Division of Information Technology

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2014-2016 Virginia Tech IT Operational Plan
(Virginia Tech. Information Technology, 2014-08-26)
This operational plan for the IT organization provides a detailed set of goals, initiatives, and tasks to realize the seven pillars of the IT strategic plan and to support the university’s long-range plan, “A Plan for a New Horizon – Envisioning Virginia Tech 2012-2018.” The content of this plan was collaboratively developed across the entire IT organization over the past year. The Operational Plan is designed to serve as a living bridge between the IT Strategic Plan and the IT Annual Report, creating a logical and traceable flow among the three documents.
Approximating Community Water System Service Areas to Explore the Demographics of SDWA Compliance in Virginia
Marcillo, Cristina; Krometis, Leigh-Anne H.; Krometis, Justin (MDPI, 2021-12-16)
Although the United States Safe Drinking Water Act (SDWA) theoretically ensures drinking water quality, recent studies have questioned the reliability and equity associated with community water system (CWS) service. This study aimed to identify SDWA violation differences (i.e., monitoring and reporting (MR) and health-based (HB)) between Virginia CWSs given associated service demographics, rurality, and system characteristics. A novel geospatial methodology delineated CWS service areas at the zip code scale to connect 2000 US Census demographics with 2006–2016 SDWA violations, with significant associations determined via negative binomial regression. The proportion of Black Americans within a service area was positively associated with the likelihood of HB violations. This effort supports the need for further investigation of racial and socioeconomic disparities in access to safe drinking water within the United States in particular and offers a geospatial strategy to explore demographics in other settings where data on infrastructure extents are limited. Further interdisciplinary efforts at multiple scales are necessary to identify the entwined causes for differential risks in adverse drinking water quality exposures and would be substantially strengthened by the mapping of official CWS service boundaries.
The Beginning of the End: A Chromosomal Assembly of the New World Malaria Mosquito Ends with a Novel Telomere
Compton, Austin; Liang, Jiangtao; Chen, Chujia; Lukyanchikova, Varvara; Qi, Yumin; Potters, Mark B.; Settlage, Robert; Miller, Dustin; Deschamps, Stephane; Mao, Chunhong; Llaca, Victor; Sharakhov, Igor V.; Tu, Zhijian Jake (Genetics Society of America, 2020-10-01)
Chromosome level assemblies are accumulating in various taxonomic groups including mosquitoes. However, even in the few reference-quality mosquito assemblies, a significant portion of the heterochromatic regions including telomeres remain unresolved. Here we produce a de novo assembly of the New World malaria mosquito, Anopheles albimanus by integrating Oxford Nanopore sequencing, Illumina, Hi-C and optical mapping. This 172.6 Mbps female assembly, which we call AalbS3, is obtained by scaffolding polished large contigs (contig N50 = 13.7 Mbps) into three chromosomes. All chromosome arms end with telomeric repeats, which is the first in mosquito assemblies and represents a significant step toward the completion of a genome assembly. These telomeres consist of tandem repeats of a novel 30-32 bp Telomeric Repeat Unit (TRU) and are confirmed by analyzing the termini of long reads and through both chromosomal in situ hybridization and a Bal31 sensitivity assay. The AalbS3 assembly included previously uncharacterized centromeric and rDNA clusters and more than doubled the content of transposable elements and other repetitive sequences. This telomere-to-telomere assembly, although still containing gaps, represents a significant step toward resolving biologically important but previously hidden genomic components. The comparison of different scaffolding methods will also inform future efforts to obtain reference-quality genomes for other mosquito species.
Building 3D Web Interoperability for the Metaverse
Havele, Anita; Polys, Nicholas F.; Behr, Johannes (ACM, 2023-10-09)
This workshop brings together participants from around the world with the goal of building a strong foundation for an open, interoperable Metaverse using the Web and the Web Standards ecosystem. The workshop will focus on four main topics: 1) The variety of relevant Standards and technology roles in the Metaverse stack, 2) the role of the 3D Web Interoperability Working Group, which has recently been chartered in the Metaverse Standards Forum, 3) scoping what the Metaverse IS NOT, and 4) how Use Cases and Scenarios can help clarify what the Metaverse IS. In this emerging space, perspectives and tradeoffs abound; we hope this workshop will push our understanding and terminology forward and also provide the community with an actionable set of common (yet extensible) referents and goals.
Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO)
Ramsey, Jolene; McIntosh, Brenley; Renfro, Daniel; Aleksander, Suzanne A.; LaBonte, Sandra; Ross, Curtis; Zweifel, Adrienne E.; Liles, Nathan; Farrar, Shabnam; Gill, Jason J.; Erill, Ivan; Ades, Sarah; Berardini, Tanya Z.; Bennett, Jennifer A.; Brady, Siobhan; Britton, Robert; Carbon, Seth; Caruso, Steven M.; Clements, Dave; Dalia, Ritu; Defelice, Meredith; Doyle, Erin L.; Friedberg, Iddo; Gurney, Susan M. R.; Hughes, Lee; Johnson, Allison; Kowalski, Jason M.; Li, Donghui; Lovering, Ruth C.; Mans, Tamara L.; McCarthy, Fiona; Moore, Sean D.; Murphy, Rebecca; Paustian, Timothy D.; Perdue, Sarah; Peterson, Celeste N.; Pruss, Birgit M.; Saha, Margaret S.; Sheehy, Robert R.; Tansey, John T.; Temple, Louise; Thorman, Alexander William; Trevino, Saul; Vollmer, Amy Cheng; Walbot, Virginia; Willey, Joanne; Siegele, Deborah A.; Hu, James C. (2021-10)
Author summary The primary scientific literature catalogs the results from publicly funded scientific research about gene function in human-readable format. Information captured from those studies in a widely adopted, machine-readable standard format comes in the form of Gene Ontology (GO) annotations about gene functions from all domains of life. Manual annotations based on inferences directly from the scientific literature, including the evidence used to make such inferences, represent the best return on investment by improving data accessibility across the biological sciences and allowing novel insights between evolutionarily related organisms. To supplement professional curation, our Community Assessment of Community Annotation with Ontologies (CACAO) project enabled annotation of the scientific literature by community annotators, in this case undergraduates, which resulted in the contribution of thousands of unique, validated entries to public resources. Importantly, the annotations described here initiated by nonexperts often deal with topics not typically covered by the experts. These annotations are now being used by scientists worldwide in their research efforts. Experimental data about gene functions curated from the primary literature have enormous value for research scientists in understanding biology. Using the Gene Ontology (GO), manual curation by experts has provided an important resource for studying gene function, especially within model organisms. Unprecedented expansion of the scientific literature and validation of the predicted proteins have increased both data value and the challenges of keeping pace. Capturing literature-based functional annotations is limited by the ability of biocurators to handle the massive and rapidly growing scientific literature. Within the community-oriented wiki framework for GO annotation called the Gene Ontology Normal Usage Tracking System (GONUTS), we describe an approach to expand biocuration through crowdsourcing with undergraduates. This multiplies the number of high-quality annotations in international databases, enriches our coverage of the literature on normal gene function, and pushes the field in new directions. From an intercollegiate competition judged by experienced biocurators, Community Assessment of Community Annotation with Ontologies (CACAO), we have contributed nearly 5,000 literature-based annotations. Many of those annotations are to organisms not currently well-represented within GO. Over a 10-year history, our community contributors have spurred changes to the ontology not traditionally covered by professional biocurators. The CACAO principle of relying on community members to participate in and shape the future of biocuration in GO is a powerful and scalable model used to promote the scientific enterprise. It also provides undergraduate students with a unique and enriching introduction to critical reading of primary literature and acquisition of marketable skills.
