1 1.441176 1 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek control +pMek model1_data1 0.225572 5.5 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek control +pMek model1_data1 0.278346 7 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek control +pMek model1_data1 0.137178 8.5 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek control +pMek model1_data1 0.196426 10 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek control +pMek model1_data2 0.121231 0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.086929466 1 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.054910478 5.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.048881617 7 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.052341248 8.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.052595374 10 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.155276 0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.24 1 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.12 5.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.12 7 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.07 8.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.07 10 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek Sorafenib +pMek model1_data3 1.724493879 1 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek UO126 +pMek model1_data3 1.683168571 5.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek UO126 +pMek model1_data3 1.470175735 7 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek UO126 +pMek model1_data3 1.557371739 8.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek UO126 +pMek model1_data3 1.559108205 10 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek UO126 +pMek model1_data3 5.857600733 1 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek UO126 +pMek model1_data3 2.857976654 5.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek UO126 +pMek model1_data3 4.607660706 7 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek UO126 +pMek model1_data3 2.789397964 8.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek UO126 +pMek model1_data3 1.623004546 10 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek UO126 From 66bc26a92fffd98e265a0bf85ea2ba372aeda376 Mon Sep 17 00:00:00 2001 From: Maren Philipps Date: Wed, 4 Dec 2024 15:26:57 +0100 Subject: [PATCH 10/17] update nominal parameters with estimated values --- .../parameters_Fiedler_BMCSystBiol2016.tsv | 44 +++++++++---------- 1 file changed, 22 insertions(+), 22 deletions(-) diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/parameters_Fiedler_BMCSystBiol2016.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/parameters_Fiedler_BMCSystBiol2016.tsv index ede65e5..88e1f7e 100644 --- a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/parameters_Fiedler_BMCSystBiol2016.tsv +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/parameters_Fiedler_BMCSystBiol2016.tsv @@ -1,23 +1,23 @@ parameterId parameterName parameterScale lowerBound upperBound nominalValue estimate -k11_k10 k_{1,1}/k{1,0} log10 1E-04 1E02 1 1 -tau1 \tau_{1} log10 1E-04 1E02 0.242822010781068 1 -tau2 \tau_{2} log10 1E-04 1E02 0.021140927521636 1 -K1_ERK0 K_1/[ERK]_0 log10 1E-04 1E02 1 1 -k11 k_{1,1} log10 1E-04 1E02 1 1 -k2 k_2 log10 1E-04 1E02 1 1 -K2 K_2 log10 1E-04 1E02 1 1 -k3_Raf0 k_3[Raf]_0 log10 1E-04 1E02 1 1 -k4 k_4 log10 1E-04 1E02 1 1 -K3 K_3 log10 1E-04 1E02 1 1 -k5_MEK0 k_5[MEK]_0 log10 1E-04 1E02 1 1 -k6 k_6 log10 1E-04 1E02 1 1 -s_pMek_rel_20140430_gel1 s_{pMek_rel,20140430,gel1} log10 1E-04 1E02 77.7404398920619 1 -s_pMek_rel_20140430_gel2 s_{pMek_rel,20140430,gel2} log10 1E-04 1E02 404.217160578548 1 -s_pMek_rel_20140505_gel1 s_{pMek_rel,20140505,gel1} log10 1E-04 1E02 392.45653075379 1 -s_pMek_rel_20140505_gel2 s_{pMek_rel,20140505,gel2} log10 1E-04 1E02 999.992845715073 1 -s_pErk_rel_20140430_gel1 s_{pErk_rel,20140430,gel1} log10 1E-04 1E02 0.369256805232789 1 -s_pErk_rel_20140430_gel2 s_{pErk_rel,20140430,gel2} log10 1E-04 1E02 0.250134156378628 1 -s_pErk_rel_20140505_gel1 s_{pErk_rel,20140505,gel1} log10 1E-04 1E02 8.92600078593847 1 -s_pErk_rel_20140505_gel2 s_{pErk_rel,20140505,gel2} log10 1E-04 1E02 2.85637035018243 1 -sigma_pMek_rel \sigma_{pMek_rel} log10 1E-10 1E02 0.000580451138215 1 -sigma_pErk_rel \sigma_{pErk_rel} log10 1E-10 1E02 0.045270131337451 1 +k11_k10 k_{1,1}/k{1,0} log10 1E-04 1E02 99.99999999999484 1 +tau1 \tau_{1} log10 1E-04 1E02 0.00010000000000000521 1 +tau2 \tau_{2} log10 1E-04 1E02 0.09288918225167495 1 +K1_ERK0 K_1/[ERK]_0 log10 1E-04 1E02 0.00010000000000012946 1 +k11 k_{1,1} log10 1E-04 1E02 26.142114172396994 1 +k2 k_2 log10 1E-04 1E02 1.757125014844015 1 +K2 K_2 log10 1E-04 1E02 1.6238964133341307 1 +k3_Raf0 k_3[Raf]_0 log10 1E-04 1E02 99.99999999999488 1 +k4 k_4 log10 1E-04 1E02 2.8508244620658574 1 +K3 K_3 log10 1E-04 1E02 0.8147224203594344 1 +k5_MEK0 k_5[MEK]_0 log10 1E-04 1E02 50.6208607696601 1 +k6 k_6 log10 1E-04 1E02 3.0464232664775106 1 +s_pMek_rel_20140430_gel1 s_{pMek_rel,20140430,gel1} log10 1E-04 1E02 9.113038276921857 