TPC 2nd submission with GC cytosol maltose accumulation

Toepfer-Lab · Jul 1, 2024 · d09c365 · d09c365
1 parent 0421dcd
commit d09c365
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Showing 132 changed files with 82,414 additions and 72,742 deletions.
diff --git a/inputs/osmolytes.csv b/inputs/osmolytes.csv
@@ -77,3 +77,4 @@ aMAL_v_gc,1
 STARCH_p_gc,0
 STARCH_p_me,0
 PALMITATE_c_gc,0
+MALTOSE_c_gc,1
diff --git a/mmon_gcm/constraintscan.py b/mmon_gcm/constraintscan.py
@@ -37,7 +37,7 @@ def generate_constraints_df(constraints_df, params_df):
     return values_df
 
 # %% ../src/functions/constraintscan.ipynb 5
-def solve_model_for_constraint_scan(constraints, fba_model, light_colour, printouts=False, maintenance=True):
+def solve_model_for_constraint_scan(constraints, fba_model, light_colour, printouts=False):
 
     solution_number = constraints.name
 
@@ -48,16 +48,10 @@ def solve_model_for_constraint_scan(constraints, fba_model, light_colour, printo
 
     for p in [1, 2, 3, 4]:
         super_model.fba_model.reactions.get_by_id(f"PROTON_ATPase_c_gc_{p}").bounds = (0, gc_atpase_upper_bound)
-
-    if maintenance:    
-        gc_maintenance_ratio = constraints.loc["Maintenance"]
-        super_model.add_maintenance(gc=True, gc_ratio=gc_maintenance_ratio, approach=4)
-    else:
-        super_model.add_maintenance(gc=True, gc_ratio=4.4270867608601426e-05, approach=4)
+        super_model.add_maintenance(gc=True)
 
     if printouts is True:
         print(f"ATPase constrained to {gc_atpase_upper_bound}")
-        print(f"GC maintenance proportion = {gc_maintenance_ratio}")
 
     if light_colour == "blue":
         super_model.fba_model.reactions.Photon_tx_gc_2.upper_bound = 0

diff --git a/mmon_gcm/runconstraintscan.py b/mmon_gcm/runconstraintscan.py
@@ -1,10 +1,10 @@
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../src/3.2_run_constraint_scan.ipynb.
 
 # %% auto 0
-__all__ = ['test', 'results_path', 'model_path', 'constraints_csv', 'light_colour', 'no_cores', 'inc_maintenance', 'constraints',
-           'model', 'batch_size', 'df', 'num_batches']
+__all__ = ['test', 'results_path', 'model_path', 'constraints_csv', 'light_colour', 'no_cores', 'constraints', 'model',
+           'batch_size', 'df', 'num_batches']
 
-# %% ../src/3.2_run_constraint_scan.ipynb 4
+# %% ../src/3.2_run_constraint_scan.ipynb 5
 import sys
 import os
 
@@ -13,22 +13,21 @@
 import pandas as pd
 from pandarallel import pandarallel
 
-# %% ../src/3.2_run_constraint_scan.ipynb 5
+# %% ../src/3.2_run_constraint_scan.ipynb 6
 test = False
 
-# %% ../src/3.2_run_constraint_scan.ipynb 7
+# %% ../src/3.2_run_constraint_scan.ipynb 8
 results_path = sys.argv[1]
 model_path = sys.argv[2]
 constraints_csv = sys.argv[3]
 light_colour = sys.argv[4]
 no_cores = int(sys.argv[5])
-inc_maintenance = eval(sys.argv[6])
 
-# %% ../src/3.2_run_constraint_scan.ipynb 8
+# %% ../src/3.2_run_constraint_scan.ipynb 9
 constraints = pd.read_csv(constraints_csv, index_col=[0], header=[0])
 model = cobra.io.load_json_model(model_path)
 
-# %% ../src/3.2_run_constraint_scan.ipynb 14
+# %% ../src/3.2_run_constraint_scan.ipynb 15
 # Define the batch size
 batch_size = 100
 
@@ -50,7 +49,7 @@
         #scan_solution = constraints.parallel_apply(
         scan_solution = current_batch.parallel_apply(
             mmon_gcm.constraintscan.solve_model_for_constraint_scan,
-            args=([model, light_colour, False, inc_maintenance]),
+            args=([model, light_colour, False]),
             axis=1,
         )
 

diff --git a/mmon_gcm/solvemodels.py b/mmon_gcm/solvemodels.py
@@ -85,10 +85,10 @@
 PPFD = 150
 arabidopsis_supermodel.constrain_photons(PPFD, printouts=True);
 
