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!