1 +s_pMek_rel_20140430_gel2 s_{pMek_rel,20140430,gel2} log10 1E-04 1E02 40.51627466624935 1 +s_pMek_rel_20140505_gel1 s_{pMek_rel,20140505,gel1} log10 1E-04 1E02 46.07048727325895 1 +s_pMek_rel_20140505_gel2 s_{pMek_rel,20140505,gel2} log10 1E-04 1E02 99.99999999999484 1 +s_pErk_rel_20140430_gel1 s_{pErk_rel,20140430,gel1} log10 1E-04 1E02 0.4021713054528761 1 +s_pErk_rel_20140430_gel2 s_{pErk_rel,20140430,gel2} log10 1E-04 1E02 0.2576150559169624 1 +s_pErk_rel_20140505_gel1 s_{pErk_rel,20140505,gel1} log10 1E-04 1E02 9.945014474175611 1 +s_pErk_rel_20140505_gel2 s_{pErk_rel,20140505,gel2} log10 1E-04 1E02 2.93201266036779 1 +sigma_pMek_rel \sigma_{pMek_rel} log10 1E-10 1E02 0.005555731242143642 1 +sigma_pErk_rel \sigma_{pErk_rel} log10 1E-10 1E02 0.042968298321873856 1 From 3c1760101a9a425d92058d48ffc4be8094c70a1c Mon Sep 17 00:00:00 2001 From: Maren Philipps Date: Wed, 4 Dec 2024 15:36:35 +0100 Subject: [PATCH 11/17] add simulated data --- .../simulatedData_Fiedler_BMCSystBiol2016.tsv | 73 +++++++++++++++++++ 1 file changed, 73 insertions(+) create mode 100644 Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/simulatedData_Fiedler_BMCSystBiol2016.tsv diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/simulatedData_Fiedler_BMCSystBiol2016.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/simulatedData_Fiedler_BMCSystBiol2016.tsv new file mode 100644 index 0000000..389b3e4 --- /dev/null +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/simulatedData_Fiedler_BMCSystBiol2016.tsv @@ -0,0 +1,73 @@ +observableId simulationConditionId simulation time observableParameters noiseParameters datasetId +pErk_rel model1_data1 0.03562601663400499 0.0 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.07699231174258513 0.25 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.14402998418113844 1.0 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.03574741674348277 5.5 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.035609796661362776 7.0 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.035628205279640356 8.5 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.03562574483699764 10.0 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.8809709849473971 0.0 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data1 1.9038893235260133 0.25 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data1 3.561617295852907 1.0 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.8839730038123768 5.5 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.8805698925260571 7.0 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.8810251064429573 8.5 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.8809642638682561 10.0 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pMek_rel model1_data1 0.053304487267850226 0.0 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.2890457361885378 0.25 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.2664185694635477 1.0 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.05326846796565126 5.5 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.05330751822204037 7.0 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.05330430271665209 8.5 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.05330448502782727 10.0 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.26947804098443656 0.0 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data1 1.4612555665641016 0.25 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data1 1.3468651113771104 1.0 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.2692959472904211 5.5 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.26949336381445216 7.0 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.26947710799552915 8.5 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.2694780296601179 10.0 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pErk_rel model1_data2 0.022820619330195413 0.0 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.037750653794211476 1.0 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.011577563362067483 5.5 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.011576634634047235 7.0 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.011576970135300398 8.5 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.011576893591693477 10.0 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.2597299468985005 0.0 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.42965421593009245 1.0 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.1317685499124472 5.5 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.13175797971380834 7.0 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.13176179817821582 8.5 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.131760927006988 10.0 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib +pMek_rel model1_data2 0.23699003356071716 0.0 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.357828707080205 1.0 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.11440162749435745 5.5 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.11477459986885565 