-# %% ../src/2.1_solvingmodel.ipynb 39
-arabidopsis_supermodel.add_maintenance(gc=True, gc_ratio=4.4270867608601426e-05);
+# %% ../src/2.1_solvingmodel.ipynb 31
+arabidopsis_supermodel.add_maintenance(gc=True, gc_ratio=4.427086760474383e-05);
 
-# %% ../src/2.1_solvingmodel.ipynb 43
+# %% ../src/2.1_solvingmodel.ipynb 35
 # Added this line to explictly set Photon constraint
 arabidopsis_supermodel.constrain_photons(PPFD, printouts=False)
 with arabidopsis_supermodel.fba_model as m:
@@ -105,10 +105,10 @@
         blue_unconstrained_wt_solution,
     ) = mmon_gcm.solving.get_pfba_fva_solution(m, rxn_list=fva_list, processes=no_processes)
 
-# %% ../src/2.1_solvingmodel.ipynb 44
+# %% ../src/2.1_solvingmodel.ipynb 36
 blue_unconstrained_wt_solution.to_csv(output_dir + f"blue_unconstrained_wt.csv")
 
-# %% ../src/2.1_solvingmodel.ipynb 46
+# %% ../src/2.1_solvingmodel.ipynb 38
 # Added this line to explictly set Photon constraint
 arabidopsis_supermodel.constrain_photons(PPFD, printouts=False)
 with arabidopsis_supermodel.fba_model as m:
@@ -124,10 +124,10 @@
         blue_unconstrained_starchko_solution,
     ) = mmon_gcm.solving.get_pfba_fva_solution(m, rxn_list=fva_list, processes=no_processes)
 
-# %% ../src/2.1_solvingmodel.ipynb 47
+# %% ../src/2.1_solvingmodel.ipynb 39
 blue_unconstrained_starchko_solution.to_csv(output_dir + "blue_unconstrained_starchko.csv")
 
-# %% ../src/2.1_solvingmodel.ipynb 50
+# %% ../src/2.1_solvingmodel.ipynb 42
 # Added this line to explictly set Photon constraint
 arabidopsis_supermodel.constrain_photons(PPFD, printouts=False)
 with arabidopsis_supermodel.fba_model as m:
@@ -144,10 +144,10 @@
         blue_constrained_wt_solution,
     ) = mmon_gcm.solving.get_pfba_fva_solution(m, rxn_list=fva_list, processes=no_processes)
 
-# %% ../src/2.1_solvingmodel.ipynb 51
+# %% ../src/2.1_solvingmodel.ipynb 43
 blue_constrained_wt_solution.to_csv(output_dir + "blue_constrained_wt.csv")
 
-# %% ../src/2.1_solvingmodel.ipynb 53
+# %% ../src/2.1_solvingmodel.ipynb 45
 # Added this line to explictly set Photon constraint
 arabidopsis_supermodel.constrain_photons(PPFD, printouts=False)
 with arabidopsis_supermodel.fba_model as m:
@@ -164,10 +164,10 @@
         blue_constrained_starchko_solution,
     ) = mmon_gcm.solving.get_pfba_fva_solution(m, rxn_list=fva_list, processes=no_processes)
 
-# %% ../src/2.1_solvingmodel.ipynb 54
+# %% ../src/2.1_solvingmodel.ipynb 46
 blue_constrained_starchko_solution.to_csv(output_dir + "blue_constrained_starchko.csv")
 
-# %% ../src/2.1_solvingmodel.ipynb 58
+# %% ../src/2.1_solvingmodel.ipynb 50
 # Added this line to explictly set Photon constraint
 arabidopsis_supermodel.constrain_photons(PPFD, printouts=False)
 with arabidopsis_supermodel.fba_model as m:
@@ -182,10 +182,10 @@
         white_unconstrained_wt_solution,
     ) = mmon_gcm.solving.get_pfba_fva_solution(m, rxn_list=fva_list, processes=no_processes)
 
-# %% ../src/2.1_solvingmodel.ipynb 59
+# %% ../src/2.1_solvingmodel.ipynb 51
 white_unconstrained_wt_solution.to_csv(output_dir + "white_unconstrained_wt.csv")
 
-# %% ../src/2.1_solvingmodel.ipynb 61
+# %% ../src/2.1_solvingmodel.ipynb 53
 # Added this line to explictly set Photon constraint
 arabidopsis_supermodel.constrain_photons(PPFD, printouts=False)
 with arabidopsis_supermodel.fba_model as m:
@@ -200,10 +200,10 @@
         white_unconstrained_starchko_solution,
     ) = mmon_gcm.solving.get_pfba_fva_solution(m, rxn_list=fva_list, processes=no_processes)
 
-# %% ../src/2.1_solvingmodel.ipynb 62
+# %% ../src/2.1_solvingmodel.ipynb 54
 white_unconstrained_starchko_solution.to_csv(output_dir + "white_unconstrained_starchko.csv")
 
