Victor Hazlewood

Bio: Victor Hazlewood is an academic researcher from University of Tennessee. The author has contributed to research in topics: Cyberinfrastructure & TeraGrid. The author has an hindex of 6, co-authored 10 publications receiving 2276 citations. Previous affiliations of Victor Hazlewood include National Institute for Computational Sciences.

XSEDE: Accelerating Scientific Discovery

Abstract: Computing in science and engineering is now ubiquitous: digital technologies underpin, accelerate, and enable new, even transformational, research in all domains. Access to an array of integrated and well-supported high-end digital services is critical for the advancement of knowledge. Driven by community needs, the Extreme Science and Engineering Discovery Environment (XSEDE) project substantially enhances the productivity of a growing community of scholars, researchers, and engineers (collectively referred to as "scientists"' throughout this article) through access to advanced digital services that support open research. XSEDE's integrated, comprehensive suite of advanced digital services federates with other high-end facilities and with campus-based resources, serving as the foundation for a national e-science infrastructure ecosystem. XSEDE's e-science infrastructure has tremendous potential for enabling new advancements in research and education. XSEDE's vision is a world of digitally enabled scholars, researchers, and engineers participating in multidisciplinary collaborations to tackle society's grand challenges.

What is campus bridging and what is XSEDE doing about it

Abstract: The term "campus bridging" was first used in the charge given to an NSF Advisory Committee for Cyberinfrastructure task force. That task force developed this description of campus bridging:"Campus bridging is the seamlessly integrated use of cyberinfrastructure operated by a scientist or engineer with other cyberinfrastructure on the scientist's campus, at other campuses, and at the regional, national, and international levels as if they were proximate to the scientist, and when working within the context of a Virtual Organization (VO) make the 'virtual' aspect of the organization irrelevant (or helpful) to the work of the VO."Campus bridging is more a viewpoint and a set of approaches to usability, software, and information concerns than a particular set of tools or software. We outline here several specific use cases that have been identified as priorities for XSEDE in the next four years. These priorities include documentation, deployment of software used entirely outside of XSEDE, and software that helps bridge from individual researcher to campus to XSEDE cyberinfrastructure. We also describe early pilot tests and means by which the user community may stay informed of campus bridging activities and participate in the implementation of Campus Bridging tools created by XSEDE. Metrics are still being developed, and will include (1) the number of campuses that adopt and use Campus Bridging tools developed by XSEDE and (2) the number of and extent to which XSEDE-developed Campus Bridging tools are adopted among other CI projects.

Methods For Creating XSEDE Compatible Clusters

Abstract: The Extreme Science and Engineering Discovery Environment has created a suite of software that is collectively known as the basic XSEDE-compatible cluster build. It has been distributed as a Rocks roll for some time. It is now available as individual RPM packages, so that it can be downloaded and installed in portions as appropriate on existing and working clusters. In this paper, we explain the concept of the XSEDE-compatible cluster and explain how to install individual components as RPMs through use of Puppet and the XSEDE compatible cluster YUM repository.

Improved Grid Security Posture through Multi-factor Authentication

Abstract: While methods of securing communication over the Internet have changed from clear text to secure encrypted channels over the last decade, the basic username-password combination for authentication has remained the mainstay in academic research computing and grid environments. Security incidents affecting grids, such as the TeraGrid stakkato incident of 2004 and 2005, has demonstrated that the use of reusable passwords for authentication can be readily exploited and can lead to a widespread security incident across the grid [1,2]. The University of Tennessee's National Institute for Computational Sciences (NICS) founded in 2008 has provided resources to the TeraGrid, including Kraken, a 1.17 petaflops Cray XT5, and has implemented and promoted the use of multi-factor authentication mechanisms since its founding. The benefits of use of this stronger authentication method has been higher productivity and resource availability for users due to no known user account compromises caused by stolen NICS user credentials that led to disabling accounts or system resources. NICS has been developing and experimenting with expanding our use of multi-factor authentication to the grid. NICS has integrated multi-factor authentication with our certificate authority so that users can now run my proxy and receive a multi-factor authenticated certificate. NICS is also exploring the federation of multi-factor authentication systems, with the goal of "one user, one token". This is especially important, as new grid resources, such as Blue Waters, will only allow multi-factor authentication, and we want the users to only carry one token, not many tokens. XSEDE, the TeraGrid successor, will also be deploying multi-factor authentication in addition to the other existing authentication methodologies. XSEDE will also work closely with science gateways and workflows to develop and maintain secure frameworks for the highest level of security possible.

