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Merge pull request #50 from siravan/master
ver 2.4.3
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‎Project.toml

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name = "CellMLToolkit"
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uuid = "03cb29e0-1ef4-4721-aa24-cf58a006576f"
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authors = ["Shahriar Iravanian <siravan@svtsim.com>"]
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version = "2.4.2"
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version = "2.4.3"
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[deps]
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EzXML = "8f5d6c58-4d21-5cfd-889c-e3ad7ee6a615"

‎README.md

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plot(sol, vars=(1,3))
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```
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Note that `model` is a directory of the CellMLToolkit package. You can find its path as
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Note that `model` is a directory of the CellMLToolkit package. You can find its path as
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```Julia
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model_root = joinpath(splitdir(pathof(CellMLToolkit))[1], "..", "models")
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prob = read_cellml(model_path, (0,100.0))
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```
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# Tutorial
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## Tutorial
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The models directory contains a few CellML model examples. Let's start with a simple one, the famous Lorenz equations!
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plot(sol, vars=8) # 8 is the index of membrane₊V
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```
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For the last example, we chose a complex model to stress the ODE solvers: [the O'Hara-Rudy left ventricular model](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002061). This model has 49 state variables, is very stiff, and is prone to oscillation. The best solver for this model is `CVODE_BDF` from the Sundial suite.
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For the next example, we chose a complex model to stress the ODE solvers: [the O'Hara-Rudy left ventricular model](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002061). This model has 49 state variables, is very stiff, and is prone to oscillation. The best solver for this model is `CVODE_BDF` from the Sundial suite.
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```Julia
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using Sundials
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```
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![](figures/ohara_rudy.png)
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## Multi-file Models (Import)
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CellML specification allows for multi-file models. In these models, the top level CellML XML file imports components from other CellML files, which in turn may import from other files. CellMLToolkit supports this functionality. It assumes that *the top-level file and all the imported files reside in the same directory*. `models/noble_1962` contained one such example:
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```julia
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ml = CellModel("models/noble_1962/Noble_1962.cellml")
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prob = ODEProblem(ml, tspan)
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sol = solve(prob, TRBDF2(), dtmax=0.5)
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```
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Note that the syntax is exactly the same as before. However, the list of the imported files are printed during `CellModel` generation:
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```
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[ Info: importing Noble62_Na_channel.cellml
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[ Info: importing Noble62_units.cellml
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[ Info: importing Noble62_K_channel.cellml
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[ Info: importing Noble62_units.cellml
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[ Info: importing Noble62_L_channel.cellml
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[ Info: importing Noble62_units.cellml
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[ Info: importing Noble62_units.cellml
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[ Info: importing Noble62_parameters.cellml
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[ Info: importing Noble62_units.cellml
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```
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Same as before, we can plot the output as
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```julia
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plot(sol, vars=2)
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```
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![](figures/noble_1962.png)

‎figures/noble_1962.png

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‎models/noble_1962/BlueSkyCatastrophy.cellml

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<?xml version='1.0'?>
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<model name="van_der_pol_model" xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#">
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<component name="main">
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<variable initial_value="0" name="t" units="dimensionless"/>
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<variable initial_value="0.9" name="x" units="dimensionless"/>
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<variable initial_value="0.4" name="y" units="dimensionless"/>
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<variable initial_value="0.2645" name="A" units="dimensionless"/>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<eq/>
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<apply>
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<diff/>
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<bvar>
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<ci>t</ci>
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</bvar>
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<ci>x</ci>
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</apply>
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<ci>y</ci>
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</apply>
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<apply>
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<eq/>
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<apply>
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<diff/>
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<bvar>
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<ci>t</ci>
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</bvar>
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<ci>y</ci>
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</apply>
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<apply>
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<plus/>
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<apply>
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<minus/>
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<apply>
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<minus/>
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<ci>x</ci>
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<apply>
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<power/>
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<ci>x</ci>
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<cn cellml:units="dimensionless">3</cn>
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</apply>
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</apply>
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<apply>
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<times/>
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<cn cellml:units="dimensionless">0.25</cn>
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<ci>y</ci>
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</apply>
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</apply>
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<apply>
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<times/>
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<ci>A</ci>
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<apply>
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<sin/>
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<ci>t</ci>
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</apply>
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</apply>
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</apply>
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</apply>
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</math>
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</component>
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</model>

