.dockerignore
.pre-commit-config.yaml
.readthedocs.yml
LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.cfg
setup.py
docker/Dockerfile
docker/cplex/cplex.installer.properties
docker/docker-scripts/docker-entrypoint.sh
docker/docker-scripts/pyinstall-solver.sh
docker/gurobi/gurobi.lic.template
docs/.gitignore
docs/Makefile
docs/conf.py
docs/gurobi.env
docs/index.rst
docs/make.bat
docs/references.bib
docs/references.rst
docs/robots.txt
docs/additional/code_repositories.rst
docs/additional/faqs.ipynb
docs/education/sb2/index.rst
docs/education/sb2/chapters/gurobi.env
docs/education/sb2/chapters/sb2_chapter1.ipynb
docs/education/sb2/chapters/sb2_chapter10.ipynb
docs/education/sb2/chapters/sb2_chapter11.ipynb
docs/education/sb2/chapters/sb2_chapter12.ipynb
docs/education/sb2/chapters/sb2_chapter13.ipynb
docs/education/sb2/chapters/sb2_chapter14.ipynb
docs/education/sb2/chapters/sb2_chapter2.ipynb
docs/education/sb2/chapters/sb2_chapter3.ipynb
docs/education/sb2/chapters/sb2_chapter4.ipynb
docs/education/sb2/chapters/sb2_chapter5.ipynb
docs/education/sb2/chapters/sb2_chapter6.ipynb
docs/education/sb2/chapters/sb2_chapter7.ipynb
docs/education/sb2/chapters/sb2_chapter8.ipynb
docs/education/sb2/chapters/sb2_chapter9.ipynb
docs/education/sb2/images/Ch1/Figure-1-1.png
docs/education/sb2/images/Ch1/Figure-1-2.png
docs/education/sb2/images/Ch1/Figure-1-3.png
docs/education/sb2/images/Ch1/Figure-1-4.png
docs/education/sb2/images/Ch1/Figure-1-5.png
docs/education/sb2/images/Ch1/Figure-1-6.png
docs/education/sb2/images/Ch1/Figure-1-7.png
docs/education/sb2/images/Ch1/Table-1-1.png
docs/education/sb2/images/Ch1/Table-1-2.png
docs/education/sb2/images/Ch1/Table-1-3.png
docs/education/sb2/images/Ch10/Figure-10-1.png
docs/education/sb2/images/Ch10/Figure-10-16.png
docs/education/sb2/images/Ch10/Figure-10-17.png
docs/education/sb2/images/Ch10/Figure-10-18.png
docs/education/sb2/images/Ch10/Figure-10-19.png
docs/education/sb2/images/Ch10/Figure-10-2.png
docs/education/sb2/images/Ch10/Figure-10-20.png
docs/education/sb2/images/Ch10/Figure-10-21.png
docs/education/sb2/images/Ch10/Figure-10-4.png
docs/education/sb2/images/Ch11/Figure-11-1.png
docs/education/sb2/images/Ch11/Figure-11-2.png
docs/education/sb2/images/Ch11/Figure-11-6.png
docs/education/sb2/images/Ch11/Figure-11-8.png
docs/education/sb2/images/Ch12/Figure-12-1.png
docs/education/sb2/images/Ch12/Figure-12-2.png
docs/education/sb2/images/Ch12/Figure-12-20.png
docs/education/sb2/images/Ch12/Figure-12-6.png
docs/education/sb2/images/Ch12/Figure-12-7.png
docs/education/sb2/images/Ch13/Figure-13-1.png
docs/education/sb2/images/Ch13/Figure-13-2.png
docs/education/sb2/images/Ch13/Figure-13-6.png
docs/education/sb2/images/Ch14/Figure-14-1.png
docs/education/sb2/images/Ch14/Figure-14-2.png
docs/education/sb2/images/Ch2/Figure-2-1.png
docs/education/sb2/images/Ch2/Figure-2-10.png
docs/education/sb2/images/Ch2/Figure-2-11.png
docs/education/sb2/images/Ch2/Figure-2-12.png
