New major features and updates
- All dependencies on R-packages of the sybil family (sybil, sybilSBML, glpkAPI, cplexAPI) are now removed. Instead, the R-package 'cobrar' now serves as a toolbox for constraint-based metabolic modeling and interface to the LP solver 'glpk'. a771d5d
- Optimised protein complex detection and prediction. fd523d8 a0b1380
- More gapseq reactions are mapped to pathways. 1d0e874
New minor features and updates
- Optimised download of reference protein sequences from UniProt. 5365dce
- log reaction in skip blast mode. 12a8e30
- Transport reactions are now added to subsystems. 690bece
- use only reviewed sequences in case of multiple candidates. 4732ccb
- enable search for reactions in pathway database. 552f28c
- improved handling of undefined subunits in protein complexes. a0b1380
Microbial physiology
- Transfer EC 2.4.1.129 to EC 2.4.99.28. 4e6663d
- L-leucine degradation via reductive Stickland reaction. bf5d31b
- New pathway for Arginine biosynthesis. 792194b
Bug fixes
- Gap-filling (minimum required growth rate is now enforced). fb7fbcb
- Gap-filling (non-feasible solutions, which are rare, are now handled and logged). 568dfa8
- Added Nickel ions to the "gut.csv" gap-fill medium. 9b5d3ac
The release name is a reference to Radiolab's podcast episode "Even the Worst Laid Plans?" (August 19, 2010), which covered a short story about microbes in the Berkeley Pit, an open pit of a former copper mine in Butte, Montana, US.