Review of Enabling Technologies to Facilitate Secure Compute Customization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aderholdt, Ferrol; Caldwell, Blake A; Hicks, Susan Elaine

High performance computing environments are often used for a wide variety of workloads ranging from simulation, data transformation and analysis, and complex workflows to name just a few. These systems may process data for a variety of users, often requiring strong separation between job allocations. There are many challenges to establishing these secure enclaves within the shared infrastructure of high-performance computing (HPC) environments. The isolation mechanisms in the system software are the basic building blocks for enabling secure compute enclaves. There are a variety of approaches and the focus of this report is to review the different virtualization technologies thatmore » facilitate the creation of secure compute enclaves. The report reviews current operating system (OS) protection mechanisms and modern virtualization technologies to better understand the performance/isolation properties. We also examine the feasibility of running ``virtualized'' computing resources as non-privileged users, and providing controlled administrative permissions for standard users running within a virtualized context. Our examination includes technologies such as Linux containers (LXC [32], Docker [15]) and full virtualization (KVM [26], Xen [5]). We categorize these different approaches to virtualization into two broad groups: OS-level virtualization and system-level virtualization. The OS-level virtualization uses containers to allow a single OS kernel to be partitioned to create Virtual Environments (VE), e.g., LXC. The resources within the host's kernel are only virtualized in the sense of separate namespaces. In contrast, system-level virtualization uses hypervisors to manage multiple OS kernels and virtualize the physical resources (hardware) to create Virtual Machines (VM), e.g., Xen, KVM. This terminology of VE and VM, detailed in Section 2, is used throughout the report to distinguish between the two different approaches to providing virtualized execution environments. As part of our technology review we analyzed several current virtualization solutions to assess their vulnerabilities. This included a review of common vulnerabilities and exposures (CVEs) for Xen, KVM, LXC and Docker to gauge their susceptibility to different attacks. The complete details are provided in Section 5 on page 33. Based on this review we concluded that system-level virtualization solutions have many more vulnerabilities than OS level virtualization solutions. As such, security mechanisms like sVirt (Section 3.3) should be considered when using system-level virtualization solutions in order to protect the host against exploits. The majority of vulnerabilities related to KVM, LXC, and Docker are in specific regions of the system. Therefore, future "zero day attacks" are likely to be in the same regions, which suggests that protecting these areas can simplify the protection of the host and maintain the isolation between users. The evaluations of virtualization technologies done thus far are discussed in Section 4. This includes experiments with 'user' namespaces in VEs, which provides the ability to isolate user privileges and allow a user to run with different UIDs within the container while mapping them to non-privileged UIDs in the host. We have identified Linux namespaces as a promising mechanism to isolate shared resources, while maintaining good performance. In Section 4.1 we describe our tests with LXC as a non-root user and leveraging namespaces to control UID/GID mappings and support controlled sharing of parallel file-systems. We highlight several of these namespace capabilities in Section 6.2.3. The other evaluations that were performed during this initial phase of work provide baseline performance data for comparing VEs and VMs to purely native execution. In Section 4.2 we performed tests using the High-Performance Computing Conjugate Gradient (HPCCG) benchmark to establish baseline performance for a scientific application when run on the Native (host) machine in contrast with execution under Docker and KVM. Our tests verified prior studies showing roughly 2-4% overheads in application execution time & MFlops when running in hypervisor-base environments (VMs) as compared to near native performance with VEs. For more details, see Figures 4.5 (page 28), 4.6 (page 28), and 4.7 (page 29). Additionally, in Section 4.3 we include network measurements for TCP bandwidth performance over the 10GigE interface in our testbed. The Native and Docker based tests achieved >= ~9Gbits/sec, while the KVM configuration only achieved 2.5Gbits/sec (Table 4.6 on page 32). This may be a configuration issue with our KVM installation, and is a point for further testing as we refine the network settings in the testbed. The initial network tests were done using a bridged networking configuration. The report outline is as follows: - Section 1 introduces the report and clarifies the scope of the proj...« less

GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research

PubMed Central

Yeung, Ka Yee

2016-01-01

Reproducibility is vital in science. For complex computational methods, it is often necessary, not just to recreate the code, but also the software and hardware environment to reproduce results. Virtual machines, and container software such as Docker, make it possible to reproduce the exact environment regardless of the underlying hardware and operating system. However, workflows that use Graphical User Interfaces (GUIs) remain difficult to replicate on different host systems as there is no high level graphical software layer common to all platforms. GUIdock allows for the facile distribution of a systems biology application along with its graphics environment. Complex graphics based workflows, ubiquitous in systems biology, can now be easily exported and reproduced on many different platforms. GUIdock uses Docker, an open source project that provides a container with only the absolutely necessary software dependencies and configures a common X Windows (X11) graphic interface on Linux, Macintosh and Windows platforms. As proof of concept, we present a Docker package that contains a Bioconductor application written in R and C++ called networkBMA for gene network inference. Our package also includes Cytoscape, a java-based platform with a graphical user interface for visualizing and analyzing gene networks, and the CyNetworkBMA app, a Cytoscape app that allows the use of networkBMA via the user-friendly Cytoscape interface. PMID:27045593

GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research.

PubMed

Hung, Ling-Hong; Kristiyanto, Daniel; Lee, Sung Bong; Yeung, Ka Yee

2016-01-01

Reproducibility is vital in science. For complex computational methods, it is often necessary, not just to recreate the code, but also the software and hardware environment to reproduce results. Virtual machines, and container software such as Docker, make it possible to reproduce the exact environment regardless of the underlying hardware and operating system. However, workflows that use Graphical User Interfaces (GUIs) remain difficult to replicate on different host systems as there is no high level graphical software layer common to all platforms. GUIdock allows for the facile distribution of a systems biology application along with its graphics environment. Complex graphics based workflows, ubiquitous in systems biology, can now be easily exported and reproduced on many different platforms. GUIdock uses Docker, an open source project that provides a container with only the absolutely necessary software dependencies and configures a common X Windows (X11) graphic interface on Linux, Macintosh and Windows platforms. As proof of concept, we present a Docker package that contains a Bioconductor application written in R and C++ called networkBMA for gene network inference. Our package also includes Cytoscape, a java-based platform with a graphical user interface for visualizing and analyzing gene networks, and the CyNetworkBMA app, a Cytoscape app that allows the use of networkBMA via the user-friendly Cytoscape interface.

Using Docker Containers to Extend Reproducibility Architecture for the NASA Earth Exchange (NEX)

NASA Technical Reports Server (NTRS)

Votava, Petr; Michaelis, Andrew; Spaulding, Ryan; Becker, Jeffrey C.

2016-01-01

NASA Earth Exchange (NEX) is a data, supercomputing and knowledge collaboratory that houses NASA satellite, climate and ancillary data where a focused community can come together to address large-scale challenges in Earth sciences. As NEX has been growing into a petabyte-size platform for analysis, experiments and data production, it has been increasingly important to enable users to easily retrace their steps, identify what datasets were produced by which process chains, and give them ability to readily reproduce their results. This can be a tedious and difficult task even for a small project, but is almost impossible on large processing pipelines. We have developed an initial reproducibility and knowledge capture solution for the NEX, however, if users want to move the code to another system, whether it is their home institution cluster, laptop or the cloud, they have to find, build and install all the required dependencies that would run their code. This can be a very tedious and tricky process and is a big impediment to moving code to data and reproducibility outside the original system. The NEX team has tried to assist users who wanted to move their code into OpenNEX on Amazon cloud by creating custom virtual machines with all the software and dependencies installed, but this, while solving some of the issues, creates a new bottleneck that requires the NEX team to be involved with any new request, updates to virtual machines and general maintenance support. In this presentation, we will describe a solution that integrates NEX and Docker to bridge the gap in code-to-data migration. The core of the solution is saemi-automatic conversion of science codes, tools and services that are already tracked and described in the NEX provenance system, to Docker - an open-source Linux container software. Docker is available on most computer platforms, easy to install and capable of seamlessly creating and/or executing any application packaged in the appropriate format. We believe this is an important step towards seamless process deployment in heterogeneous environments that will enhance community access to NASA data and tools in a scalable way, promote software reuse, and improve reproducibility of scientific results.

Using Docker Containers to Extend Reproducibility Architecture for the NASA Earth Exchange (NEX)

NASA Astrophysics Data System (ADS)

Votava, P.; Michaelis, A.; Spaulding, R.; Becker, J. C.

2016-12-01

NASA Earth Exchange (NEX) is a data, supercomputing and knowledge collaboratory that houses NASA satellite, climate and ancillary data where a focused community can come together to address large-scale challenges in Earth sciences. As NEX has been growing into a petabyte-size platform for analysis, experiments and data production, it has been increasingly important to enable users to easily retrace their steps, identify what datasets were produced by which process chains, and give them ability to readily reproduce their results. This can be a tedious and difficult task even for a small project, but is almost impossible on large processing pipelines. We have developed an initial reproducibility and knowledge capture solution for the NEX, however, if users want to move the code to another system, whether it is their home institution cluster, laptop or the cloud, they have to find, build and install all the required dependencies that would run their code. This can be a very tedious and tricky process and is a big impediment to moving code to data and reproducibility outside the original system. The NEX team has tried to assist users who wanted to move their code into OpenNEX on Amazon cloud by creating custom virtual machines with all the software and dependencies installed, but this, while solving some of the issues, creates a new bottleneck that requires the NEX team to be involved with any new request, updates to virtual machines and general maintenance support. In this presentation, we will describe a solution that integrates NEX and Docker to bridge the gap in code-to-data migration. The core of the solution is saemi-automatic conversion of science codes, tools and services that are already tracked and described in the NEX provenance system, to Docker - an open-source Linux container software. Docker is available on most computer platforms, easy to install and capable of seamlessly creating and/or executing any application packaged in the appropriate format. We believe this is an important step towards seamless process deployment in heterogeneous environments that will enhance community access to NASA data and tools in a scalable way, promote software reuse, and improve reproducibility of scientific results.

An Interactive Web-Based Analysis Framework for Remote Sensing Cloud Computing

NASA Astrophysics Data System (ADS)

Wang, X. Z.; Zhang, H. M.; Zhao, J. H.; Lin, Q. H.; Zhou, Y. C.; Li, J. H.

2015-07-01

Spatiotemporal data, especially remote sensing data, are widely used in ecological, geographical, agriculture, and military research and applications. With the development of remote sensing technology, more and more remote sensing data are accumulated and stored in the cloud. An effective way for cloud users to access and analyse these massive spatiotemporal data in the web clients becomes an urgent issue. In this paper, we proposed a new scalable, interactive and web-based cloud computing solution for massive remote sensing data analysis. We build a spatiotemporal analysis platform to provide the end-user with a safe and convenient way to access massive remote sensing data stored in the cloud. The lightweight cloud storage system used to store public data and users' private data is constructed based on open source distributed file system. In it, massive remote sensing data are stored as public data, while the intermediate and input data are stored as private data. The elastic, scalable, and flexible cloud computing environment is built using Docker, which is a technology of open-source lightweight cloud computing container in the Linux operating system. In the Docker container, open-source software such as IPython, NumPy, GDAL, and Grass GIS etc., are deployed. Users can write scripts in the IPython Notebook web page through the web browser to process data, and the scripts will be submitted to IPython kernel to be executed. By comparing the performance of remote sensing data analysis tasks executed in Docker container, KVM virtual machines and physical machines respectively, we can conclude that the cloud computing environment built by Docker makes the greatest use of the host system resources, and can handle more concurrent spatial-temporal computing tasks. Docker technology provides resource isolation mechanism in aspects of IO, CPU, and memory etc., which offers security guarantee when processing remote sensing data in the IPython Notebook. Users can write complex data processing code on the web directly, so they can design their own data processing algorithm.

Application of Docker Swarm cluster for testing programs, developed for system of devices within paradigm of Internet of things

NASA Astrophysics Data System (ADS)

Shichkina, Y. A.; Kupriyanov, M. S.; Moldachev, S. O.

2018-05-01

Today, a description of various Internet devices very often appears on the Internet. For the efficient operation of the Industrial Internet of things, it is necessary to provide a modern level of data processing starting from getting them from devices ending with returning them to devices in a processed form. Current solutions of the Internet of Things are mainly focused on the development of centralized decisions, projecting the Internet of Things on the set of cloud-based platforms that are open, but limit the ability of participants of the Internet of Things to adapt these systems to their own problems. Therefore, it is often necessary to create specialized software for specific areas of the Internet of Things. This article describes the solution of the problem of virtualization of the system of devices based on the Docker system. This solution allows developers to test any software on any number of devices forming a mesh.

BGDMdocker: a Docker workflow for data mining and visualization of bacterial pan-genomes and biosynthetic gene clusters.

PubMed

Cheng, Gong; Lu, Quan; Ma, Ling; Zhang, Guocai; Xu, Liang; Zhou, Zongshan

2017-01-01

Recently, Docker technology has received increasing attention throughout the bioinformatics community. However, its implementation has not yet been mastered by most biologists; accordingly, its application in biological research has been limited. In order to popularize this technology in the field of bioinformatics and to promote the use of publicly available bioinformatics tools, such as Dockerfiles and Images from communities, government sources, and private owners in the Docker Hub Registry and other Docker-based resources, we introduce here a complete and accurate bioinformatics workflow based on Docker. The present workflow enables analysis and visualization of pan-genomes and biosynthetic gene clusters of bacteria. This provides a new solution for bioinformatics mining of big data from various publicly available biological databases. The present step-by-step guide creates an integrative workflow through a Dockerfile to allow researchers to build their own Image and run Container easily.

BGDMdocker: a Docker workflow for data mining and visualization of bacterial pan-genomes and biosynthetic gene clusters

PubMed Central

Cheng, Gong; Zhang, Guocai; Xu, Liang

2017-01-01

Recently, Docker technology has received increasing attention throughout the bioinformatics community. However, its implementation has not yet been mastered by most biologists; accordingly, its application in biological research has been limited. In order to popularize this technology in the field of bioinformatics and to promote the use of publicly available bioinformatics tools, such as Dockerfiles and Images from communities, government sources, and private owners in the Docker Hub Registry and other Docker-based resources, we introduce here a complete and accurate bioinformatics workflow based on Docker. The present workflow enables analysis and visualization of pan-genomes and biosynthetic gene clusters of bacteria. This provides a new solution for bioinformatics mining of big data from various publicly available biological databases. The present step-by-step guide creates an integrative workflow through a Dockerfile to allow researchers to build their own Image and run Container easily. PMID:29204317

Everware toolkit. Supporting reproducible science and challenge-driven education.

NASA Astrophysics Data System (ADS)

Ustyuzhanin, A.; Head, T.; Babuschkin, I.; Tiunov, A.

2017-10-01

Modern science clearly demands for a higher level of reproducibility and collaboration. To make research fully reproducible one has to take care of several aspects: research protocol description, data access, environment preservation, workflow pipeline, and analysis script preservation. Version control systems like git help with the workflow and analysis scripts part. Virtualization techniques like Docker or Vagrant can help deal with environments. Jupyter notebooks are a powerful platform for conducting research in a collaborative manner. We present project Everware that seamlessly integrates git repository management systems such as Github or Gitlab, Docker and Jupyter helping with a) sharing results of real research and b) boosts education activities. With the help of Everware one can not only share the final artifacts of research but all the depth of the research process. This been shown to be extremely helpful during organization of several data analysis hackathons and machine learning schools. Using Everware participants could start from an existing solution instead of starting from scratch. They could start contributing immediately. Everware allows its users to make use of their own computational resources to run the workflows they are interested in, which leads to higher scalability of the toolkit.

A Steric-inhibition model for regulation of nucleotide exchange via the Dock180 family of GEFs.

PubMed

Lu, Mingjian; Kinchen, Jason M; Rossman, Kent L; Grimsley, Cynthia; Hall, Matthew; Sondek, John; Hengartner, Michael O; Yajnik, Vijay; Ravichandran, Kodi S

2005-02-22

CDM (CED-5, Dock180, Myoblast city) family members have been recently identified as novel, evolutionarily conserved guanine nucleotide exchange factors (GEFs) for Rho-family GTPases . They regulate multiple processes, including embryonic development, cell migration, apoptotic-cell engulfment, tumor invasion, and HIV-1 infection, in diverse model systems . However, the mechanism(s) of regulation of CDM proteins has not been well understood. Here, our studies on the prototype member Dock180 reveal a steric-inhibition model for regulating the Dock180 family of GEFs. At basal state, the N-terminal SH3 domain of Dock180 binds to the distant catalytic Docker domain and negatively regulates the function of Dock180. Further studies revealed that the SH3:Docker interaction sterically blocks Rac access to the Docker domain. Interestingly, ELMO binding to the SH3 domain of Dock180 disrupted the SH3:Docker interaction, facilitated Rac access to the Docker domain, and contributed to the GEF activity of the Dock180/ELMO complex. Additional genetic rescue studies in C. elegans suggested that the regulation of the Docker-domain-mediated GEF activity by the SH3 domain and its adjoining region is evolutionarily conserved. This steric-inhibition model may be a general mechanism for regulating multiple SH3-domain-containing Dock180 family members and may have implications for a variety of biological processes.

The development of an autonomous rendezvous and docking simulation using rapid integration and prototyping technology

NASA Technical Reports Server (NTRS)

Shackelford, John H.; Saugen, John D.; Wurst, Michael J.; Adler, James

1991-01-01

A generic planar 3 degree of freedom simulation was developed that supports hardware in the loop simulations, guidance and control analysis, and can directly generate flight software. This simulation was developed in a small amount of time utilizing rapid prototyping techniques. The approach taken to develop this simulation tool, the benefits seen using this approach to development, and on-going efforts to improve and extend this capability are described. The simulation is composed of 3 major elements: (1) Docker dynamics model, (2) Dockee dynamics model, and (3) Docker Control System. The docker and dockee models are based on simple planar orbital dynamics equations using a spherical earth gravity model. The docker control system is based on a phase plane approach to error correction.

The impact of Docker containers on the performance of genomic pipelines

PubMed Central

Palumbo, Emilio; Chatzou, Maria; Prieto, Pablo; Heuer, Michael L.; Notredame, Cedric

2015-01-01

Genomic pipelines consist of several pieces of third party software and, because of their experimental nature, frequent changes and updates are commonly necessary thus raising serious deployment and reproducibility issues. Docker containers are emerging as a possible solution for many of these problems, as they allow the packaging of pipelines in an isolated and self-contained manner. This makes it easy to distribute and execute pipelines in a portable manner across a wide range of computing platforms. Thus, the question that arises is to what extent the use of Docker containers might affect the performance of these pipelines. Here we address this question and conclude that Docker containers have only a minor impact on the performance of common genomic pipelines, which is negligible when the executed jobs are long in terms of computational time. PMID:26421241

The impact of Docker containers on the performance of genomic pipelines.

PubMed

Di Tommaso, Paolo; Palumbo, Emilio; Chatzou, Maria; Prieto, Pablo; Heuer, Michael L; Notredame, Cedric

2015-01-01

Genomic pipelines consist of several pieces of third party software and, because of their experimental nature, frequent changes and updates are commonly necessary thus raising serious deployment and reproducibility issues. Docker containers are emerging as a possible solution for many of these problems, as they allow the packaging of pipelines in an isolated and self-contained manner. This makes it easy to distribute and execute pipelines in a portable manner across a wide range of computing platforms. Thus, the question that arises is to what extent the use of Docker containers might affect the performance of these pipelines. Here we address this question and conclude that Docker containers have only a minor impact on the performance of common genomic pipelines, which is negligible when the executed jobs are long in terms of computational time.

Status and Roadmap of CernVM

NASA Astrophysics Data System (ADS)

Berzano, D.; Blomer, J.; Buncic, P.; Charalampidis, I.; Ganis, G.; Meusel, R.

2015-12-01

Cloud resources nowadays contribute an essential share of resources for computing in high-energy physics. Such resources can be either provided by private or public IaaS clouds (e.g. OpenStack, Amazon EC2, Google Compute Engine) or by volunteers computers (e.g. LHC@Home 2.0). In any case, experiments need to prepare a virtual machine image that provides the execution environment for the physics application at hand. The CernVM virtual machine since version 3 is a minimal and versatile virtual machine image capable of booting different operating systems. The virtual machine image is less than 20 megabyte in size. The actual operating system is delivered on demand by the CernVM File System. CernVM 3 has matured from a prototype to a production environment. It is used, for instance, to run LHC applications in the cloud, to tune event generators using a network of volunteer computers, and as a container for the historic Scientific Linux 5 and Scientific Linux 4 based software environments in the course of long-term data preservation efforts of the ALICE, CMS, and ALEPH experiments. We present experience and lessons learned from the use of CernVM at scale. We also provide an outlook on the upcoming developments. These developments include adding support for Scientific Linux 7, the use of container virtualization, such as provided by Docker, and the streamlining of virtual machine contextualization towards the cloud-init industry standard.

Data-Proximate Analysis and Visualization in the Cloud using Cloudstream, an Open-Source Application Streaming Technology Stack

NASA Astrophysics Data System (ADS)

Fisher, W. I.

2017-12-01

The rise in cloud computing, coupled with the growth of "Big Data", has lead to a migration away from local scientific data storage. The increasing size of remote scientific data sets increase, however, makes it difficult for scientists to subject them to large-scale analysis and visualization. These large datasets can take an inordinate amount of time to download; subsetting is a potential solution, but subsetting services are not yet ubiquitous. Data providers may also pay steep prices, as many cloud providers meter data based on how much data leaves their cloud service. The solution to this problem is a deceptively simple one; move data analysis and visualization tools to the cloud, so that scientists may perform data-proximate analysis and visualization. This results in increased transfer speeds, while egress costs are lowered or completely eliminated. Moving standard desktop analysis and visualization tools to the cloud is enabled via a technique called "Application Streaming". This technology allows a program to run entirely on a remote virtual machine while still allowing for interactivity and dynamic visualizations. When coupled with containerization technology such as Docker, we are able to easily deploy legacy analysis and visualization software to the cloud whilst retaining access via a desktop, netbook, a smartphone, or the next generation of hardware, whatever it may be. Unidata has created a Docker-based solution for easily adapting legacy software for Application Streaming. This technology stack, dubbed Cloudstream, allows desktop software to run in the cloud with little-to-no effort. The docker container is configured by editing text files, and the legacy software does not need to be modified in any way. This work will discuss the underlying technologies used by Cloudstream, and outline how to use Cloudstream to run and access an existing desktop application to the cloud.

BioShaDock: a community driven bioinformatics shared Docker-based tools registry

PubMed Central

Moreews, François; Sallou, Olivier; Ménager, Hervé; Le bras, Yvan; Monjeaud, Cyril; Blanchet, Christophe; Collin, Olivier

2015-01-01

Linux container technologies, as represented by Docker, provide an alternative to complex and time-consuming installation processes needed for scientific software. The ease of deployment and the process isolation they enable, as well as the reproducibility they permit across environments and versions, are among the qualities that make them interesting candidates for the construction of bioinformatic infrastructures, at any scale from single workstations to high throughput computing architectures. The Docker Hub is a public registry which can be used to distribute bioinformatic software as Docker images. However, its lack of curation and its genericity make it difficult for a bioinformatics user to find the most appropriate images needed. BioShaDock is a bioinformatics-focused Docker registry, which provides a local and fully controlled environment to build and publish bioinformatic software as portable Docker images. It provides a number of improvements over the base Docker registry on authentication and permissions management, that enable its integration in existing bioinformatic infrastructures such as computing platforms. The metadata associated with the registered images are domain-centric, including for instance concepts defined in the EDAM ontology, a shared and structured vocabulary of commonly used terms in bioinformatics. The registry also includes user defined tags to facilitate its discovery, as well as a link to the tool description in the ELIXIR registry if it already exists. If it does not, the BioShaDock registry will synchronize with the registry to create a new description in the Elixir registry, based on the BioShaDock entry metadata. This link will help users get more information on the tool such as its EDAM operations, input and output types. This allows integration with the ELIXIR Tools and Data Services Registry, thus providing the appropriate visibility of such images to the bioinformatics community. PMID:26913191

BioShaDock: a community driven bioinformatics shared Docker-based tools registry.

PubMed

Moreews, François; Sallou, Olivier; Ménager, Hervé; Le Bras, Yvan; Monjeaud, Cyril; Blanchet, Christophe; Collin, Olivier

2015-01-01

Linux container technologies, as represented by Docker, provide an alternative to complex and time-consuming installation processes needed for scientific software. The ease of deployment and the process isolation they enable, as well as the reproducibility they permit across environments and versions, are among the qualities that make them interesting candidates for the construction of bioinformatic infrastructures, at any scale from single workstations to high throughput computing architectures. The Docker Hub is a public registry which can be used to distribute bioinformatic software as Docker images. However, its lack of curation and its genericity make it difficult for a bioinformatics user to find the most appropriate images needed. BioShaDock is a bioinformatics-focused Docker registry, which provides a local and fully controlled environment to build and publish bioinformatic software as portable Docker images. It provides a number of improvements over the base Docker registry on authentication and permissions management, that enable its integration in existing bioinformatic infrastructures such as computing platforms. The metadata associated with the registered images are domain-centric, including for instance concepts defined in the EDAM ontology, a shared and structured vocabulary of commonly used terms in bioinformatics. The registry also includes user defined tags to facilitate its discovery, as well as a link to the tool description in the ELIXIR registry if it already exists. If it does not, the BioShaDock registry will synchronize with the registry to create a new description in the Elixir registry, based on the BioShaDock entry metadata. This link will help users get more information on the tool such as its EDAM operations, input and output types. This allows integration with the ELIXIR Tools and Data Services Registry, thus providing the appropriate visibility of such images to the bioinformatics community.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kowalkowski, Jim; Lyon, Adam; Paterno, Marc

Over the past few years, container technology has become increasingly promising as a means to seamlessly make our software available across a wider range of platforms. In December 2015, we decided to put together a set of docker images that serve as a demonstration of this container technology for managing a run-time environment for art-related software projects, and also serve as a set of test cases for evaluation of performance. Docker[1] containers provide a way to “wrap up a piece of software in a complete filesystem that contains everything it needs to run”. In combination with Shifter[2], such containers providemore » a way to run software developed and deployed on “typical” HEP platforms (such as SLF 6, in common use at Fermilab and on OSG platforms) on HPC facilities at NERSC. Docker containers provide a means of delivering software that can be run on a variety of hosts without needing to be compiled specially for each OS to be supported. This could substantially reduce the effort required to create and validate a new release, since one build could be suitable for use on both grid machines (both FermiGrid and OSG) as well as any machine capable of running the Docker container. In addition, docker containers may provide for a quick and easy way for users to install and use a software release in a standardized environment. This report contains the results and status of this demonstration and evaluation.« less

Use of application containers and workflows for genomic data analysis.

PubMed

Schulz, Wade L; Durant, Thomas J S; Siddon, Alexa J; Torres, Richard

2016-01-01

The rapid acquisition of biological data and development of computationally intensive analyses has led to a need for novel approaches to software deployment. In particular, the complexity of common analytic tools for genomics makes them difficult to deploy and decreases the reproducibility of computational experiments. Recent technologies that allow for application virtualization, such as Docker, allow developers and bioinformaticians to isolate these applications and deploy secure, scalable platforms that have the potential to dramatically increase the efficiency of big data processing. While limitations exist, this study demonstrates a successful implementation of a pipeline with several discrete software applications for the analysis of next-generation sequencing (NGS) data. With this approach, we significantly reduced the amount of time needed to perform clonal analysis from NGS data in acute myeloid leukemia.

An architecture for genomics analysis in a clinical setting using Galaxy and Docker

PubMed Central

Digan, W; Countouris, H; Barritault, M; Baudoin, D; Laurent-Puig, P; Blons, H; Burgun, A

2017-01-01

Abstract Next-generation sequencing is used on a daily basis to perform molecular analysis to determine subtypes of disease (e.g., in cancer) and to assist in the selection of the optimal treatment. Clinical bioinformatics handles the manipulation of the data generated by the sequencer, from the generation to the analysis and interpretation. Reproducibility and traceability are crucial issues in a clinical setting. We have designed an approach based on Docker container technology and Galaxy, the popular bioinformatics analysis support open-source software. Our solution simplifies the deployment of a small-size analytical platform and simplifies the process for the clinician. From the technical point of view, the tools embedded in the platform are isolated and versioned through Docker images. Along the Galaxy platform, we also introduce the AnalysisManager, a solution that allows single-click analysis for biologists and leverages standardized bioinformatics application programming interfaces. We added a Shiny/R interactive environment to ease the visualization of the outputs. The platform relies on containers and ensures the data traceability by recording analytical actions and by associating inputs and outputs of the tools to EDAM ontology through ReGaTe. The source code is freely available on Github at https://github.com/CARPEM/GalaxyDocker. PMID:29048555

An architecture for genomics analysis in a clinical setting using Galaxy and Docker.

PubMed

Digan, W; Countouris, H; Barritault, M; Baudoin, D; Laurent-Puig, P; Blons, H; Burgun, A; Rance, B

2017-11-01

Next-generation sequencing is used on a daily basis to perform molecular analysis to determine subtypes of disease (e.g., in cancer) and to assist in the selection of the optimal treatment. Clinical bioinformatics handles the manipulation of the data generated by the sequencer, from the generation to the analysis and interpretation. Reproducibility and traceability are crucial issues in a clinical setting. We have designed an approach based on Docker container technology and Galaxy, the popular bioinformatics analysis support open-source software. Our solution simplifies the deployment of a small-size analytical platform and simplifies the process for the clinician. From the technical point of view, the tools embedded in the platform are isolated and versioned through Docker images. Along the Galaxy platform, we also introduce the AnalysisManager, a solution that allows single-click analysis for biologists and leverages standardized bioinformatics application programming interfaces. We added a Shiny/R interactive environment to ease the visualization of the outputs. The platform relies on containers and ensures the data traceability by recording analytical actions and by associating inputs and outputs of the tools to EDAM ontology through ReGaTe. The source code is freely available on Github at https://github.com/CARPEM/GalaxyDocker. © The Author 2017. Published by Oxford University Press.

Enhanced reproducibility of SADI web service workflows with Galaxy and Docker.

PubMed

Aranguren, Mikel Egaña; Wilkinson, Mark D

2015-01-01

Semantic Web technologies have been widely applied in the life sciences, for example by data providers such as OpenLifeData and through web services frameworks such as SADI. The recently reported OpenLifeData2SADI project offers access to the vast OpenLifeData data store through SADI services. This article describes how to merge data retrieved from OpenLifeData2SADI with other SADI services using the Galaxy bioinformatics analysis platform, thus making this semantic data more amenable to complex analyses. This is demonstrated using a working example, which is made distributable and reproducible through a Docker image that includes SADI tools, along with the data and workflows that constitute the demonstration. The combination of Galaxy and Docker offers a solution for faithfully reproducing and sharing complex data retrieval and analysis workflows based on the SADI Semantic web service design patterns.

Prognostics and health management system for hydropower plant based on fog computing and docker container

NASA Astrophysics Data System (ADS)

Xiao, Jian; Zhang, Mingqiang; Tian, Haiping; Huang, Bo; Fu, Wenlong

2018-02-01

In this paper, a novel prognostics and health management system architecture for hydropower plant equipment was proposed based on fog computing and Docker container. We employed the fog node to improve the real-time processing ability of improving the cloud architecture-based prognostics and health management system and overcome the problems of long delay time, network congestion and so on. Then Storm-based stream processing of fog node was present and could calculate the health index in the edge of network. Moreover, the distributed micros-service and Docker container architecture of hydropower plants equipment prognostics and health management was also proposed. Using the micro service architecture proposed in this paper, the hydropower unit can achieve the goal of the business intercommunication and seamless integration of different equipment and different manufacturers. Finally a real application case is given in this paper.

Use of application containers and workflows for genomic data analysis

PubMed Central

Schulz, Wade L.; Durant, Thomas J. S.; Siddon, Alexa J.; Torres, Richard

2016-01-01

Background: The rapid acquisition of biological data and development of computationally intensive analyses has led to a need for novel approaches to software deployment. In particular, the complexity of common analytic tools for genomics makes them difficult to deploy and decreases the reproducibility of computational experiments. Methods: Recent technologies that allow for application virtualization, such as Docker, allow developers and bioinformaticians to isolate these applications and deploy secure, scalable platforms that have the potential to dramatically increase the efficiency of big data processing. Results: While limitations exist, this study demonstrates a successful implementation of a pipeline with several discrete software applications for the analysis of next-generation sequencing (NGS) data. Conclusions: With this approach, we significantly reduced the amount of time needed to perform clonal analysis from NGS data in acute myeloid leukemia. PMID:28163975

Docker Container Manager: A Simple Toolkit for Isolated Work with Shared Computational, Storage, and Network Resources

NASA Astrophysics Data System (ADS)

Polyakov, S. P.; Kryukov, A. P.; Demichev, A. P.

2018-01-01

We present a simple set of command line interface tools called Docker Container Manager (DCM) that allow users to create and manage Docker containers with preconfigured SSH access while keeping the users isolated from each other and restricting their access to the Docker features that could potentially disrupt the work of the server. Users can access DCM server via SSH and are automatically redirected to DCM interface tool. From there, they can create new containers, stop, restart, pause, unpause, and remove containers and view the status of the existing containers. By default, the containers are also accessible via SSH using the same private key(s) but through different server ports. Additional publicly available ports can be mapped to the respective ports of a container, allowing for some network services to be run within it. The containers are started from read-only filesystem images. Some initial images must be provided by the DCM server administrators, and after containers are configured to meet one’s needs, the changes can be saved as new images. Users can see the available images and remove their own images. DCM server administrators are provided with commands to create and delete users. All commands were implemented as Python scripts. The tools allow to deploy and debug medium-sized distributed systems for simulation in different fields on one or several local computers.

SeqBox: RNAseq/ChIPseq reproducible analysis on a consumer game computer.

PubMed

Beccuti, Marco; Cordero, Francesca; Arigoni, Maddalena; Panero, Riccardo; Amparore, Elvio G; Donatelli, Susanna; Calogero, Raffaele A

2018-03-01

Short reads sequencing technology has been used for more than a decade now. However, the analysis of RNAseq and ChIPseq data is still computational demanding and the simple access to raw data does not guarantee results reproducibility between laboratories. To address these two aspects, we developed SeqBox, a cheap, efficient and reproducible RNAseq/ChIPseq hardware/software solution based on NUC6I7KYK mini-PC (an Intel consumer game computer with a fast processor and a high performance SSD disk), and Docker container platform. In SeqBox the analysis of RNAseq and ChIPseq data is supported by a friendly GUI. This allows access to fast and reproducible analysis also to scientists with/without scripting experience. Docker container images, docker4seq package and the GUI are available at http://www.bioinformatica.unito.it/reproducibile.bioinformatics.html. beccuti@di.unito.it. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Bio-Docklets: virtualization containers for single-step execution of NGS pipelines.

PubMed

Kim, Baekdoo; Ali, Thahmina; Lijeron, Carlos; Afgan, Enis; Krampis, Konstantinos

2017-08-01

Processing of next-generation sequencing (NGS) data requires significant technical skills, involving installation, configuration, and execution of bioinformatics data pipelines, in addition to specialized postanalysis visualization and data mining software. In order to address some of these challenges, developers have leveraged virtualization containers toward seamless deployment of preconfigured bioinformatics software and pipelines on any computational platform. We present an approach for abstracting the complex data operations of multistep, bioinformatics pipelines for NGS data analysis. As examples, we have deployed 2 pipelines for RNA sequencing and chromatin immunoprecipitation sequencing, preconfigured within Docker virtualization containers we call Bio-Docklets. Each Bio-Docklet exposes a single data input and output endpoint and from a user perspective, running the pipelines as simply as running a single bioinformatics tool. This is achieved using a "meta-script" that automatically starts the Bio-Docklets and controls the pipeline execution through the BioBlend software library and the Galaxy Application Programming Interface. The pipeline output is postprocessed by integration with the Visual Omics Explorer framework, providing interactive data visualizations that users can access through a web browser. Our goal is to enable easy access to NGS data analysis pipelines for nonbioinformatics experts on any computing environment, whether a laboratory workstation, university computer cluster, or a cloud service provider. Beyond end users, the Bio-Docklets also enables developers to programmatically deploy and run a large number of pipeline instances for concurrent analysis of multiple datasets. © The Authors 2017. Published by Oxford University Press.

Bio-Docklets: virtualization containers for single-step execution of NGS pipelines

PubMed Central

Kim, Baekdoo; Ali, Thahmina; Lijeron, Carlos; Afgan, Enis

2017-01-01

Abstract Processing of next-generation sequencing (NGS) data requires significant technical skills, involving installation, configuration, and execution of bioinformatics data pipelines, in addition to specialized postanalysis visualization and data mining software. In order to address some of these challenges, developers have leveraged virtualization containers toward seamless deployment of preconfigured bioinformatics software and pipelines on any computational platform. We present an approach for abstracting the complex data operations of multistep, bioinformatics pipelines for NGS data analysis. As examples, we have deployed 2 pipelines for RNA sequencing and chromatin immunoprecipitation sequencing, preconfigured within Docker virtualization containers we call Bio-Docklets. Each Bio-Docklet exposes a single data input and output endpoint and from a user perspective, running the pipelines as simply as running a single bioinformatics tool. This is achieved using a “meta-script” that automatically starts the Bio-Docklets and controls the pipeline execution through the BioBlend software library and the Galaxy Application Programming Interface. The pipeline output is postprocessed by integration with the Visual Omics Explorer framework, providing interactive data visualizations that users can access through a web browser. Our goal is to enable easy access to NGS data analysis pipelines for nonbioinformatics experts on any computing environment, whether a laboratory workstation, university computer cluster, or a cloud service provider. Beyond end users, the Bio-Docklets also enables developers to programmatically deploy and run a large number of pipeline instances for concurrent analysis of multiple datasets. PMID:28854616

The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows

PubMed Central

O'Connor, Brian D.; Yuen, Denis; Chung, Vincent; Duncan, Andrew G.; Liu, Xiang Kun; Patricia, Janice; Paten, Benedict; Stein, Lincoln; Ferretti, Vincent

2017-01-01

As genomic datasets continue to grow, the feasibility of downloading data to a local organization and running analysis on a traditional compute environment is becoming increasingly problematic. Current large-scale projects, such as the ICGC PanCancer Analysis of Whole Genomes (PCAWG), the Data Platform for the U.S. Precision Medicine Initiative, and the NIH Big Data to Knowledge Center for Translational Genomics, are using cloud-based infrastructure to both host and perform analysis across large data sets. In PCAWG, over 5,800 whole human genomes were aligned and variant called across 14 cloud and HPC environments; the processed data was then made available on the cloud for further analysis and sharing. If run locally, an operation at this scale would have monopolized a typical academic data centre for many months, and would have presented major challenges for data storage and distribution. However, this scale is increasingly typical for genomics projects and necessitates a rethink of how analytical tools are packaged and moved to the data. For PCAWG, we embraced the use of highly portable Docker images for encapsulating and sharing complex alignment and variant calling workflows across highly variable environments. While successful, this endeavor revealed a limitation in Docker containers, namely the lack of a standardized way to describe and execute the tools encapsulated inside the container. As a result, we created the Dockstore ( https://dockstore.org), a project that brings together Docker images with standardized, machine-readable ways of describing and running the tools contained within. This service greatly improves the sharing and reuse of genomics tools and promotes interoperability with similar projects through emerging web service standards developed by the Global Alliance for Genomics and Health (GA4GH). PMID:28344774

Delivering Unidata Technology via the Cloud

NASA Astrophysics Data System (ADS)

Fisher, Ward; Oxelson Ganter, Jennifer

2016-04-01

Over the last two years, Docker has emerged as the clear leader in open-source containerization. Containerization technology provides a means by which software can be pre-configured and packaged into a single unit, i.e. a container. This container can then be easily deployed either on local or remote systems. Containerization is particularly advantageous when moving software into the cloud, as it simplifies the process. Unidata is adopting containerization as part of our commitment to migrate our technologies to the cloud. We are using a two-pronged approach in this endeavor. In addition to migrating our data-portal services to a cloud environment, we are also exploring new and novel ways to use cloud-specific technology to serve our community. This effort has resulted in several new cloud/Docker-specific projects at Unidata: "CloudStream," "CloudIDV," and "CloudControl." CloudStream is a docker-based technology stack for bringing legacy desktop software to new computing environments, without the need to invest significant engineering/development resources. CloudStream helps make it easier to run existing software in a cloud environment via a technology called "Application Streaming." CloudIDV is a CloudStream-based implementation of the Unidata Integrated Data Viewer (IDV). CloudIDV serves as a practical example of application streaming, and demonstrates how traditional software can be easily accessed and controlled via a web browser. Finally, CloudControl is a web-based dashboard which provides administrative controls for running docker-based technologies in the cloud, as well as providing user management. In this work we will give an overview of these three open-source technologies and the value they offer to our community.

The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows.

PubMed

O'Connor, Brian D; Yuen, Denis; Chung, Vincent; Duncan, Andrew G; Liu, Xiang Kun; Patricia, Janice; Paten, Benedict; Stein, Lincoln; Ferretti, Vincent

2017-01-01

As genomic datasets continue to grow, the feasibility of downloading data to a local organization and running analysis on a traditional compute environment is becoming increasingly problematic. Current large-scale projects, such as the ICGC PanCancer Analysis of Whole Genomes (PCAWG), the Data Platform for the U.S. Precision Medicine Initiative, and the NIH Big Data to Knowledge Center for Translational Genomics, are using cloud-based infrastructure to both host and perform analysis across large data sets. In PCAWG, over 5,800 whole human genomes were aligned and variant called across 14 cloud and HPC environments; the processed data was then made available on the cloud for further analysis and sharing. If run locally, an operation at this scale would have monopolized a typical academic data centre for many months, and would have presented major challenges for data storage and distribution. However, this scale is increasingly typical for genomics projects and necessitates a rethink of how analytical tools are packaged and moved to the data. For PCAWG, we embraced the use of highly portable Docker images for encapsulating and sharing complex alignment and variant calling workflows across highly variable environments. While successful, this endeavor revealed a limitation in Docker containers, namely the lack of a standardized way to describe and execute the tools encapsulated inside the container. As a result, we created the Dockstore ( https://dockstore.org), a project that brings together Docker images with standardized, machine-readable ways of describing and running the tools contained within. This service greatly improves the sharing and reuse of genomics tools and promotes interoperability with similar projects through emerging web service standards developed by the Global Alliance for Genomics and Health (GA4GH).

An Extensible Processing Framework for Eddy-covariance Data

NASA Astrophysics Data System (ADS)

Durden, D.; Fox, A. M.; Metzger, S.; Sturtevant, C.; Durden, N. P.; Luo, H.

2016-12-01

The evolution of large data collecting networks has not only led to an increase of available information, but also in the complexity of analyzing the observations. Timely dissemination of readily usable data products necessitates a streaming processing framework that is both automatable and flexible. Tower networks, such as ICOS, Ameriflux, and NEON, exemplify this issue by requiring large amounts of data to be processed from dispersed measurement sites. Eddy-covariance data from across the NEON network are expected to amount to 100 Gigabytes per day. The complexity of the algorithmic processing necessary to produce high-quality data products together with the continued development of new analysis techniques led to the development of a modular R-package, eddy4R. This allows algorithms provided by NEON and the larger community to be deployed in streaming processing, and to be used by community members alike. In order to control the processing environment, provide a proficient parallel processing structure, and certify dependencies are available during processing, we chose Docker as our "Development and Operations" (DevOps) platform. The Docker framework allows our processing algorithms to be developed, maintained and deployed at scale. Additionally, the eddy4R-Docker framework fosters community use and extensibility via pre-built Docker images and the Github distributed version control system. The capability to process large data sets is reliant upon efficient input and output of data, data compressibility to reduce compute resource loads, and the ability to easily package metadata. The Hierarchical Data Format (HDF5) is a file format that can meet these needs. A NEON standard HDF5 file structure and metadata attributes allow users to explore larger data sets in an intuitive "directory-like" structure adopting the NEON data product naming conventions.

Speeding Up Geophysical Research Using Docker Containers Within Multi-Cloud Environment.

NASA Astrophysics Data System (ADS)

Synytsky, R.; Henadiy, S.; Lobzakov, V.; Kolesnikov, L.; Starovoit, Y. O.

2016-12-01

How useful are the geophysical observations in a scope of minimizing losses from natural disasters today? Does it help to decrease number of human victims during tsunami and earthquake? Unfortunately it's still at early stage these days. It's a big goal and achievement to make such observations more useful by improving early warning and prediction systems with the help of cloud computing. Cloud computing technologies have proved the ability to speed up application development in many areas for 10 years already. Cloud unlocks new opportunities for geoscientists by providing access to modern data processing tools and algorithms including real-time high-performance computing, big data processing, artificial intelligence and others. Emerging lightweight cloud technologies, such as Docker containers, are gaining wide traction in IT due to the fact of faster and more efficient deployment of different applications in a cloud environment. It allows to deploy and manage geophysical applications and systems in minutes across multiple clouds and data centers that becomes of utmost importance for the next generation applications. In this session we'll demonstrate how Docker containers technology within multi-cloud can accelerate the development of applications specifically designed for geophysical researches.

Bringing numerous methods for expression and promoter analysis to a public cloud computing service.

PubMed

Polanski, Krzysztof; Gao, Bo; Mason, Sam A; Brown, Paul; Ott, Sascha; Denby, Katherine J; Wild, David L

2018-03-01

Every year, a large number of novel algorithms are introduced to the scientific community for a myriad of applications, but using these across different research groups is often troublesome, due to suboptimal implementations and specific dependency requirements. This does not have to be the case, as public cloud computing services can easily house tractable implementations within self-contained dependency environments, making the methods easily accessible to a wider public. We have taken 14 popular methods, the majority related to expression data or promoter analysis, developed these up to a good implementation standard and housed the tools in isolated Docker containers which we integrated into the CyVerse Discovery Environment, making these easily usable for a wide community as part of the CyVerse UK project. The integrated apps can be found at http://www.cyverse.org/discovery-environment, while the raw code is available at https://github.com/cyversewarwick and the corresponding Docker images are housed at https://hub.docker.com/r/cyversewarwick/. info@cyverse.warwick.ac.uk or D.L.Wild@warwick.ac.uk. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Secondary Use of Claims Data from the Austrian Health Insurance System with i2b2: A Pilot Study.

PubMed

Endel, Florian; Duftschmid, Georg

2016-01-01

In conformity with increasing international efforts to reuse routine health data for scientific purposes, the Main Association of Austrian Social Security Organisations provides pseudonymized claims data of the Austrian health care system for clinical research. We aimed to examine, whether an integration of the corresponding database into i2b2 would be possible and provide benefits. We applied docker-based software containers and data transformations to set up the system. To assess the benefits of i2b2 we plan to reenact the task of cohort formation of an earlier research project. The claims database was successfully integrated into i2b2. The docker-based installation approach will be published as git repository. The assessment of i2b2's benefits is currently work in progress and will be presented at the conference. Docker enables a flexible, reproducible, and resource-efficient installation of i2b2 within the restricted environment implied by our highly secured target system. First preliminary tests indicated several potential benefits of i2b2 compared to the methods applied during the earlier research project.

CommWalker: correctly evaluating modules in molecular networks in light of annotation bias.

PubMed

Luecken, M D; Page, M J T; Crosby, A J; Mason, S; Reinert, G; Deane, C M

2018-03-15

Detecting novel functional modules in molecular networks is an important step in biological research. In the absence of gold standard functional modules, functional annotations are often used to verify whether detected modules/communities have biological meaning. However, as we show, the uneven distribution of functional annotations means that such evaluation methods favor communities of well-studied proteins. We propose a novel framework for the evaluation of communities as functional modules. Our proposed framework, CommWalker, takes communities as inputs and evaluates them in their local network environment by performing short random walks. We test CommWalker's ability to overcome annotation bias using input communities from four community detection methods on two protein interaction networks. We find that modules accepted by CommWalker are similarly co-expressed as those accepted by current methods. Crucially, CommWalker performs well not only in well-annotated regions, but also in regions otherwise obscured by poor annotation. CommWalker community prioritization both faithfully captures well-validated communities and identifies functional modules that may correspond to more novel biology. The CommWalker algorithm is freely available at opig.stats.ox.ac.uk/resources or as a docker image on the Docker Hub at hub.docker.com/r/lueckenmd/commwalker/. deane@stats.ox.ac.uk. Supplementary data are available at Bioinformatics online.

Software architecture and design of the web services facilitating climate model diagnostic analysis

NASA Astrophysics Data System (ADS)

Pan, L.; Lee, S.; Zhang, J.; Tang, B.; Zhai, C.; Jiang, J. H.; Wang, W.; Bao, Q.; Qi, M.; Kubar, T. L.; Teixeira, J.

2015-12-01

Climate model diagnostic analysis is a computationally- and data-intensive task because it involves multiple numerical model outputs and satellite observation data that can both be high resolution. We have built an online tool that facilitates this process. The tool is called Climate Model Diagnostic Analyzer (CMDA). It employs the web service technology and provides a web-based user interface. The benefits of these choices include: (1) No installation of any software other than a browser, hence it is platform compatable; (2) Co-location of computation and big data on the server side, and small results and plots to be downloaded on the client side, hence high data efficiency; (3) multi-threaded implementation to achieve parallel performance on multi-core servers; and (4) cloud deployment so each user has a dedicated virtual machine. In this presentation, we will focus on the computer science aspects of this tool, namely the architectural design, the infrastructure of the web services, the implementation of the web-based user interface, the mechanism of provenance collection, the approach to virtualization, and the Amazon Cloud deployment. As an example, We will describe our methodology to transform an existing science application code into a web service using a Python wrapper interface and Python web service frameworks (i.e., Flask, Gunicorn, and Tornado). Another example is the use of Docker, a light-weight virtualization container, to distribute and deploy CMDA onto an Amazon EC2 instance. Our tool of CMDA has been successfully used in the 2014 Summer School hosted by the JPL Center for Climate Science. Students had positive feedbacks in general and we will report their comments. An enhanced version of CMDA with several new features, some requested by the 2014 students, will be used in the 2015 Summer School soon.

Reactome Pengine: A web-logic API to the homo sapiens reactome.

PubMed

Neaves, Samuel R; Tsoka, Sophia; Millard, Louise A C

2018-03-30

Existing ways of accessing data from the Reactome database are limited. Either a researcher is restricted to particular queries defined by a web application programming interface (API), or they have to download the whole database. Reactome Pengine is a web service providing a logic programming based API to the human reactome. This gives researchers greater flexibility in data access than existing APIs, as users can send their own small programs (alongside queries) to Reactome Pengine. The server and an example notebook can be found at https://apps.nms.kcl.ac.uk/reactome-pengine. Source code is available at https://github.com/samwalrus/reactome-pengine and a Docker image is available at https://hub.docker.com/r/samneaves/rp4/ . samuel.neaves@kcl.ac.uk. Supplementary data are available at Bioinformatics online.

Cyberhubs: Virtual Research Environments for Astronomy

NASA Astrophysics Data System (ADS)

Herwig, Falk; Andrassy, Robert; Annau, Nic; Clarkson, Ondrea; Côté, Benoit; D’Sa, Aaron; Jones, Sam; Moa, Belaid; O’Connell, Jericho; Porter, David; Ritter, Christian; Woodward, Paul

2018-05-01

Collaborations in astronomy and astrophysics are faced with numerous cyber-infrastructure challenges, such as large data sets, the need to combine heterogeneous data sets, and the challenge to effectively collaborate on those large, heterogeneous data sets with significant processing requirements and complex science software tools. The cyberhubs system is an easy-to-deploy package for small- to medium-sized collaborations based on the Jupyter and Docker technology, which allows web-browser-enabled, remote, interactive analytic access to shared data. It offers an initial step to address these challenges. The features and deployment steps of the system are described, as well as the requirements collection through an account of the different approaches to data structuring, handling, and available analytic tools for the NuGrid and PPMstar collaborations. NuGrid is an international collaboration that creates stellar evolution and explosion physics and nucleosynthesis simulation data. The PPMstar collaboration performs large-scale 3D stellar hydrodynamics simulations of interior convection in the late phases of stellar evolution. Examples of science that is currently performed on cyberhubs, in the areas of 3D stellar hydrodynamic simulations, stellar evolution and nucleosynthesis, and Galactic chemical evolution, are presented.

Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization.

PubMed

Wolff, Joachim; Bhardwaj, Vivek; Nothjunge, Stephan; Richard, Gautier; Renschler, Gina; Gilsbach, Ralf; Manke, Thomas; Backofen, Rolf; Ramírez, Fidel; Grüning, Björn A

2018-06-13

Galaxy HiCExplorer is a web server that facilitates the study of the 3D conformation of chromatin by allowing Hi-C data processing, analysis and visualization. With the Galaxy HiCExplorer web server, users with little bioinformatic background can perform every step of the analysis in one workflow: mapping of the raw sequence data, creation of Hi-C contact matrices, quality assessment, correction of contact matrices and identification of topological associated domains (TADs) and A/B compartments. Users can create publication ready plots of the contact matrix, A/B compartments, and TADs on a selected genomic locus, along with additional information like gene tracks or ChIP-seq signals. Galaxy HiCExplorer is freely usable at: https://hicexplorer.usegalaxy.eu and is available as a Docker container: https://github.com/deeptools/docker-galaxy-hicexplorer.

The Legacy Archive for Microwave Background Data Analysis (LAMBDA)

NASA Astrophysics Data System (ADS)

Miller, Nathan; LAMBDA

2018-01-01

The Legacy Archive for Microwave Background Data Analysis (LAMBDA) provides CMB researchers with archival data for cosmology missions, software tools, and links to other sites of interest. LAMBDA is one-stop shopping for CMB researchers. It hosts data from WMAP along with many suborbital experiments. Over the past year, LAMBDA has acquired new data from SPTpol, SPIDER and ACTPol. In addition to the primary CMB, LAMBDA also provides foreground data.LAMBDA has several ongoing efforts to provide tools for CMB researchers. These tools include a web interface for CAMB and a web interface for a CMB survey footprint database and plotting tool. Additionally, we have recently developed a Docker container with standard CMB analysis tools and demonstrations in the form of Jupyter notebooks. These containers will be publically available through Docker's container repository and the source will be available on github.

DAX - The Next Generation: Towards One Million Processes on Commodity Hardware.

PubMed

Damon, Stephen M; Boyd, Brian D; Plassard, Andrew J; Taylor, Warren; Landman, Bennett A

2017-01-01

Large scale image processing demands a standardized way of not only storage but also a method for job distribution and scheduling. The eXtensible Neuroimaging Archive Toolkit (XNAT) is one of several platforms that seeks to solve the storage issues. Distributed Automation for XNAT (DAX) is a job control and distribution manager. Recent massive data projects have revealed several bottlenecks for projects with >100,000 assessors (i.e., data processing pipelines in XNAT). In order to address these concerns, we have developed a new API, which exposes a direct connection to the database rather than REST API calls to accomplish the generation of assessors. This method, consistent with XNAT, keeps a full history for auditing purposes. Additionally, we have optimized DAX to keep track of processing status on disk (called DISKQ) rather than on XNAT, which greatly reduces load on XNAT by vastly dropping the number of API calls. Finally, we have integrated DAX into a Docker container with the idea of using it as a Docker controller to launch Docker containers of image processing pipelines. Using our new API, we reduced the time to create 1,000 assessors (a sub-cohort of our case project) from 65040 seconds to 229 seconds (a decrease of over 270 fold). DISKQ, using pyXnat, allows launching of 400 jobs in under 10 seconds which previously took 2,000 seconds. Together these updates position DAX to support projects with hundreds of thousands of scans and to run them in a time-efficient manner.