docs/education/sb2/images/Ch2/Figure-2-13.png
docs/education/sb2/images/Ch2/Figure-2-2.png
docs/education/sb2/images/Ch2/Figure-2-3.png
docs/education/sb2/images/Ch2/Figure-2-4.png
docs/education/sb2/images/Ch2/Figure-2-5.png
docs/education/sb2/images/Ch2/Figure-2-6.png
docs/education/sb2/images/Ch2/Figure-2-7.png
docs/education/sb2/images/Ch2/Figure-2-8.png
docs/education/sb2/images/Ch2/Figure-2-9.png
docs/education/sb2/images/Ch3/Figure-3-1.png
docs/education/sb2/images/Ch3/Figure-3-2.png
docs/education/sb2/images/Ch3/Figure-3-3.png
docs/education/sb2/images/Ch3/Figure-3-4.png
docs/education/sb2/images/Ch3/Figure-3-5.png
docs/education/sb2/images/Ch3/Table-3-1.png
docs/education/sb2/images/Ch5/Figure-5-1.png
docs/education/sb2/images/Ch5/Figure-5-2.png
docs/education/sb2/images/Ch5/Figure-5-3.png
docs/education/sb2/images/Ch5/Figure-5-6.png
docs/education/sb2/images/Ch5/Figure-5-8.png
docs/education/sb2/images/Ch6/Figure-6-1.png
docs/education/sb2/images/Ch6/Figure-6-5.png
docs/education/sb2/images/Ch7/Figure-7-1.png
docs/education/sb2/images/Ch7/Figure-7-2.png
docs/education/sb2/images/Ch7/Figure-7-3.png
docs/education/sb2/images/Ch7/Figure-7-4.png
docs/education/sb2/images/Ch7/Figure-7-5.png
docs/education/sb2/images/Ch7/Table-7-1.png
docs/education/sb2/images/Ch7/Table-7-2.png
docs/education/sb2/images/Ch7/Table-7-3.png
docs/education/sb2/images/Ch7/Table-7-4.png
docs/education/sb2/images/Ch7/Table-7-5.png
docs/education/sb2/images/Ch7/Table-7-6.png
docs/education/sb2/images/Ch7/Table-7-7.png
docs/education/sb2/images/Ch7/Table-7-8.png
docs/education/sb2/images/Ch7/Table-7-9.png
docs/education/sb2/images/Ch8/Figure-8-1.png
docs/education/sb2/images/Ch8/Figure-8-10.png
docs/education/sb2/images/Ch8/Figure-8-11.png
docs/education/sb2/images/Ch8/Figure-8-13.png
docs/education/sb2/images/Ch8/Figure-8-14.png
docs/education/sb2/images/Ch8/Figure-8-16.png
docs/education/sb2/images/Ch8/Figure-8-19.png
docs/education/sb2/images/Ch8/Figure-8-2.png
docs/education/sb2/images/Ch8/Figure-8-3.png
docs/education/sb2/images/Ch8/Figure-8-4.png
docs/education/sb2/images/Ch8/Figure-8-5.png
docs/education/sb2/images/Ch8/Figure-8-6.png
docs/education/sb2/images/Ch8/Table-8-1.png
docs/education/sb2/images/Ch9/Figure-9-1.png
docs/education/sb2/images/Ch9/Figure-9-11.png
docs/education/sb2/images/Ch9/Figure-9-12.png
docs/education/sb2/images/Ch9/Figure-9-17.png
docs/education/sb2/images/Ch9/Figure-9-18.png
docs/education/sb2/images/Ch9/Figure-9-2.png
docs/education/sb2/images/Ch9/Figure-9-23.png
docs/education/sb2/images/Ch9/Figure-9-3.png
docs/education/sb2/images/Ch9/Figure-9-6.png
docs/education/sb2/images/Ch9/Figure-9-7.png
docs/education/sb2/images/Ch9/Figure-9-A1.png
docs/education/sb2/images/Ch9/Figure-9-A2.png
docs/education/sb2/images/Ch9/Figure-9-A3.png
docs/education/sb2/images/Ch9/Figure-9-A4.png
docs/education/sb2/images/Ch9/Figure-9-A5.png
docs/education/sb2/model_construction/gurobi.env
