Berkeley Pit (v1.4.0)

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

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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.

Microbial circle (v1.3.1)

• same release as in v1.3, only the version number was corrected

Microbial circle

Kandinski 1923: Circles in a Circle [1]

new major features

• gapseq adapt: turn on or off growth for a list of carbon sources a647ef5 and fix growth rate 2742adb
• improved speed by protein fasta input 4259a6b 642549c ab34887 0d0123e
• pan-draft: species-level models from metagenomes 2e808c54 documentation
• gapseq test-long: fast, comprehensive test run that reconstructs ecoli core model 46f973a

new minor features

• screen for carbon sources and fermentation products 7ec79b3
• updated medium prediction f89fdbd dfaccb9 a6f2aa3 a9510ce 9047eeb
• handling of temporary files 2e34daa
• improved protein complex prediction 780e528 653be24
• integrated new uniprot API access 82ff4ad 3c936ab
• better macos/FreeBSD support b4b2c94 #145
• user-defined biomass 52dd5c8
• reference sequence download from zenodo e66a9c7
• updated rxn weight calculation 503af0e
• added M9 medium 3d31919 and updated TSB medium 73abaab
• updated pathway database metacyc v27 024476a

microbial physiology

• methanogenesis 5ba14b1 9da5f10
• rnf complex 0bea241
• bile acid pathways f715432 0293ab7
• arginine degradation fcf6deb
• aromatics degradation 140d619
• stickland fermentation 82222bd b3a904d 380d52c
• arginine degradation 4b6b6f3
• pyridoxal biosynthesis 7307765
• malolactic enzyme 02deb83
• lysin degradation 098aee6
• xylulose degradation 0ef6d9d
• inuline degradation 72ff3e0
• dehalogenation 0a77c68 deb77f2
• oxalate/formate antiporter 9e85ab1 0f03bf3
• chlorobenzene degradation 2d739a5
• glycan degradation fb3631d

bug fixes

• gpr rules e2f3209
• test script 6225829
• sbml 6fefcb5 8777e8c 8767b04 139b3b4 #153
• network coverage 0bc1278
• offline mode b27d588
• key enzyme handling 43b7241
• sequence download 55368fc 91e64d2
• gapseq find 8626e07
• gapseq find-transport 3e2d939
• output files d3a1bf2

contributors

The gapseq core team (@Waschina, @jotech) would like to thank for their support: @nicola-debernardini, @jonasoh, Anna Burrichter, @ArnaudBelcour, @jchmiel4
We appriacte all your help!

Xlthlx's moon (1.2)

• Improvement of reaction and metabolite database for archaeal metabolism (incl. methanogenesis, mevalonate pathways, chorismate biosynthesis)
• Anaerobic Degradation pathways for secondary plant metabolites (incl. daidzin, daidzein, quercetin, genistein, sulfoquinovose)
• New module for automated prediction of gapfill-/growth- medium
• Improved performance of SBML export
• gapseq version tags in main output files
• Improved prediction of reactions with multiple associated EC-numbers
• Revised reaction and metabolite database for C1-metabolism (i.e. Wood-Ljungdahl pathway)
• improved representation of nitrogen metabolism (e.g. ammonia oxidation)
• new bile acids pathways (deamination, 7dehydroxylation, epimerization)
• easier installation via conda libsbml package
• support to adjust for environmental conditions (low/high h2)
• enabled support for photosynthesis
• full model construction on the fly
• xylan degradation
• medium prediction
• improved threonine biosynthesis prediction
• updated reaction sequences (uniprot) and pathway databases (metacyc)
• revised transporter prediction
• extended nucleotide metabolism
• updated archaeal pathways

Through the guts of a beggar

A man may fish with the worm that hath eat of a king, and eat of the fish that hath fed of that worm ... a king may go a progress through the guts of a beggar (Hamlet: act 4, scene 3)

• archaea support (especially methanogens)
• new documentation
• improved fiber degradation
• extended electron bifurcation reactions
• improved anaerobic vitamine biosynthesis
• more cases of extracellular degradation
• added 'gapseq adapt' to manually improve models
• enabled photosynthesis
• many smaller bugfixes

mumbo jumbo

• official productive release
• used for results in the gapseq manuscript

Darwinian turtle

• draft model generation
• enzyme complex detection
• gapfilling by bitscore weight

Baby tiger

Preliminary release used in first studies

• pathway analysis for metacyc, kegg, seed, and custom pathways
• gapfilling of metabolic models
• draft model creation
• a lot of corrections in seed reaction database
• transporter prediction