Xenbase - Computation

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Component: COMPUTATION PROJECT SUMMARY/ABSTRACT The goal of the Computation component is to keep Xenbase operational, reliable, and responsive, to maintain and upgrade the hardware, infrastructure, software and systems necessary for peak performance and to develop and support the proposed improvements described in other sections of this application. Knowledgebases like Xenbase must integrate and process a diverse array of data and provide users with tools and interfaces to query and explore its content. These are all computational processes. In addition, Xenbase must interface with external databases and resources (NCBI, the AGR, publishers) to synchronize content and to provide annotated Xenopus data. Although invisible to the user, there is a considerable amount of computing that occurs behind the scenes every time a researcher uses Xenbase. Xenbase is a complex computing environment consisting of multiple, separate databases, many different software applications, user and curator web interfaces, and many automated data exchange pipelines. To ensure stability and enhance performance, tool sets are isolated on their own virtual machines (VMs) - we currently run ~20 VMs in our private cloud - and we constantly monitor, test, maintain, and fix bugs to keep it all running smoothly. Each time new software is implemented, we test it on isolated VMs, then optimize and integrate it with existing systems. All of this activity is contained within the Computation component and is paramount to achieving our overall project goals. In this component, we describe the computing work needed to maintain current functionality, generate custom content and the resources necessary to implement expansions and improvements over the next award cycle. Aim 1. Upgrade hardware, servers and software stack to increase capacity and expanded functionalities. Aim 2. Maintain and expand computation of Xenbase content. Aim 3. Manage and monitor networking and systems