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ModelSEED / ModelSEED-UI

ModelSEED UI (beta)
MIT License
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FBA with Genes KOs and make reaction KO actually work (currently it does nothing :(). #38

Open jplfaria opened 9 years ago

jplfaria commented 9 years ago

Currently we don't have option to do gene KOs in FBA (only reaction KOs). The implementation of reactions KOs with the search looks pretty neat, an exact same field for gene KOs would be ideal.

janakagithub commented 9 years ago

Couple of things to pay attention regarding gene KOs and why reaction KOs is more straightforward. Scenario 1. Multiple genes may mapped to a single reaction. Unless all the mapped genes are in the knockout list, the reaction is turned on Scenario 2. Multiple reactions mapped to a single gene. You KO a gene(s), and all mapped reactions may turn off.

jplfaria commented 9 years ago

Janaka, Both of your points are valid and I agree with you, still I don't think we should choose one or the other. We should have both reaction KOs and gene KOs. I am assuming most of our users know how GPRs are implemented, thus knowing the merits of doing either reaction KOs or gene KOs.

nconrad commented 9 years ago

I need to make reaction KO actually work as well. Currently, it does nothing :(

amikaili commented 7 years ago

New MODELSEED-UI production code has been released, and tagged 'v2.0', in the 'master' branch. GitHub is no longer used for bug tracking, though. Please send an email to help@modelseed.org, with the subject MODELSEED-43. The email server will post the email as a comment to the MODELSEED-43 ticket, in Jira.