Gapseq Versions Save

• 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

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

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

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

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