edkerk
commented
3 years ago Welcome to RAVEN! To help you, it would be good to find out the following information:
- RAVEN version:
... - MATLAB version:
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... - Template model:
...I assume that the template model used for gap-filling is the same as the one used to generate the draft model? What happens if you solvebalancedModelbefore removing duplicate reactions?
mfcesur
Dear Sir/Madam,
I have reconstructed a genome-scale metabolic network model using an orthology-based approach. However, "cofactors and vitamins" in the biomass equation could not be produced. Therefore, I am trying gap-filling to add the lacking reactions.
To this aim, I defined biomass formation reaction as the objective function for both template and draft models. To allow the addition of growth-related reactions via fillGaps function, I set the lower bound of the biomass formation reaction in draft model to 1e-4. Then, I removed "genes" and "rxnGeneMat" fields from the template model. After performing gap-filling, I removed duplicate reactions using checkDuplicateRxn function. Despite the addition of several reactions via fillGaps, there is no biomass formation even after gap-filling. I used the following syntax: [newConnected, cannotConnect, addedRxns, balancedModel, exitFlag] = fillGaps(dmelGEM1, human_model, true, true, false, []); dmelGEM1: draft model and human_model: template model
I would greatly appreciate if you could provide your comments or suggestions. Thank you so much for your time and consideration.
Best Regards, Müberra