UITS Research Technologies – Services Available to Regenstrief Institute 13 Oct 2015 Craig Stewart ORCID ID Executive Director, Indiana University Pervasive Technology Institute Associate Dean, Research Technologies © Trustees Indiana University 2015 Science Storage Computation Analysis/ Bio/Health Visualization Campus Education/ Grant CyberDH Gateways Software Bridging Outreach Support

Science Storage Computation Analysis/ Bio/Health Visualization Campus Education/ Grant CyberDH 2 Gateways Software Bridging Outreach Support Overview Some history UITS Research Technologies (RT) - Changing the way IU uses Cyberinfrastructure RT Service Areas - From Analysis to Visualization and everything in between Services in support of cyber risk mitigation HIPAA-aligned services Analysis and software delivery and support Visualization facilities and services

Science Storage Computation Analysis/ Bio/Health Visualization Campus Education/ Grant CyberDH 3 Gateways Software Bridging Outreach Support Some history 1980s & early 1990s – distinct IT organization at IUPUI Michael McRobbie arrives at IU as IU’s first VP for IT first full time professional bioinformatician position created at UITS IPCRES INGEN *INGEN Advanced IT Core – first ever core certified by IUSM outside of administrative umbrella of IUSM CIFASD HIPAA alignment becomes default for Research Technologies systems, INGEN Advanced IT Core becomes Advanced Biomedical IT Core (ABITC) IndianaCTSI round one IndianaCTSI round two And here we are today

Science Storage Computation Analysis/ Bio/Health Visualization Campus Education/ Grant CyberDH 4 Gateways Software Bridging Outreach Support What is Cyberinfrastructure (CI)? "Cyberinfrastructure consists of computing systems, data storage systems, advanced instruments and data repositories, visualization environments, and people, all linked together by software and high performance networks to improve research productivity and enable breakthroughs not otherwise possible.”

Science Storage Computation Analysis/ Bio/Health Visualization Campus Education/ Grant CyberDH 5 Gateways Software Bridging Outreach Support IU’s Research Cyberinfrastructure Provided by UITS Research Technologies (RT) Dedicated to supporting research & creative activity, from art to science and everything in between. Strives to support research, publications, grant support with a focus on your success. Uses local IU funds and federal grant funds to support research at IU and across the nation.

Science Storage Computation Analysis/ Bio/Health Visualization Campus Education/ Grant CyberDH 6 Gateways Software Bridging Outreach Support Where we are now – significant use by clinical and translational researchers (and most everyone else) SystemDisciplines & subdiscipline IUPUI Disciplines & IUB Total Big Red II Karst Totals

Science Storage Computation Analysis/ Bio/Health Visualization Campus Education/ Grant CyberDH 7 Gateways Software Bridging Outreach Support RT Services – Computation Fast calculations, advanced simulations, and big data analysis Big Red II – IU’s main system for high- performance parallel computing Owned solely by IU 1 petaFLOPS CPUs/GPUs 3.5 PB of scratch Available through itaccounts.iu.edu Support/consulting available Tours available

Science Storage Computation Analysis/ Bio/Health Visualization Campus Education/ Grant CyberDH 8 Gateways Software Bridging Outreach Support RT Services – Computation Fast calculations, advanced simulations, and big data analysis Karst– IU’s primary Linux cluster computing environment For research and research instruction use Serves as condominium cluster Runs Red Hat Enterprise Linux Accounts available via the Account Management Service (AMS)

Science Storage Computation Analysis/ Bio/Health Visualization Campus Education/ Grant CyberDH 9 Gateways Software Bridging Outreach Support RT Services – Computation Fast calculations, advanced simulations, and big data analysis Mason – large-memory computer cluster Supports data-intensive, high-performance computing tasks Specifically for genome researchers Uses include genome assembly software, large-scale phylogenetic software, and other genome applications

Science Storage Computation Analysis/ Bio/Health Visualization Campus Education/ Grant CyberDH 10 Gateways Software Bridging Outreach Support RT Services – Computation Fast calculations, advanced simulations, and big data analysis Research Database Complex – research databases and data applications Supports oracle and MySQL databases Strictly devoted to research Runs Red Hat Enterprise Linux Examples of research projects currently supported Collaborative Initiative on Fetal Alcohol Spectrum Disorders Indiana Spatial Data Service National Gene Vector Biorepository