7.0 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.11472507878847057 8.5 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.11473163273667024 10.0 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.5849255281066625 0.0 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.8831727744660174 1.0 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.28235968986963594 5.5 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.28328023939589553 7.0 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.2831580142387383 8.5 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.28317419032662805 10.0 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib +pErk_rel model1_data3 0.006736047578857687 1.0 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.0037868589718997466 5.5 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.0037913343479712073 7.0 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.003790745494772537 8.5 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.0037908227143303723 10.0 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.07666546006696386 1.0 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.043099648850555936 5.5 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.043150584768314015 7.0 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.0431438828112896 8.5 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.04314476167576588 10.0 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel UO126 +pMek_rel model1_data3 2.078148965157676 1.0 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 1.375499754701807 5.5 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 1.377579664273273 7.0 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 1.3772966402008164 8.5 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 1.3773351165383614 10.0 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 5.129170888183106 1.0 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 3.394931459104624 5.5 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 3.4000649754226933 7.0 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 3.39936643125794 8.5 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 3.3994613963993845 10.0 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel UO126 From 18484dcca3ded5ae94d44740e7ccb3fa21e86480 Mon Sep 17 00:00:00 2001 From: Maren Philipps Date: Wed, 4 Dec 2024 15:38:12 +0100 Subject: [PATCH 12/17] remove calibration files --- .../reformulated/opt/calibrate.py | 59 ------------------- .../reformulated/opt/sbatch.sh | 13 ---- 2 files changed, 72 deletions(-) delete mode 100644 Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/opt/calibrate.py delete mode 100644 Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/opt/sbatch.sh diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/opt/calibrate.py b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/opt/calibrate.py deleted file mode 100644 index 0b0c421..0000000 --- a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/opt/calibrate.py +++ /dev/null @@ -1,59 +0,0 @@ -import petab -import amici -import pypesto -import pypesto.petab -import pypesto.optimize -import pypesto.store -from pathlib import Path - -model_name = "Fiedler_BMCSystBiol2016" -petab_problem = petab.Problem.from_yaml(f"../{model_name}.yaml") -petab_problem_flat = petab.Problem.from_yaml(f"../{model_name}.yaml") -petab.flatten_timepoint_specific_output_overrides(petab_problem_flat) -petab_problem_flat.visualization_df = None - -pypesto_importer = pypesto.petab.PetabImporter(petab_problem_flat) -pypesto_problem = pypesto_importer.create_problem() - -result = pypesto.optimize.minimize( - pypesto_problem, - optimizer=pypesto.optimize.FidesOptimizer(), - n_starts=1000, -) - -# Save result object in hdf5 file -pypesto.store.save_to_hdf5.write_result(result, 'result.hdf5', overwrite= True) - -# Visualization -import pypesto.visualize as vis -import matplotlib.pyplot as plt - -vis.waterfall(result, size=(8, 4)) -plt.savefig('waterfall.png') -plt.close() - -from pypesto.visualize.model_fit import visualize_optimized_model_fit -visualize_optimized_model_fit( - petab_problem=petab_problem_flat, - result=result, - pypesto_problem=pypesto_problem, - return_dict=False, - start_index=0, - unflattened_petab_problem=petab_problem, -) -plt.savefig("fit.png") -plt.close() - -FITS_PATH = Path(__file__).resolve().parent / "fits" -FITS_PATH.mkdir(exist_ok=True) -for n in range(1, 20): - visualize_optimized_model_fit( - petab_problem=petab_problem_flat, - result=result, - pypesto_problem=pypesto_problem, - return_dict=False, - start_index=n, - unflattened_petab_problem=petab_problem, - ) - plt.savefig(FITS_PATH / f"fit_{str(n).rjust(2, '0')}.png") - plt.close() diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/opt/sbatch.sh b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/opt/sbatch.sh deleted file mode 100644 index 844e732..0000000 --- a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/opt/sbatch.sh +++ /dev/null @@ -1,13 +0,0 @@ -#!