DAX - the next generation: towards one million processes on commodity hardware

NASA Astrophysics Data System (ADS)

Damon, Stephen M.; Boyd, Brian D.; Plassard, Andrew J.; Taylor, Warren; Landman, Bennett A.

2017-03-01

Large scale image processing demands a standardized way of not only storage but also a method for job distribution and scheduling. The eXtensible Neuroimaging Archive Toolkit (XNAT) is one of several platforms that seeks to solve the storage issues. Distributed Automation for XNAT (DAX) is a job control and distribution manager. Recent massive data projects have revealed several bottlenecks for projects with <100,000 assessors (i.e., data processing pipelines in XNAT). In order to address these concerns, we have developed a new API, which exposes a direct connection to the database rather than REST API calls to accomplish the generation of assessors. This method, consistent with XNAT, keeps a full history for auditing purposes. Additionally, we have optimized DAX to keep track of processing status on disk (called DISKQ) rather than on XNAT, which greatly reduces load on XNAT by vastly dropping the number of API calls. Finally, we have integrated DAX into a Docker container with the idea of using it as a Docker controller to launch Docker containers of image processing pipelines. Using our new API, we reduced the time to create 1,000 assessors (a sub-cohort of our case project) from 65040 seconds to 229 seconds (a decrease of over 270 fold). DISKQ, using pyXnat, allows launching of 400 jobs in under 10 seconds which previously took 2,000 seconds. Together these updates position DAX to support projects with hundreds of thousands of scans and to run them in a time-efficient manner.

DAX - The Next Generation: Towards One Million Processes on Commodity Hardware

PubMed Central

Boyd, Brian D.; Plassard, Andrew J.; Taylor, Warren; Landman, Bennett A.

2017-01-01

Large scale image processing demands a standardized way of not only storage but also a method for job distribution and scheduling. The eXtensible Neuroimaging Archive Toolkit (XNAT) is one of several platforms that seeks to solve the storage issues. Distributed Automation for XNAT (DAX) is a job control and distribution manager. Recent massive data projects have revealed several bottlenecks for projects with >100,000 assessors (i.e., data processing pipelines in XNAT). In order to address these concerns, we have developed a new API, which exposes a direct connection to the database rather than REST API calls to accomplish the generation of assessors. This method, consistent with XNAT, keeps a full history for auditing purposes. Additionally, we have optimized DAX to keep track of processing status on disk (called DISKQ) rather than on XNAT, which greatly reduces load on XNAT by vastly dropping the number of API calls. Finally, we have integrated DAX into a Docker container with the idea of using it as a Docker controller to launch Docker containers of image processing pipelines. Using our new API, we reduced the time to create 1,000 assessors (a sub-cohort of our case project) from 65040 seconds to 229 seconds (a decrease of over 270 fold). DISKQ, using pyXnat, allows launching of 400 jobs in under 10 seconds which previously took 2,000 seconds. Together these updates position DAX to support projects with hundreds of thousands of scans and to run them in a time-efficient manner. PMID:28919661

Unidata cyberinfrastructure in the cloud: A progress report

NASA Astrophysics Data System (ADS)

Ramamurthy, Mohan

2016-04-01

Data services, software, and committed support are critical components of geosciences cyber-infrastructure that can help scientists address problems of unprecedented complexity, scale, and scope. Unidata is currently working on innovative ideas, new paradigms, and novel techniques to complement and extend its offerings. Our goal is to empower users so that they can tackle major, heretofore difficult problems. Unidata recognizes that its products and services must evolve to support new approaches to research and education. After years of hype and ambiguity, cloud computing is maturing in usability in many areas of science and education, bringing the benefits of virtualized and elastic remote services to infrastructure, software, computation, and data. Cloud environments reduce the amount of time and money spent to procure, install, and maintain new hardware and software, and reduce costs through resource pooling and shared infrastructure. Cloud services aimed at providing any resource, at any time, from any place, using any device are increasingly being embraced by all types of organizations. Given this trend and the enormous potential of cloud-based services, Unidata is moving to augment its products, services, data delivery mechanisms and applications to align with the cloud-computing paradigm. To realize the above vision, Unidata is working toward: * Providing access to many types of data from a cloud (e.g., TDS, RAMADDA and EDEX); * Deploying data-proximate tools to easily process, analyze and visualize those data in a cloud environment cloud for consumption by any one, by any device, from anywhere, at any time; * Developing and providing a range of pre-configured and well-integrated tools and services that can be deployed by any university in their own private or public cloud settings. Specifically, Unidata has developed Docker for "containerized applications", making them easy to deploy. Docker helps to create "disposable" installs and eliminates many configuration challenges. Containerized applications include tools for data transport, access, analysis, and visualization: THREDDS Data Server, Integrated Data Viewer, GEMPAK, Local Data Manager, RAMADDA Data Server, and Python tools; * Fostering partnerships with NOAA and public cloud vendors (e.g., Amazon) to harness their capabilities and resources for the benefit of the academic community.

Unidata Cyberinfrastructure in the Cloud

NASA Astrophysics Data System (ADS)

Ramamurthy, M. K.; Young, J. W.

2016-12-01

Data services, software, and user support are critical components of geosciences cyber-infrastructure to help researchers to advance science. With the maturity of and significant advances in cloud computing, it has recently emerged as an alternative new paradigm for developing and delivering a broad array of services over the Internet. Cloud computing is now mature enough in usability in many areas of science and education, bringing the benefits of virtualized and elastic remote services to infrastructure, software, computation, and data. Cloud environments reduce the amount of time and money spent to procure, install, and maintain new hardware and software, and reduce costs through resource pooling and shared infrastructure. Given the enormous potential of cloud-based services, Unidata has been moving to augment its software, services, data delivery mechanisms to align with the cloud-computing paradigm. To realize the above vision, Unidata has worked toward: * Providing access to many types of data from a cloud (e.g., via the THREDDS Data Server, RAMADDA and EDEX servers); * Deploying data-proximate tools to easily process, analyze, and visualize those data in a cloud environment cloud for consumption by any one, by any device, from anywhere, at any time; * Developing and providing a range of pre-configured and well-integrated tools and services that can be deployed by any university in their own private or public cloud settings. Specifically, Unidata has developed Docker for "containerized applications", making them easy to deploy. Docker helps to create "disposable" installs and eliminates many configuration challenges. Containerized applications include tools for data transport, access, analysis, and visualization: THREDDS Data Server, Integrated Data Viewer, GEMPAK, Local Data Manager, RAMADDA Data Server, and Python tools; * Leveraging Jupyter as a central platform and hub with its powerful set of interlinking tools to connect interactively data servers, Python scientific libraries, scripts, and workflows; * Exploring end-to-end modeling and prediction capabilities in the cloud; * Partnering with NOAA and public cloud vendors (e.g., Amazon and OCC) on the NOAA Big Data Project to harness their capabilities and resources for the benefit of the academic community.

DIaaS: Data-Intensive workflows as a service - Enabling easy composition and deployment of data-intensive workflows on Virtual Research Environments

NASA Astrophysics Data System (ADS)

Filgueira, R.; Ferreira da Silva, R.; Deelman, E.; Atkinson, M.

2016-12-01

We present the Data-Intensive workflows as a Service (DIaaS) model for enabling easy data-intensive workflow composition and deployment on clouds using containers. DIaaS model backbone is Asterism, an integrated solution for running data-intensive stream-based applications on heterogeneous systems, which combines the benefits of dispel4py with Pegasus workflow systems. The stream-based executions of an Asterism workflow are managed by dispel4py, while the data movement between different e-Infrastructures, and the coordination of the application execution are automatically managed by Pegasus. DIaaS combines Asterism framework with Docker containers to provide an integrated, complete, easy-to-use, portable approach to run data-intensive workflows on distributed platforms. Three containers integrate the DIaaS model: a Pegasus node, and an MPI and an Apache Storm clusters. Container images are described as Dockerfiles (available online at http://github.com/dispel4py/pegasus_dispel4py), linked to Docker Hub for providing continuous integration (automated image builds), and image storing and sharing. In this model, all required software (workflow systems and execution engines) for running scientific applications are packed into the containers, which significantly reduces the effort (and possible human errors) required by scientists or VRE administrators to build such systems. The most common use of DIaaS will be to act as a backend of VREs or Scientific Gateways to run data-intensive applications, deploying cloud resources upon request. We have demonstrated the feasibility of DIaaS using the data-intensive seismic ambient noise cross-correlation application (Figure 1). The application preprocesses (Phase1) and cross-correlates (Phase2) traces from several seismic stations. The application is submitted via Pegasus (Container1), and Phase1 and Phase2 are executed in the MPI (Container2) and Storm (Container3) clusters respectively. Although both phases could be executed within the same environment, this setup demonstrates the flexibility of DIaaS to run applications across e-Infrastructures. In summary, DIaaS delivers specialized software to execute data-intensive applications in a scalable, efficient, and robust manner reducing the engineering time and computational cost.

Dugong: a Docker image, based on Ubuntu Linux, focused on reproducibility and replicability for bioinformatics analyses.

PubMed

Menegidio, Fabiano B; Jabes, Daniela L; Costa de Oliveira, Regina; Nunes, Luiz R

2018-02-01

This manuscript introduces and describes Dugong, a Docker image based on Ubuntu 16.04, which automates installation of more than 3500 bioinformatics tools (along with their respective libraries and dependencies), in alternative computational environments. The software operates through a user-friendly XFCE4 graphic interface that allows software management and installation by users not fully familiarized with the Linux command line and provides the Jupyter Notebook to assist in the delivery and exchange of consistent and reproducible protocols and results across laboratories, assisting in the development of open science projects. Source code and instructions for local installation are available at https://github.com/DugongBioinformatics, under the MIT open source license. Luiz.nunes@ufabc.edu.br. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

P-MartCancer-Interactive Online Software to Enable Analysis of Shotgun Cancer Proteomic Datasets.

PubMed

Webb-Robertson, Bobbie-Jo M; Bramer, Lisa M; Jensen, Jeffrey L; Kobold, Markus A; Stratton, Kelly G; White, Amanda M; Rodland, Karin D

2017-11-01

P-MartCancer is an interactive web-based software environment that enables statistical analyses of peptide or protein data, quantitated from mass spectrometry-based global proteomics experiments, without requiring in-depth knowledge of statistical programming. P-MartCancer offers a series of statistical modules associated with quality assessment, peptide and protein statistics, protein quantification, and exploratory data analyses driven by the user via customized workflows and interactive visualization. Currently, P-MartCancer offers access and the capability to analyze multiple cancer proteomic datasets generated through the Clinical Proteomics Tumor Analysis Consortium at the peptide, gene, and protein levels. P-MartCancer is deployed as a web service (https://pmart.labworks.org/cptac.html), alternatively available via Docker Hub (https://hub.docker.com/r/pnnl/pmart-web/). Cancer Res; 77(21); e47-50. ©2017 AACR . ©2017 American Association for Cancer Research.

STAR Data Reconstruction at NERSC/Cori, an adaptable Docker container approach for HPC

NASA Astrophysics Data System (ADS)

Mustafa, Mustafa; Balewski, Jan; Lauret, Jérôme; Porter, Jefferson; Canon, Shane; Gerhardt, Lisa; Hajdu, Levente; Lukascsyk, Mark

2017-10-01

As HPC facilities grow their resources, adaptation of classic HEP/NP workflows becomes a need. Linux containers may very well offer a way to lower the bar to exploiting such resources and at the time, help collaboration to reach vast elastic resources on such facilities and address their massive current and future data processing challenges. In this proceeding, we showcase STAR data reconstruction workflow at Cori HPC system at NERSC. STAR software is packaged in a Docker image and runs at Cori in Shifter containers. We highlight two of the typical end-to-end optimization challenges for such pipelines: 1) data transfer rate which was carried over ESnet after optimizing end points and 2) scalable deployment of conditions database in an HPC environment. Our tests demonstrate equally efficient data processing workflows on Cori/HPC, comparable to standard Linux clusters.

CRISPR-DAV: CRISPR NGS data analysis and visualization pipeline.

PubMed

Wang, Xuning; Tilford, Charles; Neuhaus, Isaac; Mintier, Gabe; Guo, Qi; Feder, John N; Kirov, Stefan

2017-12-01

The simplicity and precision of CRISPR/Cas9 system has brought in a new era of gene editing. Screening for desired clones with CRISPR-mediated genomic edits in a large number of samples is made possible by next generation sequencing (NGS) due to its multiplexing. Here we present CRISPR-DAV (CRISPR Data Analysis and Visualization) pipeline to analyze the CRISPR NGS data in a high throughput manner. In the pipeline, Burrows-Wheeler Aligner and Assembly Based ReAlignment are used for small and large indel detection, and results are presented in a comprehensive set of charts and interactive alignment view. CRISPR-DAV is available at GitHub and Docker Hub repositories: https://github.com/pinetree1/crispr-dav.git and https://hub.docker.com/r/pinetree1/crispr-dav/. xuning.wang@bms.com. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

CymeR: cytometry analysis using KNIME, docker and R

PubMed Central

Muchmore, B.; Alarcón-Riquelme, M.E.

2017-01-01

Abstract Summary: Here we present open-source software for the analysis of high-dimensional cytometry data using state of the art algorithms. Importantly, use of the software requires no programming ability, and output files can either be interrogated directly in CymeR or they can be used downstream with any other cytometric data analysis platform. Also, because we use Docker to integrate the multitude of components that form the basis of CymeR, we have additionally developed a proof-of-concept of how future open-source bioinformatic programs with graphical user interfaces could be developed. Availability and Implementation: CymeR is open-source software that ties several components into a single program that is perhaps best thought of as a self-contained data analysis operating system. Please see https://github.com/bmuchmore/CymeR/wiki for detailed installation instructions. Contact: brian.muchmore@genyo.es or marta.alarcon@genyo.es PMID:27998935

CymeR: cytometry analysis using KNIME, docker and R.

PubMed

Muchmore, B; Alarcón-Riquelme, M E

2017-03-01

Here we present open-source software for the analysis of high-dimensional cytometry data using state of the art algorithms. Importantly, use of the software requires no programming ability, and output files can either be interrogated directly in CymeR or they can be used downstream with any other cytometric data analysis platform. Also, because we use Docker to integrate the multitude of components that form the basis of CymeR, we have additionally developed a proof-of-concept of how future open-source bioinformatic programs with graphical user interfaces could be developed. CymeR is open-source software that ties several components into a single program that is perhaps best thought of as a self-contained data analysis operating system. Please see https://github.com/bmuchmore/CymeR/wiki for detailed installation instructions. brian.muchmore@genyo.es or marta.alarcon@genyo.es. © The Author 2016. Published by Oxford University Press.

PhamDB: a web-based application for building Phamerator databases.

PubMed

Lamine, James G; DeJong, Randall J; Nelesen, Serita M

2016-07-01

PhamDB is a web application which creates databases of bacteriophage genes, grouped by gene similarity. It is backwards compatible with the existing Phamerator desktop software while providing an improved database creation workflow. Key features include a graphical user interface, validation of uploaded GenBank files, and abilities to import phages from existing databases, modify existing databases and queue multiple jobs. Source code and installation instructions for Linux, Windows and Mac OSX are freely available at https://github.com/jglamine/phage PhamDB is also distributed as a docker image which can be managed via Kitematic. This docker image contains the application and all third party software dependencies as a pre-configured system, and is freely available via the installation instructions provided. snelesen@calvin.edu. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

SONAR: A High-Throughput Pipeline for Inferring Antibody Ontogenies from Longitudinal Sequencing of B Cell Transcripts.

PubMed

Schramm, Chaim A; Sheng, Zizhang; Zhang, Zhenhai; Mascola, John R; Kwong, Peter D; Shapiro, Lawrence

2016-01-01

The rapid advance of massively parallel or next-generation sequencing technologies has made possible the characterization of B cell receptor repertoires in ever greater detail, and these developments have triggered a proliferation of software tools for processing and annotating these data. Of especial interest, however, is the capability to track the development of specific antibody lineages across time, which remains beyond the scope of most current programs. We have previously reported on the use of techniques such as inter- and intradonor analysis and CDR3 tracing to identify transcripts related to an antibody of interest. Here, we present Software for the Ontogenic aNalysis of Antibody Repertoires (SONAR), capable of automating both general repertoire analysis and specialized techniques for investigating specific lineages. SONAR annotates next-generation sequencing data, identifies transcripts in a lineage of interest, and tracks lineage development across multiple time points. SONAR also generates figures, such as identity-divergence plots and longitudinal phylogenetic "birthday" trees, and provides interfaces to other programs such as DNAML and BEAST. SONAR can be downloaded as a ready-to-run Docker image or manually installed on a local machine. In the latter case, it can also be configured to take advantage of a high-performance computing cluster for the most computationally intensive steps, if available. In summary, this software provides a useful new tool for the processing of large next-generation sequencing datasets and the ontogenic analysis of neutralizing antibody lineages. SONAR can be found at https://github.com/scharch/SONAR, and the Docker image can be obtained from https://hub.docker.com/r/scharch/sonar/.

Build and Execute Environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guan, Qiang

At exascale, the challenge becomes to develop applications that run at scale and use exascale platforms reliably, efficiently, and flexibly. Workflows become much more complex because they must seamlessly integrate simulation and data analytics. They must include down-sampling, post-processing, feature extraction, and visualization. Power and data transfer limitations require these analysis tasks to be run in-situ or in-transit. We expect successful workflows will comprise multiple linked simulations along with tens of analysis routines. Users will have limited development time at scale and, therefore, must have rich tools to develop, debug, test, and deploy applications. At this scale, successful workflows willmore » compose linked computations from an assortment of reliable, well-defined computation elements, ones that can come and go as required, based on the needs of the workflow over time. We propose a novel framework that utilizes both virtual machines (VMs) and software containers to create a workflow system that establishes a uniform build and execution environment (BEE) beyond the capabilities of current systems. In this environment, applications will run reliably and repeatably across heterogeneous hardware and software. Containers, both commercial (Docker and Rocket) and open-source (LXC and LXD), define a runtime that isolates all software dependencies from the machine operating system. Workflows may contain multiple containers that run different operating systems, different software, and even different versions of the same software. We will run containers in open-source virtual machines (KVM) and emulators (QEMU) so that workflows run on any machine entirely in user-space. On this platform of containers and virtual machines, we will deliver workflow software that provides services, including repeatable execution, provenance, checkpointing, and future proofing. We will capture provenance about how containers were launched and how they interact to annotate workflows for repeatable and partial re-execution. We will coordinate the physical snapshots of virtual machines with parallel programming constructs, such as barriers, to automate checkpoint and restart. We will also integrate with HPC-specific container runtimes to gain access to accelerators and other specialized hardware to preserve native performance. Containers will link development to continuous integration. When application developers check code in, it will automatically be tested on a suite of different software and hardware architectures.« less

STS-49 Endeavour/Intelsat Briefing

NASA Technical Reports Server (NTRS)

1992-01-01

Lak Virdee of Intelsat, summarizes Intelsat's role in the STS-49 Endeavour mission. He discusses the reboost hardware, giving details on the capture arm and docker adapter assembly. He describes the rendezvous between Intelsat and the Endeavour Orbiter. Mr. Virdee then answers questions from the press.

SONAR: A High-Throughput Pipeline for Inferring Antibody Ontogenies from Longitudinal Sequencing of B Cell Transcripts

PubMed Central

Schramm, Chaim A.; Sheng, Zizhang; Zhang, Zhenhai; Mascola, John R.; Kwong, Peter D.; Shapiro, Lawrence

2016-01-01

The rapid advance of massively parallel or next-generation sequencing technologies has made possible the characterization of B cell receptor repertoires in ever greater detail, and these developments have triggered a proliferation of software tools for processing and annotating these data. Of especial interest, however, is the capability to track the development of specific antibody lineages across time, which remains beyond the scope of most current programs. We have previously reported on the use of techniques such as inter- and intradonor analysis and CDR3 tracing to identify transcripts related to an antibody of interest. Here, we present Software for the Ontogenic aNalysis of Antibody Repertoires (SONAR), capable of automating both general repertoire analysis and specialized techniques for investigating specific lineages. SONAR annotates next-generation sequencing data, identifies transcripts in a lineage of interest, and tracks lineage development across multiple time points. SONAR also generates figures, such as identity–divergence plots and longitudinal phylogenetic “birthday” trees, and provides interfaces to other programs such as DNAML and BEAST. SONAR can be downloaded as a ready-to-run Docker image or manually installed on a local machine. In the latter case, it can also be configured to take advantage of a high-performance computing cluster for the most computationally intensive steps, if available. In summary, this software provides a useful new tool for the processing of large next-generation sequencing datasets and the ontogenic analysis of neutralizing antibody lineages. SONAR can be found at https://github.com/scharch/SONAR, and the Docker image can be obtained from https://hub.docker.com/r/scharch/sonar/. PMID:27708645

An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study.

PubMed

Wang, Zichen; Ma'ayan, Avi

2016-01-01

RNA-seq analysis is becoming a standard method for global gene expression profiling. However, open and standard pipelines to perform RNA-seq analysis by non-experts remain challenging due to the large size of the raw data files and the hardware requirements for running the alignment step. Here we introduce a reproducible open source RNA-seq pipeline delivered as an IPython notebook and a Docker image. The pipeline uses state-of-the-art tools and can run on various platforms with minimal configuration overhead. The pipeline enables the extraction of knowledge from typical RNA-seq studies by generating interactive principal component analysis (PCA) and hierarchical clustering (HC) plots, performing enrichment analyses against over 90 gene set libraries, and obtaining lists of small molecules that are predicted to either mimic or reverse the observed changes in mRNA expression. We apply the pipeline to a recently published RNA-seq dataset collected from human neuronal progenitors infected with the Zika virus (ZIKV). In addition to confirming the presence of cell cycle genes among the genes that are downregulated by ZIKV, our analysis uncovers significant overlap with upregulated genes that when knocked out in mice induce defects in brain morphology. This result potentially points to the molecular processes associated with the microcephaly phenotype observed in newborns from pregnant mothers infected with the virus. In addition, our analysis predicts small molecules that can either mimic or reverse the expression changes induced by ZIKV. The IPython notebook and Docker image are freely available at:  http://nbviewer.jupyter.org/github/maayanlab/Zika-RNAseq-Pipeline/blob/master/Zika.ipynb and  https://hub.docker.com/r/maayanlab/zika/.

Modeling the inhibition of quadruple mutant Plasmodium falciparum dihydrofolate reductase by pyrimethamine derivatives

NASA Astrophysics Data System (ADS)

Fogel, Gary B.; Cheung, Mars; Pittman, Eric; Hecht, David

2008-01-01

Modeling studies were performed on known inhibitors of the quadruple mutant Plasmodium falciparum dihydrofolate reductase (DHFR). GOLD was used to dock 32 pyrimethamine derivatives into the active site of DHFR obtained from the x-ray crystal structure 1J3K.pdb. Several scoring functions were evaluated and the Molegro Protein-Ligand Interaction Score was determined to have one of the best correlation to experimental p K i . In conjunction with Protein-Ligand Interaction scores, predicted binding modes and key protein-ligand interactions were evaluated and analyzed in order to develop criteria for selecting compounds having a greater chance of activity versus resistant strains of Plasmodium falciparum. This methodology will be used in future studies for selection of compounds for focused screening libraries.

Gaining Cyber Dominance

DTIC Science & Technology

2015-01-01

Robust team exercise and simulation • Air-gapped; isolation from production networks • “Train as you fight” scenarios • Advanced user and Internet...Security Onion • SIFT (Linux/Windows) • Kali • Rucksack • Docker • VTS 18 GCD Overview January 2015 © 2014 Carnegie Mellon University TEXN Architecture

IVAG: An Integrative Visualization Application for Various Types of Genomic Data Based on R-Shiny and the Docker Platform.

PubMed

Lee, Tae-Rim; Ahn, Jin Mo; Kim, Gyuhee; Kim, Sangsoo

2017-12-01

Next-generation sequencing (NGS) technology has become a trend in the genomics research area. There are many software programs and automated pipelines to analyze NGS data, which can ease the pain for traditional scientists who are not familiar with computer programming. However, downstream analyses, such as finding differentially expressed genes or visualizing linkage disequilibrium maps and genome-wide association study (GWAS) data, still remain a challenge. Here, we introduce a dockerized web application written in R using the Shiny platform to visualize pre-analyzed RNA sequencing and GWAS data. In addition, we have integrated a genome browser based on the JBrowse platform and an automated intermediate parsing process required for custom track construction, so that users can easily build and navigate their personal genome tracks with in-house datasets. This application will help scientists perform series of downstream analyses and obtain a more integrative understanding about various types of genomic data by interactively visualizing them with customizable options.

P-MartCancer–Interactive Online Software to Enable Analysis of Shotgun Cancer Proteomic Datasets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Webb-Robertson, Bobbie-Jo M.; Bramer, Lisa M.; Jensen, Jeffrey L.

P-MartCancer is a new interactive web-based software environment that enables biomedical and biological scientists to perform in-depth analyses of global proteomics data without requiring direct interaction with the data or with statistical software. P-MartCancer offers a series of statistical modules associated with quality assessment, peptide and protein statistics, protein quantification and exploratory data analyses driven by the user via customized workflows and interactive visualization. Currently, P-MartCancer offers access to multiple cancer proteomic datasets generated through the Clinical Proteomics Tumor Analysis Consortium (CPTAC) at the peptide, gene and protein levels. P-MartCancer is deployed using Azure technologies (http://pmart.labworks.org/cptac.html), the web-service is alternativelymore » available via Docker Hub (https://hub.docker.com/r/pnnl/pmart-web/) and many statistical functions can be utilized directly from an R package available on GitHub (https://github.com/pmartR).« less

ChronQC: a quality control monitoring system for clinical next generation sequencing.

PubMed

Tawari, Nilesh R; Seow, Justine Jia Wen; Perumal, Dharuman; Ow, Jack L; Ang, Shimin; Devasia, Arun George; Ng, Pauline C

2018-05-15

ChronQC is a quality control (QC) tracking system for clinical implementation of next-generation sequencing (NGS). ChronQC generates time series plots for various QC metrics to allow comparison of current runs to historical runs. ChronQC has multiple features for tracking QC data including Westgard rules for clinical validity, laboratory-defined thresholds and historical observations within a specified time period. Users can record their notes and corrective actions directly onto the plots for long-term recordkeeping. ChronQC facilitates regular monitoring of clinical NGS to enable adherence to high quality clinical standards. ChronQC is freely available on GitHub (https://github.com/nilesh-tawari/ChronQC), Docker (https://hub.docker.com/r/nileshtawari/chronqc/) and the Python Package Index. ChronQC is implemented in Python and runs on all common operating systems (Windows, Linux and Mac OS X). tawari.nilesh@gmail.com or pauline.c.ng@gmail.com. Supplementary data are available at Bioinformatics online.

CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets.

PubMed

Flobak, Åsmund; Vazquez, Miguel; Lægreid, Astrid; Valencia, Alfonso

2017-08-01

Drug synergies are sought to identify combinations of drugs particularly beneficial. User-friendly software solutions that can assist analysis of large-scale datasets are required. CImbinator is a web-service that can aid in batch-wise and in-depth analyzes of data from small-scale and large-scale drug combination screens. CImbinator offers to quantify drug combination effects, using both the commonly employed median effect equation, as well as advanced experimental mathematical models describing dose response relationships. CImbinator is written in Ruby and R. It uses the R package drc for advanced drug response modeling. CImbinator is available at http://cimbinator.bioinfo.cnio.es , the source-code is open and available at https://github.com/Rbbt-Workflows/combination_index . A Docker image is also available at https://hub.docker.com/r/mikisvaz/rbbt-ci_mbinator/ . asmund.flobak@ntnu.no or miguel.vazquez@cnio.es. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

GISpark: A Geospatial Distributed Computing Platform for Spatiotemporal Big Data

NASA Astrophysics Data System (ADS)

Wang, S.; Zhong, E.; Wang, E.; Zhong, Y.; Cai, W.; Li, S.; Gao, S.

2016-12-01

Geospatial data are growing exponentially because of the proliferation of cost effective and ubiquitous positioning technologies such as global remote-sensing satellites and location-based devices. Analyzing large amounts of geospatial data can provide great value for both industrial and scientific applications. Data- and compute- intensive characteristics inherent in geospatial big data increasingly pose great challenges to technologies of data storing, computing and analyzing. Such challenges require a scalable and efficient architecture that can store, query, analyze, and visualize large-scale spatiotemporal data. Therefore, we developed GISpark - a geospatial distributed computing platform for processing large-scale vector, raster and stream data. GISpark is constructed based on the latest virtualized computing infrastructures and distributed computing architecture. OpenStack and Docker are used to build multi-user hosting cloud computing infrastructure for GISpark. The virtual storage systems such as HDFS, Ceph, MongoDB are combined and adopted for spatiotemporal data storage management. Spark-based algorithm framework is developed for efficient parallel computing. Within this framework, SuperMap GIScript and various open-source GIS libraries can be integrated into GISpark. GISpark can also integrated with scientific computing environment (e.g., Anaconda), interactive computing web applications (e.g., Jupyter notebook), and machine learning tools (e.g., TensorFlow/Orange). The associated geospatial facilities of GISpark in conjunction with the scientific computing environment, exploratory spatial data analysis tools, temporal data management and analysis systems make up a powerful geospatial computing tool. GISpark not only provides spatiotemporal big data processing capacity in the geospatial field, but also provides spatiotemporal computational model and advanced geospatial visualization tools that deals with other domains related with spatial property. We tested the performance of the platform based on taxi trajectory analysis. Results suggested that GISpark achieves excellent run time performance in spatiotemporal big data applications.

Enhancing knowledge discovery from cancer genomics data with Galaxy

PubMed Central

Albuquerque, Marco A.; Grande, Bruno M.; Ritch, Elie J.; Pararajalingam, Prasath; Jessa, Selin; Krzywinski, Martin; Grewal, Jasleen K.; Shah, Sohrab P.; Boutros, Paul C.

2017-01-01

Abstract The field of cancer genomics has demonstrated the power of massively parallel sequencing techniques to inform on the genes and specific alterations that drive tumor onset and progression. Although large comprehensive sequence data sets continue to be made increasingly available, data analysis remains an ongoing challenge, particularly for laboratories lacking dedicated resources and bioinformatics expertise. To address this, we have produced a collection of Galaxy tools that represent many popular algorithms for detecting somatic genetic alterations from cancer genome and exome data. We developed new methods for parallelization of these tools within Galaxy to accelerate runtime and have demonstrated their usability and summarized their runtimes on multiple cloud service providers. Some tools represent extensions or refinement of existing toolkits to yield visualizations suited to cohort-wide cancer genomic analysis. For example, we present Oncocircos and Oncoprintplus, which generate data-rich summaries of exome-derived somatic mutation. Workflows that integrate these to achieve data integration and visualizations are demonstrated on a cohort of 96 diffuse large B-cell lymphomas and enabled the discovery of multiple candidate lymphoma-related genes. Our toolkit is available from our GitHub repository as Galaxy tool and dependency definitions and has been deployed using virtualization on multiple platforms including Docker. PMID:28327945

Enhancing knowledge discovery from cancer genomics data with Galaxy.

PubMed

Albuquerque, Marco A; Grande, Bruno M; Ritch, Elie J; Pararajalingam, Prasath; Jessa, Selin; Krzywinski, Martin; Grewal, Jasleen K; Shah, Sohrab P; Boutros, Paul C; Morin, Ryan D

2017-05-01

The field of cancer genomics has demonstrated the power of massively parallel sequencing techniques to inform on the genes and specific alterations that drive tumor onset and progression. Although large comprehensive sequence data sets continue to be made increasingly available, data analysis remains an ongoing challenge, particularly for laboratories lacking dedicated resources and bioinformatics expertise. To address this, we have produced a collection of Galaxy tools that represent many popular algorithms for detecting somatic genetic alterations from cancer genome and exome data. We developed new methods for parallelization of these tools within Galaxy to accelerate runtime and have demonstrated their usability and summarized their runtimes on multiple cloud service providers. Some tools represent extensions or refinement of existing toolkits to yield visualizations suited to cohort-wide cancer genomic analysis. For example, we present Oncocircos and Oncoprintplus, which generate data-rich summaries of exome-derived somatic mutation. Workflows that integrate these to achieve data integration and visualizations are demonstrated on a cohort of 96 diffuse large B-cell lymphomas and enabled the discovery of multiple candidate lymphoma-related genes. Our toolkit is available from our GitHub repository as Galaxy tool and dependency definitions and has been deployed using virtualization on multiple platforms including Docker. © The Author 2017. Published by Oxford University Press.

Reducing Time to Science: Unidata and JupyterHub Technology Using the Jetstream Cloud

NASA Astrophysics Data System (ADS)

Chastang, J.; Signell, R. P.; Fischer, J. L.

2017-12-01

Cloud computing can accelerate scientific workflows, discovery, and collaborations by reducing research and data friction. We describe the deployment of Unidata and JupyterHub technologies on the NSF-funded XSEDE Jetstream cloud. With the aid of virtual machines and Docker technology, we deploy a Unidata JupyterHub server co-located with a Local Data Manager (LDM), THREDDS data server (TDS), and RAMADDA geoscience content management system. We provide Jupyter Notebooks and the pre-built Python environments needed to run them. The notebooks can be used for instruction and as templates for scientific experimentation and discovery. We also supply a large quantity of NCEP forecast model results to allow data-proximate analysis and visualization. In addition, users can transfer data using Globus command line tools, and perform their own data-proximate analysis and visualization with Notebook technology. These data can be shared with others via a dedicated TDS server for scientific distribution and collaboration. There are many benefits of this approach. Not only is the cloud computing environment fast, reliable and scalable, but scientists can analyze, visualize, and share data using only their web browser. No local specialized desktop software or a fast internet connection is required. This environment will enable scientists to spend less time managing their software and more time doing science.

bioboxes v510

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barton, Michael; Droge, Johannes; Belmann, Peter

2017-06-22

Software is now both central and essential to modern biology, yet lack of availability, difficult installations, and complex user interfaces make software hard to obtain and use. Containerisation, as exemplified by the Docker platform, has the potential to solve the problems associated with sharing software. The developers propose bioboxes: containers with standardised interfaces to make bioinformatics software interchangeable.

In vitro guanine nucleotide exchange activity of DHR-2/DOCKER/CZH2 domains.

PubMed

Côté, Jean-François; Vuori, Kristiina

2006-01-01

Rho family GTPases regulate a large variety of biological processes, including the reorganization of the actin cytoskeleton. Like other members of the Ras superfamily of small GTP-binding proteins, Rho GTPases cycle between a GDP-bound (inactive) and a GTP-bound (active) state, and, when active, the GTPases relay extracellular signals to a large number of downstream effectors. Guanine nucleotide exchange factors (GEFs) promote the exchange of GDP for GTP on Rho GTPases, thereby activating them. Most Rho-GEFs mediate their effects through their signature domain known as the Dbl Homology-Pleckstrin Homology (DH-PH) module. Recently, we and others identified a family of evolutionarily conserved, DOCK180-related proteins that also display GEF activity toward Rho GTPases. The DOCK180-family of proteins lacks the canonical DH-PH module. Instead, they rely on a novel domain, termed DHR-2, DOCKER, or CZH2, to exchange GDP for GTP on Rho targets. In this chapter, the experimental approach that we used to uncover the exchange activity of the DHR-2 domain of DOCK180-related proteins will be described.

Bioboxes: standardised containers for interchangeable bioinformatics software.

PubMed

Belmann, Peter; Dröge, Johannes; Bremges, Andreas; McHardy, Alice C; Sczyrba, Alexander; Barton, Michael D

2015-01-01

Software is now both central and essential to modern biology, yet lack of availability, difficult installations, and complex user interfaces make software hard to obtain and use. Containerisation, as exemplified by the Docker platform, has the potential to solve the problems associated with sharing software. We propose bioboxes: containers with standardised interfaces to make bioinformatics software interchangeable.

AlgoRun: a Docker-based packaging system for platform-agnostic implemented algorithms.

PubMed

Hosny, Abdelrahman; Vera-Licona, Paola; Laubenbacher, Reinhard; Favre, Thibauld

2016-08-01

There is a growing need in bioinformatics for easy-to-use software implementations of algorithms that are usable across platforms. At the same time, reproducibility of computational results is critical and often a challenge due to source code changes over time and dependencies. The approach introduced in this paper addresses both of these needs with AlgoRun, a dedicated packaging system for implemented algorithms, using Docker technology. Implemented algorithms, packaged with AlgoRun, can be executed through a user-friendly interface directly from a web browser or via a standardized RESTful web API to allow easy integration into more complex workflows. The packaged algorithm includes the entire software execution environment, thereby eliminating the common problem of software dependencies and the irreproducibility of computations over time. AlgoRun-packaged algorithms can be published on http://algorun.org, a centralized searchable directory to find existing AlgoRun-packaged algorithms. AlgoRun is available at http://algorun.org and the source code under GPL license is available at https://github.com/algorun laubenbacher@uchc.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Binding of the cSH3 Domain of Grb2 Adaptor to Two Distinct RXXK Motifs within Gab1 Docker Employs Differential Mechanisms

PubMed Central

McDonald, Caleb B.; Seldeen, Kenneth L.; Deegan, Brian J.; Bhat, Vikas; Farooq, Amjad

2010-01-01

A ubiquitous component of cellular signaling machinery, Gab1 docker plays a pivotal role in routing extracellular information in the form of growth factors and cytokines to downstream targets such as transcription factors within the nucleus. Here, using isothermal titration calorimetry (ITC) in combination with macromolecular modeling (MM), we show that although Gab1 contains four distinct RXXK motifs, designated G1, G2, G3 and G4, only G1 and G2 motifs bind to the cSH3 domain of Grb2 adaptor and do so with distinct mechanisms. Thus, while the G1 motif strictly requires the PPRPPKP consensus sequence for high-affinity binding to the cSH3 domain, the G2 motif displays preference for the PXVXRXLKPXR consensus. Such sequential differences in the binding of G1 and G2 motifs arise from their ability to adopt distinct polyproline type II (PPII)- and 310-helical conformations upon binding to the cSH3 domain, respectively. Collectively, our study provides detailed biophysical insights into a key protein-protein interaction involved in a diverse array of signaling cascades central to health and disease. PMID:21472810

MCR Container Tools

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haas, Nicholas Q; Gillen, Robert E; Karnowski, Thomas P

MathWorks' MATLAB is widely used in academia and industry for prototyping, data analysis, data processing, etc. Many users compile their programs using the MATLAB Compiler to run on workstations/computing clusters via the free MATLAB Compiler Runtime (MCR). The MCR facilitates the execution of code calling Application Programming Interfaces (API) functions from both base MATLAB and MATLAB toolboxes. In a Linux environment, a sizable number of third-party runtime dependencies (i.e. shared libraries) are necessary. Unfortunately, to the MTLAB community's knowledge, these dependencies are not documented, leaving system administrators and/or end-users to find/install the necessary libraries either as runtime errors resulting frommore » them missing or by inspecting the header information of Executable and Linkable Format (ELF) libraries of the MCR to determine which ones are missing from the system. To address various shortcomings, Docker Images based on Community Enterprise Operating System (CentOS) 7, a derivative of Redhat Enterprise Linux (RHEL) 7, containing recent (2015-2017) MCR releases and their dependencies were created. These images, along with a provided sample Docker Compose YAML Script, can be used to create a simulated computing cluster where MATLAB Compiler created binaries can be executed using a sample Slurm Workload Manager script.« less

LHCbDIRAC as Apache Mesos microservices

NASA Astrophysics Data System (ADS)

Haen, Christophe; Couturier, Benjamin

2017-10-01

The LHCb experiment relies on LHCbDIRAC, an extension of DIRAC, to drive its offline computing. This middleware provides a development framework and a complete set of components for building distributed computing systems. These components are currently installed and run on virtual machines (VM) or bare metal hardware. Due to the increased workload, high availability is becoming more and more important for the LHCbDIRAC services, and the current installation model is showing its limitations. Apache Mesos is a cluster manager which aims at abstracting heterogeneous physical resources on which various tasks can be distributed thanks to so called “frameworks” The Marathon framework is suitable for long running tasks such as the DIRAC services, while the Chronos framework meets the needs of cron-like tasks like the DIRAC agents. A combination of the service discovery tool Consul together with HAProxy allows to expose the running containers to the outside world while hiding their dynamic placements. Such an architecture brings a greater flexibility in the deployment of LHCbDirac services, allowing for easier deployment maintenance and scaling of services on demand (e..g LHCbDirac relies on 138 services and 116 agents). Higher reliability is also easier, as clustering is part of the toolset, which allows constraints on the location of the services. This paper describes the investigations carried out to package the LHCbDIRAC and DIRAC components into Docker containers and orchestrate them using the previously described set of tools.

Scientific Platform as a Service - Tools and solutions for efficient access to and analysis of oceanographic data

NASA Astrophysics Data System (ADS)

Vines, Aleksander; Hansen, Morten W.; Korosov, Anton

2017-04-01

Existing infrastructure international and Norwegian projects, e.g., NorDataNet, NMDC and NORMAP, provide open data access through the OPeNDAP protocol following the conventions for CF (Climate and Forecast) metadata, designed to promote the processing and sharing of files created with the NetCDF application programming interface (API). This approach is now also being implemented in the Norwegian Sentinel Data Hub (satellittdata.no) to provide satellite EO data to the user community. Simultaneously with providing simplified and unified data access, these projects also seek to use and establish common standards for use and discovery metadata. This then allows development of standardized tools for data search and (subset) streaming over the internet to perform actual scientific analysis. A combinnation of software tools, which we call a Scientific Platform as a Service (SPaaS), will take advantage of these opportunities to harmonize and streamline the search, retrieval and analysis of integrated satellite and auxiliary observations of the oceans in a seamless system. The SPaaS is a cloud solution for integration of analysis tools with scientific datasets via an API. The core part of the SPaaS is a distributed metadata catalog to store granular metadata describing the structure, location and content of available satellite, model, and in situ datasets. The analysis tools include software for visualization (also online), interactive in-depth analysis, and server-based processing chains. The API conveys search requests between system nodes (i.e., interactive and server tools) and provides easy access to the metadata catalog, data repositories, and the tools. The SPaaS components are integrated in virtual machines, of which provisioning and deployment are automatized using existing state-of-the-art open-source tools (e.g., Vagrant, Ansible, Docker). The open-source code for scientific tools and virtual machine configurations is under version control at https://github.com/nansencenter/, and is coupled to an online continuous integration system (e.g., Travis CI).

eddy4R 0.2.0: a DevOps model for community-extensible processing and analysis of eddy-covariance data based on R, Git, Docker, and HDF5

NASA Astrophysics Data System (ADS)

Metzger, Stefan; Durden, David; Sturtevant, Cove; Luo, Hongyan; Pingintha-Durden, Natchaya; Sachs, Torsten; Serafimovich, Andrei; Hartmann, Jörg; Li, Jiahong; Xu, Ke; Desai, Ankur R.

2017-08-01

Large differences in instrumentation, site setup, data format, and operating system stymie the adoption of a universal computational environment for processing and analyzing eddy-covariance (EC) data. This results in limited software applicability and extensibility in addition to often substantial inconsistencies in flux estimates. Addressing these concerns, this paper presents the systematic development of portable, reproducible, and extensible EC software achieved by adopting a development and systems operation (DevOps) approach. This software development model is used for the creation of the eddy4R family of EC code packages in the open-source R language for statistical computing. These packages are community developed, iterated via the Git distributed version control system, and wrapped into a portable and reproducible Docker filesystem that is independent of the underlying host operating system. The HDF5 hierarchical data format then provides a streamlined mechanism for highly compressed and fully self-documented data ingest and output. The usefulness of the DevOps approach was evaluated for three test applications. First, the resultant EC processing software was used to analyze standard flux tower data from the first EC instruments installed at a National Ecological Observatory (NEON) field site. Second, through an aircraft test application, we demonstrate the modular extensibility of eddy4R to analyze EC data from other platforms. Third, an intercomparison with commercial-grade software showed excellent agreement (R2 = 1.0 for CO2 flux). In conjunction with this study, a Docker image containing the first two eddy4R packages and an executable example workflow, as well as first NEON EC data products are released publicly. We conclude by describing the work remaining to arrive at the automated generation of science-grade EC fluxes and benefits to the science community at large. This software development model is applicable beyond EC and more generally builds the capacity to deploy complex algorithms developed by scientists in an efficient and scalable manner. In addition, modularity permits meeting project milestones while retaining extensibility with time.

PaaS for web applications with OpenShift Origin

NASA Astrophysics Data System (ADS)

Lossent, A.; Rodriguez Peon, A.; Wagner, A.

2017-10-01

The CERN Web Frameworks team has deployed OpenShift Origin to facilitate deployment of web applications and to improving efficiency in terms of computing resource usage. OpenShift leverages Docker containers and Kubernetes orchestration to provide a Platform-as-a-service solution oriented for web applications. We will review use cases and how OpenShift was integrated with other services such as source control, web site management and authentication services.

New directions in the CernVM file system

NASA Astrophysics Data System (ADS)

Blomer, Jakob; Buncic, Predrag; Ganis, Gerardo; Hardi, Nikola; Meusel, Rene; Popescu, Radu

2017-10-01

The CernVM File System today is commonly used to host and distribute application software stacks. In addition to this core task, recent developments expand the scope of the file system into two new areas. Firstly, CernVM-FS emerges as a good match for container engines to distribute the container image contents. Compared to native container image distribution (e.g. through the “Docker registry”), CernVM-FS massively reduces the network traffic for image distribution. This has been shown, for instance, by a prototype integration of CernVM-FS into Mesos developed by Mesosphere, Inc. We present a path for a smooth integration of CernVM-FS and Docker. Secondly, CernVM-FS recently raised new interest as an option for the distribution of experiment conditions data. Here, the focus is on improved versioning capabilities of CernVM-FS that allows to link the conditions data of a run period to the state of a CernVM-FS repository. Lastly, CernVM-FS has been extended to provide a name space for physics data for the LIGO and CMS collaborations. Searching through a data namespace is often done by a central, experiment specific database service. A name space on CernVM-FS can particularly benefit from an existing, scalable infrastructure and from the POSIX file system interface.

Integrating Containers in the CERN Private Cloud

NASA Astrophysics Data System (ADS)

Noel, Bertrand; Michelino, Davide; Velten, Mathieu; Rocha, Ricardo; Trigazis, Spyridon

2017-10-01

Containers remain a hot topic in computing, with new use cases and tools appearing every day. Basic functionality such as spawning containers seems to have settled, but topics like volume support or networking are still evolving. Solutions like Docker Swarm, Kubernetes or Mesos provide similar functionality but target different use cases, exposing distinct interfaces and APIs. The CERN private cloud is made of thousands of nodes and users, with many different use cases. A single solution for container deployment would not cover every one of them, and supporting multiple solutions involves repeating the same process multiple times for integration with authentication services, storage services or networking. In this paper we describe OpenStack Magnum as the solution to offer container management in the CERN cloud. We will cover its main functionality and some advanced use cases using Docker Swarm and Kubernetes, highlighting some relevant differences between the two. We will describe the most common use cases in HEP and how we integrated popular services like CVMFS or AFS in the most transparent way possible, along with some limitations found. Finally we will look into ongoing work on advanced scheduling for both Swarm and Kubernetes, support for running batch like workloads and integration of container networking technologies with the CERN infrastructure.

Binding of the cSH3 domain of Grb2 adaptor to two distinct RXXK motifs within Gab1 docker employs differential mechanisms.

PubMed

McDonald, Caleb B; Seldeen, Kenneth L; Deegan, Brian J; Bhat, Vikas; Farooq, Amjad

2011-01-01

A ubiquitous component of cellular signaling machinery, Gab1 docker plays a pivotal role in routing extracellular information in the form of growth factors and cytokines to downstream targets such as transcription factors within the nucleus. Here, using isothermal titration calorimetry (ITC) in combination with macromolecular modeling (MM), we show that although Gab1 contains four distinct RXXK motifs, designated G1, G2, G3, and G4, only G1 and G2 motifs bind to the cSH3 domain of Grb2 adaptor and do so with distinct mechanisms. Thus, while the G1 motif strictly requires the PPRPPKP consensus sequence for high-affinity binding to the cSH3 domain, the G2 motif displays preference for the PXVXRXLKPXR consensus. Such sequential differences in the binding of G1 and G2 motifs arise from their ability to adopt distinct polyproline type II (PPII)- and 3(10) -helical conformations upon binding to the cSH3 domain, respectively. Collectively, our study provides detailed biophysical insights into a key protein-protein interaction involved in a diverse array of signaling cascades central to health and disease. Copyright © 2010 John Wiley & Sons, Ltd.

DOE Office of Scientific and Technical Information (OSTI.GOV)

P-Mart was designed specifically to allow cancer researchers to perform robust statistical processing of publicly available cancer proteomic datasets. To date an online statistical processing suite for proteomics does not exist. The P-Mart software is designed to allow statistical programmers to utilize these algorithms through packages in the R programming language as well as offering a web-based interface using the Azure cloud technology. The Azure cloud technology also allows the release of the software via Docker containers.

DaMold: A data-mining platform for variant annotation and visualization in molecular diagnostics research.

PubMed

Pandey, Ram Vinay; Pabinger, Stephan; Kriegner, Albert; Weinhäusel, Andreas

2017-07-01

Next-generation sequencing (NGS) has become a powerful and efficient tool for routine mutation screening in clinical research. As each NGS test yields hundreds of variants, the current challenge is to meaningfully interpret the data and select potential candidates. Analyzing each variant while manually investigating several relevant databases to collect specific information is a cumbersome and time-consuming process, and it requires expertise and familiarity with these databases. Thus, a tool that can seamlessly annotate variants with clinically relevant databases under one common interface would be of great help for variant annotation, cross-referencing, and visualization. This tool would allow variants to be processed in an automated and high-throughput manner and facilitate the investigation of variants in several genome browsers. Several analysis tools are available for raw sequencing-read processing and variant identification, but an automated variant filtering, annotation, cross-referencing, and visualization tool is still lacking. To fulfill these requirements, we developed DaMold, a Web-based, user-friendly tool that can filter and annotate variants and can access and compile information from 37 resources. It is easy to use, provides flexible input options, and accepts variants from NGS and Sanger sequencing as well as hotspots in VCF and BED formats. DaMold is available as an online application at http://damold.platomics.com/index.html, and as a Docker container and virtual machine at https://sourceforge.net/projects/damold/. © 2017 Wiley Periodicals, Inc.

Bringing the Unidata IDV to the Cloud

NASA Astrophysics Data System (ADS)

Fisher, W. I.; Oxelson Ganter, J.

2015-12-01

Maintaining software compatibility across new computing environments and the associated underlying hardware is a common problem for software engineers and scientific programmers. While traditional software engineering provides a suite of tools and methodologies which may mitigate this issue, they are typically ignored by developers lacking a background in software engineering. Causing further problems, these methodologies are best applied at the start of project; trying to apply them to an existing, mature project can require an immense effort. Visualization software is particularly vulnerable to this problem, given the inherent dependency on particular graphics hardware and software API's. As a result of these issues, there exists a large body of software which is simultaneously critical to the scientists who are dependent upon it, and yet increasingly difficult to maintain.The solution to this problem was partially provided with the advent of Cloud Computing; Application Streaming. This technology allows a program to run entirely on a remote virtual machine while still allowing for interactivity and dynamic visualizations, with little-to-no re-engineering required. When coupled with containerization technology such as Docker, we are able to easily bring the same visualization software to a desktop, a netbook, a smartphone, and the next generation of hardware, whatever it may be.Unidata has been able to harness Application Streaming to provide a tablet-compatible version of our visualization software, the Integrated Data Viewer (IDV). This work will examine the challenges associated with adapting the IDV to an application streaming platform, and include a brief discussion of the underlying technologies involved.

Reproducible Earth observation analytics: challenges, ideas, and a study case on containerized land use change detection

NASA Astrophysics Data System (ADS)

Appel, Marius; Nüst, Daniel; Pebesma, Edzer

2017-04-01

Geoscientific analyses of Earth observation data typically involve a long path from data acquisition to scientific results and conclusions. Before starting the actual processing, scenes must be downloaded from the providers' platforms and the computing infrastructure needs to be prepared. The computing environment often requires specialized software, which in turn might have lots of dependencies. The software is often highly customized and provided without commercial support, which leads to rather ad-hoc systems and irreproducible results. To let other scientists reproduce the analyses, the full workspace including data, code, the computing environment, and documentation must be bundled and shared. Technologies such as virtualization or containerization allow for the creation of identical computing environments with relatively little effort. Challenges, however, arise when the volume of the data is too large, when computations are done in a cluster environment, or when complex software components such as databases are used. We discuss these challenges for the example of scalable Land use change detection on Landsat imagery. We present a reproducible implementation that runs R and the scalable data management and analytical system SciDB within a Docker container. Thanks to an explicit container recipe (the Dockerfile), this enables the all-in-one reproduction including the installation of software components, the ingestion of the data, and the execution of the analysis in a well-defined environment. We furthermore discuss possibilities how the implementation could be transferred to multi-container environments in order to support reproducibility on large cluster environments.

The effect of heavy work on the musculoskeletal system of dockers.

PubMed

Waśkiewicz, J

1996-01-01

In compass of 1989-1995 all in all 388 dockers were examined, including 136 stevedores, 128 operators of mechanic equipment, 74 hoistmen and 73 retired stevedores. Out of the group of 508 stevedores that in 1989 was selected for the purpose of the study, at the end of 1995 there were 136 still working, and out of 141 operators 128 remained in employment. The number of the hoistmen working did not change. The stevedores perform heavy and a very heavy loading labour, the rest moderate and light. The highest number of changes was found in the lumbar segment of the spine-totally 56.2%, then in the sacroiliac articulations-totally 50.6%, in the cervical spine-totally 34.4%, within the shoulder girdle-33.1% and in the thoracic segment of the spine-26.3%. In stevedores these proportions were higher. A transfer to a lighter work or retirement could not inhibit the degenerative process within the musculoskeletal system. Evaluating the development of the disease in the period of observation, a progress of the pathological process was observed. No relation between the loss of fitness in stevedores and their body mass could be found. The mean time of the disease tended to increase with age of the examined. In a considerable number of the subjects a casual connection between the changes in the musculoskeletal system and the work performed was revealed.

The Cloud Area Padovana: from pilot to production

NASA Astrophysics Data System (ADS)

Andreetto, P.; Costa, F.; Crescente, A.; Dorigo, A.; Fantinel, S.; Fanzago, F.; Sgaravatto, M.; Traldi, S.; Verlato, M.; Zangrando, L.

2017-10-01

The Cloud Area Padovana has been running for almost two years. This is an OpenStack-based scientific cloud, spread across two different sites: the INFN Padova Unit and the INFN Legnaro National Labs. The hardware resources have been scaled horizontally and vertically, by upgrading some hypervisors and by adding new ones: currently it provides about 1100 cores. Some in-house developments were also integrated in the OpenStack dashboard, such as a tool for user and project registrations with direct support for the INFN-AAI Identity Provider as a new option for the user authentication. In collaboration with the EU-funded Indigo DataCloud project, the integration with Docker-based containers has been experimented with and will be available in production soon. This computing facility now satisfies the computational and storage demands of more than 70 users affiliated with about 20 research projects. We present here the architecture of this Cloud infrastructure, the tools and procedures used to operate it. We also focus on the lessons learnt in these two years, describing the problems that were found and the corrective actions that had to be applied. We also discuss about the chosen strategy for upgrades, which combines the need to promptly integrate the OpenStack new developments, the demand to reduce the downtimes of the infrastructure, and the need to limit the effort requested for such updates. We also discuss how this Cloud infrastructure is being used. In particular we focus on two big physics experiments which are intensively exploiting this computing facility: CMS and SPES. CMS deployed on the cloud a complex computational infrastructure, composed of several user interfaces for job submission in the Grid environment/local batch queues or for interactive processes; this is fully integrated with the local Tier-2 facility. To avoid a static allocation of the resources, an elastic cluster, based on cernVM, has been configured: it allows to automatically create and delete virtual machines according to the user needs. SPES, using a client-server system called TraceWin, exploits INFN’s virtual resources performing a very large number of simulations on about a thousand nodes elastically managed.

