• Open Access

Web alert: systems biology relevant to microbial metabolism

An annotated selection of World Wide Web sites relevant to the topics in Microbial Biotechnology

Authors

  • Lawrence P. Wackett

    1. McKnight Professor and Head
      Microbial Biochemistry and Biotechnology
      Department of Biochemistry Molecular Biology and Biophysics University of Minnesota St Paul, MN 55108, USA
    Search for more papers by this author

MetaCyc database

http://metacyc.org/

MetaCyc is a database of experimentally determined metabolic pathways from over 900 organisms, mostly microorganisms.

KEGG pathway database

http://www.genome.ad.jp/kegg/metabolism.html

The KEGG database consists of pathway maps that have hypertext links to further information on compounds, enzymes and genes. It extensively covers metabolism found in diverse organisms.

Biocatalysis/Biodegradation database

http://umbbd.msi.umn.edu/

The Biocatalysis/Biodegradation database is a metabolism database that focuses on catabolic pathways found in microorganisms. It is highly curated with links to many other databases.

BioPathways Consortium

http://www.biopathways.org/

The BioPathways Consortium is designed to promote the development of computational pathways biology. It does this by supporting the development and use of open technologies, standards, and resources for representing and analysing pathway information.

Pathguide: the pathway resource list

http://www.pathguide.org/

The Pathguide is a curated list of approximately 240 online biological pathway resources. A major category is for metabolic pathway resources.

BioModels database

http://www.ebi.ac.uk/biomodels/

The BioModels database stores and provides access to published mathematical models relating to biological processes. Models are linked to relevant data resources, such as publications, databases of compounds and pathways, and controlled vocabularies.

Metabolic pathfinding database

http://www.bigre.ulb.ac.be/Users/didier/pathfinding/

The metabolic pathfinding database provides tools for selecting the shortest path in a metabolic network to generate biochemically relevant pathways. The metabolic graph that is used is derived from the reactions and compounds found in the KEGG database.

Microbial metabolism prediction

http://umbbd.msi.umn.edu/predict/

The microbial metabolism prediction system uses metabolic rules to generate metabolites predicted from any starting organic compound entered by the user. The metabolic rules are based largely on reactions found in the Biocatalysis/Biodegradation database.

OptStrain:Metabolic pathway discovery and design

http://maranas.che.psu.edu/pub/pharkya-maranas05.pdf

This computational tool uses a metabolic database and combinatorial optimization to find ideal pathways for transiting from one metabolite to another. The major use is for metabolic engineering to generate valuable compounds from cheaper precursors.

Pathway tools website

http://bioinformatics.ai.sri.com/ptools/

The Pathway tools site was put up to provide access for the scientific community to computational tools to develop databases for organisms, metabolic networks and navigating through networks.

PathAligner

http://bibiserv.techfak.uni-bielefeld.de/pathaligner/

PathAligner is designed to retrieve metabolic pathways and alignment them. Metabolic pathways are reconstructed from their components: metabolites, enzymes and genes.

Evolution of molecular biology into systems biology

http://www.nature.com/nbt/journal/v22/n10/full/nbt1020.html

This web article provides an excellent historical overview of developments in molecular aspects of biology leading up to the current field of systems biology.

European systems biology

http://www.systembiology.net/

This webpage provides a list of links to resources for systems biology researchers.

Computational systems biology

http://www.genoscope.cns.fr/spip/Computational-Systems-Biology-NeMo.html

Genoscope was created to handle sequence data from the human genome project, but has more recently refocused on using systems biology, largely with microbial systems, for reducing pollution and reducing dependence on fossil fuels.

Kanehisa laboratory publications

http://kanehisa.kuicr.kyoto-u.ac.jp/

The Kanehisa laboratory, which developed the KEGG database, analyses metabolic data to derive insights into biological structure and function.

Ancillary