Segre_FBA_Tutorial

[NatalieDreux]

Part 1 Notes

Defining rxn network:

Label reactions: reacs =["x1","x2","ra","rb","ATPout","NADHout"]

Label metabolites metabs = ["A","B","ATP","NADH"]

n = len(reacs) # Number of reactions m = len(metabs) # Number of metabolites

Define values of Stoichiometric Matrix of (m,n)

S=np.array ([[ -1, -1, 1, 0, 0, 0], For metabolite A; in "x1" and "x2" --> -1; in "rA" --> +1; in "rb","ATP/NADHout" -->not invloved, [ 1, 1, 0, -1, 0, 0], For metabolite B; in x1 and x2 +1; in ra not involved; in rb =1; in ATP/NADGout; not involved, [ 1, 0, 0, 0, -1, 0], met = ATP, [ 0, 1, 0, 0, 0, -1]]) met = NADH

• each row represents [x1, x2, ra, rb, ATPout, NADHout]
  • each column represents [A, B, ATP, NADH]

[NatalieDreux]

Optimization parameters

b = vector of zeros with length (m) obj = vector of zeros with length (n)

UB[2]=1

modifying UB of third rxn (w/ zero indexing) to 1; sets constraint on individual rxn

(-1) leads to maximization when defining the objective function due to default being 'minimize'

example: obj[0]=-1 vs. obj[1]=0