SciServer Compute brings Analysis to Big Data in the Cloud

NASA Astrophysics Data System (ADS)

Raddick, Jordan; Medvedev, Dmitry; Lemson, Gerard; Souter, Barbara

2016-06-01

SciServer Compute uses Jupyter Notebooks running within server-side Docker containers attached to big data collections to bring advanced analysis to big data "in the cloud." SciServer Compute is a component in the SciServer Big-Data ecosystem under development at JHU, which will provide a stable, reproducible, sharable virtual research environment.SciServer builds on the popular CasJobs and SkyServer systems that made the Sloan Digital Sky Survey (SDSS) archive one of the most-used astronomical instruments. SciServer extends those systems with server-side computational capabilities and very large scratch storage space, and further extends their functions to a range of other scientific disciplines.Although big datasets like SDSS have revolutionized astronomy research, for further analysis, users are still restricted to downloading the selected data sets locally - but increasing data sizes make this local approach impractical. Instead, researchers need online tools that are co-located with data in a virtual research environment, enabling them to bring their analysis to the data.SciServer supports this using the popular Jupyter notebooks, which allow users to write their own Python and R scripts and execute them on the server with the data (extensions to Matlab and other languages are planned). We have written special-purpose libraries that enable querying the databases and other persistent datasets. Intermediate results can be stored in large scratch space (hundreds of TBs) and analyzed directly from within Python or R with state-of-the-art visualization and machine learning libraries. Users can store science-ready results in their permanent allocation on SciDrive, a Dropbox-like system for sharing and publishing files. Communication between the various components of the SciServer system is managed through SciServer‘s new Single Sign-on Portal.We have created a number of demos to illustrate the capabilities of SciServer Compute, including Python and R scripts accessing a range of datasets and showing the data flow between storage and compute components.Demos, documentation, and more information can be found at www.sciserver.org.SciServer is funded by the National Science Foundation Award ACI-1261715.

Data-proximate Visualization via Unidata Cloud Technologies

NASA Astrophysics Data System (ADS)

Fisher, W. I.; Oxelson Ganter, J.; Weber, J.

2016-12-01

The rise in cloud computing, coupled with the growth of "Big Data", has lead to a migration away from local scientific data storage. The increasing size of remote scientific data sets increase, however, makes it difficult for scientists to subject them to large-scale analysis and visualization. These large datasets can take an inordinate amount of time to download; subsetting is a potential solution, but subsetting services are not yet ubiquitous. Data providers may also pay steep prices, as many cloud providers meter data based on how much data leaves their cloud service.The solution to this problem is a deceptively simple one; move data analysis and visualization tools to the cloud, so that scientists may perform data-proximate analysis and visualization. This results in increased transfer speeds, while egress costs are lowered or completely eliminated. The challenge now becomes creating tools which are cloud-ready.The solution to this challenge is provided by Application Streaming. This technology allows a program to run entirely on a remote virtual machine while still allowing for interactivity and dynamic visualizations. When coupled with containerization technology such as Docker, we are able to easily deploy legacy analysis and visualization software to the cloud whilst retaining access via a desktop, netbook, a smartphone, or the next generation of hardware, whatever it may be.Unidata has harnessed Application Streaming to provide a cloud-capable version of our visualization software, the Integrated Data Viewer (IDV). This work will examine the challenges associated with adapting the IDV to an application streaming platform, and include a brief discussion of the underlying technologies involved.

Cloud-based data-proximate visualization and analysis

NASA Astrophysics Data System (ADS)

Fisher, Ward

2017-04-01

The rise in cloud computing, coupled with the growth of "Big Data", has lead to a migration away from local scientific data storage. The increasing size of remote scientific data sets increase, however, makes it difficult for scientists to subject them to large-scale analysis and visualization. These large datasets can take an inordinate amount of time to download; subsetting is a potential solution, but subsetting services are not yet ubiquitous. Data providers may also pay steep prices, as many cloud providers meter data based on how much data leaves their cloud service. The solution to this problem is a deceptively simple one; move data analysis and visualization tools to the cloud, so that scientists may perform data-proximate analysis and visualization. This results in increased transfer speeds, while egress costs are lowered or completely eliminated. The challenge now becomes creating tools which are cloud-ready. The solution to this challenge is provided by Application Streaming. This technology allows a program to run entirely on a remote virtual machine while still allowing for interactivity and dynamic visualizations. When coupled with containerization technology such as Docker, we are able to easily deploy legacy analysis and visualization software to the cloud whilst retaining access via a desktop, netbook, a smartphone, or the next generation of hardware, whatever it may be. Unidata has harnessed Application Streaming to provide a cloud-capable version of our visualization software, the Integrated Data Viewer (IDV). This work will examine the challenges associated with adapting the IDV to an application streaming platform, and include a brief discussion of the underlying technologies involved.

nRC: non-coding RNA Classifier based on structural features.

PubMed

Fiannaca, Antonino; La Rosa, Massimo; La Paglia, Laura; Rizzo, Riccardo; Urso, Alfonso

2017-01-01

Non-coding RNA (ncRNA) are small non-coding sequences involved in gene expression regulation of many biological processes and diseases. The recent discovery of a large set of different ncRNAs with biologically relevant roles has opened the way to develop methods able to discriminate between the different ncRNA classes. Moreover, the lack of knowledge about the complete mechanisms in regulative processes, together with the development of high-throughput technologies, has required the help of bioinformatics tools in addressing biologists and clinicians with a deeper comprehension of the functional roles of ncRNAs. In this work, we introduce a new ncRNA classification tool, nRC (non-coding RNA Classifier). Our approach is based on features extraction from the ncRNA secondary structure together with a supervised classification algorithm implementing a deep learning architecture based on convolutional neural networks. We tested our approach for the classification of 13 different ncRNA classes. We obtained classification scores, using the most common statistical measures. In particular, we reach an accuracy and sensitivity score of about 74%. The proposed method outperforms other similar classification methods based on secondary structure features and machine learning algorithms, including the RNAcon tool that, to date, is the reference classifier. nRC tool is freely available as a docker image at https://hub.docker.com/r/tblab/nrc/. The source code of nRC tool is also available at https://github.com/IcarPA-TBlab/nrc.

Association of atypical protein kinase C isotypes with the docker protein FRS2 in fibroblast growth factor signaling.

PubMed

Lim, Y P; Low, B C; Lim, J; Wong, E S; Guy, G R

1999-07-02

FRS2 is a docker protein that recruits signaling proteins to the plasma membrane in fibroblast growth factor signal transduction. We report here that FRS2 was associated with PKC lambda when Swiss 3T3 cells were stimulated with basic fibroblast growth factor. PKC zeta, the other member of the atypical PKC subfamily, could also bind FRS2. The association between FRS2 and PKC lambda is likely to be direct as shown by yeast two-hybrid analysis. The C-terminal fragments of FRS2 (amino acid residues 300-508) and SNT2 (amino acids 281-492), an isoform bearing 50% identity to FRS2, interacted with PKC lambda at a region (amino acids 240-562) that encompasses the catalytic domain. In vitro kinase assays revealed neither FRS2 nor SNT2 was a substrate of PKC lambda or zeta. Mutation of the alanine residue (Ala-120) to glutamate in the pseudo-substrate region of PKC lambda results in a constitutively active kinase that exhibited more than 2-fold greater binding to FRS2 in vitro than its "closed" wild-type counterpart. Tyrosine phosphorylation of FRS2 did not affect its binding to the constitutively active PKC lambda mutant, suggesting that the activation of PKC lambda is necessary and sufficient for its association with FRS2. It is likely that FRS2 serves as an anchoring protein for targeting activated atypical PKCs to the cell plasma membrane in signaling pathways.

Cancer-Related Analysis of Variants Toolkit (CRAVAT) | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

CRAVAT is an easy to use web-based tool for analysis of cancer variants (missense, nonsense, in-frame indel, frameshift indel, splice site). CRAVAT provides scores and a variety of annotations that assist in identification of important variants. Results are provided in an interactive, highly graphical webpage and include annotated 3D structure visualization. CRAVAT is also available for local or cloud-based installation as a Docker container. MuPIT provides 3D visualization of mutation clusters and functional annotation and is now integrated with CRAVAT.

Histamine in cereal dusts

PubMed Central

Nicholls, P. J.

1970-01-01

Nicholls, P. J. (1970).Brit. J. industr. Med.,27, 179-180. Histamine in cereal dusts. It has been found that workers exposed to cereal grain dusts may experience acute mild respiratory distress. An attempt has been made to explain this observation by examining the pharmacological activity of aqueous extracts of several cereal dusts from the holds of cargo ships. Histamine, but no other active agent, was found in the samples. It is unlikely that the concentration of histamine in these dusts is sufficient to cause respiratory distress in dockers unloading cereal grain cargoes. PMID:5428638

fastBMA: scalable network inference and transitive reduction.

PubMed

Hung, Ling-Hong; Shi, Kaiyuan; Wu, Migao; Young, William Chad; Raftery, Adrian E; Yeung, Ka Yee

2017-10-01

Inferring genetic networks from genome-wide expression data is extremely demanding computationally. We have developed fastBMA, a distributed, parallel, and scalable implementation of Bayesian model averaging (BMA) for this purpose. fastBMA also includes a computationally efficient module for eliminating redundant indirect edges in the network by mapping the transitive reduction to an easily solved shortest-path problem. We evaluated the performance of fastBMA on synthetic data and experimental genome-wide time series yeast and human datasets. When using a single CPU core, fastBMA is up to 100 times faster than the next fastest method, LASSO, with increased accuracy. It is a memory-efficient, parallel, and distributed application that scales to human genome-wide expression data. A 10 000-gene regulation network can be obtained in a matter of hours using a 32-core cloud cluster (2 nodes of 16 cores). fastBMA is a significant improvement over its predecessor ScanBMA. It is more accurate and orders of magnitude faster than other fast network inference methods such as the 1 based on LASSO. The improved scalability allows it to calculate networks from genome scale data in a reasonable time frame. The transitive reduction method can improve accuracy in denser networks. fastBMA is available as code (M.I.T. license) from GitHub (https://github.com/lhhunghimself/fastBMA), as part of the updated networkBMA Bioconductor package (https://www.bioconductor.org/packages/release/bioc/html/networkBMA.html) and as ready-to-deploy Docker images (https://hub.docker.com/r/biodepot/fastbma/). © The Authors 2017. Published by Oxford University Press.

SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria.

PubMed

Chevrette, Marc G; Aicheler, Fabian; Kohlbacher, Oliver; Currie, Cameron R; Medema, Marnix H

2017-10-15

Nonribosomally synthesized peptides (NRPs) are natural products with widespread applications in medicine and biotechnology. Many algorithms have been developed to predict the substrate specificities of nonribosomal peptide synthetase adenylation (A) domains from DNA sequences, which enables prioritization and dereplication, and integration with other data types in discovery efforts. However, insufficient training data and a lack of clarity regarding prediction quality have impeded optimal use. Here, we introduce prediCAT, a new phylogenetics-inspired algorithm, which quantitatively estimates the degree of predictability of each A-domain. We then systematically benchmarked all algorithms on a newly gathered, independent test set of 434 A-domain sequences, showing that active-site-motif-based algorithms outperform whole-domain-based methods. Subsequently, we developed SANDPUMA, a powerful ensemble algorithm, based on newly trained versions of all high-performing algorithms, which significantly outperforms individual methods. Finally, we deployed SANDPUMA in a systematic investigation of 7635 Actinobacteria genomes, suggesting that NRP chemical diversity is much higher than previously estimated. SANDPUMA has been integrated into the widely used antiSMASH biosynthetic gene cluster analysis pipeline and is also available as an open-source, standalone tool. SANDPUMA is freely available at https://bitbucket.org/chevrm/sandpuma and as a docker image at https://hub.docker.com/r/chevrm/sandpuma/ under the GNU Public License 3 (GPL3). chevrette@wisc.edu or marnix.medema@wur.nl. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Web Platform for Sharing Modeling Software in the Field of Nonlinear Optics

NASA Astrophysics Data System (ADS)

Dubenskaya, Julia; Kryukov, Alexander; Demichev, Andrey

2018-02-01

We describe the prototype of a Web platform intended for sharing software programs for computer modeling in the rapidly developing field of the nonlinear optics phenomena. The suggested platform is built on the top of the HUBZero open-source middleware. In addition to the basic HUBZero installation we added to our platform the capability to run Docker containers via an external application server and to send calculation programs to those containers for execution. The presented web platform provides a wide range of features and might be of benefit to nonlinear optics researchers.

SCRAM: a pipeline for fast index-free small RNA read alignment and visualization.

PubMed

Fletcher, Stephen J; Boden, Mikael; Mitter, Neena; Carroll, Bernard J

2018-03-15

Small RNAs play key roles in gene regulation, defense against viral pathogens and maintenance of genome stability, though many aspects of their biogenesis and function remain to be elucidated. SCRAM (Small Complementary RNA Mapper) is a novel, simple-to-use short read aligner and visualization suite that enhances exploration of small RNA datasets. The SCRAM pipeline is implemented in Go and Python, and is freely available under MIT license. Source code, multiplatform binaries and a Docker image can be accessed via https://sfletc.github.io/scram/. s.fletcher@uq.edu.au. Supplementary data are available at Bioinformatics online.

PEA: an integrated R toolkit for plant epitranscriptome analysis.

PubMed

Zhai, Jingjing; Song, Jie; Cheng, Qian; Tang, Yunjia; Ma, Chuang

2018-05-29

The epitranscriptome, also known as chemical modifications of RNA (CMRs), is a newly discovered layer of gene regulation, the biological importance of which emerged through analysis of only a small fraction of CMRs detected by high-throughput sequencing technologies. Understanding of the epitranscriptome is hampered by the absence of computational tools for the systematic analysis of epitranscriptome sequencing data. In addition, no tools have yet been designed for accurate prediction of CMRs in plants, or to extend epitranscriptome analysis from a fraction of the transcriptome to its entirety. Here, we introduce PEA, an integrated R toolkit to facilitate the analysis of plant epitranscriptome data. The PEA toolkit contains a comprehensive collection of functions required for read mapping, CMR calling, motif scanning and discovery, and gene functional enrichment analysis. PEA also takes advantage of machine learning technologies for transcriptome-scale CMR prediction, with high prediction accuracy, using the Positive Samples Only Learning algorithm, which addresses the two-class classification problem by using only positive samples (CMRs), in the absence of negative samples (non-CMRs). Hence PEA is a versatile epitranscriptome analysis pipeline covering CMR calling, prediction, and annotation, and we describe its application to predict N6-methyladenosine (m6A) modifications in Arabidopsis thaliana. Experimental results demonstrate that the toolkit achieved 71.6% sensitivity and 73.7% specificity, which is superior to existing m6A predictors. PEA is potentially broadly applicable to the in-depth study of epitranscriptomics. PEA Docker image is available at https://hub.docker.com/r/malab/pea, source codes and user manual are available at https://github.com/cma2015/PEA. chuangma2006@gmail.com. Supplementary data are available at Bioinformatics online.

CE-ACCE: The Cloud Enabled Advanced sCience Compute Environment

NASA Astrophysics Data System (ADS)

Cinquini, L.; Freeborn, D. J.; Hardman, S. H.; Wong, C.

2017-12-01

Traditionally, Earth Science data from NASA remote sensing instruments has been processed by building custom data processing pipelines (often based on a common workflow engine or framework) which are typically deployed and run on an internal cluster of computing resources. This approach has some intrinsic limitations: it requires each mission to develop and deploy a custom software package on top of the adopted framework; it makes use of dedicated hardware, network and storage resources, which must be specifically purchased, maintained and re-purposed at mission completion; and computing services cannot be scaled on demand beyond the capability of the available servers.More recently, the rise of Cloud computing, coupled with other advances in containerization technology (most prominently, Docker) and micro-services architecture, has enabled a new paradigm, whereby space mission data can be processed through standard system architectures, which can be seamlessly deployed and scaled on demand on either on-premise clusters, or commercial Cloud providers. In this talk, we will present one such architecture named CE-ACCE ("Cloud Enabled Advanced sCience Compute Environment"), which we have been developing at the NASA Jet Propulsion Laboratory over the past year. CE-ACCE is based on the Apache OODT ("Object Oriented Data Technology") suite of services for full data lifecycle management, which are turned into a composable array of Docker images, and complemented by a plug-in model for mission-specific customization. We have applied this infrastructure to both flying and upcoming NASA missions, such as ECOSTRESS and SMAP, and demonstrated deployment on the Amazon Cloud, either using simple EC2 instances, or advanced AWS services such as Amazon Lambda and ECS (EC2 Container Services).

ballaxy: web services for structural bioinformatics.

PubMed

Hildebrandt, Anna Katharina; Stöckel, Daniel; Fischer, Nina M; de la Garza, Luis; Krüger, Jens; Nickels, Stefan; Röttig, Marc; Schärfe, Charlotta; Schumann, Marcel; Thiel, Philipp; Lenhof, Hans-Peter; Kohlbacher, Oliver; Hildebrandt, Andreas

2015-01-01

Web-based workflow systems have gained considerable momentum in sequence-oriented bioinformatics. In structural bioinformatics, however, such systems are still relatively rare; while commercial stand-alone workflow applications are common in the pharmaceutical industry, academic researchers often still rely on command-line scripting to glue individual tools together. In this work, we address the problem of building a web-based system for workflows in structural bioinformatics. For the underlying molecular modelling engine, we opted for the BALL framework because of its extensive and well-tested functionality in the field of structural bioinformatics. The large number of molecular data structures and algorithms implemented in BALL allows for elegant and sophisticated development of new approaches in the field. We hence connected the versatile BALL library and its visualization and editing front end BALLView with the Galaxy workflow framework. The result, which we call ballaxy, enables the user to simply and intuitively create sophisticated pipelines for applications in structure-based computational biology, integrated into a standard tool for molecular modelling.  ballaxy consists of three parts: some minor modifications to the Galaxy system, a collection of tools and an integration into the BALL framework and the BALLView application for molecular modelling. Modifications to Galaxy will be submitted to the Galaxy project, and the BALL and BALLView integrations will be integrated in the next major BALL release. After acceptance of the modifications into the Galaxy project, we will publish all ballaxy tools via the Galaxy toolshed. In the meantime, all three components are available from http://www.ball-project.org/ballaxy. Also, docker images for ballaxy are available at https://registry.hub.docker.com/u/anhi/ballaxy/dockerfile/. ballaxy is licensed under the terms of the GPL. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The CDM Superfamily Protein MBC Directs Myoblast Fusion through a Mechanism That Requires Phosphatidylinositol 3,4,5-Triphosphate Binding but Is Independent of Direct Interaction with DCrk▿§

PubMed Central

Balagopalan, Lakshmi; Chen, Mei-Hui; Geisbrecht, Erika R.; Abmayr, Susan M.

2006-01-01

myoblast city (mbc), a member of the CDM superfamily, is essential in the Drosophila melanogaster embryo for fusion of myoblasts into multinucleate fibers. Using germ line clones in which both maternal and zygotic contributions were eliminated and rescue of the zygotic loss-of-function phenotype, we established that mbc is required in the fusion-competent subset of myoblasts. Along with its close orthologs Dock180 and CED-5, MBC has an SH3 domain at its N terminus, conserved internal domains termed DHR1 and DHR2 (or “Docker”), and C-terminal proline-rich domains that associate with the adapter protein DCrk. The importance of these domains has been evaluated by the ability of MBC mutations and deletions to rescue the mbc loss-of-function muscle phenotype. We demonstrate that the SH3 and Docker domains are essential. Moreover, ethyl methanesulfonate-induced mutations that change amino acids within the MBC Docker domain to residues that are conserved in other CDM family members nevertheless eliminate MBC function in the embryo, which suggests that these sites may mediate interactions specific to Drosophila MBC. A functional requirement for the conserved DHR1 domain, which binds to phosphatidylinositol 3,4,5-triphosphate, implicates phosphoinositide signaling in myoblast fusion. Finally, the proline-rich C-terminal sites mediate strong interactions with DCrk, as expected. These sites are not required for MBC to rescue the muscle loss-of-function phenotype, however, which suggests that MBC's role in myoblast fusion can be carried out independently of direct DCrk binding. PMID:17030600

Quantitative Image Feature Engine (QIFE): an Open-Source, Modular Engine for 3D Quantitative Feature Extraction from Volumetric Medical Images.

PubMed

Echegaray, Sebastian; Bakr, Shaimaa; Rubin, Daniel L; Napel, Sandy

2017-10-06

The aim of this study was to develop an open-source, modular, locally run or server-based system for 3D radiomics feature computation that can be used on any computer system and included in existing workflows for understanding associations and building predictive models between image features and clinical data, such as survival. The QIFE exploits various levels of parallelization for use on multiprocessor systems. It consists of a managing framework and four stages: input, pre-processing, feature computation, and output. Each stage contains one or more swappable components, allowing run-time customization. We benchmarked the engine using various levels of parallelization on a cohort of CT scans presenting 108 lung tumors. Two versions of the QIFE have been released: (1) the open-source MATLAB code posted to Github, (2) a compiled version loaded in a Docker container, posted to DockerHub, which can be easily deployed on any computer. The QIFE processed 108 objects (tumors) in 2:12 (h/mm) using 1 core, and 1:04 (h/mm) hours using four cores with object-level parallelization. We developed the Quantitative Image Feature Engine (QIFE), an open-source feature-extraction framework that focuses on modularity, standards, parallelism, provenance, and integration. Researchers can easily integrate it with their existing segmentation and imaging workflows by creating input and output components that implement their existing interfaces. Computational efficiency can be improved by parallelizing execution at the cost of memory usage. Different parallelization levels provide different trade-offs, and the optimal setting will depend on the size and composition of the dataset to be processed.

INDIGO-DataCloud solutions for Earth Sciences

NASA Astrophysics Data System (ADS)

Aguilar Gómez, Fernando; de Lucas, Jesús Marco; Fiore, Sandro; Monna, Stephen; Chen, Yin

2017-04-01

INDIGO-DataCloud (https://www.indigo-datacloud.eu/) is a European Commission funded project aiming to develop a data and computing platform targeting scientific communities, deployable on multiple hardware and provisioned over hybrid (private or public) e-infrastructures. The development of INDIGO solutions covers the different layers in cloud computing (IaaS, PaaS, SaaS), and provides tools to exploit resources like HPC or GPGPUs. INDIGO is oriented to support European Scientific research communities, that are well represented in the project. Twelve different Case Studies have been analyzed in detail from different fields: Biological & Medical sciences, Social sciences & Humanities, Environmental and Earth sciences and Physics & Astrophysics. INDIGO-DataCloud provides solutions to emerging challenges in Earth Science like: -Enabling an easy deployment of community services at different cloud sites. Many Earth Science research infrastructures often involve distributed observation stations across countries, and also have distributed data centers to support the corresponding data acquisition and curation. There is a need to easily deploy new data center services while the research infrastructure continuous spans. As an example: LifeWatch (ESFRI, Ecosystems and Biodiversity) uses INDIGO solutions to manage the deployment of services to perform complex hydrodynamics and water quality modelling over a Cloud Computing environment, predicting algae blooms, using the Docker technology: TOSCA requirement description, Docker repository, Orchestrator for deployment, AAI (AuthN, AuthZ) and OneData (Distributed Storage System). -Supporting Big Data Analysis. Nowadays, many Earth Science research communities produce large amounts of data and and are challenged by the difficulties of processing and analysing it. A climate models intercomparison data analysis case study for the European Network for Earth System Modelling (ENES) community has been setup, based on the Ophidia big data analysis framework and the Kepler workflow management system. Such services normally involve a large and distributed set of data and computing resources. In this regard, this case study exploits the INDIGO PaaS for a flexible and dynamic allocation of the resources at the infrastructural level. -Providing Distributed Data Storage Solutions. In order to allow scientific communities to perform heavy computation on huge datasets, INDIGO provides global data access solutions allowing researchers to access data in a distributed environment like fashion regardless of its location, and also to publish and share their research results with public or close communities. INDIGO solutions that support the access to distributed data storage (OneData) are being tested on EMSO infrastructure (Ocean Sciences and Geohazards) data. Another aspect of interest for the EMSO community is in efficient data processing by exploiting INDIGO services like PaaS Orchestrator. Further, for HPC exploitation, a new solution named Udocker has been implemented, enabling users to execute docker containers in supercomputers, without requiring administration privileges. This presentation will overview INDIGO solutions that are interesting and useful for Earth science communities and will show how they can be applied to other Case Studies.

The NASA Reanalysis Ensemble Service - Advanced Capabilities for Integrated Reanalysis Access and Intercomparison

NASA Astrophysics Data System (ADS)

Tamkin, G.; Schnase, J. L.; Duffy, D.; Li, J.; Strong, S.; Thompson, J. H.

2017-12-01

NASA's efforts to advance climate analytics-as-a-service are making new capabilities available to the research community: (1) A full-featured Reanalysis Ensemble Service (RES) comprising monthly means data from multiple reanalysis data sets, accessible through an enhanced set of extraction, analytic, arithmetic, and intercomparison operations. The operations are made accessible through NASA's climate data analytics Web services and our client-side Climate Data Services Python library, CDSlib; (2) A cloud-based, high-performance Virtual Real-Time Analytics Testbed supporting a select set of climate variables. This near real-time capability enables advanced technologies like Spark and Hadoop-based MapReduce analytics over native NetCDF files; and (3) A WPS-compliant Web service interface to our climate data analytics service that will enable greater interoperability with next-generation systems such as ESGF. The Reanalysis Ensemble Service includes the following: - New API that supports full temporal, spatial, and grid-based resolution services with sample queries - A Docker-ready RES application to deploy across platforms - Extended capabilities that enable single- and multiple reanalysis area average, vertical average, re-gridding, standard deviation, and ensemble averages - Convenient, one-stop shopping for commonly used data products from multiple reanalyses including basic sub-setting and arithmetic operations (e.g., avg, sum, max, min, var, count, anomaly) - Full support for the MERRA-2 reanalysis dataset in addition to, ECMWF ERA-Interim, NCEP CFSR, JMA JRA-55 and NOAA/ESRL 20CR… - A Jupyter notebook-based distribution mechanism designed for client use cases that combines CDSlib documentation with interactive scenarios and personalized project management - Supporting analytic services for NASA GMAO Forward Processing datasets - Basic uncertainty quantification services that combine heterogeneous ensemble products with comparative observational products (e.g., reanalysis, observational, visualization) - The ability to compute and visualize multiple reanalysis for ease of inter-comparisons - Automated tools to retrieve and prepare data collections for analytic processing

GRAbB: Selective Assembly of Genomic Regions, a New Niche for Genomic Research

PubMed Central

Zhang, Hao; van Diepeningen, Anne D.; van der Lee, Theo A. J.; Waalwijk, Cees; de Hoog, G. Sybren

2016-01-01

GRAbB (Genomic Region Assembly by Baiting) is a new program that is dedicated to assemble specific genomic regions from NGS data. This approach is especially useful when dealing with multi copy regions, such as mitochondrial genome and the rDNA repeat region, parts of the genome that are often neglected or poorly assembled, although they contain interesting information from phylogenetic or epidemiologic perspectives, but also single copy regions can be assembled. The program is capable of targeting multiple regions within a single run. Furthermore, GRAbB can be used to extract specific loci from NGS data, based on homology, like sequences that are used for barcoding. To make the assembly specific, a known part of the region, such as the sequence of a PCR amplicon or a homologous sequence from a related species must be specified. By assembling only the region of interest, the assembly process is computationally much less demanding and may lead to assemblies of better quality. In this study the different applications and functionalities of the program are demonstrated such as: exhaustive assembly (rDNA region and mitochondrial genome), extracting homologous regions or genes (IGS, RPB1, RPB2 and TEF1a), as well as extracting multiple regions within a single run. The program is also compared with MITObim, which is meant for the exhaustive assembly of a single target based on a similar query sequence. GRAbB is shown to be more efficient than MITObim in terms of speed, memory and disk usage. The other functionalities (handling multiple targets simultaneously and extracting homologous regions) of the new program are not matched by other programs. The program is available with explanatory documentation at https://github.com/b-brankovics/grabb. GRAbB has been tested on Ubuntu (12.04 and 14.04), Fedora (23), CentOS (7.1.1503) and Mac OS X (10.7). Furthermore, GRAbB is available as a docker repository: brankovics/grabb (https://hub.docker.com/r/brankovics/grabb/). PMID:27308864

GRAbB: Selective Assembly of Genomic Regions, a New Niche for Genomic Research.

PubMed

Brankovics, Balázs; Zhang, Hao; van Diepeningen, Anne D; van der Lee, Theo A J; Waalwijk, Cees; de Hoog, G Sybren

2016-06-01

GRAbB (Genomic Region Assembly by Baiting) is a new program that is dedicated to assemble specific genomic regions from NGS data. This approach is especially useful when dealing with multi copy regions, such as mitochondrial genome and the rDNA repeat region, parts of the genome that are often neglected or poorly assembled, although they contain interesting information from phylogenetic or epidemiologic perspectives, but also single copy regions can be assembled. The program is capable of targeting multiple regions within a single run. Furthermore, GRAbB can be used to extract specific loci from NGS data, based on homology, like sequences that are used for barcoding. To make the assembly specific, a known part of the region, such as the sequence of a PCR amplicon or a homologous sequence from a related species must be specified. By assembling only the region of interest, the assembly process is computationally much less demanding and may lead to assemblies of better quality. In this study the different applications and functionalities of the program are demonstrated such as: exhaustive assembly (rDNA region and mitochondrial genome), extracting homologous regions or genes (IGS, RPB1, RPB2 and TEF1a), as well as extracting multiple regions within a single run. The program is also compared with MITObim, which is meant for the exhaustive assembly of a single target based on a similar query sequence. GRAbB is shown to be more efficient than MITObim in terms of speed, memory and disk usage. The other functionalities (handling multiple targets simultaneously and extracting homologous regions) of the new program are not matched by other programs. The program is available with explanatory documentation at https://github.com/b-brankovics/grabb. GRAbB has been tested on Ubuntu (12.04 and 14.04), Fedora (23), CentOS (7.1.1503) and Mac OS X (10.7). Furthermore, GRAbB is available as a docker repository: brankovics/grabb (https://hub.docker.com/r/brankovics/grabb/).

Evolution of computational models in BioModels Database and the Physiome Model Repository.

PubMed

Scharm, Martin; Gebhardt, Tom; Touré, Vasundra; Bagnacani, Andrea; Salehzadeh-Yazdi, Ali; Wolkenhauer, Olaf; Waltemath, Dagmar

2018-04-12

A useful model is one that is being (re)used. The development of a successful model does not finish with its publication. During reuse, models are being modified, i.e. expanded, corrected, and refined. Even small changes in the encoding of a model can, however, significantly affect its interpretation. Our motivation for the present study is to identify changes in models and make them transparent and traceable. We analysed 13734 models from BioModels Database and the Physiome Model Repository. For each model, we studied the frequencies and types of updates between its first and latest release. To demonstrate the impact of changes, we explored the history of a Repressilator model in BioModels Database. We observed continuous updates in the majority of models. Surprisingly, even the early models are still being modified. We furthermore detected that many updates target annotations, which improves the information one can gain from models. To support the analysis of changes in model repositories we developed MoSt, an online tool for visualisations of changes in models. The scripts used to generate the data and figures for this study are available from GitHub https://github.com/binfalse/BiVeS-StatsGenerator and as a Docker image at https://hub.docker.com/r/binfalse/bives-statsgenerator/ . The website https://most.bio.informatik.uni-rostock.de/ provides interactive access to model versions and their evolutionary statistics. The reuse of models is still impeded by a lack of trust and documentation. A detailed and transparent documentation of all aspects of the model, including its provenance, will improve this situation. Knowledge about a model's provenance can avoid the repetition of mistakes that others already faced. More insights are gained into how the system evolves from initial findings to a profound understanding. We argue that it is the responsibility of the maintainers of model repositories to offer transparent model provenance to their users.

Canary: an atomic pipeline for clinical amplicon assays.

PubMed

Doig, Kenneth D; Ellul, Jason; Fellowes, Andrew; Thompson, Ella R; Ryland, Georgina; Blombery, Piers; Papenfuss, Anthony T; Fox, Stephen B

2017-12-15

High throughput sequencing requires bioinformatics pipelines to process large volumes of data into meaningful variants that can be translated into a clinical report. These pipelines often suffer from a number of shortcomings: they lack robustness and have many components written in multiple languages, each with a variety of resource requirements. Pipeline components must be linked together with a workflow system to achieve the processing of FASTQ files through to a VCF file of variants. Crafting these pipelines requires considerable bioinformatics and IT skills beyond the reach of many clinical laboratories. Here we present Canary, a single program that can be run on a laptop, which takes FASTQ files from amplicon assays through to an annotated VCF file ready for clinical analysis. Canary can be installed and run with a single command using Docker containerization or run as a single JAR file on a wide range of platforms. Although it is a single utility, Canary performs all the functions present in more complex and unwieldy pipelines. All variants identified by Canary are 3' shifted and represented in their most parsimonious form to provide a consistent nomenclature, irrespective of sequencing variation. Further, proximate in-phase variants are represented as a single HGVS 'delins' variant. This allows for correct nomenclature and consequences to be ascribed to complex multi-nucleotide polymorphisms (MNPs), which are otherwise difficult to represent and interpret. Variants can also be annotated with hundreds of attributes sourced from MyVariant.info to give up to date details on pathogenicity, population statistics and in-silico predictors. Canary has been used at the Peter MacCallum Cancer Centre in Melbourne for the last 2 years for the processing of clinical sequencing data. By encapsulating clinical features in a single, easily installed executable, Canary makes sequencing more accessible to all pathology laboratories. Canary is available for download as source or a Docker image at https://github.com/PapenfussLab/Canary under a GPL-3.0 License.

aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations.

PubMed

Renault, Victor; Tost, Jörg; Pichon, Fabien; Wang-Renault, Shu-Fang; Letouzé, Eric; Imbeaud, Sandrine; Zucman-Rossi, Jessica; Deleuze, Jean-François; How-Kit, Alexandre

2017-01-01

Copy number variations (CNV) include net gains or losses of part or whole chromosomal regions. They differ from copy neutral loss of heterozygosity (cn-LOH) events which do not induce any net change in the copy number and are often associated with uniparental disomy. These phenomena have long been reported to be associated with diseases and particularly in cancer. Losses/gains of genomic regions are often correlated with lower/higher gene expression. On the other hand, loss of heterozygosity (LOH) and cn-LOH are common events in cancer and may be associated with the loss of a functional tumor suppressor gene. Therefore, identifying recurrent CNV and cn-LOH events can be important as they may highlight common biological components and give insights into the development or mechanisms of a disease. However, no currently available tools allow a comprehensive whole-genome visualization of recurrent CNVs and cn-LOH in groups of samples providing absolute quantification of the aberrations leading to the loss of potentially important information. To overcome these limitations, we developed aCNViewer (Absolute CNV Viewer), a visualization tool for absolute CNVs and cn-LOH across a group of samples. aCNViewer proposes three graphical representations: dendrograms, bi-dimensional heatmaps showing chromosomal regions sharing similar abnormality patterns, and quantitative stacked histograms facilitating the identification of recurrent absolute CNVs and cn-LOH. We illustrated aCNViewer using publically available hepatocellular carcinomas (HCCs) Affymetrix SNP Array data (Fig 1A). Regions 1q and 8q present a similar percentage of total gains but significantly different copy number gain categories (p-value of 0.0103 with a Fisher exact test), validated by another cohort of HCCs (p-value of 5.6e-7) (Fig 2B). aCNViewer is implemented in python and R and is available with a GNU GPLv3 license on GitHub https://github.com/FJD-CEPH/aCNViewer and Docker https://hub.docker.com/r/fjdceph/acnviewer/. aCNViewer@cephb.fr.

Automated metadata, provenance cataloging and navigable interfaces: ensuring the usefulness of extreme-scale data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schissel, David; Greenwald, Martin

The MPO (Metadata, Provenance, Ontology) Project successfully addressed the goal of improving the usefulness and traceability of scientific data by building a system that could capture and display all steps in the process of creating, analyzing and disseminating that data. Throughout history, scientists have generated handwritten logbooks to keep track of data, their hypotheses, assumptions, experimental setup, and computational processes as well as reflections on observations and issues encountered. Over the last several decades, with the growth of personal computers, handheld devices, and the World Wide Web, the handwritten logbook has begun to be replaced by electronic logbooks. This transitionmore » has brought increased capability such as supporting multi-media, hypertext, and fast searching. However, content creation and metadata (a set of data that describes and gives information about other data) capturing has for the most part remained a manual activity just as it was with handwritten logbooks. This has led to a fragmentation of data, processing, and annotation that has only accelerated as scientific workflows continue to increase in complexity. From a scientific perspective, it is very important to be able to understand the lineage of any piece of data: who, what, when, how, and why. This is typically referred to as data provenance. The fragmentation discussed previously often means that data provenance is lost. As scientific workflows move to powerful computers and become more complex, the ability to track all of the steps involved in creating a piece of data become even more difficult. It was the goal of the MPO (Metadata, Provenance, Ontology) Project to create a system (the MPO System) that allows for automatic provenance and metadata capturing in such a way to allow easy searching and browsing. This goal needed to be accomplished in a general way so that it may be used across a broad range of scientific domains, yet allow the addition of vocabulary (Ontology) that is domain specific as is required for intelligent searching and browsing in the scientific context. Through the creation and deployment of the MPO system, the goals of the project were achieved. An enhanced metadata, provenance, and ontology storage system was created. This was combined with innovative methodologies for navigating and exploring these data using a web browser for both experimental and simulation-based scientific research. In addition, a system to allow scientists to instrument their existing workflows for automatic metadata and provenance is part of the MPO system. In that way, a scientist can continue to use their existing methodology yet easily document their work. Workflows and data provenance can be displayed either graphically or in an electronic notebook format and support advanced search features including via ontology. The MPO system was successfully used in both Climate and Magnetic Fusion Energy Research. The software for the MPO system is located at https://github.com/MPO-Group/MPO and is open source distributed under the Revised BSD License. A demonstration site of the MPO system is open to the public and is available at https://mpo.psfc.mit.edu/. A Docker container release of the command line client is available for public download using the command docker pull jcwright/mpo-cli at https://hub.docker.com/r/jcwright/mpo-cli.« less

aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations

PubMed Central

Wang-Renault, Shu-Fang; Letouzé, Eric; Imbeaud, Sandrine; Zucman-Rossi, Jessica; Deleuze, Jean-François; How-Kit, Alexandre

2017-01-01

Motivation Copy number variations (CNV) include net gains or losses of part or whole chromosomal regions. They differ from copy neutral loss of heterozygosity (cn-LOH) events which do not induce any net change in the copy number and are often associated with uniparental disomy. These phenomena have long been reported to be associated with diseases and particularly in cancer. Losses/gains of genomic regions are often correlated with lower/higher gene expression. On the other hand, loss of heterozygosity (LOH) and cn-LOH are common events in cancer and may be associated with the loss of a functional tumor suppressor gene. Therefore, identifying recurrent CNV and cn-LOH events can be important as they may highlight common biological components and give insights into the development or mechanisms of a disease. However, no currently available tools allow a comprehensive whole-genome visualization of recurrent CNVs and cn-LOH in groups of samples providing absolute quantification of the aberrations leading to the loss of potentially important information. Results To overcome these limitations, we developed aCNViewer (Absolute CNV Viewer), a visualization tool for absolute CNVs and cn-LOH across a group of samples. aCNViewer proposes three graphical representations: dendrograms, bi-dimensional heatmaps showing chromosomal regions sharing similar abnormality patterns, and quantitative stacked histograms facilitating the identification of recurrent absolute CNVs and cn-LOH. We illustrated aCNViewer using publically available hepatocellular carcinomas (HCCs) Affymetrix SNP Array data (Fig 1A). Regions 1q and 8q present a similar percentage of total gains but significantly different copy number gain categories (p-value of 0.0103 with a Fisher exact test), validated by another cohort of HCCs (p-value of 5.6e-7) (Fig 2B). Availability and implementation aCNViewer is implemented in python and R and is available with a GNU GPLv3 license on GitHub https://github.com/FJD-CEPH/aCNViewer and Docker https://hub.docker.com/r/fjdceph/acnviewer/. Contact aCNViewer@cephb.fr PMID:29261730

BioContainers: an open-source and community-driven framework for software standardization.

PubMed

da Veiga Leprevost, Felipe; Grüning, Björn A; Alves Aflitos, Saulo; Röst, Hannes L; Uszkoreit, Julian; Barsnes, Harald; Vaudel, Marc; Moreno, Pablo; Gatto, Laurent; Weber, Jonas; Bai, Mingze; Jimenez, Rafael C; Sachsenberg, Timo; Pfeuffer, Julianus; Vera Alvarez, Roberto; Griss, Johannes; Nesvizhskii, Alexey I; Perez-Riverol, Yasset

2017-08-15

BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on popular open-source projects Docker and rkt frameworks, that allow software to be installed and executed under an isolated and controlled environment. Also, it provides infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics technologies. These containers can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, cloud environments or HPC clusters). The software is freely available at github.com/BioContainers/. yperez@ebi.ac.uk. © The Author(s) 2017. Published by Oxford University Press.

BioContainers: an open-source and community-driven framework for software standardization

PubMed Central

da Veiga Leprevost, Felipe; Grüning, Björn A.; Alves Aflitos, Saulo; Röst, Hannes L.; Uszkoreit, Julian; Barsnes, Harald; Vaudel, Marc; Moreno, Pablo; Gatto, Laurent; Weber, Jonas; Bai, Mingze; Jimenez, Rafael C.; Sachsenberg, Timo; Pfeuffer, Julianus; Vera Alvarez, Roberto; Griss, Johannes; Nesvizhskii, Alexey I.; Perez-Riverol, Yasset

2017-01-01

Abstract Motivation BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on popular open-source projects Docker and rkt frameworks, that allow software to be installed and executed under an isolated and controlled environment. Also, it provides infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics technologies. These containers can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, cloud environments or HPC clusters). Availability and Implementation The software is freely available at github.com/BioContainers/. Contact yperez@ebi.ac.uk PMID:28379341

Charliecloud: Unprivileged containers for user-defined software stacks in HPC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Priedhorsky, Reid; Randles, Timothy C.

Supercomputing centers are seeing increasing demand for user-defined software stacks (UDSS), instead of or in addition to the stack provided by the center. These UDSS support user needs such as complex dependencies or build requirements, externally required configurations, portability, and consistency. The challenge for centers is to provide these services in a usable manner while minimizing the risks: security, support burden, missing functionality, and performance. We present Charliecloud, which uses the Linux user and mount namespaces to run industry-standard Docker containers with no privileged operations or daemons on center resources. Our simple approach avoids most security risks while maintaining accessmore » to the performance and functionality already on offer, doing so in less than 500 lines of code. Charliecloud promises to bring an industry-standard UDSS user workflow to existing, minimally altered HPC resources.« less

Exploring cloud and big data components for SAR archiving and analysis

NASA Astrophysics Data System (ADS)

Baker, S.; Crosby, C. J.; Meertens, C.; Phillips, D.

2017-12-01

Under the Geodesy Advancing Geoscience and EarthScope (GAGE) NSF Cooperative Agreement, UNAVCO has seen the volume of the SAR Data Archive grow at a substantial rate, from 2 TB in Y1 and 5 TB in Y2 to 41 TB in Y3 primarily due to WInSAR PI proposal management of ALOS-­2/JAXA (Japan Aerospace Exploration Agency) data and to a lesser extent Supersites and other data collections. JAXA provides a fixed number of scenes per year for each PI, and some data files are 50­-60GB each, which accounts for the large volume of data. In total, over 100TB of SAR data are in the WInSAR/UNAVCO archive and a large portion of these are available unrestricted for WInSAR members. In addition to the existing data, newer data streams from the Sentinel-1 and NISAR missions will require efficient processing pipelines and easily scalable infrastructure to handle processed results. With these growing data sizes and space concerns, the SAR archive operations migrated to the Texas Advanced Computing Center (TACC) via an NSF XSEDE proposal in spring 2017. Data are stored on an HPC system while data operations are running on Jetstream virtual machines within the same datacenter. In addition to the production data operations, testing was done in early 2017 with container based InSAR processing analysis using JupyterHub and Docker images deployed on a VM cluster on Jetstream. The JupyterHub environment is well suited for short courses and other training opportunities for the community such as labs for university courses on InSAR. UNAVCO is also exploring new processing methodologies using DC/OS (the datacenter operating system) for batch and stream processing workflows and time series analysis with Big Data open source components like the Spark, Mesos, Akka, Cassandra, Kafka (SMACK) stack. The comparison of the different methodologies will provide insight into the pros and cons for each and help the SAR community with decisions about infrastructure and software requirements to meet their research goals.

SciServer: An Online Collaborative Environment for Big Data in Research and Education

NASA Astrophysics Data System (ADS)

Raddick, Jordan; Souter, Barbara; Lemson, Gerard; Taghizadeh-Popp, Manuchehr

2017-01-01

For the past year, SciServer Compute (http://compute.sciserver.org) has offered access to big data resources running within server-side Docker containers. Compute has allowed thousands of researchers to bring advanced analysis to big datasets like the Sloan Digital Sky Survey and others, while keeping the analysis close to the data for better performance and easier read/write access. SciServer Compute is just one part of the SciServer system being developed at Johns Hopkins University, which provides an easy-to-use collaborative research environment for astronomy and many other sciences.SciServer enables these collaborative research strategies using Jupyter notebooks, in which users can write their own Python and R scripts and execute them on the same server as the data. We have written special-purpose libraries for querying, reading, and writing data. Intermediate results can be stored in large scratch space (hundreds of TBs) and analyzed directly from within Python or R with state-of-the-art visualization and machine learning libraries. Users can store science-ready results in their permanent allocation on SciDrive, a Dropbox-like system for sharing and publishing files.SciServer Compute’s virtual research environment has grown with the addition of task management and access control functions, allowing collaborators to share both data and analysis scripts securely across the world. These features also open up new possibilities for education, allowing instructors to share datasets with students and students to write analysis scripts to share with their instructors. We are leveraging these features into a new system called “SciServer Courseware,” which will allow instructors to share assignments with their students, allowing students to engage with big data in new ways.SciServer has also expanded to include more datasets beyond the Sloan Digital Sky Survey. A part of that growth has been the addition of the SkyQuery component, which allows for simple, fast cross-matching between very large astronomical datasets.Demos, documentation, and more information about all these resources can be found at www.sciserver.org.

Creating CAD designs and performing their subsequent analysis using opensource solutions in Python

NASA Astrophysics Data System (ADS)

Iakushkin, Oleg O.; Sedova, Olga S.

2018-01-01

The paper discusses the concept of a system that encapsulates the transition from geometry building to strength tests. The solution we propose views the engineer as a programmer who is capable of coding the procedure for working with the modeli.e., to outline the necessary transformations and create cases for boundary conditions. We propose a prototype of such system. In our work, we used: Python programming language to create the program; Jupyter framework to create a single workspace visualization; pythonOCC library to implement CAD; FeniCS library to implement FEM; GMSH and VTK utilities. The prototype is launched on a platform which is a dynamically expandable multi-tenant cloud service providing users with all computing resources on demand. However, the system may be deployed locally for prototyping or work that does not involve resource-intensive computing. To make it possible, we used containerization, isolating the system in a Docker container.

Leaf LIMS: A Flexible Laboratory Information Management System with a Synthetic Biology Focus.

PubMed

Craig, Thomas; Holland, Richard; D'Amore, Rosalinda; Johnson, James R; McCue, Hannah V; West, Anthony; Zulkower, Valentin; Tekotte, Hille; Cai, Yizhi; Swan, Daniel; Davey, Robert P; Hertz-Fowler, Christiane; Hall, Anthony; Caddick, Mark

2017-12-15

This paper presents Leaf LIMS, a flexible laboratory information management system (LIMS) designed to address the complexity of synthetic biology workflows. At the project's inception there was a lack of a LIMS designed specifically to address synthetic biology processes, with most systems focused on either next generation sequencing or biobanks and clinical sample handling. Leaf LIMS implements integrated project, item, and laboratory stock tracking, offering complete sample and construct genealogy, materials and lot tracking, and modular assay data capture. Hence, it enables highly configurable task-based workflows and supports data capture from project inception to completion. As such, in addition to it supporting synthetic biology it is ideal for many laboratory environments with multiple projects and users. The system is deployed as a web application through Docker and is provided under a permissive MIT license. It is freely available for download at https://leaflims.github.io .

EDEN: evolutionary dynamics within environments

PubMed Central

Münch, Philipp C.; Stecher, Bärbel; McHardy, Alice C.

2017-01-01

Abstract Summary Metagenomics revolutionized the field of microbial ecology, giving access to Gb-sized datasets of microbial communities under natural conditions. This enables fine-grained analyses of the functions of community members, studies of their association with phenotypes and environments, as well as of their microevolution and adaptation to changing environmental conditions. However, phylogenetic methods for studying adaptation and evolutionary dynamics are not able to cope with big data. EDEN is the first software for the rapid detection of protein families and regions under positive selection, as well as their associated biological processes, from meta- and pangenome data. It provides an interactive result visualization for detailed comparative analyses. Availability and implementation EDEN is available as a Docker installation under the GPL 3.0 license, allowing its use on common operating systems, at http://www.github.com/hzi-bifo/eden. Contact alice.mchardy@helmholtz-hzi.de Supplementary information Supplementary data are available at Bioinformatics online. PMID:28637301

GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the Genus Stenotrophomonas.

PubMed

Vinuesa, Pablo; Ochoa-Sánchez, Luz E; Contreras-Moreira, Bruno

2018-01-01

The massive accumulation of genome-sequences in public databases promoted the proliferation of genome-level phylogenetic analyses in many areas of biological research. However, due to diverse evolutionary and genetic processes, many loci have undesirable properties for phylogenetic reconstruction. These, if undetected, can result in erroneous or biased estimates, particularly when estimating species trees from concatenated datasets. To deal with these problems, we developed GET_PHYLOMARKERS, a pipeline designed to identify high-quality markers to estimate robust genome phylogenies from the orthologous clusters, or the pan-genome matrix (PGM), computed by GET_HOMOLOGUES. In the first context, a set of sequential filters are applied to exclude recombinant alignments and those producing anomalous or poorly resolved trees. Multiple sequence alignments and maximum likelihood (ML) phylogenies are computed in parallel on multi-core computers. A ML species tree is estimated from the concatenated set of top-ranking alignments at the DNA or protein levels, using either FastTree or IQ-TREE (IQT). The latter is used by default due to its superior performance revealed in an extensive benchmark analysis. In addition, parsimony and ML phylogenies can be estimated from the PGM. We demonstrate the practical utility of the software by analyzing 170 Stenotrophomonas genome sequences available in RefSeq and 10 new complete genomes of Mexican environmental S. maltophilia complex (Smc) isolates reported herein. A combination of core-genome and PGM analyses was used to revise the molecular systematics of the genus. An unsupervised learning approach that uses a goodness of clustering statistic identified 20 groups within the Smc at a core-genome average nucleotide identity (cgANIb) of 95.9% that are perfectly consistent with strongly supported clades on the core- and pan-genome trees. In addition, we identified 16 misclassified RefSeq genome sequences, 14 of them labeled as S. maltophilia , demonstrating the broad utility of the software for phylogenomics and geno-taxonomic studies. The code, a detailed manual and tutorials are freely available for Linux/UNIX servers under the GNU GPLv3 license at https://github.com/vinuesa/get_phylomarkers. A docker image bundling GET_PHYLOMARKERS with GET_HOMOLOGUES is available at https://hub.docker.com/r/csicunam/get_homologues/, which can be easily run on any platform.

Hydrodynamics and Water Quality forecasting over a Cloud Computing environment: INDIGO-DataCloud

NASA Astrophysics Data System (ADS)

Aguilar Gómez, Fernando; de Lucas, Jesús Marco; García, Daniel; Monteoliva, Agustín

2017-04-01

Algae Bloom due to eutrophication is an extended problem for water reservoirs and lakes that impacts directly in water quality. It can create a dead zone that lacks enough oxygen to support life and it can also be human harmful, so it must be controlled in water masses for supplying, bathing or other uses. Hydrodynamic and Water Quality modelling can contribute to forecast the status of the water system in order to alert authorities before an algae bloom event occurs. It can be used to predict scenarios and find solutions to reduce the harmful impact of the blooms. High resolution models need to process a big amount of data using a robust enough computing infrastructure. INDIGO-DataCloud (https://www.indigo-datacloud.eu/) is an European Commission funded project that aims at developing a data and computing platform targeting scientific communities, deployable on multiple hardware and provisioned over hybrid (private or public) e-infrastructures. The project addresses the development of solutions for different Case Studies using different Cloud-based alternatives. In the first INDIGO software release, a set of components are ready to manage the deployment of services to perform N number of Delft3D simulations (for calibrating or scenario definition) over a Cloud Computing environment, using the Docker technology: TOSCA requirement description, Docker repository, Orchestrator, AAI (Authorization, Authentication) and OneData (Distributed Storage System). Moreover, the Future Gateway portal based on Liferay, provides an user-friendly interface where the user can configure the simulations. Due to the data approach of INDIGO, the developed solutions can contribute to manage the full data life cycle of a project, thanks to different tools to manage datasets or even metadata. Furthermore, the cloud environment contributes to provide a dynamic, scalable and easy-to-use framework for non-IT experts users. This framework is potentially capable to automatize the processing of forecasting applying periodic tasks. For instance, a user can forecast every month the hydrodynamics and water quality status of a reservoir starting from a base model and supplying new data gathered from the instrumentation or observations. This interactive presentation aims to show the use of INDIGO solutions in a particular forecasting use case and to inspire others in the use of a Cloud framework for their applications.

wft4galaxy: a workflow testing tool for galaxy.

PubMed

Piras, Marco Enrico; Pireddu, Luca; Zanetti, Gianluigi

2017-12-01

Workflow managers for scientific analysis provide a high-level programming platform facilitating standardization, automation, collaboration and access to sophisticated computing resources. The Galaxy workflow manager provides a prime example of this type of platform. As compositions of simpler tools, workflows effectively comprise specialized computer programs implementing often very complex analysis procedures. To date, no simple way to automatically test Galaxy workflows and ensure their correctness has appeared in the literature. With wft4galaxy we offer a tool to bring automated testing to Galaxy workflows, making it feasible to bring continuous integration to their development and ensuring that defects are detected promptly. wft4galaxy can be easily installed as a regular Python program or launched directly as a Docker container-the latter reducing installation effort to a minimum. Available at https://github.com/phnmnl/wft4galaxy under the Academic Free License v3.0. marcoenrico.piras@crs4.it. © The Author 2017. Published by Oxford University Press.