Science Storage Computation Analysis/ Bio/Health Visualization Campus Education/ Grant CyberDH 11 Gateways Software Bridging Outreach Support RT Services – Analysis and software delivery and support Tools for analytics and big data research Software and application consulting – long term and short term Technical support Software packages like GIS and remote sensing software Purchase software Software licensing Benchmark and evaluate HPC systems Tutorials/documentation Public software availability Application tuning

Science Storage Computation Analysis/ Bio/Health Visualization Campus Education/ Grant CyberDH 12 Gateways Software Bridging Outreach Support RT Services – Data Storage High-quality storage services for fast access or large data sets Research File System (RFS) Centralized disk storage designed to support researchers Backed up regularly – 2 copies (IUB and IUPUI) Open to IU community – undergrads/non-IU must have sponsor 100 GB of disk storage Can utilize project areas in file system HIPAA-aligned (does not encrypt stored data – individual users responsible)

Science Storage Computation Analysis/ Bio/Health Visualization Campus Education/ Grant CyberDH 13 Gateways Software Bridging Outreach Support RT Services – Data Storage High-quality storage services for fast access or large data sets Scholarly Data Archive (SDA) Distributed tape storage for large-scale archival/near-line storage Mirrored – 2 copies (IUB and IUPUI) Open to IU community – undergrads/non-IU must have sponsor 42 PB of tape storage Supports SFTP, HSI, HPSS API HIPAA-aligned (does not encrypt stored data – individual users responsible)

Science Storage Computation Analysis/ Bio/Health Visualization Campus Education/ Grant CyberDH 14 Gateways Software Bridging Outreach Support RT Services – Visualization facilities and services Understanding advanced simulations and big data Project consultation Test and demonstrate new technologies and procedures Tours of IU visualization facilities Facility reservations Vis & Collaboration Theater Virtual Reality Theater Science on a Sphere IQ-Series - Wall/Tilt/Table Digitization & 3D Advanced Media Capture Haptic Interface Systems

Science Storage Computation Analysis/ Bio/Health Visualization Campus Education/ Grant CyberDH 15 Gateways Software Bridging Outreach Support RT Services – Visualization facilities and services IQ series – routinely installed in buildings on campus at little more than cost of components to create* * We would have to create an equitable cost structure and add to IU-RI agreement

Science Storage Computation Analysis/ Bio/Health Visualization Campus Education/ Grant CyberDH 16 Gateways Software Bridging Outreach Support RT Services – Visualization facilities and services Examples: Digital Golden Book Generating Interest in STEM using 3D 3D scanning, analysis, and printing

Science Storage Computation Analysis/ Bio/Health Visualization Campus Education/ Grant CyberDH 17 Gateways Software Bridging Outreach Support An Array of Viz Systems Immersive Theaters Ultra-Resolution Stereoscopic IUB IUPUI

Science Storage Computation Analysis/ Bio/Health Visualization Campus Education/ Grant CyberDH 18 Gateways Software Bridging Outreach Support RT Services – Services for biomedical, biological, and health-related research Clinical, genomic, and HIPAA-aligned services Examples include: The Advanced Biomedical IT Core (ABITC) Open Science Grid, Grid Operations Center Indiana CTSI HUB INResearch I2iConnect

Science Storage Computation Analysis/ Bio/Health Visualization Campus Education/ Grant CyberDH 19 Gateways Software Bridging Outreach Support RT Services – Services for biomedical, biological, and health-related research The Advanced Biomedical IT Core (ABITC) REDCAP - a HIPAA- aligned service to enable Research Electronic Data Capture by allowing research staff to design and deploy research study forms quickly and easily. REDCap may also be used to conduct electronic surveys for research. Alfresco Share – retiring – currently moving users to BOX.