Developing Applications with Networking Capabilities via End-to-End SDN (DANCES)

Abstract: The Developing Applications with Networking Capabilities via End-to-End SDN (DANCES) project [1] is a collaboration between The University of Tennessee's National Institute for Computational Sciences (UT-NICS), Pittsburgh Supercomputing Center (PSC), Pennsylvania State University (Penn State), the National Center for Supercomputing Applications (NCSA), Texas Advanced Computing Center (TACC), Georgia Institute of Technology (Georgia Tech), the Extreme Science and Engineering Discovery Environment (XSEDE), and Internet2 to investigate and develop the ability to add network bandwidth scheduling via software-defined networking (SDN) programmability to selected cyberinfrastructure services and applications. DANCES, funded by the National Science Foundation's Campus Cyberinfrastructure -- Network Infrastructure and Engineering (CC-NIE) program award numbers 1341005, 1340953, and 1340981, has field tested five vendor network devices in order to determine which implements the DANCES requirements of the OpenFlow 1.3 standard to provide the network reservation and rate-limiting capability desired to implement the goals of DANCES. Another key device selection criterion was sufficient packet buffering to handle wide area network flows without excessive packet loss. After selection of the network device a test environment was setup between UT-NICS and PSC to perform SDN tests in a simulated supercomputer center compute and data transfer resource environment. This paper describes the DANCES project, the DANCES OpenFlow 1.3 specification requirements, the determination and acquiring of a sufficient OpenFlow 1.3 network device, the provisioning of a test environment, and the test plan and results obtained so far by the DANCES team.

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

Abstract: Galaxy (homepage: https://galaxyproject.org, main public server: https://usegalaxy.org) is a web-based scientific analysis platform used by tens of thousands of scientists across the world to analyze large biomedical datasets such as those found in genomics, proteomics, metabolomics and imaging. Started in 2005, Galaxy continues to focus on three key challenges of data-driven biomedical science: making analyses accessible to all researchers, ensuring analyses are completely reproducible, and making it simple to communicate analyses so that they can be reused and extended. During the last two years, the Galaxy team and the open-source community around Galaxy have made substantial improvements to Galaxy's core framework, user interface, tools, and training materials. Framework and user interface improvements now enable Galaxy to be used for analyzing tens of thousands of datasets, and >5500 tools are now available from the Galaxy ToolShed. The Galaxy community has led an effort to create numerous high-quality tutorials focused on common types of genomic analyses. The Galaxy developer and user communities continue to grow and be integral to Galaxy's development. The number of Galaxy public servers, developers contributing to the Galaxy framework and its tools, and users of the main Galaxy server have all increased substantially.

iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data

Abstract: RNA-seq is widely used for transcriptomic profiling, but the bioinformatics analysis of resultant data can be time-consuming and challenging, especially for biologists. We aim to streamline the bioinformatic analyses of gene-level data by developing a user-friendly, interactive web application for exploratory data analysis, differential expression, and pathway analysis. iDEP (integrated Differential Expression and Pathway analysis) seamlessly connects 63 R/Bioconductor packages, 2 web services, and comprehensive annotation and pathway databases for 220 plant and animal species. The workflow can be reproduced by downloading customized R code and related pathway files. As an example, we analyzed an RNA-Seq dataset of lung fibroblasts with Hoxa1 knockdown and revealed the possible roles of SP1 and E2F1 and their target genes, including microRNAs, in blocking G1/S transition. In another example, our analysis shows that in mouse B cells without functional p53, ionizing radiation activates the MYC pathway and its downstream genes involved in cell proliferation, ribosome biogenesis, and non-coding RNA metabolism. In wildtype B cells, radiation induces p53-mediated apoptosis and DNA repair while suppressing the target genes of MYC and E2F1, and leads to growth and cell cycle arrest. iDEP helps unveil the multifaceted functions of p53 and the possible involvement of several microRNAs such as miR-92a, miR-504, and miR-30a. In both examples, we validated known molecular pathways and generated novel, testable hypotheses. Combining comprehensive analytic functionalities with massive annotation databases, iDEP ( http://ge-lab.org/idep/ ) enables biologists to easily translate transcriptomic and proteomic data into actionable insights.

Mechanical Properties of Organic Semiconductors for Stretchable, Highly Flexible, and Mechanically Robust Electronics

Abstract: Mechanical deformability underpins many of the advantages of organic semiconductors. The mechanical properties of these materials are, however, diverse, and the molecular characteristics that permit charge transport can render the materials stiff and brittle. This review is a comprehensive description of the molecular and morphological parameters that govern the mechanical properties of organic semiconductors. Particular attention is paid to ways in which mechanical deformability and electronic performance can coexist. The review begins with a discussion of flexible and stretchable devices of all types, and in particular the unique characteristics of organic semiconductors. It then discusses the mechanical properties most relevant to deformable devices. In particular, it describes how low modulus, good adhesion, and absolute extensibility prior to fracture enable robust performance, along with mechanical “imperceptibility” if worn on the skin. A description of techniques of metrology precedes a discussion...

Ruthenium atomically dispersed in carbon outperforms platinum toward hydrogen evolution in alkaline media.

Abstract: Hydrogen evolution reaction is an important process in electrochemical energy technologies. Herein, ruthenium and nitrogen codoped carbon nanowires are prepared as effective hydrogen evolution catalysts. The catalytic performance is markedly better than that of commercial platinum catalyst, with an overpotential of only -12 mV to reach the current density of 10 mV cm-2 in 1 M KOH and -47 mV in 0.1 M KOH. Comparisons with control experiments suggest that the remarkable activity is mainly ascribed to individual ruthenium atoms embedded within the carbon matrix, with minimal contributions from ruthenium nanoparticles. Consistent results are obtained in first-principles calculations, where RuCxNy moieties are found to show a much lower hydrogen binding energy than ruthenium nanoparticles, and a lower kinetic barrier for water dissociation than platinum. Among these, RuC2N2 stands out as the most active catalytic center, where both ruthenium and adjacent carbon atoms are the possible active sites.