Research and Informatics Division, University Libraries

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https://hdl.handle.net/10919/71806

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Browsing Research and Informatics Division, University Libraries by Department "University Libraries"

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    DESIGN THINKING for Visualizing Acid-Base Chemistry - Documenting a user-centered approach for designing and developing an ADA compliant online tool for visualizing acid-base chemistry
    Stamper, Michael J.; Briganti, Jonathan; Brown, Anne M.; Dietrich, Andrea M.; Godrej, Adil N.; Schreiber, Madeline E.; Walz, Anita R. (2019-07-17)
    This project created an online tool, that we call “The pkAnalyzer”. It enables the exploration of acid-conjugate base distributions in an easy to use Web interface. This project is also an example of the disciplines of Arts and Design into the STEM sciences, i.e. STEM to STEAM, and University Libraries commitment to faculty, students, and staff throughout the Virginia Tech system, in the areas of data visualization and design services to aid in the research process and communication of results. Beyond the functionality of the tool, this project involved the planning and designing a custom, modifiable, and attractive user interface (UI) and visualization that are "user-friendly", and incorporate the World Wide Web Consortium’s Web Content Accessibility Guidelines (WCAG), and falls with the Federal Governement’s Section 508 guidelines pertaining to creating and maintaining information and communications technology (ICT) that is accessible to people with disabilities relating to vision. Using a "Design Thinking" approach, all aspects of the design of this tool – User Interface (UI), User Experience (UX), Interaction Design (IxD), Graphic – were taken into account, and developed to enhance the user's experience using the tool, and undertanding of a complex chemical concept that is widely used in the basic and applied sciences and engineering.
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    Ensemble PDP-8: Eight Principles for Distributed Portals
    Fox, Edward A.; Chen, Yinlin; Akbar, Monika; Shaffer, Clifford A.; Edwards, Stephen H.; Brusilovsky, Peter; Garcia, Daniel D.; Delcambre, Lois M. L.; Decker, Felicia; Archer, David W.; Furuta, Richard; Shipman, Frank M., III; Carpenter, B. Stephen, II; Cassel, Lillian N. (2010)
    Ensemble, the National Science Digital Library (NSDL) Pathways project for Computing, builds upon a diverse group of prior NSDL, DL-I, and other projects. Ensemble has shaped its activities according to principles related to design, development, implementation, and operation of distributed portals. Here we articulate 8 key principles for distributed portals (PDPs). While our focus is on education and pedagogy, we expect that our experiences will generalize to other digital library application domains. These principles inform, facilitate, and enhance the Ensemble R&D and production activities. They allow us to provide a broad range of services, from personalization to coordination across communities. The eight PDPs can be briefly summarized as: (1) Articulation across communities using ontologies. (2) Browsing tailored to collections. (3) Integration across interfaces and virtual environments. (4) Metadata interoperability and integration. (5) Social graph construction using logging and metrics. (6) Superimposed information and annotation integrated across distributed systems. (7) Streamlined user access with IDs. (8) Web 2.0 multiple social network system interconnection.
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    Integration of VT ETD-db with Banner
    Volpe, James; McMillan, Gail; Fox, Edward A. (Department of Computer Science, Virginia Polytechnic Institute & State University, 2008)
    The Electronic Thesis and Dissertation database (ETD-db) was developed at Virginia Tech by Digital Library and Archives for the VT Graduate School and the Networked Digital Library of Theses and Dissertations (NDLTD). The software is freely available and over 100 universities worldwide have implemented the ETD-db system. One drawback of the system is the dependence on user keyed data. At Virginia Tech, like most other universities, there is an administrative database that could provide much of this information. The Banner Administrative System is the central administration system at Virginia Tech. Banner’s underlying database software is from Oracle. This paper will demonstrate how the ETD-db can be seamlessly integrated with an Oracle database or more specifically the Banner Administrative System, to improve the integrity of the data for ETDs.
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    Introduction to Copyright for Extension Master Gardeners
    Haugen, Inga (Virginia Tech, 2021-02-24)
    This presentation will discuss Copyright. This was an introduction module made for Extension Master Gardeners but may be useful for others.
