.gitignore
.readthedocs.yaml
LICENSE
README.md
for_local_use.py
requirements.txt
setup.py
test_script.py
useful_parameters.json
.github/workflows/python-app.yml
docs/Makefile
docs/api.rst
docs/conf.py
docs/for_local_use.rst
docs/index.rst
docs/make.bat
docs/mobspy.data_handler.rst
docs/mobspy.modules.rst
docs/mobspy.parameter_scripts.rst
docs/mobspy.parameters.rst
docs/mobspy.plot_params.rst
docs/mobspy.plot_scripts.rst
docs/mobspy.rst
docs/mobspy.sbml_simulator.rst
docs/mobspy.simulation_logging.rst
docs/modules.rst
docs/setup.rst
docs/test_script.rst
docs/Notebooks/01_Basic_Intro.ipynb
docs/Notebooks/02_Reaction_Inheritance.ipynb
docs/Notebooks/03_Characteristics.ipynb
docs/Notebooks/04_Characteristic_restriction.ipynb
docs/Notebooks/05_For_Loops.ipynb
docs/Notebooks/06_Order_Matters.ipynb
docs/Notebooks/07_Initial_Condition.ipynb
docs/Notebooks/08_Units.ipynb
docs/Notebooks/09_Result_Data.ipynb
docs/Notebooks/10_Reaction_Rates.ipynb
docs/Notebooks/11_Looping_Through_Species.ipynb
docs/Notebooks/12_Born_Species.ipynb
docs/Notebooks/13_Events.ipynb
docs/Notebooks/14_Concatenating_Simulations.ipynb
docs/_autosummary/mobspy.rst
docs/_build/doctrees/api.doctree
docs/_build/doctrees/environment.pickle
docs/_build/doctrees/for_local_use.doctree
docs/_build/doctrees/index.doctree
docs/_build/doctrees/mobspy.data_handler.doctree
docs/_build/doctrees/mobspy.doctree
docs/_build/doctrees/mobspy.modules.doctree
docs/_build/doctrees/mobspy.parameter_scripts.doctree
docs/_build/doctrees/mobspy.parameters.doctree
docs/_build/doctrees/mobspy.plot_params.doctree
docs/_build/doctrees/mobspy.plot_scripts.doctree
docs/_build/doctrees/mobspy.sbml_simulator.doctree
docs/_build/doctrees/mobspy.simulation_logging.doctree
docs/_build/doctrees/modules.doctree
docs/_build/doctrees/setup.doctree
docs/_build/doctrees/test_script.doctree
docs/_build/doctrees/Notebooks/01_Basic_Intro.doctree
docs/_build/doctrees/Notebooks/02_Reaction_Inheritance.doctree
docs/_build/doctrees/Notebooks/03_Characteristics.doctree
docs/_build/doctrees/Notebooks/04_Characteristic_restriction.doctree
docs/_build/doctrees/Notebooks/05_For_Loops.doctree
docs/_build/doctrees/Notebooks/06_Order_Matters.doctree
docs/_build/doctrees/Notebooks/07_Initial_Condition.doctree
docs/_build/doctrees/Notebooks/08_Units.doctree
docs/_build/doctrees/Notebooks/09_Result_Data.doctree
docs/_build/doctrees/Notebooks/10_Reaction_Rates.doctree
docs/_build/doctrees/Notebooks/11_Looping_Through_Species.doctree
docs/_build/doctrees/Notebooks/12_Born_Species.doctree
docs/_build/doctrees/Notebooks/13_Events.doctree
docs/_build/doctrees/Notebooks/14_Concatenating_Simulations.doctree
docs/_build/doctrees/_autosummary/mobspy.doctree
docs/_build/doctrees/nbsphinx/Notebooks_01_Basic_Intro_13_1.png
docs/_build/doctrees/nbsphinx/Notebooks_01_Basic_Intro_18_0.png
docs/_build/doctrees/nbsphinx/Notebooks_01_Basic_Intro_21_1.png
docs/_build/doctrees/nbsphinx/Notebooks_01_Basic_Intro_3_1.png
docs/_build/doctrees/nbsphinx/Notebooks_09_Result_Data_1_1.png
docs/_build/doctrees/nbsphinx/Notebooks_09_Result_Data_3_0.png
docs/_build/doctrees/nbsphinx/Notebooks_09_Result_Data_5_0.png
docs/_build/doctrees/nbsphinx/Notebooks_09_Result_Data_9_1.png
docs/_build/doctrees/nbsphinx/Notebooks_10_Reaction_Rates_11_1.png
docs/_build/doctrees/nbsphinx/Notebooks_13_Events_11_2.png
docs/_build/doctrees/nbsphinx/Notebooks_13_Events_1_2.png
