D1276 Nucleic Acids Research, 2012, Vol. 40, Database issue commentary could enrich the evaluation of hypotheses generated from phylogenetic inference. DATABASE AVAILABILITY EcoliWiki is freely available via the EcoliWiki website (http://ecoliwiki.net). SUPPLEMENTARY DATA Supplementary Data are available at Supplementary Methods. NAR Online: ACKNOWLEDGEMENTS We would like to thank Yasha Hartberg and Jerry Tsai for inspiring our initial experiments with wikis for annotation. We thank Lincoln Stein and Mike Cherry for hosting J.C.H. during early development of EcoliWiki and for valuable insights into model organism databases and com- munity annotation. Peter Karp generously helped us use EcoCyc to seed EcoliWiki with content about E. coli genes. Barry Wanner and Paul Thomas, as PIs of the EcoliHub and PortEco projects provided the subcontracts to support this work. Dave Clements helped contribute documentation and debugging. Jim Wilson donated the code for the project and Drew Endy graciously shared his laboratory’s edited/updated version of the T7 GenBank ﬁle. Gunnar von Heijne provided an updated version of TMHMM. We especially want to thank Jim Anderson at National Institutes of Health for deciding that wikis were a promising avenue for data resources, the biological wiki community for generously sharing their experience, information and code, and the users and contributors to EcoliWiki content. FUNDING EcoliWiki is funded as a component of PortEco from subcontracts from grant U24 GM077905-01 (2006-2009) and 1U24GM088849-01 (2009-present) from the NIH/ NIGMS. Funding for open access charge: NIH 1U24GM088849-01. Conﬂict of interest statement. None declared. REFERENCES 1. Gama-Castro,S., Salgado,H., Peralta-Gil,M., Santos-Zavaleta,A., Muniz-Rascado,L., Solano-Lira,H., Jimenez-Jacinto,V., Weiss,V., Garcia-Sotelo,J.S., Lopez-Fuentes,A. et al. (2011) RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units). Nucleic Acids Res., 39, D98–D105. 2. Glasner,J.D., Liss,P., Plunkett,G. III, Darling,A., Prasad,T., Rusch,M., Byrnes,A., Gilson,M., Biehl,B., Blattner,F.R. et al. (2003) ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res., 31, 147–151. 3. Keseler,I.M., Collado-Vides,J., Santos-Zavaleta,A., Peralta-Gil,M., Gama-Castro,S., Muniz-Rascado,L., Bonavides-Martinez,C., Paley,S., Krummenacker,M., Altman,T. et al. (2011) EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res., 39, D583–D590. 4. Misra,R.V., Horler,R.S., Reindl,W., Goryanin,II. and Thomas,G.H. (2005) EchoBASE: an integrated post-genomic database for Escherichia coli. Nucleic Acids Res., 33, D329–D333. 5. Rudd,K.E. (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res., 28, 60–64. 6. Medigue,C., Viari,A., Henaut,A. and Danchin,A. (1993) Colibri: a functional data base for the Escherichia coli genome. Microbiol. Rev., 57, 623–654. 7. Florez,L.A., Roppel,S.F., Schmeisky,A.G., Lammers,C.R. and Stulke,J. (2009) A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki. Database, 2009, bap012. 8. Hu,J.C., Karp,P.D., Keseler,I.M., Krummenacker,M. and Siegele,D.A. (2009) What we can learn about Escherichia coli through application of Gene Ontology. Trends Microbiol., 17, 269–278. 9. Lee,T.L. (2008) Big data: open-source format needed to aid wiki collaboration. Nature, 455, 461. 10. Hu,J.C., Aramayo,R., Bolser,D., Conway,T., Elsik,C.G., Gribskov,M., Kelder,T., Kihara,D., Knight,T.F. Jr, Pico,A.R. et al. (2008) The emerging world of wikis. Science, 320, 1289–1290. 11. Hayashi,K., Morooka,N., Yamamoto,Y., Fujita,K., Isono,K., Choi,S., Ohtsubo,E., Baba,T., Wanner,B.L., Mori,H. et al. (2006) Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Mol. Syst. Biol., 2, 2006 0007. 12. Blattner,F.R., Plunkett,G. III, Bloch,C.A., Perna,N.T., Burland,V., Riley,M., Collado-Vides,J., Glasner,J.D., Rode,C.K., Mayhew,G.F. et al. (1997) The complete genome sequence of Escherichia coli K-12. Science, 277, 1453–1462. 13. Durfee,T., Nelson,R., Baldwin,S., Plunkett,G. III, Burland,V., Mau,B., Petrosino,J.F., Qin,X., Muzny,D.M., Ayele,M. et al. (2008) The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J. Bacteriol., 190, 2597–2606. 14. Ferenci,T., Zhou,Z., Betteridge,T., Ren,Y., Liu,Y., Feng,L., Reeves,P.R. and Wang,L. (2009) Genomic sequencing reveals regulatory mutations and recombinational events in the widely used MC4100 lineage of Escherichia coli K-12. J. Bacteriol., 191, 4025–4029. 15. Jeong,H., Barbe,V., Lee,C.H., Vallenet,D., Yu,D.S., Choi,S.H., Couloux,A., Lee,S.W., Yoon,S.H., Cattolico,L. et al. (2009) Genome sequences of Escherichia coli B strains REL606 and BL21(DE3). J. Mol. Biol., 394, 644–652. 16. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403–410. 17. Demerec,M., Adelberg,E.A., Clark,A.J. and Hartman,P.E. (1966) A proposal for a uniform nomenclature in bacterial genetics. Genetics, 54, 61–76. 18. Sayers,E.W., Barrett,T., Benson,D.A., Bolton,E., Bryant,S.H., Canese,K., Chetvernin,V., Church,D.M., DiCuccio,M., Federhen,S. et al. (2011) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 39, D38–D51. 19. UniProt Consortium. (2011) Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res., 39, D214–D219. 20. Finn,R.D., Mistry,J., Tate,J., Coggill,P., Heger,A., Pollington,J.E., Gavin,O.L., Gunasekaran,P., Ceric,G., Forslund,K. et al. (2010) The Pfam protein families database. Nucleic Acids Res., 38, D211–D222. 21. Scheer,M., Grote,A., Chang,A., Schomburg,I., Munaretto,C., Rother,M., Sohngen,C., Stelzer,M., Thiele,J. and Schomburg,D. (2011) BRENDA, the enzyme information system in 2011. Nucleic Acids Res., 39, D670–D676. 22. Kiefer,F., Arnold,K., Kunzli,M., Bordoli,L. and Schwede,T. (2009) The SWISS-MODEL Repository and associated resources. Nucleic Acids Res., 37, D387–D392. 23. Pieper,U., Webb,B.M., Barkan,D.T., Schneidman-Duhovny,D., Schlessinger,A., Braberg,H., Yang,Z., Meng,E.C., Pettersen,E.F., Huang,C.C. et al. (2011) ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res., 39, D465–D474.