A database of global coastal conditions
Castaneda-Guzman, Mariana; Mantilla-Saltos, Gabriel; Murray, Kris A.; Settlage, Robert; Escobar, Luis E. (2021-11-26)
Remote sensing satellite imagery has the potential to monitor and understand dynamic environmental phenomena by retrieving information about Earth's surface. Marine ecosystems, however, have been studied with less intensity than terrestrial ecosystems due, in part, to data limitations. Data on sea surface temperature (SST) and Chlorophyll-a (Chlo-a) can provide quantitative information of environmental conditions in coastal regions at a high spatial and temporal resolutions. Using the exclusive economic zone of coastal regions as the study area, we compiled monthly and annual statistics of SST and Chlo-a globally for 2003 to 2020. This ready-to-use dataset aims to reduce the computational time and costs for local-, regional-, continental-, and global-level studies of coastal areas. Data may be of interest to researchers in the areas of ecology, oceanography, biogeography, fisheries, and global change. Target applications of the database include environmental monitoring of biodiversity and marine microorganisms, and environmental anomalies.
Deficiency in the endocytic adaptor proteins PHETA1/2 impairs renal and craniofacial development
Ates, Kristin M.; Wang, Tong; Moreland, Trevor; Veeranan-Karmegam, Rajalakshmi; Ma, Manxiu; Jeter, Chelsi; Anand, Priya; Wenzel, Wolfgang; Kim, Hyung-Goo; Wolfe, Lynne A.; Stephen, Joshi; Adams, David R.; Markello, Thomas; Tifft, Cynthia J.; Settlage, Robert E.; Gahl, William A.; Gonsalvez, Graydon B.; Malicdan, May Christine; Flanagan-Steet, Heather; Pan, Yuchin Albert (2020-05)
A critical barrier in the treatment of endosomal and lysosomal diseases is the lack of understanding of the in vivo functions of the putative causative genes. We addressed this by investigating a key pair of endocytic adaptor proteins, PH domain-containing endocytic trafficking adaptor 1 and 2 (PHETA1/2; also known as FAM109A/B, Ses1/2, IPIP27A/B), which interact with the protein product of OCRL, the causative gene for Lowe syndrome. Here, we conducted the first study of PHETA1/2 in vivo, utilizing the zebrafish system. We found that impairment of both zebrafish orthologs, phetal and pheta2, disrupted endocytosis and ciliogenesis in renal tissues. In addition, pheta1/2 mutant animals exhibited reduced jaw size and delayed chondrocyte differentiation, indicating a role in craniofacial development. Deficiency of pheta1/2 resulted in dysregulation of cathepsin K, which led to an increased abundance of type II collagen in craniofacial cartilages, a marker of immature cartilage extracellular matrix. Cathepsin K inhibition rescued the craniofacial phenotypes in the pheta1/2 double mutants. The abnormal renal and craniofacial phenotypes in the pheta1/2 mutant animals were consistent with the clinical presentation of a patient with a de novo arginine (R) to cysteine (C) variant (R6C) of PHETA1. Expressing the patient-specific variant in zebrafish exacerbated craniofacial deficits, suggesting that the R6C allele acts in a dominant-negative manner. Together, these results provide insights into the in vivo roles of PHETA1/2 and suggest that the R6C variant is contributory to the pathogenesis of disease in the patient. This article has an associated First Person interview with the first author of the paper.
Description of non-Darcy flows in porous medium systems
Dye, A. L.; McClure, J. E.; Miller, C. T.; Gray, W. G. (American Physical Society, 2013-03-18)
Fluid flow through isotropic and anisotropic porous medium systems is investigated for a range of Reynolds numbers corresponding to both Darcy and non-Darcy regimes. A non-dimensional formulation is developed for a Forchheimer approximation of the momentum balance, and lattice Boltzmann simulations are used to elucidate the effects of porous medium characteristics on macroscale constitutive relation parameters. The geometric orientation tensor of the solid phase is posited as a morphological measure of leading-order importance for the description of anisotropic flows. Simulation results are presented to confirm this hypothesis, and parameter correlations are developed to predict closure relation coefficients as a function of porous medium porosity, specific interfacial area of the solid phase, and the geometric orientation tensor. The developed correlations provide improved estimates of model coefficients compared to available estimates and extend predictive capabilities to fully determine macroscopic momentum parameters for three-dimensional flows in anisotropic porous media.
