title: TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei.
abstract: The metabolic network of a cell represents the catabolic and anabolic reactions that interconvert small molecules (metabolites) through the activity of enzymes, transporters and non-catalyzed chemical reactions. Our understanding of individual metabolic networks is increasing as we learn more about the enzymes that are active in particular cells under particular conditions and as technologies advance to allow detailed measurements of the cellular metabolome. Metabolic network databases are of increasing importance in allowing us to contextualise data sets emerging from transcriptomic, proteomic and metabolomic experiments. Here we present a dynamic database, TrypanoCyc (http://www.metexplore.fr/trypanocyc/), which describes the generic and condition-specific metabolic network of Trypanosoma brucei, a parasitic protozoan responsible for human and animal African trypanosomiasis. In addition to enabling navigation through the BioCyc-based TrypanoCyc interface, we have also implemented a network-based representation of the information through MetExplore, yielding a novel environment in which to visualise the metabolism of this important parasite.
authors.affiliation: Institut National de la Recherche Agronomique (INRA), UMR1331, TOXALIM (Research Centre in Food Toxicology), Université de Toulouse, Toulouse, France.
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authors.lastname: Shameer
authors.affiliation: The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Flora J
authors.initials: FJ
authors.lastname: Logan-Klumpler
authors.affiliation: Institut National de la Recherche Agronomique (INRA), UMR1331, TOXALIM (Research Centre in Food Toxicology), Université de Toulouse, Toulouse, France.
authors.forename: Florence
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authors.lastname: Vinson
authors.affiliation: Institut National de la Recherche Agronomique (INRA), UMR441, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Auzeville, France.
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authors.lastname: Cottret
authors.affiliation: Institut National de la Recherche Agronomique (INRA), UMR1331, TOXALIM (Research Centre in Food Toxicology), Université de Toulouse, Toulouse, France.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Merlet
authors.affiliation: University of Glasgow, Glasgow, Scotland, G12 8QQ, UK.
authors.forename: Fiona
authors.initials: F
authors.lastname: Achcar
authors.affiliation: Ludwig-Maximilians-Universität München, Biocenter, 82152-Martinsried, Germany.
authors.forename: Michael
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authors.lastname: Boshart
authors.affiliation: The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Matthew
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authors.affiliation: Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, UK.
authors.forename: Rainer
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authors.affiliation: CNRS, Bordeaux, 33076, France.
authors.forename: Frédéric
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authors.lastname: Bringaud
authors.affiliation: University of Bern, Bern, CH-3012, Switzerland.
authors.forename: Peter
authors.initials: P
authors.lastname: Bütikofer
authors.affiliation: University of Glasgow, Glasgow, Scotland, G12 8QQ, UK.
authors.forename: Amy M
authors.initials: AM
authors.lastname: Cattanach
authors.affiliation: The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Bridget
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authors.lastname: Bannerman-Chukualim
authors.affiliation: Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia.
authors.forename: Darren J
authors.initials: DJ
authors.lastname: Creek
authors.affiliation: University of Glasgow, Glasgow, Scotland, G12 8QQ, UK.
authors.forename: Kathryn
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authors.lastname: Crouch
authors.affiliation: University of Glasgow, Glasgow, Scotland, G12 8QQ, UK.
authors.forename: Harry P
authors.initials: HP
authors.lastname: de Koning
authors.affiliation: European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, UK.
authors.forename: Hubert
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authors.affiliation: ISSC, UNESCO, F-75732 CEDEX 15, Paris, France.
authors.forename: Charles
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authors.lastname: Ebikeme
authors.affiliation: University of Dundee, Dundee, Scotland, DD1 4HN, UK.
authors.forename: Alan H
authors.initials: AH
authors.lastname: Fairlamb
authors.affiliation: University of Dundee, Dundee, Scotland, DD1 4HN, UK.
authors.forename: Michael A J
authors.initials: MA
authors.lastname: Ferguson
authors.affiliation: Divisionof Biomedical and Life Sciences, Lancaster University, Bailrigg, Lancaster, LA1 4YG, UK.
