- Author:
- Dewan Sarwar <sarwarcse@gmail.com>
- Date:
- 2019-01-31 16:34:20+13:00
- Desc:
- Testing with Max's suggested way of annotation for weinstein_1995_max model
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/584/rawfile/848b6a8fb585337adc4f3805c0ed682a6a5fd379/test.xml
<sedML xmlns="http://sed-ml.org/sed-ml/level1/version2" xmlns:cellml="http://www.cellml.org/cellml/1.1#" level="1"
version="2">
<listOfSimulations>
<uniformTimeCourse id="simulation1" initialTime="0" numberOfPoints="1000" outputEndTime="1" outputStartTime="0">
<algorithm kisaoID="KISAO:0000019">
<listOfAlgorithmParameters>
<algorithmParameter kisaoID="KISAO:0000211" value="1e-7"/>
<algorithmParameter kisaoID="KISAO:0000475" value="BDF"/>
<algorithmParameter kisaoID="KISAO:0000481" value="true"/>
<algorithmParameter kisaoID="KISAO:0000476" value="Newton"/>
<algorithmParameter kisaoID="KISAO:0000477" value="Dense"/>
<algorithmParameter kisaoID="KISAO:0000480" value="0"/>
<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:0000479" value="0"/>
</listOfAlgorithmParameters>
</algorithm>
</uniformTimeCourse>
</listOfSimulations>
<listOfModels>
<model id="model" language="urn:sedml:language:cellml.1_1" source="weinstein_1995.cellml"/>
</listOfModels>
<listOfTasks>
<repeatedTask id="repeatedTask" range="once" resetModel="true">
<listOfRanges>
<vectorRange id="once">
<value>1</value>
</vectorRange>
</listOfRanges>
<listOfSubTasks>
<subTask order="1" task="task1"/>
</listOfSubTasks>
</repeatedTask>
<task id="task1" modelReference="model" simulationReference="simulation1"/>
</listOfTasks>
<listOfDataGenerators>
<Protocol id="1"
name="myAttrib" ploty="undefined"/>
<Protocol id="2"
name="V vs I"
opby="http://identifiers.org/opb/OPB_00318"
opbx="http://identifiers.org/opb/OPB_00506"
chebi="undefined"
fma="http://purl.obolibrary.org/obo/FMA_84666"
sparqly="protocol2Currrent"
sparqlx="protocol2Potential"
time="undefined"
ploty="undefined"/>
<Protocol id="3A"
name="concentration/flux vs concentration 3A"
opby="http://identifiers.org/opb/OPB_00593"
opbx="http://identifiers.org/opb/OPB_00340"
chebi="http://purl.obolibrary.org/obo/CHEBI_29101"
fma="http://purl.obolibrary.org/obo/FMA_74550"
sparqly="protocol3Flux"
sparqlx="protocol1Concentration"
time="undefined"
ploty="plot (dimensionless)"/>
<Protocol id="3B"
name="concentration/flux vs concentration 3B"
opby="http://identifiers.org/opb/OPB_00593"
opbx="http://identifiers.org/opb/OPB_00340"
chebi="http://purl.obolibrary.org/obo/CHEBI_29101"
fma="http://purl.obolibrary.org/obo/FMA_74550"
sparqly="protocol3Flux"
sparqlx="protocol1Concentration"
time="undefined"
ploty="plot (dimensionless)"/>
<Protocol id="4A"
name="1/flux vs concentration 4A"
opby="http://identifiers.org/opb/OPB_00593"
opbx="http://identifiers.org/opb/OPB_00340"
chebi="http://purl.obolibrary.org/obo/CHEBI_28938"
fma="http://purl.obolibrary.org/obo/FMA_74550"
sparqly="protocol3Flux"
sparqlx="protocol4Concentration"
time="undefined"
ploty="plot (mM)"/>
<Protocol id="4B"
name="1/flux vs concentration 4B"
opby="http://identifiers.org/opb/OPB_00593"
opbx="http://identifiers.org/opb/OPB_00340"
chebi="http://purl.obolibrary.org/obo/CHEBI_28938"
