visualization-friendly version of Carbon dioxide flux

Question

visualization-friendly version of Carbon dioxide flux

djinnome opened this issue a year ago · comments

Jeremy Zucker commented a year ago

Create a source CO2 flux that is distinguishable from CO2 exchange
Remove bicarbonate <-> CO2 reaction from Rhodosporidium (or restrict the maximum flux) to prevent Cyano from getting more carbon that it should

Jeremy Zucker · Answer 1 · Thu Jun 22 2023 05:08:23 GMT+0800 (China Standard Time)

Currently blocking the ability to use flux visualization Alluvial plots

Andrew McNaughton · Answer 2 · Thu Jul 27 2023 06:50:29 GMT+0800 (China Standard Time)

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.

Jeremy Zucker · Answer 3 · Thu Jul 27 2023 07:35:40 GMT+0800 (China Standard Time)

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 @djinnome<https://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 GitHub<#99 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AABDGUX37PAOEXVDJZY7GT3XSGNMBANCNFSM6AAAAAAZPJSPNA>. You are receiving this because you were mentioned.Message ID: ***@***.***>

Andrew McNaughton · Answer 4 · Fri Jul 28 2023 01:43:25 GMT+0800 (China Standard Time)

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?

Andrew McNaughton · Answer 5 · Fri Jul 28 2023 01:46:04 GMT+0800 (China Standard Time)

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

Andrew McNaughton · Answer 6 · Fri Jul 28 2023 01:59:40 GMT+0800 (China Standard Time)

Issue is being addressed in the ConsortiumModels Repo: PNNL-CompBio/ConsortiumModels#5