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.
- Further improving model reconstruction and gapfilling to prevent overproduction ATP
- Adding support for building models from multiple annotation sources (with LLNL team)
- Adding support for metagenome model reconstruction
- Adding model characterization tools to support pathway analysis, auxotrophy prediction, and reaction classification
- Removing outdated, obfuscated, and nonfunctional apps
- The ability to reconstruct a model for plants has been moved, and it is now available in the Reconstruct Plant Metabolism App.
- The gram-negative and gram-positive templates have been updated. The “Automatic selection” will use the updated templates.
- The old templates (legacy) can be manually selected in the parameter dropdown. It is important to note that models built using the older templates will lead to different results if your genome(s) was annotated with the latest version of RAST. We do not recommend this practice. If you are trying to use older templates for reproducibility purposes please use a genome annotated with the older version of RAST
- In tha FBA App - Gene Knockouts functionality now allows search of genes associated with the model removing the need to manually type gene names
- Biochemistry DB is now searchable when adding new reactions and compound to to the model with the Edit Metabolic Model App
- view_flux_network App has been deprecated.
- build_multiple_metabolic_models. In addition to individual genomes, genome sets can now be used as an input for model reconstruction
- improving the model reconstruction pipeline to prevent the overproduction of ATP by draft metabolic models
- added KBase paper citation in PLOS format to utilities, added citations to Gapfill Metabolic Model, and created RELEASE_NOTES.md file
- Refinements to auxotrophy method
- Patch for _check_job failures
- Make sure GAAPI does not provide CDSs in feature list
- Fixes for media importer
- Correcting unit scale in SBML export
- Update app citations
- 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.
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