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BBDTC Updates

Get the latest updates on the Biomedical Big Data Training Collaborative, including VM hosting and architecture, import/export Xblocks, and the BBDTC toolbox. Learn about the goals and vision of the collaborative and explore the user interface, repository content, and course viewer. Discover the Virtual Machine Toolbox and upcoming courses. Stay informed with the BBDTC updates.

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BBDTC Updates

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  1. BBDTC Updates Biomedical Big Data Training Collaborative biobigdata.ucsd.edu

  2. Outline • Introduction to BBDTC and updates • BBDTC VM Hosting &Architecture • Import/ Export Xblocks • BBDTC Toolbox • Demo

  3. Biomedical Big Data Training Collaborative (BBDTC) • BBDTC is a collaborative environment that promotes training and education in biomedical big data research. • Our vision is to provide free and easy access to the high-qualityknowledge and data community effort around biomedical big data research. • We have 4 main goals: • Course framework development • Curriculum Content development • Virtual Machine Toolbox development • Community engagement

  4. Biomedical Big Data Training Collaborative BBDTC User Interface • Repository Content • Viewer Course Builder Interface • Course Viewer • Interface • Social Media • Aspects Virtual Machine Toolbox

  5. BBDTC website is up! • Experimental HUBzero website is up and evolving • Full Course on Scalable Bioinformatics Bootcamp Course • NBCR Summer Training: “Data to Structural Models” Our first course using the BBDTC MOOC platform will be piloted August 17-21, 2015 • First version of ability to run toolbox Amazon VMs related to a course • Downloadable toolbox: Virtualbox image • Ongoing work to import xBlocks for existing edX courses

  6. Design of HUBzero-based System Architecture and Extensions edX xBlocks import Current System Components

  7. BBDTC Course Structure We have verified and tested features of the BBDTC course building interface and linked the VM toolbox framework to an existing full course on "Scalable Bioinformatics Bootcamp" available through the BBDTC portal.

  8. Scalable Bioinformatics Bootcamp Course

  9. Xblocks Import/Export

  10. XBlocks • Xblocks is a format for defining educational material as a hierarchy of information ‘blocks’. • Blocks can be composed of other blocks. • Each block can represent something as small as a paragraph of text, or a test question, or a link to a video. • Blocks can be composed of other blocks. A block can be as large as the course itself. • Blocks can be reshuffled and reused to create new courses.

  11. Import/Export • Import/

  12. Biomedical Big Data Toolbox The BBDTC system supports two categories of Virtual Machine Toolboxes: a Downloadable VM toolbox and an Amazon EC2 VM toolbox. • Downloadable VM toolbox: In this category, the software tools are shared as a downloadable light-weight Virtualbox Image. The downloadable VM toolbox allow users to get a standardized software tool environment with with their required software dependencies and the necessary test data on their personal machines. • Amazon EC2 VM Toolbox: This category provides a ready-to-go solution for scalable big data experiments. The users will be able to access an Amazon EC2 Virtual Machines through the BBDTC website. The system utilizes noVNC, a HTML5 based VNC client.

  13. Amazon EC2 VM access through BBDTC using noVNC

  14. How was BBDTC built? • HUBzero as a base • Hosting on SDSC Cloud VM • Scaling up in the future

  15. What is HUBzero? • Uses the Joomla! Content Management System as its core. • Classic LAMP-stack Web Application. • Configured and Extended to support research and educational endeavors largely out of the box. • Uses an earlier virtualization technology (OpenVZ) to host applications and their dependencies on the server itself. • Users ‘remote-desktop’ from a web-browser window.

  16. HUBzero Architecture

  17. SDSC VM Hosting • Current Usage: • 4 cores (2 virtual CPUs) (200% of base system) • 50GB of disk(50% of base system) • 10GB of memory(?% of base system) • Current Allocation: • 8 cores • 1TB of disk • 24GB of memory

  18. Upgrades are Easy

  19. Accurately gauge usage in real-time

  20. …or over time

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