/bin/bash -#SBATCH --job-name fied -#SBATCH --output log/%j.log -#SBATCH --nodes 1 -#SBATCH --ntasks 1 -#SBATCH --cpus-per-task 48 -#SBATCH --time 07-00:00:00 -#SBATCH --mail-type=BEGIN,END,FAIL -#SBATCH --mail-user=maren.philipps@uni-bonn.de - -source home/maren/prerequisites.sh -source /home/maren/devenv/bin/activate -python calibrate.py From 5f76b4abb207b6aaa7a5932a2cb14820f99fc27b Mon Sep 17 00:00:00 2001 From: Maren Philipps Date: Wed, 4 Dec 2024 15:49:02 +0100 Subject: [PATCH 13/17] remove visualisation file --- .../reformulated/Fiedler_BMCSystBiol2016.yaml | 2 -- .../visualizationSpecification_Fiedler_BMCSystBiol2016.tsv | 7 ------- 2 files changed, 9 deletions(-) delete mode 100644 Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/visualizationSpecification_Fiedler_BMCSystBiol2016.tsv diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/Fiedler_BMCSystBiol2016.yaml b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/Fiedler_BMCSystBiol2016.yaml index 67687dd..9561aa9 100644 --- a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/Fiedler_BMCSystBiol2016.yaml +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/Fiedler_BMCSystBiol2016.yaml @@ -9,5 +9,3 @@ problems: - observables_Fiedler_BMCSystBiol2016.tsv sbml_files: - model_Fiedler_BMCSystBiol2016.xml - visualization_files: - - visualizationSpecification_Fiedler_BMCSystBiol2016.tsv diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/visualizationSpecification_Fiedler_BMCSystBiol2016.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/visualizationSpecification_Fiedler_BMCSystBiol2016.tsv deleted file mode 100644 index 7d7378c..0000000 --- a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/visualizationSpecification_Fiedler_BMCSystBiol2016.tsv +++ /dev/null @@ -1,7 +0,0 @@ -plotId plotName plotTypeSimulation plotTypeData xLabel yValues yLabel datasetId -Fig8c_pMek_control relative pMek - control LinePlot replicate time [h] pMek_rel relative pMek [UI] control -Fig8c_pMek_Sorafenib relative pMek - 5 muM Sorafenib LinePlot replicate time [h] pMek_rel relative pMek [UI] Sorafenib -Fig8c_pMek_UO126 relative pMek - 30 muM UO126 LinePlot replicate time [h] pMek_rel relative pMek [UI] UO126 -Fig8c_pErk_control relative pErk - control LinePlot replicate time [h] pErk_rel relative pErk [UI] control -Fig8c_pErk_Sorafenib relative pMrk - 5 muM Sorafenib LinePlot replicate time [h] pErk_rel relative pErk [UI] Sorafenib -Fig8c_pErk_UO126 relative pMrk - 30 muM UO126 LinePlot replicate time [h] pErk_rel relative pErk [UI] UO126 From 5a7909d045629ae490383b93dcf322635815b283 Mon Sep 17 00:00:00 2001 From: Maren Philipps Date: Sat, 4 Jan 2025 20:12:22 +0100 Subject: [PATCH 14/17] change ID --- .../reformulated/Fiedler_BMCSystBiol2016.yaml | 11 ----------- .../reformulated/Fiedler_BMCSystBiol2016_rel.yaml | 11 +++++++++++ ...rimentalCondition_Fiedler_BMCSystBiol2016_rel.tsv} | 0 ...> measurementData_Fiedler_BMCSystBiol2016_rel.tsv} | 0 ...2016.xml => model_Fiedler_BMCSystBiol2016_rel.xml} | 2 +- ...sv => observables_Fiedler_BMCSystBiol2016_rel.tsv} | 0 ...tsv => parameters_Fiedler_BMCSystBiol2016_rel.tsv} | 0 ...alizationSpecification_Fiedler_BMCSystBiol2016.tsv | 7 +++++++ 8 files changed, 19 insertions(+), 12 deletions(-) delete mode 100644 Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/Fiedler_BMCSystBiol2016.yaml create mode 100644 Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/Fiedler_BMCSystBiol2016_rel.yaml rename Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/{experimentalCondition_Fiedler_BMCSystBiol2016.tsv => experimentalCondition_Fiedler_BMCSystBiol2016_rel.tsv} (100%) rename Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/{measurementData_Fiedler_BMCSystBiol2016.tsv => measurementData_Fiedler_BMCSystBiol2016_rel.tsv} (100%) rename Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/{model_Fiedler_BMCSystBiol2016.xml => model_Fiedler_BMCSystBiol2016_rel.xml} (99%) rename Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/{observables_Fiedler_BMCSystBiol2016.tsv => observables_Fiedler_BMCSystBiol2016_rel.tsv} (100%) rename Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/{parameters_Fiedler_BMCSystBiol2016.tsv => parameters_Fiedler_BMCSystBiol2016_rel.tsv} (100%) create mode 100644 Benchmark-Models/Fiedler_BMCSystBiol2016/visualizationSpecification_Fiedler_BMCSystBiol2016.tsv diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/Fiedler_BMCSystBiol2016.yaml b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/Fiedler_BMCSystBiol2016.yaml deleted file mode 100644 index 9561aa9..0000000 --- a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/Fiedler_BMCSystBiol2016.yaml +++ /dev/null @@ -1,11 +0,0 @@ -format_version: 1 -parameter_file: parameters_Fiedler_BMCSystBiol2016.tsv -problems: -- condition_files: - - experimentalCondition_Fiedler_BMCSystBiol2016.tsv - measurement_files: - - measurementData_Fiedler_BMCSystBiol2016.tsv - observable_files: - - observables_Fiedler_BMCSystBiol2016.tsv - sbml_files: - - model_Fiedler_BMCSystBiol2016.xml diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/Fiedler_BMCSystBiol2016_rel.yaml b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/Fiedler_BMCSystBiol2016_rel.yaml new file mode 100644 index 0000000..e7c8468 --- /dev/null +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/Fiedler_BMCSystBiol2016_rel.yaml @@ -0,0 +1,11 @@ +format_version: 1 +parameter_file: parameters_Fiedler_BMCSystBiol_rel.tsv +problems: +- condition_files: + - experimentalCondition_Fiedler_BMCSystBiol_rel.tsv + measurement_files: + - measurementData_Fiedler_BMCSystBiol_rel.tsv + observable_files: + - observables_Fiedler_BMCSystBiol_rel.tsv + sbml_files: + - model_Fiedler_BMCSystBiol_rel.xml diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/experimentalCondition_Fiedler_BMCSystBiol2016.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/experimentalCondition_Fiedler_BMCSystBiol2016_rel.tsv similarity index 100% rename from Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/experimentalCondition_Fiedler_BMCSystBiol2016.tsv rename to Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/experimentalCondition_Fiedler_BMCSystBiol2016_rel.tsv diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/measurementData_Fiedler_BMCSystBiol2016.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/measurementData_Fiedler_BMCSystBiol2016_rel.tsv similarity index 100% rename from Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/measurementData_Fiedler_BMCSystBiol2016.tsv rename to Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/measurementData_Fiedler_BMCSystBiol2016_rel.tsv diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/model_Fiedler_BMCSystBiol2016.xml b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/model_Fiedler_BMCSystBiol2016_rel.xml similarity index 99% rename from Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/model_Fiedler_BMCSystBiol2016.xml rename to Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/model_Fiedler_BMCSystBiol2016_rel.xml index e5e1d64..3acfd63 100644 --- a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/model_Fiedler_BMCSystBiol2016.xml +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/model_Fiedler_BMCSystBiol2016_rel.xml @@ -1,6 +1,6 @@ - + diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/observables_Fiedler_BMCSystBiol2016.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/observables_Fiedler_BMCSystBiol2016_rel.tsv similarity index 100% rename from Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/observables_Fiedler_BMCSystBiol2016.tsv rename to Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/observables_Fiedler_BMCSystBiol2016_rel.tsv diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/parameters_Fiedler_BMCSystBiol2016.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/parameters_Fiedler_BMCSystBiol2016_rel.tsv similarity index 100% rename from Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/parameters_Fiedler_BMCSystBiol2016.tsv rename to Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/parameters_Fiedler_BMCSystBiol2016_rel.tsv diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/visualizationSpecification_Fiedler_BMCSystBiol2016.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/visualizationSpecification_Fiedler_BMCSystBiol2016.tsv new file mode 100644 index 0000000..6ac3521 --- /dev/null +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/visualizationSpecification_Fiedler_BMCSystBiol2016.tsv @@ -0,0 +1,7 @@ +plotId plotName plotTypeSimulation plotTypeData xLabel yValues yLabel datasetId +pMek_control pMek - control LinePlot replicate time [h] pMek pMek control +pMek_Sorafenib pMek - 5 muM Sorafenib LinePlot replicate time [h] pMek pMek Sorafenib +pMek_UO126 pMek - 30 muM UO126 LinePlot replicate time [h] pMek pMek UO126 +pErk_control pErk - control LinePlot replicate time [h] pErk pErk control +pErk_Sorafenib pErk - 5 muM Sorafenib LinePlot replicate time [h] pErk pErk Sorafenib +pErk_UO126 pErk - 30 muM UO126 LinePlot replicate time [h] pErk pErk UO126 From e68524c62a14c003e98a2077981653aa92ef2ac2 Mon Sep 17 00:00:00 2001 From: Maren Philipps Date: Sat, 4 Jan 2025 20:14:20 +0100 Subject: [PATCH 15/17] update simulated data --- .../simulatedData_Fiedler_BMCSystBiol2016.tsv | 146 +++++++++--------- 1 file changed, 73 insertions(+), 73 deletions(-) diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/simulatedData_Fiedler_BMCSystBiol2016.