Optimization won't finish in time limit

[wshao1]

Hi! Is it possible to use Human-GEM as the input model? The optimization steps are taking longer than the default time limit of 3000 seconds, but I am not sure what is a reasonable time to expect, or if Human-GEM is small enough for deltaFBA to work.

Any advice would be appreciated!

[ravisudharsh]

Hello! Using human genome scale metabolic models is quite possible. There always exists a tradeoff between incorporating too many constraints and the optimization time. I would recommend incorporating constraints (via transcriptomics and/or metabolomics) in incremental fashion, starting from the most essential to the least and subsequently testing the L1 and/or L2 minimizations. I hope this helps! Best of luck, Ravi

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On Thu, Sep 19, 2024 at 5:53 AM wshao1 ***@***.***> wrote: Hi! Is it possible to use Human-GEM as the input model? The optimization steps are taking longer than the default time limit of 3000 seconds, but I am not sure what is a reasonable time to expect, or if Human-GEM is small enough for deltaFBA to work. Any advice would be appreciated! — Reply to this email directly, view it on GitHub <#2>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYCBQW2YYC5VF34NFXVRDDZXJDDHAVCNFSM6AAAAABOO75ZMCVHI2DSMVQWIX3LMV43ASLTON2WKOZSGUZTKMRRHEYDOOA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[wshao1]

Thanks Ravi! Does the speed of the L1/L2 minimization depend on the constraint set in Step 1 (i.e. number of up/down-regulated reactions to maintain)?