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!

Contributors

jotech, jonasoh, and 4 other contributors

Assets 2

10 Feb 10:41

jotech

v1.2

fbb651e

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

Assets 2

25 Sep 12:04

jotech

v1.1

91e477d

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)