W32 Nucleic Acids Research, 2009, Vol. 37, Web Server issue SUPPLEMENTARY DATA Supplementary Data are available at NAR Online. ACKNOWLEDGEMENTS We thank Andrew Pohorille of NASA’s Division of Astrobiology and Fundamental Biology who provided seed support for BioLingua/BioBIKE. Others who have contributed signiﬁcantly to this work include Pat Langley, Marc Santoro, Michiko Kato, James Mastro, Bogdan Mihai, Emily Niman, Craig Noe, Peter Seibel, Hien Truong, Andy Whittam, Richard Waldinger, Carolyn Talcott and Merill Knapp. Richard Waldinger and several anonymous reviewers provided valuable comments on various drafts of this article. FUNDING National Science Foundation (DBI-0516378, DBI- 0850146 to J.E.); the National Aeronautics and Space Administration (JRIs: NCC2-5555, NCC2-5462, NCC2- 5471 to J.S.); software grants from Franz, Inc. and LispWorks, Inc. Funding for open access charge: Jeﬀ Shrager. Conﬂict of interest statement. None declared. REFERENCES 1. Massar,J.P., Travers,M., Elhai,J. and Shrager,J. (2005) BioLingua: a programmable knowledge environment for biologists. Bioinformatics, 21, 199–207. 2. Kanehisa,M., Goto,S., Hattori,M., Aoki-Kinoshita,K.F., Itoh,M., Kawashima,S., Katayama,T., Araki,M. and Hirakawa,M. (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res., 34, D354–D357. 3. Altschul,S.F., Madden,T.L., Schaﬀer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389–3402. 4. Ihaka,R. and Gentleman,R. (1996) R: a language for data analysis and graphics. J. Comput. Graphical Stat., 5, 299–314. 5. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-speciﬁc gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673–4680. 6. Bailey,T.L., Williams,N., Misleh,C. and Li,W.W. (2006) MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res., 34, W369–W373. 7. Washietl,S., Hofacker,I.L. and Stadler,P.F. (2005) Fast and reliable prediction of noncoding RNAs. Proc. Natl Acad. Sci. USA, 102, 2454–2459. 8. Felsenstein,J. (2005) PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle. 9. Green,T.R.G. and Petre,M. (1996) Usability analysis of visual programming environments: a ‘cognitive dimensions’ framework. J. Visual. Lang. Comput., 7, 131–174. 10. Ow,S.Y., Cardona,L., Taton,A., Magnuson,A., Lindblad,P., Stensjo¨ ,K. and Wright,P.C. (2009) Quantitative overview of N2 Fixation in Nostoc punctiforme ATCC 29133 through cellular enrichments and iTRAQ shotgun proteomics. J. Proteome Res., 8, 187–198. 11. Elhai,J., Kato,M., Cousins,S., Lindblad,P. and Costa,J.L. (2008) Very small mobile repeated elements in cyanobacterial genomes. Genome Res., 18, 1484–1499. 12. Maglott,D., Ostell,J., Pruitt,K.D. and Tatsuova,T. (2007) Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res., 35, D26–D31. 13. Markowitz,V.M., Szeto,E., Palaniappan,K., Grechkin,Y., Chu,K., Chen,I-M.A., Dubchak,I., Anderson,I., Lykidis,A., Mavromatis,K., Ivanova,N.N. and Kyrpides,N.C. (2008) The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res., 36, D528–D533. 14. Johnson,M., Zaratskaya,I., Raytselis,Y., Merezhuk,Y., McGinnis,S. and Madden,T.L. (2008) NCBI Blast: a better web interface. Nucleic Acids Res., 36, W5–W9. 15. Hull,D., Wolstencroft,K., Stevens,R., Goble,C., Pocock,M.R., Li,P. and Oinn,T. (2006) Taverna: a tool for building and running workﬂows of services. Nucleic Acids Res., 34, W729–W732. 16. Stajich,J.E., Block,D., Boulez,K., Brenner,S.E., Chervitz,S.A., Dagdigian,C., Fuellen,G., Gilbert,J.G., Korf,I., Lapp,H. et al. (2002) The Bioperl toolkit: Perl modules for the life sciences. Genome Res., 12, 1611–1618. 17. Shrager,J., Waldinger,R., Stickel,M. and Massar,J.P. (2007) Deductive Biocomputing. PLoS ONE, 2, e339. 18. Travers,M., Massar,J.P. and Shrager,J. (2005) The (re)birth of the knowledge operating system. Proceedings of the International Lisp Conference. Assoc. of Lisp Users (ALU), Stanford, CA, pp. 357–365. 19. Clamp,M., Cuﬀ,J., Searle,S.M. and Barton,G.J. (2004) The Jalview Java alignment editor. Bioinformatics, 20, 426–427. 20. Alhapel,A., Darley,D.J., Wagener,N., Eckel,E., Elsner,N. and Pierik,A.J. (2006) Molecular and functional analysis of nicotinate catabolism in Eubacterium barkeri. Proc. Acad. Sci. USA, 103, 12341–12346.