National Center for Genome Analysis Program Year 3 Report – September 15, 2013 – September 14, 2014

On September 15, 2011, Indiana University (IU) received three years of support to establish the National Center for Genome Analysis Support (NCGAS). This technical report describes the activities of the third 12 months of NCGASThe facilities supported by the Research Technologies division at Indiana University are supported by a number of grants. The authors would like to acknowledge that although the National Center for Genome Analysis Support is funded by NSF 1062432, our work would not be possible without the generous support of the following awards received by our parent organization, the Pervasive Technology Institute at Indiana University. • The Indiana University Pervasive Technology Institute was supported in part by two grants from the Lilly Endowment, Inc. • NCGAS has also been supported directly by the Indiana METACyt Initiative. The Indiana METACyt Initiative of Indiana University is supported in part by the Lilly Endowment, Inc. • This material is based in part upon work supported by the National Science Foundation under Grant No. CNS-0521433. Any opinions, findings and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation (NSF)

Optimizing the National Cyberinfrastructure for Lower Bioinformatic Costs: Making the Most of Resources for Publicly Funded Research

Presented at the RNA-Seq Conference, June 18-20, 2013 in Boston MassachusettsOverviews of NCGAS mission, cyberinfrastructure, and server-on-demand resources and of XSEDE for larger-scale resources.This material is based upon work supported by the National Science Foundation under Grants No. ABI-1062432. This work was supported in part by the Lilly Endowment, Inc. and the Indiana University Pervasive Technology Institute Any opinions presented here are those of the presenter(s) and do not necessarily represent the opinions of the National Science Foundation or any other funding agencie

Cybersecurity Leadership

The presentation, part of the Tobias Leadership Conference, Indianapolis, IN, 1 May 2015, discusses cybersecurity leadership through four interrelated topics: strategy, policy and governance, security practice, and developing cybersecurity leaders

The New Divisia Monetary Aggregates

This is the publisher's version, also available electronically from http://www.jstor.org/stable/183199

National Center for Genome Analysis Program Year 2 Report – September 15, 2012 – September 14, 2013

On September 15, 2011, Indiana University (IU) received three years of support to establish the National Center for Genome Analysis Support (NCGAS). This technical report describes the activities of the second 12 months of NCGASThe facilities supported by the Research Technologies division at Indiana University are supported by a number of grants. The authors would like to acknowledge that although the National Center for Genome Analysis Support is funded by NSF 1062432, our work would not be possible without the generous support of the following awards received by our parent organization, the Pervasive Technology Institute at Indiana University. • The Indiana University Pervasive Technology Institute was supported in part by two grants from the Lilly Endowment, Inc. • NCGAS has also been supported directly by the Indiana METACyt Initiative. The Indiana METACyt Initiative of Indiana University is supported in part by the Lilly Endowment, Inc. • This material is based in part upon work supported by the National Science Foundation under Grant No. CNS-0521433. Any opinions, findings and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation (NSF)

Research IT maturity models for academic health centers: Early development and initial evaluation

This paper proposes the creation and application of maturity models to guide institutional strategic investment in research informatics and information technology (research IT) and to provide the ability to measure readiness for clinical and research infrastructure as well as sustainability of expertise. Conducting effective and efficient research in health science increasingly relies upon robust research IT systems and capabilities. Academic health centers are increasing investments in health IT systems to address operational pressures, including rapidly growing data, technological advances, and increasing security and regulatory challenges associated with data access requirements. Current approaches for planning and investment in research IT infrastructure vary across institutions and lack comparable guidance for evaluating investments, resulting in inconsistent approaches to research IT implementation across peer academic health centers as well as uncertainty in linking research IT investments to institutional goals. Maturity models address these issues through coupling the assessment of current organizational state with readiness for deployment of potential research IT investment, which can inform leadership strategy. Pilot work in maturity model development has ranged from using them as a catalyst for engaging medical school IT leaders in planning at a single institution to developing initial maturity indices that have been applied and refined across peer medical schools

Discrimination of Juvenile Red Snapper Otolith Chemical Signatures from Gulf of Mexico Nursery Regions

