FUNDING French projects (ANR REGLIS NT05-3 45205 and ANR MIRI BLAN08-1335497); French-UK projects (ANR- BBSRC MetNet4SysBio ANR-07-BSYS 003 02 and ANR-BBSRC SysTryp). Funding for open access charge: University of Glasgow. Conﬂict of interest statement. None declared. REFERENCES 1. Fiehn,O. (2001) Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks. Comp. Funct. Genomics, 2, 155–168. 2. Francke,C., Siezen,R.J. and Teusink,B. (2005) Reconstructing the metabolic network of a bacterium from its genome. Trends Microbiol., 13, 550–558. 3. Lacroix,V., Cottret,L., The´ bault,P. and Sagot,M.-F. (2008) An introduction to metabolic networks and their structural analysis. IEEE/ACM Trans. Comput. Biol. Bioinform., 5, 594–617. 4. Kanehisa,M., Goto,S., Furumichi,M., Tanabe,M. and Hirakawa,M. (2010) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res., 38, D355–D360. 5. Caspi,R., Altman,T., Dale,J.M., Dreher,K., Fulcher,C.A., Gilham,F., Kaipa,P., Karthikeyan,A.S., Kothari,A., Krummenacker,M. et al. (2010) The metacyc database of metabolic pathways and enzymes and the biocyc collection of pathway/genome databases. Nucleic Acids Res., 38, D473–D479. 6. Suhre,K. and Schmitt-Kopplin,P. (2008) MassTRIX: mass translator into pathways. Nucleic Acids Res., 36, W481–W484. 7. Okuda,S., Yamada,T., Hamajima,M., Itoh,M., Katayama,T., Bork,P., Goto,S. and Kanehisa,M. (2008) KEGG Atlas mapping for global analysis of metabolic pathways. Nucleic Acids Res., 36, W423–W426. 8. Paley,S.M. and Karp,P.D. (2006) The pathway tools cellular overview diagram and omics viewer. Nucleic Acids Res., 34, 3771–3778. 9. Kono,N., Arakawa,K., Ogawa,R., Kido,N., Oshita,K., Ikegami,K., Tamaki,S. and Tomita,M. (2009) Pathway projector: web-based zoomable pathway browser using kegg atlas and google maps api. PLoS ONE, 4, e7710 [11 November 2009, Epub ahead of print]. 10. Ginsburg,H. (2009) Caveat emptor: limitations of the automated reconstruction of metabolic pathways in Plasmodium. Trends Parasitol., 25, 37–43. 11. Yeh,I., Hanekamp,T., Tsoka,S., Karp,P.D. and Altman,R.B. (2004) Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery. Genome Res., 14, 917–924. Nucleic Acids Research, 2010, Vol. 38, Web Server issue W137 12. Handorf,T., Ebenho¨ h,O. and Heinrich,R. (2005) Expanding metabolic networks: scopes of compounds, robustness, and evolution. J. Mol. Evol., 61, 498–512. 13. Evsikov,A.V., Dolan,M.E., Genrich,M.P., Patek,E. and Bult,C.J. (2009) Mousecyc: a curated biochemical pathways database for the laboratory mouse. Genome Biol., 10, R84. 14. Keseler,I.M., Bonavides-Martı` nez,C., Collado-Vides,J., Gama- Castro,S., Gunsalus,R.P., Johnson,D.A., Krummenacker,M., Nolan,L.M., Paley,S., Paulsen,I.T. et al. (2009) Ecocyc: a comprehensive view of Escherichia coli biology. Nucleic Acids Res., 37, D464–D470. 15. Romero,P., Wagg,J., Green,M.L., Kaiser,D., Krummenacker,M. and Karp,P.D. (2005) Computational prediction of human metabolic pathways from the complete human genome. Genome Biol., 6, R2. 16. Vallenet,D., Labarre,L., Rouy,Z., Barbe,V., Bocs,S., Cruveiller,S., Lajus,A., Pascal,G., Scarpelli,C. and Me´ digue,C. (2006) Mage: a microbial genome annotation system supported by synteny results. Nucleic Acids Res., 34, 53–65. 17. Zhang,P., Foerster,H., Tissier,C.P., Mueller,L., Paley,S., Karp,P.D. and Rhee,S.Y. (2005) Metacyc and aracyc. metabolic pathway databases for plant research. Plant Physiol., 138, 27–37. 18. Arita,M. (2004) The metabolic world of Escherichia coli is not small. Proc. Natl Acad. Sci. USA, 101, 1543–1547. 19. Shannon,P., Markiel,A., Ozier,O., Baliga,N.S., Wang,J.T., Ramage,D., Amin,N., Schwikowski,B. and Ideker,T. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res., 13, 2498–2504. 20. Finney,A. and Hucka,M. (2003) Systems biology markup language: level 2 and beyond. Biochem. Soc. Trans., 31(Pt 6), 1472–1473. 21. Green,M.L. and Karp,P.D. (2004) A bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinformatics, 5, 76. 22. Kind,T. and Fiehn,O. (2006) Metabolomic database annotations via query of elemental compositions: mass accuracy is insuﬃcient even at less than 1 ppm. BMC Bioinformatics, 7, 234. 23. Jourdan,F., Cottret,L., Wildridge,D., Scheltema,R., Hillenweck,A., Barrett,M.P., Zalko,D., Watson,D.G. and Debrauwer,L. (2010) Use of reconstituted metabolic networks to assist in metabolomic data visualization and mining. Metabolomics, doi:10.1007/ s11306-009-0196-9. 24. Handorf,T., Christian,N., Ebenho¨ h,O. and Kahn,D. (2007) An environmental perspective on metabolism. J. Theor. Biol., 252, 530–537. 25. Wishart,D.S., Knox,C., Guo,A., Eisner,R., Young,N., Gautam,B., Hau,D.D., Psychogios,N., Dong,E., Bouatra,S. et al. (2009) Hmdb: a knowledgebase for the human metabolome. Nucleic Acids Res., 37, D603–D610. 26. Liu,W.-C., Lin,W.-H., Davis,A.J., Jorda` n,F., Yang,H.-T. and Hwang,M.-J. (2007) A network perspective on the topological importance of enzymes and their phylogenetic conservation. BMC Bioinformatics, 8, 121.