search

PNNL-CompBio / CONCERTO

Continuous integration and validation for genome-scale metabolic model consortia
Apache License 2.0
3 stars 3 forks source link

visualization-friendly version of Carbon dioxide flux #99

Open djinnome opened 1 year ago

djinnome commented 1 year ago
djinnome commented 1 year ago

Currently blocking the ability to use flux visualization Alluvial plots

mcnaughtonadm commented 11 months ago

Just want to confirm @djinnome. For the second task here, removing the HCO3 <-> CO2 reaction. Is this something we want to alter permanently in https://github.com/PNNL-CompBio/RToru-GEM/tree/main or just temporarily for the visualization? Just want to know where I need to make the method.

djinnome commented 11 months ago

Let’s do it temporarily first. If it gives us what we expect, we can create a PR to modify it in the model.

From: Andrew McNaughton @.> Date: Wednesday, July 26, 2023 at 6:50 PM To: PNNL-CompBio/CONCERTO @.> Cc: Zucker, Jeremy D @.>, Mention @.> Subject: Re: [PNNL-CompBio/CONCERTO] visualization-friendly version of Carbon dioxide flux (Issue #99) Check twice before you click! This email originated from outside PNNL.

Just want to confirm @djinnomehttps://github.com/djinnome. For the second task here, removing the HCO3 <-> CO2 reaction. Is this something we want to alter permanently in https://github.com/PNNL-CompBio/RToru-GEM/tree/main or just temporarily for the visualization? Just want to know where I need to make the method.

— Reply to this email directly, view it on GitHubhttps://github.com/PNNL-CompBio/CONCERTO/issues/99#issuecomment-1652645793, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AABDGUX37PAOEXVDJZY7GT3XSGNMBANCNFSM6AAAAAAZPJSPNA. You are receiving this because you were mentioned.Message ID: @.***>

mcnaughtonadm commented 11 months ago

The reaction in Rhodosporidium that is transferring HCO3 <-> CO2 is the CYNTAH__Rhodosporidium reaction which is: 'cynt_c__Rhodosporidium + 3.0 h_c__Rhodosporidium + hco3_c__Rhodosporidium --> 2.0 co2_c__Rhodosporidium + nh4_c__Rhodosporidium' is this okay since it's only moving h3O3 to co2 and not reversible?

mcnaughtonadm commented 11 months ago

Also the HCO3E__Rhodosporidium reaction but this one I can just remove: 'co2_c__Rhodosporidium + h2o_c__Rhodosporidium <=> h_c__Rhodosporidium + hco3_c__Rhodosporidium'

mcnaughtonadm commented 11 months ago

Issue is being addressed in the ConsortiumModels Repo: https://github.com/PNNL-CompBio/ConsortiumModels/pull/5