docs/_build/doctrees/nbsphinx/Notebooks_13_Events_4_3.png
docs/_build/doctrees/nbsphinx/Notebooks_13_Events_8_1.png
docs/_build/doctrees/nbsphinx/Notebooks_14_Concatenating_Simulations_1_1.png
docs/_build/doctrees/nbsphinx/Notebooks_14_Concatenating_Simulations_3_1.png
docs/_build/doctrees/nbsphinx/Notebooks_14_Concatenating_Simulations_5_1.png
docs/_build/doctrees/nbsphinx/Notebooks/01_Basic_Intro.ipynb
docs/_build/doctrees/nbsphinx/Notebooks/02_Reaction_Inheritance.ipynb
docs/_build/doctrees/nbsphinx/Notebooks/03_Characteristics.ipynb
docs/_build/doctrees/nbsphinx/Notebooks/04_Characteristic_restriction.ipynb
docs/_build/doctrees/nbsphinx/Notebooks/05_For_Loops.ipynb
docs/_build/doctrees/nbsphinx/Notebooks/06_Order_Matters.ipynb
docs/_build/doctrees/nbsphinx/Notebooks/07_Initial_Condition.ipynb
docs/_build/doctrees/nbsphinx/Notebooks/08_Units.ipynb
docs/_build/doctrees/nbsphinx/Notebooks/09_Result_Data.ipynb
docs/_build/doctrees/nbsphinx/Notebooks/10_Reaction_Rates.ipynb
docs/_build/doctrees/nbsphinx/Notebooks/11_Looping_Through_Species.ipynb
docs/_build/doctrees/nbsphinx/Notebooks/12_Born_Species.ipynb
docs/_build/doctrees/nbsphinx/Notebooks/13_Events.ipynb
docs/_build/doctrees/nbsphinx/Notebooks/14_Concatenating_Simulations.ipynb
docs/_build/html/.buildinfo
docs/_build/html/api.html
docs/_build/html/for_local_use.html
docs/_build/html/genindex.html
docs/_build/html/index.html
docs/_build/html/mobspy.data_handler.html
docs/_build/html/mobspy.html
docs/_build/html/mobspy.modules.html
docs/_build/html/mobspy.parameter_scripts.html
docs/_build/html/mobspy.parameters.html
docs/_build/html/mobspy.plot_params.html
docs/_build/html/mobspy.plot_scripts.html
docs/_build/html/mobspy.sbml_simulator.html
docs/_build/html/mobspy.simulation_logging.html
docs/_build/html/modules.html
docs/_build/html/objects.inv
docs/_build/html/py-modindex.html
docs/_build/html/search.html
docs/_build/html/searchindex.js
docs/_build/html/setup.html
docs/_build/html/test_script.html
docs/_build/html/Notebooks/01_Basic_Intro.html
docs/_build/html/Notebooks/01_Basic_Intro.ipynb
docs/_build/html/Notebooks/02_Reaction_Inheritance.html
docs/_build/html/Notebooks/02_Reaction_Inheritance.ipynb
docs/_build/html/Notebooks/03_Characteristics.html
docs/_build/html/Notebooks/03_Characteristics.ipynb
docs/_build/html/Notebooks/04_Characteristic_restriction.html
docs/_build/html/Notebooks/04_Characteristic_restriction.ipynb
docs/_build/html/Notebooks/05_For_Loops.html
docs/_build/html/Notebooks/05_For_Loops.ipynb
docs/_build/html/Notebooks/06_Order_Matters.html
docs/_build/html/Notebooks/06_Order_Matters.ipynb
docs/_build/html/Notebooks/07_Initial_Condition.html
docs/_build/html/Notebooks/07_Initial_Condition.ipynb
docs/_build/html/Notebooks/08_Units.html
docs/_build/html/Notebooks/08_Units.ipynb
docs/_build/html/Notebooks/09_Result_Data.html
docs/_build/html/Notebooks/09_Result_Data.ipynb
docs/_build/html/Notebooks/10_Reaction_Rates.html
docs/_build/html/Notebooks/10_Reaction_Rates.ipynb
docs/_build/html/Notebooks/11_Looping_Through_Species.html
docs/_build/html/Notebooks/11_Looping_Through_Species.ipynb
docs/_build/html/Notebooks/12_Born_Species.html
docs/_build/html/Notebooks/12_Born_Species.ipynb
docs/_build/html/Notebooks/13_Events.html
docs/_build/html/Notebooks/13_Events.ipynb
docs/_build/html/Notebooks/14_Concatenating_Simulations.html
docs/_build/html/Notebooks/14_Concatenating_Simulations.ipynb
