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AnalizeHaCaTModel.md

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Aalize the HaCaT Normal Cell line model.

We read the Recon2.2 of biomodels, if you whant to download uncomment the second line.

import cobra
#!wget http://www.ebi.ac.uk/biomodels-main/download?mid=MODEL1603150001 -O recon2.2.xml
Recon2 = cobra.io.read_sbml_model("Models/recon2.2.xml")

Reading the default model

hacat_model=cobra.io.read_sbml_model("Models/hgu133APlus2_hacat_model_0418_DEMEM6429_n5.sbml")

Calculating growth default growth_rate and duplication time

import math
growth_rate = math.log(2)/22.5
print(growth_rate*1.20)
#duplication time
print(math.log(2)/0.008)
0.03696784962986375
86.64339756999316

Define the default bounds for the defined DMEM 6429 medium

#Biomass bounds
for rxex in hacat_model.exchanges:
    rxex.bounds=(-0.01,1)
    
### DMEM 6429 medium
#### AminoAcids

hacat_model.reactions.EX_ala_L_LPAREN_e_RPAREN_.lower_bound=-1
hacat_model.reactions.EX_arg_L_LPAREN_e_RPAREN_.lower_bound=-1
hacat_model.reactions.EX_asn_L_LPAREN_e_RPAREN_.lower_bound=-1
hacat_model.reactions.EX_asp_L_LPAREN_e_RPAREN_.lower_bound=-1
hacat_model.reactions.EX_cys_L_LPAREN_e_RPAREN_.lower_bound=-1
hacat_model.reactions.EX_gln_L_LPAREN_e_RPAREN_.lower_bound=-1
hacat_model.reactions.EX_glu_L_LPAREN_e_RPAREN_.lower_bound=-1
hacat_model.reactions.EX_gly_LPAREN_e_RPAREN_.lower_bound=-1
hacat_model.reactions.EX_his_L_LPAREN_e_RPAREN_.lower_bound=-1
hacat_model.reactions.EX_ile_L_LPAREN_e_RPAREN_.lower_bound=-1
hacat_model.reactions.EX_leu_L_LPAREN_e_RPAREN_.lower_bound=-1
hacat_model.reactions.EX_lys_L_LPAREN_e_RPAREN_.lower_bound=-1 
hacat_model.reactions.EX_met_L_LPAREN_e_RPAREN_.lower_bound=-1
hacat_model.reactions.EX_phe_L_LPAREN_e_RPAREN_.lower_bound=-1
hacat_model.reactions.EX_pro_L_LPAREN_e_RPAREN_.lower_bound=-1
hacat_model.reactions.EX_ser_L_LPAREN_e_RPAREN_.lower_bound=-1
hacat_model.reactions.EX_thr_L_LPAREN_e_RPAREN_.lower_bound=-1
hacat_model.reactions.EX_trp_L_LPAREN_e_RPAREN_.lower_bound=-1
hacat_model.reactions.EX_tyr_L_LPAREN_e_RPAREN_.lower_bound=-1
hacat_model.reactions.EX_val_L_LPAREN_e_RPAREN_.lower_bound=-1

### DMEM 6429 medium
#Carbon Sources
hacat_model.reactions.EX_glc_LPAREN_e_RPAREN_.lower_bound=-4.5
hacat_model.reactions.EX_pyr_LPAREN_e_RPAREN_.lower_bound= -1
### DMEM 6429 medium
#Minerals, vitamins, other
hacat_model.reactions.EX_chol_LPAREN_e_RPAREN_.lower_bound=-1
hacat_model.reactions.EX_fe2_LPAREN_e_RPAREN_.lower_bound=-1
hacat_model.reactions.EX_fol_LPAREN_e_RPAREN_.lower_single_gene_deletionbound=-1
hacat_model.reactions.EX_h2o_LPAREN_e_RPAREN_.lower_bound=-10
hacat_model.reactions.EX_inost_LPAREN_e_RPAREN_.lower_bound=-1
hacat_model.reactions.EX_pi_LPAREN_e_RPAREN_.lower_bound=-10
hacat_model.reactions.EX_ribflv_LPAREN_e_RPAREN_.lower_bound=-1
hacat_model.reactions.EX_so4_LPAREN_e_RPAREN_.lower_bound=-1
#EXTRA
hacat_model.reactions.EX_o2_LPAREN_e_RPAREN_.bounds=(-1000,0)
hacat_model.reactions.biomass_reaction.lower_bound=0.008
hacat_model.reactions.biomass_reaction.upper_bound=0.037


fba_solution = hacat_model.optimize()
hacat_model.optimize()

Calculate FBA and parsimonius FBA

fba_solution.fluxes.to_csv('hacat_fba_fluxes_221117_DEMEM6429_n5.csv')

pfba_solution = cobra.flux_analysis.pfba(hacat_model)

Save result to file

pfba_solution.fluxes.to_csv('hacat_pfba_fluxes_221117_DEMEM6429_n5.csv')

Calculate the Flux Variability analisis

hacat_model.summary(fva=1.00)