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/simulatedData_Fiedler_BMCSystBiol2016.tsv index 77a5836..134774d 100644 --- a/Benchmark-Models/Fiedler_BMCSystBiol2016/simulatedData_Fiedler_BMCSystBiol2016.tsv +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/simulatedData_Fiedler_BMCSystBiol2016.tsv @@ -1,73 +1,73 @@ -observableId preequilibrationConditionId simulationConditionId simulation time observableParameters noiseParameters -pErk model1_data1 0.03361643271144515 0.0 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk -pErk model1_data1 0.08384600871194502 0.25 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk -pErk model1_data1 0.14529413431664095 1.0 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk -pErk model1_data1 0.03373888438216745 5.5 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk -pErk model1_data1 0.03361660721448361 7.0 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk -pErk model1_data1 0.033614606544540175 8.5 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk -pErk model1_data1 0.03361682359235068 10.0 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk -pErk model1_data1 0.8126060252664574 0.0 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk -pErk model1_data1 2.0267995851526917 0.25 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk -pErk model1_data1 3.5121778088422517 1.0 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk -pErk model1_data1 0.8155660349226578 5.5 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk -pErk model1_data1 0.8126102435076284 7.0 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk -pErk model1_data1 0.812561881551303 8.5 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk -pErk model1_data1 0.8126154739840452 10.0 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk -pMek model1_data1 0.04863500550105047 0.0 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek -pMek model1_data1 0.28579620668392197 0.25 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek -pMek model1_data1 0.28761271518189074 1.0 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek -pMek model1_data1 0.04892443748331804 5.5 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek -pMek model1_data1 0.04861268829425418 7.0 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek -pMek model1_data1 0.048635535764149945 8.5 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek -pMek model1_data1 0.04863522217188459 10.0 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek -pMek model1_data1 0.24552376547695293 0.0 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek -pMek model1_data1 1.4427830345891586 0.25 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek -pMek model1_data1 1.45195330200966 1.0 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek -pMek model1_data1 0.24698490297254252 5.5 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek -pMek model1_data1 0.24541110167459282 7.0 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek -pMek model1_data1 0.2455264424005296 8.5 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek -pMek model1_data1 0.2455248592948422 10.0 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek -pErk model1_data2 0.022771734786134104 0.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data2 0.03631870697453655 1.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data2 0.011295410041568654 5.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data2 0.011240689927851936 7.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data2 0.01124690853273153 8.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data2 0.011246374775472459 10.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data2 0.2600384889733869 0.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data2 0.41473615303461114 1.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data2 0.12898628001468046 5.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data2 0.1283614116934487 7.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data2 0.12843242414074793 8.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data2 0.12842632897793177 10.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pMek model1_data2 0.25288130419190086 0.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data2 0.38089387885488346 1.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data2 0.11921586344671047 5.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data2 0.11881098439949271 7.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data2 0.11887339130720243 8.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data2 0.11886560414931766 10.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data2 0.6256030660476078 0.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data2 0.9422933783572799 1.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data2 0.29492812816711056 5.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data2 0.29392649788001884 7.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data2 0.29408088633087925 8.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data2 0.29406162168075384 10.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pErk model1_data3 0.00678828316965931 1.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data3 0.0041676476822826445 5.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data3 0.00416424385399046 7.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data3 0.004164954335288319 8.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data3 0.004164841688668539 10.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data3 0.07751780506580175 1.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data3 0.04759184208197086 5.