title: BioMiner--modeling, analyzing, and visualizing biochemical pathways and networks.
abstract: BACKGROUND
  Understanding the biochemistry of a newly sequenced organism is an essential task for post-genomic analysis. Since, however, genome and array data grow much faster than biochemical information, it is necessary to infer reactions by comparative analysis. No integrated and easy to use software tool for this purpose exists as yet.
  
  
  RESULTS
  We present a new software system--BioMiner--for analyzing and visualizing biochemical pathways and networks. BioMiner is based on a new comprehensive, extensible and reusable data model--BioCore--which can be used to model biochemical pathways and networks. As a first application we present PathFinder, a new tool predicting biochemical pathways by comparing groups of related organisms based on sequence similarity. We successfully tested PathFinder with a number of experiments, e.g. the well studied glycolysis in bacteria. Additionally, an application called PathViewer for the visualization of metabolic networks is presented. PathViewer is the first application we are aware of which supports the graphical comparison of metabolic networks of different organisms.
  
  
  BACKGROUND
  http://www.zbi.uni-saarland.de/chair/projects/BioMiner
  
  
  BACKGROUND
  Additional information on experimental results can be found on our web site.
authors.affiliation: Center for Bioinformatics, Saarland University, Saarbrücken, Germany.
authors.forename: M
authors.initials: M
authors.lastname: Sirava
authors.forename: T
authors.initials: T
authors.lastname: Schäfer
authors.forename: M
authors.initials: M
authors.lastname: Eiglsperger
authors.forename: M
authors.initials: M
authors.lastname: Kaufmann
authors.forename: O
authors.initials: O
authors.lastname: Kohlbacher
authors.forename: E
authors.initials: E
authors.lastname: Bornberg-Bauer
authors.forename: H P
authors.initials: HP
authors.lastname: Lenhof
mesh_terms: D001671:Biochemistry / Q000379:methods; D003196:Computer Graphics; D003198:Computer Simulation; D004734:Energy Metabolism / Q000502:physiology*; D005786:Gene Expression Regulation / Q000502:physiology*; D008954:Models, Biological; D009097:Multienzyme Complexes / Q000378:metabolism; D015398:Signal Transduction / Q000502:physiology*; D012984:Software; D014584:User-Computer Interface
chemical_list: D009097:Multienzyme Complexes