Create a single deletation analisis using the hacat_model

import pandas
from time import time

import cobra.test

from cobra.flux_analysis import (
    single_gene_deletion, single_reaction_deletion, double_gene_deletion,
    double_reaction_deletion)

deletion_results=single_reaction_deletion(hacat_model, hacat_model.reactions)

Print the deletation results which are distint than optimal

deletion_results[deletion_results.status != 'optimal']

Ref: Doubling time of human cancerous cell lines 16.2 Hrs http://bionumbers.hms.harvard.edu/bionumber.aspx?&id=100685&ver=21

Analisis of model exchanges. We close all fluxes except the once necesary to analize the main type of metabilism test for max ATP hydrolysis flux from only o2 and the defined carbon

closedModel=hacat_model.copy()
closedModel.add_reaction(Recon2.reactions.DM_atp_c_)
closedModel.objective="DM_atp_c_"

for rx in closedModel.exchanges:
    rx.upper_bound= 100
    rx.lower_bound= -0.00000001
    

#Biomass
closedModel.reactions.biomass_other.lower_bound=0
closedModel.reactions.biomass_carbohydrate.lower_bound=0
closedModel.reactions.biomass_DNA.lower_bound=0
closedModel.reactions.biomass_lipid.lower_bound=0
closedModel.reactions.biomass_protein.lower_bound=0
closedModel.reactions.biomass_RNA.lower_bound=0
closedModel.reactions.biomass_reaction.lower_bound=0
closedModel.reactions.biomass_reaction.upper_bound=0


#closedModel.reactions.r1147.bounds=(0,0)
#closedModel.reactions.r2375.bounds=(0,0)
# test for max ATP hydrolysis flux from only o2 and the defined carbon
# source
# glucose aerobic

closedModel.reactions.EX_o2_LPAREN_e_RPAREN_.bounds=(-1000,0.0)
closedModel.reactions.EX_h2o_LPAREN_e_RPAREN_.bounds=(-1000,1000)
closedModel.reactions.EX_co2_LPAREN_e_RPAREN_.bounds=(-0.0,1000)
closedModel.reactions.EX_glc_LPAREN_e_RPAREN_.bounds=(-1,-1)
closedModel.optimize()

Analisis of parcimonius FBA of the closed model with different carbon sources.

parsimonius FBA for glutamine anaerobic medium

cobra.flux_analysis.pfba(closedModel).fluxes.to_csv('hacat_pfba_fluxes_221117_DEMEM6429_n5_glucose_aerobic.csv')
closedModel=hacat_model.copy()
closedModel.add_reaction(Recon2.reactions.DM_atp_c_)
closedModel.objective="DM_atp_c_"

for rx in closedModel.exchanges:
    rx.upper_bound= 100
    rx.lower_bound= -0.00000001
    

#Biomass
closedModel.reactions.biomass_other.lower_bound=0
closedModel.reactions.biomass_carbohydrate.lower_bound=0
closedModel.reactions.biomass_DNA.lower_bound=0
closedModel.reactions.biomass_lipid.lower_bound=0
closedModel.reactions.biomass_protein.lower_bound=0
closedModel.reactions.biomass_RNA.lower_bound=0
closedModel.reactions.biomass_reaction.lower_bound=0
closedModel.reactions.biomass_reaction.upper_bound=0

# test for max ATP hydrolysis flux from only o2 and the defined carbon
# source
# glucose anaerobic

closedModel.reactions.EX_o2_LPAREN_e_RPAREN_.bounds=(0,0)
closedModel.reactions.EX_h2o_LPAREN_e_RPAREN_.bounds=(-1000,1000)
closedModel.reactions.EX_co2_LPAREN_e_RPAREN_.bounds=(0.0,1000)
closedModel.reactions.EX_glc_LPAREN_e_RPAREN_.bounds=(-1,-1)
closedModel.optimize()
cobra.flux_analysis.pfba(closedModel).fluxes.to_csv('hacat_pfba_fluxes_221117_DEMEM6429_n5_glucose_anaerobic.csv')

parsimonius FBA for glutamine aerobic medium

closedModel=hacat_model.copy()
closedModel.add_reaction(Recon2.reactions.DM_atp_c_)
closedModel.objective="DM_atp_c_"

for rx in closedModel.exchanges:
    rx.upper_bound= 100
    rx.lower_bound= -0.00000001
    

#Biomass
closedModel.reactions.biomass_other.lower_bound=0
closedModel.reactions.biomass_carbohydrate.lower_bound=0
closedModel.reactions.biomass_DNA.lower_bound=0
closedModel.reactions.biomass_lipid.lower_bound=0
closedModel.reactions.biomass_protein.lower_bound=0
closedModel.reactions.biomass_RNA.lower_bound=0
closedModel.reactions.biomass_reaction.lower_bound=0
closedModel.reactions.biomass_reaction.upper_bound=0