authors.forename: Michael L
authors.initials: ML
authors.lastname: Ginger
authors.affiliation: University of Liverpool, Liverpool, Merseyside L69 3BX, UK.
authors.forename: Christiane
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authors.lastname: Hertz-Fowler
authors.affiliation: Chalmers University of Technology, Kemivägen 10, 412 96, Göteborg, Sweden.
authors.forename: Eduard J
authors.initials: EJ
authors.lastname: Kerkhoven
authors.affiliation: Swiss Tropical and Public Health Institute, Socinstr. 57, Basel 4051, Switzerland.
authors.forename: Pascal
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authors.lastname: Mäser
authors.affiliation: University of Edinburgh, Mayfield Road, Edinburgh EH9 3JU, UK.
authors.forename: Paul A M
authors.initials: PA
authors.lastname: Michels
authors.affiliation: University of Glasgow, Glasgow, Scotland, G12 8QQ, UK.
authors.forename: Archana
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authors.lastname: Nayak
authors.affiliation: Texas Tech University, Lubbock, TX, USA.
authors.forename: David W
authors.initials: DW
authors.lastname: Nes
authors.affiliation: Trinity College Dublin, Dublin 2, Ireland.
authors.forename: Derek P
authors.initials: DP
authors.lastname: Nolan
authors.affiliation: Biomatters Inc. 60 Park Place, Suite 2100, Newark, NJ, USA.
authors.forename: Christian
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authors.lastname: Olsen
authors.affiliation: University of Liverpool, Liverpool, Merseyside L69 3BX, UK.
authors.forename: Fatima
authors.initials: F
authors.lastname: Silva-Franco
authors.affiliation: University of St Andrews, St Andrews, Scotland, KY16 9ST, UK.
authors.forename: Terry K
authors.initials: TK
authors.lastname: Smith
authors.affiliation: LSHTM, London, WC1E 7HT, UK.
authors.forename: Martin C
authors.initials: MC
authors.lastname: Taylor
authors.affiliation: Utrecht University, Utrecht, 3508 TD, The Netherlands Erasmus University Medical Center, Rotterdam, 3015 CE, The Netherlands.
authors.forename: Aloysius G M
authors.initials: AG
authors.lastname: Tielens
authors.affiliation: Divisionof Biomedical and Life Sciences, Lancaster University, Bailrigg, Lancaster, LA1 4YG, UK.
authors.forename: Michael D
authors.initials: MD
authors.lastname: Urbaniak
authors.affiliation: Erasmus University Medical Center, Rotterdam, 3015 CE, The Netherlands.
authors.forename: Jaap J
authors.initials: JJ
authors.lastname: van Hellemond
authors.affiliation: University of Glasgow, Glasgow, Scotland, G12 8QQ, UK.
authors.forename: Isabel M
authors.initials: IM
authors.lastname: Vincent
authors.affiliation: Queen Mary University of London, London E1 4NS, UK.
authors.forename: Shane R
authors.initials: SR
authors.lastname: Wilkinson
authors.affiliation: University of Dundee, Dundee, Scotland, DD1 4HN, UK.
authors.forename: Susan
authors.initials: S
authors.lastname: Wyllie
authors.affiliation: University of Louvain, Brussels, B-1200, Belgium.
authors.forename: Fred R
authors.initials: FR
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authors.affiliation: University of Glasgow, Glasgow, Scotland, G12 8QQ, UK Fabien.Jourdan@toulouse.inra.fr.
authors.forename: Michael P
authors.initials: MP
authors.lastname: Barrett
authors.affiliation: Institut National de la Recherche Agronomique (INRA), UMR1331, TOXALIM (Research Centre in Food Toxicology), Université de Toulouse, Toulouse, France Fabien.Jourdan@toulouse.inra.fr.
authors.forename: Fabien
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authors.lastname: Jourdan
mesh_terms: D057225:Data Mining; D062126:Databases, Chemical; D020407:Internet; D053858:Metabolic Networks and Pathways; D040901:Proteomics; D014346:Trypanosoma brucei brucei / Q000235:genetics / Q000378:metabolism*