Hello community.
Currently I am trying to reconstruct metabolic model out of some of my genomes. I learned Optflux. This tool can import SBML file and carry out FBA and other simulations. However, my problem is, I can generate a compatible SBML file for it.
I have tried KBase. I found my genome there and followed the instructions to construct a gap-filled model. Once that was done, I downloaded the model in SBML format and tried to import it into Optflux. It was not a smooth process, I needed to replace all the pipes and so on before Optflux can read in most of information. Then I tried "Wild type simulation". The program just popped up "infeasible problem" and refused to go on. Without any documentations or hints, I just don't know where should I look at to find a solution.
However, this small practice also makes it clear, that I just miss a lots of basis in the workflow. For this reason, I would like to ask you guys for some good modeling tutorials, so I can learn the whole thing from a Fasta file to FBA and gene knockout simulations. Any suggestion is appreciated!
Old post but the best resources I have encountered are from DTU. The department Biosustain are maintainers of COBRApy and Cameo. They have a very nice introduction course for Cameo written by Nikolaus Sonnenschein . Link to Cameo