| docs/misc/metadata hierarchy.txt | |
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| docs/references.bib | |
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| docs/references.rst | |
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| docs/requirements.rtd.txt | |
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| docs/requirements.txt | |
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| examples/Read and plot wc_simulate dataframe.ipynb | |
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| examples/config/debug.default.cfg | |
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| examples/jupyter_examples/Example simulation run.ipynb | |
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| examples/transcription_translation_hybrid_model/model.xlsx | |
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| examples/translation_metabolism_hybrid_model/model.xlsx | |
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| migrations/data_schema_migration_conf--wc_sim--wc_lang--2019-06-25-22-43-31.yaml | |
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| migrations/data_schema_migration_conf--wc_sim--wc_lang--2019-07-12-12-55-44.yaml | |
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| multialg_analysis/README.txt | |
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| multialg_analysis/data/plots/ode_modes_species_trajectories.pdf | |
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| multialg_analysis/data/run_ode_solver.xlsx | |
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| multialg_analysis/data/run_ode_solver_one_step.xlsx | |
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| multialg_analysis/data/run_ode_solver_w_internal.tsv | |
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| multialg_analysis/data/run_ode_solver_w_internal.xlsx | |
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| presentation_2020_07_06_WC_sim_for_H1_model/model_core_expression_usage.tsv | |
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| pytest.ini | |
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| requirements.txt | |
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| setup.cfg | |
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| wc_sim/config/core.default.cfg | |
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| wc_sim/config/core.schema.cfg | |
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| wc_sim/config/debug.default.cfg | |
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| wc_sim/on_ROSS/try_c_and_python/callbacks.c | |
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| wc_sim/on_ROSS/try_c_and_python/spammodule.c | |
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| docs/conf.py | 98 |
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| examples/config/__init__.py | 0 |
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| examples/config/core.py | 33 | B 4 hrs |
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| examples/debug_logs.py | 10 | A 30 mins |
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| examples/plot_predictions.py | 34 |
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| examples/transcription_translation_hybrid_model/run_with_custom_code.py | 207 | B 6 hrs |
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| examples/transcription_translation_hybrid_model/run_with_wc_sim.py | 72 | C 1 day |
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| examples/translation_metabolism_hybrid_model/run.py | 91 | F 3 days |
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| multialg_analysis/code/analyze_ode_steps.py | 73 | A 50 mins |
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| presentation_2020_07_06_WC_sim_for_H1_model/expr_dependencies_figs.py | 21 |
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| presentation_2020_07_06_WC_sim_for_H1_model/h1_model_properties.py | 98 | A 3 hrs |
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| setup.py | 60 |
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| temp_wc_analysis/__init__.py | 0 |
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| temp_wc_analysis/analysis.py | 76 | B 5 hrs |
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| temp_wc_analysis/exercise.py | 85 | A 1 hr |
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| temp_wc_analysis/plot_specie_pop.py | 139 | A 2 hrs |
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| wc_sim/future_multialgorithm_simulation.py | 71 |
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| wc_sim/on_ROSS/try_c_and_python/python_call_c.py | 14 |
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| wc_sim/on_ROSS/try_c_and_python/python_with_c_callback.py | 33 | A 2 hrs |
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| wc_sim/testing/analyze_tolerances.py | 209 | C 1 day |
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