Designing for Social Interactions in a Virtual Art Gallery
Polys, Nicholas F.; Roshan, Samridhi; Newton, Emily; Narula, Muskaan; Thai, Bao-Tran (ACM, 2022-11-02)
The dawn of a new digital world has emerged with new ways to communicate and collaborate with other people across the globe. Metaverses and Mirror Worlds have broadened our perspectives on the ways we can utilize 3D virtual environments. A Mirror World is a 3D virtual space that depicts a real-life place or environment that people may want to see physically or would like to manipulate to create something new. A perfect example of this would be an art gallery which provides people an outlet to express themselves through various art forms and be able to socialize and have that human interaction that is needed during times when physical presence may be difficult. This project strives to improve user social interactions and make spatial control easier and more fluid in a virtual art gallery, while also incorporating the existing metaphor of permission and user privileges used in synchronous collaborative environments. We worked to create ways for people to be invited into group chats based on proximity, allowing users to give their consent as to who they want to talk to and who they will allow to share control within the space. We also implemented a way to view the space as a 3D map that highlights pieces of artwork around the space for people to teleport to and view at ease. To demonstrate this shared viewing and navigation experience we also focused on incorporating audio and spatial interaction features within the art gallery prototype of X3D and glTF models, images and audio, and HTML user interface.
Development of a Responsible Policy Index to Improve Statutory and Self-Regulatory Policies that Protect Children’s Diet and Health in the America’s Region
Rincón-Gallardo Patiño, Sofía; Rajamohan, Srijith; Meaney, Kathleen; Coupey, Eloise; Serrano, Elena L.; Hedrick, Valisa E.; da Silva Gomes, Fabio; Polys, Nicholas F.; Kraak, Vivica (MDPI, 2020-01-13)
In 2010, 193 Member States of the World Health Organization (WHO) endorsed World Health Assembly Resolution WHA63.14 to restrict the marketing of food and beverage products high in fat, sugar and salt (HFSS) to children to prevent obesity and non-communicable diseases (NCDs). No study has examined HFSS marketing policies across the WHO regional office countries in the Americas. Between 2018 and 2019, a transdisciplinary team examined policies to restrict HFSS food and beverage product marketing to children to develop a responsible policy index (RESPI) that provides a quality score based on policy characteristics and marketing techniques. After designing the RESPI, we conducted a comprehensive literature review through October 2019 to examine policies in 14 countries in the WHO Americans Region. We categorized policies (n = 38) as either self-regulatory or statutory and calculated the RESPI scores, ranked from 0 (lowest) to 10 (highest). Results showed Brazil, Canada, Chile, and Uruguay had the highest RESPI scores associated with statutory policies that restricted point of sale, cartoon, licensed media characters and celebrities; and HFSS products in schools and child care settings, and broadcast and print media. Policymakers can use the RESPI tool to evaluate marketing policies within and across geopolitical boundaries to protect children’s diet and health.
Division of Information Technology Annual Report - Fiscal Year 2018
(Virginia Tech. Information Technology, 2018)
The Division of Information Technology provides and supports core technology services that are essential to the successful functioning of the university. These include ongoing services, innovations to existing services, and a select number of new services that add functionality or build on existing capabilities. The current strategic plan provides guidance and direction for our service portfolio through 2018. Our annual report for FY 2018 provides an opportunity to review and reflect on the outcomes of the past year, to assess the effectiveness of the division in adapting to meet the university’s needs, and to provide actionable insights that support the ongoing work and continued development of the Division of Information Technology. This report is organized by the division’s “pillars,” which were introduced in the 2012-2018 Division of IT Strategic Plan, and upon which we in the division have focused our priorities. It is also informed by current visioning efforts including Beyond Boundaries and our own internal initiative to develop a new strategic plan for our organization.
Division of Information Technology Annual Report - Fiscal Year 2019
(Virginia Tech, 2019)
As described in this annual report, our work in FY 2019 focused on supporting the teaching and learning, research and discovery, and outreach and engagement missions of Virginia Tech and strengthening the Division of IT through the seven pillars of the IT Strategic Plan for 2012-2018.
Division of Information Technology Annual Report, Fiscal Year 2020
(Virginia Tech, 2020)
This is the 2020 annual report for the Division of IT at Virginia Tech.