fma="http://purl.obolibrary.org/obo/FMA_74550"
sparqly="protocol3Flux"
sparqlx="protocol4Concentration"
time="undefined"
ploty="plot (mM)"/>
<Protocol id="2A"
name="flux vs external pH 2A"
opby="http://identifiers.org/opb/OPB_00593"
opbx="http://identifiers.org/opb/OPB_00340"
chebi="http://purl.obolibrary.org/obo/CHEBI_15378"
fma="http://purl.obolibrary.org/obo/FMA_74550"
sparqly="protocol3Flux"
sparqlx="protocol2AConcentration"
time="undefined"
ploty="plot (dimensionless)"/>
<Protocol id="2B"
name="1/flux vs concentration 2B"
opby="http://identifiers.org/opb/OPB_00593"
opbx="http://identifiers.org/opb/OPB_00340"
chebi="http://purl.obolibrary.org/obo/CHEBI_15378"
fma="http://purl.obolibrary.org/obo/FMA_74550"
sparqly="protocol3Flux"
sparqlx="protocol2AConcentration"
time="undefined"
ploty="plot (dimensionless)"/>
<Protocol id="experimental"
name="experimental"
opby="http://identifiers.org/opb/OPB_00340"
opbx="http://identifiers.org/opb/OPB_01023"
chebi="http://purl.obolibrary.org/obo/CHEBI_29101"
fma="http://purl.obolibrary.org/obo/FMA_74550"
sparqly="protocol1Concentration"
sparqlx="protocol1Time"
time="/cellml:model/cellml:component[@name='environment']/cellml:variable[@name='time']"
ploty="experimental"/>
<dataGenerator id="xDataGenerator1_1">
<listOfVariables>
<variable id="xVariable1_1"
target="xtarget"
taskReference="repeatedTask"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci>xVariable1_1</ci>
</math>
</dataGenerator>
<dataGenerator id="yDataGenerator1_1">
<listOfVariables>
<variable id="yVariable1_1"
target="ytarget"
taskReference="repeatedTask"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci>yVariable1_1</ci>
</math>
</dataGenerator>
</listOfDataGenerators>
<listOfOutputs>
<plot2D id="plot1">
<annotation>
<properties xmlns="http://www.opencor.ws/">
<backgroundColor>#ffffff</backgroundColor>
<fontSize>10</fontSize>
<foregroundColor>#000000</foregroundColor>
<height>1</height>
<gridLines>
<style>dot</style>
<width>1</width>
<color>#a0a0a4</color>
</gridLines>
<legend>false</legend>
<pointCoordinates>
<style>dash</style>
<width>1</width>
<color>#b0008080</color>
<fontColor>#ffffff</fontColor>
</pointCoordinates>
<surroundingArea>
<backgroundColor>#f0f0f0</backgroundColor>
<foregroundColor>#000000</foregroundColor>
</surroundingArea>
<title/>
<xAxis>
<logarithmicScale>false</logarithmicScale>
<title/>
</xAxis>
<yAxis>
<logarithmicScale>false</logarithmicScale>
<title/>
</yAxis>
<zoomRegion>
<style>solid</style>
<width>1</width>
<color>#b0800000</color>
<fontColor>#ffffff</fontColor>
<filled>true</filled>
<fillColor>#30ffff00</fillColor>
</zoomRegion>
</properties>
</annotation>
<listOfCurves>
<curve id="curve1_1" logX="false" logY="false" xDataReference="xDataGenerator1_1"
yDataReference="yDataGenerator1_1">
<annotation>
<properties xmlns="http://www.opencor.ws/">
<title/>
<line>
<style>solid</style>
<width>1</width>
<color>#000080</color>
</line>
<symbol>
<style>none</style>
<size>8</size>
<color>#000080</color>
<filled>true</filled>
<fillColor>#ffffff</fillColor>
</symbol>
</properties>
</annotation>
</curve>
</listOfCurves>
</plot2D>
</listOfOutputs>
</sedML>
