This SDK Module contains methods relating to the reconstruction and analysis of metabolic models in KBase. Check out the Developer Guide for an overview on the module structure and help getting started.
- Refinements to auxotrophy method
- Fix Propagate Model with full genome refs
- Fix GC content calculation for community models
- Phenotype simulation will not fail if gapfilling is unsuccessful
- Fixed PUBLIC-290 check mass balance report name
- Switched to use of genome apis for compatibility with new object types (SCT-932)
- Switched to resolved refs (#/#/#) for input objects
- Ensured all compound information is copied into community models
- Correct faulty reference for custom media compounds
- Auxotropy local method
- Hotfix: remove link which was breaking UI for propagate models app
- Fixed PUBLIC-256 build multiple metabolic saving to same name
- Fixed metabolic model upload for compounds with dashes and spaces
- Fixed Gapfilling drops compounds from biomass to grow
- Added View Flux Network app which visualises a FBA solution in an interactive diagram
- Removed View FBA Expression Comparison app which is no longer needed due to the report from Compare FLux with Expression App
- Refactored all apps to accept IDs as permanent numerical references (eg. 133/124/1) and updated tests & UI accordingly
- Use reference chains to ensure that a model does not become uneditable if its genome is inaccessible.
- Updated table parseing to accept '\r' line delimination and error if uploaded phenotype set is empty
- Updated SBML parsing to address compound duplication bug and prefix all ids in SBML export to be compliant with SBML schema.
- Update Edit Media and Edit Model UI to ensure that users provide all needed parameters when loading a new compound
- Added the ability to specify custom bounds on additional compounds and reactions in a phenotype set
- Model download now includes many additional information types like thermodynamics, pathways and chemical structure
- Flux information from phenotype sets are retained for inspection
- Fixed duplicate compartments in propagate model
- Fixed Genome ID not being updated for propagate model
- Corrected bugs in media editing and SBML model upload
- Adding internal functional support for batch FBA (no UI yet)
- Inchikey and SMILES may be uploaded to models
- Makes TSV & Excel importers case insensitive
- Clarified media parameter on Build and Gapfill Metabolic Model
- Updated compare metabolic model to accept model references(not names)
- Updated build multiple metabolic models to accept model references(not names)
- Allowing different solvers to be passed into FBA object
- Adding sink to activate Biotin biosynthesis in SBML export
- Allowing gapfilled compartmentalized reactions to be added to model
- Fixing issue with genome client in KBase
- Supporting generic media
- Update Travis file
-Fixing R_ bug in model import
-Updated service to support new authentication procedure -Added batch version of model reconstruction
-Fixing minor bug in SBML exporter
-New model editor -New media editor -New bulk export tool
-Improved reports generated by most methods -Moved all upload and download code for model objects into this repository -Fixed model comparison tool
-Ability to gapfill a model on all phenotype conditions either cumulatively or iteratively
-Fixed a bug in the numbering of gapfill solution objects when a model is consecutively gapfilled multiple times
-Integration of probabilistic gapfilling -Improved multiple-model comparison -Improved model and media editors -Improved error handling in methods -Support for large-scale analysis of many models, media, or genomes at once
This was the initial public release of the modeling tools as an SDK module. For release notes before this time, see https://github.com/kbase/KBaseFBAModeling.