Computational Component 1: Computational Support for all Echinobase Objectives SUMMARY Echinobase is the only centralized and curated repository of genomic features for multiple species of echinoderms. The primary mode of access to Echinobase resources is through a web information system that displays content stored in annotation databases as useful and informative web pages and applications. This requires maintaining data and applications in a secure, high performance, web-accessible environment and ensuring that this system remains at peak performance through regular upgrading and maintenance of all software and hardware. This component addresses these needs by implementing a system build from a clone of Xenbase, the Xenopus model organism database. Through this approach Echinobase will acquire the database with a customized Chado schema, a java based web app, and various other tools developed and optimized by Xenbase personnel. In particular Echinobase will acquire a searchable gene expression database, and highly automated curation pipelines. Automated pipelines will be customized to load and contain echinoderm-specific data (i.e. genomes, transcriptomes, annotations, etc). The website frontend will be modified to project a unique Echinobase user interface that supports the unique features of Echinobase and its users preferences. Thus, through this proposal, Echinobase leverages more than 10 years and $8 million of Xenbase development and expertise. This provides an extensive improvement in functionality for Echinobase at a fraction of the cost of providing updates in isolation. This innovative and cost saving approach supports both expanded functionalities of Echinobase (i.e. the addition of a gene expression database) as well as broader initiatives of database coalescence. Computational support will be provided for the deployment of BioTapestry, a gene regulatory network modeling and viewing software addition proposed to integrate with Echinobase. This component will also provide critical support the data, curation, and software innovations from the other components of this application; it is the backbone of the entirety of Echinobase.
