FBA generates results but pFBA does not.

[Sanu Shameer]

Hi All

I've been stuck on this for a while now....

I am a working with a C3 leaf model model (attached). optimizeCbModel works on my model and constraint used.

-----------------------------------CODE----------------------------------

source_model = initializeDielLeafModel('/home/sanu/diel_leaf_model.xml');

PPFD = 500;
net_rate = 11.1895;

%set PPFD
indx_light_Day = find(source_model.rxns=="Photon_tx1");
[source_model.lb(indx_light_Day), source_model.ub(indx_light_Day)] = deal(PPFD);
disp(strcat('photon uptake = ',num2str(PPFD)))

%set maintenance
indx_ATPase_Day = find(source_model.rxns=="ATPase_tx1");
[source_model.lb(indx_ATPase_Day), source_model.ub(indx_ATPase_Day)] = deal(0);
disp(strcat('ATPase flux = ',num2str(0)))

%set Vc flux
indx_Vc_Day = find(source_model.rxns=="RIBULOSE_BISPHOSPHATE_CARBOXYLASE_RXN_p1");
[source_model.lb(indx_Vc_Day), source_model.ub(indx_Vc_Day)] = deal(net_rate);
disp(strcat('Vc = ',num2str(net_rate)))

FBAsoln = optimizeCbModel(source_model,"max");

-----------------------------------OUTPUT--------------------------------

The resulting FBAsoln struct fields and values are as follows:

full = 1563x1 double

obj = 0.2298

rcost = 1563x1 double

dual = 1419x1 double

solver = 'glpk'

algorithm = 'default'

stat = 1

origStat = 5

time = 0.2228

basis = []

x = 1563x1 double

f = 0.2298

y = 1419x1 double

w = 1563x1 double

v = 1563x1 double

--------------------------------------------------------------------------------

But pFBA(source_model,'GeneOption',0,'skipclass',1) doesn't seem to work (upperbounds of the irreversible model still remains the default value, which is a 1000 in my case).

I decided to write my own simple pFBA function to figure out what was happening.

-----------------------------------CODE----------------------------------

FBAsoln = optimizeCbModel(source_model,"max");

[irr_model,matchRev,rev2irrev,irrev2rev] = convertToIrreversible(source_model);

indx_obj = find(irr_model.c == 1);
[irr_model.lb(indx_obj), irr_model.ub(indx_obj)] = deal(FBAsoln.x(indx_obj));

irr_model.c = irr_model.c * 0;
irr_model.c = irr_model.c + 1;

FBAsoln2 = optimizeCbModel(irr_model,'min');

-------------------------------OUTPUT-----------------------------------

The final FBAsoln2 struct fields and values are as follows:

full = 2065x1 double

obj = 0

rcost = 2065x1 double

dual = 1419x1 double

solver = 'glpk'

algorithm = 'default'

stat = 0

origStat = 110

time = 0.2434

basis = []

f = 0

x = []

--------------------------------------------------------------------------------

I can't seem to figure out why the minimization of sum of fluxes does not seem to work.

Please let me know if you can figure out what I am doing wrong,

Thanks in advance,

Sanu

[Anne Richelle]

Hi Sanu,

seems that this is a solver issue: if you use gurobi instead of glpk it works fine.

Let me know if it works for you

[Sanu Shameer]

Hi Anne

Changing the solver worked. I did not have 'gurobi' installed so I used the 'matlab' solver instead and it worked. Thanks a lot :-)

Best Regards

Sanu