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Bioinformatics Our group runs the Xenopus model organism database, Xenbase. This DB integrates developmental and genomic data on frog development. It is presently a DB2/websphere implementation running on linux. It includes a diverse range of information ranging from gene sequences, scientific literature, images, movies, anatomy and more. We are presently developing a detailed anatomical and developmental ontology to bridge these different data forms and enhance high-level querying. This database implemented a unique community based data annotation system and has many innovative features. More info: xenbase.org the Xenopus model organism database 3dexpress.org, our db2 database of 3d gene expression patterns using UV mapping (use firefox with a shockwave plugin) Visit the Xenopus database front end Key references: Hellsten, U, Harland, R.M., Gilchrist, M.J., Hendrix, D., Jurka, J., Kapitonov, V., Ovcharenko, I., Putnam, N.H., Shu, S., Taher, L, Blitz, I.L., Blumberg, B., Dichmann, D.S., Dubchak, I., Amaya, E., Detter, J.C., Fletcher, R., Gerhard, D.S., Goodstein, D., Graves, T., Grigoriev, I.V., Grimwood, .J, Kawashima, T., Lindquist, E., Lucas, S.M., Mead, P.E., Mitros, T., Ogino, H., Ohta, Y., Poliakov, A.V., Pollet, N., Robert, J., Salamov, A., Sater, A.K., Schmutz, J., Terry, A., Vize, P.D., Warren, W.C., Wells, D., Wills, A., Wilson, R.K., Zimmerman, L.B., Zorn, A.M., Grainger, R., Grammer, T., Khokha, M.K., Richardson, P.M. and Rokhsar, D.S. (2010) The genome of the western clawed frog Xenopus tropicalis. Science 328: 633-636. Jeff B. Bowes, Kevin A. Snyder, Erik Segerdell, Chris J. Jarabek, Kenan Azam, Aaron M. Zorn and Peter D. Vize (2010). Xenbase: Gene expression and improved integration. Nucl. Acids Res. doi:10.1093/nar/gkp953 Segerdell, E., Bowes, J.B., Pollet, N. and Vize, P.D. (2008) The Xenopus Anatomical Ontology: a comprehensive map of development in a model vertebrate. BMC Developmental Biology 2008, 8: 92-98. Bowes, J.B., Snyder, K.. Segerdell, E., Gibb, R., Jarabek, C., Noumen, E., Pollet, N. and Vize, P.D. (2008). Xenbase: a Xenopus biology and genomics resource. Nucl. Acids. Res. 36: D761-D767. Vize, P.D. and Gerth, V.E. (2007). Adaptation of videogame UVW mapping to 3D visualization of gene expression patterns. Proc. SPIE, in press. Gerth, V.E., Katsuyama, K., Snyder, K., Bowes, J.B., Kitayama, A., Ueno, N. and Vize, P.D. (2007) Projecting 2D gene expression data into 3 and 4D space. Devel. Dynamics, 236: 1036-1043. Gerth, V.E., Zhou, X. and Vize, P.D. (2005). Nephrin expression and 3D morphogenesis of the Xenopus pronephric glomus. Developmental Dynamics, 233: 1131-1139 Gerth, V.E. and Vize, P.D. (2004). A Java tool for dynamic web-based 3D visualization of anatomy and overlapping gene or protein expression patterns. Bioinformatics, (see PubMed). Vize, P.D. (2004). Internet tools for cell and developmental biologists. In "The Internet for Molecular Biologists", R.Horton and C. Sansom Eds. The Practical Approach Series, Oxford University Press. ISBN 0199638888 Bowes, J.B. and Vize, P.D. (2003). Xenopus informatics. Current Genomics 4: 653-664 Vize, P.D. (2001). On-line analysis of development. Bioessays, 23: 549-554

Example of one of the 14,000 gene records generated by Xenbase