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Merge pull request #197 from m-philipps/model_Raia_CancerResearch2011
Fix RaiaCancerResearch2011
2 parents 5f8a33c + a6b5856 commit ce89204

4 files changed

Lines changed: 11 additions & 10 deletions

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‎Benchmark-Models/Raia_CancerResearch2011/Raia_CancerResearch2011.yaml‎

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- model_Raia_CancerResearch2011.xml
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visualization_files:
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- visualizationSpecification_Raia_CancerResearch2011.tsv
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‎Benchmark-Models/Raia_CancerResearch2011/model_Raia_CancerResearch2011.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
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<model id="Raia_CancerResearch2011" name="il13_jak2_stat5">
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<model id="Raia_CancerResearch2011" name="Raia_CancerResearch2011">
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<notes>
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<body xmlns="http://www.w3.org/1999/xhtml">
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<pre>PEtab implementation of the model from Raia et al. (2011), Cancer Res February 1 2011 (71) (3) 693-704</pre>

‎Benchmark-Models/Raia_CancerResearch2011/observables_Raia_CancerResearch2011.tsv‎

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observableId observableName observableFormula noiseFormula observableTransformation noiseDistribution
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observable_CD274mRNA CD274mRNA * observableParameter1_observable_CD274mRNA noiseParameter1_observable_CD274mRNA + noiseParameter2_observable_CD274mRNA * observable_CD274mRNA lin normal
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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
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observable_RecSurf IL13_Rec + Rec + p_IL13_Rec noiseParameter1_observable_RecSurf + noiseParameter2_observable_RecSurf * observable_RecSurf lin normal
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observable_SOCS3 SOCS3 noiseParameter1_observable_SOCS3 + noiseParameter2_observable_SOCS3 * observable_SOCS3 lin normal
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observable_SOCS3mRNA SOCS3mRNA * observableParameter1_observable_SOCS3mRNA noiseParameter1_observable_SOCS3mRNA + noiseParameter2_observable_SOCS3mRNA * observable_SOCS3mRNA lin normal
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observable_pIL4Ra observableParameter1_observable_pIL4Ra * (p_IL13_Rec + p_IL13_Rec_i) noiseParameter1_observable_pIL4Ra + noiseParameter2_observable_pIL4Ra * observable_pIL4Ra lin normal
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observable_pJAK2 pJAK2 * observableParameter1_observable_pJAK2 noiseParameter1_observable_pJAK2 + noiseParameter2_observable_pJAK2 * observable_pJAK2 lin normal
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observable_pSTAT5 pSTAT5 noiseParameter1_observable_pSTAT5 + noiseParameter2_observable_pSTAT5 * observable_pSTAT5 lin normal
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observable_CD274mRNA CD274mRNA * observableParameter1_observable_CD274mRNA noiseParameter1_observable_CD274mRNA + noiseParameter2_observable_CD274mRNA * (CD274mRNA * observableParameter1_observable_CD274mRNA) lin normal
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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
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observable_RecSurf IL13_Rec + Rec + p_IL13_Rec noiseParameter1_observable_RecSurf + noiseParameter2_observable_RecSurf * (IL13_Rec + Rec + p_IL13_Rec) lin normal
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observable_SOCS3 SOCS3 noiseParameter1_observable_SOCS3 + noiseParameter2_observable_SOCS3 * SOCS3 lin normal
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observable_SOCS3mRNA SOCS3mRNA * observableParameter1_observable_SOCS3mRNA noiseParameter1_observable_SOCS3mRNA + noiseParameter2_observable_SOCS3mRNA * (SOCS3mRNA * observableParameter1_observable_SOCS3mRNA) lin normal
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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
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observable_pJAK2 pJAK2 * observableParameter1_observable_pJAK2 noiseParameter1_observable_pJAK2 + noiseParameter2_observable_pJAK2 * (pJAK2 * observableParameter1_observable_pJAK2) lin normal
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observable_pSTAT5 pSTAT5 noiseParameter1_observable_pSTAT5 + noiseParameter2_observable_pSTAT5 * pSTAT5 lin normal

‎src/python/setup.cfg‎

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[options]
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install_requires =
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petab >= 0.1.28
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petab >= 0.2.5
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python_requires = >= 3.8
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zip_safe = False

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