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    Introduction to Creative Commons for Extension Master Gardeners
    Haugen, Inga (Virginia Tech, 2021-02-24)
    This presentaion will discuss Creative Commons. This was a overview for the Extension Master Gardeners but may be useful for others.
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    Introduction to Fair Use for Extension Master Gardeners
    Haugen, Inga (Virginia Tech, 2021-02-24)
    This presentation will discuss Fair Use. This was presented to Extension Master Gardeners but may be useful for others as well. The Fair Use LibGuide was used as well as the ala.org website
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    Molecular evolution of genes encoding allergen proteins in the peanuts genus Arachis: Structural and functional implications
    Hilu, Khidir W.; Friend, Sheena A.; Vallanadu, Viruthika; Brown, Anne M.; Hollingsworth, Louis R. IV (PLOS, 2019-11-01)
    Food allergies are severe immune responses to plant and animal products mediated by immunoglobulin E (IgE). Peanuts (Arachis hypogaea L.) are among the top 15 crops that feed the world. However, peanuts is among the “big eight food allergens”, and allergies induced by peanuts are a significant public health problem and a life-threatening concern. Targeted mutation studies in peanuts demonstrate that single residue alterations in these allergen proteins could result in substantial reduction in allergenicity. Knowledge of peanut allergen proteins is confined to the allotetraploid crop and its two progenitors. We explored frequencies and positions of natural mutations in the hyperallergenic homologues Ara h 2 and Ara h 6 in newly generated sequences for 24 Arachis wild species and the crop species, assessed potential mutational impact on allergenicity using immunoblots and structural modeling, and evaluated whether these mutations follow evolutionary trends. We uncovered a wealth of natural mutations, both substitutions and gaps, including the elimination of immunodominant epitopes in some species. These molecular alterations appear to be associated with substantial reductions in allergenicity. The study demonstrated that Ara h 2 and Ara h 6 follow contrasting modes of natural selection and opposing mutational patterns, particularly in epitope regions. Phylogenetic analysis revealed a progressive trend towards immunodominant epitope evolution in Ara h 2. The findings provide valuable insight into the interactions among mutations, protein structure and immune system response, thus presenting a valuable platform for future manipulation of allergens to minimize, treat or eliminate allergenicity. The study strongly encourages exploration of genepools of economically important plants in allergenicity research.
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    On Utilization of Contributory Storage in Desktop Grids
    Miller, Chreston; Butler, Patrick; Shah, Ankur; Butt, Ali R. (Department of Computer Science, Virginia Polytechnic Institute & State University, 2007)
    The availability of desktop grids and shared computing platforms has popularized the use of contributory resources, such as desktops, as computing substrates for a variety of applications. However, addressing the exponentially growing storage demands of applications, especially in a contributory environment, remains a challenging research problem. In this report, we propose a transparent distributed storage system that harnesses the storage contributed by grid participants arranged in a peer-to-peer network to yield a scalable, robust, and self-organizing system. The novelty of our work lies in (i) design simplicity to facilitate actual use; (ii) support for easy integration with grid platforms; (iii) ingenious use of striping and error coding techniques to support very large data files; and (iv) the use of multicast techniques for data replication. Experimental results through simulations and an actual implementation show that our system can provide reliable and efficient storage with large file support for desktop grid applications.
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    Protocols
    Singh, Ajeet; Chen, Yinlin; Santhanam, Srinivasa; Zhu, Weihua (2009-10-09)
    This module addresses the concepts, development and implementation of digital library protocols and covers the roles of protocols in information retrieval systems (IR) and Service Oriented Architectures (SOA).
  • Scalable Storage for Digital Libraries
    Mather, Paul (Department of Computer Science, Virginia Polytechnic Institute & State University, 2002-10-01)
    I propose a storage system optimised for digital libraries. Its key features are its heterogeneous scalability; its integration and exploitation of rich semantic metadata associated with digital objects; its use of a name space; and its aggressive performance optimisation in the digital library domain.
