GitHub - haydengallo/glv_dfba

This is a repo for constraining dFBA with gLV population dynamics to infer more realistic underlying metabolic dynamics as compared to traditional FBA approaches.

required scipy=1.13.1

Name		Name	Last commit message	Last commit date
__pycache__		__pycache__
.DS_Store		.DS_Store
.current_global_0x38b279fd0		.current_global_0x38b279fd0
.current_package_0x38b279fd0		.current_package_0x38b279fd0
.current_script_0x38b279fd0		.current_script_0x38b279fd0
AD_gLV_FBA_test.ipynb		AD_gLV_FBA_test.ipynb
COMETS_Venturelli_sims_panGenus_parallel.py		COMETS_Venturelli_sims_panGenus_parallel.py
FVA_testing.ipynb		FVA_testing.ipynb
MC_SA.ipynb		MC_SA.ipynb
MDSINE_FBA.py		MDSINE_FBA.py
README.md		README.md
Testing_MDSINE_pkl_objects.ipynb		Testing_MDSINE_pkl_objects.ipynb
Testing_MDSINE_pkl_objects_alt.ipynb		Testing_MDSINE_pkl_objects_alt.ipynb
batch_sims_from_posterior.py		batch_sims_from_posterior.py
cobra_env.yml		cobra_env.yml
cobra_glv_fba.yml		cobra_glv_fba.yml
dfba_glv_implement.ipynb		dfba_glv_implement.ipynb
dfba_glv_implement_bayes_testing.ipynb		dfba_glv_implement_bayes_testing.ipynb
flux_sampling_simulations_plotting.ipynb		flux_sampling_simulations_plotting.ipynb
gLV_FBA_Venturelli.ipynb		gLV_FBA_Venturelli.ipynb
gLV_FBA_Venturelli.py		gLV_FBA_Venturelli.py
gLV_FBA_Venturelli_sims_panGenus.py		gLV_FBA_Venturelli_sims_panGenus.py
gLV_FBA_Venturelli_sims_panGenus_parallel.py		gLV_FBA_Venturelli_sims_panGenus_parallel.py
gLV_FBA_Venturelli_sims_panGenus_parallel_hpc.py		gLV_FBA_Venturelli_sims_panGenus_parallel_hpc.py
gLV_FBA_Venturelli_sims_panGenus_parallel_test_2.py		gLV_FBA_Venturelli_sims_panGenus_parallel_test_2.py
gLV_FBA_WD_Kennedy_et_al.ipynb		gLV_FBA_WD_Kennedy_et_al.ipynb
gap_filling_AGORA.ipynb		gap_filling_AGORA.ipynb
growths_50_samps_08_05_2026.npy		growths_50_samps_08_05_2026.npy
helper_functions.py		helper_functions.py
interactions_50_samps_08_05_2026.npy		interactions_50_samps_08_05_2026.npy
median_grow.csv		median_grow.csv
median_interactions.csv		median_interactions.csv
median_perturbations_test.csv		median_perturbations_test.csv
multiple_datasets_fitting.ipynb		multiple_datasets_fitting.ipynb
perturbations_50_samps_08_05_2026.npy		perturbations_50_samps_08_05_2026.npy
plots.ipynb		plots.ipynb
run.py		run.py
run_3_species.py		run_3_species.py
stability_analysis_testing.ipynb		stability_analysis_testing.ipynb
testing_FBA_after_MDSINE.ipynb		testing_FBA_after_MDSINE.ipynb
testing_FBA_after_MDSINE.py		testing_FBA_after_MDSINE.py
testing_mouse_GEM.ipynb		testing_mouse_GEM.ipynb

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