Age-0 red snapper Lutjanus campechanus from the 2005-2007 year-classes were sampled in six regions across the Gulf of Mexico (Gulf) to develop nursery signatures from otolith element : Ca ratios (Ba:Ca, Mg:Ca, Mn:Ca, Sr:Ca, and Li:Ca) and stable isotope delta values (delta C-13 and delta O-18). Element : Ca ratios were analyzed with sector field inductively coupled plasma mass spectrometry on dissolved right sagittae; isotope ratio mass spectrometry was employed to analyze pulverized left otoliths for delta C-13 and delta O-18. Otolith chemical signatures were significantly different among regions in each year. Year-class-specific quadratic discriminant function analysis (QDFA) distinguished nursery regions with an accuracy of 82% for 2005, 70% for 2006, and 72% for 2007. However, samples were not obtained from all six study regions in 2005 and 2006. A QDFA of all year-classes combined produced an overall classification accuracy of 70%, thus indicating that region-specific otolith chemical signatures from adjacent sampling years could be used as surrogates for regions where samples were not obtained in a given year

Report of NSF Workshop Series on Scientific Software Security Innovation Institute

Many individuals attended these workshops and contributed to the writing of this report. They are named in the report itself.Over the period of 2010‐2011, a series of two workshops were held in response to NSF Dear Colleague Letter NSF 10‐050 calling for exploratory workshops to consider requirements for Scientific Software Innovation Institutes (S2I2s). The specific topic of the workshop series was the potential benefits of a security-­‐focused software institute that would serve the entire NSF research and development community. The first workshop was held on August 6th, 2010 in Arlington, VA and represented an initial exploration of the topic. The second workshop was held on October 26th, 2011 in Chicago, IL and its goals were to 1) Extend our understanding of relevant needs of MREFC and large NSF Projects, 2) refine outcome from first workshop with broader community input, and 3) vet concepts for a trusted cyberinfrastructure institute. This report summarizes the findings of these workshops.This material is based upon work supported by the National Science Foundation under grant number 1043843. 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

Cyberinfrastructure resources enabling creation of the loblolly pine reference transcriptome

This paper was presented at XSEDE 15 conference.Today's genomics technologies generate more sequence data than ever before possible, and at substantially lower costs, serving researchers across biological disciplines in transformative ways. Building transcriptome assemblies from RNA sequencing reads is one application of next-generation sequencing (NGS) that has held a central role in biological discovery in both model and non- model organisms, with and without whole genome sequence references. A major limitation in effective building of transcriptome references is no longer the sequencing data generation itself, but the computing infrastructure and expertise needed to assemble, analyze and manage the data. Here we describe a currently available resource dedicated to achieving such goals, and its use for extensive RNA assembly of up to 1.3 billion reads representing the massive transcriptome of loblolly pine, using four major assembly software installations. The Mason cluster, an XSEDE second tier resource at Indiana University, provides the necessary fast CPU cycles, large memory, and high I/O throughput for conducting large-scale genomics research. The National Center for Genome Analysis Support, or NCGAS, provides technical support in using HPC systems, bioinformatic support for determining the appropriate method to analyze a given dataset, and practical assistance in running computations. We demonstrate that a sufficient supercomputing resource and good workflow design are elements that are essential to large eukaryotic genomics and transcriptomics projects such as the complex transcriptome of loblolly pine, gene expression data that inform annotation and functional interpretation of the largest genome sequence reference to date.This work was supported in part by USDA NIFA grant 2011- 67009-30030, PineRefSeq, led by the University of California, Davis, and NCGAS funded by NSF under award No. 1062432

Application of Otolith Chemical Signatures to Estimate Population Connectivity of Red Snapper In the Western Gulf of Mexico

Otolith chemical signatures of Red Snapper Lutjanus campechanus from six nursery regions were used to estimate the sources of recruits to four sampling regions in the western Gulf of Mexico (Gulf) and to estimate whether postsettlement mixing of Red Snapper occurs between the U.S. and Mexican portions of the western Gulf. In a previous study, region-specific otolith signatures (element : Ca ratios: Ba:Ca, Mg:Ca, Mn:Ca, Sr:Ca, and Li:Ca; stable isotope delta values: δ13C and δ18O) were developed based on age-0 Red Snapper (2005–2007 year-classes) sampled from the six nursery areas. In the present study, subadult and adult Red Snapper (ages 1–3) belonging to those same year-classes were collected from four sampling regions within the western Gulf (two regions in U.S. waters; two regions along the Mexican continental shelf) during summer in 2006–2008. Left sagittal otoliths were used to age subadults and adults to the corresponding nursery year-classes, and right sagittal otoliths were cored for chemical analysis. Off the southwestern U.S. coast, the sampled age-1–3 Red Snapper included locally derived recruits as well as recruits from the northwestern Gulf nursery region. However, analytical results were inconclusive with respect to estimating the connectivity between Red Snapper populations in U.S. and Mexican waters of the western Gulf