Question: Any tutorial for metabolic model reconstruction?
1
gravatar for Dgg32
4.5 years ago by
Dgg3260
Bremen
Dgg3260 wrote:

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 popuped "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!

 

 

 

 

optflux kbase model • 1.6k views
ADD COMMENTlink modified 3.2 years ago by flight50560 • written 4.5 years ago by Dgg3260
0
gravatar for flight505
3.2 years ago by
flight50560
Denmark/DTU
flight50560 wrote:

Hi i just wanted to follow up on your old post. i am also looking for a good tutorial describing in detail the process, how to as well as trouble shooting of reconstructing metabolic model as well as testing the model. Any recommendations?? - thanks

ADD COMMENTlink written 3.2 years ago by flight50560

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

ADD REPLYlink modified 5 months ago • written 6 months ago by flight50560
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