Models: slight updates to our SED-ML files and COMBINE archives.

opencor · Jan 9, 2020 · ed5fa03 · ed5fa03
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Showing 17 changed files with 47 additions and 33 deletions.
diff --git a/models/tests/combine/fink_slepchenko_moraru_watras_schaff_loew_2000v2.omex b/models/tests/combine/fink_slepchenko_moraru_watras_schaff_loew_2000v2.omex
diff --git a/models/tests/combine/lorenz.omex b/models/tests/combine/lorenz.omex
diff --git a/models/tests/combine/no_master_file.omex b/models/tests/combine/no_master_file.omex
diff --git a/models/tests/combine/noble_1962.omex b/models/tests/combine/noble_1962.omex
diff --git a/models/tests/combine/smith_chase_nokes_shaw_wake_2004.omex b/models/tests/combine/smith_chase_nokes_shaw_wake_2004.omex
diff --git a/models/tests/combine/two_master_files.omex b/models/tests/combine/two_master_files.omex
diff --git a/models/tests/sedml/noble_1962_V_iK.sedml b/models/tests/sedml/noble_1962_V_iK.sedml
@@ -1,10 +1,10 @@
 <?xml version='1.0' encoding='UTF-8'?>
-<sedML level="1" version="2" xmlns="http://sed-ml.org/sed-ml/level1/version2" xmlns:cellml="http://www.cellml.org/cellml/1.0#">
+<sedML level="1" version="3" xmlns="http://sed-ml.org/sed-ml/level1/version3" xmlns:cellml="http://www.cellml.org/cellml/1.0#">
     <listOfSimulations>
         <uniformTimeCourse id="simulation1" initialTime="0" numberOfPoints="1000" outputEndTime="1000" outputStartTime="0">
             <algorithm kisaoID="KISAO:0000019">
                 <listOfAlgorithmParameters>
-                    <algorithmParameter kisaoID="KISAO:0000211" value="1e-7"/>
+                    <algorithmParameter kisaoID="KISAO:0000211" value="1e-07"/>
                     <algorithmParameter kisaoID="KISAO:0000475" value="BDF"/>
                     <algorithmParameter kisaoID="KISAO:0000481" value="true"/>
                     <algorithmParameter kisaoID="KISAO:0000476" value="Newton"/>
@@ -13,7 +13,7 @@
                     <algorithmParameter kisaoID="KISAO:0000415" value="500"/>
                     <algorithmParameter kisaoID="KISAO:0000467" value="0"/>
                     <algorithmParameter kisaoID="KISAO:0000478" value="Banded"/>
-                    <algorithmParameter kisaoID="KISAO:0000209" value="1e-7"/>
+                    <algorithmParameter kisaoID="KISAO:0000209" value="1e-07"/>
                     <algorithmParameter kisaoID="KISAO:0000479" value="0"/>
                 </listOfAlgorithmParameters>
             </algorithm>

diff --git a/models/tests/sedml/noble_1962_V_time.sedml b/models/tests/sedml/noble_1962_V_time.sedml
@@ -1,10 +1,10 @@
 <?xml version='1.0' encoding='UTF-8'?>
-<sedML level="1" version="2" xmlns="http://sed-ml.org/sed-ml/level1/version2" xmlns:cellml="http://www.cellml.org/cellml/1.0#">
+<sedML level="1" version="3" xmlns="http://sed-ml.org/sed-ml/level1/version3" xmlns:cellml="http://www.cellml.org/cellml/1.0#">
     <listOfSimulations>
         <uniformTimeCourse id="simulation1" initialTime="0" numberOfPoints="1000" outputEndTime="1000" outputStartTime="0">
             <algorithm kisaoID="KISAO:0000019">
                 <listOfAlgorithmParameters>
-                    <algorithmParameter kisaoID="KISAO:0000211" value="1e-7"/>
+                    <algorithmParameter kisaoID="KISAO:0000211" value="1e-07"/>
                     <algorithmParameter kisaoID="KISAO:0000475" value="BDF"/>
                     <algorithmParameter kisaoID="KISAO:0000481" value="true"/>
                     <algorithmParameter kisaoID="KISAO:0000476" value="Newton"/>
@@ -13,7 +13,7 @@
                     <algorithmParameter kisaoID="KISAO:0000415" value="500"/>
