Name		Name	Last commit message	Last commit date
parent directory ..
CMakeLists.txt		CMakeLists.txt
README.md		README.md
createSteadystateExampleSBML.py		createSteadystateExampleSBML.py
create_steadystate_amici_model.py		create_steadystate_amici_model.py
exampleSteadystateScaledTest.h		exampleSteadystateScaledTest.h
main.cpp		main.cpp
main_multicondition.cpp		main_multicondition.cpp
main_simulator.cpp		main_simulator.cpp
parpeExampleSteadystateBasic.ipynb		parpeExampleSteadystateBasic.ipynb
parpeExampleSteadystateHierarchical.ipynb		parpeExampleSteadystateHierarchical.ipynb
parpeExampleSteadystateMinibatch.ipynb		parpeExampleSteadystateMinibatch.ipynb
recreateExampleData.sh		recreateExampleData.sh
steadyStateMultiConditionDataprovider.cpp		steadyStateMultiConditionDataprovider.cpp
steadyStateMultiConditionDataprovider.h		steadyStateMultiConditionDataprovider.h
steadystateProblem.cpp		steadystateProblem.cpp
steadystateProblem.h		steadystateProblem.h
steadystateProblemParallel.cpp		steadystateProblemParallel.cpp
steadystateProblemParallel.h		steadystateProblemParallel.h
test_steadystate.py		test_steadystate.py

README.md

parPE steadystate example

This directory contains file to generate a simple parameter estimation problem and some Jupyter notebooks to demonstrate basic parPE usage.

parpeExampleSteadystateBasic.ipynb describes the parameter estimation problem and demonstrates basic parPE usage
parpeExampleSteadystateHierarchical.ipynb demonstrates the hierarchical optimization approach implemented in parPE
parpeExampleSteadystateMinibatch.ipynb demonstrates the use of mini-batch optimization implemented in parPE

The example problem is generated by

createSteadystateExampleSBML.py: Create SBML model from scratch
create_steadystate_amici_model.py: Create example artificial measurements and other PEtab files