Merge pull request #197 from m-philipps/model_Raia_CancerResearch2011

Fix RaiaCancerResearch2011
Benchmarking-Initiative · Dec 13, 2023 · ce89204 · ce89204
2 parents 5f8a33c + a6b5856
commit ce89204
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Showing 4 changed files with 11 additions and 10 deletions.
diff --git 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
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
-  <model id="Raia_CancerResearch2011" name="il13_jak2_stat5">
+  <model id="Raia_CancerResearch2011" name="Raia_CancerResearch2011">
     <notes>
       <body xmlns="http://www.w3.org/1999/xhtml">
         <pre>PEtab implementation of the model from Raia et al. (2011), Cancer Res February 1 2011 (71) (3) 693-704</pre>

diff --git 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
@@ -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
Original file line number	Diff line number	Diff line change
Expand Up		@@ -11,3 +11,4 @@ problems:
		- model_Raia_CancerResearch2011.xml
		visualization_files:
		- visualizationSpecification_Raia_CancerResearch2011.tsv