Hi Michel
I don't think that there currently is a utility function that does
what you are looking for. One reason for this is, that it is not
totally straight forward.
How do you define "produce"?
Are you only looking for reactions, which have the compound on the
right hand side of the equation (i.e. a positive stoichiometric
coefficient?), if so, what about a strictly reverse reaction,
which has a ub of 0, and a lower bound < 0 and the compound
with a coefficient of 1. That reaction would never be able to
produce the compound.
You would also have to take into account all reversible reactions
consuming the compound, as they can in fact also produce the
compound.
I will add some parameters to findRxnsFromMets to allow searching for consuming/producing reactions respecting the above explanations, and hopefully this will be in soon.
Best
Thomas
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ATPID = findMetIDs(model, 'atp_c') % find the MetID of atp_c
Sfull = full(model.S); % convert the spare double to a matrix
ATP_Coeff = Sfull(ATPID,:) % Find all coefficients involving 'atp_c'
IndATP_Prod = find(ATP_Coeff > 0) % Find Rxn ID for ATP producing Rxn
i = 0
Prod_FBA = 0
Coeff = 0
Gross_ATP_Prod = 0
for i = 1:length(IndATP_Prod)
Prod_FBA(i) = FBAsolution.x(IndATP_Prod(i)) % A Flux balance analysis must be run before this code and the results are stored in 'FBAsolution'
Coeff(i) = Sfull(ATPID, IndATP_Prod(i)) % Find coefficients
Gross_ATP_Prod(i) = Prod_FBA(i) * abs(Coeff(i))
end
Gross_ATP_Prod_cytosol = sum(Gross_ATP_Prod) % This is the gross ATP production flux in the cytosol
Hi Michel
I don't think that there currently is a utility function that does what you are looking for. One reason for this is, that it is not totally straight forward.
How do you define "produce"?
Are you only looking for reactions, which have the compound on the right hand side of the equation (i.e. a positive stoichiometric coefficient?), if so, what about a strictly reverse reaction, which has a ub of 0, and a lower bound < 0 and the compound with a coefficient of 1. That reaction would never be able to produce the compound.
You would also have to take into account all reversible reactions consuming the compound, as they can in fact also produce the compound.
I will add some parameters to findRxnsFromMets to allow searching for consuming/producing reactions respecting the above explanations, and hopefully this will be in soon.
Best
Thomas
On 21.11.18 19:46, 'Michel_Lavoie' via COBRA Toolbox wrote:
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Hi all,--I would like to select all the reactions leading to production of ATP in my cobra model, but I do not know how to do that. I know the function (findRxnsFromMets(model,...), but I was only able toextract from the network a list of reactions involving ATP production and ATP consumption. What commands should I use to select only the reactions leading to ATP production (and not consumption) in my Cobra Model?Thank you again for your help,Michel
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