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data3 0.04755297256350257 7.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data3 0.04756108580058681 8.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data3 0.047559799449016726 10.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pMek model1_data3 2.0430841389034655 1.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data3 1.377916119880504 5.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data3 1.378050495730159 7.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data3 1.3781283022947328 8.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data3 1.3781066885745035 10.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data3 5.05438591269406 1.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data3 3.408826730423337 5.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data3 3.4091591628418403 7.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data3 3.40935164850428 8.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data3 3.4092981783211544 10.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek +observableId simulationConditionId simulation time observableParameters noiseParameters datasetId +pErk model1_data1 0.03361643271144515 0.0 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control +pErk model1_data1 0.08384600871194502 0.25 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control +pErk model1_data1 0.14529413431664095 1.0 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control +pErk model1_data1 0.03373888438216745 5.5 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control +pErk model1_data1 0.03361660721448361 7.0 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control +pErk model1_data1 0.033614606544540175 8.5 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control +pErk model1_data1 0.03361682359235068 10.0 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control +pErk model1_data1 0.8126060252664574 0.0 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk control +pErk model1_data1 2.0267995851526917 0.25 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk control +pErk model1_data1 3.5121778088422517 1.0 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk control +pErk model1_data1 0.8155660349226578 5.5 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk control +pErk model1_data1 0.8126102435076284 7.0 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk control +pErk model1_data1 0.812561881551303 8.5 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk control +pErk model1_data1 0.8126154739840452 10.0 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk control +pMek model1_data1 0.04863500550105047 0.0 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek control +pMek model1_data1 0.28579620668392197 0.25 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek control +pMek model1_data1 0.28761271518189074 1.0 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek control +pMek model1_data1 0.04892443748331804 5.5 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek control +pMek model1_data1 0.04861268829425418 7.0 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek control +pMek model1_data1 0.048635535764149945 8.5 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek control +pMek model1_data1 0.04863522217188459 10.0 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek control +pMek model1_data1 0.24552376547695293 0.0 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek control +pMek model1_data1 1.4427830345891586 0.25 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek control +pMek model1_data1 1.45195330200966 1.0 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek control +pMek model1_data1 0.24698490297254252 5.5 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek control +pMek model1_data1 0.24541110167459282 7.0 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek control +pMek model1_data1 0.2455264424005296 8.5 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek control +pMek model1_data1 0.2455248592948422 10.0 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek control +pErk model1_data2 0.022771734786134104 0.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.03631870697453655 1.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.011295410041568654 5.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.011240689927851936 7.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.01124690853273153 8.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.011246374775472459 10.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.2600384889733869 0.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.41473615303461114 1.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.12898628001468046 5.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.1283614116934487 7.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.12843242414074793 8.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.12842632897793177 10.