Patch for SBML compatible units (for PR #320)#2
Open
ayush9pandey wants to merge 14 commits into
Open
Conversation
…r unit features for correct sbml handling of units
… (and similar other high values) in uM, so the 7. Transport_Models.ipynb needed to be fixed with reasonable parameter values.
Owner
|
Thanks for these changes, @ayush9pandey! The changes in this PR look OK, but they are applied to the murrayrm:pure_update-01Jan2026 branch rather than the murrayrm:parameter_update-22Nov2025 branch, so I'm going to try to cherry pick the changes and apply them to parameter_update-22Nov2025. |
Author
|
My bad. Thank you for cherry picking. If it's preferable, we could close this PR and I could open a new one on the correct branch. |
murrayrm
force-pushed
the
pure_update-01Jan2026
branch
from
7a12846 to
56ba17c
Compare
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Hi @murrayrm
I have added support for parameter unit updates in PR BuildACell#320 in sbmlutil.py so that the parameter units are correctly processed and are written to SBML.
In addition, I have suggested a change: delete gfp_expression.py example and instead add a tutorial style notebook to be consistent with other notebooks. So, I have added a number 10... notebook and added more code in there to compare cell-based mixtures.