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Infer reactions #266

Merged
merged 40 commits into from
Sep 27, 2022
Merged

Infer reactions #266

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430f796
files added and changed
skeating Jul 15, 2021
f07dd77
fix strict include build
skeating Jul 16, 2021
2a2861f
add rr converter
skeating Aug 8, 2022
8d8b297
merged files from alessandro
skeating Aug 9, 2022
924a58e
started tests for new funcs
skeating Aug 10, 2022
671c9aa
adding tests for new ast funcs
skeating Aug 12, 2022
39d8669
added tests for decompose
skeating Aug 12, 2022
fddf359
sorting decompose
skeating Aug 15, 2022
ae64773
testing derivatives
skeating Aug 18, 2022
0b76a84
test deriv minus
skeating Aug 19, 2022
efb6911
power and divide
skeating Aug 20, 2022
68ae4f7
got first bit of infer hidden species working
skeating Aug 26, 2022
db1bf5e
Merge branch 'development' into infer-rns
skeating Aug 26, 2022
6c81d71
put in all tests
skeating Aug 26, 2022
814dfd1
working hidden vars example
skeating Aug 29, 2022
9a58dd3
sorting more
skeating Aug 31, 2022
1ce90a0
creating a class to do expression rearrangement and analysis for Fage…
skeating Sep 1, 2022
cbb8338
further analysis
skeating Sep 1, 2022
0fb3eca
catch dxdt != ode
skeating Sep 2, 2022
70f8eed
sorted create term
skeating Sep 3, 2022
b0f0cdc
more complicated expressions
skeating Sep 3, 2022
65bebf7
dont sub k-x if already done k-x-y
skeating Sep 3, 2022
327ce76
these produce same results with copasi
skeating Sep 5, 2022
6403774
numbers for z
skeating Sep 5, 2022
2881c7b
sort param initial value
skeating Sep 6, 2022
3e1a36f
find same exp more than once
skeating Sep 7, 2022
1d0bb0e
detect k-x-y
skeating Sep 7, 2022
02876ab
replace -x+y with y-x
skeating Sep 8, 2022
47acf53
replace k+w-x with z+w
skeating Sep 8, 2022
b790290
sorted k+v-x-y
skeating Sep 10, 2022
06be5cd
adding k-x+w-y
skeating Sep 15, 2022
cd42507
calculate initial values correctly
skeating Sep 15, 2022
6be2c2b
sorting names of new variables
skeating Sep 16, 2022
370e969
fix issues on win gha
skeating Sep 17, 2022
df98d67
linux doesnt like ASTNodeType_t::
skeating Sep 17, 2022
a7056ee
dont use std::to_string
skeating Sep 17, 2022
d8c9565
catch errors now
skeating Sep 17, 2022
12806b7
c++ 20 fixes
skeating Sep 17, 2022
6927356
missed one char *
skeating Sep 17, 2022
536ad07
- plug leaks
fbergmann Sep 27, 2022
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1,515 changes: 1,515 additions & 0 deletions dev/tests/model1-raterules.xml
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1,511 changes: 1,511 additions & 0 deletions dev/tests/model1-reactions.xml
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3,716 changes: 3,716 additions & 0 deletions dev/tests/model2-raterules.xml
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2,766 changes: 2,766 additions & 0 deletions dev/tests/model2-reactions.xml
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226 changes: 226 additions & 0 deletions dev/tests/model3-raterules.xml
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<?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="New_Model" name="Greene2019 - Differentiate Spontaneous and Induced Evolution to Drug Resistance During Cancer Treatment" substanceUnits="substance" timeUnits="time" volumeUnits="volume" areaUnits="area" lengthUnits="length" extentUnits="substance">
<listOfUnitDefinitions>
<unitDefinition id="length" name="length">
<listOfUnits>
<unit kind="metre" exponent="1" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="area" name="area">
<listOfUnits>
<unit kind="metre" exponent="2" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="volume" name="volume">
<listOfUnits>
<unit kind="litre" exponent="1" scale="-3" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="time" name="time">
<listOfUnits>
<unit kind="second" exponent="1" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="substance" name="substance">
<listOfUnits>
<unit kind="mole" exponent="1" scale="-3" multiplier="1"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment metaid="COPASI1" id="compartment" name="compartment" spatialDimensions="3" size="1" units="volume" constant="true"/>
