Xenbase

Xenbase is a Model Organism Database (MOD), providing informatics resources, as well as genomic and biological data on Xenopus frogs.Xenbase has been available since 1999, and covers both X. laevis and X. tropicalis Xenopus varieties. As of 2013 all of its services are running on virtual machines in a private cloud environment, making it one of the first MODs to do so. Other than hosting genomics data and tools, Xenbase supports the Xenopus research community though profiles for researchers and laboratories, and job and events postings. Xenbase is a Model Organism Database (MOD), providing informatics resources, as well as genomic and biological data on Xenopus frogs.Xenbase has been available since 1999, and covers both X. laevis and X. tropicalis Xenopus varieties. As of 2013 all of its services are running on virtual machines in a private cloud environment, making it one of the first MODs to do so. Other than hosting genomics data and tools, Xenbase supports the Xenopus research community though profiles for researchers and laboratories, and job and events postings. Xenbase runs in a cloud environment. Its virtual machines are running in a VMware vSphere environment on two servers, with automatic load balancing and fault tolerance. Xenbase software uses Java, JSP, JavaScript, AJAX, XML, and CSS. It also uses IBM's WebSphere Application Server and the IBM DB2 database. The Xenopus model organism is responsible for large amounts of new knowledge on embryonic development and cell biology. Xenopus has a number of unique experimental advantages as a vertebrate model. Paramount among these is the robustness of early embryos and their amenability to microinjection and microsurgery. This makes them a particularly attractive system for testing the ectopic activity of gene products and loss-of-function experiments using antagonizing reagents such as morpholinos, dominant-negatives and neomorphic proteins. Morpholinos are synthetic oligonucleotides that can be used to inhibit nuclear RNA splicing or mRNA translation and are the common gene inhibition reagent in Xenopus as neither siRNA or miRNA have yet been shown to reproducibly function in frog embryos. Xenopus embryos develop very quickly and form a full set of differentiated tissues within days of fertilization, allowing rapid analysis of the effects of manipulating embryonic gene expression. The large size of embryos and amenability to microinjection also makes them extremely well suited to microarray approaches. Furthermore, these same characteristics make Xenopus, one of the few vertebrate model organisms suited for chemical screens. Xenbase provides a large database of images illustrating the full genome, movies detailing embryogenesis, and multiple online tools useful for designing and conducting experiments using Xenopus. Xenopus can be used to model human diseases caused by common genes. Xenbase supports this by mapping Disease Ontology and OMIM diseases to Xenopus genes and publications. Xenbase provides many tools useful for both professional research as well as academic learning. Highlighted below are a few of the tools, along with a brief description. For full details on provided tools, users are referred to Xenbase's publications . A detailed introduction to using Xenabse comes in . The Nobel Prize for Medicine or Physiology was awarded to John B. Gurdon and Shinya Yamanaka on October 8, 2012. for nuclear reprogramming in Xenopus. Importance: Gurdon's experiments challenged the dogma of the time which suggested that the nucleus of a differentiated cell is committed to their fate (Example: a liver cell nucleus remains a liver cell nucleus and cannot return to an undifferentiated state).