Why does the original Recon3D_301 include hundreds of blocked reactions?

[KrsickaD]

I'am trying to run FBA on the Recon3D_301 model [http://bigg.ucsd.edu/models/Recon3D]. The set of blocked reactions (flux < 1e-6) include hundreds of reactions, even if I do not apply any constraints before the optimization. Any suggestions?

import cobra
import csv
import json

cobra.Configuration().solver = "glpk"

model = cobra.io.load_json_model(filename)

model.objective = "BIOMASS_reaction"

solution = model.optimize('maximize',True)

blocked_reactions = [reaction for reaction in model.reactions if abs(solution.__getitem__(reaction.id)) < 1e-6]

for reaction in blocked_reactions:
blocked_metabolites = set()
for metabolite in reaction.metabolites:
    for metabolite, stoichiometry in reaction.metabolites.items():
        if stoichiometry > 0:  # only metabolic products
            blocked_metabolites.add(metabolite.id)
  
with open(output_file, "a", newline="", encoding="utf-8") as f:
    writer = csv.writer(f)
    writer.writerow([reaction.id,','.join(blocked_metabolites)])
               
print(f"Analysis complete. Results saved in {output_file}")

[cdiener]

Your analysis is not really looking for blocked reactions. Only for fluxes that are zero when optimizing the biomass. Fluxes can be zero when optimizing biomass without the reaction being blocked. For that you usually need an FVA but COBRAPY also has a function to find blocked reactions a little faster:

In [1]: from cobra.io import read_sbml_model

In [2]: from cobra.flux_analysis import find_blocked_reactions

In [3]: recon3 = read_sbml_model("Recon3D.xml")

In [4]: recon3.solver = "glpk"

In [5]: blocked = find_blocked_reactions(recon3)

In [6]: blocked
Out[6]: []