Enzyme2

Enzyme2 is a command line tool to process and evaluate metabolic networks and microarray data. It uses the Affymetrix (Microarray), BioCyc (Pathway/Genome) and GO (Ontology) databases.

Alternatively, you can also use Bioconductor, Cytoscape, Galaxy, Mayday, MeV or Vanted for metabolic networks and microarray data analysis.

Version 4.9.29

This program is owned by Heiko Stark. It can be used free of charge for non-commercial use. For the common citations in publications please use the following entry “Enzyme2 software (Heiko Stark, Jena, Germany, URL: http://starkrats.de).


An installer for Windows and Linux can be found here: Software

enzyme2 32bit (Windows, ReactOS & Wine/Darwine)
enzyme2 64bit (Windows & Wine/Darwine)

enzyme2 32bit (Linux)
enzyme2 64bit (Linux)

Note: Intel 32bit runs also on 64bit systems, but only with 4GB memory!

//!enzyme2
// This is a comment for the enzyme macro - you can use this macro like a programing language
// For more infos, please see http://stark-jena.de | enzyme
// Copyright (c) 2011-201 by Heiko Stark

load.metacycle "reactions.dat"
load.metacycle.compound "compounds.dat"
load.metacycle.enzyme "enzrxns.dat" // fill up enzyme names
load.metacycle.gene "genes.dat" // fill up gene names
load.metacycle.pathway "pathways.dat" // fill up pathway names

print "How many organisms? : " organism.size // only if you use more than one organism
print "How many metabolites? : " metabolite.size
print "How many reactions? : " reaction.size
print "How many enzymes? : " reaction.enzyme.size // only if you load additional enzymes (load.metacycle.enzyme)
print "How many reaction genes? : " reaction.gene.size // only if you load additional genes (load.metacycle.gene)
print "How many genes? : " regulator.gene.size // only if you load additional genes (load.metacycle.gene)
print "How many pathways? : " reaction.pathway.size // only if you load additional pathways (load.metacycle.pathway)

load.ontology "gene_ontology_ext.obo"
load.kegg "mmu.list"

annotation.clear 
database.save "database.fast" // full database

//!enzyme2
// This is a comment for the enzyme macro - you can use this macro like a programing language
// For more infos, please see http://stark-jena.de | enzyme
// Copyright (c) 2011-2015 by Heiko Stark

// Show statistics
metabolite.clearname := true // false S###S | true metabolite
metabolite.withlocation := true // false metabolite | true metabolite[?]

ifexists "database.fast"
then
	load.database "database.fast"
end
else
	print "No database found!"
	stop
end

print "How many organisms? : " organism.size // only if you use more than one organism
print "How many metabolites? : " metabolite.size
print "How many reactions? : " reaction.size

io.dir.hardchange "Complete"
pathway.complete
print "Reactions: " pathway.size

pathway.save "pathway.list" index
pathway.save "pathway.eclist" ec
pathway.save "pathway.namelist" name
pathway.savepathways "pathways.name" sortname
pathway.savepathways "pathways.count" sortcount
pathway.savepathways "pathways.index" sortindex
pathway.savepathways "pathways.group" group
pathway.saveignore "pathwayignore.eclist" ec
pathway.savemetaused "pathwaymetaused.list" index
pathway.savemetaused "pathwaymetaused.namelist" name
pathway.savemetacount "pathwaymetacount.list" index
pathway.savemetacount "pathwaymetacount.namelist" name

metabolite.clearname := false
pathway.savemetatool "pathway.dat" index auto
metabolite.clearname := true

pathway.savemetatool "pathway.ecdat" ec auto
pathway.savegml "pathway.gml" 18

metabolite.clearname := false
reaction.save "reaction.idlist" index
metabolite.clearname := true

reaction.save "reaction.eclist" ec
reaction.save "reaction.list" index
// metabolite.sort // after sorting the metabolite the reaction is empty
metabolite.save "metabolite.list" index

Used for the Gerontoshield project.


And used for these investigations:


If you want to send me a bug report or have some suggestions about what future versions of ‘enzyme2’ should support you can contact me either by email (bugs[@]starkrats[dot]de).