Shifter: Containers for HPC

NASA Astrophysics Data System (ADS)

Gerhardt, Lisa; Bhimji, Wahid; Canon, Shane; Fasel, Markus; Jacobsen, Doug; Mustafa, Mustafa; Porter, Jeff; Tsulaia, Vakho

2017-10-01

Bringing HEP computing to HPC can be difficult. Software stacks are often very complicated with numerous dependencies that are difficult to get installed on an HPC system. To address this issue, NERSC has created Shifter, a framework that delivers Docker-like functionality to HPC. It works by extracting images from native formats and converting them to a common format that is optimally tuned for the HPC environment. We have used Shifter to deliver the CVMFS software stack for ALICE, ATLAS, and STAR on the supercomputers at NERSC. As well as enabling the distribution multi-TB sized CVMFS stacks to HPC, this approach also offers performance advantages. Software startup times are significantly reduced and load times scale with minimal variation to 1000s of nodes. We profile several successful examples of scientists using Shifter to make scientific analysis easily customizable and scalable. We will describe the Shifter framework and several efforts in HEP and NP to use Shifter to deliver their software on the Cori HPC system.

[Asbestos import in Italy: the transit through Livorno harbour from 1957 to 1995].

PubMed

Nemo, Alessandro; Boccuzzi, Maria Teresa; Silvestri, Stefano

2009-01-01

This work aims to describe quantities, type of packaging and geographical area of origin of the asbestos fibres unloaded in Livorno harbour between 1957 and 1995. Historical data, available for this period, were collected from Il Messaggero Marittimo, a periodical journal dealing with Livorno harbour activities. Collaboration between the local Health and Safety Unit (ASL 6) and the Institute for Study and Prevention of Cancer (ISPO), both Regional Institutions of the National Health Service, made it possible to carry out this work. The computation of the collected data for the whole period allows the description of the quantities, year by year and the assessment of the percentage imported through Livorno on the total tonnage imported in Italy during the same period. The detection of the geographical areas of origin allowed to estimate the quantities subdivided by type of fibre (serpentine/amphiboles). These results will help the historical assessment of occupational asbestos exposure of the Livorno dockers.

OpenNEX, a private-public partnership in support of the national climate assessment

NASA Astrophysics Data System (ADS)

Nemani, R. R.; Wang, W.; Michaelis, A.; Votava, P.; Ganguly, S.

2016-12-01

The NASA Earth Exchange (NEX) is a collaborative computing platform that has been developed with the objective of bringing scientists together with the software tools, massive global datasets, and supercomputing resources necessary to accelerate research in Earth systems science and global change. NEX is funded as an enabling tool for sustaining the national climate assessment. Over the past five years, researchers have used the NEX platform and produced a number of data sets highly relevant to the National Climate Assessment. These include high-resolution climate projections using different downscaling techniques and trends in historical climate from satellite data. To enable a broader community in exploiting the above datasets, the NEX team partnered with public cloud providers to create the OpenNEX platform. OpenNEX provides ready access to NEX data holdings on a number of public cloud platforms along with pertinent analysis tools and workflows in the form of Machine Images and Docker Containers, lectures and tutorials by experts. We will showcase some of the applications of OpenNEX data and tools by the community on Amazon Web Services, Google Cloud and the NEX Sandbox.

Building a Billion Spatio-Temporal Object Search and Visualization Platform

NASA Astrophysics Data System (ADS)

Kakkar, D.; Lewis, B.

2017-10-01

With funding from the Sloan Foundation and Harvard Dataverse, the Harvard Center for Geographic Analysis (CGA) has developed a prototype spatio-temporal visualization platform called the Billion Object Platform or BOP. The goal of the project is to lower barriers for scholars who wish to access large, streaming, spatio-temporal datasets. The BOP is now loaded with the latest billion geo-tweets, and is fed a real-time stream of about 1 million tweets per day. The geo-tweets are enriched with sentiment and census/admin boundary codes when they enter the system. The system is open source and is currently hosted on Massachusetts Open Cloud (MOC), an OpenStack environment with all components deployed in Docker orchestrated by Kontena. This paper will provide an overview of the BOP architecture, which is built on an open source stack consisting of Apache Lucene, Solr, Kafka, Zookeeper, Swagger, scikit-learn, OpenLayers, and AngularJS. The paper will further discuss the approach used for harvesting, enriching, streaming, storing, indexing, visualizing and querying a billion streaming geo-tweets.

A low-complexity add-on score for protein remote homology search with COMER.

PubMed

Margelevicius, Mindaugas

2018-06-15

Protein sequence alignment forms the basis for comparative modeling, the most reliable approach to protein structure prediction, among many other applications. Alignment between sequence families, or profile-profile alignment, represents one of the most, if not the most, sensitive means for homology detection but still necessitates improvement. We aim at improving the quality of profile-profile alignments and the sensitivity induced by them by refining profile-profile substitution scores. We have developed a new score that represents an additional component of profile-profile substitution scores. A comprehensive evaluation shows that the new add-on score statistically significantly improves both the sensitivity and the alignment quality of the COMER method. We discuss why the score leads to the improvement and its almost optimal computational complexity that makes it easily implementable in any profile-profile alignment method. An implementation of the add-on score in the open-source COMER software and data are available at https://sourceforge.net/projects/comer. The COMER software is also available on Github at https://github.com/minmarg/comer and as a Docker image (minmar/comer). Supplementary data are available at Bioinformatics online.

Sirepo for Synchrotron Radiation Workshop

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nagler, Robert; Moeller, Paul; Rakitin, Maksim

Sirepo is an open source framework for cloud computing. The graphical user interface (GUI) for Sirepo, also known as the client, executes in any HTML5 compliant web browser on any computing platform, including tablets. The client is built in JavaScript, making use of the following open source libraries: Bootstrap, which is fundamental for cross-platform web applications; AngularJS, which provides a model–view–controller (MVC) architecture and GUI components; and D3.js, which provides interactive plots and data-driven transformations. The Sirepo server is built on the following Python technologies: Flask, which is a lightweight framework for web development; Jinja, which is a secure andmore » widely used templating language; and Werkzeug, a utility library that is compliant with the WSGI standard. We use Nginx as the HTTP server and proxy, which provides a scalable event-driven architecture. The physics codes supported by Sirepo execute inside a Docker container. One of the codes supported by Sirepo is the Synchrotron Radiation Workshop (SRW). SRW computes synchrotron radiation from relativistic electrons in arbitrary magnetic fields and propagates the radiation wavefronts through optical beamlines. SRW is open source and is primarily supported by Dr. Oleg Chubar of NSLS-II at Brookhaven National Laboratory.« less

GC31G-1182: Opennex, a Private-Public Partnership in Support of the National Climate Assessment

NASA Technical Reports Server (NTRS)

Nemani, Ramakrishna R.; Wang, Weile; Michaelis, Andrew; Votava, Petr; Ganguly, Sangram

2016-01-01

The NASA Earth Exchange (NEX) is a collaborative computing platform that has been developed with the objective of bringing scientists together with the software tools, massive global datasets, and supercomputing resources necessary to accelerate research in Earth systems science and global change. NEX is funded as an enabling tool for sustaining the national climate assessment. Over the past five years, researchers have used the NEX platform and produced a number of data sets highly relevant to the National Climate Assessment. These include high-resolution climate projections using different downscaling techniques and trends in historical climate from satellite data. To enable a broader community in exploiting the above datasets, the NEX team partnered with public cloud providers to create the OpenNEX platform. OpenNEX provides ready access to NEX data holdings on a number of public cloud platforms along with pertinent analysis tools and workflows in the form of Machine Images and Docker Containers, lectures and tutorials by experts. We will showcase some of the applications of OpenNEX data and tools by the community on Amazon Web Services, Google Cloud and the NEX Sandbox.

Community and Virtual Community.

ERIC Educational Resources Information Center

Ellis, David; Oldridge, Rachel; Vasconcelos, Ana

2004-01-01

Presents a literature review that covers the following topics related to virtual communities: (1) information and virtual community; (2) virtual communities and communities of practice; (3) virtual communities and virtual arenas, including virtual community networks; and (4) networked virtual communities. (Contains 175 references.) (MES)

Virtual Team Governance: Addressing the Governance Mechanisms and Virtual Team Performance

NASA Astrophysics Data System (ADS)

Zhan, Yihong; Bai, Yu; Liu, Ziheng

As technology has improved and collaborative software has been developed, virtual teams with geographically dispersed members spread across diverse physical locations have become increasingly prominent. Virtual team is supported by advancing communication technologies, which makes virtual teams able to largely transcend time and space. Virtual teams have changed the corporate landscape, which are more complex and dynamic than traditional teams since the members of virtual teams are spread on diverse geographical locations and their roles in the virtual team are different. Therefore, how to realize good governance of virtual team and arrive at good virtual team performance is becoming critical and challenging. Good virtual team governance is essential for a high-performance virtual team. This paper explores the performance and the governance mechanism of virtual team. It establishes a model to explain the relationship between the performance and the governance mechanisms in virtual teams. This paper is focusing on managing virtual teams. It aims to find the strategies to help business organizations to improve the performance of their virtual teams and arrive at the objectives of good virtual team management.

Personal Virtual Libraries

ERIC Educational Resources Information Center

Pappas, Marjorie L.

2004-01-01

Virtual libraries are becoming more and more common. Most states have a virtual library. A growing number of public libraries have a virtual presence on the Web. Virtual libraries are a growing addition to school library media collections. The next logical step would be personal virtual libraries. A personal virtual library (PVL) is a collection…

Models and algorithm of optimization launch and deployment of virtual network functions in the virtual data center

NASA Astrophysics Data System (ADS)

Bolodurina, I. P.; Parfenov, D. I.

2017-10-01

The goal of our investigation is optimization of network work in virtual data center. The advantage of modern infrastructure virtualization lies in the possibility to use software-defined networks. However, the existing optimization of algorithmic solutions does not take into account specific features working with multiple classes of virtual network functions. The current paper describes models characterizing the basic structures of object of virtual data center. They including: a level distribution model of software-defined infrastructure virtual data center, a generalized model of a virtual network function, a neural network model of the identification of virtual network functions. We also developed an efficient algorithm for the optimization technology of containerization of virtual network functions in virtual data center. We propose an efficient algorithm for placing virtual network functions. In our investigation we also generalize the well renowned heuristic and deterministic algorithms of Karmakar-Karp.

Working Group Reports and Presentations: Virtual Worlds and Virtual Exploration

NASA Technical Reports Server (NTRS)

LAmoreaux, Claudia

2006-01-01

Scientists and engineers are continually developing innovative methods to capitalize on recent developments in computational power. Virtual worlds and virtual exploration present a new toolset for project design, implementation, and resolution. Replication of the physical world in the virtual domain provides stimulating displays to augment current data analysis techniques and to encourage public participation. In addition, the virtual domain provides stakeholders with a low cost, low risk design and test environment. The following document defines a virtual world and virtual exploration, categorizes the chief motivations for virtual exploration, elaborates upon specific objectives, identifies roadblocks and enablers for realizing the benefits, and highlights the more immediate areas of implementation (i.e. the action items). While the document attempts a comprehensive evaluation of virtual worlds and virtual exploration, the innovative nature of the opportunities presented precludes completeness. The authors strongly encourage readers to derive additional means of utilizing the virtual exploration toolset.

Bicycle: a bioinformatics pipeline to analyze bisulfite sequencing data.

PubMed

Graña, Osvaldo; López-Fernández, Hugo; Fdez-Riverola, Florentino; González Pisano, David; Glez-Peña, Daniel

2018-04-15

High-throughput sequencing of bisulfite-converted DNA is a technique used to measure DNA methylation levels. Although a considerable number of computational pipelines have been developed to analyze such data, none of them tackles all the peculiarities of the analysis together, revealing limitations that can force the user to manually perform additional steps needed for a complete processing of the data. This article presents bicycle, an integrated, flexible analysis pipeline for bisulfite sequencing data. Bicycle analyzes whole genome bisulfite sequencing data, targeted bisulfite sequencing data and hydroxymethylation data. To show how bicycle overtakes other available pipelines, we compared them on a defined number of features that are summarized in a table. We also tested bicycle with both simulated and real datasets, to show its level of performance, and compared it to different state-of-the-art methylation analysis pipelines. Bicycle is publicly available under GNU LGPL v3.0 license at http://www.sing-group.org/bicycle. Users can also download a customized Ubuntu LiveCD including bicycle and other bisulfite sequencing data pipelines compared here. In addition, a docker image with bicycle and its dependencies, which allows a straightforward use of bicycle in any platform (e.g. Linux, OS X or Windows), is also available. ograna@cnio.es or dgpena@uvigo.es. Supplementary data are available at Bioinformatics online.

Tools for open geospatial science

NASA Astrophysics Data System (ADS)

Petras, V.; Petrasova, A.; Mitasova, H.

2017-12-01

Open science uses open source to deal with reproducibility challenges in data and computational sciences. However, just using open source software or making the code public does not make the research reproducible. Moreover, the scientists face the challenge of learning new unfamiliar tools and workflows. In this contribution, we will look at a graduate-level course syllabus covering several software tools which make validation and reuse by a wider professional community possible. For the novices in the open science arena, we will look at how scripting languages such as Python and Bash help us reproduce research (starting with our own work). Jupyter Notebook will be introduced as a code editor, data exploration tool, and a lab notebook. We will see how Git helps us not to get lost in revisions and how Docker is used to wrap all the parts together using a single text file so that figures for a scientific paper or a technical report can be generated with a single command. We will look at examples of software and publications in the geospatial domain which use these tools and principles. Scientific contributions to GRASS GIS, a powerful open source desktop GIS and geoprocessing backend, will serve as an example of why and how to publish new algorithms and tools as part of a bigger open source project.

Sirepo - Warp

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nagler, Robert; Moeller, Paul

Sirepo is an open source framework for cloud computing. The graphical user interface (GUI) for Sirepo, also known as the client, executes in any HTML5 compliant web browser on any computing platform, including tablets. The client is built in JavaScript, making use of the following open source libraries: Bootstrap, which is fundamental for cross-platform web applications; AngularJS, which provides a model–view–controller (MVC) architecture and GUI components; and D3.js, which provides interactive plots and data-driven transformations. The Sirepo server is built on the following Python technologies: Flask, which is a lightweight framework for web development; Jin-ja, which is a secure andmore » widely used templating language; and Werkzeug, a utility library that is compliant with the WSGI standard. We use Nginx as the HTTP server and proxy, which provides a scalable event-driven architecture. The physics codes supported by Sirepo execute inside a Docker container. One of the codes supported by Sirepo is Warp. Warp is a particle-in-cell (PIC) code de-signed to simulate high-intensity charged particle beams and plasmas in both the electrostatic and electromagnetic regimes, with a wide variety of integrated physics models and diagnostics. At pre-sent, Sirepo supports a small subset of Warp’s capabilities. Warp is open source and is part of the Berkeley Lab Accelerator Simulation Toolkit.« less

Title list of documents made publicly available, November 1-30, 1995

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1996-01-01

The Title List of Documents Made Publicly Available is a monthly publication. It contains descriptions of the information received and generated by the U.S. Nuclear Regulatory Commission (NRC). This information includes (1) docketed material associated with civilian nuclear power plants and other uses of radioactive materials and (2) nondocketed material received and generated by NRC pertinent to its role as a regulatory agency. As used here, docketed does not refer to Court dockets; it refers to the system by which NRC maintains its regulatory records. This series of documents is indexed by a Personal Author Index, a Corporate Source Indexmore » and a Report Number Index. The docketed information contained in the Title List includes the information formerly issued through the Department of Energy publication Power Reactor Docker Information, last published in January 1979. NRC documents that are publicly available may be examined without charge at the NRC Public Document Room (PDR). Duplicate copies may be obtained for a fee. Standing orders for certain categories of documents are also available. Clients may search for and order desired titles through the PDR computerized Bibliographic Retrieval System, which is accessible both at the PDR and remotely. The PDR is staffed by professional technical librarians, who provide reference assistance to users.« less

Geographically distributed Batch System as a Service: the INDIGO-DataCloud approach exploiting HTCondor

NASA Astrophysics Data System (ADS)

Aiftimiei, D. C.; Antonacci, M.; Bagnasco, S.; Boccali, T.; Bucchi, R.; Caballer, M.; Costantini, A.; Donvito, G.; Gaido, L.; Italiano, A.; Michelotto, D.; Panella, M.; Salomoni, D.; Vallero, S.

2017-10-01

One of the challenges a scientific computing center has to face is to keep delivering well consolidated computational frameworks (i.e. the batch computing farm), while conforming to modern computing paradigms. The aim is to ease system administration at all levels (from hardware to applications) and to provide a smooth end-user experience. Within the INDIGO- DataCloud project, we adopt two different approaches to implement a PaaS-level, on-demand Batch Farm Service based on HTCondor and Mesos. In the first approach, described in this paper, the various HTCondor daemons are packaged inside pre-configured Docker images and deployed as Long Running Services through Marathon, profiting from its health checks and failover capabilities. In the second approach, we are going to implement an ad-hoc HTCondor framework for Mesos. Container-to-container communication and isolation have been addressed exploring a solution based on overlay networks (based on the Calico Project). Finally, we have studied the possibility to deploy an HTCondor cluster that spans over different sites, exploiting the Condor Connection Broker component, that allows communication across a private network boundary or firewall as in case of multi-site deployments. In this paper, we are going to describe and motivate our implementation choices and to show the results of the first tests performed.

ASaiM: a Galaxy-based framework to analyze microbiota data.

PubMed

Batut, Bérénice; Gravouil, Kévin; Defois, Clémence; Hiltemann, Saskia; Brugère, Jean-François; Peyretaillade, Eric; Peyret, Pierre

2018-05-22

New generations of sequencing platforms coupled to numerous bioinformatics tools has led to rapid technological progress in metagenomics and metatranscriptomics to investigate complex microorganism communities. Nevertheless, a combination of different bioinformatic tools remains necessary to draw conclusions out of microbiota studies. Modular and user-friendly tools would greatly improve such studies. We therefore developed ASaiM, an Open-Source Galaxy-based framework dedicated to microbiota data analyses. ASaiM provides an extensive collection of tools to assemble, extract, explore and visualize microbiota information from raw metataxonomic, metagenomic or metatranscriptomic sequences. To guide the analyses, several customizable workflows are included and are supported by tutorials and Galaxy interactive tours, which guide users through the analyses step by step. ASaiM is implemented as a Galaxy Docker flavour. It is scalable to thousands of datasets, but also can be used on a normal PC. The associated source code is available under Apache 2 license at https://github.com/ASaiM/framework and documentation can be found online (http://asaim.readthedocs.io). Based on the Galaxy framework, ASaiM offers a sophisticated environment with a variety of tools, workflows, documentation and training to scientists working on complex microorganism communities. It makes analysis and exploration analyses of microbiota data easy, quick, transparent, reproducible and shareable.

Logistic Model to Support Service Modularity for the Promotion of Reusability in a Web Objects-Enabled IoT Environment.

PubMed

Kibria, Muhammad Golam; Ali, Sajjad; Jarwar, Muhammad Aslam; Kumar, Sunil; Chong, Ilyoung

2017-09-22

Due to a very large number of connected virtual objects in the surrounding environment, intelligent service features in the Internet of Things requires the reuse of existing virtual objects and composite virtual objects. If a new virtual object is created for each new service request, then the number of virtual object would increase exponentially. The Web of Objects applies the principle of service modularity in terms of virtual objects and composite virtual objects. Service modularity is a key concept in the Web Objects-Enabled Internet of Things (IoT) environment which allows for the reuse of existing virtual objects and composite virtual objects in heterogeneous ontologies. In the case of similar service requests occurring at the same, or different locations, the already-instantiated virtual objects and their composites that exist in the same, or different ontologies can be reused. In this case, similar types of virtual objects and composite virtual objects are searched and matched. Their reuse avoids duplication under similar circumstances, and reduces the time it takes to search and instantiate them from their repositories, where similar functionalities are provided by similar types of virtual objects and their composites. Controlling and maintaining a virtual object means controlling and maintaining a real-world object in the real world. Even though the functional costs of virtual objects are just a fraction of those for deploying and maintaining real-world objects, this article focuses on reusing virtual objects and composite virtual objects, as well as discusses similarity matching of virtual objects and composite virtual objects. This article proposes a logistic model that supports service modularity for the promotion of reusability in the Web Objects-enabled IoT environment. Necessary functional components and a flowchart of an algorithm for reusing composite virtual objects are discussed. Also, to realize the service modularity, a use case scenario is studied and implemented.

Logistic Model to Support Service Modularity for the Promotion of Reusability in a Web Objects-Enabled IoT Environment

PubMed Central

Chong, Ilyoung

2017-01-01

Due to a very large number of connected virtual objects in the surrounding environment, intelligent service features in the Internet of Things requires the reuse of existing virtual objects and composite virtual objects. If a new virtual object is created for each new service request, then the number of virtual object would increase exponentially. The Web of Objects applies the principle of service modularity in terms of virtual objects and composite virtual objects. Service modularity is a key concept in the Web Objects-Enabled Internet of Things (IoT) environment which allows for the reuse of existing virtual objects and composite virtual objects in heterogeneous ontologies. In the case of similar service requests occurring at the same, or different locations, the already-instantiated virtual objects and their composites that exist in the same, or different ontologies can be reused. In this case, similar types of virtual objects and composite virtual objects are searched and matched. Their reuse avoids duplication under similar circumstances, and reduces the time it takes to search and instantiate them from their repositories, where similar functionalities are provided by similar types of virtual objects and their composites. Controlling and maintaining a virtual object means controlling and maintaining a real-world object in the real world. Even though the functional costs of virtual objects are just a fraction of those for deploying and maintaining real-world objects, this article focuses on reusing virtual objects and composite virtual objects, as well as discusses similarity matching of virtual objects and composite virtual objects. This article proposes a logistic model that supports service modularity for the promotion of reusability in the Web Objects-enabled IoT environment. Necessary functional components and a flowchart of an algorithm for reusing composite virtual objects are discussed. Also, to realize the service modularity, a use case scenario is studied and implemented. PMID:28937590

Estimating Distance in Real and Virtual Environments: Does Order Make a Difference?

PubMed Central

Ziemer, Christine J.; Plumert, Jodie M.; Cremer, James F.; Kearney, Joseph K.

2010-01-01

This investigation examined how the order in which people experience real and virtual environments influences their distance estimates. Participants made two sets of distance estimates in one of the following conditions: 1) real environment first, virtual environment second; 2) virtual environment first, real environment second; 3) real environment first, real environment second; or 4) virtual environment first, virtual environment second. In Experiment 1, participants imagined how long it would take to walk to targets in real and virtual environments. Participants’ first estimates were significantly more accurate in the real than in the virtual environment. When the second environment was the same as the first environment (real-real and virtual-virtual), participants’ second estimates were also more accurate in the real than in the virtual environment. When the second environment differed from the first environment (real-virtual and virtual-real), however, participants’ second estimates did not differ significantly across the two environments. A second experiment in which participants walked blindfolded to targets in the real environment and imagined how long it would take to walk to targets in the virtual environment replicated these results. These subtle, yet persistent order effects suggest that memory can play an important role in distance perception. PMID:19525540

Sensitivity-based virtual fields for the non-linear virtual fields method

NASA Astrophysics Data System (ADS)

Marek, Aleksander; Davis, Frances M.; Pierron, Fabrice

2017-09-01

The virtual fields method is an approach to inversely identify material parameters using full-field deformation data. In this manuscript, a new set of automatically-defined virtual fields for non-linear constitutive models has been proposed. These new sensitivity-based virtual fields reduce the influence of noise on the parameter identification. The sensitivity-based virtual fields were applied to a numerical example involving small strain plasticity; however, the general formulation derived for these virtual fields is applicable to any non-linear constitutive model. To quantify the improvement offered by these new virtual fields, they were compared with stiffness-based and manually defined virtual fields. The proposed sensitivity-based virtual fields were consistently able to identify plastic model parameters and outperform the stiffness-based and manually defined virtual fields when the data was corrupted by noise.

Efficient operating system level virtualization techniques for cloud resources

NASA Astrophysics Data System (ADS)

Ansu, R.; Samiksha; Anju, S.; Singh, K. John

2017-11-01

Cloud computing is an advancing technology which provides the servcies of Infrastructure, Platform and Software. Virtualization and Computer utility are the keys of Cloud computing. The numbers of cloud users are increasing day by day. So it is the need of the hour to make resources available on demand to satisfy user requirements. The technique in which resources namely storage, processing power, memory and network or I/O are abstracted is known as Virtualization. For executing the operating systems various virtualization techniques are available. They are: Full System Virtualization and Para Virtualization. In Full Virtualization, the whole architecture of hardware is duplicated virtually. No modifications are required in Guest OS as the OS deals with the VM hypervisor directly. In Para Virtualization, modifications of OS is required to run in parallel with other OS. For the Guest OS to access the hardware, the host OS must provide a Virtual Machine Interface. OS virtualization has many advantages such as migrating applications transparently, consolidation of server, online maintenance of OS and providing security. This paper briefs both the virtualization techniques and discusses the issues in OS level virtualization.

Starting and Operating Live Virtual Reference Services: A How-To-Do-It Manual for Librarians. How-To-Do-It Manuals for Librarians, Number 118.

ERIC Educational Resources Information Center

Meola, Marc; Stormont, Sam

This guide discusses the essentials of live virtual reference, preparing for virtual reference, and implementing and incorporating virtual reference. Chapter 1, "Understanding Live Virtual Reference," lays out what virtual reference is and how it compares to other forms of reference. Chapter 2, "Offering Live Virtual Reference," presents ten…

Virtual healthcare delivery: defined, modeled, and predictive barriers to implementation identified.

PubMed

Harrop, V M

2001-01-01

Provider organizations lack: 1. a definition of "virtual" healthcare delivery relative to the products, services, and processes offered by dot.coms, web-compact disk healthcare content providers, telemedicine, and telecommunications companies, and 2. a model for integrating real and virtual healthcare delivery. This paper defines virtual healthcare delivery as asynchronous, outsourced, and anonymous, then proposes a 2x2 Real-Virtual Healthcare Delivery model focused on real and virtual patients and real and virtual provider organizations. Using this model, provider organizations can systematically deconstruct healthcare delivery in the real world and reconstruct appropriate pieces in the virtual world. Observed barriers to virtual healthcare delivery are: resistance to telecommunication integrated delivery networks and outsourcing; confusion over virtual infrastructure requirements for telemedicine and full-service web portals, and the impact of integrated delivery networks and outsourcing on extant cultural norms and revenue generating practices. To remain competitive provider organizations must integrate real and virtual healthcare delivery.

Virtual healthcare delivery: defined, modeled, and predictive barriers to implementation identified.

PubMed Central

Harrop, V. M.

2001-01-01

Provider organizations lack: 1. a definition of "virtual" healthcare delivery relative to the products, services, and processes offered by dot.coms, web-compact disk healthcare content providers, telemedicine, and telecommunications companies, and 2. a model for integrating real and virtual healthcare delivery. This paper defines virtual healthcare delivery as asynchronous, outsourced, and anonymous, then proposes a 2x2 Real-Virtual Healthcare Delivery model focused on real and virtual patients and real and virtual provider organizations. Using this model, provider organizations can systematically deconstruct healthcare delivery in the real world and reconstruct appropriate pieces in the virtual world. Observed barriers to virtual healthcare delivery are: resistance to telecommunication integrated delivery networks and outsourcing; confusion over virtual infrastructure requirements for telemedicine and full-service web portals, and the impact of integrated delivery networks and outsourcing on extant cultural norms and revenue generating practices. To remain competitive provider organizations must integrate real and virtual healthcare delivery. PMID:11825189

Virtual Oscillator Controls | Grid Modernization | NREL

Science.gov Websites

Virtual Oscillator Controls Virtual Oscillator Controls NREL is developing virtual oscillator Santa-Barbara, and SunPower. Publications Synthesizing Virtual Oscillators To Control Islanded Inverters Synchronization of Parallel Single-Phase Inverters Using Virtual Oscillator Control, IEEE Transactions on Power

Fully Three-Dimensional Virtual-Reality System

NASA Technical Reports Server (NTRS)

Beckman, Brian C.

1994-01-01

Proposed virtual-reality system presents visual displays to simulate free flight in three-dimensional space. System, virtual space pod, is testbed for control and navigation schemes. Unlike most virtual-reality systems, virtual space pod would not depend for orientation on ground plane, which hinders free flight in three dimensions. Space pod provides comfortable seating, convenient controls, and dynamic virtual-space images for virtual traveler. Controls include buttons plus joysticks with six degrees of freedom.

Tools for Teaching Virtual Teams: A Comparative Resource Review

ERIC Educational Resources Information Center

Larson, Barbara; Leung, Opal; Mullane, Kenneth

2017-01-01

As the ubiquity of virtual work--and particularly virtual project teams--increases in the professional environment, management and other professional programs are increasingly teaching students skills related to virtual work. One of the most common forms of teaching virtual work skills is a virtual team project, in which students collaborate with…

Infrastructure Suitability Assessment Modeling for Cloud Computing Solutions

DTIC Science & Technology

2011-09-01

Virtualization vs . Para-Virtualization .......................................................10 Figure 4. Modeling alternatives in relation to model...the conceptual difference between full virtualization and para-virtualization. Figure 3. Full Virtualization vs . Para-Virtualization 2. XEN...Besides Microsoft’s own client implementations, dubbed “Remote Desktop Con- nection Client” for Windows® and Apple ® operating systems, various open

Exploring Virtual Reality for Classroom Use: The Virtual Reality and Education Lab at East Carolina University.

ERIC Educational Resources Information Center

Auld, Lawrence W. S.; Pantelidis, Veronica S.

1994-01-01

Describes the Virtual Reality and Education Lab (VREL) established at East Carolina University to study the implications of virtual reality for elementary and secondary education. Highlights include virtual reality software evaluation; hardware evaluation; computer-based curriculum objectives which could use virtual reality; and keeping current…

Virtual goods recommendations in virtual worlds.

PubMed

Chen, Kuan-Yu; Liao, Hsiu-Yu; Chen, Jyun-Hung; Liu, Duen-Ren

2015-01-01

Virtual worlds (VWs) are computer-simulated environments which allow users to create their own virtual character as an avatar. With the rapidly growing user volume in VWs, platform providers launch virtual goods in haste and stampede users to increase sales revenue. However, the rapidity of development incurs virtual unrelated items which will be difficult to remarket. It not only wastes virtual global companies' intelligence resources, but also makes it difficult for users to find suitable virtual goods fit for their virtual home in daily virtual life. In the VWs, users decorate their houses, visit others' homes, create families, host parties, and so forth. Users establish their social life circles through these activities. This research proposes a novel virtual goods recommendation method based on these social interactions. The contact strength and contact influence result from interactions with social neighbors and influence users' buying intention. Our research highlights the importance of social interactions in virtual goods recommendation. The experiment's data were retrieved from an online VW platform, and the results show that the proposed method, considering social interactions and social life circle, has better performance than existing recommendation methods.

A Low-cost System for Generating Near-realistic Virtual Actors

NASA Astrophysics Data System (ADS)

Afifi, Mahmoud; Hussain, Khaled F.; Ibrahim, Hosny M.; Omar, Nagwa M.

2015-06-01

Generating virtual actors is one of the most challenging fields in computer graphics. The reconstruction of a realistic virtual actor has been paid attention by the academic research and the film industry to generate human-like virtual actors. Many movies were acted by human-like virtual actors, where the audience cannot distinguish between real and virtual actors. The synthesis of realistic virtual actors is considered a complex process. Many techniques are used to generate a realistic virtual actor; however they usually require expensive hardware equipment. In this paper, a low-cost system that generates near-realistic virtual actors is presented. The facial features of the real actor are blended with a virtual head that is attached to the actor's body. Comparing with other techniques that generate virtual actors, the proposed system is considered a low-cost system that requires only one camera that records the scene without using any expensive hardware equipment. The results of our system show that the system generates good near-realistic virtual actors that can be used on many applications.

Virtual Goods Recommendations in Virtual Worlds

PubMed Central

Chen, Kuan-Yu; Liao, Hsiu-Yu; Chen, Jyun-Hung; Liu, Duen-Ren

2015-01-01

Virtual worlds (VWs) are computer-simulated environments which allow users to create their own virtual character as an avatar. With the rapidly growing user volume in VWs, platform providers launch virtual goods in haste and stampede users to increase sales revenue. However, the rapidity of development incurs virtual unrelated items which will be difficult to remarket. It not only wastes virtual global companies' intelligence resources, but also makes it difficult for users to find suitable virtual goods fit for their virtual home in daily virtual life. In the VWs, users decorate their houses, visit others' homes, create families, host parties, and so forth. Users establish their social life circles through these activities. This research proposes a novel virtual goods recommendation method based on these social interactions. The contact strength and contact influence result from interactions with social neighbors and influence users' buying intention. Our research highlights the importance of social interactions in virtual goods recommendation. The experiment's data were retrieved from an online VW platform, and the results show that the proposed method, considering social interactions and social life circle, has better performance than existing recommendation methods. PMID:25834837

Using virtual machine monitors to overcome the challenges of monitoring and managing virtualized cloud infrastructures

NASA Astrophysics Data System (ADS)

Bamiah, Mervat Adib; Brohi, Sarfraz Nawaz; Chuprat, Suriayati

2012-01-01

Virtualization is one of the hottest research topics nowadays. Several academic researchers and developers from IT industry are designing approaches for solving security and manageability issues of Virtual Machines (VMs) residing on virtualized cloud infrastructures. Moving the application from a physical to a virtual platform increases the efficiency, flexibility and reduces management cost as well as effort. Cloud computing is adopting the paradigm of virtualization, using this technique, memory, CPU and computational power is provided to clients' VMs by utilizing the underlying physical hardware. Beside these advantages there are few challenges faced by adopting virtualization such as management of VMs and network traffic, unexpected additional cost and resource allocation. Virtual Machine Monitor (VMM) or hypervisor is the tool used by cloud providers to manage the VMs on cloud. There are several heterogeneous hypervisors provided by various vendors that include VMware, Hyper-V, Xen and Kernel Virtual Machine (KVM). Considering the challenge of VM management, this paper describes several techniques to monitor and manage virtualized cloud infrastructures.

iVirtualWorld: A Domain-Oriented End-User Development Environment for Building 3D Virtual Chemistry Experiments

ERIC Educational Resources Information Center

Zhong, Ying

2013-01-01

Virtual worlds are well-suited for building virtual laboratories for educational purposes to complement hands-on physical laboratories. However, educators may face technical challenges because developing virtual worlds requires skills in programming and 3D design. Current virtual world building tools are developed for users who have programming…

Using smartphone technology to deliver a virtual pedestrian environment: usability and validation.

PubMed

Schwebel, David C; Severson, Joan; He, Yefei

2017-09-01

Various programs effectively teach children to cross streets more safely, but all are labor- and cost-intensive. Recent developments in mobile phone technology offer opportunity to deliver virtual reality pedestrian environments to mobile smartphone platforms. Such an environment may offer a cost- and labor-effective strategy to teach children to cross streets safely. This study evaluated usability, feasibility, and validity of a smartphone-based virtual pedestrian environment. A total of 68 adults completed 12 virtual crossings within each of two virtual pedestrian environments, one delivered by smartphone and the other a semi-immersive kiosk virtual environment. Participants completed self-report measures of perceived realism and simulator sickness experienced in each virtual environment, plus self-reported demographic and personality characteristics. All participants followed system instructions and used the smartphone-based virtual environment without difficulty. No significant simulator sickness was reported or observed. Users rated the smartphone virtual environment as highly realistic. Convergent validity was detected, with many aspects of pedestrian behavior in the smartphone-based virtual environment matching behavior in the kiosk virtual environment. Anticipated correlations between personality and kiosk virtual reality pedestrian behavior emerged for the smartphone-based system. A smartphone-based virtual environment can be usable and valid. Future research should develop and evaluate such a training system.

Validation of virtual reality as a tool to understand and prevent child pedestrian injury.

PubMed

Schwebel, David C; Gaines, Joanna; Severson, Joan

2008-07-01

In recent years, virtual reality has emerged as an innovative tool for health-related education and training. Among the many benefits of virtual reality is the opportunity for novice users to engage unsupervised in a safe environment when the real environment might be dangerous. Virtual environments are only useful for health-related research, however, if behavior in the virtual world validly matches behavior in the real world. This study was designed to test the validity of an immersive, interactive virtual pedestrian environment. A sample of 102 children and 74 adults was recruited to complete simulated road-crossings in both the virtual environment and the identical real environment. In both the child and adult samples, construct validity was demonstrated via significant correlations between behavior in the virtual and real worlds. Results also indicate construct validity through developmental differences in behavior; convergent validity by showing correlations between parent-reported child temperament and behavior in the virtual world; internal reliability of various measures of pedestrian safety in the virtual world; and face validity, as measured by users' self-reported perception of realism in the virtual world. We discuss issues of generalizability to other virtual environments, and the implications for application of virtual reality to understanding and preventing pediatric pedestrian injuries.

Virtual World Currency Value Fluctuation Prediction System Based on User Sentiment Analysis.

PubMed

Kim, Young Bin; Lee, Sang Hyeok; Kang, Shin Jin; Choi, Myung Jin; Lee, Jung; Kim, Chang Hun

2015-01-01

In this paper, we present a method for predicting the value of virtual currencies used in virtual gaming environments that support multiple users, such as massively multiplayer online role-playing games (MMORPGs). Predicting virtual currency values in a virtual gaming environment has rarely been explored; it is difficult to apply real-world methods for predicting fluctuating currency values or shares to the virtual gaming world on account of differences in domains between the two worlds. To address this issue, we herein predict virtual currency value fluctuations by collecting user opinion data from a virtual community and analyzing user sentiments or emotions from the opinion data. The proposed method is straightforward and applicable to predicting virtual currencies as well as to gaming environments, including MMORPGs. We test the proposed method using large-scale MMORPGs and demonstrate that virtual currencies can be effectively and efficiently predicted with it.

Effects of virtualization on a scientific application - Running a hyperspectral radiative transfer code on virtual machines.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tikotekar, Anand A; Vallee, Geoffroy R; Naughton III, Thomas J

2008-01-01

The topic of system-level virtualization has recently begun to receive interest for high performance computing (HPC). This is in part due to the isolation and encapsulation offered by the virtual machine. These traits enable applications to customize their environments and maintain consistent software configurations in their virtual domains. Additionally, there are mechanisms that can be used for fault tolerance like live virtual machine migration. Given these attractive benefits to virtualization, a fundamental question arises, how does this effect my scientific application? We use this as the premise for our paper and observe a real-world scientific code running on a Xenmore » virtual machine. We studied the effects of running a radiative transfer simulation, Hydrolight, on a virtual machine. We discuss our methodology and report observations regarding the usage of virtualization with this application.« less

Interference Cognizant Network Scheduling

NASA Technical Reports Server (NTRS)

Hall, Brendan (Inventor); Bonk, Ted (Inventor); DeLay, Benjamin F. (Inventor); Varadarajan, Srivatsan (Inventor); Smithgall, William Todd (Inventor)

2017-01-01

Systems and methods for interference cognizant network scheduling are provided. In certain embodiments, a method of scheduling communications in a network comprises identifying a bin of a global timeline for scheduling an unscheduled virtual link, wherein a bin is a segment of the timeline; identifying a pre-scheduled virtual link in the bin; and determining if the pre-scheduled and unscheduled virtual links share a port. In certain embodiments, if the unscheduled and pre-scheduled virtual links don't share a port, scheduling transmission of the unscheduled virtual link to overlap with the scheduled transmission of the pre-scheduled virtual link; and if the unscheduled and pre-scheduled virtual links share a port: determining a start time delay for the unscheduled virtual link based on the port; and scheduling transmission of the unscheduled virtual link in the bin based on the start time delay to overlap part of the scheduled transmission of the pre-scheduled virtual link.

Computer network defense system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Urias, Vincent; Stout, William M. S.; Loverro, Caleb

A method and apparatus for protecting virtual machines. A computer system creates a copy of a group of the virtual machines in an operating network in a deception network to form a group of cloned virtual machines in the deception network when the group of the virtual machines is accessed by an adversary. The computer system creates an emulation of components from the operating network in the deception network. The components are accessible by the group of the cloned virtual machines as if the group of the cloned virtual machines was in the operating network. The computer system moves networkmore » connections for the group of the virtual machines in the operating network used by the adversary from the group of the virtual machines in the operating network to the group of the cloned virtual machines, enabling protecting the group of the virtual machines from actions performed by the adversary.« less

Virtual World Currency Value Fluctuation Prediction System Based on User Sentiment Analysis

PubMed Central

Kim, Young Bin; Lee, Sang Hyeok; Kang, Shin Jin; Choi, Myung Jin; Lee, Jung; Kim, Chang Hun

2015-01-01

In this paper, we present a method for predicting the value of virtual currencies used in virtual gaming environments that support multiple users, such as massively multiplayer online role-playing games (MMORPGs). Predicting virtual currency values in a virtual gaming environment has rarely been explored; it is difficult to apply real-world methods for predicting fluctuating currency values or shares to the virtual gaming world on account of differences in domains between the two worlds. To address this issue, we herein predict virtual currency value fluctuations by collecting user opinion data from a virtual community and analyzing user sentiments or emotions from the opinion data. The proposed method is straightforward and applicable to predicting virtual currencies as well as to gaming environments, including MMORPGs. We test the proposed method using large-scale MMORPGs and demonstrate that virtual currencies can be effectively and efficiently predicted with it. PMID:26241496

Mapping, Awareness, And Virtualization Network Administrator Training Tool Virtualization Module

DTIC Science & Technology

2016-03-01

AND VIRTUALIZATION NETWORK ADMINISTRATOR TRAINING TOOL VIRTUALIZATION MODULE by Erik W. Berndt March 2016 Thesis Advisor: John Gibson...REPORT TYPE AND DATES COVERED Master’s thesis 4. TITLE AND SUBTITLE MAPPING, AWARENESS, AND VIRTUALIZATION NETWORK ADMINISTRATOR TRAINING TOOL... VIRTUALIZATION MODULE 5. FUNDING NUMBERS 6. AUTHOR(S) Erik W. Berndt 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) Naval Postgraduate School

Virtual Reality as Innovative Approach to the Interior Designing

NASA Astrophysics Data System (ADS)

Kaleja, Pavol; Kozlovská, Mária

2017-06-01

We can observe significant potential of information and communication technologies (ICT) in interior designing field, by development of software and hardware virtual reality tools. Using ICT tools offer realistic perception of proposal in its initial idea (the study). A group of real-time visualization, supported by hardware tools like Oculus Rift HTC Vive, provides free walkthrough and movement in virtual interior with the possibility of virtual designing. By improving of ICT software tools for designing in virtual reality we can achieve still more realistic virtual environment. The contribution presented proposal of an innovative approach of interior designing in virtual reality, using the latest software and hardware ICT virtual reality technologies

[Development of a virtual model of fibro-bronchoscopy].

PubMed

Solar, Mauricio; Ducoing, Eugenio

2011-09-01

A virtual model of fibro-bronchoscopy is reported. The virtual model represents in 3D the trachea and the bronchi creating a virtual world of the bronchial tree. The bronchoscope is modeled to look over the bronchial tree imitating the displacement and rotation of the real bronchoscope. The parameters of the virtual model were gradually adjusted according to expert opinion and allowed the training of specialists with a virtual bronchoscope of great realism. The virtual bronchial tree provides clues of reality regarding the movement of the bronchoscope, creating the illusion that the virtual instrument is behaving as the real one with all the benefits in costs that this means.

Recent evolution of China's virtual water trade: analysis of selected crops and considerations for policy

NASA Astrophysics Data System (ADS)

Shi, J.; Liu, J.; Pinter, L.

2014-04-01

China has dramatically increased its virtual water import over recent years. Many studies have focused on the quantity of traded virtual water, but very few go into analysing geographic distribution and the properties of China's virtual water trade network. This paper provides a calculation and analysis of the crop-related virtual water trade network of China based on 27 major primary crops between 1986 and 2009. The results show that China is a net importer of virtual water from water-abundant areas of North America and South America, and a net virtual water exporter to water-stressed areas of Asia, Africa, and Europe. Virtual water import is far larger than virtual water export, and in both import and export a small number of trade partners control the supply chain. Grain crops are the major contributors to virtual water trade, and among grain crops, soybeans, mostly imported from the US, Brazil and Argentina, are the most significant. In order to mitigate water scarcity and secure the food supply, virtual water should actively be incorporated into national water management strategies. And the sources of virtual water import need to be further diversified to reduce supply chain risks and increase resilience.

Innovative application of virtual display technique in virtual museum

NASA Astrophysics Data System (ADS)

Zhang, Jiankang

2017-09-01

Virtual museum refers to display and simulate the functions of real museum on the Internet in the form of 3 Dimensions virtual reality by applying interactive programs. Based on Virtual Reality Modeling Language, virtual museum building and its effective interaction with the offline museum lie in making full use of 3 Dimensions panorama technique, virtual reality technique and augmented reality technique, and innovatively taking advantages of dynamic environment modeling technique, real-time 3 Dimensions graphics generating technique, system integration technique and other key virtual reality techniques to make sure the overall design of virtual museum.3 Dimensions panorama technique, also known as panoramic photography or virtual reality, is a technique based on static images of the reality. Virtual reality technique is a kind of computer simulation system which can create and experience the interactive 3 Dimensions dynamic visual world. Augmented reality, also known as mixed reality, is a technique which simulates and mixes the information (visual, sound, taste, touch, etc.) that is difficult for human to experience in reality. These technologies make virtual museum come true. It will not only bring better experience and convenience to the public, but also be conducive to improve the influence and cultural functions of the real museum.

History and geography of virtual water trade

NASA Astrophysics Data System (ADS)

Carr, J. A.; D'Odorico, P.; Laio, F.; Ridolfi, L.

2012-12-01

The global trade of goods is associated with a virtual transfer of the water required for their production. The way changes in trade affect the virtual redistribution of freshwater resources has been recently documented through the analysis of the virtual water network. It is, however, unclear how these changes are contributed by different types of products and regions of the world. Here we show how the global patterns of virtual water transport are contributed by the trade of different commodity types, including plant, animal, luxury (e.g., coffee, tea, and alcohol), and other products (non-edible plant and animal products typically used for manufacturing). Major contributors to the virtual water network exhibit different trade patterns with regard to these commodity types with the net importers of virtual water relying on the supply of virtual water from a small percentage of the global population. Discrepancies exist among the different commodity networks. Surprisingly, while the total virtual water flux through the network has increased between 1986 and 2008, the global proportions associated with the four commodity groups have remained relatively stable. Here we discuss some major changes in the global patterns of virtual water trade with a focus on the increase in regional dependencies on foreign virtual water. The increase in virtual water trade and the percentage of the total virtual water flux in the network corresponding to plant, animals, luxury, and other commodities.

Learning Rationales and Virtual Reality Technology in Education.

ERIC Educational Resources Information Center

Chiou, Guey-Fa

1995-01-01

Defines and describes virtual reality technology and differentiates between virtual learning environment, learning material, and learning tools. Links learning rationales to virtual reality technology to pave conceptual foundations for application of virtual reality technology education. Constructivism, case-based learning, problem-based learning,…

Approaches to virtual screening and screening library selection.

PubMed

Wildman, Scott A

2013-01-01

The ease of access to virtual screening (VS) software in recent years has resulted in a large increase in literature reports. Over 300 publications in the last year report the use of virtual screening techniques to identify new chemical matter or present the development of new virtual screening techniques. The increased use is accompanied by a corresponding increase in misuse and misinterpretation of virtual screening results. This review aims to identify many of the common difficulties associated with virtual screening and allow researchers to better assess the reliability of their virtual screening effort.

Virtual performer: single camera 3D measuring system for interaction in virtual space

NASA Astrophysics Data System (ADS)

Sakamoto, Kunio; Taneji, Shoto

2006-10-01

The authors developed interaction media systems in the 3D virtual space. In these systems, the musician virtually plays an instrument like the theremin in the virtual space or the performer plays a show using the virtual character such as a puppet. This interactive virtual media system consists of the image capture, measuring performer's position, detecting and recognizing motions and synthesizing video image using the personal computer. In this paper, we propose some applications of interaction media systems; a virtual musical instrument and superimposing CG character. Moreover, this paper describes the measuring method of the positions of the performer, his/her head and both eyes using a single camera.

Virtual Simulations: A Creative, Evidence-Based Approach to Develop and Educate Nurses.

PubMed

Leibold, Nancyruth; Schwarz, Laura

2017-02-01

The use of virtual simulations in nursing is an innovative strategy that is increasing in application. There are several terms related to virtual simulation; although some are used interchangeably, the meanings are not the same. This article presents examples of virtual simulation, virtual worlds, and virtual patients in continuing education, staff development, and academic nursing education. Virtual simulations in nursing use technology to provide safe, as realistic as possible clinical practice for nurses and nursing students. Virtual simulations are useful for learning new skills; practicing a skill that puts content, high-order thinking, and psychomotor elements together; skill competency learning; and assessment for low-volume, high-risk skills. The purpose of this article is to describe the related terms, examples, uses, theoretical frameworks, challenges, and evidence related to virtual simulations in nursing.

Virtual Reality and the Virtual Library.

ERIC Educational Resources Information Center

Oppenheim, Charles

1993-01-01

Explains virtual reality, including proper and improper uses of the term, and suggests ways that libraries might be affected by it. Highlights include elements of virtual reality systems; possible virtual reality applications, including architecture, the chemical industry, transport planning, armed forces, and entertainment; and the virtual…

[Virtual microscopy in pathology teaching and postgraduate training (continuing education)].

PubMed

Sinn, H P; Andrulis, M; Mogler, C; Schirmacher, P

2008-11-01

As with conventional microscopy, virtual microscopy permits histological tissue sections to be viewed on a computer screen with a free choice of viewing areas and a wide range of magnifications. This, combined with the possibility of linking virtual microscopy to E-Learning courses, make virtual microscopy an ideal tool for teaching and postgraduate training in pathology. Uses of virtual microscopy in pathology teaching include blended learning with the presentation of digital teaching slides in the internet parallel to presentation in the histology lab, extending student access to histology slides beyond the lab. Other uses are student self-learning in the Internet, as well as the presentation of virtual slides in the classroom with or without replacing real microscopes. Successful integration of virtual microscopy depends on its embedding in the virtual classroom and the creation of interactive E-learning content. Applications derived from this include the use of virtual microscopy in video clips, podcasts, SCORM modules and the presentation of virtual microscopy using interactive whiteboards in the classroom.

[Virtual water content of livestock products in China].

PubMed

Wang, Hong-rui; Wang, Jun-hong

2006-04-01

The paper expatiated the virtual water content concept of livestock products and the study meaning on developing virtual water trade of livestock products in China, then summarized the calculation methods on virtual water and virtual water trade of livestock products. Based on these, the paper analyzed and researched every province virtual water content of livestock products in details, then elicited various situation of every province virtual water content of livestock products in China by year. Moreover, it compared virtual water content of livestock products with local water resources. The study indicated the following results: (1) The virtual water content of livestock products is increasing rapidly in China recently, especially poultry eggs and pork. (2) The distribution of virtual water content of livestock products is not balanced, mainly lies in North China, East China and so on; (3) The increasing production of livestock in Beijing City, Tianjin City, Hebei, Nei Monggol, Liaononing, Jilin, Shandong, Henan and Ningxia province and autonom ous region will bring pressure to local water shortage.

Virtual Network Configuration Management System for Data Center Operations and Management

NASA Astrophysics Data System (ADS)

Okita, Hideki; Yoshizawa, Masahiro; Uehara, Keitaro; Mizuno, Kazuhiko; Tarui, Toshiaki; Naono, Ken

Virtualization technologies are widely deployed in data centers to improve system utilization. However, they increase the workload for operators, who have to manage the structure of virtual networks in data centers. A virtual-network management system which automates the integration of the configurations of the virtual networks is provided. The proposed system collects the configurations from server virtualization platforms and VLAN-supported switches, and integrates these configurations according to a newly developed XML-based management information model for virtual-network configurations. Preliminary evaluations show that the proposed system helps operators by reducing the time to acquire the configurations from devices and correct the inconsistency of operators' configuration management database by about 40 percent. Further, they also show that the proposed system has excellent scalability; the system takes less than 20 minutes to acquire the virtual-network configurations from a large scale network that includes 300 virtual machines. These results imply that the proposed system is effective for improving the configuration management process for virtual networks in data centers.

Reasons to Use Virtual Reality in Education and Training Courses and a Model to Determine When to Use Virtual Reality

ERIC Educational Resources Information Center

Pantelidis, Veronica S.

2009-01-01

Many studies have been conducted on the use of virtual reality in education and training. This article lists examples of such research. Reasons to use virtual reality are discussed. Advantages and disadvantages of using virtual reality are presented, as well as suggestions on when to use and when not to use virtual reality. A model that can be…

Virtual button interface

DOEpatents

Jones, Jake S.

1999-01-01

An apparatus and method of issuing commands to a computer by a user interfacing with a virtual reality environment. To issue a command, the user directs gaze at a virtual button within the virtual reality environment, causing a perceptible change in the virtual button, which then sends a command corresponding to the virtual button to the computer, optionally after a confirming action is performed by the user, such as depressing a thumb switch.

Virtual Reality: The Future of Animated Virtual Instructor, the Technology and Its Emergence to a Productive E-Learning Environment.

ERIC Educational Resources Information Center

Jiman, Juhanita

This paper discusses the use of Virtual Reality (VR) in e-learning environments where an intelligent three-dimensional (3D) virtual person plays the role of an instructor. With the existence of this virtual instructor, it is hoped that the teaching and learning in the e-environment will be more effective and productive. This virtual 3D animated…

Worse than imagined: Unidentified virtual water flows in China.

PubMed

Cai, Beiming; Wang, Chencheng; Zhang, Bing

2017-07-01

The impact of virtual water flows on regional water scarcity in China had been deeply discussed in previous research. However, these studies only focused on water quantity, the impact of virtual water flows on water quality has been largely neglected. In this study, we incorporate the blue water footprint related with water quantity and grey water footprint related with water quality into virtual water flow analysis based on the multiregional input-output model of 2007. The results find that the interprovincial virtual flows accounts for 23.4% of China's water footprint. The virtual grey water flows are 8.65 times greater than the virtual blue water flows; the virtual blue water and grey water flows are 91.8 and 794.6 Gm 3 /y, respectively. The use of the indicators related with water quantity to represent virtual water flows in previous studies will underestimate their impact on water resources. In addition, the virtual water flows are mainly derived from agriculture, chemical industry and petroleum processing and the coking industry, which account for 66.8%, 7.1% and 6.2% of the total virtual water flows, respectively. Virtual water flows have intensified both quantity- and quality-induced water scarcity of export regions, where low-value-added but water-intensive and high-pollution goods are produced. Our study on virtual water flows can inform effective water use policy for both water resources and water pollution in China. Our methodology about virtual water flows also can be used in global scale or other countries if data available. Copyright © 2017 Elsevier Ltd. All rights reserved.

Creating an Online Library To Support a Virtual Learning Community.

ERIC Educational Resources Information Center

Sandelands, Eric

1998-01-01

International Management Centres (IMC), an independent business school, and Anbar Electronic Intelligence (AEI), a database publisher, have created a virtual library for IMC's virtual business school. Topics discussed include action learning; IMC's partnership with AEI; the virtual university model; designing virtual library resources; and…

Identifying the Priorities and Practices of Virtual School Educators Using Action Research

ERIC Educational Resources Information Center

Dawson, Kara; Dana, Nancy Fichtman; Wolkenhauer, Rachel; Krell, Desi

2013-01-01

This study examined the nature of thirty virtual educators' action research questions during a yearlong action research professional development experience within a large, state-funded virtual school. Virtual educators included instructional personnel (i.e., individuals responsible for teaching virtual courses) and noninstructional personnel…

Magical Stories: Blending Virtual Reality and Artificial Intelligence.

