Services and support for IU School of Medicine and Clinical Affairs Schools by the UITS/PTI Advanced Biomedical Information Technology Core and Research Technologies Division in FY 2013 - Extended Version

The report presents information on services delivered in FY 2013 by ABITC and RT to the IU School of Medicine and the other Clinical Affairs schools that include the Schools of Nursing, Dentistry, Health and Rehabilitation Sciences, and Optometry; the Fairbanks School of Public Health at IUPUI; the School of Public Health at IU Bloomington; and the School of Social Work

Extensible Terascale Facility (ETF): Indiana-Purdue Grid (IP-Grid)

NSF Award ID: ACI-0338618 Project Dates: 10/1/03-9/30/0

Taxonomy Visualization in Support of the Semi-Automatic Validation and Optimization of Organizational Schemas

Never before in history, mankind had access to and produced so much data, information, knowledge, and expertise as today. To organize, access, and manage these highly valuable assets effectively, we use taxonomies, classification hierarchies, ontologies, and controlled vocabularies among others. We create directory structures for our files. We use organizational hierarchies to structure our work environment. However, the design and continuous update of these organizational schemas that potentially have thousands of class nodes to organize millions of entities is challenging for any human being. The Taxonomy Visualization and Validation (TV) tool introduced in this paper supports the semi-automatic validation and optimization of organizational schemas such as file directories, classification hierarchies, taxonomies, or any other structure imposed on a data set as a means of organization, structuring, and naming. By showing the “goodness of fit” of a schema and the potentially millions of entities it organizes, the TV eases the identification and reclassification of misclassified information entities, the identification of classes that grew over-proportionally, the evaluation of the size and homogeneity of existing classes, the examination of the “well-formedness” of an organizational schema, etc. The TV is exemplarily applied to display the United States Patent and Trademark Office patent classification, which organizes more than three million patents into about 160,000 distinct patent classes. The paper concludes with a discussion and an outlook to future work

January 1 - December 31, 2012

This report summarizes training, education, and outreach activities for calendar 2012 of PTI and affiliated organizations, including the School of Informatics and Computing, Office of the Vice President for Information Technology, and Maurer School of Law. Reported activities include those led by PTI Research Centers (Center for Applied Cybersecurity Research, Center for Research in Extreme Scale Technologies, Data to Insight Center, Digital Science Center) and Service and Cyberinfrastructure Centers (Research Technologies Division of University Information Technology Services, National Center for Genome Assembly Support

2012 Annual Report - Advanced Biomedical Information Technology Core

This material is based upon work supported in part by the following funding agencies and grant awards: • Lilly Endowment, for its support of the Indiana Genomics Initiative (INGEN) – 2000; Indiana Metabolomics and Cytomics Initiative (METACyt); Indiana Pervasive Computing Research (IPCRES) initiative and Pervasive Technology Institute (1999 and 2008 respectively) • National Science Foundation under grants 01116050 MRI: Creation of the AVIDD Data Facility: A Distributed Facility for Managing, Analyzing and Visualizing Instrument-Driven Data (Michael A. McRobbie, PI); 0521433 MRI: Acquisition of a High-Speed, High Capacity Storage System to Support Scientific Computing: The Data Capacitor (Craig A. Stewart, PI); 0521433 ABI Development: National Center for Genome Analysis Support (Craig A. Stewart, PI) • National Institutes of Health NIAAA awards U24 AA014818-01 (Craig A. Stewart, PI) and U24 AA014818-04 (William K. Barnett, PI) Informatics Core for the Collaborative Initiative on Fetal Alcohol Spectrum Disorder • Subcontracts through the following NIH grant awards: 5P40RR024928 (Kenneth Cornetta, PI), 2U01AA014809 (Tatiana Foroud, PI), 1DP2OD007363-01 (Alexander Niculescu, PI), UL1RR025761-01 (Anantha Shekhar, PI), 3UL1RR025761-04S2 (Anantha Shekhar, PI), and 3UL1RR025761-04S3 (Anantha Shekhar, PI) • Funding from the general funds of Indiana University Any opinions expressed in this document are those of the authors and do not necessarily reflect the views of the funding agencies above

DLI-2: Creating the Digital Music Library: Final Report to the National Science Foundation

Indiana University’s Variations2 Digital Music Library project focused on three chief areas of research and development: system architecture, including content representation and metadata standards; component-based application architecture; and network services. We tested and evaluated commercial technologies, primarily for multimedia and storage management; developed custom software solutions for the needs of the music library community; integrated commercial and custom software products; and tested and evaluated prototype systems for music instruction and library services, locally at Indiana University, and at a number of satellite sites, in the U.S. and overseas. This document is the project's final report to the National Science Foundation.This work was sponsored by the National Science Foundation under award no. 9909068, as part of the DLI-2 initiative

Indiana University Pervasive Technology Institute – Research Technologies: XSEDE Service Provider and XSEDE subcontract report (PY1: 1 July 2011 to 30 June 2012)

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 NSF or XSEDE leadership.This document is a summary of the activities of the Research Technologies division of UITS, a Service & Cyberinfrastructure Center affiliated with the Indiana University Pervasive Technology Institute, as part of the eXtreme Science and Engineering Discovery Environment (XSEDE) during XSEDE Program Year 1 (1 July 2011 – 30 June 2012). This document consists of three parts: - Section 2 of this document describes IU’s activities as an XSEDE Service Provider, using the format prescribed by XSEDE for reporting such activities. - Section 3 of this document describes IU’s activities as part of XSEDE management, operations, and support activities funded under a subcontract from the National Center for Supercomputer Applications (NCSA), the lead organization for XSEDE. This section is organized by the XSEDE Work Breakdown Structure (WBS) plan. - Appendix 1 is a summary table of IU’s education, outreach, and training events funded and supported in whole or in part by IU’s subcontract from NCSA as part of XSEDE.This document was developed with support from National Science Foundation (NSF) grant OCI-1053575