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)

A Roadmap for Using NSF Cyberinfrastructure with InCommon

This document provides a Roadmap for using the InCommon identity federation to enable researchers to access NSF cyberinfrastructure (CI) via their campus authentication service. It presents benefits and challenges of using InCommon for NSF cyberinfrastructure, and guidance in overcoming the challenges.NSF OCI-1040777, IU Pervasive Technology Institut

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)

Distinct trajectories of leisure time physical activity and predictors of trajectory class membership: a 22 year cohort study

<p>Abstract</p> <p>Background</p> <p>Prospective studies linking social factors to long term patterns of physical activity are lacking. In this 22 year longitudinal study, we seek to identify long term patterns of involvement in leisure time physical activity (LTPA), and explore socioeconomic and demographic predictors of distinct LTPA trajectories.</p> <p>Methods</p> <p>Among 2102 individuals aged 18–60 years in 1981 who participated in the 1981 Canada Fitness Survey/1988 Campbell's Survey of Well-Being, 1186 (56.4%) completed questionnaires for the 2002/04 follow-up. Complete data on LTPA at all 3 surveys were available for 884 participants. Latent class growth analysis was used to identify major classes of LTPA trajectories; predictors of class membership were identified using polytomous logistic regression.</p> <p>Results</p> <p>Four latent classes were identified: <it>inactive</it>, <it>increasers</it>, <it>active</it>, and <it>decreasers </it>(53%, 26%, 12%, and 9% of participants, respectively). Women, older participants, those with lower household income, and with lower educational attainment, were significantly less likely to follow <it>active </it>(Vs. <it>inactive</it>) trajectories of LTPA. Disadvantaged groups with respect to education and income were also significantly more likely to follow <it>decreasing </it>(Vs. <it>active</it>) trajectories.</p> <p>Conclusion</p> <p>There is a need for continued efforts to increase overall population levels of LTPA, particularly among socially disadvantaged groups with respect to income and education, who are most likely to experience unfavorable trajectories of LTPA.</p

Noncovariant gauge fixing in the quantum Dirac field theory of atoms and molecules

Starting from the Weyl gauge formulation of quantum electrodynamics (QED), the formalism of quantum-mechanical gauge fixing is extended using techniques from nonrelativistic QED. This involves expressing the redundant gauge degrees of freedom through an arbitrary functional of the gauge-invariant transverse degrees of freedom. Particular choices of functional can be made to yield the Coulomb gauge and Poincar\'{e} gauge representations. The Hamiltonian we derive therefore serves as a good starting point for the description of atoms and molecules by means of a relativistic Dirac field. We discuss important implications for the ontology of noncovariant canonical QED due to the gauge freedom that remains present in our formulation.Comment: 8 pages, 0 figure

Sustained Software for Cyberinfrastructure - Analyses of Successful Efforts with a Focus on NSF-Funded Software

Reliable software that provides needed functionality is clearly essential for an effective distributed cyberinfrastructure (CI) that supports comprehensive, balanced, and flexible distributed CI that, in turn, supports science and engineering applications. The purpose of this study was to understand what factors lead to software projects being well sustained over the long run, focusing on software created with funding from the US National Science Foundation (NSF) and/or used by researchers funded by the NSF. We surveyed NSF-funded researchers and performed in-depth studies of software projects that have been sustained over many years. Successful projects generally used open-source software licenses and employed good software engineering practices and test practices. However, many projects that have not been well sustained over time also meet these criteria. The features that stood out about successful projects included deeply committed leadership and some sort of user forum or conference at least annually. In some cases, software project leaders have employed multiple financial strategies over the course of a decades-old software project. Such well-sustained software is used in major distributed CI projects that support thousands of users, and this software is critical to the operation of major distributed CI facilities in the US. The findings of our study identify some characteristics of software that is relevant to the NSF-supported research community, and that has been sustained over many years

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

Influence of the state of light on the optically induced interparticle interaction

A general expression for the energy of interparticle interaction induced by an arbitrary mode of light is determined using quantum electrodynamics, and it is shown that the Casimir-Polder potential is included within this quantum result. Equations are also derived for the corresponding coupling induced by multimode number states of light, and the dependence of the pair energy on the Poynting vector and polarization state is determined. Attention is then focused on the interactions between particles trapped in counterpropagating coherent beams, both with and without interference, and it is shown that the results afford insights into the multiparticle structures that can be optically fabricated with counterpropagating input. Brief consideration is also given to the effect of squeezing the optical coherent state. Extending previous studies of optical binding in Laguerre-Gaussian beams, results are given for the case of particles trapped at radially different locations within the beam structure. Finally, consideration is given to interparticle interactions induced by broadband light, and it is shown how the length of optically fabricated particle chains can be controlled by the use of wavelength filters

Information technology in support of research, scholarship, and creative activities: A strategic plan for Research Technologies – a division of UITS and a PTI Service and Cyberinfrastructure Center

Stewart, C.A., M.R. Link, E. Wernert, W.K. Barnett, T.M. Miller. 2012. Information technology in support of research, scholarship, and creative activities: A strategic plan for Research Technologies – a division of UITS and a PTI Service and Cyberinfrastructure Center. Indiana University, Bloomington, IN. PTI Technical Report PTI-TR12-007.IU is currently executing its second information technology strategic plan – Empowering People: Indiana University's Strategic Plan for Information Technology 2009 (hereafter referred to as Empowering People). In this document, we set out long-term goals for the Research Technologies (RT) division of UITS, reaffirm specific goals set for RT for 2019, describe Actions within Empowering People for which RT is responsible, and describe the new internal structure of Research Technologies. The mission of the Research Technologies division of UITS is to develop, deliver, and support advanced technology solutions that improve productivity of and enable new possibilities in research, scholarly endeavors, and creative activity at Indiana University and beyond; and to complement this with education and technology translation activities to improve the quality of life of people in Indiana, the nation, and the world

Optical Thomas-Reiche-Kuhn sum rules

The Thomas-Reiche-Kuhn sum rule is a fundamental consequence of the position-momentum commutation relation for an atomic electron and it provides an important constraint on the transition matrix elements for an atom. Analogously, the commutation relations for the electromagnetic field operators in a magnetodielectric medium constrain the properties of the dispersion relations for the medium through four sum rules for the allowed phase and group velocities for polaritons propagating through the medium. These rules apply to all bulk media including the metamaterials designed to provide negative refractive indices. An immediate consequence of this is that it is not possible to construct a medium in which all the polariton modes for a given wavelength lie in the negative-index region