Adjusting metE expression.

CovertLab · Feb 16, 2024 · ccab0d4 · ccab0d4
1 parent 4fbe48f
commit ccab0d4
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Showing 3 changed files with 338 additions and 3 deletions.
diff --git a/ecoli/experiments/metabolism_redux_sim.py b/ecoli/experiments/metabolism_redux_sim.py
@@ -63,8 +63,8 @@ def run_ecoli_with_metabolism_redux_classic(
         raw_output=False,
         save=True,
         save_times=[1, 200, 400, 600, 800, 1000, 1200, 1300, 1400, 1500, 3000, 4500, 5000],
-        condition = "with_aa", # basal, with_aa
-        fixed_media = "minimal_plus_amino_acids" # minimal, minimal_plus_amino_acids
+        condition = "basal", # basal, with_aa
+        fixed_media = "minimal" # minimal, minimal_plus_amino_acids
 ):
     # filename = 'default'
     sim = EcoliSim.from_file(CONFIG_DIR_PATH + filename + ".json")

diff --git a/ecoli/library/sim_data.py b/ecoli/library/sim_data.py
@@ -39,7 +39,7 @@ def __init__(
         total_time=10,
         fixed_media = None,
         media_timeline=((0, 'minimal'),),   # have to change both media_timeline and condition
-        condition = 'with_aa',
+        condition = 'basal',
         operons=True,
         trna_charging=True,
         ppgpp_regulation=True,

diff --git a/notebooks/cofactors/cofactors_jl.ipynb b/notebooks/cofactors/cofactors_jl.ipynb