KarrLab/obj_tables

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examples/thermodynamic_metabolic_model/notes.txt

Summary

Maintainability
Test Coverage
No explicit definition of compartments
Missing several columns from metabolite and reaction tables
Use different reaction ids in different workbooks

All metabolites in ecoli457 except 5:
    f1p
    fru
    gal
    gal1p
    glcn

All reactions in ecoli457 except 12:
    EX_fru(e)
    EX_gal(e)
    EX_glcn(e)
    FRUK
    FRUpts
    G3PD5
    GALabc
    GALKr
    GlcnUpt
    GLYK
    GNK
    UGLT

Reactions have same stoichiometry and directionality except 2:
    ACS: (2) pi vs ppi
    FUM_SEC: includes proton symport vs no symport

Reactions have same reversibility except 5
    ACKr
    FUM
    FUM_SEC
    GlycUpt
    PTAr

Reversed direction of some reactions for consistency with Khodayari and Maranas
    [e]: <=> glyc

Mapped all but 14 fluxes to specific reactions:
    PFK-FBP
    Middle_EMP
    Low_EMP
    PYK-PPS
    ED
    PPP_ED_branch
    Early_PPP
    Non-ox_PPP
    Early_TCA
    Int_TCA
    MDH+MQO
    ME
    Glx_Cycle
    Growth_rate

Mapped all ΔG to specific reactions