ERIC Educational Resources Information Center

McLellan, Hilary

Artificial intelligence (AI) techniques and virtual reality (VR) make possible powerful interactive stories, and this paper focuses on examples of virtual characters in three dimensional (3-D) worlds. Waldern, a virtual reality game designer, has theorized about and implemented software design of virtual teammates and opponents that incorporate AI…

An Investigation of Communication in Virtual High Schools

ERIC Educational Resources Information Center

Belair, Marley

2012-01-01

Virtual schooling is an increasing trend for secondary education. Research of the communication practices in virtual schools has provided a myriad of suggestions for virtual school policies. The purpose of this qualitative study was to investigate the activities and processes involved in the daily rituals of virtual school teachers and learners…

77 FR 23512 - Advisory Committee on Apprenticeship; virtual meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-19

...; virtual meeting AGENCY: Employment and Training Administration (ETA), Labor. ACTION: Notice of a virtual....S.C. APP. 1), notice is hereby given to announce a open virtual meeting of the Advisory Committee on... the public. A virtual meeting of the ACA provides cost savings and a greater degree of public...

The Virtual Reference Librarian's Handbook.

ERIC Educational Resources Information Center

Lipow, Anne Grodzins

This book is a practical guide to librarians and their administrators who are thinking about or in the early stages of providing virtual reference service. Part 1, "The Decision to Go Virtual," provides a context for thinking about virtual reference, including the benefits and problems, getting in the virtual frame of mind, and shopping…

CEDS Addresses: Virtual and Blended Learning

ERIC Educational Resources Information Center

US Department of Education, 2015

2015-01-01

The Common Education Data Standards (CEDS) common data vocabulary supports the collection and use of information about virtual and blended learning. The data element "Virtual Indicator", introduced in version 3 of CEDS, supports a range of virtual learning-related use cases. The Virtual Indicator element may be related to a Course…

Virtual button interface

DOEpatents

Jones, J.S.

1999-01-12

An apparatus and method of issuing commands to a computer by a user interfacing with a virtual reality environment are disclosed. To issue a command, the user directs gaze at a virtual button within the virtual reality environment, causing a perceptible change in the virtual button, which then sends a command corresponding to the virtual button to the computer, optionally after a confirming action is performed by the user, such as depressing a thumb switch. 4 figs.

An Intelligent Virtual Human System For Providing Healthcare Information And Support

DTIC Science & Technology

2011-01-01

for clinical purposes. Shifts in the social and scientific landscape have now set the stage for the next major movement in Clinical Virtual Reality ...College; dMadigan Army Medical Center Army Abstract. Over the last 15 years, a virtual revolution has taken place in the use of Virtual Reality ... Virtual Reality with the “birth” of intelligent virtual humans. Seminal research and development has appeared in the creation of highly interactive

A Descriptive Study of the Factors Influencing the Degree to Which Fourth-, Fifth-, and Sixth-Grade Virtual Education Students Perceive a Sense of Virtual Community

ERIC Educational Resources Information Center

Gerth, Dana A.

2013-01-01

Review of literature revealed a shortage of research describing the development of K-12 virtual communities and the absence of a tool to measure sense of virtual community in K-12 virtual education students. The purpose of this descriptive, quantitative study was to examine the perception of a sense of virtual community from the perspective of…

Modulation of thermal pain-related brain activity with virtual reality: evidence from fMRI.

PubMed

Hoffman, Hunter G; Richards, Todd L; Coda, Barbara; Bills, Aric R; Blough, David; Richards, Anne L; Sharar, Sam R

2004-06-07

This study investigated the neural correlates of virtual reality analgesia. Virtual reality significantly reduced subjective pain ratings (i.e. analgesia). Using fMRI, pain-related brain activity was measured for each participant during conditions of no virtual reality and during virtual reality (order randomized). As predicted, virtual reality significantly reduced pain-related brain activity in all five regions of interest; the anterior cingulate cortex, primary and secondary somatosensory cortex, insula, and thalamus (p<0.002, corrected). Results showed direct modulation of human brain pain responses by virtual reality distraction. Copyright 2004 Lippincott Williams and Wilkins

Multisensory Integration in the Virtual Hand Illusion with Active Movement

PubMed Central

Satoh, Satoru; Hachimura, Kozaburo

2016-01-01

Improving the sense of immersion is one of the core issues in virtual reality. Perceptual illusions of ownership can be perceived over a virtual body in a multisensory virtual reality environment. Rubber Hand and Virtual Hand Illusions showed that body ownership can be manipulated by applying suitable visual and tactile stimulation. In this study, we investigate the effects of multisensory integration in the Virtual Hand Illusion with active movement. A virtual xylophone playing system which can interactively provide synchronous visual, tactile, and auditory stimulation was constructed. We conducted two experiments regarding different movement conditions and different sensory stimulations. Our results demonstrate that multisensory integration with free active movement can improve the sense of immersion in virtual reality. PMID:27847822

Designing communication and remote controlling of virtual instrument network system

NASA Astrophysics Data System (ADS)

Lei, Lin; Wang, Houjun; Zhou, Xue; Zhou, Wenjian

2005-01-01

In this paper, a virtual instrument network through the LAN and finally remote control of virtual instruments is realized based on virtual instrument and LabWindows/CVI software platform. The virtual instrument network system is made up of three subsystems. There are server subsystem, telnet client subsystem and local instrument control subsystem. This paper introduced virtual instrument network structure in detail based on LabWindows. Application procedure design of virtual instrument network communication, the Client/the programming mode of the server, remote PC and server communication far realizing, the control power of the workstation is transmitted, server program and so on essential technical were introduced. And virtual instruments network may connect to entire Internet on. Above-mentioned technology, through measuring the application in the electronic measurement virtual instrument network that is already built up, has verified the actual using value of the technology. Experiment and application validate that this design is resultful.

Health care globalization: a need for virtual leadership.

PubMed

Holland, J Brian; Malvey, Donna; Fottler, Myron D

2009-01-01

As health care organizations expand and move into global markets, they face many leadership challenges, including the difficulty of leading individuals who are geographically dispersed. This article provides global managers with guidelines for leading and motivating individuals or teams from a distance while overcoming the typical challenges that "virtual leaders" and "virtual teams" face: employee isolation, confusion, language barriers, cultural differences, and technological breakdowns. Fortunately, technological advances in communications have provided various methods to accommodate geographically dispersed or "global virtual teams." Health care leaders now have the ability to lead global teams from afar by becoming "virtual leaders" with a responsibility to lead a "virtual team." Three models of globalization presented and discussed are outsourcing of health care services, medical tourism, and telerobotics. These models require global managers to lead virtually, and a positive relationship between the virtual leader and the virtual team member is vital in the success of global health care organizations.

Virtual reality system for treatment of the fear of public speaking using image-based rendering and moving pictures.

PubMed

Lee, Jae M; Ku, Jeong H; Jang, Dong P; Kim, Dong H; Choi, Young H; Kim, In Y; Kim, Sun I

2002-06-01

The fear of speaking is often cited as the world's most common social phobia. The rapid growth of computer technology enabled us to use virtual reality (VR) for the treatment of the fear of public speaking. There have been two techniques used to construct a virtual environment for the treatment of the fear of public speaking: model-based and movie-based. Virtual audiences and virtual environments made by model-based technique are unrealistic and unnatural. The movie-based technique has a disadvantage in that each virtual audience cannot be controlled respectively, because all virtual audiences are included in one moving picture file. To address this disadvantage, this paper presents a virtual environment made by using image-based rendering (IBR) and chroma keying simultaneously. IBR enables us to make the virtual environment realistic because the images are stitched panoramically with the photos taken from a digital camera. And the use of chroma keying allows a virtual audience to be controlled individually. In addition, a real-time capture technique was applied in constructing the virtual environment to give the subjects more interaction, in that they can talk with a therapist or another subject.

Manually locating physical and virtual reality objects.

PubMed

Chen, Karen B; Kimmel, Ryan A; Bartholomew, Aaron; Ponto, Kevin; Gleicher, Michael L; Radwin, Robert G

2014-09-01

In this study, we compared how users locate physical and equivalent three-dimensional images of virtual objects in a cave automatic virtual environment (CAVE) using the hand to examine how human performance (accuracy, time, and approach) is affected by object size, location, and distance. Virtual reality (VR) offers the promise to flexibly simulate arbitrary environments for studying human performance. Previously, VR researchers primarily considered differences between virtual and physical distance estimation rather than reaching for close-up objects. Fourteen participants completed manual targeting tasks that involved reaching for corners on equivalent physical and virtual boxes of three different sizes. Predicted errors were calculated from a geometric model based on user interpupillary distance, eye location, distance from the eyes to the projector screen, and object. Users were 1.64 times less accurate (p < .001) and spent 1.49 times more time (p = .01) targeting virtual versus physical box corners using the hands. Predicted virtual targeting errors were on average 1.53 times (p < .05) greater than the observed errors for farther virtual targets but not significantly different for close-up virtual targets. Target size, location, and distance, in addition to binocular disparity, affected virtual object targeting inaccuracy. Observed virtual box inaccuracy was less than predicted for farther locations, suggesting possible influence of cues other than binocular vision. Human physical interaction with objects in VR for simulation, training, and prototyping involving reaching and manually handling virtual objects in a CAVE are more accurate than predicted when locating farther objects.

Virtual Manufacturing Techniques Designed and Applied to Manufacturing Activities in the Manufacturing Integration and Technology Branch

NASA Technical Reports Server (NTRS)

Shearrow, Charles A.

1999-01-01

One of the identified goals of EM3 is to implement virtual manufacturing by the time the year 2000 has ended. To realize this goal of a true virtual manufacturing enterprise the initial development of a machinability database and the infrastructure must be completed. This will consist of the containment of the existing EM-NET problems and developing machine, tooling, and common materials databases. To integrate the virtual manufacturing enterprise with normal day to day operations the development of a parallel virtual manufacturing machinability database, virtual manufacturing database, virtual manufacturing paradigm, implementation/integration procedure, and testable verification models must be constructed. Common and virtual machinability databases will include the four distinct areas of machine tools, available tooling, common machine tool loads, and a materials database. The machine tools database will include the machine envelope, special machine attachments, tooling capacity, location within NASA-JSC or with a contractor, and availability/scheduling. The tooling database will include available standard tooling, custom in-house tooling, tool properties, and availability. The common materials database will include materials thickness ranges, strengths, types, and their availability. The virtual manufacturing databases will consist of virtual machines and virtual tooling directly related to the common and machinability databases. The items to be completed are the design and construction of the machinability databases, virtual manufacturing paradigm for NASA-JSC, implementation timeline, VNC model of one bridge mill and troubleshoot existing software and hardware problems with EN4NET. The final step of this virtual manufacturing project will be to integrate other production sites into the databases bringing JSC's EM3 into a position of becoming a clearing house for NASA's digital manufacturing needs creating a true virtual manufacturing enterprise.

Evaluating Remapped Physical Reach for Hand Interactions with Passive Haptics in Virtual Reality.

PubMed

Han, Dustin T; Suhail, Mohamed; Ragan, Eric D

2018-04-01

Virtual reality often uses motion tracking to incorporate physical hand movements into interaction techniques for selection and manipulation of virtual objects. To increase realism and allow direct hand interaction, real-world physical objects can be aligned with virtual objects to provide tactile feedback and physical grasping. However, unless a physical space is custom configured to match a specific virtual reality experience, the ability to perfectly match the physical and virtual objects is limited. Our research addresses this challenge by studying methods that allow one physical object to be mapped to multiple virtual objects that can exist at different virtual locations in an egocentric reference frame. We study two such techniques: one that introduces a static translational offset between the virtual and physical hand before a reaching action, and one that dynamically interpolates the position of the virtual hand during a reaching motion. We conducted two experiments to assess how the two methods affect reaching effectiveness, comfort, and ability to adapt to the remapping techniques when reaching for objects with different types of mismatches between physical and virtual locations. We also present a case study to demonstrate how the hand remapping techniques could be used in an immersive game application to support realistic hand interaction while optimizing usability. Overall, the translational technique performed better than the interpolated reach technique and was more robust for situations with larger mismatches between virtual and physical objects.

The European Virtual Observatory EURO-VO | Euro-VO

Science.gov Websites

: VOTECH EuroVO-DCA EuroVO-AIDA EuroVO-ICE The European Virtual Observatory EURO-VO The Virtual Observatory news Workshop on Virtual Observatory Tools and their Applications, Krakow, Poland June 16-18, organized present the Astronomical Virtual Observatory at the Copernicus (European Earth Observation Programme) Big

75 FR 17913 - Sunshine Act; Notice of Virtual Public Forum for EAC Standards Board

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-08

... ELECTION ASSISTANCE COMMISSION Sunshine Act; Notice of Virtual Public Forum for EAC Standards... Standards Board Virtual Meeting Room at http://www.eac.gov . Once at the main page of EAC's Web site, viewers should click the link to the Standards Board Virtual Meeting Room. The virtual meeting room will...

Virtual Teaming and Collaboration Technology: A Study of Influences on Virtual Project Outcomes

ERIC Educational Resources Information Center

Broils, Gary C.

2014-01-01

The purpose of this quantitative correlational study was to explore the relationships between the independent variables, contextual factors for virtual teams and collaboration technology, and the dependent variable, virtual project outcomes. The problem leading to the need for the study is a lower success rate for virtual projects compared to…

Virtual School Startups: Founder Processes in American K-12 Public Virtual Schools

ERIC Educational Resources Information Center

Taylor, Brett D.; McNair, Delores E.

2018-01-01

Traditional school districts do not have a lot of experience with virtual schools and have lost students to state and charter virtual schools. To retain students and offer alternative learning opportunities, more public districts are starting their own virtual schools. This study was an examination of foundational processes at three California…

Realistic terrain visualization based on 3D virtual world technology

NASA Astrophysics Data System (ADS)

Huang, Fengru; Lin, Hui; Chen, Bin; Xiao, Cai

2009-09-01

The rapid advances in information technologies, e.g., network, graphics processing, and virtual world, have provided challenges and opportunities for new capabilities in information systems, Internet applications, and virtual geographic environments, especially geographic visualization and collaboration. In order to achieve meaningful geographic capabilities, we need to explore and understand how these technologies can be used to construct virtual geographic environments to help to engage geographic research. The generation of three-dimensional (3D) terrain plays an important part in geographical visualization, computer simulation, and virtual geographic environment applications. The paper introduces concepts and technologies of virtual worlds and virtual geographic environments, explores integration of realistic terrain and other geographic objects and phenomena of natural geographic environment based on SL/OpenSim virtual world technologies. Realistic 3D terrain visualization is a foundation of construction of a mirror world or a sand box model of the earth landscape and geographic environment. The capabilities of interaction and collaboration on geographic information are discussed as well. Further virtual geographic applications can be developed based on the foundation work of realistic terrain visualization in virtual environments.

Realistic terrain visualization based on 3D virtual world technology

NASA Astrophysics Data System (ADS)

Huang, Fengru; Lin, Hui; Chen, Bin; Xiao, Cai

2010-11-01

The rapid advances in information technologies, e.g., network, graphics processing, and virtual world, have provided challenges and opportunities for new capabilities in information systems, Internet applications, and virtual geographic environments, especially geographic visualization and collaboration. In order to achieve meaningful geographic capabilities, we need to explore and understand how these technologies can be used to construct virtual geographic environments to help to engage geographic research. The generation of three-dimensional (3D) terrain plays an important part in geographical visualization, computer simulation, and virtual geographic environment applications. The paper introduces concepts and technologies of virtual worlds and virtual geographic environments, explores integration of realistic terrain and other geographic objects and phenomena of natural geographic environment based on SL/OpenSim virtual world technologies. Realistic 3D terrain visualization is a foundation of construction of a mirror world or a sand box model of the earth landscape and geographic environment. The capabilities of interaction and collaboration on geographic information are discussed as well. Further virtual geographic applications can be developed based on the foundation work of realistic terrain visualization in virtual environments.

Virtual reality in the treatment of persecutory delusions: randomised controlled experimental study testing how to reduce delusional conviction.

PubMed

Freeman, Daniel; Bradley, Jonathan; Antley, Angus; Bourke, Emilie; DeWeever, Natalie; Evans, Nicole; Černis, Emma; Sheaves, Bryony; Waite, Felicity; Dunn, Graham; Slater, Mel; Clark, David M

2016-07-01

Persecutory delusions may be unfounded threat beliefs maintained by safety-seeking behaviours that prevent disconfirmatory evidence being successfully processed. Use of virtual reality could facilitate new learning. To test the hypothesis that enabling patients to test the threat predictions of persecutory delusions in virtual reality social environments with the dropping of safety-seeking behaviours (virtual reality cognitive therapy) would lead to greater delusion reduction than exposure alone (virtual reality exposure). Conviction in delusions and distress in a real-world situation were assessed in 30 patients with persecutory delusions. Patients were then randomised to virtual reality cognitive therapy or virtual reality exposure, both with 30 min in graded virtual reality social environments. Delusion conviction and real-world distress were then reassessed. In comparison with exposure, virtual reality cognitive therapy led to large reductions in delusional conviction (reduction 22.0%, P = 0.024, Cohen's d = 1.3) and real-world distress (reduction 19.6%, P = 0.020, Cohen's d = 0.8). Cognitive therapy using virtual reality could prove highly effective in treating delusions. © The Royal College of Psychiatrists 2016.

Evolution-based Virtual Content Insertion with Visually Virtual Interactions in Videos

NASA Astrophysics Data System (ADS)

Chang, Chia-Hu; Wu, Ja-Ling

With the development of content-based multimedia analysis, virtual content insertion has been widely used and studied for video enrichment and multimedia advertising. However, how to automatically insert a user-selected virtual content into personal videos in a less-intrusive manner, with an attractive representation, is a challenging problem. In this chapter, we present an evolution-based virtual content insertion system which can insert virtual contents into videos with evolved animations according to predefined behaviors emulating the characteristics of evolutionary biology. The videos are considered not only as carriers of message conveyed by the virtual content but also as the environment in which the lifelike virtual contents live. Thus, the inserted virtual content will be affected by the videos to trigger a series of artificial evolutions and evolve its appearances and behaviors while interacting with video contents. By inserting virtual contents into videos through the system, users can easily create entertaining storylines and turn their personal videos into visually appealing ones. In addition, it would bring a new opportunity to increase the advertising revenue for video assets of the media industry and online video-sharing websites.

Virtual reality in the treatment of persecutory delusions: randomised controlled experimental study testing how to reduce delusional conviction

PubMed Central

Freeman, Daniel; Bradley, Jonathan; Antley, Angus; Bourke, Emilie; DeWeever, Natalie; Evans, Nicole; Černis, Emma; Sheaves, Bryony; Waite, Felicity; Dunn, Graham; Slater, Mel; Clark, David M.

2016-01-01

Background Persecutory delusions may be unfounded threat beliefs maintained by safety-seeking behaviours that prevent disconfirmatory evidence being successfully processed. Use of virtual reality could facilitate new learning. Aims To test the hypothesis that enabling patients to test the threat predictions of persecutory delusions in virtual reality social environments with the dropping of safety-seeking behaviours (virtual reality cognitive therapy) would lead to greater delusion reduction than exposure alone (virtual reality exposure). Method Conviction in delusions and distress in a real-world situation were assessed in 30 patients with persecutory delusions. Patients were then randomised to virtual reality cognitive therapy or virtual reality exposure, both with 30 min in graded virtual reality social environments. Delusion conviction and real-world distress were then reassessed. Results In comparison with exposure, virtual reality cognitive therapy led to large reductions in delusional conviction (reduction 22.0%, P = 0.024, Cohen's d = 1.3) and real-world distress (reduction 19.6%, P = 0.020, Cohen's d = 0.8). Conclusion Cognitive therapy using virtual reality could prove highly effective in treating delusions. PMID:27151071

The effect of extended sensory range via the EyeCane sensory substitution device on the characteristics of visionless virtual navigation.

PubMed

Maidenbaum, Shachar; Levy-Tzedek, Shelly; Chebat, Daniel Robert; Namer-Furstenberg, Rinat; Amedi, Amir

2014-01-01

Mobility training programs for helping the blind navigate through unknown places with a White-Cane significantly improve their mobility. However, what is the effect of new assistive technologies, offering more information to the blind user, on the underlying premises of these programs such as navigation patterns? We developed the virtual-EyeCane, a minimalistic sensory substitution device translating single-point-distance into auditory cues identical to the EyeCane's in the real world. We compared performance in virtual environments when using the virtual-EyeCane, a virtual-White-Cane, no device and visual navigation. We show that the characteristics of virtual-EyeCane navigation differ from navigation with a virtual-White-Cane or no device, and that virtual-EyeCane users complete more levels successfully, taking shorter paths and with less collisions than these groups, and we demonstrate the relative similarity of virtual-EyeCane and visual navigation patterns. This suggests that additional distance information indeed changes navigation patterns from virtual-White-Cane use, and brings them closer to visual navigation.

Virtual reality and paranoid ideations in people with an 'at-risk mental state' for psychosis.

PubMed

Valmaggia, Lucia R; Freeman, Daniel; Green, Catherine; Garety, Philippa; Swapp, David; Antley, Angus; Prescott, Corinne; Fowler, David; Kuipers, Elizabeth; Bebbington, Paul; Slater, Mel; Broome, Matthew; McGuire, Philip K

2007-12-01

Virtual reality provides a means of studying paranoid thinking in controlled laboratory conditions. However, this method has not been used with a clinical group. To establish the feasibility and safety of using virtual reality methodology in people with an at-risk mental state and to investigate the applicability of a cognitive model of paranoia to this group. Twenty-one participants with an at-risk mental state were assessed before and after entering a virtual reality environment depicting the inside of an underground train. Virtual reality did not raise levels of distress at the time of testing or cause adverse experiences over the subsequent week. Individuals attributed mental states to virtual reality characters including hostile intent. Persecutory ideation in virtual reality was predicted by higher levels of trait paranoia, anxiety, stress, immersion in virtual reality, perseveration and interpersonal sensitivity. Virtual reality is an acceptable experimental technique for use with individuals with at-risk mental states. Paranoia in virtual reality was understandable in terms of the cognitive model of persecutory delusions.

Virtual Visits and Patient-Centered Care: Results of a Patient Survey and Observational Study

PubMed Central

2017-01-01

Background Virtual visits are clinical interactions in health care that do not involve the patient and provider being in the same room at the same time. The use of virtual visits is growing rapidly in health care. Some health systems are integrating virtual visits into primary care as a complement to existing modes of care, in part reflecting a growing focus on patient-centered care. There is, however, limited empirical evidence about how patients view this new form of care and how it affects overall health system use. Objective Descriptive objectives were to assess users and providers of virtual visits, including the reasons patients give for use. The analytic objective was to assess empirically the influence of virtual visits on overall primary care use and costs, including whether virtual care is with a known or a new primary care physician. Methods The study took place in British Columbia, Canada, where virtual visits have been publicly funded since October 2012. A survey of patients who used virtual visits and an observational study of users and nonusers of virtual visits were conducted. Comparison groups included two groups: (1) all other BC residents, and (2) a group matched (3:1) to the cohort. The first virtual visit was used as the intervention and the main outcome measures were total primary care visits and costs. Results During 2013-2014, there were 7286 virtual visit encounters, involving 5441 patients and 144 physicians. Younger patients and physicians were more likely to use and provide virtual visits (P<.001), with no differences by sex. Older and sicker patients were more likely to see a known provider, whereas the lowest socioeconomic groups were the least likely (P<.001). The survey of 399 virtual visit patients indicated that virtual visits were liked by patients, with 372 (93.2%) of respondents saying their virtual visit was of high quality and 364 (91.2%) reporting their virtual visit was “very” or “somewhat” helpful to resolve their health issue. Segmented regression analysis and the corresponding regression parameter estimates suggested virtual visits appear to have the potential to decrease primary care costs by approximately Can $4 per quarter (Can –$3.79, P=.12), but that benefit is most associated with seeing a known provider (Can –$8.68, P<.001). Conclusions Virtual visits may be one means of making the health system more patient-centered, but careful attention needs to be paid to how these services are integrated into existing health care delivery systems. PMID:28550006

Efficient Generation and Selection of Virtual Populations in Quantitative Systems Pharmacology Models.

PubMed

Allen, R J; Rieger, T R; Musante, C J

2016-03-01

Quantitative systems pharmacology models mechanistically describe a biological system and the effect of drug treatment on system behavior. Because these models rarely are identifiable from the available data, the uncertainty in physiological parameters may be sampled to create alternative parameterizations of the model, sometimes termed "virtual patients." In order to reproduce the statistics of a clinical population, virtual patients are often weighted to form a virtual population that reflects the baseline characteristics of the clinical cohort. Here we introduce a novel technique to efficiently generate virtual patients and, from this ensemble, demonstrate how to select a virtual population that matches the observed data without the need for weighting. This approach improves confidence in model predictions by mitigating the risk that spurious virtual patients become overrepresented in virtual populations.

Laser device

DOEpatents

Scott, Jill R.; Tremblay, Paul L.

2008-08-19

A laser device includes a virtual source configured to aim laser energy that originates from a true source. The virtual source has a vertical rotational axis during vertical motion of the virtual source and the vertical axis passes through an exit point from which the laser energy emanates independent of virtual source position. The emanating laser energy is collinear with an orientation line. The laser device includes a virtual source manipulation mechanism that positions the virtual source. The manipulation mechanism has a center of lateral pivot approximately coincident with a lateral index and a center of vertical pivot approximately coincident with a vertical index. The vertical index and lateral index intersect at an index origin. The virtual source and manipulation mechanism auto align the orientation line through the index origin during virtual source motion.

Sense of presence and anxiety during virtual social interactions between a human and virtual humans.

PubMed

Morina, Nexhmedin; Brinkman, Willem-Paul; Hartanto, Dwi; Emmelkamp, Paul M G

2014-01-01

Virtual reality exposure therapy (VRET) has been shown to be effective in treatment of anxiety disorders. Yet, there is lack of research on the extent to which interaction between the individual and virtual humans can be successfully implanted to increase levels of anxiety for therapeutic purposes. This proof-of-concept pilot study aimed at examining levels of the sense of presence and anxiety during exposure to virtual environments involving social interaction with virtual humans and using different virtual reality displays. A non-clinical sample of 38 participants was randomly assigned to either a head-mounted display (HMD) with motion tracker and sterescopic view condition or a one-screen projection-based virtual reality display condition. Participants in both conditions engaged in free speech dialogues with virtual humans controlled by research assistants. It was hypothesized that exposure to virtual social interactions will elicit moderate levels of sense of presence and anxiety in both groups. Further it was expected that participants in the HMD condition will report higher scores of sense of presence and anxiety than participants in the one-screen projection-based display condition. Results revealed that in both conditions virtual social interactions were associated with moderate levels of sense of presence and anxiety. Additionally, participants in the HMD condition reported significantly higher levels of presence than those in the one-screen projection-based display condition (p = .001). However, contrary to the expectations neither the average level of anxiety nor the highest level of anxiety during exposure to social virtual environments differed between the groups (p = .97 and p = .75, respectively). The findings suggest that virtual social interactions can be successfully applied in VRET to enhance sense of presence and anxiety. Furthermore, our results indicate that one-screen projection-based displays can successfully activate levels of anxiety in social virtual environments. The outcome can prove helpful in using low-cost projection-based virtual reality environments for treating individuals with social phobia.

The role of virtual articulator in prosthetic and restorative dentistry.

PubMed

Koralakunte, Pavankumar Ravi; Aljanakh, Mohammad

2014-07-01

Virtual reality is a computer based technology linked with the future of dentistry and dental practice. The virtual articulator is one such application in prosthetic and restorative dentistry based on virtual reality that will significantly reduce the limitations of the mechanical articulator, and by simulation of real patient data, allow analyses with regard to static and dynamic occlusion as well as to jaw relation. It is the purpose of this article to present the concepts and strategies for a future replacement of the mechanical articulator by a virtual one. Also, a brief note on virtual reality haptic system has been highlighted along with newly developed touch enabled virtual articulator.

The Application of Leap Motion in Astronaut Virtual Training

NASA Astrophysics Data System (ADS)

Qingchao, Xie; Jiangang, Chao

2017-03-01

With the development of computer vision, virtual reality has been applied in astronaut virtual training. As an advanced optic equipment to track hand, Leap Motion can provide precise and fluid tracking of hands. Leap Motion is suitable to be used as gesture input device in astronaut virtual training. This paper built an astronaut virtual training based Leap Motion, and established the mathematics model of hands occlusion. At last the ability of Leap Motion to handle occlusion was analysed. A virtual assembly simulation platform was developed for astronaut training, and occlusion gesture would influence the recognition process. The experimental result can guide astronaut virtual training.

Recent evolution of China's virtual water trade: analysis of selected crops and considerations for policy

NASA Astrophysics Data System (ADS)

Shi, J.; Liu, J.; Pinter, L.

2013-09-01

China has dramatically increased its virtual water import unconsciously for recent years. Many studies have focused on the quantity of traded virtual water but very few go into analysing geographic distribution and the properties of China's virtual water trade network. This paper provides a calculation and analysis of the crop-related virtual water trade network of China based on 27 major primary crops between 1986 and 2009. The results show that China is a net importer of virtual water from water-abundant areas of North and South America, and a net virtual water exporter to water-stressed areas of Asia, Africa, and Europe. Virtual water import is far larger than virtual water export and in both import and export a small number of trade partners control the supply chain. Grain crops are the major contributors to virtual water trade, and among grain crops soybeans, mostly imported from the US, Brazil and Argentina are the most significant. As crop yield and crop water productivity in North and South America are generally higher than those in Asia and Africa, the effect of China's crop-related virtual water trade positively contributes to optimizing crop water use efficiency at the global scale. In order to mitigate water scarcity and secure the food supply, virtual water should be actively incorporated into national water management strategies. From the national perspective, China should reduce the export and increase the import of water-intensive crops. But the sources of virtual water import need to be further diversified to reduce supply chain risks and increase resilience.

Spatial organization and drivers of the virtual water trade: a community-structure analysis

NASA Astrophysics Data System (ADS)

D'Odorico, Paolo; Carr, Joel; Laio, Francesco; Ridolfi, Luca

2012-09-01

The trade of agricultural commodities can be associated with a virtual transfer of the local freshwater resources used for the production of these goods. Thus, trade of food products virtually transfers large amounts of water from areas of food production to far consumption regions, a process termed the ‘globalization of water’. We consider the (time-varying) community structure of the virtual water network for the years 1986-2008. The communities are groups of countries with dense internal connections, while the connections are sparser among different communities. Between 1986 and 2008, the ratio between virtual water flows within communities and the total global trade of virtual water has continuously increased, indicating the existence of well defined clusters of virtual water transfers. In some cases (e.g. Central and North America and Europe in recent years) the virtual water communities correspond to geographically coherent regions, suggesting the occurrence of an ongoing process of regionalization of water resources. However, most communities also include countries located on different ‘sides’ of the world. As such, geographic proximity only partly explains the community structure of virtual water trade. Similarly, the global distribution of people and wealth, whose effect on the virtual water trade is expressed through simple ‘gravity models’, is unable to explain the strength of virtual water communities observed in the past few decades. A gravity model based on the availability of and demand for virtual water in different countries has higher explanatory power, but the drivers of the virtual water fluxes are yet to be adequately identified.

Results of a massive experiment on virtual currency endowments and money demand.

PubMed

Živić, Nenad; Andjelković, Igor; Özden, Tolga; Dekić, Milovan; Castronova, Edward

2017-01-01

We use a 575,000-subject, 28-day experiment to investigate monetary policy in a virtual setting. The experiment tests the effect of virtual currency endowments on player retention and virtual currency demand. An increase in endowments of a virtual currency should lower the demand for the currency in the short run. However, in the long run, we would expect money demand to rise in response to inflation in the virtual world. We test for this behavior in a virtual field experiment in the football management game Top11. 575,000 players were selected at random and allocated to different "shards" or versions of the world. The shards differed only in terms of the initial money endowment offered to new players. Money demand was observed for 28 days as players used real money to purchase additional virtual currency. The results indicate that player money purchases were significantly higher in the shards where higher endowments were given. This suggests that a positive change in the money supply in a virtual context leads to inflation and increased money demand, and does so much more quickly than in real-world economies. Differences between virtual and real currency behavior will become more interesting as virtual currency becomes a bigger part of the real economy.

Virtual reality simulators and training in laparoscopic surgery.

PubMed

Yiannakopoulou, Eugenia; Nikiteas, Nikolaos; Perrea, Despina; Tsigris, Christos

2015-01-01

Virtual reality simulators provide basic skills training without supervision in a controlled environment, free of pressure of operating on patients. Skills obtained through virtual reality simulation training can be transferred on the operating room. However, relative evidence is limited with data available only for basic surgical skills and for laparoscopic cholecystectomy. No data exist on the effect of virtual reality simulation on performance on advanced surgical procedures. Evidence suggests that performance on virtual reality simulators reliably distinguishes experienced from novice surgeons Limited available data suggest that independent approach on virtual reality simulation training is not different from proctored approach. The effect of virtual reality simulators training on acquisition of basic surgical skills does not seem to be different from the effect the physical simulators. Limited data exist on the effect of virtual reality simulation training on the acquisition of visual spatial perception and stress coping skills. Undoubtedly, virtual reality simulation training provides an alternative means of improving performance in laparoscopic surgery. However, future research efforts should focus on the effect of virtual reality simulation on performance in the context of advanced surgical procedure, on standardization of training, on the possibility of synergistic effect of virtual reality simulation training combined with mental training, on personalized training. Copyright © 2014 Surgical Associates Ltd. Published by Elsevier Ltd. All rights reserved.

Evaluation of the Use of a Virtual Patient on Student Competence and Confidence in Performing Simulated Clinic Visits.

PubMed

Taglieri, Catherine A; Crosby, Steven J; Zimmerman, Kristin; Schneider, Tulip; Patel, Dhiren K

2017-06-01

Objective. To assess the effect of incorporating virtual patient activities in a pharmacy skills lab on student competence and confidence when conducting real-time comprehensive clinic visits with mock patients. Methods. Students were randomly assigned to a control or intervention group. The control group completed the clinic visit prior to completing virtual patient activities. The intervention group completed the virtual patient activities prior to the clinic visit. Student proficiency was evaluated in the mock lab. All students completed additional exercises with the virtual patient and were subsequently assessed. Student impressions were assessed via a pre- and post-experience survey. Results. Student performance conducting clinic visits was higher in the intervention group compared to the control group. Overall student performance continued to improve in the subsequent module. There was no change in student confidence from pre- to post-experience. Student rating of the ease of use and realistic simulation of the virtual patient increased; however, student rating of the helpfulness of the virtual patient decreased. Despite student rating of the helpfulness of the virtual patient program, student performance improved. Conclusion. Virtual patient activities enhanced student performance during mock clinic visits. Students felt the virtual patient realistically simulated a real patient. Virtual patients may provide additional learning opportunities for students.

Results of a massive experiment on virtual currency endowments and money demand

PubMed Central

Živić, Nenad; Andjelković, Igor; Özden, Tolga; Dekić, Milovan

2017-01-01

We use a 575,000-subject, 28-day experiment to investigate monetary policy in a virtual setting. The experiment tests the effect of virtual currency endowments on player retention and virtual currency demand. An increase in endowments of a virtual currency should lower the demand for the currency in the short run. However, in the long run, we would expect money demand to rise in response to inflation in the virtual world. We test for this behavior in a virtual field experiment in the football management game Top11. 575,000 players were selected at random and allocated to different “shards” or versions of the world. The shards differed only in terms of the initial money endowment offered to new players. Money demand was observed for 28 days as players used real money to purchase additional virtual currency. The results indicate that player money purchases were significantly higher in the shards where higher endowments were given. This suggests that a positive change in the money supply in a virtual context leads to inflation and increased money demand, and does so much more quickly than in real-world economies. Differences between virtual and real currency behavior will become more interesting as virtual currency becomes a bigger part of the real economy. PMID:29045494

Case-Based Learning in Virtual Groups--Collaborative Problem Solving Activities and Learning Outcomes in a Virtual Professional Training Course

ERIC Educational Resources Information Center

Kopp, Birgitta; Hasenbein, Melanie; Mandl, Heinz

2014-01-01

This article analyzes the collaborative problem solving activities and learning outcomes of five groups that worked on two different complex cases in a virtual professional training course. In this asynchronous virtual learning environment, all knowledge management content was delivered virtually and collaboration took place through forums. To…

Effect of Virtual Analytical Chemistry Laboratory on Enhancing Student Research Skills and Practices

ERIC Educational Resources Information Center

Bortnik, Boris; Stozhko, Natalia; Pervukhina, Irina; Tchernysheva, Albina; Belysheva, Galina

2017-01-01

This article aims to determine the effect of a virtual chemistry laboratory on university student achievement. The article describes a model of a laboratory course that includes a virtual component. This virtual component is viewed as a tool of student pre-lab autonomous learning. It presents electronic resources designed for a virtual laboratory…

75 FR 17912 - Sunshine Act; Notice of Virtual Public Forum for EAC Board of Advisors

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-08

... ELECTION ASSISTANCE COMMISSION Sunshine Act; Notice of Virtual Public Forum for EAC Board of...: EAC Board of Advisors Virtual Meeting Room at http://www.eac.gov . Once at the main page of EAC's Web site, viewers should click the link to the Board of Advisors Virtual Meeting Room. The virtual meeting...

From Cognitive Capability to Social Reform? Shifting Perceptions of Learning in Immersive Virtual Worlds

ERIC Educational Resources Information Center

Savin-Baden, Maggi

2008-01-01

Learning in immersive virtual worlds (simulations and virtual worlds such as Second Life) could become a central learning approach in many curricula, but the socio-political impact of virtual world learning on higher education remains under-researched. Much of the recent research into learning in immersive virtual worlds centres around games and…

Catching the Bug: How Virtual Coaching Improves Teaching

ERIC Educational Resources Information Center

Allen, Megan

2014-01-01

In this article the author describes virtual coaching and why it is so effective. The following six points of virtual coaching are explained: (1) Also known as bug-in-ear coaching, virtual coaching is not new; (2) Virtual coaching can save money and time; (3) Bug-in-ear coaching increases the frequency of observations for novice teachers; (4) It…

Using a Virtual Class to Demonstrate Computer-Mediated Group Dynamics Concepts

ERIC Educational Resources Information Center

Franz, Timothy M.; Vicker, Lauren A.

2010-01-01

We report about an active learning demonstration designed to use a virtual class to present computer-mediated group communication course concepts to show that students can learn about these concepts in a virtual class. We designated 1 class period as a virtual rather than face-to-face class, when class members "attended" virtually using…

The virtues of virtual reality in exposure therapy.

PubMed

Gega, Lina

2017-04-01

Virtual reality can be more effective and less burdensome than real-life exposure. Optimal virtual reality delivery should incorporate in situ direct dialogues with a therapist, discourage safety behaviours, allow for a mismatch between virtual and real exposure tasks, and encourage self-directed real-life practice between and beyond virtual reality sessions. © The Royal College of Psychiatrists 2017.

Virtual reality for emergency training

DOE Office of Scientific and Technical Information (OSTI.GOV)

Altinkemer, K.

1995-12-31

Virtual reality is a sequence of scenes generated by a computer as a response to the five different senses. These senses are sight, sound, taste, touch, smell. Other senses that can be used in virtual reality include balance, pheromonal, and immunological senses. Many application areas include: leisure and entertainment, medicine, architecture, engineering, manufacturing, and training. Virtual reality is especially important when it is used for emergency training and management of natural disasters including earthquakes, floods, tornados and other situations which are hard to emulate. Classical training methods for these extraordinary environments lack the realistic surroundings that virtual reality can provide.more » In order for virtual reality to be a successful training tool the design needs to include certain aspects; such as how real virtual reality should be and how much fixed cost is entailed in setting up the virtual reality trainer. There are also pricing questions regarding the price per training session on virtual reality trainer, and the appropriate training time length(s).« less

Virtual Worlds for Virtual Organizing

NASA Astrophysics Data System (ADS)

Rhoten, Diana; Lutters, Wayne

The members and resources of a virtual organization are dispersed across time and space, yet they function as a coherent entity through the use of technologies, networks, and alliances. As virtual organizations proliferate and become increasingly important in society, many may exploit the technical architecture s of virtual worlds, which are the confluence of computer-mediated communication, telepresence, and virtual reality originally created for gaming. A brief socio-technical history describes their early origins and the waves of progress followed by stasis that brought us to the current period of renewed enthusiasm. Examination of contemporary examples demonstrates how three genres of virtual worlds have enabled new arenas for virtual organizing: developer-defined closed worlds, user-modifiable quasi-open worlds, and user-generated open worlds. Among expected future trends are an increase in collaboration born virtually rather than imported from existing organizations, a tension between high-fidelity recreations of the physical world and hyper-stylized imaginations of fantasy worlds, and the growth of specialized worlds optimized for particular sectors, companies, or cultures.

A Typology of Ethnographic Scales for Virtual Worlds

NASA Astrophysics Data System (ADS)

Boellstorff, Tom

This chapter outlines a typology of genres of ethnographic research with regard to virtual worlds, informed by extensive research the author has completed both in Second Life and in Indonesia. It begins by identifying four confusions about virtual worlds: they are not games, they need not be graphical or even visual, they are not mass media, and they need not be defined in terms of escapist role-playing. A three-part typology of methods for ethnographic research in virtual worlds focuses on the relationship between research design and ethnographic scale. One class of methods for researching virtual worlds with regard to ethnographic scale explores interfaces between virtual worlds and the actual world, whereas a second examines interfaces between two or more virtual worlds. The third class involves studying a single virtual world in its own terms. Recognizing that all three approaches have merit for particular research purposes, ethnography of virtual worlds can be a vibrant field of research, contributing to central debates about human selfhood and sociality.

Evaluation of the cognitive effects of travel technique in complex real and virtual environments.

PubMed

Suma, Evan A; Finkelstein, Samantha L; Reid, Myra; V Babu, Sabarish; Ulinski, Amy C; Hodges, Larry F

2010-01-01

We report a series of experiments conducted to investigate the effects of travel technique on information gathering and cognition in complex virtual environments. In the first experiment, participants completed a non-branching multilevel 3D maze at their own pace using either real walking or one of two virtual travel techniques. In the second experiment, we constructed a real-world maze with branching pathways and modeled an identical virtual environment. Participants explored either the real or virtual maze for a predetermined amount of time using real walking or a virtual travel technique. Our results across experiments suggest that for complex environments requiring a large number of turns, virtual travel is an acceptable substitute for real walking if the goal of the application involves learning or reasoning based on information presented in the virtual world. However, for applications that require fast, efficient navigation or travel that closely resembles real-world behavior, real walking has advantages over common joystick-based virtual travel techniques.

Modulation of visually evoked movement responses in moving virtual environments.

PubMed

Reed-Jones, Rebecca J; Vallis, Lori Ann

2009-01-01

Virtual-reality technology is being increasingly used to understand how humans perceive and act in the moving world around them. What is currently not clear is how virtual reality technology is perceived by human participants and what virtual scenes are effective in evoking movement responses to visual stimuli. We investigated the effect of virtual-scene context on human responses to a virtual visual perturbation. We hypothesised that exposure to a natural scene that matched the visual expectancies of the natural world would create a perceptual set towards presence, and thus visual guidance of body movement in a subsequently presented virtual scene. Results supported this hypothesis; responses to a virtual visual perturbation presented in an ambiguous virtual scene were increased when participants first viewed a scene that consisted of natural landmarks which provided 'real-world' visual motion cues. Further research in this area will provide a basis of knowledge for the effective use of this technology in the study of human movement responses.

Virtual hand: a 3D tactile interface to virtual environments

NASA Astrophysics Data System (ADS)

Rogowitz, Bernice E.; Borrel, Paul

2008-02-01

We introduce a novel system that allows users to experience the sensation of touch in a computer graphics environment. In this system, the user places his/her hand on an array of pins, which is moved about space on a 6 degree-of-freedom robot arm. The surface of the pins defines a surface in the virtual world. This "virtual hand" can move about the virtual world. When the virtual hand encounters an object in the virtual world, the heights of the pins are adjusted so that they represent the object's shape, surface, and texture. A control system integrates pin and robot arm motions to transmit information about objects in the computer graphics world to the user. It also allows the user to edit, change and move the virtual objects, shapes and textures. This system provides a general framework for touching, manipulating, and modifying objects in a 3-D computer graphics environment, which may be useful in a wide range of applications, including computer games, computer aided design systems, and immersive virtual worlds.

An Interactive and Comprehensive Working Environment for High-Energy Physics Software with Python and Jupyter Notebooks

NASA Astrophysics Data System (ADS)

Braun, N.; Hauth, T.; Pulvermacher, C.; Ritter, M.

2017-10-01

Today’s analyses for high-energy physics (HEP) experiments involve processing a large amount of data with highly specialized algorithms. The contemporary workflow from recorded data to final results is based on the execution of small scripts - often written in Python or ROOT macros which call complex compiled algorithms in the background - to perform fitting procedures and generate plots. During recent years interactive programming environments, such as Jupyter, became popular. Jupyter allows to develop Python-based applications, so-called notebooks, which bundle code, documentation and results, e.g. plots. Advantages over classical script-based approaches is the feature to recompute only parts of the analysis code, which allows for fast and iterative development, and a web-based user frontend, which can be hosted centrally and only requires a browser on the user side. In our novel approach, Python and Jupyter are tightly integrated into the Belle II Analysis Software Framework (basf2), currently being developed for the Belle II experiment in Japan. This allows to develop code in Jupyter notebooks for every aspect of the event simulation, reconstruction and analysis chain. These interactive notebooks can be hosted as a centralized web service via jupyterhub with docker and used by all scientists of the Belle II Collaboration. Because of its generality and encapsulation, the setup can easily be scaled to large installations.

ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data

PubMed Central

Krestel, Ralf; Ohler, Uwe; Vingron, Martin; Marsico, Annalisa

2017-01-01

Abstract RNA-binding proteins (RBPs) play an important role in RNA post-transcriptional regulation and recognize target RNAs via sequence-structure motifs. The extent to which RNA structure influences protein binding in the presence or absence of a sequence motif is still poorly understood. Existing RNA motif finders either take the structure of the RNA only partially into account, or employ models which are not directly interpretable as sequence-structure motifs. We developed ssHMM, an RNA motif finder based on a hidden Markov model (HMM) and Gibbs sampling which fully captures the relationship between RNA sequence and secondary structure preference of a given RBP. Compared to previous methods which output separate logos for sequence and structure, it directly produces a combined sequence-structure motif when trained on a large set of sequences. ssHMM’s model is visualized intuitively as a graph and facilitates biological interpretation. ssHMM can be used to find novel bona fide sequence-structure motifs of uncharacterized RBPs, such as the one presented here for the YY1 protein. ssHMM reaches a high motif recovery rate on synthetic data, it recovers known RBP motifs from CLIP-Seq data, and scales linearly on the input size, being considerably faster than MEMERIS and RNAcontext on large datasets while being on par with GraphProt. It is freely available on Github and as a Docker image. PMID:28977546

GES DISC Data Recipes in Jupyter Notebooks

NASA Astrophysics Data System (ADS)

Li, A.; Banavige, B.; Garimella, K.; Rice, J.; Shen, S.; Liu, Z.

2017-12-01

The Earth Science Data and Information System (ESDIS) Project manages twelve Distributed Active Archive Centers (DAACs) which are geographically dispersed across the United States. The DAACs are responsible for ingesting, processing, archiving, and distributing Earth science data produced from various sources (satellites, aircraft, field measurements, etc.). In response to projections of an exponential increase in data production, there has been a recent effort to prototype various DAAC activities in the cloud computing environment. This, in turn, led to the creation of an initiative, called the Cloud Analysis Toolkit to Enable Earth Science (CATEES), to develop a Python software package in order to transition Earth science data processing to the cloud. This project, in particular, supports CATEES and has two primary goals. One, transition data recipes created by the Goddard Earth Science Data and Information Service Center (GES DISC) DAAC into an interactive and educational environment using Jupyter Notebooks. Two, acclimate Earth scientists to cloud computing. To accomplish these goals, we create Jupyter Notebooks to compartmentalize the different steps of data analysis and help users obtain and parse data from the command line. We also develop a Docker container, comprised of Jupyter Notebooks, Python library dependencies, and command line tools, and configure it into an easy to deploy package. The end result is an end-to-end product that simulates the use case of end users working in the cloud computing environment.

A De-Identification Pipeline for Ultrasound Medical Images in DICOM Format.

PubMed

Monteiro, Eriksson; Costa, Carlos; Oliveira, José Luís

2017-05-01

Clinical data sharing between healthcare institutions, and between practitioners is often hindered by privacy protection requirements. This problem is critical in collaborative scenarios where data sharing is fundamental for establishing a workflow among parties. The anonymization of patient information burned in DICOM images requires elaborate processes somewhat more complex than simple de-identification of textual information. Usually, before sharing, there is a need for manual removal of specific areas containing sensitive information in the images. In this paper, we present a pipeline for ultrasound medical image de-identification, provided as a free anonymization REST service for medical image applications, and a Software-as-a-Service to streamline automatic de-identification of medical images, which is freely available for end-users. The proposed approach applies image processing functions and machine-learning models to bring about an automatic system to anonymize medical images. To perform character recognition, we evaluated several machine-learning models, being Convolutional Neural Networks (CNN) selected as the best approach. For accessing the system quality, 500 processed images were manually inspected showing an anonymization rate of 89.2%. The tool can be accessed at https://bioinformatics.ua.pt/dicom/anonymizer and it is available with the most recent version of Google Chrome, Mozilla Firefox and Safari. A Docker image containing the proposed service is also publicly available for the community.

Virtual and live social facilitation while exergaming: competitiveness moderates exercise intensity.

PubMed

Snyder, Amanda L; Anderson-Hanley, Cay; Arciero, Paul J

2012-04-01

Grounded in social facilitation theory, this study compared the impact on exercise intensity of a virtual versus a live competitor, when riding a virtual reality-enhanced stationary bike ("cybercycle"). It was hypothesized that competitiveness would moderate effects. Twenty-three female college students were exposed to three conditions on a cybercycle: solo training, virtual competitor, and live competitor. After training without a competitor (solo condition for familiarization with equipment), participants competed against a virtual avatar or live rider (random order of presentation). A repeated-measures analysis revealed a significant condition (virtual/live) by competitiveness (high/low) interaction for exercise intensity (watts). More competitive participants exhibited significantly greater exercise intensity when competing against a live versus virtual competitor. The implication is that live competitors can have an added social facilitation effect and influence exercise intensity, although competitiveness moderates this effect.

Efficient Generation and Selection of Virtual Populations in Quantitative Systems Pharmacology Models

PubMed Central

Rieger, TR; Musante, CJ

2016-01-01

Quantitative systems pharmacology models mechanistically describe a biological system and the effect of drug treatment on system behavior. Because these models rarely are identifiable from the available data, the uncertainty in physiological parameters may be sampled to create alternative parameterizations of the model, sometimes termed “virtual patients.” In order to reproduce the statistics of a clinical population, virtual patients are often weighted to form a virtual population that reflects the baseline characteristics of the clinical cohort. Here we introduce a novel technique to efficiently generate virtual patients and, from this ensemble, demonstrate how to select a virtual population that matches the observed data without the need for weighting. This approach improves confidence in model predictions by mitigating the risk that spurious virtual patients become overrepresented in virtual populations. PMID:27069777

Grasping trajectories in a virtual environment adhere to Weber's law.

PubMed

Ozana, Aviad; Berman, Sigal; Ganel, Tzvi

2018-06-01

Virtual-reality and telerobotic devices simulate local motor control of virtual objects within computerized environments. Here, we explored grasping kinematics within a virtual environment and tested whether, as in normal 3D grasping, trajectories in the virtual environment are performed analytically, violating Weber's law with respect to object's size. Participants were asked to grasp a series of 2D objects using a haptic system, which projected their movements to a virtual space presented on a computer screen. The apparatus also provided object-specific haptic information upon "touching" the edges of the virtual targets. The results showed that grasping movements performed within the virtual environment did not produce the typical analytical trajectory pattern obtained during 3D grasping. Unlike as in 3D grasping, grasping trajectories in the virtual environment adhered to Weber's law, which indicates relative resolution in size processing. In addition, the trajectory patterns differed from typical trajectories obtained during 3D grasping, with longer times to complete the movement, and with maximum grip apertures appearing relatively early in the movement. The results suggest that grasping movements within a virtual environment could differ from those performed in real space, and are subjected to irrelevant effects of perceptual information. Such atypical pattern of visuomotor control may be mediated by the lack of complete transparency between the interface and the virtual environment in terms of the provided visual and haptic feedback. Possible implications of the findings to movement control within robotic and virtual environments are further discussed.

A threat to a virtual hand elicits motor cortex activation.

PubMed

González-Franco, Mar; Peck, Tabitha C; Rodríguez-Fornells, Antoni; Slater, Mel

2014-03-01

We report an experiment where participants observed an attack on their virtual body as experienced in an immersive virtual reality (IVR) system. Participants sat by a table with their right hand resting upon it. In IVR, they saw a virtual table that was registered with the real one, and they had a virtual body that substituted their real body seen from a first person perspective. The virtual right hand was collocated with their real right hand. Event-related brain potentials were recorded in two conditions, one where the participant's virtual hand was attacked with a knife and a control condition where the knife only struck the virtual table. Significantly greater P450 potentials were obtained in the attack condition confirming our expectations that participants had a strong illusion of the virtual hand being their own, which was also strongly supported by questionnaire responses. Higher levels of subjective virtual hand ownership correlated with larger P450 amplitudes. Mu-rhythm event-related desynchronization in the motor cortex and readiness potential (C3-C4) negativity were clearly observed when the virtual hand was threatened-as would be expected, if the real hand was threatened and the participant tried to avoid harm. Our results support the idea that event-related potentials may provide a promising non-subjective measure of virtual embodiment. They also support previous experiments on pain observation and are placed into context of similar experiments and studies of body perception and body ownership within cognitive neuroscience.

The Role of Virtual Articulator in Prosthetic and Restorative Dentistry

PubMed Central

Aljanakh, Mohammad

2014-01-01

Virtual reality is a computer based technology linked with the future of dentistry and dental practice. The virtual articulator is one such application in prosthetic and restorative dentistry based on virtual reality that will significantly reduce the limitations of the mechanical articulator, and by simulation of real patient data, allow analyses with regard to static and dynamic occlusion as well as to jaw relation. It is the purpose of this article to present the concepts and strategies for a future replacement of the mechanical articulator by a virtual one. Also, a brief note on virtual reality haptic system has been highlighted along with newly developed touch enabled virtual articulator. PMID:25177664

Towards a Methodology for Managing Competencies in Virtual Teams - A Systemic Approach

NASA Astrophysics Data System (ADS)

Schumacher, Marinita; Stal-Le Cardinal, Julie; Bocquet, Jean-Claude

Virtual instruments and tools are future trends in Engineering which are a response to the growing complexity of engineering tasks, the facility of communication and strong collaborations on the international market. Outsourcing, off-shoring, and the globalization of organisations’ activities have resulted in the formation of virtual product development teams. Individuals who are working in virtual teams must be equipped with diversified competencies that provide a basis for virtual team building. Thanks to the systemic approach of the functional analysis our paper responds to the need of a methodology of competence management to build virtual teams that are active in virtual design projects in the area of New Product Development (NPD).

Sounds of silence: How to animate virtual worlds with sound

NASA Technical Reports Server (NTRS)

Astheimer, Peter

1993-01-01

Sounds are an integral and sometimes annoying part of our daily life. Virtual worlds which imitate natural environments gain a lot of authenticity from fast, high quality visualization combined with sound effects. Sounds help to increase the degree of immersion for human dwellers in imaginary worlds significantly. The virtual reality toolkit of IGD (Institute for Computer Graphics) features a broad range of standard visual and advanced real-time audio components which interpret an object-oriented definition of the scene. The virtual reality system 'Virtual Design' realized with the toolkit enables the designer of virtual worlds to create a true audiovisual environment. Several examples on video demonstrate the usage of the audio features in Virtual Design.