                     <algorithmParameter kisaoID="KISAO:0000467" value="0"/>
                     <algorithmParameter kisaoID="KISAO:0000478" value="Banded"/>
-                    <algorithmParameter kisaoID="KISAO:0000209" value="1e-7"/>
+                    <algorithmParameter kisaoID="KISAO:0000209" value="1e-07"/>
                     <algorithmParameter kisaoID="KISAO:0000479" value="0"/>
                 </listOfAlgorithmParameters>
             </algorithm>

diff --git a/models/tests/sedml/noble_1962_gL_time.sedml b/models/tests/sedml/noble_1962_gL_time.sedml
@@ -1,10 +1,10 @@
 <?xml version='1.0' encoding='UTF-8'?>
-<sedML level="1" version="2" xmlns="http://sed-ml.org/sed-ml/level1/version2" xmlns:cellml="http://www.cellml.org/cellml/1.0#">
+<sedML level="1" version="3" xmlns="http://sed-ml.org/sed-ml/level1/version3" xmlns:cellml="http://www.cellml.org/cellml/1.0#">
     <listOfSimulations>
         <uniformTimeCourse id="simulation1" initialTime="0" numberOfPoints="1000" outputEndTime="1000" outputStartTime="0">
             <algorithm kisaoID="KISAO:0000019">
                 <listOfAlgorithmParameters>
-                    <algorithmParameter kisaoID="KISAO:0000211" value="1e-7"/>
+                    <algorithmParameter kisaoID="KISAO:0000211" value="1e-07"/>
                     <algorithmParameter kisaoID="KISAO:0000475" value="BDF"/>
                     <algorithmParameter kisaoID="KISAO:0000481" value="true"/>
                     <algorithmParameter kisaoID="KISAO:0000476" value="Newton"/>
@@ -13,7 +13,7 @@
                     <algorithmParameter kisaoID="KISAO:0000415" value="500"/>
                     <algorithmParameter kisaoID="KISAO:0000467" value="0"/>
                     <algorithmParameter kisaoID="KISAO:0000478" value="Banded"/>
-                    <algorithmParameter kisaoID="KISAO:0000209" value="1e-7"/>
+                    <algorithmParameter kisaoID="KISAO:0000209" value="1e-07"/>
                     <algorithmParameter kisaoID="KISAO:0000479" value="0"/>
                 </listOfAlgorithmParameters>
             </algorithm>

diff --git a/models/tests/sedml/noble_1962_iK_V.sedml b/models/tests/sedml/noble_1962_iK_V.sedml
@@ -1,10 +1,10 @@
 <?xml version='1.0' encoding='UTF-8'?>
-<sedML level="1" version="2" xmlns="http://sed-ml.org/sed-ml/level1/version2" xmlns:cellml="http://www.cellml.org/cellml/1.0#">
+<sedML level="1" version="3" xmlns="http://sed-ml.org/sed-ml/level1/version3" xmlns:cellml="http://www.cellml.org/cellml/1.0#">
     <listOfSimulations>
         <uniformTimeCourse id="simulation1" initialTime="0" numberOfPoints="1000" outputEndTime="1000" outputStartTime="0">
             <algorithm kisaoID="KISAO:0000019">
                 <listOfAlgorithmParameters>
-                    <algorithmParameter kisaoID="KISAO:0000211" value="1e-7"/>
+                    <algorithmParameter kisaoID="KISAO:0000211" value="1e-07"/>
                     <algorithmParameter kisaoID="KISAO:0000475" value="BDF"/>
                     <algorithmParameter kisaoID="KISAO:0000481" value="true"/>
                     <algorithmParameter kisaoID="KISAO:0000476" value="Newton"/>
@@ -13,7 +13,7 @@
                     <algorithmParameter kisaoID="KISAO:0000415" value="500"/>
                     <algorithmParameter kisaoID="KISAO:0000467" value="0"/>
                     <algorithmParameter kisaoID="KISAO:0000478" value="Banded"/>
-                    <algorithmParameter kisaoID="KISAO:0000209" value="1e-7"/>
+                    <algorithmParameter kisaoID="KISAO:0000209" value="1e-07"/>