‎models/noble_1962/BlueSkyCatastrophy.sedml

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<?xml version='1.0' encoding='UTF-8'?>
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<sedML level="1" version="2" xmlns="http://sed-ml.org/sed-ml/level1/version2" xmlns:cellml="http://www.cellml.org/cellml/1.1#">
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<listOfSimulations>
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<uniformTimeCourse id="simulation1" initialTime="0" numberOfPoints="50000" outputEndTime="500" outputStartTime="0">
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<algorithm kisaoID="KISAO:0000019">
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<listOfAlgorithmParameters>
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<algorithmParameter kisaoID="KISAO:0000211" value="1e-07"/>
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<algorithmParameter kisaoID="KISAO:0000475" value="BDF"/>
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<algorithmParameter kisaoID="KISAO:0000481" value="true"/>
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<algorithmParameter kisaoID="KISAO:0000476" value="Newton"/>
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<algorithmParameter kisaoID="KISAO:0000477" value="Dense"/>
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<algorithmParameter kisaoID="KISAO:0000480" value="0"/>
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<algorithmParameter kisaoID="KISAO:0000415" value="500"/>
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<algorithmParameter kisaoID="KISAO:0000467" value="0"/>
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<algorithmParameter kisaoID="KISAO:0000478" value="Banded"/>
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<algorithmParameter kisaoID="KISAO:0000209" value="1e-07"/>
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<algorithmParameter kisaoID="KISAO:0000479" value="0"/>
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</listOfAlgorithmParameters>
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</algorithm>
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</uniformTimeCourse>
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</listOfSimulations>
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<listOfModels>
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<model id="model" language="urn:sedml:language:cellml.1_1" source="BlueSkyCatastrophy.cellml"/>
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</listOfModels>
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<listOfTasks>
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<repeatedTask id="repeatedTask" range="once" resetModel="true">
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<listOfRanges>
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<vectorRange id="once">
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<value> 1 </value>
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</vectorRange>
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</listOfRanges>
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<listOfSubTasks>
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<subTask order="1" task="task1"/>
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</listOfSubTasks>
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</repeatedTask>
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<task id="task1" modelReference="model" simulationReference="simulation1"/>
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</listOfTasks>
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<listOfDataGenerators>
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<dataGenerator id="xDataGenerator1_1">
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<listOfVariables>
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<variable id="xVariable1_1" target="/cellml:model/cellml:component[@name='main']/cellml:variable[@name='t']" taskReference="repeatedTask"/>
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</listOfVariables>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<ci> xVariable1_1 </ci>
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</math>
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</dataGenerator>
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<dataGenerator id="yDataGenerator1_1">
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<listOfVariables>
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<variable id="yVariable1_1" target="/cellml:model/cellml:component[@name='main']/cellml:variable[@name='x']" taskReference="repeatedTask"/>
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</listOfVariables>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<ci> yVariable1_1 </ci>
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</math>
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</dataGenerator>
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<dataGenerator id="xDataGenerator2_1">
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<listOfVariables>
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<variable id="xVariable2_1" target="/cellml:model/cellml:component[@name='main']/cellml:variable[@name='x']" taskReference="repeatedTask"/>
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</listOfVariables>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<ci> xVariable2_1 </ci>
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</math>
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</dataGenerator>
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<dataGenerator id="yDataGenerator2_1">
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<listOfVariables>
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<variable id="yVariable2_1" target="/cellml:model/cellml:component[@name='main']/cellml:variable[@name='y']" taskReference="repeatedTask"/>
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</listOfVariables>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<ci> yVariable2_1 </ci>
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</math>
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</dataGenerator>
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</listOfDataGenerators>
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<listOfOutputs>
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<plot2D id="plot1">
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<listOfCurves>
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<curve id="curve1_1" logX="false" logY="false" xDataReference="xDataGenerator1_1" yDataReference="yDataGenerator1_1"/>
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</listOfCurves>
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</plot2D>
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<plot2D id="plot2">
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<listOfCurves>
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<curve id="curve2_1" logX="false" logY="false" xDataReference="xDataGenerator2_1" yDataReference="yDataGenerator2_1"/>
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</listOfCurves>
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</plot2D>
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</listOfOutputs>
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</sedML>