Photorealistic virtual anatomy based on Chinese Visible Human data.

PubMed

Heng, P A; Zhang, S X; Xie, Y M; Wong, T T; Chui, Y P; Cheng, C Y

2006-04-01

Virtual reality based learning of human anatomy is feasible when a database of 3D organ models is available for the learner to explore, visualize, and dissect in virtual space interactively. In this article, we present our latest work on photorealistic virtual anatomy applications based on the Chinese Visible Human (CVH) data. We have focused on the development of state-of-the-art virtual environments that feature interactive photo-realistic visualization and dissection of virtual anatomical models constructed from ultra-high resolution CVH datasets. We also outline our latest progress in applying these highly accurate virtual and functional organ models to generate realistic look and feel to advanced surgical simulators. (c) 2006 Wiley-Liss, Inc.

The specificity of memory enhancement during interaction with a virtual environment.

PubMed

Brooks, B M; Attree, E A; Rose, F D; Clifford, B R; Leadbetter, A G

1999-01-01

Two experiments investigated differences between active and passive participation in a computer-generated virtual environment in terms of spatial memory, object memory, and object location memory. It was found that active participants, who controlled their movements in the virtual environment using a joystick, recalled the spatial layout of the virtual environment better than passive participants, who merely watched the active participants' progress. Conversely, there were no significant differences between the active and passive participants' recall or recognition of the virtual objects, nor in their recall of the correct locations of objects in the virtual environment. These findings are discussed in terms of subject-performed task research and the specificity of memory enhancement in virtual environments.

Understanding the Dimensions of Virtual Teams: A Study of Professional Students in India

ERIC Educational Resources Information Center

Gupta, Shubhi; Pathak, Govind Swaroop

2017-01-01

Despite several efforts to bring about a clear phenomenon of virtual teams, there is still some confusion as to how virtual teams should be defined. It is probably because the characteristics of virtual teams and relationships among them have not been consistent. To address this gap, the present study explores the nature of virtual teams by…

The Development of the Virtual Learning Media of the Sacred Object Artwork

ERIC Educational Resources Information Center

Nuanmeesri, Sumitra; Jamornmongkolpilai, Saran

2018-01-01

This research aimed to develop the virtual learning media of the sacred object artwork by applying the concept of the virtual technology in order to publicize knowledge on the cultural wisdom of the sacred object artwork. It was done by designing and developing the virtual learning media of the sacred object artwork for the virtual presentation.…

Emergence of Virtual Communities as Means of Communication: A Case Study on Virtual Health Care Communities

ERIC Educational Resources Information Center

Argan, Mehpare Tokay; Argan, Metin; Suher, Idil K.

2011-01-01

Like in all areas, virtual communities make their presence felt in the area of healthcare too. Virtual communities play an important role in healthcare in terms of gathering information on healthcare, sharing of personal interests and providing social support. Virtual communities provide a way for a group of peers to communicate with each other.…

The Effects of "Live Virtual Classroom" on Students' Achievement and Students' Opinions about "Live Virtual Classroom" at Distance Education

ERIC Educational Resources Information Center

Yilmaz, Ozgur

2015-01-01

This study was performed to investigate the effects of live virtual classroom on students' achievement and to determine students' opinions about the live virtual physics classroom at distance learning. 63 second-year Distance Computer Education & Instructional Technology students enrolled in this study. At the live virtual physics classroom,…

Virtual Reality and Computer-Enhanced Training Applied to Wheeled Mobility: An Overview of Work in Pittsburgh

ERIC Educational Resources Information Center

Cooper, Rory A.; Ding, Dan; Simpson, Richard; Fitzgerald, Shirley G.; Spaeth, Donald M.; Guo, Songfeng; Koontz, Alicia M.; Cooper, Rosemarie; Kim, Jongbae; Boninger, Michael L.

2005-01-01

Some aspects of assistive technology can be enhanced by the application of virtual reality. Although virtual simulation offers a range of new possibilities, learning to navigate in a virtual environment is not equivalent to learning to navigate in the real world. Therefore, virtual reality simulation is advocated as a useful preparation for…

Virtual Reality

DTIC Science & Technology

1993-04-01

until exhausted. SECURITY CLASSIFICATION OF THIS PAGE All other editions are obsolete. UNCLASSIFIED " VIRTUAL REALITY JAMES F. DAILEY, LIEUTENANT COLONEL...US" This paper reviews the exciting field of virtual reality . The author describes the basic concepts of virtual reality and finds that its numerous...potential benefits to society could revolutionize everyday life. The various components that make up a virtual reality system are described in detail

A Study Comparing the Pedagogical Effectiveness of Virtual Worlds and of Classical Methods

DTIC Science & Technology

2014-08-01

Approved for public release; distribution is unlimited. A Study Comparing the Pedagogical Effectiveness of Virtual Worlds and of Classical Methods...ABSTRACT A Study Comparing the Pedagogical Effectiveness of Virtual Worlds and of Classical Methods Report Title This experiment tests whether a virtual... PEDAGOGICAL EFFECTIVENESS OF VIRTUAL WORLDS AND OF TRADITIONAL TRAINING METHODS A Thesis by BENJAMIN PETERS

A Review of Virtual Character's Emotion Model

NASA Astrophysics Data System (ADS)

Liu, Zhen

2008-11-01

Emotional virtual characters are essential to digital entertainment, an emotion is related to virtual environment and a virtual character's inner variables, emotion model of virtual character is a hot topic in many fields, domain knowledge is very important for modeling emotion, and the current research of emotion expression in the world was also summarized, and some new research directions of emotion model are presented.

The Virtual Desktop: Options and Challenges in Selecting a Secure Desktop Infrastructure Based on Virtualization

DTIC Science & Technology

2011-10-01

Fortunately, some products offer centralized management and deployment tools for local desktop implementation . Figure 5 illustrates the... implementation of a secure desktop infrastructure based on virtualization. It includes an overview of desktop virtualization, including an in-depth...environment in the data centre, whereas LHVD places it on the endpoint itself. Desktop virtualization implementation considerations and potential

The Effect of Realistic Appearance of Virtual Characters in Immersive Environments - Does the Character's Personality Play a Role?

PubMed

Zibrek, Katja; Kokkinara, Elena; Mcdonnell, Rachel

2018-04-01

Virtual characters that appear almost photo-realistic have been shown to induce negative responses from viewers in traditional media, such as film and video games. This effect, described as the uncanny valley, is the reason why realism is often avoided when the aim is to create an appealing virtual character. In Virtual Reality, there have been few attempts to investigate this phenomenon and the implications of rendering virtual characters with high levels of realism on user enjoyment. In this paper, we conducted a large-scale experiment on over one thousand members of the public in order to gather information on how virtual characters are perceived in interactive virtual reality games. We were particularly interested in whether different render styles (realistic, cartoon, etc.) would directly influence appeal, or if a character's personality was the most important indicator of appeal. We used a number of perceptual metrics such as subjective ratings, proximity, and attribution bias in order to test our hypothesis. Our main result shows that affinity towards virtual characters is a complex interaction between the character's appearance and personality, and that realism is in fact a positive choice for virtual characters in virtual reality.

Development of a Virtual Museum Including a 4d Presentation of Building History in Virtual Reality

NASA Astrophysics Data System (ADS)

Kersten, T. P.; Tschirschwitz, F.; Deggim, S.

2017-02-01

In the last two decades the definition of the term "virtual museum" changed due to rapid technological developments. Using today's available 3D technologies a virtual museum is no longer just a presentation of collections on the Internet or a virtual tour of an exhibition using panoramic photography. On one hand, a virtual museum should enhance a museum visitor's experience by providing access to additional materials for review and knowledge deepening either before or after the real visit. On the other hand, a virtual museum should also be used as teaching material in the context of museum education. The laboratory for Photogrammetry & Laser Scanning of the HafenCity University Hamburg has developed a virtual museum (VM) of the museum "Alt-Segeberger Bürgerhaus", a historic town house. The VM offers two options for visitors wishing to explore the museum without travelling to the city of Bad Segeberg, Schleswig-Holstein, Germany. Option a, an interactive computer-based, tour for visitors to explore the exhibition and to collect information of interest or option b, to immerse into virtual reality in 3D with the HTC Vive Virtual Reality System.

[Research on the virtual water composition and virtual water trade for agriculture in Beijing].

PubMed

Wang, Hong-rui; Wang, Yan; Wang, Jun-hong; Dong, Yan-yan; Han, Zhao-xing

2007-12-01

Based on the irrigation norm of typical district and county, and revised by the isoline map of Chinese crops water demand, the change of crops program was analyzed as well as the agricultural water use and its GDP benefits. Then the virtual water was calculated for years. At last, the input-output method was used to calculate the trade of virtual water in Beijing. As the results, the virtual water for cereal crops has been decreasing in Beijing, from 1.832 x 10(9) m3 in 1990 to 4.283 x 10(8) m3 in 2004. Otherwise the virtual water for technical crops has been increasing, which is from 9.06 x 10(8) m3 in 1990 to 1.492 x 10(9) m3 in 2004. On the whole, the virtual water for crops has been decreasing in Beijing. From the angle of primary products Beijing is a virtual water importing area. Virtual water importing of annual average is 2.37 x 10(8) m3, which is about 5.93% of the total water of Beijing. Virtual water has been an important supplement of local real water of Beijing.

Virtual Visits and Patient-Centered Care: Results of a Patient Survey and Observational Study.

PubMed

McGrail, Kimberlyn Marie; Ahuja, Megan Alyssa; Leaver, Chad Andrew

2017-05-26

Virtual visits are clinical interactions in health care that do not involve the patient and provider being in the same room at the same time. The use of virtual visits is growing rapidly in health care. Some health systems are integrating virtual visits into primary care as a complement to existing modes of care, in part reflecting a growing focus on patient-centered care. There is, however, limited empirical evidence about how patients view this new form of care and how it affects overall health system use. Descriptive objectives were to assess users and providers of virtual visits, including the reasons patients give for use. The analytic objective was to assess empirically the influence of virtual visits on overall primary care use and costs, including whether virtual care is with a known or a new primary care physician. The study took place in British Columbia, Canada, where virtual visits have been publicly funded since October 2012. A survey of patients who used virtual visits and an observational study of users and nonusers of virtual visits were conducted. Comparison groups included two groups: (1) all other BC residents, and (2) a group matched (3:1) to the cohort. The first virtual visit was used as the intervention and the main outcome measures were total primary care visits and costs. During 2013-2014, there were 7286 virtual visit encounters, involving 5441 patients and 144 physicians. Younger patients and physicians were more likely to use and provide virtual visits (P<.001), with no differences by sex. Older and sicker patients were more likely to see a known provider, whereas the lowest socioeconomic groups were the least likely (P<.001). The survey of 399 virtual visit patients indicated that virtual visits were liked by patients, with 372 (93.2%) of respondents saying their virtual visit was of high quality and 364 (91.2%) reporting their virtual visit was "very" or "somewhat" helpful to resolve their health issue. Segmented regression analysis and the corresponding regression parameter estimates suggested virtual visits appear to have the potential to decrease primary care costs by approximately Can $4 per quarter (Can -$3.79, P=.12), but that benefit is most associated with seeing a known provider (Can -$8.68, P<.001). Virtual visits may be one means of making the health system more patient-centered, but careful attention needs to be paid to how these services are integrated into existing health care delivery systems. ©Kimberlyn Marie McGrail, Megan Alyssa Ahuja, Chad Andrew Leaver. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 26.05.2017.

Virtual imaging in sports broadcasting: an overview

NASA Astrophysics Data System (ADS)

Tan, Yi

2003-04-01

Virtual imaging technology is being used to augment television broadcasts -- virtual objects are seamlessly inserted into the video stream to appear as real entities to TV audiences. Virtual advertisements, the main application of this technology, are providing opportunities to improve the commercial value of television programming while enhancing the contents and the entertainment aspect of these programs. State-of-the-art technologies, such as image recognition, motion tracking and chroma keying, are central to a virtual imaging system. This paper reviews the general framework, the key techniques, and the sports broadcasting applications of virtual imaging technology.

Virtual reality: past, present and future.

PubMed

Gobbetti, E; Scateni, R

1998-01-01

This report provides a short survey of the field of virtual reality, highlighting application domains, technological requirements, and currently available solutions. The report is organized as follows: section 1 presents the background and motivation of virtual environment research and identifies typical application domain, section 2 discusses the characteristics a virtual reality system must have in order to exploit the perceptual and spatial skills of users, section 3 surveys current input/output devices for virtual reality, section 4 surveys current software approaches to support the creation of virtual reality systems, and section 5 summarizes the report.

An Algorithm for Creating Virtual Controls Using Integrated and Harmonized Longitudinal Data.

PubMed

Hansen, William B; Chen, Shyh-Huei; Saldana, Santiago; Ip, Edward H

2018-06-01

We introduce a strategy for creating virtual control groups-cases generated through computer algorithms that, when aggregated, may serve as experimental comparators where live controls are difficult to recruit, such as when programs are widely disseminated and randomization is not feasible. We integrated and harmonized data from eight archived longitudinal adolescent-focused data sets spanning the decades from 1980 to 2010. Collectively, these studies examined numerous psychosocial variables and assessed past 30-day alcohol, cigarette, and marijuana use. Additional treatment and control group data from two archived randomized control trials were used to test the virtual control algorithm. Both randomized controlled trials (RCTs) assessed intentions, normative beliefs, and values as well as past 30-day alcohol, cigarette, and marijuana use. We developed an algorithm that used percentile scores from the integrated data set to create age- and gender-specific latent psychosocial scores. The algorithm matched treatment case observed psychosocial scores at pretest to create a virtual control case that figuratively "matured" based on age-related changes, holding the virtual case's percentile constant. Virtual controls matched treatment case occurrence, eliminating differential attrition as a threat to validity. Virtual case substance use was estimated from the virtual case's latent psychosocial score using logistic regression coefficients derived from analyzing the treatment group. Averaging across virtual cases created group estimates of prevalence. Two criteria were established to evaluate the adequacy of virtual control cases: (1) virtual control group pretest drug prevalence rates should match those of the treatment group and (2) virtual control group patterns of drug prevalence over time should match live controls. The algorithm successfully matched pretest prevalence for both RCTs. Increases in prevalence were observed, although there were discrepancies between live and virtual control outcomes. This study provides an initial framework for creating virtual controls using a step-by-step procedure that can now be revised and validated using other prevention trial data.

Can a virtual supermarket bring realism into the lab? Comparing shopping behavior using virtual and pictorial store representations to behavior in a physical store.

PubMed

van Herpen, Erica; van den Broek, Eva; van Trijp, Hans C M; Yu, Tian

2016-12-01

Immersive virtual reality techniques present new opportunities for research into consumer behavior. The current study examines whether the increased realism of a virtual store compared to pictorial (2D) stimuli elicits consumer behavior that is more in line with behavior in a physical store. We examine the number, variety, and type of products selected, amount of money spent, and responses to price promotions and shelf display, in three product categories (fruit & vegetables, milk, and biscuits). We find that virtual reality elicits behavior that is more similar to behavior in the physical store compared to the picture condition for the number of products selected (Milk: M store  = 1.19, M virtual  = 1.53, M pictures  = 2.58) and amount of money spent (Milk: M store  = 1.27, M virtual  = 1.53, M pictures  = 2.60 Euro), and for the selection of products from different areas of the shelf, both vertically (purchases from top shelves, milk and biscuits: P store  = 21.6%, P virtual  = 33.4%, P pictures  = 50.0%) and horizontally (purchase from left shelf, biscuits: P store  = 35.5%, P virtual  = 53.3%, P pictures  = 66.7%). This indicates that virtual reality can improve realism in responses to shelf allocation. Virtual reality was not able to diminish other differences between lab and physical store: participants bought more products and spent more money (for biscuits and fruit & vegetables), bought more national brands, and responded more strongly to price promotions in both virtual reality and pictorial representations than in the physical store. Implications for the use of virtual reality in studies of consumer food choice behavior as well as for future improvement of virtual reality techniques are discussed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Theft of Virtual Property — Towards Security Requirements for Virtual Worlds

NASA Astrophysics Data System (ADS)

Beyer, Anja

The article is focused to introduce the topic of information technology security for Virtual Worlds to a security experts’ audience. Virtual Worlds are Web 2.0 applications where the users cruise through the world with their individually shaped avatars to find either amusement, challenges or the next best business deal. People do invest a lot of time but beyond they invest in buying virtual assets like fantasy witcheries, wepaons, armour, houses, clothes,...etc with the power of real world money. Although it is called “virtual” (which is often put on the same level as “not existent”) there is a real value behind it. In November 2007 dutch police arrested a seventeen years old teenager who was suspicted to have stolen virtual items in a Virtual World called Habbo Hotel [Reuters07]. In order to successfully provide security mechanisms into Virtual Worlds it is necessarry to fully understand the domain for which the security mechansims are defined. As Virtual Worlds must be clasified into the domain of Social Software the article starts with an overview of how to understand Web 2.0 and gives a short introduction to Virtual Worlds. The article then provides a consideration of assets of Virtual Worlds participants, describes how these assets can be threatened and gives an overview of appopriate security requirements and completes with an outlook of possible countermeasures.

Virtual Realities and the Future of Text.

ERIC Educational Resources Information Center

Marcus, Stephen

1992-01-01

Discusses issues surrounding virtual reality and "virtual books." Suggests that those who are exploring the territory of virtual realities are already helping to expand and enrich expectations and visions for integrating technology into reading and writing. (RS)

A Survey of Middleware for Sensor and Network Virtualization

PubMed Central

Khalid, Zubair; Fisal, Norsheila; Rozaini, Mohd.

2014-01-01

Wireless Sensor Network (WSN) is leading to a new paradigm of Internet of Everything (IoE). WSNs have a wide range of applications but are usually deployed in a particular application. However, the future of WSNs lies in the aggregation and allocation of resources, serving diverse applications. WSN virtualization by the middleware is an emerging concept that enables aggregation of multiple independent heterogeneous devices, networks, radios and software platforms; and enhancing application development. WSN virtualization, middleware can further be categorized into sensor virtualization and network virtualization. Middleware for WSN virtualization poses several challenges like efficient decoupling of networks, devices and software. In this paper efforts have been put forward to bring an overview of the previous and current middleware designs for WSN virtualization, the design goals, software architectures, abstracted services, testbeds and programming techniques. Furthermore, the paper also presents the proposed model, challenges and future opportunities for further research in the middleware designs for WSN virtualization. PMID:25615737

Virtual Remediation Versus Methylphenidate to Improve Distractibility in Children With ADHD: A Controlled Randomized Clinical Trial Study.

PubMed

Bioulac, Stéphanie; Micoulaud-Franchi, Jean-Arthur; Maire, Jenna; Bouvard, Manuel P; Rizzo, Albert A; Sagaspe, Patricia; Philip, Pierre

2018-03-01

Virtual environments have been used to assess children with ADHD but have never been tested as therapeutic tools. We tested a new virtual classroom cognitive remediation program to improve symptoms in children with ADHD. In this randomized clinical trial, 51 children with ADHD (7-11 years) were assigned to a virtual cognitive remediation group, a methylphenidate group, or a psychotherapy group. All children were evaluated before and after therapy with an ADHD Rating Scale, a Continuous Performance Test (CPT), and a virtual classroom task. After therapy by virtual remediation, children exhibited significantly higher numbers of correct hits on the virtual classroom and CPT. These improvements were equivalent to those observed with methylphenidate treatment. Our study demonstrates for the first time that a cognitive remediation program delivered in a virtual classroom reduces distractibility in children with ADHD and could replace methylphenidate treatment in specific cases.

Crushing virtual cigarettes reduces tobacco addiction and treatment discontinuation.

PubMed

Girard, Benoit; Turcotte, Vincent; Bouchard, Stéphane; Girard, Bruno

2009-10-01

Pilot studies revealed promising results regarding crushing virtual cigarettes to reduce tobacco addiction. In this study, 91 regular smokers were randomly assigned to two treatment conditions that differ only by the action performed in the virtual environment: crushing virtual cigarettes or grasping virtual balls. All participants also received minimal psychosocial support from nurses during each of 12 visits to the clinic. An affordable virtual reality system was used (eMagin HMD) with a virtual environment created by modifying a 3D game. Results revealed that crushing virtual cigarettes during 4 weekly sessions led to a statistically significant reduction in nicotine addiction (assessed with the Fagerström test), abstinence rate (confirmed with exhaled carbon monoxide), and drop-out rate from the 12-week psychosocial minimal-support treatment program. Increased retention in the program is discussed as a potential explanation for treatment success, and hypotheses are raised about self-efficacy, motivation, and learning.

A web-based platform for virtual screening.

PubMed

Watson, Paul; Verdonk, Marcel; Hartshorn, Michael J

2003-09-01

A fully integrated, web-based, virtual screening platform has been developed to allow rapid virtual screening of large numbers of compounds. ORACLE is used to store information at all stages of the process. The system includes a large database of historical compounds from high throughput screenings (HTS) chemical suppliers, ATLAS, containing over 3.1 million unique compounds with their associated physiochemical properties (ClogP, MW, etc.). The database can be screened using a web-based interface to produce compound subsets for virtual screening or virtual library (VL) enumeration. In order to carry out the latter task within ORACLE a reaction data cartridge has been developed. Virtual libraries can be enumerated rapidly using the web-based interface to the cartridge. The compound subsets can be seamlessly submitted for virtual screening experiments, and the results can be viewed via another web-based interface allowing ad hoc querying of the virtual screening data stored in ORACLE.

Exploring Infiniband Hardware Virtualization in OpenNebula towards Efficient High-Performance Computing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pais Pitta de Lacerda Ruivo, Tiago; Bernabeu Altayo, Gerard; Garzoglio, Gabriele

2014-11-11

has been widely accepted that software virtualization has a big negative impact on high-performance computing (HPC) application performance. This work explores the potential use of Infiniband hardware virtualization in an OpenNebula cloud towards the efficient support of MPI-based workloads. We have implemented, deployed, and tested an Infiniband network on the FermiCloud private Infrastructure-as-a-Service (IaaS) cloud. To avoid software virtualization towards minimizing the virtualization overhead, we employed a technique called Single Root Input/Output Virtualization (SRIOV). Our solution spanned modifications to the Linux’s Hypervisor as well as the OpenNebula manager. We evaluated the performance of the hardware virtualization on up to 56more » virtual machines connected by up to 8 DDR Infiniband network links, with micro-benchmarks (latency and bandwidth) as well as w a MPI-intensive application (the HPL Linpack benchmark).« less

Virtual Laboratories and Virtual Worlds

NASA Astrophysics Data System (ADS)

Hut, Piet

2008-05-01

Since we cannot put stars in a laboratory, astrophysicists had to wait till the invention of computers before becoming laboratory scientists. For half a century now, we have been conducting experiments in our virtual laboratories. However, we ourselves have remained behind the keyboard, with the screen of the monitor separating us from the world we are simulating. Recently, 3D on-line technology, developed first for games but now deployed in virtual worlds like Second Life, is beginning to make it possible for astrophysicists to enter their virtual labs themselves, in virtual form as avatars. This has several advantages, from new possibilities to explore the results of the simulations to a shared presence in a virtual lab with remote collaborators on different continents. I will report my experiences with the use of Qwaq Forums, a virtual world developed by a new company (see http://www.qwaq.com).

A survey of middleware for sensor and network virtualization.

PubMed

Khalid, Zubair; Fisal, Norsheila; Rozaini, Mohd

2014-12-12

Wireless Sensor Network (WSN) is leading to a new paradigm of Internet of Everything (IoE). WSNs have a wide range of applications but are usually deployed in a particular application. However, the future of WSNs lies in the aggregation and allocation of resources, serving diverse applications. WSN virtualization by the middleware is an emerging concept that enables aggregation of multiple independent heterogeneous devices, networks, radios and software platforms; and enhancing application development. WSN virtualization, middleware can further be categorized into sensor virtualization and network virtualization. Middleware for WSN virtualization poses several challenges like efficient decoupling of networks, devices and software. In this paper efforts have been put forward to bring an overview of the previous and current middleware designs for WSN virtualization, the design goals, software architectures, abstracted services, testbeds and programming techniques. Furthermore, the paper also presents the proposed model, challenges and future opportunities for further research in the middleware designs for WSN virtualization.

Virtual environments simulation in research reactor

NASA Astrophysics Data System (ADS)

Muhamad, Shalina Bt. Sheik; Bahrin, Muhammad Hannan Bin

2017-01-01

Virtual reality based simulations are interactive and engaging. It has the useful potential in improving safety training. Virtual reality technology can be used to train workers who are unfamiliar with the physical layout of an area. In this study, a simulation program based on the virtual environment at research reactor was developed. The platform used for virtual simulation is 3DVia software for which it's rendering capabilities, physics for movement and collision and interactive navigation features have been taken advantage of. A real research reactor was virtually modelled and simulated with the model of avatars adopted to simulate walking. Collision detection algorithms were developed for various parts of the 3D building and avatars to restrain the avatars to certain regions of the virtual environment. A user can control the avatar to move around inside the virtual environment. Thus, this work can assist in the training of personnel, as in evaluating the radiological safety of the research reactor facility.

Virtual Screening with AutoDock: Theory and Practice

PubMed Central

Cosconati, Sandro; Forli, Stefano; Perryman, Alex L.; Harris, Rodney; Goodsell, David S.; Olson, Arthur J.

2011-01-01

Importance to the field Virtual screening is a computer-based technique for identifying promising compounds to bind to a target molecule of known structure. Given the rapidly increasing number of protein and nucleic acid structures, virtual screening continues to grow as an effective method for the discovery of new inhibitors and drug molecules. Areas covered in this review We describe virtual screening methods that are available in the AutoDock suite of programs, and several of our successes in using AutoDock virtual screening in pharmaceutical lead discovery. What the reader will gain A general overview of the challenges of virtual screening is presented, along with the tools available in the AutoDock suite of programs for addressing these challenges. Take home message Virtual screening is an effective tool for the discovery of compounds for use as leads in drug discovery, and the free, open source program AutoDock is an effective tool for virtual screening. PMID:21532931

Approaching Authentic Assessment: Using Virtual School Teachers' Expertise to Develop an Understanding of Full Time K-8 Virtual School Teacher Practices

ERIC Educational Resources Information Center

Seamster, Christina Lambert

2016-01-01

According to Molnar (2014), full time virtual school education lacks a measurement tool that accurately measures effective virtual teacher practice. Using both qualitative and quantitative methods, the current study sought to understand the common practices among full time K-8 virtual school teachers, the extent to which teachers believed such…

Will Anything Useful Come Out of Virtual Reality? Examination of a Naval Application

DTIC Science & Technology

1993-05-01

The term virtual reality can encompass varying meanings, but some generally accepted attributes of a virtual environment are that it is immersive...technology, but at present there are few practical applications which are utilizing the broad range of virtual reality technology. This paper will discuss an...Operability, operator functions, Virtual reality , Man-machine interface, Decision aids/decision making, Decision support. ASW.

Therapists' perception of benefits and costs of using virtual reality treatments.

PubMed

Segal, Robert; Bhatia, Maneet; Drapeau, Martin

2011-01-01

Research indicates that virtual reality is effective in the treatment of many psychological difficulties and is being used more frequently. However, little is known about therapists' perception of the benefits and costs related to the use of virtual therapy in treatment delivery. In the present study, 271 therapists completed an online questionnaire that assessed their perceptions about the potential benefits and costs of using virtual reality in psychotherapy. Results indicated that therapists perceived the potential benefits as outweighing the potential costs. Therapists' self-reported knowledge of virtual reality, theoretical orientation, and interest in using virtual reality were found to be associated with perceptual measures. These findings contribute to the current knowledge of the perception of virtual reality amongst psychotherapists.

The NASA Goddard Space Flight Center Virtual Science Fair

NASA Technical Reports Server (NTRS)

Bolognese, Jeff; Walden, Harvey; Obenschain, Arthur F. (Technical Monitor)

2002-01-01

This report describes the development of the NASA Goddard Space Flight Center Virtual Science Fair, including its history and outgrowth from the traditional regional science fairs supported by NASA. The results of the 1999 Virtual Science Fair pilot program, the mechanics of running the 2000 Virtual Science Fair and its results, and comments and suggestions for future Virtual Science Fairs are provided. The appendices to the report include the original proposal for this project, the judging criteria, the user's guide and the judge's guide to the Virtual Science Fair Web site, the Fair publicity brochure and the Fair award designs, judges' and students' responses to survey questions about the Virtual Science Fair, and lists of student entries to both the 1999 and 2000 Fairs.

G2H--graphics-to-haptic virtual environment development tool for PC's.

PubMed

Acosta, E; Temkin, B; Krummel, T M; Heinrichs, W L

2000-01-01

For surgical training and preparations, the existing surgical virtual environments have shown great improvement. However, these improvements are more in the visual aspect. The incorporation of haptics into virtual reality base surgical simulations would enhance the sense of realism greatly. To aid in the development of the haptic surgical virtual environment we have created a graphics to haptic, G2H, virtual environment developer tool. G2H transforms graphical virtual environments (created or imported) to haptic virtual environments without programming. The G2H capability has been demonstrated using the complex 3D pelvic model of Lucy 2.0, the Stanford Visible Female. The pelvis was made haptic using G2H without any further programming effort.

Virtual Reality: An Overview.

ERIC Educational Resources Information Center

Franchi, Jorge

1994-01-01

Highlights of this overview of virtual reality include optics; interface devices; virtual worlds; potential applications, including medicine and archaeology; problems, including costs; current research and development; future possibilities; and a listing of vendors and suppliers of virtual reality products. (Contains 11 references.) (LRW)

75 FR 33760 - Information Collection; Virtual Incident Procurement (VIPR) System Existing Vendor Survey

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-15

... DEPARTMENT OF AGRICULTURE Forest Service Information Collection; Virtual Incident Procurement... from all interested individuals and organizations on the new information collection, Virtual Incident....t., Monday through Friday. SUPPLEMENTARY INFORMATION: Title: Virtual Incident Procurement (VIPR...

Virtual Reality and Its Potential Application in Education and Training.

ERIC Educational Resources Information Center

Milheim, William D.

1995-01-01

An overview is provided of current trends in virtual reality research and development, including discussion of hardware, types of virtual reality, and potential problems with virtual reality. Implications for education and training are explored. (Author/JKP)

Interreality: A New Paradigm for E-health.

PubMed

Riva, Giuseppe

2009-01-01

"Interreality" is a personalized immersive e-therapy whose main novelty is a hybrid, closed-loop empowering experience bridging physical and virtual worlds. The main feature of interreality is a twofold link between the virtual and the real world: (a) behavior in the physical world influences the experience in the virtual one; (b) behavior in the virtual world influences the experience in the real one. This is achieved through: (1) 3D Shared Virtual Worlds: role-playing experiences in which one or more users interact with one another within a 3D world; (2) Bio and Activity Sensors (From the Real to the Virtual World): They are used to track the emotional/health/activity status of the user and to influence his/her experience in the virtual world (aspect, activity and access); (3) Mobile Internet Appliances (From the Virtual to the Real One): In interreality, the social and individual user activity in the virtual world has a direct link with the users' life through a mobile phone/digital assistant. The different technologies that are involved in the interreality vision and its clinical rationale are addressed and discussed.

Virtual collaboration in the online educational setting: a concept analysis.

PubMed

Breen, Henny

2013-01-01

This study was designed to explore the concept of virtual collaboration within the context of an online learning environment in an academic setting. Rodgers' method of evolutionary concept analysis was used to provide a contextual view of the concept to identify attributes, antecedents, and consequences of virtual collaboration. Commonly used terms to describe virtual collaboration are collaborative and cooperative learning, group work, group interaction, group learning, and teamwork. A constructivist pedagogy, group-based process with a shared purpose, support, and web-based technology is required for virtual collaboration to take place. Consequences of virtual collaboration are higher order thinking and learning to work with others. A comprehensive definition of virtual collaboration is offered as an outcome of this analysis. Clarification of virtual collaboration prior to using it as a pedagogical tool in the online learning environment will enhance nursing education with the changes in nursing curriculum being implemented today. Further research is recommended to describe the developmental stages of the collaborative process among nursing students in online education and how virtual collaboration facilitates collaboration in practice. © 2013 Wiley Periodicals, Inc.

Formalizing and Promoting Collaboration in 3D Virtual Environments - A Blueprint for the Creation of Group Interaction Patterns

NASA Astrophysics Data System (ADS)

Schmeil, Andreas; Eppler, Martin J.

Despite the fact that virtual worlds and other types of multi-user 3D collaboration spaces have long been subjects of research and of application experiences, it still remains unclear how to best benefit from meeting with colleagues and peers in a virtual environment with the aim of working together. Making use of the potential of virtual embodiment, i.e. being immersed in a space as a personal avatar, allows for innovative new forms of collaboration. In this paper, we present a framework that serves as a systematic formalization of collaboration elements in virtual environments. The framework is based on the semiotic distinctions among pragmatic, semantic and syntactic perspectives. It serves as a blueprint to guide users in designing, implementing, and executing virtual collaboration patterns tailored to their needs. We present two team and two community collaboration pattern examples as a result of the application of the framework: Virtual Meeting, Virtual Design Studio, Spatial Group Configuration, and Virtual Knowledge Fair. In conclusion, we also point out future research directions for this emerging domain.

Virtual endoscopic imaging of the spine.

PubMed

Kotani, Toshiaki; Nagaya, Shigeyuki; Sonoda, Masaru; Akazawa, Tsutomu; Lumawig, Jose Miguel T; Nemoto, Tetsuharu; Koshi, Takana; Kamiya, Koshiro; Hirosawa, Naoya; Minami, Shohei

2012-05-20

Prospective trial of virtual endoscopy in spinal surgery. To investigate the utility of virtual endoscopy of the spine in conjunction with spinal surgery. Several studies have described clinical applications of virtual endoscopy to visualize the inside of the bronchi, paranasal sinus, stomach, small intestine, pancreatic duct, and bile duct, but, to date, no study has described the use of virtual endoscopy in the spine. Virtual endoscopy is a realistic 3-dimensional intraluminal simulation of tubular structures that is generated by postprocessing of computed tomographic data sets. Five patients with spinal disease were selected: 2 patients with degenerative disease, 2 patients with spinal deformity, and 1 patient with spinal injury. Virtual endoscopy software allows an observer to explore the spinal canal with a mouse, using multislice computed tomographic data. Our study found that virtual endoscopy of the spine has advantages compared with standard imaging methods because surgeons can noninvasively explore the spinal canal in all directions. Virtual endoscopy of the spine may be useful to surgeons for diagnosis, preoperative planning, and postoperative assessment by obviating the need to mentally construct a 3-dimensional picture of the spinal canal from 2-dimensional computed tomographic scans.

Coercive Narratives, Motivation and Role Playing in Virtual Worlds

DTIC Science & Technology

2002-01-01

resource for making immersive virtual environments highly engaging. Interaction also appeals to our natural desire to discover. Reading a book contains...participation in an open-ended Virtual Environment (VE). I intend to take advantage of a participants’ natural tendency to prefer interaction when possible...I hope this work will expand the potential of experience within virtual worlds. K e y w o r d s : Immersive Environments , Virtual Environments

Proof-of-Concept Part Task Trainer for Close Air Support Procedures

DTIC Science & Technology

2016-06-01

TVDL Tactical Video Down Link VE Virtual Environment VR Virtual Reality WTI Weapons and Tactics Instructor xvii ACKNOWLEDGMENTS I would first...in training of USMC pilots for close air support operations? • What is the feasibility of developing a prototype virtual reality (VR) system that...Chapter IV provides a review of virtual reality (VR)/ virtual environment (VE) and part-task trainers currently used in military training

A Virtual Reality-Based Simulation of Abdominal Surgery

DTIC Science & Technology

1994-06-30

415) 591-7881 In! IhNiI 1 SHORT TITLE: A Virtual Reality -Based Simulation of Abdominal Surgery REPORTING PERIOD: October 31, 1993-June 30, 1994 The...Report - A Virtual Reality -Based Simulation Of Abdominal Surgery Page 2 June 21, 1994 TECHNICAL REPORT SUMMARY Virtual Reality is a marriage between...applications of this technology. Virtual reality systems can be used to teach surgical anatomy, diagnose surgical problems, plan operations. simulate and

Mixed virtual reality simulation--taking endoscopic simulation one step further.

PubMed

Courteille, O; Felländer-Tsai, L; Hedman, L; Kjellin, A; Enochsson, L; Lindgren, G; Fors, U

2011-01-01

This pilot study aimed to assess medical students' appraisals of a "mixed" virtual reality simulation for endoscopic surgery (with a virtual patient case in addition to a virtual colonoscopy) as well as the impact of this simulation set-up on students' performance. Findings indicate that virtual patients can enhance contextualization of simulated endoscopy and thus facilitate an authentic learning environment, which is important in order to increase motivation.

Simplified Virtualization in a HEP/NP Environment with Condor

NASA Astrophysics Data System (ADS)

Strecker-Kellogg, W.; Caramarcu, C.; Hollowell, C.; Wong, T.

2012-12-01

In this work we will address the development of a simple prototype virtualized worker node cluster, using Scientific Linux 6.x as a base OS, KVM and the libvirt API for virtualization, and the Condor batch software to manage virtual machines. The discussion in this paper provides details on our experience with building, configuring, and deploying the various components from bare metal, including the base OS, creation and distribution of the virtualized OS images and the integration of batch services with the virtual machines. Our focus was on simplicity and interoperability with our existing architecture.

Virtual facebow technique.

PubMed

Solaberrieta, Eneko; Garmendia, Asier; Minguez, Rikardo; Brizuela, Aritza; Pradies, Guillermo

2015-12-01

This article describes a virtual technique for transferring the location of a digitized cast from the patient to a virtual articulator (virtual facebow transfer). Using a virtual procedure, the maxillary digital cast is transferred to a virtual articulator by means of reverse engineering devices. The following devices necessary to carry out this protocol are available in many contemporary practices: an intraoral scanner, a digital camera, and specific software. Results prove the viability of integrating different tools and software and of completely integrating this procedure into a dental digital workflow. Copyright © 2015 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.

Perception of Virtual Audiences.

PubMed

Chollet, Mathieu; Scherer, Stefan

2017-01-01

A growing body of evidence shows that virtual audiences are a valuable tool in the treatment of social anxiety, and recent works show that it also a useful in public-speaking training programs. However, little research has focused on how such audiences are perceived and on how the behavior of virtual audiences can be manipulated to create various types of stimuli. The authors used a crowdsourcing methodology to create a virtual audience nonverbal behavior model and, with it, created a dataset of videos with virtual audiences containing varying behaviors. Using this dataset, they investigated how virtual audiences are perceived and which factors affect this perception.

Virtualization and cloud computing in dentistry.

PubMed

Chow, Frank; Muftu, Ali; Shorter, Richard

2014-01-01

The use of virtualization and cloud computing has changed the way we use computers. Virtualization is a method of placing software called a hypervisor on the hardware of a computer or a host operating system. It allows a guest operating system to run on top of the physical computer with a virtual machine (i.e., virtual computer). Virtualization allows multiple virtual computers to run on top of one physical computer and to share its hardware resources, such as printers, scanners, and modems. This increases the efficient use of the computer by decreasing costs (e.g., hardware, electricity administration, and management) since only one physical computer is needed and running. This virtualization platform is the basis for cloud computing. It has expanded into areas of server and storage virtualization. One of the commonly used dental storage systems is cloud storage. Patient information is encrypted as required by the Health Insurance Portability and Accountability Act (HIPAA) and stored on off-site private cloud services for a monthly service fee. As computer costs continue to increase, so too will the need for more storage and processing power. Virtual and cloud computing will be a method for dentists to minimize costs and maximize computer efficiency in the near future. This article will provide some useful information on current uses of cloud computing.

Middle school students' learning of mechanics concepts through engagement in different sequences of physical and virtual experiments

NASA Astrophysics Data System (ADS)

Sullivan, Sarah; Gnesdilow, Dana; Puntambekar, Sadhana; Kim, Jee-Seon

2017-08-01

Physical and virtual experimentation are thought to have different affordances for supporting students' learning. Research investigating the use of physical and virtual experiments to support students' learning has identified a variety of, sometimes conflicting, outcomes. Unanswered questions remain about how physical and virtual experiments may impact students' learning and for which contexts and content areas they may be most effective. Using a quasi-experimental design, we examined eighth grade students' (N = 100) learning of physics concepts related to pulleys depending on the sequence of physical and virtual labs they engaged in. Five classes of students were assigned to either the: physical first condition (PF) (n = 55), where students performed a physical pulley experiment and then performed the same experiment virtually, or virtual first condition (VF) (n = 45), with the opposite sequence. Repeated measures ANOVA's were conducted to examine how physical and virtual labs impacted students' learning of specific physics concepts. While we did not find clear-cut support that one sequence was better, we did find evidence that participating in virtual experiments may be more beneficial for learning certain physics concepts, such as work and mechanical advantage. Our findings support the idea that if time or physical materials are limited, using virtual experiments may help students understand work and mechanical advantage.

Factors to keep in mind when introducing virtual microscopy.

PubMed

Glatz-Krieger, Katharina; Spornitz, Udo; Spatz, Alain; Mihatsch, Michael J; Glatz, Dieter

2006-03-01

Digitization of glass slides and delivery of so-called virtual slides (VS) emulating a real microscope over the Internet have become reality due to recent improvements in technology. We have implemented a virtual microscope for instruction of medical students and for continuing medical education. Up to 30,000 images per slide are captured using a microscope with an automated stage. The images are post-processed and then served by a plain hypertext transfer protocol (http)-server. A virtual slide client (vMic) based on Macromedia's Flash MX, a highly accepted technology available on every modern Web browser, has been developed. All necessary virtual slide parameters are stored in an XML file together with the image. Evaluation of the courses by questionnaire indicated that most students and many but not all pathologists regard virtual slides as an adequate replacement for traditional slides. All our virtual slides are publicly accessible over the World Wide Web (WWW) at http://vmic.unibas.ch . Recently, several commercially available virtual slide acquisition systems (VSAS) have been developed that use various technologies to acquire and distribute virtual slides. These systems differ in speed, image quality, compatibility, viewer functionalities and price. This paper gives an overview of the factors to keep in mind when introducing virtual microscopy.

Motor learning from virtual reality to natural environments in individuals with Duchenne muscular dystrophy.

PubMed

Quadrado, Virgínia Helena; Silva, Talita Dias da; Favero, Francis Meire; Tonks, James; Massetti, Thais; Monteiro, Carlos Bandeira de Mello

2017-11-10

To examine whether performance improvements in the virtual environment generalize to the natural environment. we had 64 individuals, 32 of which were individuals with DMD and 32 were typically developing individuals. The groups practiced two coincidence timing tasks. In the more tangible button-press task, the individuals were required to 'intercept' a falling virtual object at the moment it reached the interception point by pressing a key on the computer. In the more abstract task, they were instructed to 'intercept' the virtual object by making a hand movement in a virtual environment using a webcam. For individuals with DMD, conducting a coincidence timing task in a virtual environment facilitated transfer to the real environment. However, we emphasize that a task practiced in a virtual environment should have higher rates of difficulties than a task practiced in a real environment. IMPLICATIONS FOR REHABILITATION Virtual environments can be used to promote improved performance in ?real-world? environments. Virtual environments offer the opportunity to create paradigms similar ?real-life? tasks, however task complexity and difficulty levels can be manipulated, graded and enhanced to increase likelihood of success in transfer of learning and performance. Individuals with DMD, in particular, showed immediate performance benefits after using virtual reality.

Distributed virtual environment for emergency medical training

NASA Astrophysics Data System (ADS)

Stytz, Martin R.; Banks, Sheila B.; Garcia, Brian W.; Godsell-Stytz, Gayl M.

1997-07-01

In many professions where individuals must work in a team in a high stress environment to accomplish a time-critical task, individual and team performance can benefit from joint training using distributed virtual environments (DVEs). One professional field that lacks but needs a high-fidelity team training environment is the field of emergency medicine. Currently, emergency department (ED) medical personnel train by using words to create a metal picture of a situation for the physician and staff, who then cooperate to solve the problems portrayed by the word picture. The need in emergency medicine for realistic virtual team training is critical because ED staff typically encounter rarely occurring but life threatening situations only once in their careers and because ED teams currently have no realistic environment in which to practice their team skills. The resulting lack of experience and teamwork makes diagnosis and treatment more difficult. Virtual environment based training has the potential to redress these shortfalls. The objective of our research is to develop a state-of-the-art virtual environment for emergency medicine team training. The virtual emergency room (VER) allows ED physicians and medical staff to realistically prepare for emergency medical situations by performing triage, diagnosis, and treatment on virtual patients within an environment that provides them with the tools they require and the team environment they need to realistically perform these three tasks. There are several issues that must be addressed before this vision is realized. The key issues deal with distribution of computations; the doctor and staff interface to the virtual patient and ED equipment; the accurate simulation of individual patient organs' response to injury, medication, and treatment; and an accurate modeling of the symptoms and appearance of the patient while maintaining a real-time interaction capability. Our ongoing work addresses all of these issues. In this paper we report on our prototype VER system and its distributed system architecture for an emergency department distributed virtual environment for emergency medical staff training. The virtual environment enables emergency department physicians and staff to develop their diagnostic and treatment skills using the virtual tools they need to perform diagnostic and treatment tasks. Virtual human imagery, and real-time virtual human response are used to create the virtual patient and present a scenario. Patient vital signs are available to the emergency department team as they manage the virtual case. The work reported here consists of the system architectures we developed for the distributed components of the virtual emergency room. The architectures we describe consist of the network level architecture as well as the software architecture for each actor within the virtual emergency room. We describe the role of distributed interactive simulation and other enabling technologies within the virtual emergency room project.

Virtualization for the LHCb Online system

NASA Astrophysics Data System (ADS)

Bonaccorsi, Enrico; Brarda, Loic; Moine, Gary; Neufeld, Niko

2011-12-01

Virtualization has long been advertised by the IT-industry as a way to cut down cost, optimise resource usage and manage the complexity in large data-centers. The great number and the huge heterogeneity of hardware, both industrial and custom-made, has up to now led to reluctance in the adoption of virtualization in the IT infrastructure of large experiment installations. Our experience in the LHCb experiment has shown that virtualization improves the availability and the manageability of the whole system. We have done an evaluation of available hypervisors / virtualization solutions and find that the Microsoft HV technology provides a high level of maturity and flexibility for our purpose. We present the results of these comparison tests, describing in detail, the architecture of our virtualization infrastructure with a special emphasis on the security for services visible to the outside world. Security is achieved by a sophisticated combination of VLANs, firewalls and virtual routing - the cost and benefits of this solution are analysed. We have adapted our cluster management tools, notably Quattor, for the needs of virtual machines and this allows us to migrate smoothly services on physical machines to the virtualized infrastructure. The procedures for migration will also be described. In the final part of the document we describe our recent R&D activities aiming to replacing the SAN-backend for the virtualization by a cheaper iSCSI solution - this will allow to move all servers and related services to the virtualized infrastructure, excepting the ones doing hardware control via non-commodity PCI plugin cards.

Virtual Labs and Virtual Worlds

NASA Astrophysics Data System (ADS)

Boehler, Ted

2006-12-01

Virtual Labs and Virtual Worlds Coastline Community College has under development several virtual lab simulations and activities that range from biology, to language labs, to virtual discussion environments. Imagine a virtual world that students enter online, by logging onto their computer from home or anywhere they have web access. Upon entering this world they select a personalized identity represented by a digitized character (avatar) that can freely move about, interact with the environment, and communicate with other characters. In these virtual worlds, buildings, gathering places, conference rooms, labs, science rooms, and a variety of other “real world” elements are evident. When characters move about and encounter other people (players) they may freely communicate. They can examine things, manipulate objects, read signs, watch video clips, hear sounds, and jump to other locations. Goals of critical thinking, social interaction, peer collaboration, group support, and enhanced learning can be achieved in surprising new ways with this innovative approach to peer-to-peer communication in a virtual discussion world. In this presentation, short demos will be given of several online learning environments including a virtual biology lab, a marine science module, a Spanish lab, and a virtual discussion world. Coastline College has been a leader in the development of distance learning and media-based education for nearly 30 years and currently offers courses through PDA, Internet, DVD, CD-ROM, TV, and Videoconferencing technologies. Its distance learning program serves over 20,000 students every year. sponsor Jerry Meisner

An Audio Architecture Integrating Sound and Live Voice for Virtual Environments

DTIC Science & Technology

2002-09-01

implementation of a virtual environment. As real world training locations become scarce and training budgets are trimmed, training system developers ...look more and more towards virtual environments as the answer. Virtual environments provide training system developers with several key benefits

Building Virtuality into University-Based Human Resources Policy in China's Universities

ERIC Educational Resources Information Center

Guoliang, Zhang

2005-01-01

On the basis of discussing the notion of virtual human resources and its structure, this paper analyzes the necessity of building up virtual university teaching staff and proposes a model for the structural makeup of virtual university teaching staff.

Optimizing Virtual Network Functions Placement in Virtual Data Center Infrastructure Using Machine Learning

NASA Astrophysics Data System (ADS)

Bolodurina, I. P.; Parfenov, D. I.

2018-01-01

We have elaborated a neural network model of virtual network flow identification based on the statistical properties of flows circulating in the network of the data center and characteristics that describe the content of packets transmitted through network objects. This enabled us to establish the optimal set of attributes to identify virtual network functions. We have established an algorithm for optimizing the placement of virtual data functions using the data obtained in our research. Our approach uses a hybrid method of visualization using virtual machines and containers, which enables to reduce the infrastructure load and the response time in the network of the virtual data center. The algorithmic solution is based on neural networks, which enables to scale it at any number of the network function copies.

The NASA Goddard Space Flight Center Virtual Science Fair

NASA Technical Reports Server (NTRS)

Bolognese, Jeff; Walden, Harvey; Obenschain, Arthur F. (Technical Monitor)

2001-01-01

This report describes the development of the NASA Goddard Space Flight Center Virtual Science Fair, including its history and outgrowth from the traditional regional science fairs supported by NASA. The results of the 1999 Virtual Science Fair pilot program, the mechanics of running the 2000 Virtual Science Fair and its results, and comments and suggestions for future Virtual Science Fairs are provided. The appendices to the report contain supporting documentation, including the original proposal for this project, the judging criteria, the user's guide and the judge's guide to the Virtual Science Fair Web site, the Fair publicity brochure and the Fair award designs, judges' and students' responses to survey questions about the Virtual Science Fair, and lists of student entries to both the 1999 and 2000 Fairs.

Dynamic Extension of a Virtualized Cluster by using Cloud Resources

NASA Astrophysics Data System (ADS)

Oberst, Oliver; Hauth, Thomas; Kernert, David; Riedel, Stephan; Quast, Günter

2012-12-01

The specific requirements concerning the software environment within the HEP community constrain the choice of resource providers for the outsourcing of computing infrastructure. The use of virtualization in HPC clusters and in the context of cloud resources is therefore a subject of recent developments in scientific computing. The dynamic virtualization of worker nodes in common batch systems provided by ViBatch serves each user with a dynamically virtualized subset of worker nodes on a local cluster. Now it can be transparently extended by the use of common open source cloud interfaces like OpenNebula or Eucalyptus, launching a subset of the virtual worker nodes within the cloud. This paper demonstrates how a dynamically virtualized computing cluster is combined with cloud resources by attaching remotely started virtual worker nodes to the local batch system.

[Distribution of virtual water of crops in Beijing].

PubMed

Wang, Hong-Rui; Dong, Yan-Yan; Wang, Jun-Hong; Wang, Yan; Han, Zhao-Xing

2007-11-01

Virtual water content of grains and vegetables in Beijing's districts is calculated and analyzed for many years by irrigating water quota method, which is compared with the distribution and exploitation of groundwater in Beijing. The results indicate the virtual water content of grains shows a downward trend in all the districts, but the grain production in Yanqing district brings great pressure to the local groundwater. Secondly, the virtual water content of vegetables shows an upward trend in Shunyi District, Daxing district and Pinggu District and is accounting for more and more gradually. Thirdly, the total virtual water volume of grains is decreasing, and the total virtual water volume of vegetables is increasing and the total virtual water volume of crops in Beijing is reducing in recent years, which corresponds with the structural adjustment of policies.

Novel interactive virtual showcase based on 3D multitouch technology

NASA Astrophysics Data System (ADS)

Yang, Tao; Liu, Yue; Lu, You; Wang, Yongtian

2009-11-01

A new interactive virtual showcase is proposed in this paper. With the help of virtual reality technology, the user of the proposed system can watch the virtual objects floating in the air from all four sides and interact with the virtual objects by touching the four surfaces of the virtual showcase. Unlike traditional multitouch system, this system cannot only realize multi-touch on a plane to implement 2D translation, 2D scaling, and 2D rotation of the objects; it can also realize the 3D interaction of the virtual objects by recognizing and analyzing the multi-touch that can be simultaneously captured from the four planes. Experimental results show the potential of the proposed system to be applied in the exhibition of historical relics and other precious goods.

Controlling social stress in virtual reality environments.

PubMed

Hartanto, Dwi; Kampmann, Isabel L; Morina, Nexhmedin; Emmelkamp, Paul G M; Neerincx, Mark A; Brinkman, Willem-Paul

2014-01-01

Virtual reality exposure therapy has been proposed as a viable alternative in the treatment of anxiety disorders, including social anxiety disorder. Therapists could benefit from extensive control of anxiety eliciting stimuli during virtual exposure. Two stimuli controls are studied in this study: the social dialogue situation, and the dialogue feedback responses (negative or positive) between a human and a virtual character. In the first study, 16 participants were exposed in three virtual reality scenarios: a neutral virtual world, blind date scenario, and job interview scenario. Results showed a significant difference between the three virtual scenarios in the level of self-reported anxiety and heart rate. In the second study, 24 participants were exposed to a job interview scenario in a virtual environment where the ratio between negative and positive dialogue feedback responses of a virtual character was systematically varied on-the-fly. Results yielded that within a dialogue the more positive dialogue feedback resulted in less self-reported anxiety, lower heart rate, and longer answers, while more negative dialogue feedback of the virtual character resulted in the opposite. The correlations between on the one hand the dialogue stressor ratio and on the other hand the means of SUD score, heart rate and audio length in the eight dialogue conditions showed a strong relationship: r(6) = 0.91, p = 0.002; r(6) = 0.76, p = 0.028 and r(6) = -0.94, p = 0.001 respectively. Furthermore, more anticipatory anxiety reported before exposure was found to coincide with more self-reported anxiety, and shorter answers during the virtual exposure. These results demonstrate that social dialogues in a virtual environment can be effectively manipulated for therapeutic purposes.

Virtual bystanders in a language lesson: examining the effect of social evaluation, vicarious experience, cognitive consistency and praising on students' beliefs, self-efficacy and anxiety in a virtual reality environment.

PubMed

Qu, Chao; Ling, Yun; Heynderickx, Ingrid; Brinkman, Willem-Paul

2015-01-01

Bystanders in a real world's social setting have the ability to influence people's beliefs and behavior. This study examines whether this effect can be recreated in a virtual environment, by exposing people to virtual bystanders in a classroom setting. Participants (n = 26) first witnessed virtual students answering questions from an English teacher, after which they were also asked to answer questions from the teacher as part of a simulated training for spoken English. During the experiment the attitudes of the other virtual students in the classroom was manipulated; they could whisper either positive or negative remarks to each other when a virtual student was talking or when a participant was talking. The results show that the expressed attitude of virtual bystanders towards the participants affected their self-efficacy, and their avoidance behavior. Furthermore, the experience of witnessing bystanders commenting negatively on the performance of other students raised the participants' heart rate when it was their turn to speak. Two-way interaction effects were also found on self-reported anxiety and self-efficacy. After witnessing bystanders' positive attitude towards peer students, participants' self-efficacy when answering questions received a boost when bystanders were also positive towards them, and a blow when bystanders reversed their attitude by being negative towards them. Still, inconsistency, instead of consistency, between the bystanders' attitudes towards virtual peers and the participants was not found to result in a larger change in the participants' beliefs. Finally the results also reveal that virtual flattering or destructive criticizing affected the participants' beliefs not only about the virtual bystanders, but also about the neutral teacher. Together these findings show that virtual bystanders in a classroom can affect people's beliefs, anxiety and behavior.