Division of Information Technology Annual Report, Fiscal Year 2021
(Virginia Tech, 2021)
This is the 2021 annual report for the Division of IT at Virginia Tech.
Division of Information Technology Annual Report, Fiscal Year 2022
(Virginia Tech, 2023)
This is the 2022 annual report for the Division of IT at Virginia Tech.
Effect of Topology and Geometric Structure on Collective Motion in the Vicsek Model
McClure, James E.; Abaid, Nicole (Frontiers, 2022-03-08)
In this work, we explore how the emergence of collective motion in a system of particles is influenced by the structure of their domain. Using the Vicsek model to generate flocking, we simulate two-dimensional systems that are confined based on varying obstacle arrangements. The presence of obstacles alters the topological structure of the domain where collective motion occurs, which, in turn, alters the scaling behavior. We evaluate these trends by considering the scaling exponent and critical noise threshold for the Vicsek model, as well as the associated diffusion properties of the system. We show that obstacles tend to inhibit collective motion by forcing particles to traverse the system based on curved trajectories that reflect the domain topology. Our results highlight key challenges related to the development of a more comprehensive understanding of geometric structure's influence on collective behavior.
Enhancing Brain Flow Visualization with Automated 3D Data Processing: A Study on DCE-MRI Data from Mice with Tumors
Mohammed, Ayat; Polys, Nicholas F.; Cunningham, Jessica; Munson, Jennifer M.; Chutkowski, James; Liang, Hun; Park, Daniel; Rockne, Russell; Woodall, Ryan; Esparza, Cora (ACM, 2023-10-09)
Enhancing the process of generating entirely automated visualization schemes of complex fluid flow patterns within brain tumors is critical for gaining insights into their movements and behaviors. This study focused on optimizing and automating the processing of 3D volumetric and vector field data sets obtained from DCE-MRI (Dynamic Contrast-Enhanced Magnetic Resonance Imaging) scans. It is crucial to maintain performance, preserve data quality and resolution, and provide an accessible platform for biomedical scientists. In this paper, we represent an innovative approach to enhance fluid flow visualization of brain tumors through scalable visualization techniques. New techniques have been designed, benchmarked, and authenticated to produce X3D visualizations in Web3D environments using Python, and ParaView. The proposed approach does not only enhance fluid flow visualization in the context of brain tumor research but also provides a reproducible and transparent framework for future studies with both human and mouse scans.
Fusobacterium Genomics Using MinION and Illumina Sequencing Enables Genome Completion and Correction
Todd, S. Michelle; Settlage, Robert E.; Lahmers, Kevin K.; Slade, Daniel J. (American Society for Microbiology, 2018)
Understanding the virulence mechanisms of human pathogens from the genus Fusobacterium has been hindered by a lack of properly assembled and annotated genomes. Here we report the first complete genomes for seven Fusobacterium strains, as well as resequencing of the reference strain Fusobacterium nucleatum subsp. nucleatum ATCC 25586 (total of seven species; total of eight genomes). A highly efficient and cost-effective sequencing pipeline was achieved using sample multiplexing for short-read Illumina (150 bp) and long-read Oxford Nanopore Min- ION (80 kbp) platforms, coupled with genome assembly using the open-source software Unicycler. Compared to currently available draft assemblies (previously 24 to 67 contigs), these genomes are highly accurate and consist of only one complete chromosome. We present the complete genome sequence of F. nucleatum subsp. nucleatum ATCC 23726, a genetically tractable and biomedically important strain and, in addition, reveal that the previous F. nucleatum subsp. nucleatum ATCC 25586 genome assembly contains a 452-kb genomic inversion that has been corrected using our sequencing and assembly pipeline. To enable genomic analyses by the scientific community, we concurrently used these genomes to launch FusoPortal, a repository of interactive and downloadable genomic data, genome maps, gene annotations, and protein functional analyses and classifications. In summary, this report provides detailed methods for accurately sequencing, assembling, and annotating Fusobacterium genomes, while focusing on using open-source software to foster the availability of reproducible and open data. This resource will enhance efforts to properly identify virulence proteins that may contribute to a repertoire of diseases that includes periodontitis, preterm birth, and colorectal cancer.
