Genome scale modelling FBA example

[abshah1]

Hi,
I'm creating a model of a metabolic network for my Uni project. I need to use FBA and MFA, and I was wondering if anyone has FBA and MFA models that I could use to build my own. Any help would be greatly appreciated.
Thanks

[Midnighter]

Hello @abshah1,

For which organism do you want to build a model? Maybe one exists already? There are multiple model databases out there by now. Other than that our documentation is a great place to start and you could check out KBase if you really need to create a new reconstruction from a genome.

[abshah1]

Hi @Midnighter

Thank you for your response, I will check those sites out.
I am trying to optimise a metabolic reaction network, that includes the glycolysis pathway, the pentose phosphate pathway, the citric acid cycle, and the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway, in an attempt to overproduce high value compunds like terpenes. The organism used is cyanobacteria. The method involves applying FBA, MFA and Optknock.

[Midnighter]

For OptKnock you should take a look at cameo or maybe you would like to use a visual online tool like https://caffeine.dd-decaf.eu/. I don't know about your specific cyanobacterium but I know that some have been published. Take a look at BioModels, for example.