start docs revamp

COBREXA · Feb 1, 2024 · 5b3072c · 5b3072c
1 parent 8545a99
commit 5b3072c
Showing 1 changed file with 8 additions and 9 deletions.
diff --git a/docs/src/examples/06-mmdf.jl b/docs/src/examples/06-mmdf.jl
@@ -37,7 +37,6 @@ import Downloads: download
 # Additionally to COBREXA, and the model format package, we will need a solver
 # -- let's use GLPK here:
 
-using COBREXA
 import JSONFBCModels
 import GLPK
 
@@ -85,16 +84,16 @@ reaction_standard_gibbs_free_energies = Dict{String,Float64}(
 # other reactions.
 
 reference_flux = Dict(
-    "ENO" => 1.0,
+    "ENO" => 2.0,
     "FBA" => 1.0,
-    "GAPD" => 1.0,
+    "GAPD" => 2.0,
     "GLCpts" => 1.0,
-    "LDH_D" => -1.0,
+    "LDH_D" => -2.0,
     "PFK" => 1.0,
     "PGI" => 1.0,
-    "PGK" => -1.0,
-    "PGM" => -1.0,
-    "PYK" => 1.0,
+    "PGK" => -2.0,
+    "PGM" => -2.0,
+    "PYK" => 2.0,
     "TPI" => 1.0,
 )
 
@@ -114,8 +113,8 @@ mmdf_solution = max_min_driving_force_analysis(
         "atp" => ("atp_c", "adp_c", 10.0),
         "nadh" => ("nadh_c", "nad_c", 0.13),
     ),
-    proton_metabolites = ["h_c", "h_e"],
-    water_metabolites = ["h2o_c", "h2o_e"],
+    proton_metabolites = ["h_c"],
+    water_metabolites = ["h2o_c"],
     concentration_lower_bound = 1e-6, # M
     concentration_upper_bound = 1e-1, # M
     T = 298.15, # Kelvin