Controlling Social Stress in Virtual Reality Environments

PubMed Central

Hartanto, Dwi; Kampmann, Isabel L.; Morina, Nexhmedin; Emmelkamp, Paul G. M.; Neerincx, Mark A.; Brinkman, Willem-Paul

2014-01-01

Virtual reality exposure therapy has been proposed as a viable alternative in the treatment of anxiety disorders, including social anxiety disorder. Therapists could benefit from extensive control of anxiety eliciting stimuli during virtual exposure. Two stimuli controls are studied in this study: the social dialogue situation, and the dialogue feedback responses (negative or positive) between a human and a virtual character. In the first study, 16 participants were exposed in three virtual reality scenarios: a neutral virtual world, blind date scenario, and job interview scenario. Results showed a significant difference between the three virtual scenarios in the level of self-reported anxiety and heart rate. In the second study, 24 participants were exposed to a job interview scenario in a virtual environment where the ratio between negative and positive dialogue feedback responses of a virtual character was systematically varied on-the-fly. Results yielded that within a dialogue the more positive dialogue feedback resulted in less self-reported anxiety, lower heart rate, and longer answers, while more negative dialogue feedback of the virtual character resulted in the opposite. The correlations between on the one hand the dialogue stressor ratio and on the other hand the means of SUD score, heart rate and audio length in the eight dialogue conditions showed a strong relationship: r(6) = 0.91, p = 0.002; r(6) = 0.76, p = 0.028 and r(6) = −0.94, p = 0.001 respectively. Furthermore, more anticipatory anxiety reported before exposure was found to coincide with more self-reported anxiety, and shorter answers during the virtual exposure. These results demonstrate that social dialogues in a virtual environment can be effectively manipulated for therapeutic purposes. PMID:24671006

Virtual microscopy: an evaluation of its validity and diagnostic performance in routine histologic diagnosis of skin tumors.

PubMed

Nielsen, Patricia Switten; Lindebjerg, Jan; Rasmussen, Jan; Starklint, Henrik; Waldstrøm, Marianne; Nielsen, Bjarne

2010-12-01

Digitization of histologic slides is associated with many advantages, and its use in routine diagnosis holds great promise. Nevertheless, few articles evaluate virtual microscopy in routine settings. This study is an evaluation of the validity and diagnostic performance of virtual microscopy in routine histologic diagnosis of skin tumors. Our aim is to investigate whether conventional microscopy of skin tumors can be replaced by virtual microscopy. Ninety-six skin tumors and skin-tumor-like changes were consecutively gathered over a 1-week period. Specimens were routinely processed, and digital slides were captured on Mirax Scan (Carl Zeiss MicroImaging, Göttingen, Germany). Four pathologists evaluated the 96 virtual slides and the associated 96 conventional slides twice with intermediate time intervals of at least 3 weeks. Virtual slides that caused difficulties were reevaluated to identify possible reasons for this. The accuracy was 89.2% for virtual microscopy and 92.7% for conventional microscopy. All κ coefficients expressed very good intra- and interobserver agreement. The sensitivities were 85.7% (78.0%-91.0%) and 92.0% (85.5%-95.7%) for virtual and conventional microscopy, respectively. The difference between the sensitivities was 6.3% (0.8%-12.6%). The subsequent reevaluation showed that virtual slides were as useful as conventional slides when rendering a diagnosis. Differences seen are presumed to be due to the pathologists' lack of experience using the virtual microscope. We conclude that it is feasible to make histologic diagnosis on the skin tumor types represented in this study using virtual microscopy after pathologists have completed a period of training. Larger studies should be conducted to verify whether virtual microscopy can replace conventional microscopy in routine practice. Copyright © 2010 Elsevier Inc. All rights reserved.

Virtual Reality Exploration and Planning for Precision Colorectal Surgery.

PubMed

Guerriero, Ludovica; Quero, Giuseppe; Diana, Michele; Soler, Luc; Agnus, Vincent; Marescaux, Jacques; Corcione, Francesco

2018-06-01

Medical software can build a digital clone of the patient with 3-dimensional reconstruction of Digital Imaging and Communication in Medicine images. The virtual clone can be manipulated (rotations, zooms, etc), and the various organs can be selectively displayed or hidden to facilitate a virtual reality preoperative surgical exploration and planning. We present preliminary cases showing the potential interest of virtual reality in colorectal surgery for both cases of diverticular disease and colonic neoplasms. This was a single-center feasibility study. The study was conducted at a tertiary care institution. Two patients underwent a laparoscopic left hemicolectomy for diverticular disease, and 1 patient underwent a laparoscopic right hemicolectomy for cancer. The 3-dimensional virtual models were obtained from preoperative CT scans. The virtual model was used to perform preoperative exploration and planning. Intraoperatively, one of the surgeons was manipulating the virtual reality model, using the touch screen of a tablet, which was interactively displayed to the surgical team. The main outcome was evaluation of the precision of virtual reality in colorectal surgery planning and exploration. In 1 patient undergoing laparoscopic left hemicolectomy, an abnormal origin of the left colic artery beginning as an extremely short common trunk from the inferior mesenteric artery was clearly seen in the virtual reality model. This finding was missed by the radiologist on CT scan. The precise identification of this vascular variant granted a safe and adequate surgery. In the remaining cases, the virtual reality model helped to precisely estimate the vascular anatomy, providing key landmarks for a safer dissection. A larger sample size would be necessary to definitively assess the efficacy of virtual reality in colorectal surgery. Virtual reality can provide an enhanced understanding of crucial anatomical details, both preoperatively and intraoperatively, which could contribute to improve safety in colorectal surgery.

Recent history and geography of virtual water trade.

PubMed

Carr, Joel A; D'Odorico, Paolo; Laio, Francesco; Ridolfi, Luca

2013-01-01

The global trade of goods is associated with a virtual transfer of the water required for their production. The way changes in trade affect the virtual redistribution of freshwater resources has been recently documented through the analysis of the virtual water network. It is, however, unclear how these changes are contributed by different types of products and regions of the world. Here we show how the global patterns of virtual water transport are contributed by the trade of different commodity types, including plant, animal, luxury (e.g., coffee, tea, and alcohol), and other products. Major contributors to the virtual water network exhibit different trade patterns with regard to these commodity types. The net importers rely on the supply of virtual water from a small percentage of the global population. However, discrepancies exist among the different commodity networks. While the total virtual water flux through the network has increased between 1986 and 2010, the proportions associated with the four commodity groups have remained relatively stable. However, some of the major players have shown significant changes in the virtual water imports and exports associated with those commodity groups. For instance, China has switched from being a net exporter of virtual water associated with other products (non-edible plant and animal products typically used for manufacturing) to being the largest importer, accounting for 31% of the total water virtually transported with these products. Conversely, in the case of The United states of America, the commodity proportions have remained overall unchanged throughout the study period: the virtual water exports from The United States of America are dominated by plant products, whereas the imports are comprised mainly of animal and luxury products.

Software platform virtualization in chemistry research and university teaching

PubMed Central

2009-01-01

Background Modern chemistry laboratories operate with a wide range of software applications under different operating systems, such as Windows, LINUX or Mac OS X. Instead of installing software on different computers it is possible to install those applications on a single computer using Virtual Machine software. Software platform virtualization allows a single guest operating system to execute multiple other operating systems on the same computer. We apply and discuss the use of virtual machines in chemistry research and teaching laboratories. Results Virtual machines are commonly used for cheminformatics software development and testing. Benchmarking multiple chemistry software packages we have confirmed that the computational speed penalty for using virtual machines is low and around 5% to 10%. Software virtualization in a teaching environment allows faster deployment and easy use of commercial and open source software in hands-on computer teaching labs. Conclusion Software virtualization in chemistry, mass spectrometry and cheminformatics is needed for software testing and development of software for different operating systems. In order to obtain maximum performance the virtualization software should be multi-core enabled and allow the use of multiprocessor configurations in the virtual machine environment. Server consolidation, by running multiple tasks and operating systems on a single physical machine, can lead to lower maintenance and hardware costs especially in small research labs. The use of virtual machines can prevent software virus infections and security breaches when used as a sandbox system for internet access and software testing. Complex software setups can be created with virtual machines and are easily deployed later to multiple computers for hands-on teaching classes. We discuss the popularity of bioinformatics compared to cheminformatics as well as the missing cheminformatics education at universities worldwide. PMID:20150997

Software platform virtualization in chemistry research and university teaching.

PubMed

Kind, Tobias; Leamy, Tim; Leary, Julie A; Fiehn, Oliver

2009-11-16

Modern chemistry laboratories operate with a wide range of software applications under different operating systems, such as Windows, LINUX or Mac OS X. Instead of installing software on different computers it is possible to install those applications on a single computer using Virtual Machine software. Software platform virtualization allows a single guest operating system to execute multiple other operating systems on the same computer. We apply and discuss the use of virtual machines in chemistry research and teaching laboratories. Virtual machines are commonly used for cheminformatics software development and testing. Benchmarking multiple chemistry software packages we have confirmed that the computational speed penalty for using virtual machines is low and around 5% to 10%. Software virtualization in a teaching environment allows faster deployment and easy use of commercial and open source software in hands-on computer teaching labs. Software virtualization in chemistry, mass spectrometry and cheminformatics is needed for software testing and development of software for different operating systems. In order to obtain maximum performance the virtualization software should be multi-core enabled and allow the use of multiprocessor configurations in the virtual machine environment. Server consolidation, by running multiple tasks and operating systems on a single physical machine, can lead to lower maintenance and hardware costs especially in small research labs. The use of virtual machines can prevent software virus infections and security breaches when used as a sandbox system for internet access and software testing. Complex software setups can be created with virtual machines and are easily deployed later to multiple computers for hands-on teaching classes. We discuss the popularity of bioinformatics compared to cheminformatics as well as the missing cheminformatics education at universities worldwide.

Recent History and Geography of Virtual Water Trade

PubMed Central

Carr, Joel A.; D’Odorico, Paolo; Laio, Francesco; Ridolfi, Luca

2013-01-01

The global trade of goods is associated with a virtual transfer of the water required for their production. The way changes in trade affect the virtual redistribution of freshwater resources has been recently documented through the analysis of the virtual water network. It is, however, unclear how these changes are contributed by different types of products and regions of the world. Here we show how the global patterns of virtual water transport are contributed by the trade of different commodity types, including plant, animal, luxury (e.g., coffee, tea, and alcohol), and other products. Major contributors to the virtual water network exhibit different trade patterns with regard to these commodity types. The net importers rely on the supply of virtual water from a small percentage of the global population. However, discrepancies exist among the different commodity networks. While the total virtual water flux through the network has increased between 1986 and 2010, the proportions associated with the four commodity groups have remained relatively stable. However, some of the major players have shown significant changes in the virtual water imports and exports associated with those commodity groups. For instance, China has switched from being a net exporter of virtual water associated with other products (non-edible plant and animal products typically used for manufacturing) to being the largest importer, accounting for 31% of the total water virtually transported with these products. Conversely, in the case of The United states of America, the commodity proportions have remained overall unchanged throughout the study period: the virtual water exports from The United States of America are dominated by plant products, whereas the imports are comprised mainly of animal and luxury products. PMID:23457481

Rapid prototyping, astronaut training, and experiment control and supervision: distributed virtual worlds for COLUMBUS, the European Space Laboratory module

NASA Astrophysics Data System (ADS)

Freund, Eckhard; Rossmann, Juergen

2002-02-01

In 2004, the European COLUMBUS Module is to be attached to the International Space Station. On the way to the successful planning, deployment and operation of the module, computer generated and animated models are being used to optimize performance. Under contract of the German Space Agency DLR, it has become IRF's task to provide a Projective Virtual Reality System to provide a virtual world built after the planned layout of the COLUMBUS module let astronauts and experimentators practice operational procedures and the handling of experiments. The key features of the system currently being realized comprise the possibility for distributed multi-user access to the virtual lab and the visualization of real-world experiment data. Through the capabilities to share the virtual world, cooperative operations can be practiced easily, but also trainers and trainees can work together more effectively sharing the virtual environment. The capability to visualize real-world data will be used to introduce measured data of experiments into the virtual world online in order to realistically interact with the science-reference model hardware: The user's actions in the virtual world are translated into corresponding changes of the inputs of the science reference model hardware; the measured data is than in turn fed back into the virtual world. During the operation of COLUMBUS, the capabilities for distributed access and the capabilities to visualize measured data through the use of metaphors and augmentations of the virtual world may be used to provide virtual access to the COLUMBUS module, e.g. via Internet. Currently, finishing touches are being put to the system. In November 2001 the virtual world shall be operational, so that besides the design and the key ideas, first experimental results can be presented.

ISMCR 1994: Topical Workshop on Virtual Reality. Proceedings of the Fourth International Symposium on Measurement and Control in Robotics

NASA Technical Reports Server (NTRS)

1994-01-01

This symposium on measurement and control in robotics included sessions on: (1) rendering, including tactile perception and applied virtual reality; (2) applications in simulated medical procedures and telerobotics; (3) tracking sensors in a virtual environment; (4) displays for virtual reality applications; (5) sensory feedback including a virtual environment application with partial gravity simulation; and (6) applications in education, entertainment, technical writing, and animation.

[Virtual bronchoscopy: the correlation between endoscopic simulation and bronchoscopic findings].

PubMed

Salvolini, L; Gasparini, S; Baldelli, S; Bichi Secchi, E; Amici, F

1997-11-01

We carried out a preliminary clinical validation of 3D spiral CT virtual endoscopic reconstructions of the tracheobronchial tree, by comparing virtual bronchoscopic images with actual endoscopic findings. Twenty-two patients with tracheobronchial disease suspected at preliminary clinical, cytopathological and plain chest film findings were submitted to spiral CT of the chest and bronchoscopy. CT was repeated after endobronchial therapy in 2 cases. Virtual endoscopic shaded-surface-display views of the tracheobronchial tree were reconstructed from reformatted CT data with an Advantage Navigator software. Virtual bronchoscopic images were preliminarily evaluated with a semi-quantitative quality score (excellent/good/fair/poor). The depiction of consecutive airway branches was then considered. Virtual bronchoscopies were finally submitted to double-blind comparison with actual endoscopies. Virtual image quality was considered excellent in 8 cases, good in 14 and fair in 2. Virtual exploration was stopped at the lobar bronchi in one case only; the origin of segmental bronchi was depicted in 23 cases and that of some subsegmental branches in 2 cases. Agreement between actual and virtual bronchoscopic findings was good in all cases but 3 where it was nevertheless considered satisfactory. The yield of clinically useful information differed in 8/24 cases: virtual reconstructions provided more information than bronchoscopy in 5 cases and vice versa in 3. Virtual reconstructions are limited in that the procedure is long and difficult and needing a strictly standardized threshold value not to alter virtual findings. Moreover, the reconstructed surface lacks transparency, there is the partial volume effect and the branches < or = 4 pixels phi and/or meandering ones are difficult to explore. Our preliminary data are encouraging. Segmental bronchi were depicted in nearly all cases, except for the branches involved by disease. Obstructing lesions could be bypassed in some cases, making an indication for endoscopic laser therapy. Future didactic perspectives and applications to minimally invasive or virtual reality-assisted therapy seem promising, even though actual clinical applications require further studies.

The Virtual Maternity Clinic: a teaching and learning innovation for midwifery education.

PubMed

Phillips, Diane; Duke, Maxine; Nagle, Cate; Macfarlane, Susie; Karantzas, Gery; Patterson, Denise

2013-10-01

There are challenges for midwifery students in developing skill and competency due to limited placements in antenatal clinics. The Virtual Maternity Clinic, an online resource, was developed to support student learning in professional midwifery practice. Identifying students' perceptions of the Virtual Maternity Clinic; learning about the impact of the Virtual Maternity Clinic on the students' experience of its use and access; and learning about the level of student satisfaction of the Virtual Maternity Clinic. Two interventions were used including pre and post evaluations of the online learning resource with data obtained from questionnaires using open ended and dichotomous responses and rating scales. The pre-Virtual Maternity Clinic intervention used a qualitative design and the post-Virtual Maternity Clinic intervention applied both qualitative and quantitative approaches. Three campuses of Deakin University, located in Victoria, Australia. Midwifery students enrolled in the Bachelor of Nursing/Bachelor of Midwifery and Graduate Diploma of Midwifery were recruited across three campuses of Deakin University (n=140). Thematic analysis of the pre-Virtual Maternity Clinic intervention (return rate n=119) related to students' expectations of this resource. The data for the post-Virtual Maternity Clinic intervention (return rate n=42) including open-ended responses were thematically analysed; dichotomous data examined in the form of frequencies and percentages of agreement and disagreement; and 5-rating scales were analysed using Pearson's correlations (α=.05, two-tailed). Results showed from the pre-Virtual Maternity Clinic intervention that students previously had placements in antenatal clinics were optimistic about the online learning resource. The post-Virtual Maternity Clinic intervention results indicated that students were satisfied with the Virtual Maternity Clinic as a learning resource despite some technological issues. The Virtual Maternity Clinic provides benefits for students in repeated observation of the practice of the midwife to support their professional learning and practice development. Copyright © 2012 Elsevier Ltd. All rights reserved.

Knowledge-Driven Design of Virtual Patient Simulations

ERIC Educational Resources Information Center

Vergara, Victor; Caudell, Thomas; Goldsmith, Timothy; Panaiotis; Alverson, Dale

2009-01-01

Virtual worlds provide unique opportunities for instructors to promote, study, and evaluate student learning and comprehension. In this article, Victor Vergara, Thomas Caudell, Timothy Goldsmith, Panaiotis, and Dale Alverson explore the advantages of using virtual reality environments to create simulations for medical students. Virtual simulations…

Virtual Reality in the Classroom.

ERIC Educational Resources Information Center

Pantelidis, Veronica S.

1993-01-01

Considers the concept of virtual reality; reviews its history; describes general uses of virtual reality, including entertainment, medicine, and design applications; discusses classroom uses of virtual reality, including a software program called Virtus WalkThrough for use with a computer monitor; and suggests future possibilities. (34 references)…

Fast localized orthonormal virtual orbitals which depend smoothly on nuclear coordinates.

PubMed

Subotnik, Joseph E; Dutoi, Anthony D; Head-Gordon, Martin

2005-09-15

We present here an algorithm for computing stable, well-defined localized orthonormal virtual orbitals which depend smoothly on nuclear coordinates. The algorithm is very fast, limited only by diagonalization of two matrices with dimension the size of the number of virtual orbitals. Furthermore, we require no more than quadratic (in the number of electrons) storage. The basic premise behind our algorithm is that one can decompose any given atomic-orbital (AO) vector space as a minimal basis space (which includes the occupied and valence virtual spaces) and a hard-virtual (HV) space (which includes everything else). The valence virtual space localizes easily with standard methods, while the hard-virtual space is constructed to be atom centered and automatically local. The orbitals presented here may be computed almost as quickly as projecting the AO basis onto the virtual space and are almost as local (according to orbital variance), while our orbitals are orthonormal (rather than redundant and nonorthogonal). We expect this algorithm to find use in local-correlation methods.

Using voice input and audio feedback to enhance the reality of a virtual experience

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miner, N.E.

1994-04-01

Virtual Reality (VR) is a rapidly emerging technology which allows participants to experience a virtual environment through stimulation of the participant`s senses. Intuitive and natural interactions with the virtual world help to create a realistic experience. Typically, a participant is immersed in a virtual environment through the use of a 3-D viewer. Realistic, computer-generated environment models and accurate tracking of a participant`s view are important factors for adding realism to a virtual experience. Stimulating a participant`s sense of sound and providing a natural form of communication for interacting with the virtual world are equally important. This paper discusses the advantagesmore » and importance of incorporating voice recognition and audio feedback capabilities into a virtual world experience. Various approaches and levels of complexity are discussed. Examples of the use of voice and sound are presented through the description of a research application developed in the VR laboratory at Sandia National Laboratories.« less

European Pharmacy Students' Experience With Virtual Patient Technology

PubMed Central

Madeira, Filipe

2012-01-01

Objective. To describe how virtual patients are being used to simulate real-life clinical scenarios in undergraduate pharmacy education in Europe. Methods. One hundred ninety-four participants at the 2011 Congress of the European Pharmaceutical Students Association (EPSA) completed an exploratory cross-sectional survey instrument. Results. Of the 46 universities and 23 countries represented at the EPSA Congress, only 12 students from 6 universities in 6 different countries reported having experience with virtual patient technology. The students were satisfied with the virtual patient technology and considered it more useful as a teaching and learning tool than an assessment tool. Respondents who had not used virtual patient technology expressed support regarding its potential benefits in pharmacy education. French and Dutch students were significantly less interested in virtual patient technology than were their counterparts from other European countries. Conclusion. The limited use of virtual patients in pharmacy education in Europe suggests the need for initiatives to increase the use of virtual patient technology and the benefits of computer-assisted learning in pharmacy education. PMID:22919082

Virtual reality training improves balance function.

PubMed

Mao, Yurong; Chen, Peiming; Li, Le; Huang, Dongfeng

2014-09-01

Virtual reality is a new technology that simulates a three-dimensional virtual world on a computer and enables the generation of visual, audio, and haptic feedback for the full immersion of users. Users can interact with and observe objects in three-dimensional visual space without limitation. At present, virtual reality training has been widely used in rehabilitation therapy for balance dysfunction. This paper summarizes related articles and other articles suggesting that virtual reality training can improve balance dysfunction in patients after neurological diseases. When patients perform virtual reality training, the prefrontal, parietal cortical areas and other motor cortical networks are activated. These activations may be involved in the reconstruction of neurons in the cerebral cortex. Growing evidence from clinical studies reveals that virtual reality training improves the neurological function of patients with spinal cord injury, cerebral palsy and other neurological impairments. These findings suggest that virtual reality training can activate the cerebral cortex and improve the spatial orientation capacity of patients, thus facilitating the cortex to control balance and increase motion function.

Virtual reality training improves balance function

PubMed Central

Mao, Yurong; Chen, Peiming; Li, Le; Huang, Dongfeng

2014-01-01

Virtual reality is a new technology that simulates a three-dimensional virtual world on a computer and enables the generation of visual, audio, and haptic feedback for the full immersion of users. Users can interact with and observe objects in three-dimensional visual space without limitation. At present, virtual reality training has been widely used in rehabilitation therapy for balance dysfunction. This paper summarizes related articles and other articles suggesting that virtual reality training can improve balance dysfunction in patients after neurological diseases. When patients perform virtual reality training, the prefrontal, parietal cortical areas and other motor cortical networks are activated. These activations may be involved in the reconstruction of neurons in the cerebral cortex. Growing evidence from clinical studies reveals that virtual reality training improves the neurological function of patients with spinal cord injury, cerebral palsy and other neurological impairments. These findings suggest that virtual reality training can activate the cerebral cortex and improve the spatial orientation capacity of patients, thus facilitating the cortex to control balance and increase motion function. PMID:25368651

Evaluation of virtual simulation in a master's-level nurse education certificate program.

PubMed

Foronda, Cynthia; Lippincott, Christine; Gattamorta, Karina

2014-11-01

Master's-level, nurse education certificate students performed virtual clinical simulations as a portion of their clinical practicum. Virtual clinical simulation is an innovative pedagogy using avatars in Web-based platforms to provide simulated clinical experiences. The purpose of this mixed-methods study was to evaluate nurse educator students' experience with virtual simulation and the effect of virtual simulation on confidence in teaching ability. Aggregated quantitative results yielded no significant change in confidence in teaching ability. Individually, some students indicated change of either increased or decreased confidence, whereas others exhibited no change in confidence after engaging in virtual simulation. Qualitative findings revealed a process of precursors of anxiety and frustration with technical difficulties followed by outcomes of appreciation and learning. Instructor support was a mediating factor to decrease anxiety and technical difficulties. This study served as a starting point regarding the application of a virtual world to teach the art of instruction. As the movement toward online education continues, educators should further explore use of virtual simulation to prepare nurse educators.

Can virtual reality be used to conduct mass prophylaxis clinic training? A pilot program.

PubMed

Yellowlees, Peter; Cook, James N; Marks, Shayna L; Wolfe, Daniel; Mangin, Elanor

2008-03-01

To create and evaluate a pilot bioterrorism defense training environment using virtual reality technology. The present pilot project used Second Life, an internet-based virtual world system, to construct a virtual reality environment to mimic an actual setting that might be used as a Strategic National Stockpile (SNS) distribution site for northern California in the event of a bioterrorist attack. Scripted characters were integrated into the system as mock patients to analyze various clinic workflow scenarios. Users tested the virtual environment over two sessions. Thirteen users who toured the environment were asked to complete an evaluation survey. Respondents reported that the virtual reality system was relevant to their practice and had potential as a method of bioterrorism defense training. Computer simulations of bioterrorism defense training scenarios are feasible with existing personal computer technology. The use of internet-connected virtual environments holds promise for bioterrorism defense training. Recommendations are made for public health agencies regarding the implementation and benefits of using virtual reality for mass prophylaxis clinic training.

European pharmacy students' experience with virtual patient technology.

PubMed

Cavaco, Afonso Miguel; Madeira, Filipe

2012-08-10

To describe how virtual patients are being used to simulate real-life clinical scenarios in undergraduate pharmacy education in Europe. One hundred ninety-four participants at the 2011 Congress of the European Pharmaceutical Students Association (EPSA) completed an exploratory cross-sectional survey instrument. Of the 46 universities and 23 countries represented at the EPSA Congress, only 12 students from 6 universities in 6 different countries reported having experience with virtual patient technology. The students were satisfied with the virtual patient technology and considered it more useful as a teaching and learning tool than an assessment tool. Respondents who had not used virtual patient technology expressed support regarding its potential benefits in pharmacy education. French and Dutch students were significantly less interested in virtual patient technology than were their counterparts from other European countries. The limited use of virtual patients in pharmacy education in Europe suggests the need for initiatives to increase the use of virtual patient technology and the benefits of computer-assisted learning in pharmacy education.

Investigation on Consumers’ Behaviour towards Energy Saving through Utilisation of Virtual SED (Smart Energy Displays) in Residential Building

NASA Astrophysics Data System (ADS)

Adlisia Puspa Harani, Sandhika

2018-05-01

The study is conducted by gathering data from interviews an in-home experiment, to examine the impacts of both virtual and physical SED toward user engagement. Business opportunity and benefits of virtual SED for stake holders are also discussed in this study. The research was conducted by interviewing method to respondens in Nottingham, UK. By comparing consumers’ energy saving behaviour from physical and virtual SED users, virtual SED shows similar level of effectiveness as physical SED, but there is no evidence that the virtual versions are better than the physical ones in terms of reducing energy consumption. Nevertheless, virtual SED can be more beneficial for consumers who can get easier access. They also help educating users to be more concern about energy issue. Energy suppliers get benefits by having virtual versions of SED, in which they can reduce production and distribution costs, as well as diminishing waste from physical SED.

Increasing Accessibility to the Blind of Virtual Environments, Using a Virtual Mobility Aid Based On the "EyeCane": Feasibility Study

PubMed Central

Maidenbaum, Shachar; Levy-Tzedek, Shelly; Chebat, Daniel-Robert; Amedi, Amir

2013-01-01

Virtual worlds and environments are becoming an increasingly central part of our lives, yet they are still far from accessible to the blind. This is especially unfortunate as such environments hold great potential for them for uses such as social interaction, online education and especially for use with familiarizing the visually impaired user with a real environment virtually from the comfort and safety of his own home before visiting it in the real world. We have implemented a simple algorithm to improve this situation using single-point depth information, enabling the blind to use a virtual cane, modeled on the “EyeCane” electronic travel aid, within any virtual environment with minimal pre-processing. Use of the Virtual-EyeCane, enables this experience to potentially be later used in real world environments with identical stimuli to those from the virtual environment. We show the fast-learned practical use of this algorithm for navigation in simple environments. PMID:23977316

Evaluation of procedural learning transfer from a virtual environment to a real situation: a case study on tank maintenance training.

PubMed

Ganier, Franck; Hoareau, Charlotte; Tisseau, Jacques

2014-01-01

Virtual reality opens new opportunities for operator training in complex tasks. It lowers costs and has fewer constraints than traditional training. The ultimate goal of virtual training is to transfer knowledge gained in a virtual environment to an actual real-world setting. This study tested whether a maintenance procedure could be learnt equally well by virtual-environment and conventional training. Forty-two adults were divided into three equally sized groups: virtual training (GVT® [generic virtual training]), conventional training (using a real tank suspension and preparation station) and control (no training). Participants then performed the procedure individually in the real environment. Both training types (conventional and virtual) produced similar levels of performance when the procedure was carried out in real conditions. Performance level for the two trained groups was better in terms of success and time taken to complete the task, time spent consulting job instructions and number of times the instructor provided guidance.

Shared virtual environments for aerospace training

NASA Technical Reports Server (NTRS)

Loftin, R. Bowen; Voss, Mark

1994-01-01

Virtual environments have the potential to significantly enhance the training of NASA astronauts and ground-based personnel for a variety of activities. A critical requirement is the need to share virtual environments, in real or near real time, between remote sites. It has been hypothesized that the training of international astronaut crews could be done more cheaply and effectively by utilizing such shared virtual environments in the early stages of mission preparation. The Software Technology Branch at NASA's Johnson Space Center has developed the capability for multiple users to simultaneously share the same virtual environment. Each user generates the graphics needed to create the virtual environment. All changes of object position and state are communicated to all users so that each virtual environment maintains its 'currency.' Examples of these shared environments will be discussed and plans for the utilization of the Department of Defense's Distributed Interactive Simulation (DIS) protocols for shared virtual environments will be presented. Finally, the impact of this technology on training and education in general will be explored.

Hierarchical virtual screening approaches in small molecule drug discovery.

PubMed

Kumar, Ashutosh; Zhang, Kam Y J

2015-01-01

Virtual screening has played a significant role in the discovery of small molecule inhibitors of therapeutic targets in last two decades. Various ligand and structure-based virtual screening approaches are employed to identify small molecule ligands for proteins of interest. These approaches are often combined in either hierarchical or parallel manner to take advantage of the strength and avoid the limitations associated with individual methods. Hierarchical combination of ligand and structure-based virtual screening approaches has received noteworthy success in numerous drug discovery campaigns. In hierarchical virtual screening, several filters using ligand and structure-based approaches are sequentially applied to reduce a large screening library to a number small enough for experimental testing. In this review, we focus on different hierarchical virtual screening strategies and their application in the discovery of small molecule modulators of important drug targets. Several virtual screening studies are discussed to demonstrate the successful application of hierarchical virtual screening in small molecule drug discovery. Copyright © 2014 Elsevier Inc. All rights reserved.

The electronic-commerce-oriented virtual merchandise model

NASA Astrophysics Data System (ADS)

Fang, Xiaocui; Lu, Dongming

2004-03-01

Electronic commerce has been the trend of commerce activities. Providing with Virtual Reality interface, electronic commerce has better expressing capacity and interaction means. But most of the applications of virtual reality technology in EC, 3D model is only the appearance description of merchandises. There is almost no information concerned with commerce information and interaction information. This resulted in disjunction of virtual model and commerce information. So we present Electronic Commerce oriented Virtual Merchandise Model (ECVMM), which combined a model with commerce information, interaction information and figure information of virtual merchandise. ECVMM with abundant information provides better support to information obtainment and communication in electronic commerce.

Psychological benefits of virtual reality for patients in rehabilitation therapy.

PubMed

Chen, Chih-Hung; Jeng, Ming-Chang; Fung, Chin-Ping; Doong, Ji-Liang; Chuang, Tien-Yow

2009-05-01

Whether virtual rehabilitation is beneficial has not been determined. To investigate the psychological benefits of virtual reality in rehabilitation. An experimental group underwent therapy with a virtual-reality-based exercise bike, and a control group underwent the therapy without virtual-reality equipment. Hospital laboratory. 30 patients suffering from spinal-cord injury. A designed rehabilitation therapy. Endurance, Borg's rating-of-perceived-exertion scale, the Activation-Deactivation Adjective Check List (AD-ACL), and the Simulator Sickness Questionnaire. The differences between the experimental and control groups were significant for AD-ACL calmness and tension. A virtual-reality-based rehabilitation program can ease patients' tension and induce calm.

Virtual reality exposure therapy for combat-related posttraumatic stress disorder.

PubMed

Rothbaum, Barbara O; Rizzo, Albert Skip; Difede, JoAnn

2010-10-01

Posttraumatic stress disorder (PTSD) is a chronic, debilitating, psychological condition that occurs in a subset of individuals who experience or witness life-threatening traumatic events. PTSD is highly prevalent in those who served in the military. In this paper, we present the underlying theoretical foundations and existing research on virtual reality exposure therapy, a recently emerging treatment for PTSD. Three virtual reality scenarios used to treat PTSD in active duty military and combat veterans and survivors of terrorism are presented: Virtual Vietnam, Virtual Iraq, and Virtual World Trade Center. Preliminary results of ongoing trials are presented. © 2010 Association for Research in Nervous and Mental Disease.

Analysing neutron scattering data using McStas virtual experiments

NASA Astrophysics Data System (ADS)

Udby, L.; Willendrup, P. K.; Knudsen, E.; Niedermayer, Ch.; Filges, U.; Christensen, N. B.; Farhi, E.; Wells, B. O.; Lefmann, K.

2011-04-01

With the intention of developing a new data analysis method using virtual experiments we have built a detailed virtual model of the cold triple-axis spectrometer RITA-II at PSI, Switzerland, using the McStas neutron ray-tracing package. The parameters characterising the virtual instrument were carefully tuned against real experiments. In the present paper we show that virtual experiments reproduce experimentally observed linewidths within 1-3% for a variety of samples. Furthermore we show that the detailed knowledge of the instrumental resolution found from virtual experiments, including sample mosaicity, can be used for quantitative estimates of linewidth broadening resulting from, e.g., finite domain sizes in single-crystal samples.

An information model for a virtual private optical network (OVPN) using virtual routers (VRs)

NASA Astrophysics Data System (ADS)

Vo, Viet Minh Nhat

2002-05-01

This paper describes a virtual private optical network architecture (Optical VPN - OVPN) based on virtual router (VR). It improves over architectures suggested for virtual private networks by using virtual routers with optical networks. The new things in this architecture are necessary changes to adapt to devices and protocols used in optical networks. This paper also presents information models for the OVPN: at the architecture level and at the service level. These are extensions to the DEN (directory enable network) and CIM (Common Information Model) for OVPNs using VRs. The goal is to propose a common management model using policies.

Network Hardware Virtualization for Application Provisioning in Core Networks

DOE PAGES

Gumaste, Ashwin; Das, Tamal; Khandwala, Kandarp; ...

2017-02-03

We present that service providers and vendors are moving toward a network virtualized core, whereby multiple applications would be treated on their own merit in programmable hardware. Such a network would have the advantage of being customized for user requirements and allow provisioning of next generation services that are built specifically to meet user needs. In this article, we articulate the impact of network virtualization on networks that provide customized services and how a provider's business can grow with network virtualization. We outline a decision map that allows mapping of applications with technology that is supported in network-virtualization - orientedmore » equipment. Analogies to the world of virtual machines and generic virtualization show that hardware supporting network virtualization will facilitate new customer needs while optimizing the provider network from the cost and performance perspectives. A key conclusion of the article is that growth would yield sizable revenue when providers plan ahead in terms of supporting network-virtualization-oriented technology in their networks. To be precise, providers have to incorporate into their growth plans network elements capable of new service deployments while protecting network neutrality. Finally, a simulation study validates our NV-induced model.« less

Virtual gaming simulation of a mental health assessment: A usability study.

PubMed

Verkuyl, Margaret; Romaniuk, Daria; Mastrilli, Paula

2018-05-18

Providing safe and realistic virtual simulations could be an effective way to facilitate the transition from the classroom to clinical practice. As nursing programs begin to include virtual simulations as a learning strategy; it is critical to first assess the technology for ease of use and usefulness. A virtual gaming simulation was developed, and a usability study was conducted to assess its ease of use and usefulness for students and faculty. The Technology Acceptance Model provided the framework for the study, which included expert review and testing by nursing faculty and nursing students. This study highlighted the importance of assessing ease of use and usefulness in a virtual game simulation and provided feedback for the development of an effective virtual gaming simulation. The study participants said the virtual gaming simulation was engaging, realistic and similar to a clinical experience. Participants found the game easy to use and useful. Testing provided the development team with ideas to improve the user interface. The usability methodology provided is a replicable approach to testing virtual experiences before a research study or before implementing virtual experiences into curriculum. Copyright © 2018 Elsevier Ltd. All rights reserved.

Development of a virtual reality training system for endoscope-assisted submandibular gland removal.

PubMed

Miki, Takehiro; Iwai, Toshinori; Kotani, Kazunori; Dang, Jianwu; Sawada, Hideyuki; Miyake, Minoru

2016-11-01

Endoscope-assisted surgery has widely been adopted as a basic surgical procedure, with various training systems using virtual reality developed for this procedure. In the present study, a basic training system comprising virtual reality for the removal of submandibular glands under endoscope assistance was developed. The efficacy of the training system was verified in novice oral surgeons. A virtual reality training system was developed using existing haptic devices. Virtual reality models were constructed from computed tomography data to ensure anatomical accuracy. Novice oral surgeons were trained using the developed virtual reality training system. The developed virtual reality training system included models of the submandibular gland and surrounding connective tissues and blood vessels entering the submandibular gland. Cutting or abrasion of the connective tissue and manipulations, such as elevation of blood vessels, were reproduced by the virtual reality system. A training program using the developed system was devised. Novice oral surgeons were trained in accordance with the devised training program. Our virtual reality training system for endoscope-assisted removal of the submandibular gland is effective in the training of novice oral surgeons in endoscope-assisted surgery. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Virtual study groups and online Observed Structured Clinical Examinations practices - enabling trainees to enable themselves.

PubMed

Davidson, Dennisa; Evans, Lois

2018-03-01

To explore online study groups as augmentation tools in preparing for the Royal Australian and New Zealand College of Psychiatrists Observed Structured Clinical Examinations (OSCE) for fellowship. An online survey of New Zealand trainees was carried out to assess exam preparedness and openness to virtual study groups and results analysed. Relevant material around virtual study groups for fellowship examinations was reviewed and used to inform a pilot virtual study group. Four New Zealand trainees took part in the pilot project, looking at using a virtual platform to augment OSCE preparation. Of the 50 respondents 36% felt adequately prepared for the OSCE. Sixty-four per cent were interested in using a virtual platform to augment their study. Virtual study groups were noted to be especially important for rural trainees, none of whom felt able to form study groups for themselves. The pilot virtual study group was trialled successfully. All four trainees reported the experience as subjectively beneficial to their examination preparation. Virtual platforms hold promise as an augmentation strategy for exam preparation, especially for rural trainees who are more geographically isolated and less likely to have peers preparing for the same examinations.

A virtual work space for both hands manipulation with coherency between kinesthetic and visual sensation

NASA Technical Reports Server (NTRS)

Ishii, Masahiro; Sukanya, P.; Sato, Makoto

1994-01-01

This paper describes the construction of a virtual work space for tasks performed by two handed manipulation. We intend to provide a virtual environment that encourages users to accomplish tasks as they usually act in a real environment. Our approach uses a three dimensional spatial interface device that allows the user to handle virtual objects by hand and be able to feel some physical properties such as contact, weight, etc. We investigated suitable conditions for constructing our virtual work space by simulating some basic assembly work, a face and fit task. We then selected the conditions under which the subjects felt most comfortable in performing this task and set up our virtual work space. Finally, we verified the possibility of performing more complex tasks in this virtual work space by providing simple virtual models and then let the subjects create new models by assembling these components. The subjects can naturally perform assembly operations and accomplish the task. Our evaluation shows that this virtual work space has the potential to be used for performing tasks that require two-handed manipulation or cooperation between both hands in a natural manner.

Alleviating the water scarcity in the North China Plain: the role of virtual water and real water transfer

NASA Astrophysics Data System (ADS)

Zhang, Zhuoying; Yang, Hong; Shi, Minjun

2016-04-01

The North China Plain is the most water scarce region in China. Its water security is closely relevant to interregional water movement, which can be realized by real water transfers and/or virtual water transfers. This study investigates the roles of virtual water trade and real water transfer using Interregional Input-Output model. The results show that the region is receiving 19.4 billion m3/year of virtual water from the interregional trade, while exporting 16.4 billion m3/year of virtual water in the international trade. In balance, the region has a net virtual water gain of 3 billion m3/year from outside. Its virtual water inflow is dominated by agricultural products from other provinces, totalling 16.6 billion m3/year, whilst its virtual water export is dominated by manufacturing sectors to other countries, totalling 11.7 billion m3/year. Both virtual water import and real water transfer from South to North Water Diversion Project are important water supplements for the region. The results of this study provide useful scientific references for the establishment of combating strategies to deal with the water scarcity in the future.

Network Hardware Virtualization for Application Provisioning in Core Networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gumaste, Ashwin; Das, Tamal; Khandwala, Kandarp

We present that service providers and vendors are moving toward a network virtualized core, whereby multiple applications would be treated on their own merit in programmable hardware. Such a network would have the advantage of being customized for user requirements and allow provisioning of next generation services that are built specifically to meet user needs. In this article, we articulate the impact of network virtualization on networks that provide customized services and how a provider's business can grow with network virtualization. We outline a decision map that allows mapping of applications with technology that is supported in network-virtualization - orientedmore » equipment. Analogies to the world of virtual machines and generic virtualization show that hardware supporting network virtualization will facilitate new customer needs while optimizing the provider network from the cost and performance perspectives. A key conclusion of the article is that growth would yield sizable revenue when providers plan ahead in terms of supporting network-virtualization-oriented technology in their networks. To be precise, providers have to incorporate into their growth plans network elements capable of new service deployments while protecting network neutrality. Finally, a simulation study validates our NV-induced model.« less

Virtual Learning Effectiveness: An Examination of the Process

ERIC Educational Resources Information Center

Stonebraker, Peter W.; Hazeltine, James E.

2004-01-01

This study defines, examines, and measures the effectiveness of a corporate virtual learning program. Initially, distinctions between traditional and virtual learning and university and corporate programs are defined. Then, based on the literature, an integrative model of the perceived effectiveness of a virtual learning environment is developed…

The Virtual Reality Roving Vehicle Project.

ERIC Educational Resources Information Center

Winn, William

1995-01-01

Describes the Virtual Reality Roving Vehicle project developed at the University of Washington to teach students in grades 4 through 12 about virtual reality. Topics include teacher workshops; virtual worlds created by students; learning outcomes compared with traditional instruction; and the effect of student characteristics, including gender, on…

Virtual Reality: Toward Fundamental Improvements in Simulation-Based Training.

ERIC Educational Resources Information Center

Thurman, Richard A.; Mattoon, Joseph S.

1994-01-01

Considers the role and effectiveness of virtual reality in simulation-based training. The theoretical and practical implications of verity, integration, and natural versus artificial interface are discussed; a three-dimensional classification scheme for virtual reality is described; and the relationship between virtual reality and other…

Virtual Education: Guidelines for Using Games Technology

ERIC Educational Resources Information Center

Schofield, Damian

2014-01-01

Advanced three-dimensional virtual environment technology, similar to that used by the film and computer games industry, can allow educational developers to rapidly create realistic online virtual environments. This technology has been used to generate a range of interactive Virtual Reality (VR) learning environments across a spectrum of…

World Reaction to Virtual Space

NASA Technical Reports Server (NTRS)

1999-01-01

DRaW Computing developed virtual reality software for the International Space Station. Open Worlds, as the software has been named, can be made to support Java scripting and virtual reality hardware devices. Open Worlds permits the use of VRML script nodes to add virtual reality capabilities to the user's applications.

Virtual Reference Services.

ERIC Educational Resources Information Center

Brewer, Sally

2003-01-01

As the need to access information increases, school librarians must create virtual libraries. Linked to reliable reference resources, the virtual library extends the physical collection and library hours and lets students learn to use Web-based resources in a protected learning environment. The growing number of virtual schools increases the need…

Virtual Reality in Schools: The Ultimate Educational Technology.

ERIC Educational Resources Information Center

Reid, Robert D.; Sykes, Wylmarie

1999-01-01

Discusses the use of virtual reality as an educational tool. Highlights include examples of virtual reality in public schools that lead to a more active learning process, simulated environments, integrating virtual reality into any curriculum, benefits to teachers and students, and overcoming barriers to implementation. (LRW)

Learning Area and Perimeter with Virtual Manipulatives

ERIC Educational Resources Information Center

Bouck, Emily; Flanagan, Sara; Bouck, Mary

2015-01-01

Manipulatives are considered a best practice for educating students with disabilities, but little research exists which examines virtual manipulatives as tool for supporting students in mathematics. This project investigated the use of a virtual manipulative through the National Library of Virtual Manipulatives--polynominoes (i.e., tiles)--as a…

Study on virtual instrument developing system based on intelligent virtual control

NASA Astrophysics Data System (ADS)

Tang, Baoping; Cheng, Fabin; Qin, Shuren

2005-01-01

The paper introduces a non-programming developing system of a virtual instument (VI), i.e., a virtual measurement instrument developing system (VMIDS) based on intelligent virtual control (IVC). The background of the IVC-based VMIDS is described briefly, and the hierarchical message bus (HMB)-based software architecture of VMIDS is discussed in detail. The three parts and functions of VMIDS are introduced, and the process of non-programming developing VI is further described.

The need for virtual reality simulators in dental education: A review.

PubMed

Roy, Elby; Bakr, Mahmoud M; George, Roy

2017-04-01

Virtual reality simulators are becoming an essential part of modern education. The benefits of Virtual reality in dentistry is constantly being assessed as a method or an adjunct to improve fine motor skills, hand-eye coordination in pre-clinical settings and overcome the monetary and intellectual challenges involved with such training. This article, while providing an overview of the virtual reality dental simulators, also looks at the link between virtual reality simulation and current pedagogical knowledge.

Local concurrent error detection and correction in data structures using virtual backpointers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, C.C.J.; Chen, P.P.; Fuchs, W.K.

1989-11-01

A new technique, based on virtual backpointers, is presented in this paper for local concurrent error detection and correction in linked data structures. Two new data structures utilizing virtual backpointers, the Virtual Double-Linked List and the B-Tree and Virtual Backpointers, are described. For these structures, double errors within a fixed-size checking window can be detected in constant time and single errors detected during forward moves can be corrected in constant time.

AR Feels "Softer" than VR: Haptic Perception of Stiffness in Augmented versus Virtual Reality.

PubMed

Gaffary, Yoren; Le Gouis, Benoit; Marchal, Maud; Argelaguet, Ferran; Arnaldi, Bruno; Lecuyer, Anatole

2017-11-01

Does it feel the same when you touch an object in Augmented Reality (AR) or in Virtual Reality (VR)? In this paper we study and compare the haptic perception of stiffness of a virtual object in two situations: (1) a purely virtual environment versus (2) a real and augmented environment. We have designed an experimental setup based on a Microsoft HoloLens and a haptic force-feedback device, enabling to press a virtual piston, and compare its stiffness successively in either Augmented Reality (the virtual piston is surrounded by several real objects all located inside a cardboard box) or in Virtual Reality (the same virtual piston is displayed in a fully virtual scene composed of the same other objects). We have conducted a psychophysical experiment with 12 participants. Our results show a surprising bias in perception between the two conditions. The virtual piston is on average perceived stiffer in the VR condition compared to the AR condition. For instance, when the piston had the same stiffness in AR and VR, participants would select the VR piston as the stiffer one in 60% of cases. This suggests a psychological effect as if objects in AR would feel "softer" than in pure VR. Taken together, our results open new perspectives on perception in AR versus VR, and pave the way to future studies aiming at characterizing potential perceptual biases.

Walking training associated with virtual reality-based training increases walking speed of individuals with chronic stroke: systematic review with meta-analysis.

PubMed

Rodrigues-Baroni, Juliana M; Nascimento, Lucas R; Ada, Louise; Teixeira-Salmela, Luci F

2014-01-01

To systematically review the available evidence on the efficacy of walking training associated with virtual reality-based training in patients with stroke. The specific questions were: Is walking training associated with virtual reality-based training effective in increasing walking speed after stroke? Is this type of intervention more effective in increasing walking speed, than non-virtual reality-based walking interventions? A systematic review with meta-analysis of randomized clinical trials was conducted. Participants were adults with chronic stroke and the experimental intervention was walking training associated with virtual reality-based training to increase walking speed. The outcome data regarding walking speed were extracted from the eligible trials and were combined using a meta-analysis approach. Seven trials representing eight comparisons were included in this systematic review. Overall, the virtual reality-based training increased walking speed by 0.17 m/s (IC 95% 0.08 to 0.26), compared with placebo/nothing or non-walking interventions. In addition, the virtual reality-based training increased walking speed by 0.15 m/s (IC 95% 0.05 to 0.24), compared with non-virtual reality walking interventions. This review provided evidence that walking training associated with virtual reality-based training was effective in increasing walking speed after stroke, and resulted in better results than non-virtual reality interventions.

Controlling Within-Field Sheep Movement Using Virtual Fencing.

PubMed

Marini, Danila; Llewellyn, Rick; Belson, Sue; Lee, Caroline

2018-02-26

Virtual fencing has the potential to greatly improve livestock movement, grazing efficiency, and land management by farmers; however, relatively little work has been done to test the potential of virtual fencing with sheep. Commercial dog training equipment, comprising of a collar and GPS hand-held unit were used to implement a virtual fence in a commercial setting. Six, 5-6 year-old Merino wethers, which were naïve to virtual fencing were GPS tracked for their use of a paddock (80 × 20 m) throughout the experiment. The virtual fence was effective at preventing a small group of sheep from entering the exclusion zone. The probability of a sheep receiving an electrical stimulus following an audio cue was low (19%), and declined over the testing period. It took an average of eight interactions with the fence for an association to be made between the audio and stimulus cue, with all of the animals responding to the audio alone by the third day. Following the removal of the virtual fence, sheep were willing to cross the previous location of the virtual fence after 30 min of being in the paddock. This is an important aspect in the implementation of virtual fencing as a grazing management tool and further enforces that the sheep in this study were able to associate the audio with the virtual fence and not the physical location itself.

Head-mounted active noise control system with virtual sensing technique

NASA Astrophysics Data System (ADS)

Miyazaki, Nobuhiro; Kajikawa, Yoshinobu

2015-03-01

In this paper, we apply a virtual sensing technique to a head-mounted active noise control (ANC) system we have already proposed. The proposed ANC system can reduce narrowband noise while improving the noise reduction ability at the desired locations. A head-mounted ANC system based on an adaptive feedback structure can reduce noise with periodicity or narrowband components. However, since quiet zones are formed only at the locations of error microphones, an adequate noise reduction cannot be achieved at the locations where error microphones cannot be placed such as near the eardrums. A solution to this problem is to apply a virtual sensing technique. A virtual sensing ANC system can achieve higher noise reduction at the desired locations by measuring the system models from physical sensors to virtual sensors, which will be used in the online operation of the virtual sensing ANC algorithm. Hence, we attempt to achieve the maximum noise reduction near the eardrums by applying the virtual sensing technique to the head-mounted ANC system. However, it is impossible to place the microphone near the eardrums. Therefore, the system models from physical sensors to virtual sensors are estimated using the Head And Torso Simulator (HATS) instead of human ears. Some simulation, experimental, and subjective assessment results demonstrate that the head-mounted ANC system with virtual sensing is superior to that without virtual sensing in terms of the noise reduction ability at the desired locations.

Man, mind, and machine: the past and future of virtual reality simulation in neurologic surgery.

PubMed

Robison, R Aaron; Liu, Charles Y; Apuzzo, Michael L J

2011-11-01

To review virtual reality in neurosurgery, including the history of simulation and virtual reality and some of the current implementations; to examine some of the technical challenges involved; and to propose a potential paradigm for the development of virtual reality in neurosurgery going forward. A search was made on PubMed using key words surgical simulation, virtual reality, haptics, collision detection, and volumetric modeling to assess the current status of virtual reality in neurosurgery. Based on previous results, investigators extrapolated the possible integration of existing efforts and potential future directions. Simulation has a rich history in surgical training, and there are numerous currently existing applications and systems that involve virtual reality. All existing applications are limited to specific task-oriented functions and typically sacrifice visual realism for real-time interactivity or vice versa, owing to numerous technical challenges in rendering a virtual space in real time, including graphic and tissue modeling, collision detection, and direction of the haptic interface. With ongoing technical advancements in computer hardware and graphic and physical rendering, incremental or modular development of a fully immersive, multipurpose virtual reality neurosurgical simulator is feasible. The use of virtual reality in neurosurgery is predicted to change the nature of neurosurgical education, and to play an increased role in surgical rehearsal and the continuing education and credentialing of surgical practitioners. Copyright © 2011 Elsevier Inc. All rights reserved.

Walking training associated with virtual reality-based training increases walking speed of individuals with chronic stroke: systematic review with meta-analysis

PubMed Central

Rodrigues-Baroni, Juliana M.; Nascimento, Lucas R.; Ada, Louise; Teixeira-Salmela, Luci F.

2014-01-01

OBJECTIVE: To systematically review the available evidence on the efficacy of walking training associated with virtual reality-based training in patients with stroke. The specific questions were: Is walking training associated with virtual reality-based training effective in increasing walking speed after stroke? Is this type of intervention more effective in increasing walking speed, than non-virtual reality-based walking interventions? METHOD: A systematic review with meta-analysis of randomized clinical trials was conducted. Participants were adults with chronic stroke and the experimental intervention was walking training associated with virtual reality-based training to increase walking speed. The outcome data regarding walking speed were extracted from the eligible trials and were combined using a meta-analysis approach. RESULTS: Seven trials representing eight comparisons were included in this systematic review. Overall, the virtual reality-based training increased walking speed by 0.17 m/s (IC 95% 0.08 to 0.26), compared with placebo/nothing or non-walking interventions. In addition, the virtual reality-based training increased walking speed by 0.15 m/s (IC 95% 0.05 to 0.24), compared with non-virtual reality walking interventions. CONCLUSIONS: This review provided evidence that walking training associated with virtual reality-based training was effective in increasing walking speed after stroke, and resulted in better results than non-virtual reality interventions. PMID:25590442

Recognition profile of emotions in natural and virtual faces.

PubMed

Dyck, Miriam; Winbeck, Maren; Leiberg, Susanne; Chen, Yuhan; Gur, Ruben C; Gur, Rurben C; Mathiak, Klaus

2008-01-01

Computer-generated virtual faces become increasingly realistic including the simulation of emotional expressions. These faces can be used as well-controlled, realistic and dynamic stimuli in emotion research. However, the validity of virtual facial expressions in comparison to natural emotion displays still needs to be shown for the different emotions and different age groups. Thirty-two healthy volunteers between the age of 20 and 60 rated pictures of natural human faces and faces of virtual characters (avatars) with respect to the expressed emotions: happiness, sadness, anger, fear, disgust, and neutral. Results indicate that virtual emotions were recognized comparable to natural ones. Recognition differences in virtual and natural faces depended on specific emotions: whereas disgust was difficult to convey with the current avatar technology, virtual sadness and fear achieved better recognition results than natural faces. Furthermore, emotion recognition rates decreased for virtual but not natural faces in participants over the age of 40. This specific age effect suggests that media exposure has an influence on emotion recognition. Virtual and natural facial displays of emotion may be equally effective. Improved technology (e.g. better modelling of the naso-labial area) may lead to even better results as compared to trained actors. Due to the ease with which virtual human faces can be animated and manipulated, validated artificial emotional expressions will be of major relevance in future research and therapeutic applications.