‎models/noble_1962/Firstorder.cellml

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<model name="first_order_model" xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#">
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<component name="main">
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<variable initial_value="0" name="t" units="dimensionless"/>
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<variable initial_value="5" name="y" units="dimensionless"/>
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<variable initial_value="1" name="a" units="dimensionless"/>
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<variable initial_value="2" name="b" units="dimensionless"/>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<eq/>
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<apply>
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<diff/>
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<bvar>
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<ci>t</ci>
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</bvar>
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<ci>y</ci>
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</apply>
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<apply>
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<plus/>
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<apply>
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<times/>
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<apply>
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<minus/>
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<ci>a</ci>
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</apply>
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<ci>y</ci>
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</apply>
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<ci>b</ci>
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</apply>
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</apply>
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</math>
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</component>
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</model>

‎models/noble_1962/Firstorder.rst

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Exponential decay: A simple first order ODE
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-------------------------------------------
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Used as the simplest example of a first order differential equation, this model consists of a `single equation <Firstorder.cellml/cellml_math>`_. One of the simulation experiments for this model described in the tutorial can be obtained by loading the `corresponding SED-ML document <Firstorder.sedml>`__ into OpenCOR and executing the simulation - which can be achived by choosing the **Launch with OpenCOR** link from the *Views Available* listing.

‎models/noble_1962/Firstorder.sedml

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<?xml version='1.0' encoding='UTF-8'?>
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<sedML level="1" version="2" xmlns="http://sed-ml.org/sed-ml/level1/version2" xmlns:cellml="http://www.cellml.org/cellml/1.1#">
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<listOfSimulations>
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<uniformTimeCourse id="simulation1" initialTime="0" numberOfPoints="100" outputEndTime="10" outputStartTime="0">
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<algorithm kisaoID="KISAO:0000019">
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<listOfAlgorithmParameters>
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<algorithmParameter kisaoID="KISAO:0000211" value="1e-07"/>
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<algorithmParameter kisaoID="KISAO:0000475" value="BDF"/>
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<algorithmParameter kisaoID="KISAO:0000481" value="true"/>
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<algorithmParameter kisaoID="KISAO:0000476" value="Newton"/>
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<algorithmParameter kisaoID="KISAO:0000477" value="Dense"/>
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<algorithmParameter kisaoID="KISAO:0000480" value="0"/>
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<algorithmParameter kisaoID="KISAO:0000415" value="500"/>
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<algorithmParameter kisaoID="KISAO:0000467" value="0"/>
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<algorithmParameter kisaoID="KISAO:0000478" value="Banded"/>
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<algorithmParameter kisaoID="KISAO:0000209" value="1e-07"/>
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<algorithmParameter kisaoID="KISAO:0000479" value="0"/>
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</listOfAlgorithmParameters>
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</algorithm>
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</uniformTimeCourse>
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</listOfSimulations>
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<listOfModels>
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<model id="model" language="urn:sedml:language:cellml.1_1" source="Firstorder.cellml"/>
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</listOfModels>
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<listOfTasks>
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<repeatedTask id="repeatedTask" range="once" resetModel="true">
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<listOfRanges>
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<vectorRange id="once">
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<value> 1 </value>
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</vectorRange>
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</listOfRanges>
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<listOfSubTasks>
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<subTask order="1" task="task1"/>
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</listOfSubTasks>
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</repeatedTask>
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<task id="task1" modelReference="model" simulationReference="simulation1"/>
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</listOfTasks>
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<listOfDataGenerators>
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<dataGenerator id="xDataGenerator1_1">
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<listOfVariables>
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<variable id="xVariable1_1" target="/cellml:model/cellml:component[@name='main']/cellml:variable[@name='t']" taskReference="repeatedTask"/>
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</listOfVariables>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<ci> xVariable1_1 </ci>
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</math>
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</dataGenerator>
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<dataGenerator id="yDataGenerator1_1">
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<listOfVariables>
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<variable id="yVariable1_1" target="/cellml:model/cellml:component[@name='main']/cellml:variable[@name='y']" taskReference="repeatedTask"/>
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</listOfVariables>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<ci> yVariable1_1 </ci>
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</math>
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</dataGenerator>
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</listOfDataGenerators>
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<listOfOutputs>
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<plot2D id="plot1">
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<listOfCurves>
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<curve id="curve1_1" logX="false" logY="false" xDataReference="xDataGenerator1_1" yDataReference="yDataGenerator1_1"/>
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</listOfCurves>
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</plot2D>
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</listOfOutputs>
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</sedML>

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