Patrial FBC2 extension support #7
Open
Conversation
This file contains 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
Adding an 'SBMLResourceIdentifiers' class for importing references on Genes, Proteins, Metabolites, and Reactions. SBML importer can now read geneProduct FBC objects and turn them into Protein objects. Importer also reads “is” and “isEncodedBy” MIRIAM biological qualifiers and parses them into SBMLResourceIdentifiers. Correctly reading the fbc:upperFluxBound and fbc:lowerFluxBound values. Clarifying some exceptions in rangedNumber, Proteins, and Genes. Additional checking for SBML import to work nicely with versions of the library lacking FBC. Extracting chemical formula from FBC SBML attribute for metabolites. Adding code to track 'non-canonical' proteins - i.e. proteins that represent unknown connectors between genes and reactions. Untangling a series of circular import dependencies that prevented modular testing of parts of the JQMM including sbmlio.
Changes to reflect the slight change in calling convention needed by the dependency untangling.
|
Note: We need this to use jQMM with P. putida, as the only up-to-date models are in SBML3. |
|
ok, cool |
|
If you give me a link to the model you use, I can test it... |
|
The putida model isn't ready yet... we have to convert the identifiers to BiGG format. Can we just test with the smbl3 version of iJR904 (http://bigg.ucsd.edu/static/models/iJR904.xml)? |
|
iJR904 works fine - it's one of the models I used to test Arrowland. |
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Outdated suggestions cannot be applied.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.
Support for reading SBML3 files with FBC2 extension. Note that WRITING SBML3 with FBC2 is not supported in these changes. Writing SBML will still result in a non-FBC2-format file.