                     <algorithmParameter kisaoID="KISAO:0000479" value="0"/>
                 </listOfAlgorithmParameters>
             </algorithm>

diff --git a/models/tests/sedml/noble_1962_iK_time.sedml b/models/tests/sedml/noble_1962_iK_time.sedml
@@ -1,10 +1,10 @@
 <?xml version='1.0' encoding='UTF-8'?>
-<sedML level="1" version="2" xmlns="http://sed-ml.org/sed-ml/level1/version2" xmlns:cellml="http://www.cellml.org/cellml/1.0#">
+<sedML level="1" version="3" xmlns="http://sed-ml.org/sed-ml/level1/version3" xmlns:cellml="http://www.cellml.org/cellml/1.0#">
     <listOfSimulations>
         <uniformTimeCourse id="simulation1" initialTime="0" numberOfPoints="1000" outputEndTime="1000" outputStartTime="0">
             <algorithm kisaoID="KISAO:0000019">
                 <listOfAlgorithmParameters>
-                    <algorithmParameter kisaoID="KISAO:0000211" value="1e-7"/>
+                    <algorithmParameter kisaoID="KISAO:0000211" value="1e-07"/>
                     <algorithmParameter kisaoID="KISAO:0000475" value="BDF"/>
                     <algorithmParameter kisaoID="KISAO:0000481" value="true"/>
                     <algorithmParameter kisaoID="KISAO:0000476" value="Newton"/>
@@ -13,7 +13,7 @@
                     <algorithmParameter kisaoID="KISAO:0000415" value="500"/>
                     <algorithmParameter kisaoID="KISAO:0000467" value="0"/>
                     <algorithmParameter kisaoID="KISAO:0000478" value="Banded"/>
-                    <algorithmParameter kisaoID="KISAO:0000209" value="1e-7"/>
+                    <algorithmParameter kisaoID="KISAO:0000209" value="1e-07"/>
                     <algorithmParameter kisaoID="KISAO:0000479" value="0"/>
                 </listOfAlgorithmParameters>
             </algorithm>

diff --git a/models/tests/sedml/noble_1962_local.sedml b/models/tests/sedml/noble_1962_local.sedml
@@ -1,10 +1,10 @@
 <?xml version='1.0' encoding='UTF-8'?>
-<sedML level="1" version="2" xmlns="http://sed-ml.org/sed-ml/level1/version2" xmlns:cellml="http://www.cellml.org/cellml/1.0#">
+<sedML level="1" version="3" xmlns="http://sed-ml.org/sed-ml/level1/version3" xmlns:cellml="http://www.cellml.org/cellml/1.0#">
     <listOfSimulations>
         <uniformTimeCourse id="simulation1" initialTime="0" numberOfPoints="60" outputEndTime="3000" outputStartTime="0">
             <algorithm kisaoID="KISAO:0000019">
                 <listOfAlgorithmParameters>
-                    <algorithmParameter kisaoID="KISAO:0000211" value="1e-7"/>
+                    <algorithmParameter kisaoID="KISAO:0000211" value="1e-07"/>
                     <algorithmParameter kisaoID="KISAO:0000475" value="BDF"/>
                     <algorithmParameter kisaoID="KISAO:0000481" value="true"/>
                     <algorithmParameter kisaoID="KISAO:0000476" value="Newton"/>
@@ -13,7 +13,7 @@
                     <algorithmParameter kisaoID="KISAO:0000415" value="500"/>
                     <algorithmParameter kisaoID="KISAO:0000467" value="0"/>
                     <algorithmParameter kisaoID="KISAO:0000478" value="Banded"/>
-                    <algorithmParameter kisaoID="KISAO:0000209" value="1e-7"/>
+                    <algorithmParameter kisaoID="KISAO:0000209" value="1e-07"/>
                     <algorithmParameter kisaoID="KISAO:0000479" value="0"/>
                 </listOfAlgorithmParameters>
             </algorithm>
@@ -196,6 +196,7 @@
                 <curve id="curve1_1" logX="false" logY="false" xDataReference="xDataGenerator1_1" yDataReference="yDataGenerator1_1">
                     <annotation>
                         <properties xmlns="http://www.opencor.ws/">
