Biomedical Big Data Training Collaborative biobigdata.ucsd.edu BBDTC UPDATES Biomedical Big Data Training Collaborative biobigdata.ucsd.edu

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

Biomedical Big Data Training Collaborative biobigdata.ucsd.edu 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-quality knowledge 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 Biomedical Big Data Training Collaborative (BBDTC)

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

Biomedical Big Data Training Collaborative biobigdata.ucsd.edu 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 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 BBDTC website is up!

Biomedical Big Data Training Collaborative biobigdata.ucsd.edu Design of HUBzero-based System Architecture and Extensions edX xBlocks import Current System Components

Biomedical Big Data Training Collaborative biobigdata.ucsd.edu 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.

Biomedical Big Data Training Collaborative biobigdata.ucsd.edu Scalable Bioinformatics Bootcamp Course

Biomedical Big Data Training Collaborative biobigdata.ucsd.edu Xblocks Import/Export

Biomedical Big Data Training Collaborative biobigdata.ucsd.edu 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.

Biomedical Big Data Training Collaborative biobigdata.ucsd.edu Import/Export Import/

Biomedical Big Data Training Collaborative biobigdata.ucsd.edu Biomedical Big Data Toolbox The BBDTC system supports two categories of Virtual Machine Toolboxes: a Downloadable VM toolbox and an Amazon EC2 VM toolbox. i) 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. i) 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.

Biomedical Big Data Training Collaborative biobigdata.ucsd.edu Amazon EC2 VM access through BBDTC using noVNC

Biomedical Big Data Training Collaborative biobigdata.ucsd.edu

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

Biomedical Big Data Training Collaborative biobigdata.ucsd.edu 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.

Biomedical Big Data Training Collaborative biobigdata.ucsd.edu HUBzero Architecture

Biomedical Big Data Training Collaborative biobigdata.ucsd.edu 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

Biomedical Big Data Training Collaborative biobigdata.ucsd.edu Upgrades are Easy

Biomedical Big Data Training Collaborative biobigdata.ucsd.edu Accurately gauge usage in real-time

Biomedical Big Data Training Collaborative biobigdata.ucsd.edu …or over time