diff --git a/Benchmark-Models/Raia_CancerResearch2011/Raia_CancerResearch2011.yaml b/Benchmark-Models/Raia_CancerResearch2011/Raia_CancerResearch2011.yaml index 4ac6086..db384ca 100644 --- a/Benchmark-Models/Raia_CancerResearch2011/Raia_CancerResearch2011.yaml +++ b/Benchmark-Models/Raia_CancerResearch2011/Raia_CancerResearch2011.yaml @@ -11,3 +11,4 @@ problems: - model_Raia_CancerResearch2011.xml visualization_files: - visualizationSpecification_Raia_CancerResearch2011.tsv + diff --git a/Benchmark-Models/Raia_CancerResearch2011/model_Raia_CancerResearch2011.xml b/Benchmark-Models/Raia_CancerResearch2011/model_Raia_CancerResearch2011.xml index c9381f7..5455306 100644 --- a/Benchmark-Models/Raia_CancerResearch2011/model_Raia_CancerResearch2011.xml +++ b/Benchmark-Models/Raia_CancerResearch2011/model_Raia_CancerResearch2011.xml @@ -1,6 +1,6 @@ - + 
PEtab implementation of the model from Raia et al. (2011), Cancer Res February 1 2011 (71) (3) 693-704
diff --git a/Benchmark-Models/Raia_CancerResearch2011/observables_Raia_CancerResearch2011.tsv b/Benchmark-Models/Raia_CancerResearch2011/observables_Raia_CancerResearch2011.tsv index 4bf1ba0..44e4175 100644 --- a/Benchmark-Models/Raia_CancerResearch2011/observables_Raia_CancerResearch2011.tsv +++ b/Benchmark-Models/Raia_CancerResearch2011/observables_Raia_CancerResearch2011.tsv @@ -1,9 +1,9 @@ observableId observableName observableFormula noiseFormula observableTransformation noiseDistribution -observable_CD274mRNA CD274mRNA * observableParameter1_observable_CD274mRNA noiseParameter1_observable_CD274mRNA + noiseParameter2_observable_CD274mRNA * observable_CD274mRNA lin normal -observable_IL13_cell observableParameter1_observable_IL13_cell * (IL13_Rec + IL13_DecoyR + p_IL13_Rec + p_IL13_Rec_i) noiseParameter1_observable_IL13_cell + noiseParameter2_observable_IL13_cell * observable_IL13_cell lin normal -observable_RecSurf IL13_Rec + Rec + p_IL13_Rec noiseParameter1_observable_RecSurf + noiseParameter2_observable_RecSurf * observable_RecSurf lin normal -observable_SOCS3 SOCS3 noiseParameter1_observable_SOCS3 + noiseParameter2_observable_SOCS3 * observable_SOCS3 lin normal -observable_SOCS3mRNA SOCS3mRNA * observableParameter1_observable_SOCS3mRNA noiseParameter1_observable_SOCS3mRNA + noiseParameter2_observable_SOCS3mRNA * observable_SOCS3mRNA lin normal -observable_pIL4Ra observableParameter1_observable_pIL4Ra * (p_IL13_Rec + p_IL13_Rec_i) noiseParameter1_observable_pIL4Ra + noiseParameter2_observable_pIL4Ra * observable_pIL4Ra lin normal -observable_pJAK2 pJAK2 * observableParameter1_observable_pJAK2 noiseParameter1_observable_pJAK2 + noiseParameter2_observable_pJAK2 * observable_pJAK2 lin normal -observable_pSTAT5 pSTAT5 noiseParameter1_observable_pSTAT5 + noiseParameter2_observable_pSTAT5 * observable_pSTAT5 lin normal +observable_CD274mRNA CD274mRNA * observableParameter1_observable_CD274mRNA noiseParameter1_observable_CD274mRNA + noiseParameter2_observable_CD274mRNA * (CD274mRNA * observableParameter1_observable_CD274mRNA) lin normal +observable_IL13_cell observableParameter1_observable_IL13_cell * (IL13_Rec + IL13_DecoyR + p_IL13_Rec + p_IL13_Rec_i) noiseParameter1_observable_IL13_cell + noiseParameter2_observable_IL13_cell * (observableParameter1_observable_IL13_cell * (IL13_Rec + IL13_DecoyR + p_IL13_Rec + p_IL13_Rec_i)) lin normal +observable_RecSurf IL13_Rec + Rec + p_IL13_Rec noiseParameter1_observable_RecSurf + noiseParameter2_observable_RecSurf * (IL13_Rec + Rec + p_IL13_Rec) lin normal +observable_SOCS3 SOCS3 noiseParameter1_observable_SOCS3 + noiseParameter2_observable_SOCS3 * SOCS3 lin normal +observable_SOCS3mRNA SOCS3mRNA * observableParameter1_observable_SOCS3mRNA noiseParameter1_observable_SOCS3mRNA + noiseParameter2_observable_SOCS3mRNA * (SOCS3mRNA * observableParameter1_observable_SOCS3mRNA) lin normal +observable_pIL4Ra observableParameter1_observable_pIL4Ra * (p_IL13_Rec + p_IL13_Rec_i) noiseParameter1_observable_pIL4Ra + noiseParameter2_observable_pIL4Ra * (observableParameter1_observable_pIL4Ra * (p_IL13_Rec + p_IL13_Rec_i)) lin normal +observable_pJAK2 pJAK2 * observableParameter1_observable_pJAK2 noiseParameter1_observable_pJAK2 + noiseParameter2_observable_pJAK2 * (pJAK2 * observableParameter1_observable_pJAK2) lin normal +observable_pSTAT5 pSTAT5 noiseParameter1_observable_pSTAT5 + noiseParameter2_observable_pSTAT5 * pSTAT5 lin normal diff --git a/src/python/setup.cfg b/src/python/setup.cfg index 91f1ed2..aebb862 100644 --- a/src/python/setup.cfg +++ b/src/python/setup.cfg @@ -16,7 +16,7 @@ license_file = LICENSE [options] install_requires = - petab >= 0.1.28 + petab >= 0.2.5 python_requires = >= 3.8 zip_safe = False