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    Science of Digital Libraries(SciDL)
    Fox, Edward A.; Carroll, John M.; Fan, Patrick; Cassel, Lillian N.; Zubair, Mohammad; Maly, Kurt; McMillan, Gail; Ramakrishnan, Naren; Halbert, Martin (Department of Computer Science, Virginia Polytechnic Institute & State University, 2003)
    Our purpose is to ensure that people and institutions better manage information through digital libraries (DLs). Thus we address a fundamental human and social need, which is particularly urgent in the modern Information (and Knowledge) Age. Our goal is to significantly advance both the theory and state-of-theart of DLs (and other advanced information systems) - thoroughly validating our approach using highly visible testbeds. Our research objective is to leverage our formal, theory-based approach to the problems of defining, understanding, modeling, building, personalizing, and evaluating DLs. We will construct models and tools based on that theory so organizations and individuals can easily create and maintain fully functional DLs, whose components can interoperate with corresponding components of related DLs. This research should be highly meritorious intellectually. We bring together a team of senior researchers with expertise in information retrieval, human-computer interaction, scenario-based design, personalization, and componentized system development and expect to make important contributions in each of those areas. Of crucial import, however, is that we will integrate our prior research and experience to achieve breakthrough advances in the field of DLs, regarding theory, methodology, systems, and evaluation. We will extend the 5S theory, which has identified five key dimensions or onstructs underlying effective DLs: Streams, Structures, Spaces, Scenarios, and Societies. We will use that theory to describe and develop metamodels, models, and systems, which can be tailored to disciplines and/or groups, as well as personalized. We will disseminate our findings as well as provide toolkits as open source software, encouraging wide use. We will validate our work using testbeds, ensuring broad impact. We will put powerful tools into the hands of digital librarians so they may easily plan and configure tailored systems, to support an extensible set of services, including publishing, discovery, searching, browsing, recommending, and access control, handling diverse types of collections, and varied genres and classes of digital objects. With these tools, end-users will for be able to design personal DLs. Testbeds are crucial to validate scientific theories and will be thoroughly integrated into SciDL research and evaluation. We will focus on two application domains, which together should allow comprehensive validation and increase the significance of SciDL's impact on scholarly communities. One is education (through CITIDEL); the other is libraries (through DLA and OCKHAM). CITIDEL deals with content from publishers (e.g, ACM Digital Library), corporate research efforts e.g., CiteSeer), volunteer initiatives (e.g., DBLP, based on the database and logic rogramming literature), CS departments (e.g., NCSTRL, mostly technical reports), educational initiatives (e.g., Computer Science Teaching Center), and universities (e.g., theses and dissertations). DLA is a unit of the Virginia Tech library that virtually publishes scholarly communication such as faculty-edited journals and rare and unique resources including image collections and finding aids from Special Collections. The OCKHAM initiative, calling for simplicity in the library world, emphasizes a three-part solution: lightweightprotocols, component-based development, and open reference models. It provides a framework to research the deployment of the SciDL approach in libraries. Thus our choice of testbeds also will nsure that our research will have additional benefit to and impact on the fields of computing and library and information science, supporting transformations in how we learn and deal with information.
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    Towards Use And Reuse Driven Big Data Management
    Xie, Zhiwu; Chen, Yinlin; Griffin, Julie; Walters, Tyler; Tarazaga, Pablo Alberto; Kasarda, Mary E. (2015-06-03)
    We propose a use and reuse driven big data management approach that fuses the data repository and data processing capabilities in a co-located, public cloud. It answers to the urgent data management needs from the growing number of researchers who don’t fit in the big science/small science dichotomy. This approach will allow researchers to more easily use, manage, and collaborate around big data sets, as well as give librarians the opportunity to work alongside the researchers to preserve and curate data while it is still fresh and being actively used. This also provides the technological foundation to foster a sharing culture more aligned with the open source software development paradigm than the lone-wolf, gift-exchanging small science sharing or the top-down, highly structured big science sharing. To materialize this vision, we provide a system architecture consisting of a scalable digital repository system coupled with the co-located cloud storage and cloud computing, as well as a job scheduler and a deployment management system. Motivated by Virginia Tech’s Goodwin Hall instrumentation project, we implemented and evaluated a prototype. The results show not only sufficient capacities for this particular case, but also near perfect linear storage and data processing scalabilities under moderately high workload.