-# %% ../src/2.1_solvingmodel.ipynb 65
+# %% ../src/2.1_solvingmodel.ipynb 57
 # Added this line to explictly set Photon constraint
 arabidopsis_supermodel.constrain_photons(PPFD, printouts=False)
 with arabidopsis_supermodel.fba_model as m:
@@ -218,10 +218,10 @@
         white_constrained_wt_solution,
     ) = mmon_gcm.solving.get_pfba_fva_solution(m, rxn_list=fva_list, processes=no_processes)
 
-# %% ../src/2.1_solvingmodel.ipynb 66
+# %% ../src/2.1_solvingmodel.ipynb 58
 white_constrained_wt_solution.to_csv(output_dir + "white_constrained_wt.csv")
 
-# %% ../src/2.1_solvingmodel.ipynb 68
+# %% ../src/2.1_solvingmodel.ipynb 60
 # Added this line to explictly set Photon constraint
 arabidopsis_supermodel.constrain_photons(PPFD, printouts=False)
 with arabidopsis_supermodel.fba_model as m:
@@ -236,10 +236,10 @@
         white_constrained_starchko_solution,
     ) = mmon_gcm.solving.get_pfba_fva_solution(m, rxn_list=fva_list, processes=no_processes)
 
-# %% ../src/2.1_solvingmodel.ipynb 69
+# %% ../src/2.1_solvingmodel.ipynb 61
 white_constrained_starchko_solution.to_csv(output_dir + "white_constrained_starchko.csv")
 
-# %% ../src/2.1_solvingmodel.ipynb 73
+# %% ../src/2.1_solvingmodel.ipynb 65
 # Added this line to explictly set Photon constraint
 arabidopsis_supermodel.constrain_photons(PPFD, printouts=False)
 with arabidopsis_supermodel.fba_model as m:
@@ -257,10 +257,10 @@
         nops_unconstrained_wt_solution,
     ) = mmon_gcm.solving.get_pfba_fva_solution(m, rxn_list=fva_list, processes=no_processes)
 
-# %% ../src/2.1_solvingmodel.ipynb 74
+# %% ../src/2.1_solvingmodel.ipynb 66
 nops_unconstrained_wt_solution.to_csv(output_dir + "nops_unconstrained_wt.csv")
 
-# %% ../src/2.1_solvingmodel.ipynb 76
+# %% ../src/2.1_solvingmodel.ipynb 68
 # Added this line to explictly set Photon constraint
 arabidopsis_supermodel.constrain_photons(PPFD, printouts=False)
 with arabidopsis_supermodel.fba_model as m:
@@ -277,10 +277,10 @@
         nops_unconstrained_starchko_solution,
     ) = mmon_gcm.solving.get_pfba_fva_solution(m, rxn_list=fva_list, processes=no_processes)
 
-# %% ../src/2.1_solvingmodel.ipynb 77
+# %% ../src/2.1_solvingmodel.ipynb 69
 nops_unconstrained_starchko_solution.to_csv(output_dir + "nops_unconstrained_starchko.csv")
 
-# %% ../src/2.1_solvingmodel.ipynb 80
+# %% ../src/2.1_solvingmodel.ipynb 72
 # Added this line to explictly set Photon constraint
 arabidopsis_supermodel.constrain_photons(PPFD, printouts=False)
 with arabidopsis_supermodel.fba_model as m:
@@ -298,10 +298,10 @@
         nops_unconstrained_wt_solution,
     ) = mmon_gcm.solving.get_pfba_fva_solution(m, rxn_list=fva_list, processes=no_processes)
 
-# %% ../src/2.1_solvingmodel.ipynb 81
+# %% ../src/2.1_solvingmodel.ipynb 73
 nops_unconstrained_wt_solution.to_csv(output_dir + "nops_constrained_wt.csv")
 
-# %% ../src/2.1_solvingmodel.ipynb 83
+# %% ../src/2.1_solvingmodel.ipynb 75
 # Added this line to explictly set Photon constraint
 arabidopsis_supermodel.constrain_photons(PPFD, printouts=False)
 with arabidopsis_supermodel.fba_model as m:
@@ -318,5 +318,5 @@
         nops_unconstrained_starchko_solution,
     ) = mmon_gcm.solving.get_pfba_fva_solution(m, rxn_list=fva_list, processes=no_processes)
 
-# %% ../src/2.1_solvingmodel.ipynb 84
+# %% ../src/2.1_solvingmodel.ipynb 76
 nops_unconstrained_starchko_solution.to_csv(output_dir + "nops_constrained_starchko.csv")
diff --git a/mmon_gcm/supermodel.py b/mmon_gcm/supermodel.py
@@ -214,7 +214,7 @@ def constrain_photons(self, PPFD, printouts=False):
         return self
 
     def add_maintenance(self, me=True, gc=True, gc_scaling=1, 
-                        printouts=False, gc_ratio=4.4270867608601426e-05):
+                        printouts=False, gc_ratio=4.427086760474383e-05): #gc_ratio from 2.0_compute_maintenance
         """
         This function constrains the maintenance reactions in the model
         relative to the input of photons into the model.