docs/_build/html/_autosummary/mobspy.html
docs/_build/html/_images/Notebooks_01_Basic_Intro_13_1.png
docs/_build/html/_images/Notebooks_01_Basic_Intro_18_0.png
docs/_build/html/_images/Notebooks_01_Basic_Intro_21_1.png
docs/_build/html/_images/Notebooks_01_Basic_Intro_3_1.png
docs/_build/html/_images/Notebooks_09_Result_Data_1_1.png
docs/_build/html/_images/Notebooks_09_Result_Data_3_0.png
docs/_build/html/_images/Notebooks_09_Result_Data_5_0.png
docs/_build/html/_images/Notebooks_09_Result_Data_9_1.png
docs/_build/html/_images/Notebooks_10_Reaction_Rates_11_1.png
docs/_build/html/_images/Notebooks_13_Events_11_2.png
docs/_build/html/_images/Notebooks_13_Events_1_2.png
docs/_build/html/_images/Notebooks_13_Events_4_3.png
docs/_build/html/_images/Notebooks_13_Events_8_1.png
docs/_build/html/_images/Notebooks_14_Concatenating_Simulations_1_1.png
docs/_build/html/_images/Notebooks_14_Concatenating_Simulations_3_1.png
docs/_build/html/_images/Notebooks_14_Concatenating_Simulations_5_1.png
docs/_build/html/_sources/api.rst.txt
docs/_build/html/_sources/for_local_use.rst.txt
docs/_build/html/_sources/index.rst.txt
docs/_build/html/_sources/mobspy.data_handler.rst.txt
docs/_build/html/_sources/mobspy.modules.rst.txt
docs/_build/html/_sources/mobspy.parameter_scripts.rst.txt
docs/_build/html/_sources/mobspy.parameters.rst.txt
docs/_build/html/_sources/mobspy.plot_params.rst.txt
docs/_build/html/_sources/mobspy.plot_scripts.rst.txt
docs/_build/html/_sources/mobspy.rst.txt
docs/_build/html/_sources/mobspy.sbml_simulator.rst.txt
docs/_build/html/_sources/mobspy.simulation_logging.rst.txt
docs/_build/html/_sources/modules.rst.txt
docs/_build/html/_sources/setup.rst.txt
docs/_build/html/_sources/test_script.rst.txt
docs/_build/html/_sources/Notebooks/01_Basic_Intro.ipynb.txt
docs/_build/html/_sources/Notebooks/02_Reaction_Inheritance.ipynb.txt
docs/_build/html/_sources/Notebooks/03_Characteristics.ipynb.txt
docs/_build/html/_sources/Notebooks/04_Characteristic_restriction.ipynb.txt
docs/_build/html/_sources/Notebooks/05_For_Loops.ipynb.txt
docs/_build/html/_sources/Notebooks/06_Order_Matters.ipynb.txt
docs/_build/html/_sources/Notebooks/07_Initial_Condition.ipynb.txt
docs/_build/html/_sources/Notebooks/08_Units.ipynb.txt
docs/_build/html/_sources/Notebooks/09_Result_Data.ipynb.txt
docs/_build/html/_sources/Notebooks/10_Reaction_Rates.ipynb.txt
docs/_build/html/_sources/Notebooks/11_Looping_Through_Species.ipynb.txt
docs/_build/html/_sources/Notebooks/12_Born_Species.ipynb.txt
docs/_build/html/_sources/Notebooks/13_Events.ipynb.txt
docs/_build/html/_sources/Notebooks/14_Concatenating_Simulations.ipynb.txt
docs/_build/html/_sources/_autosummary/mobspy.rst.txt
docs/_build/html/_static/_sphinx_javascript_frameworks_compat.js
docs/_build/html/_static/basic.css
docs/_build/html/_static/doctools.js
docs/_build/html/_static/documentation_options.js
docs/_build/html/_static/file.png
docs/_build/html/_static/jquery.js
docs/_build/html/_static/language_data.js
docs/_build/html/_static/minus.png
docs/_build/html/_static/nbsphinx-broken-thumbnail.svg
docs/_build/html/_static/nbsphinx-code-cells.css
docs/_build/html/_static/nbsphinx-gallery.css
docs/_build/html/_static/nbsphinx-no-thumbnail.svg
docs/_build/html/_static/plus.png
docs/_build/html/_static/pygments.css
docs/_build/html/_static/searchtools.js
docs/_build/html/_static/sphinx_highlight.js