# glutamine aerobic
closedModel.reactions.EX_o2_LPAREN_e_RPAREN_.bounds=(-1000,0)
closedModel.reactions.EX_h2o_LPAREN_e_RPAREN_.bounds=(-1000,1000)
closedModel.reactions.EX_co2_LPAREN_e_RPAREN_.bounds=(0,1000)
closedModel.reactions.EX_gln_L_LPAREN_e_RPAREN_.bounds=(-1,-1)

closedModel.optimize()
cobra.flux_analysis.pfba(closedModel).fluxes.to_csv('hacat_pfba_fluxes_221117_DEMEM6429_n5_glutamine_aerobic.csv')

parsimonius FBA for glutamine anaerobic medium

closedModel=hacat_model.copy()
closedModel.add_reaction(Recon2.reactions.DM_atp_c_)
closedModel.objective="DM_atp_c_"

for rx in closedModel.exchanges:
    rx.upper_bound= 100
    rx.lower_bound= -0.00000001 #-0.00474 #this is the minimum value
    

#Biomass
closedModel.reactions.biomass_other.lower_bound=0
closedModel.reactions.biomass_carbohydrate.lower_bound=0
closedModel.reactions.biomass_DNA.lower_bound=0
closedModel.reactions.biomass_lipid.lower_bound=0
closedModel.reactions.biomass_protein.lower_bound=0
closedModel.reactions.biomass_RNA.lower_bound=0
closedModel.reactions.biomass_reaction.lower_bound=0
closedModel.reactions.biomass_reaction.upper_bound=0

# glutamine anaerobic
closedModel.reactions.EX_o2_LPAREN_e_RPAREN_.bounds=(0,0)
closedModel.reactions.EX_h2o_LPAREN_e_RPAREN_.bounds=(-1000,1000)
closedModel.reactions.EX_co2_LPAREN_e_RPAREN_.bounds=(0,1000)
closedModel.reactions.EX_gln_L_LPAREN_e_RPAREN_.bounds=(-1,-1)

closedModel.optimize()
cobra.flux_analysis.pfba(closedModel).fluxes.to_csv('hacat_pfba_fluxes_221117_DEMEM6429_n5_glutamine_anaerobic.csv')
closedModel=hacat_model.copy()
closedModel.add_reaction(Recon2.reactions.DM_atp_c_)
closedModel.objective="DM_atp_c_"

for rx in closedModel.exchanges:
    rx.upper_bound= 100
    rx.lower_bound= -0.00000001 #-0.00474
    
    
#Biomass
closedModel.reactions.biomass_other.lower_bound=0
closedModel.reactions.biomass_carbohydrate.lower_bound=0
closedModel.reactions.biomass_DNA.lower_bound=0
closedModel.reactions.biomass_lipid.lower_bound=0
closedModel.reactions.biomass_protein.lower_bound=0
closedModel.reactions.biomass_RNA.lower_bound=0
closedModel.reactions.biomass_reaction.lower_bound=0
closedModel.reactions.biomass_reaction.upper_bound=0


## fru aerobic
closedModel.reactions.EX_o2_LPAREN_e_RPAREN_.bounds=(-1000,0)
closedModel.reactions.EX_h2o_LPAREN_e_RPAREN_.bounds=(-1000,1000)
closedModel.reactions.EX_co2_LPAREN_e_RPAREN_.bounds=(0,1000)
closedModel.reactions.EX_fru_LPAREN_e_RPAREN_.bounds=(-1,-1)

closedModel.optimize()
cobra.flux_analysis.pfba(closedModel).fluxes.to_csv('hacat_pfba_fluxes_221117_DEMEM6429_n5_fructose_aerobic.csv')
closedModel=hacat_model.copy()
closedModel.add_reaction(Recon2.reactions.DM_atp_c_)
closedModel.objective="DM_atp_c_"

for rx in closedModel.exchanges:
    rx.upper_bound= 100
    rx.lower_bound= -0.00000001
    
    
#Biomass
closedModel.reactions.biomass_other.lower_bound=0
closedModel.reactions.biomass_carbohydrate.lower_bound=0
closedModel.reactions.biomass_DNA.lower_bound=0
closedModel.reactions.biomass_lipid.lower_bound=0
closedModel.reactions.biomass_protein.lower_bound=0
closedModel.reactions.biomass_RNA.lower_bound=0
closedModel.reactions.biomass_reaction.lower_bound=0
closedModel.reactions.biomass_reaction.upper_bound=0


## fru aerobic
closedModel.reactions.EX_o2_LPAREN_e_RPAREN_.bounds=(0,0)
closedModel.reactions.EX_h2o_LPAREN_e_RPAREN_.bounds=(-1000,1000)
closedModel.reactions.EX_co2_LPAREN_e_RPAREN_.bounds=(0,1000)
closedModel.reactions.EX_fru_LPAREN_e_RPAREN_.bounds=(-1,-1)

closedModel.optimize()
cobra.flux_analysis.pfba(closedModel).fluxes.to_csv('hacat_pfba_fluxes_221117_DEMEM6429_n5_fructose_anaerobic.csv')
closedModel=hacat_model.copy()
for rx in closedModel.reactions:
    rx.bounds=(-0.001,0.001)
    fba=closedModel.optimize()
    fba2=hacat_model.optimize()
    if(fba.f != fba2.f/2 ):
        print(rx.id)