diff --git a/models/4_stage_GC.json b/models/4_stage_GC.json
@@ -106604,7 +106604,7 @@
 "Heteroglycans_c_me_1":1.0,
 "MALTOSE_c_me_1":-1.0
 },
-"lower_bound":-1000.0,
+"lower_bound":0,
 "upper_bound":1000.0,
 "gene_reaction_rule":"",
 "subsystem":"NA",
@@ -106626,7 +106626,7 @@
 "Heteroglycans_c_me_2":1.0,
 "MALTOSE_c_me_2":-1.0
 },
-"lower_bound":-1000.0,
+"lower_bound":0,
 "upper_bound":1000.0,
 "gene_reaction_rule":"",
 "subsystem":"NA",
@@ -106648,7 +106648,7 @@
 "Heteroglycans_c_me_3":1.0,
 "MALTOSE_c_me_3":-1.0
 },
-"lower_bound":-1000.0,
+"lower_bound":0,
 "upper_bound":1000.0,
 "gene_reaction_rule":"",
 "subsystem":"NA",
@@ -106670,7 +106670,7 @@
 "Heteroglycans_c_me_4":1.0,
 "MALTOSE_c_me_4":-1.0
 },
-"lower_bound":-1000.0,
+"lower_bound":0,
 "upper_bound":1000.0,
 "gene_reaction_rule":"",
 "subsystem":"NA",
@@ -106692,7 +106692,7 @@
 "Heteroglycans_c_gc_1":1.0,
 "MALTOSE_c_gc_1":-1.0
 },
-"lower_bound":-1000.0,
+"lower_bound":0,
 "upper_bound":1000.0,
 "gene_reaction_rule":"",
 "subsystem":"NA",
@@ -106714,7 +106714,7 @@
 "Heteroglycans_c_gc_2":1.0,
 "MALTOSE_c_gc_2":-1.0
 },
-"lower_bound":-1000.0,
+"lower_bound":0,
 "upper_bound":1000.0,
 "gene_reaction_rule":"",
 "subsystem":"NA",
@@ -106736,7 +106736,7 @@
 "Heteroglycans_c_gc_3":1.0,
 "MALTOSE_c_gc_3":-1.0
 },
-"lower_bound":-1000.0,
+"lower_bound":0,
 "upper_bound":1000.0,
 "gene_reaction_rule":"",
 "subsystem":"NA",
@@ -106758,7 +106758,7 @@
 "Heteroglycans_c_gc_4":1.0,
 "MALTOSE_c_gc_4":-1.0
 },
-"lower_bound":-1000.0,
+"lower_bound":0,
 "upper_bound":1000.0,
 "gene_reaction_rule":"",
 "subsystem":"NA",
@@ -237645,6 +237645,54 @@
 "gene_reaction_rule":""
 },
 {
+"id":"MALTOSE_c_gc_Linker_1",
+"name":"MALTOSE_c_gc_Linker_1",
+"metabolites":{
+"MALTOSE_c_gc_1":-0.16666666666666666,
+"MALTOSE_c_gc_2":2.0,
+"pseudoOs_c_gc_1":1
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":""
+},
+{
+"id":"MALTOSE_c_gc_Linker_2",
+"name":"MALTOSE_c_gc_Linker_2",
+"metabolites":{
+"MALTOSE_c_gc_2":-2.0,
+"MALTOSE_c_gc_3":0.08695652173913043,
+"pseudoOs_c_gc_2":1
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":""
+},
+{
+"id":"MALTOSE_c_gc_Linker_3",
+"name":"MALTOSE_c_gc_Linker_3",
+"metabolites":{
+"MALTOSE_c_gc_3":-0.08695652173913043,
+"MALTOSE_c_gc_4":0.16666666666666666,
+"pseudoOs_c_gc_3":1
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":""
+},
+{
+"id":"MALTOSE_c_gc_Linker_4",
+"name":"MALTOSE_c_gc_Linker_4",
+"metabolites":{
+"MALTOSE_c_gc_1":0.16666666666666666,
+"MALTOSE_c_gc_4":-0.16666666666666666,
+"pseudoOs_c_gc_4":1
+},
+"lower_bound":0.0,
+"upper_bound":1000.0,
+"gene_reaction_rule":""
+},
+{
 "id":"pseudoOs_constraint_a_1",
 "name":"pseudoOs_constraint_a_1",
 "metabolites":{