docs/_build/html/_static/css/badge_only.css
docs/_build/html/_static/css/theme.css
docs/_build/html/_static/css/fonts/Roboto-Slab-Bold.woff
docs/_build/html/_static/css/fonts/Roboto-Slab-Bold.woff2
docs/_build/html/_static/css/fonts/Roboto-Slab-Regular.woff
docs/_build/html/_static/css/fonts/Roboto-Slab-Regular.woff2
docs/_build/html/_static/css/fonts/fontawesome-webfont.eot
docs/_build/html/_static/css/fonts/fontawesome-webfont.svg
docs/_build/html/_static/css/fonts/fontawesome-webfont.ttf
docs/_build/html/_static/css/fonts/fontawesome-webfont.woff
docs/_build/html/_static/css/fonts/fontawesome-webfont.woff2
docs/_build/html/_static/css/fonts/lato-bold-italic.woff
docs/_build/html/_static/css/fonts/lato-bold-italic.woff2
docs/_build/html/_static/css/fonts/lato-bold.woff
docs/_build/html/_static/css/fonts/lato-bold.woff2
docs/_build/html/_static/css/fonts/lato-normal-italic.woff
docs/_build/html/_static/css/fonts/lato-normal-italic.woff2
docs/_build/html/_static/css/fonts/lato-normal.woff
docs/_build/html/_static/css/fonts/lato-normal.woff2
docs/_build/html/_static/js/badge_only.js
docs/_build/html/_static/js/html5shiv-printshiv.min.js
docs/_build/html/_static/js/html5shiv.min.js
docs/_build/html/_static/js/theme.js
example_models/Tutorial Notebooks/01_Basic_Intro.ipynb
example_models/Tutorial Notebooks/02_Reaction_Inheritance.ipynb
example_models/Tutorial Notebooks/03_Characteristics.ipynb
example_models/Tutorial Notebooks/04_Characteristic_restriction.ipynb
example_models/Tutorial Notebooks/05_For_Loops.ipynb
example_models/Tutorial Notebooks/06_Order_Matters.ipynb
example_models/Tutorial Notebooks/07_Initial_Condition.ipynb
example_models/Tutorial Notebooks/08_Units_and_Output.ipynb
example_models/Tutorial Notebooks/09_Result_Data.ipynb
example_models/Tutorial Notebooks/10_Reaction_Rates.ipynb
example_models/Tutorial Notebooks/11_Looping_Through_Species.ipynb
example_models/Tutorial Notebooks/12_Born_Species.ipynb
example_models/Tutorial Notebooks/13_Events.ipynb
example_models/Tutorial Notebooks/14_Concatenating_Simulations.ipynb
example_models/Tutorial Notebooks/15_Assignments.ipynb
example_models/Tutorial Notebooks/16_Rev_All_Any.ipynb
example_models/Tutorial Notebooks/images/Matching_Meta.png
example_models/Tutorial Notebooks/images/vectorial_space.png
example_models/application_models/AB_2CD.py
example_models/application_models/AND_gate.py
example_models/application_models/CRISPR_Oscillator.py
example_models/application_models/For_The_Trees.py
example_models/application_models/NOR_gate.py
example_models/application_models/donor_receptor.py
example_models/application_models/oscillator.py
example_models/application_models/positive_phage_feedback_loop.py
example_models/application_models/random_walk.py
example_models/application_models/simple_infection.py
example_models/application_models/simple_repressor.py
example_models/application_models/simple_rule_based_and_gate.py
images/img.png
mobspy/__init__.py
mobspy/_version.py
mobspy/simulation.py
mobspy/variables_and_operators.py
mobspy.egg-info/PKG-INFO
mobspy.egg-info/SOURCES.txt
mobspy.egg-info/dependency_links.txt
mobspy.egg-info/requires.txt
mobspy.egg-info/top_level.txt
mobspy/data_handler/__init__.py
mobspy/data_handler/process_result_data.py
mobspy/data_handler/time_series_object.py
mobspy/import_manager/__init__.py
mobspy/import_manager/lazy_import_class.py
mobspy/import_manager/profiler_import_time_test.py
