working code making 2 plots

vivarium-collective · Dec 15, 2023 · 2411be6 · 2411be6
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diff --git a/Notebook/.ipynb_checkpoints/FBA-experiment_Alteromonas-checkpoint.ipynb b/Notebook/.ipynb_checkpoints/FBA-experiment_Alteromonas-checkpoint.ipynb
diff --git a/Notebook/Delete_FBA-experiment_Alteromonas.ipynb b/Notebook/Delete_FBA-experiment_Alteromonas.ipynb
diff --git a/Notebook/FBA-experiment_Alteromonas.ipynb b/Notebook/FBA-experiment_Alteromonas.ipynb
diff --git a/vivarium_microbiome/output/ex/Ex_Exchange for Acetate_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/Ex_Exchange for Acetate_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/Ex_Exchange for Butyrate_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/Ex_Exchange for Butyrate_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/Ex_Exchange for CO2_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/Ex_Exchange for CO2_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/Ex_Exchange for Cbl_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/Ex_Exchange for Cbl_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/Ex_Exchange for Enterobactin_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/Ex_Exchange for Enterobactin_e0_top_flux_changes.png
diff --git a/...ium_microbiome/output/ex/Ex_Exchange for Fe-enterochlin_e0_top_flux_changes.png b/...ium_microbiome/output/ex/Ex_Exchange for Fe-enterochlin_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/Ex_Exchange for Folate_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/Ex_Exchange for Folate_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/Ex_Exchange for Formate_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/Ex_Exchange for Formate_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/Ex_Exchange for Glycerol_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/Ex_Exchange for Glycerol_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/Ex_Exchange for H+_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/Ex_Exchange for H+_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/Ex_Exchange for H2O_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/Ex_Exchange for H2O_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/Ex_Exchange for L-Alanine_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/Ex_Exchange for L-Alanine_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/Ex_Exchange for L-Aspartate_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/Ex_Exchange for L-Aspartate_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/Ex_Exchange for L-Glutamine_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/Ex_Exchange for L-Glutamine_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/Ex_Exchange for L-Threonine_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/Ex_Exchange for L-Threonine_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/Ex_Exchange for Methanol_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/Ex_Exchange for Methanol_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/Ex_Exchange for NH3_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/Ex_Exchange for NH3_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/Ex_Exchange for Na+_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/Ex_Exchange for Na+_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/Ex_Exchange for Niacin_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/Ex_Exchange for Niacin_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/Ex_Exchange for Nitrite_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/Ex_Exchange for Nitrite_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/Ex_Exchange for Palmitate_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/Ex_Exchange for Palmitate_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/Ex_Exchange for Pyridoxal_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/Ex_Exchange for Pyridoxal_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/Ex_Exchange for Thiamin_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/Ex_Exchange for Thiamin_e0_top_flux_changes.png
diff --git a/...um_microbiome/output/ex/up_Ex_Exchange for Acetoacetate_e0_top_flux_changes.png b/...um_microbiome/output/ex/up_Ex_Exchange for Acetoacetate_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/up_Ex_Exchange for BIOT_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/up_Ex_Exchange for BIOT_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/up_Ex_Exchange for Ca2+_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/up_Ex_Exchange for Ca2+_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/up_Ex_Exchange for Cl-_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/up_Ex_Exchange for Cl-_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/up_Ex_Exchange for Co2+_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/up_Ex_Exchange for Co2+_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/up_Ex_Exchange for Cu2+_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/up_Ex_Exchange for Cu2+_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/up_Ex_Exchange for D-Glucose_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/up_Ex_Exchange for D-Glucose_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/up_Ex_Exchange for Glycine_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/up_Ex_Exchange for Glycine_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/up_Ex_Exchange for Heme_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/up_Ex_Exchange for Heme_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/up_Ex_Exchange for K+_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/up_Ex_Exchange for K+_e0_top_flux_changes.png