</listOfCompartments>
<listOfParameters>
<parameter metaid="COPASI5" id="S_0" name="S_0" value="0.01" constant="true"/>
<parameter metaid="COPASI6" id="R_0" name="R_0" value="0" constant="true"/>
<parameter metaid="COPASI7" id="V_d" name="V_d" value="0.1" constant="true"/>
<parameter metaid="COPASI8" id="V_c" name="V_c" value="0.9" constant="true"/>
<parameter metaid="COPASI9" id="epsilon" name="epsilon" value="1e-06" constant="true"/>
<parameter metaid="COPASI10" id="d" name="d" value="1" constant="true"/>
<parameter metaid="COPASI11" id="p_r" name="p_r" value="0.2" constant="true"/>
<parameter metaid="COPASI12" id="u_on" name="u_on" value="1.5" constant="true"/>
<parameter metaid="COPASI13" id="delta_ton" name="delta_ton" value="1" constant="true"/>
<parameter metaid="COPASI14" id="delta_toff" name="delta_toff" value="3" constant="true"/>
<parameter metaid="COPASI15" id="u" name="u" value="0" constant="false"/>
<parameter metaid="COPASI16" id="alpha" name="alpha" value="0.01" constant="true"/>
<parameter metaid="COPASI4" id="Tumor_Volume_V" name="Tumor Volume V" value="0.01" constant="false"/>
<parameter metaid="COPASI3" id="Sensitive_tumor_S" name="Sensitive tumor S" value="0.01" constant="false"/>
<parameter metaid="COPASI2" id="Resistant_tumor_R" name="Resistant tumor R" value="0" constant="false"/>
</listOfParameters>
<listOfInitialAssignments>
<initialAssignment symbol="Sensitive_tumor_S">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> S_0 </ci>
</math>
</initialAssignment>
</listOfInitialAssignments>
<listOfRules>
<assignmentRule variable="Tumor_Volume_V">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<ci> Resistant_tumor_R </ci>
<ci> Sensitive_tumor_S </ci>
</apply>
</math>
</assignmentRule>
<rateRule variable="Resistant_tumor_R">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<apply>
<times/>
<cn> 1 </cn>
<apply>
<divide/>
<apply>
<times/>
<ci> compartment </ci>
<apply>
<plus/>
<ci> epsilon </ci>
<apply>
<times/>
<ci> alpha </ci>
<ci> u </ci>
</apply>
</apply>
<ci> Sensitive_tumor_S </ci>
</apply>
<ci> compartment </ci>
</apply>
</apply>
<apply>
<times/>
<cn> 1 </cn>
<apply>
<divide/>
<apply>
<times/>
<ci> compartment </ci>
<ci> p_r </ci>
<apply>
<minus/>
<cn> 1 </cn>
<apply>
<plus/>
<ci> Sensitive_tumor_S </ci>
<ci> Resistant_tumor_R </ci>
</apply>
</apply>
<ci> Resistant_tumor_R </ci>
</apply>
<ci> compartment </ci>
</apply>
</apply>
</apply>
</math>
</rateRule>
<rateRule variable="Sensitive_tumor_S">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<apply>
<times/>
<apply>
<minus/>
<cn> 1 </cn>
</apply>
<apply>
<divide/>
<apply>
<times/>
<ci> compartment </ci>
<apply>
<plus/>
<ci> epsilon </ci>
<apply>
<times/>
<ci> alpha </ci>
<ci> u </ci>
</apply>
</apply>
<ci> Sensitive_tumor_S </ci>
</apply>
<ci> compartment </ci>
</apply>
</apply>
<apply>
<times/>
<cn> 1 </cn>
<apply>
<divide/>
<apply>
<times/>
<ci> compartment </ci>
<apply>
<minus/>
<cn> 1 </cn>
<apply>
<plus/>
<ci> Sensitive_tumor_S </ci>
<ci> Resistant_tumor_R </ci>
</apply>
</apply>
<ci> Sensitive_tumor_S </ci>
</apply>
<ci> compartment </ci>
</apply>
</apply>
<apply>
<times/>
<apply>
<minus/>
<cn> 1 </cn>
</apply>
<apply>
<divide/>
<apply>
<times/>
<ci> compartment </ci>
<ci> d </ci>
<ci> u </ci>
<ci> Sensitive_tumor_S </ci>
</apply>
<ci> compartment </ci>
</apply>
</apply>
</apply>
</math>
</rateRule>
</listOfRules>
<listOfEvents>
<event metaid="COPASI17" id="treatment" name="treatment" useValuesFromTriggerTime="true">
<trigger initialValue="false" persistent="true">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<and/>
<apply>
<gt/>
<ci> Tumor_Volume_V </ci>
<ci> V_d </ci>
</apply>
<apply>
<eq/>
<ci> u </ci>
<cn> 0 </cn>
</apply>
</apply>
</math>
</trigger>
<listOfEventAssignments>
<eventAssignment variable="u">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<ci> u </ci>
<ci> u_on </ci>
</apply>
</math>
</eventAssignment>
</listOfEventAssignments>
</event>
</listOfEvents>
</model>
</sbml>
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