Fast BOF #115
Open
Fast BOF #115
Conversation
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
Incorporate changes from maintenance branch into allchanges branch
Make all original tests run
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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Outdated suggestions cannot be applied.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.
One aspect hampering the use of Medusa for certain applications is the need to construct a list of GEMs prior to creating and analyzing the ensemble. Indeed, in many situations, it is computationally less expensive to create and analyze each member of the fly. This feature allows for directly populating the ensemble without needing to first generate each individual member, for one specific situation. This feature allows for directly populating an ensemble where members only differ w.r.t. their biomass objective function (BOF) definition. Note that as BOF coefficients can be set to zero, metabolites can either be omitted or admitted to the BOF. Changes made:
maintenance,refactor_populate_features_base, andtestBoundsbranches, I can undo this if this is inconvenientHappy to discuss if functions like these would be a good fit for Medusa, or if they should be ported elsewhere.