mobspy/modules/__init__.py
mobspy/modules/assignments_implementation.py
mobspy/modules/class_of_meta_specie_named_any.py
mobspy/modules/compiler.py
mobspy/modules/context_related_scripts.py
mobspy/modules/event_functions.py
mobspy/modules/function_rate_code.py
mobspy/modules/logic_operator_objects.py
mobspy/modules/meta_class.py
mobspy/modules/meta_class_utils.py
mobspy/modules/mobspy_expressions.py
mobspy/modules/mobspy_parameters.py
mobspy/modules/order_operators.py
mobspy/modules/reaction_construction_nb.py
mobspy/modules/set_counts_module.py
mobspy/modules/species_string_generator.py
mobspy/modules/unit_handler.py
mobspy/modules/user_functions.py
mobspy/parameter_estimation_data_loader/__init__.py
mobspy/parameter_estimation_data_loader/data_loader.py
mobspy/parameter_estimation_data_loader/parameter_estimation_scripts.py
mobspy/parameter_scripts/__init__.py
mobspy/parameter_scripts/parameter_reader.py
mobspy/parameter_scripts/parametric_sweeps.py
mobspy/parameters/README.md
mobspy/parameters/__init__.py
mobspy/parameters/default_reader.py
mobspy/parameters/example_reader.py
mobspy/patch_scripts/__init__.py
mobspy/patch_scripts/basico_task_parametrization.py
mobspy/plot_params/__init__.py
mobspy/plot_params/default_plot_reader.py
mobspy/plot_params/example_plot_reader.py
mobspy/plot_scripts/__init__.py
mobspy/plot_scripts/default_plots.py
mobspy/plot_scripts/hierarchical_plot.py
mobspy/plot_scripts/process_plot_data.py
mobspy/plot_scripts/statistics_calculations.py
mobspy/sbml_simulator/SBMLWriter.py
mobspy/sbml_simulator/__init__.py
mobspy/sbml_simulator/builder.py
mobspy/sbml_simulator/run.py
mobspy/sbml_simulator/__pycache__/SBMLWriter.cpython-310.pyc
mobspy/sbml_simulator/__pycache__/__init__.cpython-310.pyc
mobspy/sbml_simulator/__pycache__/builder.cpython-310.pyc
mobspy/sbml_simulator/__pycache__/run.cpython-310.pyc
mobspy/simulation_logging/__init__.py
mobspy/simulation_logging/log_scripts.py
test_plot_images/constant_tree.png
test_plot_images/deterministic_tree.png
test_plot_images/stochastic_tree.png
test_tools/model_1.txt
test_tools/model_10.txt
test_tools/model_11.txt
test_tools/model_12.txt
test_tools/model_13.txt
test_tools/model_14.txt
test_tools/model_15.txt
test_tools/model_16.txt
test_tools/model_17.txt
test_tools/model_18.txt
test_tools/model_19.txt
test_tools/model_2.txt
test_tools/model_20.txt
test_tools/model_21.txt
test_tools/model_22.txt
test_tools/model_23.txt
test_tools/model_24.txt
test_tools/model_25.txt
test_tools/model_26.txt
test_tools/model_27.txt
test_tools/model_28.txt
test_tools/model_29.txt
test_tools/model_3.txt
test_tools/model_30.txt
test_tools/model_31.txt
test_tools/model_32.txt
test_tools/model_33.txt
test_tools/model_34.txt
test_tools/model_35.txt
test_tools/model_36.txt
test_tools/model_37.txt
test_tools/model_38.txt
test_tools/model_39.txt
test_tools/model_4.txt
test_tools/model_40.txt
test_tools/model_41.txt
test_tools/model_42.txt
test_tools/model_43.txt
test_tools/model_44.txt
test_tools/model_45.txt
test_tools/model_46.txt
test_tools/model_47.txt
test_tools/model_48.txt
test_tools/model_49.txt
test_tools/model_5.txt
test_tools/model_50.txt
test_tools/model_51.txt
test_tools/model_52.txt
test_tools/model_53.txt
test_tools/model_54.txt
test_tools/model_55.txt
test_tools/model_56.txt
test_tools/model_6.txt
test_tools/model_7.txt
test_tools/model_8.txt
test_tools/model_9.txt