Tech-2 Technology Development -2 describes the new features that we need to add to Xenbase in order to achieve our overall goals. Xenbase has a long list of essential additions and upgrades to be performed. This prioritized list was developed through feedback from the External Advisory Board (EAB), the Xenopus PI meeting and user surveys. These projects will require work at multiple levels of our software stack, from database modifications, web application development and user interfaces, to upgrades, maintenance, testing, bug fixing. Our experienced development team will continue to seek input from other MODs leveraging solutions that have working in other Resources.
Our specific aims are:
Aim 1 - Deploy JBrowse and WebApollo Aim 2 - Develop Support Vector Machine tools Aim 3 - Build support for new content types including robust graph display and visualization tools, protein-protein and gene interaction content, Non-coding RNAs and alternative splicing support and genome editing support.

National Institute of Health (NIH)
Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD)
Biotechnology Resource Grants (P41)
Project #
Application #
Study Section
Special Emphasis Panel (ZHD1)
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Cincinnati Children's Hospital Medical Center
United States
Zip Code
Vize, Peter D; Zorn, Aaron M (2017) Xenopus genomic data and browser resources. Dev Biol 426:194-199
Session, Adam M; Uno, Yoshinobu; Kwon, Taejoon et al. (2016) Genome evolution in the allotetraploid frog Xenopus laevis. Nature 538:336-343
Deans, Andrew R; Lewis, Suzanna E; Huala, Eva et al. (2015) Finding our way through phenotypes. PLoS Biol 13:e1002033
Vize, Peter D; Liu, Yu; Karimi, Kamran (2015) Database and Informatic Challenges in Representing Both Diploid and Tetraploid Xenopus Species in Xenbase. Cytogenet Genome Res 145:278-82
Grant, Ian M; Balcha, Dawit; Hao, Tong et al. (2015) The Xenopus ORFeome: A resource that enables functional genomics. Dev Biol 408:345-57
James-Zorn, Christina; Ponferrada, Virgillio G; Burns, Kevin A et al. (2015) Xenbase: Core features, data acquisition, and data processing. Genesis 53:486-97
Karpinka, J Brad; Fortriede, Joshua D; Burns, Kevin A et al. (2015) Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes. Nucleic Acids Res 43:D756-63
Karimi, Kamran; Vize, Peter D (2014) The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud. Database (Oxford) 2014:
Segerdell, Erik; Ponferrada, Virgilio G; James-Zorn, Christina et al. (2013) Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase. J Biomed Semantics 4:31
James-Zorn, Christina; Ponferrada, Virgilio G; Jarabek, Chris J et al. (2013) Xenbase: expansion and updates of the Xenopus model organism database. Nucleic Acids Res 41:D865-70

Showing the most recent 10 out of 18 publications