These are chat archives for opencobra/cobrapy

Feb 2018
Feb 19 2018 15:14
Hi all.
I am trying to track the flux of a metabolite and its derivatives through a network.
Is there a systematic way of doing this? Maybe somebody has already written method that prints a nice summary or something?
For example, suppose I optimize a model. Then I want to know where the glucose is going. Ideally the method should detect that glucose is being consumed by the reactions of glycolysis, and then pyruvate is going into the mitochondria, etc.
Moritz E. Beber
Feb 19 2018 15:49
I don't have any code that does exactly what you want. My approach would be to build a bipartite graph of the active reactions (flux > 0) and then find the (shortest) path from the glucose node to the biomass reaction node? You can get a summary for an individual metabolite but that only lists in-/out-fluxes.
You will have to remove co-factors or else build a reaction-centric network from the hypergraph representation.
Synchon Mandal
Feb 19 2018 17:18

Hello everyone!

I found out that cobrapy is participating in Google Summer of Code '18. I am an user of cobrapy and I am really interested in contributing to this project. How would I go about applying for this internship? Thanks in advance!

Moritz E. Beber
Feb 19 2018 18:43
Hi @synchon, please take a look here and especially the section about 'Applying'. Basically, you use the existing project ideas or your own ones to develop a project proposal. It's best if you discuss your plan with us early on so you don't surprise us with an application out of the blue.