.codespellrc
.gitignore
.readthedocs.yaml
AUTHORS.txt
CONTRIBUTING.md
LICENSE.txt
README.md
concretization.txt
pyproject.toml
setup.sh
setup_no_spack.sh
.ci/setup.sh
.github/workflows/format.yml
.github/workflows/integration_tests.yml
.github/workflows/publish.yml
.github/workflows/unit_tests.yml
docs/conf.py
docs/contributing.rst
docs/dualrun.drawio.svg
docs/index.rst
docs/modules.rst
docs/multiscale_run.rst
docs/orchestration_scheme.drawio.svg
docs/requirements.txt
docs/simulation_config.rst
multiscale_run/__init__.py
multiscale_run/bloodflow_manager.py
multiscale_run/cli.py
multiscale_run/config.py
multiscale_run/connection_manager.py
multiscale_run/metabolism_manager.py
multiscale_run/neurodamus_manager.py
multiscale_run/preprocessor.py
multiscale_run/reporter.py
multiscale_run/simulation.py
multiscale_run/steps_manager.py
multiscale_run/utils.py
multiscale_run.egg-info/PKG-INFO
multiscale_run.egg-info/SOURCES.txt
multiscale_run.egg-info/dependency_links.txt
multiscale_run.egg-info/entry_points.txt
multiscale_run.egg-info/requires.txt
multiscale_run.egg-info/top_level.txt
multiscale_run/metabolism/__init__.py
multiscale_run/metabolism/constants.py
multiscale_run/metabolism/indexes.py
multiscale_run/metabolism/initial_conditions.py
multiscale_run/metabolism/model.py
multiscale_run/templates/__init__.py
multiscale_run/templates/msr.schema.json
multiscale_run/templates/postproc.ipynb
multiscale_run/templates/simulation.sbatch.jinja
multiscale_run/templates/tiny_CI/circuit_config.json
multiscale_run/templates/tiny_CI/node_sets.json
multiscale_run/templates/tiny_CI/simulation_config.json
old/.gitlab-ci.yml
old/README.md
old/quadrun.graphml
old/quadrun.png
old/simulation.py
old/ci/.ci/setup.sh
old/ci/.ci/test_init_julia_create.sh
old/ci/.ci/test_integration.sh
old/ci/.ci/test_pytest.sh
old/ci/.ci/test_simulation.sh
old/ci/workflows/check-packaging.yml
old/ci/workflows/publish.yml
old/data/metabolism/ATDMP.jl
old/data/metabolism/ETC.jl
old/data/metabolism/GLC_transport.jl
old/data/metabolism/GLYCOLYSIS.jl
old/data/metabolism/MAS.jl
old/data/metabolism/PPP_a.jl
old/data/metabolism/PPP_n.jl
old/data/metabolism/TCA.jl
old/data/metabolism/bf_input.jl
old/data/metabolism/creatine.jl
old/data/metabolism/ephys_parameters.jl
old/data/metabolism/gaba.jl
old/data/metabolism/general_parameters.jl
old/data/metabolism/generalisations.jl
old/data/metabolism/gltgln.jl
old/data/metabolism/glycogen.jl
old/data/metabolism/gshgssg.jl
old/data/metabolism/ketones.jl
old/data/metabolism/lactate.jl
old/data/metabolism/pyrCarb.jl
old/data/metabolism/pyrTrCytoMito.jl
old/data/metabolism/u0.csv
old/data/metabolism/u0_db_refined_selected_oct2021.jl
old/data/metabolism/variables_idxs.jl
old/metabolism/ODE_system.jl
old/metabolism/ODE_system_aged.jl
old/metabolism/ODE_system_young.jl
old/metabolism/README.md
old/templates/rat_sscxS1HL_V10/circuit_config.json
old/templates/rat_sscxS1HL_V10/node_sets.json
old/templates/rat_sscxS1HL_V10/simulation_config.json
old/templates/rat_sscxS1HL_V6/circuit_config.json
old/templates/rat_sscxS1HL_V6/node_sets.json
old/templates/rat_sscxS1HL_V6/simulation_config.json
old/templates/tiny_CI/circuit_config.json
old/templates/tiny_CI/node_sets.json
old/templates/tiny_CI/simulation_config.json
old/tests/contrib/update_currents.sh
old/tests/integration/autogen_mesh.py
old/tests/integration/connect_neurodamus2steps.py
old/tests/integration/preprocessor.py
old/tests/integration/simulation_config.json
old/tests/metabolism/jl_model_tests.ipynb
old/tests/metabolism/py_jl_tests.ipynb
old/tests/pytests/test_metabolism.py
old/tests/pytests/test_steps.py
tests/__init__.py
tests/unit/__init__.py
tests/unit/test_cli.py
tests/unit/test_config.py
tests/unit/test_metab_solver.py
tests/unit/test_preprocessor.py
tests/unit/test_reporter.py
tests/unit/test_utils.py
tests/unit/test_folder/simulation_config.json