diff --git a/...rium_microbiome/output/ex/up_Ex_Exchange for L-Arginine_e0_top_flux_changes.png b/...rium_microbiome/output/ex/up_Ex_Exchange for L-Arginine_e0_top_flux_changes.png
diff --git a/...um_microbiome/output/ex/up_Ex_Exchange for L-Asparagine_e0_top_flux_changes.png b/...um_microbiome/output/ex/up_Ex_Exchange for L-Asparagine_e0_top_flux_changes.png
diff --git a/...rium_microbiome/output/ex/up_Ex_Exchange for L-Cysteine_e0_top_flux_changes.png b/...rium_microbiome/output/ex/up_Ex_Exchange for L-Cysteine_e0_top_flux_changes.png
diff --git a/...ium_microbiome/output/ex/up_Ex_Exchange for L-Glutamate_e0_top_flux_changes.png b/...ium_microbiome/output/ex/up_Ex_Exchange for L-Glutamate_e0_top_flux_changes.png
diff --git a/...ium_microbiome/output/ex/up_Ex_Exchange for L-Histidine_e0_top_flux_changes.png b/...ium_microbiome/output/ex/up_Ex_Exchange for L-Histidine_e0_top_flux_changes.png
diff --git a/...um_microbiome/output/ex/up_Ex_Exchange for L-Isoleucine_e0_top_flux_changes.png b/...um_microbiome/output/ex/up_Ex_Exchange for L-Isoleucine_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/up_Ex_Exchange for L-Leucine_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/up_Ex_Exchange for L-Leucine_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/up_Ex_Exchange for L-Lysine_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/up_Ex_Exchange for L-Lysine_e0_top_flux_changes.png
diff --git a/...um_microbiome/output/ex/up_Ex_Exchange for L-Methionine_e0_top_flux_changes.png b/...um_microbiome/output/ex/up_Ex_Exchange for L-Methionine_e0_top_flux_changes.png
diff --git a/...microbiome/output/ex/up_Ex_Exchange for L-Phenylalanine_e0_top_flux_changes.png b/...microbiome/output/ex/up_Ex_Exchange for L-Phenylalanine_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/up_Ex_Exchange for L-Proline_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/up_Ex_Exchange for L-Proline_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/up_Ex_Exchange for L-Serine_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/up_Ex_Exchange for L-Serine_e0_top_flux_changes.png
diff --git a/...um_microbiome/output/ex/up_Ex_Exchange for L-Tryptophan_e0_top_flux_changes.png b/...um_microbiome/output/ex/up_Ex_Exchange for L-Tryptophan_e0_top_flux_changes.png
diff --git a/...rium_microbiome/output/ex/up_Ex_Exchange for L-Tyrosine_e0_top_flux_changes.png b/...rium_microbiome/output/ex/up_Ex_Exchange for L-Tyrosine_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/up_Ex_Exchange for L-Valine_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/up_Ex_Exchange for L-Valine_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/up_Ex_Exchange for Mg_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/up_Ex_Exchange for Mg_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/up_Ex_Exchange for Mn2+_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/up_Ex_Exchange for Mn2+_e0_top_flux_changes.png
diff --git a/...m_microbiome/output/ex/up_Ex_Exchange for Myristic acid_e0_top_flux_changes.png b/...m_microbiome/output/ex/up_Ex_Exchange for Myristic acid_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/up_Ex_Exchange for O2_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/up_Ex_Exchange for O2_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/up_Ex_Exchange for PAN_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/up_Ex_Exchange for PAN_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/up_Ex_Exchange for Phosphate_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/up_Ex_Exchange for Phosphate_e0_top_flux_changes.png
diff --git a/...rium_microbiome/output/ex/up_Ex_Exchange for Putrescine_e0_top_flux_changes.png b/...rium_microbiome/output/ex/up_Ex_Exchange for Putrescine_e0_top_flux_changes.png
diff --git a/...rium_microbiome/output/ex/up_Ex_Exchange for Riboflavin_e0_top_flux_changes.png b/...rium_microbiome/output/ex/up_Ex_Exchange for Riboflavin_e0_top_flux_changes.png
diff --git a/...me/output/ex/up_Ex_Exchange for S-Adenosyl-L-methionine_e0_top_flux_changes.png b/...me/output/ex/up_Ex_Exchange for S-Adenosyl-L-methionine_e0_top_flux_changes.png
diff --git a/...rium_microbiome/output/ex/up_Ex_Exchange for Spermidine_e0_top_flux_changes.png b/...rium_microbiome/output/ex/up_Ex_Exchange for Spermidine_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/up_Ex_Exchange for Sulfate_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/up_Ex_Exchange for Sulfate_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/up_Ex_Exchange for Zn2+_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/up_Ex_Exchange for Zn2+_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/up_Ex_Exchange for fe3_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/up_Ex_Exchange for fe3_e0_top_flux_changes.png
diff --git a/vivarium_microbiome/output/ex/up_Ex_Exchange for ocdca_e0_top_flux_changes.png b/vivarium_microbiome/output/ex/up_Ex_Exchange for ocdca_e0_top_flux_changes.png