Genome-wide identification of enhancers and transcription factors regulating the myogenic differentiation of bovine satellite cells
Lyu, Pengcheng; Settlage, Robert E.; Jiang, Honglin (2021-12-16)
Background Satellite cells are the myogenic precursor cells in adult skeletal muscle. The objective of this study was to identify enhancers and transcription factors that regulate gene expression during the differentiation of bovine satellite cells into myotubes. Results Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) was performed to identify genomic regions where lysine 27 of H3 histone is acetylated (H3K27ac), i.e., active enhancers, from bovine satellite cells before and during differentiation into myotubes. A total of 19,027 and 47,669 H3K27ac-marked enhancers were consistently identified from two biological replicates of before- and during-differentiation bovine satellite cells, respectively. Of these enhancers, 5882 were specific to before-differentiation, 35,723 to during-differentiation, and 13,199 common to before- and during-differentiation bovine satellite cells. Whereas most of the before- or during-differentiation-specific H3K27ac-marked enhancers were located distally to the transcription start site, the enhancers common to before- and during-differentiation were located both distally and proximally to the transcription start site. The three sets of H3K27ac-marked enhancers were associated with functionally different genes and enriched with different transcription factor binding sites. Specifically, many of the H3K27ac-marked enhancers specific to during-differentiation bovine satellite cells were associated with genes involved in muscle structure and development, and were enriched with binding sites for the MyoD, AP-1, KLF, TEAD, and MEF2 families of transcription factors. A positive role was validated for Fos and FosB, two AP-1 family transcription factors, in the differentiation of bovine satellite cells into myotubes by siRNA-mediated knockdown. Conclusions Tens of thousands of H3K27ac-marked active enhancers have been identified from bovine satellite cells before or during differentiation. These enhancers contain binding sites not only for transcription factors whose role in satellite cell differentiation is well known but also for transcription factors whose role in satellite cell differentiation is unknown. These enhancers and transcription factors are valuable resources for understanding the complex mechanism that mediates gene expression during satellite cell differentiation. Because satellite cell differentiation is a key step in skeletal muscle growth, the enhancers, the transcription factors, and their target genes identified in this study are also valuable resources for identifying and interpreting skeletal muscle trait-associated DNA variants in cattle.
Hermes: Boosting the Performance of Machine-Learning-Based Intrusion Detection System through Geometric Feature Learning
Zhang, Chaoyu; Shi, Shanghao; Wang, Ning; Xu, Xiangxiang; Li, Shaoyu; Zheng, Lizhong; Marchany, Randy; Gardner, Mark; Hou, Y. Thomas; Lou, Wenjing (ACM, 2024-10-14)
Anomaly-Based Intrusion Detection Systems (IDSs) have been extensively researched for their ability to detect zero-day attacks. These systems establish a baseline of normal behavior using benign traffic data and flag deviations from this norm as potential threats. They generally experience higher false alarm rates than signature-based IDSs. Unlike image data, where the observed features provide immediate utility, raw network traffic necessitates additional processing for effective detection. It is challenging to learn useful patterns directly from raw traffic data or simple traffic statistics (e.g., connection duration, package inter-arrival time) as the complex relationships are difficult to distinguish. Therefore, some feature engineering becomes imperative to extract and transform raw data into new feature representations that can directly improve the detection capability and reduce the false positive rate. We propose a geometric feature learning method to optimize the feature extraction process. We employ contrastive feature learning to learn a feature space where normal traffic instances reside in a compact cluster. We further utilize H-Score feature learning to maximize the compactness of the cluster representing the normal behavior, enhancing the subsequent anomaly detection performance. Our evaluations using the NSL-KDD and N-BaloT datasets demonstrate that the proposed IDS powered by feature learning can consistently outperform state-of-the-art anomaly-based IDS methods by significantly lowering the false positive rate. Furthermore, we deploy the proposed IDS on a Raspberry Pi 4 and demonstrate its applicability on resource-constrained Internet of Things (IoT) devices, highlighting its versatility for diverse application scenarios.

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