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Version 1.6 introduces a significant number of new models to the repository. We describe the addition of 23 new models that valuably expand the portion of the phylogenetic tree covered by BiGG Models. The models include updates for four E. coli strains, S. aureus, and M. tuberculosis H37Rv and new models for five Plasmodium strains, stage specific models for Trypanosoma cruzi, C. difficile, and A. baumannii. We also expand the functionality for hosting multi-strain models, which have proven to be insightful in a variety of studies centered on comparisons of related strains. These multistrain collections are available for download on the model pages for iYL1228, STM_v1_0, and iCN718.
BiGG Models v1.4 introduces four new genome-scale models and a host of improvements, including:
- Merged reactions with identical stoichiometry but running in reverse directions. NOTE: Some BiGG IDs were affected by this change. For more details, see #261.
- DNA and protein sequences for genes
- Updated external database links with MetaNetX v3
- Added a new universal model on the Data Access page
- Added more info to namespace downloads on the Data Access page, including old identifiers
- More corrected formulae and charges
- Corrected gene mapping for yeast model
- Upgraded to ModelPolisher v1.7
- All Python 3 for bigg_models and cobradb
- And more: https://github.com/SBRG/bigg_models/issues?q=is%3Aissue+milestone%3Av1.4
This release removes a number of duplicate metabolites and reactions in BiGG.
A new model has been added: iCHOv1
ModelPolisher has been updated to version 1.5.
BiGG Models is out of beta!
This release adds a few new features and a ton of bug fixes:
- Added a model, iAF1260b
- New downloads for the entire reaction and metabolite namespaces
- External database link for reactions thanks to MetaNetX
- Upgraded to Escher 1.4. Now, clicking metabolites and reactions on the Escher map takes you to the BiGG page.
- Fixed some erroneous charges and objectives
- Comments are now handled directly with GitHub issues
- Using the latest release of ModelPolisher v1.2
The first BiGG Models release. This release is described in our publication:
King ZA, Lu JS, Dräger A, Miller PC, Federowicz S, Lerman JA, Ebrahim A, Palsson BO, and Lewis NE. (2015). BiGG Models: A platform for integrating, standardizing, and sharing genome-scale models. Nucl Acids Res. doi:10.1093/nar/gkv1049.