Science Storage Computation Analysis/ Bio/Health Visualization Campus Education/ Grant CyberDH 20 Gateways Software Bridging Outreach Support RT Services – Services for biomedical, biological, and health-related research National Center for Genome Analysis Support Consulting for biologists undertaking genome analysis and genomic researchers Genome analysis software Optimization Hardening Enhancement Data storage Results archiving Delivery and assistance in use of supercomputer clusters Funded by the National Science Foundation

Science Storage Computation Analysis/ Bio/Health Visualization Campus Education/ Grant CyberDH 21 Gateways Software Bridging Outreach Support Federally funded resources Open Science Grid (High-throughput Computing) XSEDE including IU-led Jetstream

Science Storage Computation Analysis/ Bio/Health Visualization Campus Education/ Grant CyberDH 22 Gateways Software Bridging Outreach Support RT Services – Education and Outreach Can help you figure out which RT services might benefit your research; will help with planning events regarding IU Cyberinfrastructure In-person classes and workshops Infoshares tailored to your campus, department, class Tours of facilities like the Data Center or Science on a Sphere On-line tutorials and workshops Represents IU at conferences and within HPC organizations

Science Storage Computation Analysis/ Bio/Health Visualization Campus Education/ Grant CyberDH 23 Gateways Software Bridging Outreach Support RT Services – Grant support and custom fee-based services Helps with proposals that require cyberinfrastructure. Application development and custom programming for a fee. Data Management Plans Facilities Statements Letters of Support Application Development Custom programming

Science Storage Computation Analysis/ Bio/Health Visualization Campus Education/ Grant CyberDH 24 Gateways Software Bridging Outreach Support Summary of discussion We all agree that the missions of Regenstrief Institute and IU are aligned and becoming closer over time, but we also have to deal with the technicalities of the legal structure of RI since we often work in areas impacted by contracts and licenses with software vendors. We are in uncharted territory and will make some of this up as we go along. Tactical issues -We will continue to work together on SAS licensing issues. -Purchase of Karst nodes and use of Karst desktop environment (along with purchase of disk space dedicated to RI) seems like a good option for processing. -Oracle extracts are a current performance bottleneck. Strategic Issues -Need to revisit and update the Master agreement – structure of and problems in current (outdated) agreement. -We need to take a strategic look at RI workflows. Eric Wernert will initiate such a review as soon as he has filled a vacant position in his group (search is underway).

Science Storage Computation Analysis/ Bio/Health Visualization Campus Education/ Grant CyberDH 25 Gateways Software Bridging Outreach Support Contact Information Contacts: Craig A. Stewart - Eric Wernert – Scott Michael - Sign up for CI Newsletter at View all the research services on IU Mobile and at

Science Storage Computation Analysis/ Bio/Health Visualization Campus Education/ Grant CyberDH 26 Gateways Software Bridging Outreach Support Acknowledgments & Disclaimers Please cite as Jetstream is supported by NSF award (Craig Stewart, PI) XSEDE is supported by NSF award (John Towns, UIUC, PI) This work was also supported by the Indiana University Pervasive Technology Institute, which was initiated with major funding from the Lilly Endowment, Inc. Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation (NSF) or other supporting organizations.

Science Storage Computation Analysis/ Bio/Health Visualization Campus Education/ Grant CyberDH 27 Gateways Software Bridging Outreach Support License Terms Stewart, C.A UITS Research Technologies – Services Available to Regenstrief Institute. Presentation. Presented at Regenstrief Institute, Indiana University Purdue University Indianapolis, Indianapolis. 13 October Items indicated with a © are under copyright and used here with permission. Such items may not be reused without permission from the holder of copyright except where license terms noted on a slide permit reuse. Except where otherwise noted, contents of this presentation are copyright 2014 by the Trustees of Indiana University. This document is released under the Creative Commons Attribution 3.0 Unported license ( This license includes the following terms: You are free to share – to copy, distribute and transmit the work and to remix – to adapt the work under the following conditions: attribution – you must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work). For any reuse or distribution, you must make clear to others the license terms of this work. Jetstream is supported by NSF award (Craig Stewart, PI) XSEDE is supported by NSF award (John Towns, UIUC, PI) This work was also supported by the Indiana University Pervasive Technology Institute, which was initiated with major funding from the Lilly Endowment, Inc. Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation (NSF) or other supporting organizations.