From 5a7909d045629ae490383b93dcf322635815b283 Mon Sep 17 00:00:00 2001
From: Maren Philipps <maren.philipps@uni-bonn.de>
Date: Sat, 4 Jan 2025 20:12:22 +0100
Subject: [PATCH] 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 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:render="http://www.sbml.org/sbml/level3/version1/render/version1" level="3" version="1" layout:required="false" render:required="false">
-  <model metaid="COPASI0" id="Fiedler_BMCSystBiol2016" name="Fiedler_BMCSystBiol2016" substanceUnits="substance" timeUnits="time" volumeUnits="volume" areaUnits="area" lengthUnits="length" extentUnits="substance">
+  <model metaid="COPASI0" id="Fiedler_BMCSystBiol2016_rel" name="Fiedler_BMCSystBiol2016_rel" substanceUnits="substance" timeUnits="time" volumeUnits="volume" areaUnits="area" lengthUnits="length" extentUnits="substance">
     <annotation>
       <COPASI xmlns="http://www.copasi.org/static/sbml">
         <rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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