docs/education/sb2/model_construction/sb2_amp_salvage_network.ipynb
docs/education/sb2/model_construction/sb2_glycolysis.ipynb
docs/education/sb2/model_construction/sb2_hemoglobin.ipynb
docs/education/sb2/model_construction/sb2_pentose_phosphate_pathway.ipynb
docs/education/sb2/model_construction/sb2_pfk.ipynb
docs/gallery/index.rst
docs/gallery/media/escher_toy_animation.mp4
docs/gallery/visualization/animating_simulations.ipynb
docs/gallery/visualization/catalytic_potential_visualizations.ipynb
docs/gallery/visualization/gurobi.env
docs/gallery/workflows/constructing_glycolysis.ipynb
docs/gallery/workflows/gurobi.env
docs/images/masspy-logo.svg
docs/images/multicompartment.png
docs/images/phosphate_trafficking.png
docs/installation/docker.rst
docs/installation/docker_detailed.rst
docs/installation/quickstart.rst
docs/installation/solvers.rst
docs/tutorials/cobra_to_mass.ipynb
docs/tutorials/compartments.ipynb
docs/tutorials/constructing_models.ipynb
docs/tutorials/dynamic_simulation.ipynb
docs/tutorials/ensemble_modeling.ipynb
docs/tutorials/enzyme_modules.ipynb
docs/tutorials/getting_started_with_masspy.ipynb
docs/tutorials/global_configuration.ipynb
docs/tutorials/gurobi.env
docs/tutorials/import_export_optimization.ipynb
docs/tutorials/network_visualization.ipynb
docs/tutorials/plot_visualization.ipynb
docs/tutorials/quality_assurance.ipynb
docs/tutorials/reading_writing_models.ipynb
docs/tutorials/thermo_concentrations.ipynb
release-notes/0.1.0.md
release-notes/0.1.1.md
release-notes/0.1.3.md
release-notes/0.1.4.md
release-notes/next-release.md
src/mass/__init__.py
src/mass/exceptions.py
src/mass/core/__init__.py
src/mass/core/mass_configuration.py
src/mass/core/mass_metabolite.py
src/mass/core/mass_model.py
src/mass/core/mass_reaction.py
src/mass/core/mass_solution.py
src/mass/core/units.py
src/mass/enzyme_modules/__init__.py
src/mass/enzyme_modules/enzyme_module.py
src/mass/enzyme_modules/enzyme_module_dict.py
src/mass/enzyme_modules/enzyme_module_form.py
src/mass/enzyme_modules/enzyme_module_reaction.py
src/mass/example_data/__init__.py
src/mass/example_data/maps/RBC.glycolysis.map.json
src/mass/example_data/maps/multicompartment_map.json
src/mass/example_data/maps/phosphate_trafficking_map.json
src/mass/example_data/maps/sb2_RBC_map.json
src/mass/example_data/maps/sb2_amp_salvage_network_map.json
src/mass/example_data/maps/sb2_glycolysis_map.json
src/mass/example_data/maps/sb2_pentose_phosphate_pathway_map.json
src/mass/example_data/maps/simple_toy_map.json
src/mass/example_data/models/Glycolysis.json
src/mass/example_data/models/Glycolysis_FKRM.json
src/mass/example_data/models/Glycolysis_Hb_HEX1.json
src/mass/example_data/models/Glycolysis_Hb_PFK.json
src/mass/example_data/models/Glycolysis_Hb_PYK.json
src/mass/example_data/models/Hemoglobin.json
src/mass/example_data/models/Model_to_Repair.json
src/mass/example_data/models/MultiCompartment.json
src/mass/example_data/models/Phosphate_Trafficking.json
