.gitignore
.readthedocs.yaml
LICENSE
README.md
debugging_script.py
extra_requires.txt
for_local_use.py
requirements.txt
setup.py
test_fractional_products.py
test_hybrid_sim.py
test_logging.py
test_multiline.py
test_np.py
test_ode_syntax.py
test_script.py
test_units.py
testconfig_units.yaml
testutils.py
useful_parameters.json
.github/workflows/python-app.yml
_static/images/img.png
docs/Makefile
docs/application.rst
docs/conf.py
docs/index.rst
docs/make.bat
docs/readme.rst
docs/requirements.txt
docs/tutorial.rst
docs/_templates/autosummary/module.rst
docs/example_models/application_models/AB_2CD.py
docs/example_models/application_models/AND_gate.py
docs/example_models/application_models/CRISPR_Oscillator.py
docs/example_models/application_models/For_The_Trees.py
docs/example_models/application_models/NOR_gate.py
docs/example_models/application_models/donor_receptor.py
docs/example_models/application_models/oscillator.py
docs/example_models/application_models/positive_phage_feedback_loop.py
docs/example_models/application_models/random_walk.py
docs/example_models/application_models/simple_infection.py
docs/example_models/application_models/simple_repressor.py
docs/example_models/application_models/simple_rule_based_and_gate.py
docs/example_models/journal_models/Antimony_Comparison.py
docs/example_models/journal_models/BioCRNpyler_1.py
docs/example_models/journal_models/BioCRNpyler_2.py
docs/example_models/journal_models/BioNetGen_Comparison.py
docs/example_models/journal_models/BioNetGen_multi_state.txt
docs/example_models/journal_models/Bistable_Gut_Inflammation.py
docs/example_models/journal_models/For_The_Trees.py
docs/example_models/journal_models/Kappa_comp_v1.py
docs/example_models/journal_models/Logical_XOR_Gate.py
docs/example_models/journal_models/Mutual_Annihilation.py
docs/example_models/journal_models/Phage_Transmission_System.py
docs/example_models/journal_models/PySB_Comparison.py
docs/example_models/journal_models/Synchronized_Cycles_of_Bacterial_Lysis.py
docs/example_models/journal_models/comparision_bioCRNpyler.py
docs/example_models/journal_models/hello_pysb.py
docs/example_models/journal_models/kappa_model.png
docs/example_models/tutorial_notebooks/01_Basic_Intro.ipynb
docs/example_models/tutorial_notebooks/02_Reaction_Inheritance.ipynb
docs/example_models/tutorial_notebooks/03_Characteristics.ipynb
docs/example_models/tutorial_notebooks/04_Characteristic_restriction.ipynb
docs/example_models/tutorial_notebooks/05_For_Loops.ipynb
docs/example_models/tutorial_notebooks/06_Order_Matters.ipynb
docs/example_models/tutorial_notebooks/07_Initial_Condition.ipynb
docs/example_models/tutorial_notebooks/08_Units_and_Output.ipynb
docs/example_models/tutorial_notebooks/09_Result_Data.ipynb
docs/example_models/tutorial_notebooks/10_Reaction_Rates.ipynb
docs/example_models/tutorial_notebooks/11_Looping_Through_Species.ipynb
docs/example_models/tutorial_notebooks/12_Born_Species.ipynb
docs/example_models/tutorial_notebooks/13_Events.ipynb
docs/example_models/tutorial_notebooks/14_Concatenating_Simulations.ipynb
docs/example_models/tutorial_notebooks/15_Assignments.ipynb
docs/example_models/tutorial_notebooks/16_Rev_All_Any.ipynb
docs/example_models/tutorial_notebooks/17_Export_Model.ipynb
docs/example_models/tutorial_notebooks/18_Reversible_Reactions.ipynb
docs/example_models/tutorial_notebooks/19_Plot_Configuration.ipynb
docs/example_models/tutorial_notebooks/20_Update_Model_After_Compilation.ipynb
docs/example_models/tutorial_notebooks/images/cycling_species.svg
docs/example_models/tutorial_notebooks/images/vectorial_space.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/compiler_operator_functions.py
mobspy/modules/context_related_scripts.py
mobspy/modules/event_functions.py
mobspy/modules/function_rate_code.py
mobspy/modules/functions.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/ode_operator.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
mobspy/simulator_object/__init__.py
mobspy/simulator_object/simulator_object_functions.py
test_plot_images/read_me.txt
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_57.txt
test_tools/model_58.txt
test_tools/model_59.txt
test_tools/model_6.txt
test_tools/model_60.txt
test_tools/model_61.txt
test_tools/model_62.txt
test_tools/model_63.txt
test_tools/model_64.txt
test_tools/model_65.txt
test_tools/model_66.txt
test_tools/model_7.txt
test_tools/model_8.txt
test_tools/model_9.txt
test_tools/model_ode_applied_to_species.txt
test_tools/model_ode_compartments.txt
test_tools/model_ode_complex_expressions.txt
test_tools/model_ode_inheritance.txt
test_tools/model_ode_neg.txt
test_tools/model_ode_neg_test.txt
test_tools/model_ode_syntax_basic.txt
test_tools/model_ode_syntax_two_species.txt
test_tools/model_ode_with_functions.txt