Open Caseses100 opened 8 months ago
Could you please specify (or link) which model file you exactly used?
I used the ecYeastGEM.xml model that I retrieved via this link: https://github.com/SysBioChalmers/ecModels/blob/d0e2ebf0c440e81f777b069fd52af037e006ea3d/ecYeastGEM/model/ecYeastGEM.xml
From: Eduard Kerkhoven @.> Sent: maandag 18 maart 2024 10:58 To: SysBioChalmers/GECKO @.> Cc: Effie Leijten @.>; Author @.> Subject: Re: [SysBioChalmers/GECKO] Bug detected: model.summary does not match expected phenotype for ecYeastGEM.xml for different carbon sources (Issue #368)
You don't often get email from @.*** Learn why this is importanthttps://aka.ms/LearnAboutSenderIdentification
Could you please specify (or link) which model file you exactly used?
— Reply to this email directly, view it on GitHubhttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FSysBioChalmers%2FGECKO%2Fissues%2F368%23issuecomment-2003399684&data=05%7C02%7Ce.m.leijten%40tudelft.nl%7Cbf7c9993eb3147179c0d08dc4731e8c3%7C096e524d692940308cd38ab42de0887b%7C0%7C0%7C638463526873917109%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=7n8%2Bqm5L%2FpZzpXTR0MgNz62WQerdUoFi%2FfHHNV9OnMk%3D&reserved=0, or unsubscribehttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FBHB645L6NMFGP5FL43L6Z6LYY23C3AVCNFSM6AAAAABE3HAY62VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMBTGM4TSNRYGQ&data=05%7C02%7Ce.m.leijten%40tudelft.nl%7Cbf7c9993eb3147179c0d08dc4731e8c3%7C096e524d692940308cd38ab42de0887b%7C0%7C0%7C638463526873917109%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=OKO1HX3ZWgBDGxZXhX%2FouLsBB8giy18jkNe2SjhsK%2Fs%3D&reserved=0. You are receiving this because you authored the thread.Message ID: @.***>
Description of the bug:
For my research I'm using the ecYeastGEM model to evaluate what happens to fluxes if I incorporate certain knockouts or gene insertions in S. cerevisiae. As certain knockouts completely stop certain fluxes of the 'central carbon metabolism' I need to run the model in altered media with different carbon sources (i.e. with a medium with altered medium exchanges). To check that this medium alteration step works, I've been running the ecYeastGEM model (without any genetic modifications implemented) on glucose and on ethanol. For glucose, I expect to see a secretion of ethanol and carbon dioxide (crabtree effect). For ethanol, I expect only carbon dioxide. I use the model.summary() to evaluate the model's outputs.
However, I do not get this as outputs.
For growth on glucose, I get a 100% carbon dioxide secretion as output.
Secretion
Metabolite Reaction Flux C-Number C-Flux s_0458[e] r_1672 -2.413 1 100.00% s_0776[e] r_1814 -5.578E-06 2 0.00% s_0805[e] r_2100 -3.92 0 0.00% s_0450[c] r_2111 -0.08797 0 0.00%
For growth on ethanol, I also get 100% carbon dioxide secretion as output.
Secretion
Metabolite Reaction Flux C-Number C-Flux s_0458[e] r_1672 -690.5 1 100.00% s_0776[e] r_1814 -0.002075 2 0.00% s_0805[e] r_2100 -2241 0 0.00% s_0450[c] r_2111 -32.11 0 0.00%
Reproducing these results:
System information
I hereby confirm that:
main
branch of the repository.