src/mass/example_data/models/SB2_AMPSalvageNetwork.json
src/mass/example_data/models/SB2_Glycolysis.json
src/mass/example_data/models/SB2_Hemoglobin.json
src/mass/example_data/models/SB2_PFK.json
src/mass/example_data/models/SB2_PentosePhosphatePathway.json
src/mass/example_data/models/Simple_Toy.json
src/mass/example_data/models/Simple_Toy.xml
src/mass/example_data/models/WholeCellRBC_MA_Rates.json
src/mass/example_data/models/WholeCellRBC_MA_Rates.xml
src/mass/example_data/models/WholeCellRBC_MM_Rates.json
src/mass/example_data/models/WholeCellRBC_MM_Rates.xml
src/mass/example_data/models/textbook.json
src/mass/example_data/models/textbook.xml
src/mass/io/__init__.py
src/mass/io/dict.py
src/mass/io/json.py
src/mass/io/sbml.py
src/mass/simulation/__init__.py
src/mass/simulation/ensemble.py
src/mass/simulation/simulation.py
src/mass/thermo/__init__.py
src/mass/thermo/conc_solution.py
src/mass/thermo/conc_solver.py
src/mass/thermo/conc_sampling/__init__.py
src/mass/thermo/conc_sampling/conc_achr.py
src/mass/thermo/conc_sampling/conc_hr_sampler.py
src/mass/thermo/conc_sampling/conc_optgp.py
src/mass/thermo/conc_sampling/conc_sampling.py
src/mass/util/__init__.py
src/mass/util/dict_with_id.py
src/mass/util/expressions.py
src/mass/util/matrix.py
src/mass/util/qcqa.py
src/mass/util/util.py
src/mass/visualization/__init__.py
src/mass/visualization/comparison.py
src/mass/visualization/phase_portraits.py
src/mass/visualization/time_profiles.py
src/mass/visualization/visualization_util.py
src/masspy.egg-info/PKG-INFO
src/masspy.egg-info/SOURCES.txt
src/masspy.egg-info/dependency_links.txt
src/masspy.egg-info/requires.txt
src/masspy.egg-info/top_level.txt
src/masspy.egg-info/zip-safe
tests/__init__.py
tests/test_mass.py
tests/data/maps/RBC.glycolysis.map.json
tests/data/maps/multicompartment_map.json
tests/data/maps/phosphate_trafficking_map.json
tests/data/maps/sb2_RBC_map.json
tests/data/maps/sb2_amp_salvage_network_map.json
tests/data/maps/sb2_glycolysis_map.json
tests/data/maps/sb2_pentose_phosphate_pathway_map.json
tests/data/maps/simple_toy_map.json
tests/data/models/Glycolysis.json
tests/data/models/Glycolysis_FKRM.json
tests/data/models/Glycolysis_Hb_HEX1.json
tests/data/models/Glycolysis_Hb_PFK.json
tests/data/models/Glycolysis_Hb_PYK.json
tests/data/models/Hemoglobin.json
tests/data/models/Model_to_Repair.json
tests/data/models/MultiCompartment.json
tests/data/models/Phosphate_Trafficking.json
tests/data/models/SB2_AMPSalvageNetwork.json
tests/data/models/SB2_Glycolysis.json
tests/data/models/SB2_Hemoglobin.json
tests/data/models/SB2_PFK.json
tests/data/models/SB2_PentosePhosphatePathway.json
tests/data/models/Simple_Toy.json
tests/data/models/Simple_Toy.xml
tests/data/models/WholeCellRBC_MA_Rates.json
tests/data/models/WholeCellRBC_MA_Rates.xml
tests/data/models/WholeCellRBC_MM_Rates.json
tests/data/models/WholeCellRBC_MM_Rates.xml
tests/data/models/textbook.json
tests/data/models/textbook.xml