+                            <selected>true</selected>
                             <title>V</title>
                             <line>
                                 <style>solid</style>
@@ -260,6 +261,7 @@
                 <curve id="curve2_1" logX="false" logY="false" xDataReference="xDataGenerator2_1" yDataReference="yDataGenerator2_1">
                     <annotation>
                         <properties xmlns="http://www.opencor.ws/">
+                            <selected>true</selected>
                             <title>Sodium</title>
                             <line>
                                 <style>dot</style>
@@ -279,6 +281,7 @@
                 <curve id="curve2_2" logX="false" logY="false" xDataReference="xDataGenerator2_2" yDataReference="yDataGenerator2_2">
                     <annotation>
                         <properties xmlns="http://www.opencor.ws/">
+                            <selected>true</selected>
                             <title>Potassium</title>
                             <line>
                                 <style>dot</style>
@@ -298,6 +301,7 @@
                 <curve id="curve2_3" logX="false" logY="false" xDataReference="xDataGenerator2_3" yDataReference="yDataGenerator2_3">
                     <annotation>
                         <properties xmlns="http://www.opencor.ws/">
+                            <selected>true</selected>
                             <title>Leak</title>
                             <line>
                                 <style>dot</style>
@@ -362,6 +366,7 @@
                 <curve id="curve3_1" logX="false" logY="false" xDataReference="xDataGenerator3_1" yDataReference="yDataGenerator3_1">
                     <annotation>
                         <properties xmlns="http://www.opencor.ws/">
+                            <selected>true</selected>
                             <title>m</title>
                             <line>
                                 <style>dot</style>
@@ -381,6 +386,7 @@
                 <curve id="curve3_2" logX="false" logY="false" xDataReference="xDataGenerator3_2" yDataReference="yDataGenerator3_2">
                     <annotation>
                         <properties xmlns="http://www.opencor.ws/">
+                            <selected>true</selected>
                             <title>h</title>
                             <line>
                                 <style>dot</style>
@@ -400,6 +406,7 @@
                 <curve id="curve3_3" logX="false" logY="false" xDataReference="xDataGenerator3_3" yDataReference="yDataGenerator3_3">
                     <annotation>
                         <properties xmlns="http://www.opencor.ws/">
+                            <selected>true</selected>
                             <title>n</title>
                             <line>
                                 <style>dot</style>

diff --git a/models/tests/sedml/noble_1962_remote.sedml b/models/tests/sedml/noble_1962_remote.sedml
@@ -1,10 +1,10 @@
 <?xml version='1.0' encoding='UTF-8'?>
-<sedML level="1" version="2" xmlns="http://sed-ml.org/sed-ml/level1/version2" xmlns:cellml="http://www.cellml.org/cellml/1.0#">
+<sedML level="1" version="3" xmlns="http://sed-ml.org/sed-ml/level1/version3" xmlns:cellml="http://www.cellml.org/cellml/1.0#">
     <listOfSimulations>
         <uniformTimeCourse id="simulation1" initialTime="0" numberOfPoints="60" outputEndTime="3" outputStartTime="0">
             <algorithm kisaoID="KISAO:0000019">
                 <listOfAlgorithmParameters>
-                    <algorithmParameter kisaoID="KISAO:0000211" value="1e-7"/>