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk Sorafenib +pMek model1_data2 0.25288130419190086 0.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.38089387885488346 1.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.11921586344671047 5.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.11881098439949271 7.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.11887339130720243 8.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.11886560414931766 10.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.6256030660476078 0.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.9422933783572799 1.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.29492812816711056 5.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.29392649788001884 7.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.29408088633087925 8.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.29406162168075384 10.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek Sorafenib +pErk model1_data3 0.00678828316965931 1.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk UO126 +pErk model1_data3 0.0041676476822826445 5.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk UO126 +pErk model1_data3 0.00416424385399046 7.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk UO126 +pErk model1_data3 0.004164954335288319 8.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk UO126 +pErk model1_data3 0.004164841688668539 10.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk UO126 +pErk model1_data3 0.07751780506580175 1.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk UO126 +pErk model1_data3 0.04759184208197086 5.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk UO126 +pErk model1_data3 0.04755297256350257 7.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk UO126 +pErk model1_data3 0.04756108580058681 8.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk UO126 +pErk model1_data3 0.047559799449016726 10.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk UO126 +pMek model1_data3 2.0430841389034655 1.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek UO126 +pMek model1_data3 1.377916119880504 5.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek UO126 +pMek model1_data3 1.378050495730159 7.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek UO126 +pMek model1_data3 1.3781283022947328 8.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek UO126 +pMek model1_data3 1.3781066885745035 10.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek UO126 +pMek model1_data3 5.05438591269406 1.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek UO126 +pMek model1_data3 3.408826730423337 5.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek UO126 +pMek model1_data3 3.4091591628418403 7.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek UO126 +pMek model1_data3 3.40935164850428 8.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek UO126 +pMek model1_data3 3.4092981783211544 10.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek UO126 From 908c3ef287a500045035178c06f5aa00cabb4052 Mon Sep 17 00:00:00 2001 From: Maren Philipps Date: Sat, 4 Jan 2025 20:26:52 +0100 Subject: [PATCH 16/17] fix ID in file names --- .../reformulated/Fiedler_BMCSystBiol2016_rel.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/Fiedler_BMCSystBiol2016_rel.yaml b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/Fiedler_BMCSystBiol2016_rel.yaml index e7c8468..3b4e7e2 100644 --- a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/Fiedler_BMCSystBiol2016_rel.yaml +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/Fiedler_BMCSystBiol2016_rel.yaml @@ -1,11 +1,11 @@ format_version: 1 -parameter_file: parameters_Fiedler_BMCSystBiol_rel.tsv +parameter_file: parameters_Fiedler_BMCSystBiol2016_rel.tsv problems: - condition_files: - - experimentalCondition_Fiedler_BMCSystBiol_rel.tsv + - experimentalCondition_Fiedler_BMCSystBiol2016_rel.tsv measurement_files: - - measurementData_Fiedler_BMCSystBiol_rel.tsv + - measurementData_Fiedler_BMCSystBiol2016_rel.tsv observable_files: - - observables_Fiedler_BMCSystBiol_rel.tsv + - observables_Fiedler_BMCSystBiol2016_rel.tsv sbml_files: - - model_Fiedler_BMCSystBiol_rel.xml + - model_Fiedler_BMCSystBiol2016_rel.xml From 2abb2254f369d8ea18d0b0d4d5c1d8107853cc11 Mon Sep 17 00:00:00 2001 From: Maren Philipps Date: Sat, 4 Jan 2025 22:33:29 +0100 Subject: [PATCH 17/17] add annotation with identifier --- .../model_Fiedler_BMCSystBiol2016_rel.xml | 20 +++++++++---------- 1 file changed, 9 insertions(+), 11 deletions(-) diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/model_Fiedler_BMCSystBiol2016_rel.xml b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/model_Fiedler_BMCSystBiol2016_rel.xml index 3acfd63..3f93af6 100644 --- a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/model_Fiedler_BMCSystBiol2016_rel.xml +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/model_Fiedler_BMCSystBiol2016_rel.xml @@ -2,17 +2,15 @@ - - - - - - 2024-10-06T10:20:09Z - - - - - + + + + + + + + +