+                    <algorithmParameter kisaoID="KISAO:0000211" value="1e-07"/>
                     <algorithmParameter kisaoID="KISAO:0000475" value="BDF"/>
                     <algorithmParameter kisaoID="KISAO:0000481" value="true"/>
                     <algorithmParameter kisaoID="KISAO:0000476" value="Newton"/>
@@ -13,7 +13,7 @@
                     <algorithmParameter kisaoID="KISAO:0000415" value="500"/>
                     <algorithmParameter kisaoID="KISAO:0000467" value="0"/>
                     <algorithmParameter kisaoID="KISAO:0000478" value="Banded"/>
-                    <algorithmParameter kisaoID="KISAO:0000209" value="1e-7"/>
+                    <algorithmParameter kisaoID="KISAO:0000209" value="1e-07"/>
                     <algorithmParameter kisaoID="KISAO:0000479" value="0"/>
                 </listOfAlgorithmParameters>
             </algorithm>
@@ -196,6 +196,7 @@
                 <curve id="curve1_1" logX="false" logY="false" xDataReference="xDataGenerator1_1" yDataReference="yDataGenerator1_1">
                     <annotation>
                         <properties xmlns="http://www.opencor.ws/">
+                            <selected>true</selected>
                             <title>V</title>
                             <line>
                                 <style>solid</style>
@@ -260,6 +261,7 @@
                 <curve id="curve2_1" logX="false" logY="false" xDataReference="xDataGenerator2_1" yDataReference="yDataGenerator2_1">
                     <annotation>
                         <properties xmlns="http://www.opencor.ws/">
+                            <selected>true</selected>
                             <title>Sodium</title>
                             <line>
                                 <style>dot</style>
@@ -279,6 +281,7 @@
                 <curve id="curve2_2" logX="false" logY="false" xDataReference="xDataGenerator2_2" yDataReference="yDataGenerator2_2">
                     <annotation>
                         <properties xmlns="http://www.opencor.ws/">
+                            <selected>true</selected>
                             <title>Potassium</title>
                             <line>
                                 <style>dot</style>
@@ -298,6 +301,7 @@
                 <curve id="curve2_3" logX="false" logY="false" xDataReference="xDataGenerator2_3" yDataReference="yDataGenerator2_3">
                     <annotation>
                         <properties xmlns="http://www.opencor.ws/">
+                            <selected>true</selected>
                             <title>Leak</title>
                             <line>
                                 <style>dot</style>
@@ -362,6 +366,7 @@
                 <curve id="curve3_1" logX="false" logY="false" xDataReference="xDataGenerator3_1" yDataReference="yDataGenerator3_1">
                     <annotation>
                         <properties xmlns="http://www.opencor.ws/">
+                            <selected>true</selected>
                             <title>m</title>
                             <line>
                                 <style>dot</style>
@@ -381,6 +386,7 @@
                 <curve id="curve3_2" logX="false" logY="false" xDataReference="xDataGenerator3_2" yDataReference="yDataGenerator3_2">
                     <annotation>
                         <properties xmlns="http://www.opencor.ws/">
+                            <selected>true</selected>
                             <title>h</title>
                             <line>
                                 <style>dot</style>
@@ -400,6 +406,7 @@
                 <curve id="curve3_3" logX="false" logY="false" xDataReference="xDataGenerator3_3" yDataReference="yDataGenerator3_3">
                     <annotation>
                         <properties xmlns="http://www.opencor.ws/">
+                            <selected>true</selected>
                             <title>n</title>
                             <line>
                                 <style>dot</style>

diff --git a/models/tests/sedml/noble_1962_time_V.sedml b/models/tests/sedml/noble_1962_time_V.sedml
@@ -1,10 +1,10 @@
 <?xml version='1.0' encoding='UTF-8'?>
-<sedML level="1" version="2" xmlns="http://sed-ml.org/sed-ml/level1/version2" xmlns:cellml="http://www.cellml.org/cellml/1.0#">
+<sedML level="1" version="3" xmlns="http://sed-ml.org/sed-ml/level1/version3" xmlns:cellml="http://www.cellml.org/cellml/1.0#">
     <listOfSimulations>
         <uniformTimeCourse id="simulation1" initialTime="0" numberOfPoints="1000" outputEndTime="1000" outputStartTime="0">
             <algorithm kisaoID="KISAO:0000019">
                 <listOfAlgorithmParameters>
-                    <algorithmParameter kisaoID="KISAO:0000211" value="1e-7"/>
+                    <algorithmParameter kisaoID="KISAO:0000211" value="1e-07"/>
                     <algorithmParameter kisaoID="KISAO:0000475" value="BDF"/>
                     <algorithmParameter kisaoID="KISAO:0000481" value="true"/>
                     <algorithmParameter kisaoID="KISAO:0000476" value="Newton"/>
@@ -13,7 +13,7 @@
                     <algorithmParameter kisaoID="KISAO:0000415" value="500"/>
                     <algorithmParameter kisaoID="KISAO:0000467" value="0"/>
                     <algorithmParameter kisaoID="KISAO:0000478" value="Banded"/>
-                    <algorithmParameter kisaoID="KISAO:0000209" value="1e-7"/>
+                    <algorithmParameter kisaoID="KISAO:0000209" value="1e-07"/>
                     <algorithmParameter kisaoID="KISAO:0000479" value="0"/>
                 </listOfAlgorithmParameters>
             </algorithm>

diff --git a/models/tests/sedml/noble_1962_time_gL.sedml b/models/tests/sedml/noble_1962_time_gL.sedml
@@ -1,10 +1,10 @@
 <?xml version='1.0' encoding='UTF-8'?>
-<sedML level="1" version="2" xmlns="http://sed-ml.org/sed-ml/level1/version2" xmlns:cellml="http://www.cellml.org/cellml/1.0#">
+<sedML level="1" version="3" xmlns="http://sed-ml.org/sed-ml/level1/version3" xmlns:cellml="http://www.cellml.org/cellml/1.0#">
     <listOfSimulations>
         <uniformTimeCourse id="simulation1" initialTime="0" numberOfPoints="1000" outputEndTime="1000" outputStartTime="0">
             <algorithm kisaoID="KISAO:0000019">
                 <listOfAlgorithmParameters>
-                    <algorithmParameter kisaoID="KISAO:0000211" value="1e-7"/>
+                    <algorithmParameter kisaoID="KISAO:0000211" value="1e-07"/>
                     <algorithmParameter kisaoID="KISAO:0000475" value="BDF"/>
                     <algorithmParameter kisaoID="KISAO:0000481" value="true"/>
                     <algorithmParameter kisaoID="KISAO:0000476" value="Newton"/>
@@ -13,7 +13,7 @@
                     <algorithmParameter kisaoID="KISAO:0000415" value="500"/>
                     <algorithmParameter kisaoID="KISAO:0000467" value="0"/>
                     <algorithmParameter kisaoID="KISAO:0000478" value="Banded"/>
-                    <algorithmParameter kisaoID="KISAO:0000209" value="1e-7"/>
+                    <algorithmParameter kisaoID="KISAO:0000209" value="1e-07"/>
                     <algorithmParameter kisaoID="KISAO:0000479" value="0"/>
                 </listOfAlgorithmParameters>
             </algorithm>