Towards a Digital Body: The Virtual Arm Illusion

PubMed Central

Slater, Mel; Perez-Marcos, Daniel; Ehrsson, H. Henrik; Sanchez-Vives, Maria V.

2008-01-01

The integration of the human brain with computers is an interesting new area of applied neuroscience, where one application is replacement of a person's real body by a virtual representation. Here we demonstrate that a virtual limb can be made to feel part of your body if appropriate multisensory correlations are provided. We report an illusion that is invoked through tactile stimulation on a person's hidden real right hand with synchronous virtual visual stimulation on an aligned 3D stereo virtual arm projecting horizontally out of their shoulder. An experiment with 21 male participants showed displacement of ownership towards the virtual hand, as illustrated by questionnaire responses and proprioceptive drift. A control experiment with asynchronous tapping was carried out with a different set of 20 male participants who did not experience the illusion. After 5 min of stimulation the virtual arm rotated. Evidence suggests that the extent of the illusion was also correlated with the degree of muscle activity onset in the right arm as measured by EMG during this period that the arm was rotating, for the synchronous but not the asynchronous condition. A completely virtual object can therefore be experienced as part of one's self, which opens up the possibility that an entire virtual body could be felt as one's own in future virtual reality applications or online games, and be an invaluable tool for the understanding of the brain mechanisms underlying body ownership. PMID:18958207

Welcome to Wonderland: The Influence of the Size and Shape of a Virtual Hand On the Perceived Size and Shape of Virtual Objects

PubMed Central

Linkenauger, Sally A.; Leyrer, Markus; Bülthoff, Heinrich H.; Mohler, Betty J.

2013-01-01

The notion of body-based scaling suggests that our body and its action capabilities are used to scale the spatial layout of the environment. Here we present four studies supporting this perspective by showing that the hand acts as a metric which individuals use to scale the apparent sizes of objects in the environment. However to test this, one must be able to manipulate the size and/or dimensions of the perceiver’s hand which is difficult in the real world due to impliability of hand dimensions. To overcome this limitation, we used virtual reality to manipulate dimensions of participants’ fully-tracked, virtual hands to investigate its influence on the perceived size and shape of virtual objects. In a series of experiments, using several measures, we show that individuals’ estimations of the sizes of virtual objects differ depending on the size of their virtual hand in the direction consistent with the body-based scaling hypothesis. Additionally, we found that these effects were specific to participants’ virtual hands rather than another avatar’s hands or a salient familiar-sized object. While these studies provide support for a body-based approach to the scaling of the spatial layout, they also demonstrate the influence of virtual bodies on perception of virtual environments. PMID:23874681

Recognition Profile of Emotions in Natural and Virtual Faces

PubMed Central

Dyck, Miriam; Winbeck, Maren; Leiberg, Susanne; Chen, Yuhan; Gur, Rurben C.; Mathiak, Klaus

2008-01-01

Background Computer-generated virtual faces become increasingly realistic including the simulation of emotional expressions. These faces can be used as well-controlled, realistic and dynamic stimuli in emotion research. However, the validity of virtual facial expressions in comparison to natural emotion displays still needs to be shown for the different emotions and different age groups. Methodology/Principal Findings Thirty-two healthy volunteers between the age of 20 and 60 rated pictures of natural human faces and faces of virtual characters (avatars) with respect to the expressed emotions: happiness, sadness, anger, fear, disgust, and neutral. Results indicate that virtual emotions were recognized comparable to natural ones. Recognition differences in virtual and natural faces depended on specific emotions: whereas disgust was difficult to convey with the current avatar technology, virtual sadness and fear achieved better recognition results than natural faces. Furthermore, emotion recognition rates decreased for virtual but not natural faces in participants over the age of 40. This specific age effect suggests that media exposure has an influence on emotion recognition. Conclusions/Significance Virtual and natural facial displays of emotion may be equally effective. Improved technology (e.g. better modelling of the naso-labial area) may lead to even better results as compared to trained actors. Due to the ease with which virtual human faces can be animated and manipulated, validated artificial emotional expressions will be of major relevance in future research and therapeutic applications. PMID:18985152

Virtual Collaboration Readiness Measurement a Case Study in the Automobile Industry

NASA Astrophysics Data System (ADS)

Ziarati, Koorush; Khayami, Raouf; Parvinnia, Elham; Afroozi Milani, Ghazal

In end of the last century information and communication technology caused a veritable evolution in the world of business and commerce. Globalization has changed all the commerce equations and business plans. Old companies have to change their strategies if they want to survive after this technological revolution. A new form of collaboration between the distributed and networked organizations has emerged as the "Virtual Organization" paradigm. A company can not join a virtual organization before obtaining a virtual maturity. This maturity shows the readiness of the company to begin a virtual collaboration. In this paper, based on the coherent and formal definition of virtual organizations, the criteria for measuring the readiness of companies are proposed. Our criteria are confirmed, modified or combined by using the factor analysis method on a sufficient number of virtual companies in the automobile manufacturing industry.

Intelligent Motion and Interaction Within Virtual Environments

NASA Technical Reports Server (NTRS)

Ellis, Stephen R. (Editor); Slater, Mel (Editor); Alexander, Thomas (Editor)

2007-01-01

What makes virtual actors and objects in virtual environments seem real? How can the illusion of their reality be supported? What sorts of training or user-interface applications benefit from realistic user-environment interactions? These are some of the central questions that designers of virtual environments face. To be sure simulation realism is not necessarily the major, or even a required goal, of a virtual environment intended to communicate specific information. But for some applications in entertainment, marketing, or aspects of vehicle simulation training, realism is essential. The following chapters will examine how a sense of truly interacting with dynamic, intelligent agents may arise in users of virtual environments. These chapters are based on presentations at the London conference on Intelligent Motion and Interaction within a Virtual Environments which was held at University College, London, U.K., 15-17 September 2003.

Cybersickness and Anxiety During Simulated Motion: Implications for VRET.

PubMed

Bruck, Susan; Watters, Paul

2009-01-01

Some clinicians have suggested using virtual reality environments to deliver psychological interventions to treat anxiety disorders. However, given a significant body of work on cybersickness symptoms which may arise in virtual environments - especially those involving simulated motion - we tested (a) whether being exposed to a virtual reality environment alone causes anxiety to increase, and (b) whether exposure to simulated motion in a virtual reality environment increases anxiety. Using a repeated measures design, we used Kim's Anxiety Scale questionnaire to compare baseline anxiety, anxiety after virtual environment exposure, and anxiety after simulated motion. While there was no significant effect on anxiety for being in a virtual environment with no simulated motion, the introduction of simulated motion caused anxiety to significantly increase, but not to a severe or extreme level. The implications of this work for virtual reality exposure therapy (VRET) are discussed.

Deploying Embodied AI into Virtual Worlds

NASA Astrophysics Data System (ADS)

Burden, David J. H.

The last two years have seen the start of commercial activity within virtual worlds. Unlike computer games where Non-Player-Character avatars are common, in most virtual worlds they are the exception — and until recently in Second Life they were non-existent. However there is real commercial scope for Als in these worlds — in roles from virtual sales staff and tutors to personal assistants. Deploying an embodied AI into a virtual world offers a unique opportunity to evaluate embodied Als, and to develop them within an environment where human and computer are on almost equal terms. This paper presents an architecture being used for the deployment of chatbot driven avatars within the Second Life virtual world, looks at the challenges of deploying an AI within such a virtual world, the possible implications for the Turing Test, and identifies research directions for the future.

Virtual patient simulation at US and Canadian medical schools.

PubMed

Huang, Grace; Reynolds, Robby; Candler, Chris

2007-05-01

"Virtual patients" are computer-based simulations designed to complement clinical training. These applications possess numerous educational benefits but are costly to develop. Few medical schools can afford to create them. The purpose of this inventory was to gather information regarding in-house virtual patient development at U.S. and Canadian medical schools to promote the sharing of existing cases and future collaboration. From February to September 2005, the authors contacted 142 U.S. and Canadian medical schools and requested that they report on virtual patient simulation activities at their respective institutions. The inventory elicited information regarding the pedagogic and technical characteristics of each virtual patient application. The schools were also asked to report on their willingness to share virtual patients. Twenty-six out of 108 responding schools reported that they were producing virtual patients. Twelve schools provided additional data on 103 cases and 111 virtual patients. The vast majority of virtual patients were media rich and were associated with significant production costs and time. The reported virtual patient cases tended to focus on primary care disciplines and did not as a whole exhibit racial or ethnic diversity. Funding sources, production costs, and production duration influenced the extent of schools' willingness to share. Broader access to and cooperative development of these resources would allow medical schools to enhance their clinical curricula. Virtual patient development should include basic science objectives for more integrative learning, simulate the consequences of clinical decision making, and include additional cases in cultural competency. Together, these efforts can enhance medical education despite external constraints on clinical training.

Collaborative Research: Bringing Problem Solving in the Field into the Classroom: Developing and Assessing Virtual Field Trips for Teaching Sedimentary and Introductory Geology

NASA Astrophysics Data System (ADS)

Wang, P.; Caldwell, M.

2012-12-01

Coastal Florida offers a unique setting for the facilitation of learning about a variety of modern sedimentary environments. Despite the conflicting concept of "virtual" and "actual" field trip, and the uncertainties associated with the implementation and effectiveness, virtual trips provide likely the only way to reach a large diversified student population and eliminate travel time and expenses. In addition, with rapidly improving web and visualization technology, field trips can be simulated virtually. It is therefore essential to systematically develop and assess the educational effectiveness of virtual field trips. This project is developing, implementing, and assessing a series of virtual field trips for teaching undergraduate sedimentary geology at a large four-year research university and introductory geology at a large two-year community college. The virtual field trip is based on a four-day actual field trip for a senior level sedimentary geology class. Two versions of the virtual field trip, one for advanced class and one for introductory class, are being produced. The educational outcome of the virtual field trip will be compared to that from actual field trip. This presentation summarizes Year 1 achievements of the three-year project. The filming, editing, and initial production of the virtual field trip have been completed. Formative assessments were conducted by the Coalition for Science Literacy at the University of South Florida. Once tested and refined, the virtual field trips will be disseminated through broadly used web portals and workshops at regional and national meetings.

Seeing an Embodied Virtual Hand is Analgesic Contingent on Colocation.

PubMed

Nierula, Birgit; Martini, Matteo; Matamala-Gomez, Marta; Slater, Mel; Sanchez-Vives, Maria V

2017-06-01

Seeing one's own body has been reported to have analgesic properties. Analgesia has also been described when seeing an embodied virtual body colocated with the real one. However, there is controversy regarding whether this effect holds true when seeing an illusory-owned body part, such as during the rubber-hand illusion. A critical difference between these paradigms is the distance between the real and surrogate body part. Colocation of the real and surrogate arm is possible in an immersive virtual environment, but not during illusory ownership of a rubber arm. The present study aimed at testing whether the distance between a real and a virtual arm can explain such differences in terms of pain modulation. Using a paradigm of embodiment of a virtual body allowed us to evaluate heat pain thresholds at colocation and at a 30-cm distance between the real and the virtual arm. We observed a significantly higher heat pain threshold at colocation than at a 30-cm distance. The analgesic effects of seeing a virtual colocated arm were eliminated by increasing the distance between the real and the virtual arm, which explains why seeing an illusorily owned rubber arm does not consistently result in analgesia. These findings are relevant for the use of virtual reality in pain management. Looking at a virtual body has analgesic properties similar to looking at one's real body. We identify the importance of colocation between a real and a surrogate body for this to occur and thereby resolve a scientific controversy. This information is useful for exploiting immersive virtual reality in pain management. Copyright © 2017. Published by Elsevier Inc.

Kinematic evaluation of virtual walking trajectories.

PubMed

Cirio, Gabriel; Olivier, Anne-Hélène; Marchal, Maud; Pettré, Julien

2013-04-01

Virtual walking, a fundamental task in Virtual Reality (VR), is greatly influenced by the locomotion interface being used, by the specificities of input and output devices, and by the way the virtual environment is represented. No matter how virtual walking is controlled, the generation of realistic virtual trajectories is absolutely required for some applications, especially those dedicated to the study of walking behaviors in VR, navigation through virtual places for architecture, rehabilitation and training. Previous studies focused on evaluating the realism of locomotion trajectories have mostly considered the result of the locomotion task (efficiency, accuracy) and its subjective perception (presence, cybersickness). Few focused on the locomotion trajectory itself, but in situation of geometrically constrained task. In this paper, we study the realism of unconstrained trajectories produced during virtual walking by addressing the following question: did the user reach his destination by virtually walking along a trajectory he would have followed in similar real conditions? To this end, we propose a comprehensive evaluation framework consisting on a set of trajectographical criteria and a locomotion model to generate reference trajectories. We consider a simple locomotion task where users walk between two oriented points in space. The travel path is analyzed both geometrically and temporally in comparison to simulated reference trajectories. In addition, we demonstrate the framework over a user study which considered an initial set of common and frequent virtual walking conditions, namely different input devices, output display devices, control laws, and visualization modalities. The study provides insight into the relative contributions of each condition to the overall realism of the resulting virtual trajectories.

The Informal Workplace Learning Experiences of Virtual Team Members: A Look at the Role of Collaborative Technologies

ERIC Educational Resources Information Center

Jones, Frankie S.

2007-01-01

This qualitative study explored how collaborative technologies influence the informal learning experiences of virtual team members. Inputs revealed as critical to virtual informal learning were integrated, collaborative technological systems; positive relationships and trust; and organizational support and virtual team management. These inputs…

Brain Activity on Navigation in Virtual Environments.

ERIC Educational Resources Information Center

Mikropoulos, Tassos A.

2001-01-01

Assessed the cognitive processing that takes place in virtual environments by measuring electrical brain activity using Fast Fourier Transform analysis. University students performed the same task in a real and a virtual environment, and eye movement measurements showed that all subjects were more attentive when navigating in the virtual world.…

NREL, EPRI Validate Advanced Microgrid Controller with ESIF's Virtual

Science.gov Websites

Microgrid Controller with ESIF's Virtual Microgrid Model NREL, EPRI Validate Advanced Microgrid Controller with ESIF's Virtual Microgrid Model NREL is working with the Electric Power Research Institute (EPRI Energy Systems Integration Facility, by connecting it to a virtual model of a microgrid. NREL researchers

Sniffing Out Efficacy: Sniffy Lite, a Virtual Animal Lab

ERIC Educational Resources Information Center

Venneman, Sandy S.; Knowles, Laura, Ruth

2005-01-01

We investigated the benefits of using a virtual laboratory, Sniffy Lite CD-ROM (Alloway, Wilson, Graham, & Krames, 2000), as a supplemental teaching tool to present schedules of reinforcement in operant conditioning. Our results suggest that using the virtual laboratory significantly enhanced understanding. Students who used the virtual laboratory…

A Systematic Framework of Virtual Laboratories Using Mobile Agent and Design Pattern Technologies

ERIC Educational Resources Information Center

Li, Yi-Hsung; Dow, Chyi-Ren; Lin, Cheng-Min; Chen, Sheng-Chang; Hsu, Fu-Wei

2009-01-01

Innovations in network and information technology have transformed traditional classroom lectures into new approaches that have given universities the opportunity to create a virtual laboratory. However, there is no systematic framework in existing approaches for the development of virtual laboratories. Further, developing a virtual laboratory…

The Investigation of Teacher Communication Practices in Virtual High School

ERIC Educational Resources Information Center

Belair, Marley

2011-01-01

Virtual schooling is an increasing trend for secondary education. Research of the communication practices in virtual schools has provided a myriad of suggestions for virtual school policies. Although transactional distance has been investigated in relation to certain aspects of the communication process, a small-scale qualitative study has not…

Librarians without Borders? Virtual Reference Service to Unaffiliated Users

ERIC Educational Resources Information Center

Kibbee, Jo

2006-01-01

The author investigates issues faced by academic research libraries in providing virtual reference services to unaffiliated users. These libraries generally welcome visitors who use on-site collections and reference services, but are these altruistic policies feasible in a virtual environment? This paper reviews the use of virtual reference…

Can Virtual Schools Thrive in the Real World?

ERIC Educational Resources Information Center

Wang, Yinying; Decker, Janet R.

2014-01-01

Despite the relatively large number of students enrolled in Ohio's virtual schools, it is unclear how virtual schools compare to their traditional school counterparts on measures of student achievement. To provide some insight, we compared the school performance from 2007-2011 at Ohio's virtual and traditional schools. The results suggest that…

Virtual Reality: Emerging Applications and Future Directions

ERIC Educational Resources Information Center

Ludlow, Barbara L.

2015-01-01

Virtual reality is an emerging technology that has resulted in rapid expansion in the development of virtual immersive environments for use as educational simulations in schools, colleges and universities. This article presents an overview of virtual reality, describes a number of applications currently being used by special educators for…

A Practical Guide, with Theoretical Underpinnings, for Creating Effective Virtual Reality Learning Environments

ERIC Educational Resources Information Center

O'Connor, Eileen A.; Domingo, Jelia

2017-01-01

With the advent of open source virtual environments, the associated cost reductions, and the more flexible options, avatar-based virtual reality environments are within reach of educators. By using and repurposing readily available virtual environments, instructors can bring engaging, community-building, and immersive learning opportunities to…

Software Engineering Infrastructure in a Large Virtual Campus

ERIC Educational Resources Information Center

Cristobal, Jesus; Merino, Jorge; Navarro, Antonio; Peralta, Miguel; Roldan, Yolanda; Silveira, Rosa Maria

2011-01-01

Purpose: The design, construction and deployment of a large virtual campus are a complex issue. Present virtual campuses are made of several software applications that complement e-learning platforms. In order to develop and maintain such virtual campuses, a complex software engineering infrastructure is needed. This paper aims to analyse the…

Virtual Schools in the U.S. 2017

ERIC Educational Resources Information Center

Molnar, Alex; Miron, Gary; Gulosino, Charisse; Shank, Christopher; Davidson, Caryn; Barbour, Michael; Huerta, Luis; Shafter, Sheryl Rankin; Rice, Jennifer King; Nitkin, David

2017-01-01

In the five years since the first National Education Policy Center (NEPC) "Annual Report on Virtual Education" was released in 2013, virtual education has continued to be a focal point for policymakers. Proponents argue that virtual education can expand student choices and improve the efficiency of public education. In particular,…

Virtual Reality: A Dream Come True or a Nightmare.

ERIC Educational Resources Information Center

Cornell, Richard; Bailey, Dan

Virtual Reality (VR) is a new medium which allows total stimulation of one's senses through human/computer interfaces. VR has applications in training simulators, nano-science, medicine, entertainment, electronic technology, and manufacturing. This paper focuses on some current and potential problems of virtual reality and virtual environments…

A Virtual Education: Guidelines for Using Games Technology

ERIC Educational Resources Information Center

Schofield, Damian

2014-01-01

Advanced three-dimensional virtual environment technology, similar to that used by the film and computer games industry, can allow educational developers to rapidly create realistic online vir-tual environments. This technology has been used to generate a range of interactive Virtual Real-ity (VR) learning environments across a spectrum of…

Synchronous Learning Best Practices: An Action Research Study

ERIC Educational Resources Information Center

Warden, Clyde A.; Stanworth, James O.; Ren, Jian Biao; Warden, Antony R.

2013-01-01

Low cost and significant advances in technology now allow instructors to create their own virtual learning environments. Creating social interactions within a virtual space that emulates the physical classroom remains challenging. While students are familiar with virtual worlds and video meetings, they are inexperienced as virtual learners. Over a…

Ethnography in a Virtual World

ERIC Educational Resources Information Center

Shumar, Wesley; Madison, Nora

2013-01-01

This article situates the discussion of virtual ethnography within the larger political/economic changes of twenty-first century consumer capitalism and suggests that increasingly our entire social world is a virtual world and that there were very particular utopian and dystopian framings of virtual community growing out of that history. The…

Share (And Not) Share Alike: Improving Virtual Team Climate and Decision Performance

ERIC Educational Resources Information Center

Cordes, Sean

2017-01-01

Virtual teams face unique communication and collaboration challenges that impact climate development and performance. First, virtual teams rely on technology mediated communication which can constrain communication. Second, team members lack skill for adapting process to the virtual setting. A collaboration process structure was designed to…

Finding Information on the State Virtual Libraries

ERIC Educational Resources Information Center

Pappas, Marjorie L.

2004-01-01

The number of state virtual libraries is rapidly expanding. These virtual libraries might include collections of subscription databases; state weblinks and resources; digital collections of primary source documents; and a state union catalog or links to school, public, and academic library catalogs. Most of these virtual libraries include an…

A "Virtual Spin" on the Teaching of Probability

ERIC Educational Resources Information Center

Beck, Shari A.; Huse, Vanessa E.

2007-01-01

This article, which describes integrating virtual manipulatives with the teaching of probability at the elementary level, puts a "virtual spin" on the teaching of probability to provide more opportunities for students to experience successful learning. The traditional use of concrete manipulatives is enhanced with virtual coins and spinners from…

Virtual Scavenger Hunt: An AI-Powered Virtual Environment Designed for Training Individuals in Effective Teamwork, and Analyzing Cross-Cultural Behavior

DTIC Science & Technology

2009-03-20

involved the development of an environment within the Multiverse virtual world, oriented toward allowing individuals to acquire and reinforce skills via...PetBrain software G2: Creation of a scavenger hunt scenario in the Multiverse virtual world, in which humans and AIs can collaboratively play scavenger...carried out by Novamente LLC for AOARD during June 2008 ? February 2009. It involved the development of an environment within the Multiverse virtual world

The Benefits and Risks of Virtual Bidding in Multi-Settlement Markets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Isemonger, Alan G.

2006-11-15

While it is possible that multi-settlement markets can exist without virtual trading, it is equally clear that virtual trading can provide many market benefits. The main one: In the absence of explicit virtual bidding (EVB), the price arbitrage trades that are benign in other commodity markets affect the reliability of the underlying electricity markets, resulting in a situation where EVB is most useful when it neutralizes the deleterious reliability effects of implicit virtual bidding and physical arbitrage. (author)

Ring-based ultrasonic virtual point detector with applications to photoacoustic tomography

NASA Astrophysics Data System (ADS)

Yang, Xinmai; Li, Meng-Lin; Wang, Lihong V.

2007-06-01

An ultrasonic virtual point detector is constructed using the center of a ring transducer. The virtual point detector provides ideal omnidirectional detection free of any aperture effect. Compared with a real point detector, the virtual one has lower thermal noise and can be scanned with its center inside a physically inaccessible medium. When applied to photoacoustic tomography, the virtual point detector provides both high spatial resolution and high signal-to-noise ratio. It can also be potentially applied to other ultrasound-related technologies.

Simulators and virtual reality in surgical education.

PubMed

Chou, Betty; Handa, Victoria L

2006-06-01

This article explores the pros and cons of virtual reality simulators, their abilities to train and assess surgical skills, and their potential future applications. Computer-based virtual reality simulators and more conventional box trainers are compared and contrasted. The virtual reality simulator provides objective assessment of surgical skills and immediate feedback further to enhance training. With this ability to provide standardized, unbiased assessment of surgical skills, the virtual reality trainer has the potential to be a tool for selecting, instructing, certifying, and recertifying gynecologists.

Blade runner. Blade server and virtualization technology can help hospitals save money--but they are far from silver bullets.

PubMed

Lawrence, Daphne

2009-03-01

Blade servers and virtualization can reduce infrastructure, maintenance, heating, electric, cooling and equipment costs. Blade server technology is evolving and some elements may become obsolete. There is very little interoperability between blades. Hospitals can virtualize 40 to 60 percent of their servers, and old servers can be reused for testing. Not all applications lend themselves to virtualization--especially those with high memory requirements. CIOs should engage their vendors in virtualization discussions.

Generation IV Nuclear Energy Systems Construction Cost Reductions through the Use of Virtual Environments - Task 4 Report: Virtual Mockup Maintenance Task Evaluation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Timothy Shaw; Anthony Baratta; Vaughn Whisker

2005-02-28

Task 4 report of 3 year DOE NERI-sponsored effort evaluating immersive virtual reality (CAVE) technology for design review, construction planning, and maintenance planning and training for next generation nuclear power plants. Program covers development of full-scale virtual mockups generated from 3D CAD data presented in a CAVE visualization facility. This report focuses on using Full-scale virtual mockups for nuclear power plant training applications.

Methods and systems relating to an augmented virtuality environment

DOEpatents

Nielsen, Curtis W; Anderson, Matthew O; McKay, Mark D; Wadsworth, Derek C; Boyce, Jodie R; Hruska, Ryan C; Koudelka, John A; Whetten, Jonathan; Bruemmer, David J

2014-05-20

Systems and methods relating to an augmented virtuality system are disclosed. A method of operating an augmented virtuality system may comprise displaying imagery of a real-world environment in an operating picture. The method may further include displaying a plurality of virtual icons in the operating picture representing at least some assets of a plurality of assets positioned in the real-world environment. Additionally, the method may include displaying at least one virtual item in the operating picture representing data sensed by one or more of the assets of the plurality of assets and remotely controlling at least one asset of the plurality of assets by interacting with a virtual icon associated with the at least one asset.

Virtual network embedding in cross-domain network based on topology and resource attributes

NASA Astrophysics Data System (ADS)

Zhu, Lei; Zhang, Zhizhong; Feng, Linlin; Liu, Lilan

2018-03-01

Aiming at the network architecture ossification and the diversity of access technologies issues, this paper researches the cross-domain virtual network embedding algorithm. By analysing the topological attribute from the local and global perspective of nodes in the virtual network and the physical network, combined with the local network resource property, we rank the embedding priority of the nodes with PCA and TOPSIS methods. Besides, the link load distribution is considered. Above all, We proposed an cross-domain virtual network embedding algorithm based on topology and resource attributes. The simulation results depicts that our algorithm increases the acceptance rate of multi-domain virtual network requests, compared with the existing virtual network embedding algorithm.

Research on virtual Guzheng based on Kinect

NASA Astrophysics Data System (ADS)

Li, Shuyao; Xu, Kuangyi; Zhang, Heng

2018-05-01

There are a lot of researches on virtual instruments, but there are few on classical Chinese instruments, and the techniques used are very limited. This paper uses Unity 3D and Kinect camera combined with virtual reality technology and gesture recognition method to design a virtual playing system of Guzheng, a traditional Chinese musical instrument, with demonstration function. In this paper, the real scene obtained by Kinect camera is fused with virtual Guzheng in Unity 3D. The depth data obtained by Kinect and the Suzuki85 algorithm are used to recognize the relative position of the user's right hand and the virtual Guzheng, and the hand gesture of the user is recognized by Kinect.

Virtual reality in surgical training.

PubMed

Lange, T; Indelicato, D J; Rosen, J M

2000-01-01

Virtual reality in surgery and, more specifically, in surgical training, faces a number of challenges in the future. These challenges are building realistic models of the human body, creating interface tools to view, hear, touch, feel, and manipulate these human body models, and integrating virtual reality systems into medical education and treatment. A final system would encompass simulators specifically for surgery, performance machines, telemedicine, and telesurgery. Each of these areas will need significant improvement for virtual reality to impact medicine successfully in the next century. This article gives an overview of, and the challenges faced by, current systems in the fast-changing field of virtual reality technology, and provides a set of specific milestones for a truly realistic virtual human body.

Surgery applications of virtual reality

NASA Technical Reports Server (NTRS)

Rosen, Joseph

1994-01-01

Virtual reality is a computer-generated technology which allows information to be displayed in a simulated, bus lifelike, environment. In this simulated 'world', users can move and interact as if they were actually a part of that world. This new technology will be useful in many different fields, including the field of surgery. Virtual reality systems can be used to teach surgical anatomy, diagnose surgical problems, plan operations, simulate and perform surgical procedures (telesurgery), and predict the outcomes of surgery. The authors of this paper describe the basic components of a virtual reality surgical system. These components include: the virtual world, the virtual tools, the anatomical model, the software platform, the host computer, the interface, and the head-coupled display. In the chapter they also review the progress towards using virtual reality for surgical training, planning, telesurgery, and predicting outcomes. Finally, the authors present a training system being developed for the practice of new procedures in abdominal surgery.

Cognitive training on stroke patients via virtual reality-based serious games.

PubMed

Gamito, Pedro; Oliveira, Jorge; Coelho, Carla; Morais, Diogo; Lopes, Paulo; Pacheco, José; Brito, Rodrigo; Soares, Fabio; Santos, Nuno; Barata, Ana Filipa

2017-02-01

Use of virtual reality environments in cognitive rehabilitation offers cost benefits and other advantages. In order to test the effectiveness of a virtual reality application for neuropsychological rehabilitation, a cognitive training program using virtual reality was applied to stroke patients. A virtual reality-based serious games application for cognitive training was developed, with attention and memory tasks consisting of daily life activities. Twenty stroke patients were randomly assigned to two conditions: exposure to the intervention, and waiting list control. The results showed significant improvements in attention and memory functions in the intervention group, but not in the controls. Overall findings provide further support for the use of VR cognitive training applications in neuropsychological rehabilitation. Implications for Rehabilitation Improvements in memory and attention functions following a virtual reality-based serious games intervention. Training of daily-life activities using a virtual reality application. Accessibility to training contents.

Development of a virtual speaking simulator using Image Based Rendering.

PubMed

Lee, J M; Kim, H; Oh, M J; Ku, J H; Jang, D P; Kim, I Y; Kim, S I

2002-01-01

The fear of speaking is often cited as the world's most common social phobia. The rapid growth of computer technology has enabled the use of virtual reality (VR) for the treatment of the fear of public speaking. There are two techniques for building virtual environments for the treatment of this fear: a model-based and a movie-based method. Both methods have the weakness that they are unrealistic and not controllable individually. To understand these disadvantages, this paper presents a virtual environment produced with Image Based Rendering (IBR) and a chroma-key simultaneously. IBR enables the creation of realistic virtual environments where the images are stitched panoramically with the photos taken from a digital camera. And the use of chroma-keys puts virtual audience members under individual control in the environment. In addition, real time capture technique is used in constructing the virtual environments enabling spoken interaction between the subject and a therapist or another subject.

Leading virtual teams: hierarchical leadership, structural supports, and shared team leadership.

PubMed

Hoch, Julia E; Kozlowski, Steve W J

2014-05-01

Using a field sample of 101 virtual teams, this research empirically evaluates the impact of traditional hierarchical leadership, structural supports, and shared team leadership on team performance. Building on Bell and Kozlowski's (2002) work, we expected structural supports and shared team leadership to be more, and hierarchical leadership to be less, strongly related to team performance when teams were more virtual in nature. As predicted, results from moderation analyses indicated that the extent to which teams were more virtual attenuated relations between hierarchical leadership and team performance but strengthened relations for structural supports and team performance. However, shared team leadership was significantly related to team performance regardless of the degree of virtuality. Results are discussed in terms of needed research extensions for understanding leadership processes in virtual teams and practical implications for leading virtual teams. (c) 2014 APA, all rights reserved.

Virtual optical network mapping and core allocation in elastic optical networks using multi-core fibers

NASA Astrophysics Data System (ADS)

Xuan, Hejun; Wang, Yuping; Xu, Zhanqi; Hao, Shanshan; Wang, Xiaoli

2017-11-01

Virtualization technology can greatly improve the efficiency of the networks by allowing the virtual optical networks to share the resources of the physical networks. However, it will face some challenges, such as finding the efficient strategies for virtual nodes mapping, virtual links mapping and spectrum assignment. It is even more complex and challenging when the physical elastic optical networks using multi-core fibers. To tackle these challenges, we establish a constrained optimization model to determine the optimal schemes of optical network mapping, core allocation and spectrum assignment. To solve the model efficiently, tailor-made encoding scheme, crossover and mutation operators are designed. Based on these, an efficient genetic algorithm is proposed to obtain the optimal schemes of the virtual nodes mapping, virtual links mapping, core allocation. The simulation experiments are conducted on three widely used networks, and the experimental results show the effectiveness of the proposed model and algorithm.

Distributed attitude synchronization of formation flying via consensus-based virtual structure

NASA Astrophysics Data System (ADS)

Cong, Bing-Long; Liu, Xiang-Dong; Chen, Zhen

2011-06-01

This paper presents a general framework for synchronized multiple spacecraft rotations via consensus-based virtual structure. In this framework, attitude control systems for formation spacecrafts and virtual structure are designed separately. Both parametric uncertainty and external disturbance are taken into account. A time-varying sliding mode control (TVSMC) algorithm is designed to improve the robustness of the actual attitude control system. As for the virtual attitude control system, a behavioral consensus algorithm is presented to accomplish the attitude maneuver of the entire formation and guarantee a consistent attitude among the local virtual structure counterparts during the attitude maneuver. A multiple virtual sub-structures (MVSSs) system is introduced to enhance current virtual structure scheme when large amounts of spacecrafts are involved in the formation. The attitude of spacecraft is represented by modified Rodrigues parameter (MRP) for its non-redundancy. Finally, a numerical simulation with three synchronization situations is employed to illustrate the effectiveness of the proposed strategy.

[Virtual reality in neurosurgery].

PubMed

Tronnier, V M; Staubert, A; Bonsanto, M M; Wirtz, C R; Kunze, S

2000-03-01

Virtual reality enables users to immerse themselves in a virtual three-dimensional world and to interact in this world. The simulation is different from the kind in computer games, in which the viewer is active but acts in a nonrealistic world, or on the TV screen, where we are passively driven in an active world. In virtual reality elements look realistic, they change their characteristics and have almost real-world unpredictability. Virtual reality is not only implemented in gambling dens and the entertainment industry but also in manufacturing processes (cars, furniture etc.), military applications and medicine. Especially the last two areas are strongly correlated, because telemedicine or telesurgery was originated for military reasons to operate on war victims from a secure distance or to perform surgery on astronauts in an orbiting space station. In medicine and especially neurosurgery virtual-reality methods are used for education, surgical planning and simulation on a virtual patient.

Architecture of web services in the enhancement of real-time 3D video virtualization in cloud environment

NASA Astrophysics Data System (ADS)

Bada, Adedayo; Wang, Qi; Alcaraz-Calero, Jose M.; Grecos, Christos

2016-04-01

This paper proposes a new approach to improving the application of 3D video rendering and streaming by jointly exploring and optimizing both cloud-based virtualization and web-based delivery. The proposed web service architecture firstly establishes a software virtualization layer based on QEMU (Quick Emulator), an open-source virtualization software that has been able to virtualize system components except for 3D rendering, which is still in its infancy. The architecture then explores the cloud environment to boost the speed of the rendering at the QEMU software virtualization layer. The capabilities and inherent limitations of Virgil 3D, which is one of the most advanced 3D virtual Graphics Processing Unit (GPU) available, are analyzed through benchmarking experiments and integrated into the architecture to further speed up the rendering. Experimental results are reported and analyzed to demonstrate the benefits of the proposed approach.

Revisiting Parametric Types and Virtual Classes

NASA Astrophysics Data System (ADS)

Madsen, Anders Bach; Ernst, Erik

This paper presents a conceptually oriented updated view on the relationship between parametric types and virtual classes. The traditional view is that parametric types excel at structurally oriented composition and decomposition, and virtual classes excel at specifying mutually recursive families of classes whose relationships are preserved in derived families. Conversely, while class families can be specified using a large number of F-bounded type parameters, this approach is complex and fragile; and it is difficult to use traditional virtual classes to specify object composition in a structural manner, because virtual classes are closely tied to nominal typing. This paper adds new insight about the dichotomy between these two approaches; it illustrates how virtual constraints and type refinements, as recently introduced in gbeta and Scala, enable structural treatment of virtual types; finally, it shows how a novel kind of dynamic type check can detect compatibility among entire families of classes.

A 360° Vision for Virtual Organizations Characterization and Modelling: Two Intentional Level Aspects

NASA Astrophysics Data System (ADS)

Priego-Roche, Luz-María; Rieu, Dominique; Front, Agnès

Nowadays, organizations aiming to be successful in an increasingly competitive market tend to group together into virtual organizations. Designing the information system (IS) of such virtual organizations on the basis of the IS of those participating is a real challenge. The IS of a virtual organization plays an important role in the collaboration and cooperation of the participants organizations and in reaching the common goal. This article proposes criteria allowing virtual organizations to be identified and classified at an intentional level, as well as the information necessary for designing the organizations’ IS. Instantiation of criteria for a specific virtual organization and its participants, will allow simple graphical models to be generated in a modelling tool. The models will be used as bases for the IS design at organizational and operational levels. The approach is illustrated by the example of the virtual organization UGRT (a regional stockbreeders union in Tabasco, Mexico).

Future Evolution of Virtual Worlds as Communication Environments

NASA Astrophysics Data System (ADS)

Prisco, Giulio

Extensive experience creating locations and activities inside virtual worlds provides the basis for contemplating their future. Users of virtual worlds are diverse in their goals for these online environments; for example, immersionists want them to be alternative realities disconnected from real life, whereas augmentationists want them to be communication media supporting real-life activities. As the technology improves, the diversity of virtual worlds will increase along with their significance. Many will incorporate more advanced virtual reality, or serve as major media for long-distance collaboration, or become the venues for futurist social movements. Key issues are how people can create their own virtual worlds, travel across worlds, and experience a variety of multimedia immersive environments. This chapter concludes by noting the view among some computer scientists that future technologies will permit uploading human personalities to artificial intelligence avatars, thereby enhancing human beings and rendering the virtual worlds entirely real.

Agreements in Virtual Organizations

NASA Astrophysics Data System (ADS)

Pankowska, Malgorzata

This chapter is an attempt to explain the important impact that contract theory delivers with respect to the concept of virtual organization. The author believes that not enough research has been conducted in order to transfer theoretical foundations for networking to the phenomena of virtual organizations and open autonomic computing environment to ensure the controllability and management of them. The main research problem of this chapter is to explain the significance of agreements for virtual organizations governance. The first part of this chapter comprises explanations of differences among virtual machines and virtual organizations for further descriptions of the significance of the first ones to the development of the second. Next, the virtual organization development tendencies are presented and problems of IT governance in highly distributed organizational environment are discussed. The last part of this chapter covers analysis of contracts and agreements management for governance in open computing environments.

Runtime Performance and Virtual Network Control Alternatives in VM-Based High-Fidelity Network Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yoginath, Srikanth B; Perumalla, Kalyan S; Henz, Brian J

2012-01-01

In prior work (Yoginath and Perumalla, 2011; Yoginath, Perumalla and Henz, 2012), the motivation, challenges and issues were articulated in favor of virtual time ordering of Virtual Machines (VMs) in network simulations hosted on multi-core machines. Two major components in the overall virtualization challenge are (1) virtual timeline establishment and scheduling of VMs, and (2) virtualization of inter-VM communication. Here, we extend prior work by presenting scaling results for the first component, with experiment results on up to 128 VMs scheduled in virtual time order on a single 12-core host. We also explore the solution space of design alternatives formore » the second component, and present performance results from a multi-threaded, multi-queue implementation of inter-VM network control for synchronized execution with VM scheduling, incorporated in our NetWarp simulation system.« less

CycloPs: generating virtual libraries of cyclized and constrained peptides including nonnatural amino acids.

PubMed

Duffy, Fergal J; Verniere, Mélanie; Devocelle, Marc; Bernard, Elise; Shields, Denis C; Chubb, Anthony J

2011-04-25

We introduce CycloPs, software for the generation of virtual libraries of constrained peptides including natural and nonnatural commercially available amino acids. The software is written in the cross-platform Python programming language, and features include generating virtual libraries in one-dimensional SMILES and three-dimensional SDF formats, suitable for virtual screening. The stand-alone software is capable of filtering the virtual libraries using empirical measurements, including peptide synthesizability by standard peptide synthesis techniques, stability, and the druglike properties of the peptide. The software and accompanying Web interface is designed to enable the rapid generation of large, structurally diverse, synthesizable virtual libraries of constrained peptides quickly and conveniently, for use in virtual screening experiments. The stand-alone software, and the Web interface for evaluating these empirical properties of a single peptide, are available at http://bioware.ucd.ie .

Virtual Technologies to Develop Visual-Spatial Ability in Engineering Students

ERIC Educational Resources Information Center

Roca-González, Cristina; Martin-Gutierrez, Jorge; García-Dominguez, Melchor; Carrodeguas, Mª del Carmen Mato

2017-01-01

The present study assessed a short training experiment to improve spatial abilities using two tools based on virtual technologies: one focused on manipulation of specific geometric virtual pieces, and the other consisting of virtual orienteering game. The two tools can help improve spatial abilities required for many engineering problem-solving…

Understanding the Adaptive Use of Virtual World Technology Capabilities and Trust in Virtual Teams

ERIC Educational Resources Information Center

Owens, Dawn

2012-01-01

In an environment of global competition and constant technological change, the use of virtual teams has become commonplace for many organizations. Virtual team members are geographically and temporally dispersed, experience cultural diversity, and lack shared social context and face-to-face encounters considered as irreplaceable for building and…

How Do Virtual World Experiences Bring about Learning? A Critical Review of Theories

ERIC Educational Resources Information Center

Loke, Swee-Kin

2015-01-01

While students do learn real-world knowledge and skills in virtual worlds, educators have yet to adequately theorise how students' virtual world experiences bring about this learning. This paper critically reviewed theories currently used to underpin empirical work in virtual worlds for education. In particular, it evaluated how applicable these…

The Effect of Desktop Illumination Realism on a User's Sense of Presence in a Virtual Learning Environment

ERIC Educational Resources Information Center

Ehrlich, Justin

2010-01-01

The application of virtual reality is becoming ever more important as technology reaches new heights allowing virtual environments (VE) complete with global illumination. One successful application of virtual environments is educational interventions meant to treat individuals with autism spectrum disorder (ASD). VEs are effective with these…

The Intersection of Virtual Organizations and the Library: A Case Study

ERIC Educational Resources Information Center

Carlson, Jake; Yatcilla, Jane Kinkus

2010-01-01

The proliferation of virtual organizations is changing the nature and practice of research. These changes present a challenge to Libraries, as their traditional roles and services do not translate well to virtual organizations. However, virtual organizations also offer opportunities for librarians to participate in shaping the next generation of…

Middle School Students' Learning of Mechanics Concepts through Engagement in Different Sequences of Physical and Virtual Experiments

ERIC Educational Resources Information Center

Sullivan, Sarah; Gnesdilow, Dana; Puntambekar, Sadhana; Kim, Jee-Seon

2017-01-01

Physical and virtual experimentation are thought to have different affordances for supporting students' learning. Research investigating the use of physical and virtual experiments to support students' learning has identified a variety of, sometimes conflicting, outcomes. Unanswered questions remain about how physical and virtual experiments may…

Managing Global Virtual Teams across Classrooms, Students and Faculty

ERIC Educational Resources Information Center

Shea, Timothy P.; Sherer, Pamela D.; Quilling, Rosemary D.; Blewett, Craig N.

2011-01-01

Virtual teams are becoming commonplace in business today so our business school students should have experience in effectively working in virtual teams. Based on a month-long virtual team project conducted by the authors between classes in South Africa and the United States, this paper discusses the opportunities and challenges of using global…

Moving beyond Assumptions: The Use of Virtual Reference Data in an Academic Library

ERIC Educational Resources Information Center

Nolen, David S.; Powers, Amanda Clay; Zhang, Li; Xu, Yue; Cannady, Rachel E.; Li, Judy

2012-01-01

The Mississippi State University Libraries' Virtual Reference Service collected statistics about virtual reference usage. Analysis of the data collected by an entry survey from chat and e-mail transactions provided librarians with concrete information about what patron groups were the highest and lowest users of virtual reference services. These…

Home | Society of Women Engineers

Science.gov Websites

virtual instruction by industry experts and are accessible to members. Find a Learning Activity Explore on ways to engage and promote an inclusive culture. Learn More... Experience WE17 Virtual Access> ;> Check out what you missed with Virtual Conference Access Purchase the Virtual Conference on SWE's

Virtual Frog Dissection Kit Version 2.2

Science.gov Websites

Virtual Frog Dissection Kit This award-winning interactive program is part of the "Whole Frog " project. You can interactively dissect a (digitized) frog named Fluffy, and play the Virtual Frog animals other than the frog that have a computer-graphics based virtual dissection page. We get frequent

Using a Virtual History Conference to Teach the Iraq War

ERIC Educational Resources Information Center

Gilley, Bruce

2013-01-01

In teaching the causes of the Iraq War, the use of "virtual history" can be employed in a conference setting in which different individuals are assigned to different plausible counterfactuals they use to construct virtual histories. The Iraq War lends itself to the virtual history approach because of the availability of many plausible…

The Impact of Virtual Collaboration and Collaboration Technologies on Knowledge Transfer and Team Performance in Distributed Organizations

ERIC Educational Resources Information Center

Ngoma, Ngoma Sylvestre

2013-01-01

Virtual teams are increasingly viewed as a powerful determinant of competitive advantage in geographically distributed organizations. This study was designed to provide insights into the interdependencies between virtual collaboration, collaboration technologies, knowledge transfer, and virtual team performance in an effort to understand whether…

The Study on Virtual Medical Instrument based on LabVIEW.

PubMed

Chengwei, Li; Limei, Zhang; Xiaoming, Hu

2005-01-01

With the increasing performance of computer, the virtual instrument technology has greatly advanced over the years, and then virtual medical instrument technology becomes available. This paper presents the virtual medical instrument, and then as an example, an application of a signal acquisition, processing and analysis system using LabVIEW is also given.

The Potential of Using Virtual Reality Technology in Physical Activity Settings

ERIC Educational Resources Information Center

Pasco, Denis

2013-01-01

In recent years, virtual reality technology has been successfully used for learning purposes. The purposes of the article are to examine current research on the role of virtual reality in physical activity settings and discuss potential application of using virtual reality technology to enhance learning in physical education. The article starts…

Virtual human versus human administration of photographic lineups.

PubMed

Daugherty, Brent; Babu, Sabarish; Wallendael, Lori Van; Cutler, Brian; Hodges, Larry F

2008-01-01

One solution to mistaken identification by a crime's victims and eyewitnesses is to use a virtual officer to conduct identification procedures. Results from a study comparing a virtual officer with a live human investigator indicate that the virtual officer performs comparably to the human in terms of identification accuracy, emotional affect, and ease of use.

The Problem Patron and the Academic Library Web Site as Virtual Reference Desk.

ERIC Educational Resources Information Center

Taylor, Daniel; Porter, George S.

2002-01-01

Considers problem library patrons in a virtual environment based on experiences at California Institute of Technology's Web site and its use for virtual reference. Discusses the virtual reference desk concept; global visibility and access to the World Wide Web; problematic email; and advantages in the electronic environment. (LRW)

Virtual Worlds? "Outlook Good"

ERIC Educational Resources Information Center

Kelton, AJ

2008-01-01

Many people believed that virtual worlds would end up like the eight-track audiotape: a memory of something no longer used (or useful). Yet today there are hundreds of higher education institutions represented in three-dimensional (3D) virtual worlds such as Active Worlds and Second Life. The movement toward the virtual realm as a viable teaching…

Technology Counts 2012: Virtual Shift

ERIC Educational Resources Information Center

Education Week, 2012

2012-01-01

Virtual education is moving into that intersection where rising popularity meets calls for greater accountability. How the virtual education movement responds to those calls will have a significant impact on how it evolves in K-12 over the next five to 10 years. This report tackles this shift in the virtual education landscape. It examines the…

Development and Management of Virtual Schools: Issues and Trends

ERIC Educational Resources Information Center

Cavanaugh, Catherine, Ed.

2004-01-01

Virtual schools are a result of widespread changes in knowledge about learning, in available technology and in society. Virtual schooling is growing in popularity and will continue to attract students because of the benefits it offers over traditional schooling. Stakeholders in virtual schools need information to guide their decisions. For the…

Technical Problems Experienced in the Transformation of Virtual Worlds into an Education Environment and Coping Strategies

ERIC Educational Resources Information Center

Coban, Murat; Karakus, Turkan; Karaman, Asiye; Gunay, Fatma; Goktas, Yuksel

2015-01-01

Research into virtual worlds demonstrates that to successfully use virtual world platforms in different disciplines, certain limitations and potential difficulties of these platforms must be overcome. The current study extends previous research by investigating problems in integrating virtual worlds in education with a longitudinal observation of…

Learning Ethics through Virtual Fieldtrips: Teaching Ethical Theories through Virtual Experiences

ERIC Educational Resources Information Center

Houser, Rick; Thoma, Steve; Coppock, Amanda; Mazer, Matthew; Midkiff, Lewis; Younanian, Marisa; Young, Sarah

2011-01-01

Teaching ethical reasoning is considered an important component of the undergraduate learning experience. A recent approach to teaching using experiential learning is through virtual worlds such as Second Life. We discuss how ethics may be taught using experiential learning in the virtual world of Second Life. Participants in the class in this…

Risks and Uncertainties in Virtual Worlds: An Educators' Perspective

ERIC Educational Resources Information Center

Farahmand, Fariborz; Yadav, Aman; Spafford, Eugene H.

2013-01-01

Virtual worlds present tremendous advantages to cyberlearning. For example, in virtual worlds users can socialize with others, build objects and share them, customize parts of the world and hold lectures, do experiments, or share data. However, virtual worlds pose a wide range of security, privacy, and safety concerns. This may lead educators to…

On Being Bored and Lost (in Virtuality)

ERIC Educational Resources Information Center

Moore, Kristen; Pflugfelder, Ehren Helmut

2010-01-01

Education in virtual worlds has the potential, it seems, for engaging students in innovative ways and for enabling new discourses on a host of issues. Virtual locations like "Second Life," "Kaneva," or "World of Warcraft," among other multi-user virtual environments (MUVEs), also come with unique challenges for educators as they consider the…

Virtual Virtuosos: A Case Study in Learning Music in Virtual Learning Environments in Spain

ERIC Educational Resources Information Center

Alberich-Artal, Enric; Sangra, Albert

2012-01-01

In recent years, the development of Information and Communication Technologies (ICT) has contributed to the generation of a number of interesting initiatives in the field of music education and training in virtual learning environments. However, music education initiatives employing virtual learning environments have replicated and perpetuated the…

Education about Hallucinations Using an Internet Virtual Reality System: A Qualitative Survey

ERIC Educational Resources Information Center

Yellowlees, Peter M.; Cook, James N.

2006-01-01

Objective: The authors evaluate an Internet virtual reality technology as an education tool about the hallucinations of psychosis. Method: This is a pilot project using Second Life, an Internet-based virtual reality system, in which a virtual reality environment was constructed to simulate the auditory and visual hallucinations of two patients…

Teaching with Virtual Worlds: Factors to Consider for Instructional Use of Second Life

ERIC Educational Resources Information Center

Mayrath, Michael C.; Traphagan, Tomoko; Jarmon, Leslie; Trivedi, Avani; Resta, Paul

2010-01-01

Substantial evidence now supports pedagogical applications of virtual worlds; however, most research supporting virtual worlds for education has been conducted using researcher-developed Multi-User Virtual Environments (MUVE). Second Life (SL) is a MUVE that has been adopted by a large number of academic institutions; however, little research has…

Effects of Exercise in Immersive Virtual Environments on Cortical Neural Oscillations and Mental State

PubMed Central

Vogt, Tobias; Herpers, Rainer; Askew, Christopher D.; Scherfgen, David; Strüder, Heiko K.; Schneider, Stefan

2015-01-01

Virtual reality environments are increasingly being used to encourage individuals to exercise more regularly, including as part of treatment those with mental health or neurological disorders. The success of virtual environments likely depends on whether a sense of presence can be established, where participants become fully immersed in the virtual environment. Exposure to virtual environments is associated with physiological responses, including cortical activation changes. Whether the addition of a real exercise within a virtual environment alters sense of presence perception, or the accompanying physiological changes, is not known. In a randomized and controlled study design, moderate-intensity Exercise (i.e., self-paced cycling) and No-Exercise (i.e., automatic propulsion) trials were performed within three levels of virtual environment exposure. Each trial was 5 minutes in duration and was followed by posttrial assessments of heart rate, perceived sense of presence, EEG, and mental state. Changes in psychological strain and physical state were generally mirrored by neural activation patterns. Furthermore, these changes indicated that exercise augments the demands of virtual environment exposures and this likely contributed to an enhanced sense of presence. PMID:26366305

Energy Consumption Management of Virtual Cloud Computing Platform

NASA Astrophysics Data System (ADS)

Li, Lin

2017-11-01

For energy consumption management research on virtual cloud computing platforms, energy consumption management of virtual computers and cloud computing platform should be understood deeper. Only in this way can problems faced by energy consumption management be solved. In solving problems, the key to solutions points to data centers with high energy consumption, so people are in great need to use a new scientific technique. Virtualization technology and cloud computing have become powerful tools in people’s real life, work and production because they have strong strength and many advantages. Virtualization technology and cloud computing now is in a rapid developing trend. It has very high resource utilization rate. In this way, the presence of virtualization and cloud computing technologies is very necessary in the constantly developing information age. This paper has summarized, explained and further analyzed energy consumption management questions of the virtual cloud computing platform. It eventually gives people a clearer understanding of energy consumption management of virtual cloud computing platform and brings more help to various aspects of people’s live, work and son on.

Virtual reality measures in neuropsychological assessment: a meta-analytic review.

PubMed

Neguț, Alexandra; Matu, Silviu-Andrei; Sava, Florin Alin; David, Daniel

2016-02-01

Virtual reality-based assessment is a new paradigm for neuropsychological evaluation, that might provide an ecological assessment, compared to paper-and-pencil or computerized neuropsychological assessment. Previous research has focused on the use of virtual reality in neuropsychological assessment, but no meta-analysis focused on the sensitivity of virtual reality-based measures of cognitive processes in measuring cognitive processes in various populations. We found eighteen studies that compared the cognitive performance between clinical and healthy controls on virtual reality measures. Based on a random effects model, the results indicated a large effect size in favor of healthy controls (g = .95). For executive functions, memory and visuospatial analysis, subgroup analysis revealed moderate to large effect sizes, with superior performance in the case of healthy controls. Participants' mean age, type of clinical condition, type of exploration within virtual reality environments, and the presence of distractors were significant moderators. Our findings support the sensitivity of virtual reality-based measures in detecting cognitive impairment. They highlight the possibility of using virtual reality measures for neuropsychological assessment in research applications, as well as in clinical practice.

Effects of virtual reality-based bilateral upper-extremity training on brain activity in post-stroke patients.

PubMed

Lee, Su-Hyun; Kim, Yu-Mi; Lee, Byoung-Hee

2015-07-01

[Purpose] This study investigated the therapeutic effects of virtual reality-based bilateral upper-extremity training on brain activity in patients with stroke. [Subjects and Methods] Eighteen chronic stroke patients were divided into two groups: the virtual reality-based bilateral upper-extremity training group (n = 10) and the bilateral upper-limb training group (n = 8). The virtual reality-based bilateral upper-extremity training group performed bilateral upper-extremity exercises in a virtual reality environment, while the bilateral upper-limb training group performed only bilateral upper-extremity exercise. All training was conducted 30 minutes per day, three times per week for six weeks, followed by brain activity evaluation. [Results] Electroencephalography showed significant increases in concentration in the frontopolar 2 and frontal 4 areas, and significant increases in brain activity in the frontopolar 1 and frontal 3 areas in the virtual reality-based bilateral upper-extremity training group. [Conclusion] Virtual reality-based bilateral upper-extremity training can improve the brain activity of stroke patients. Thus, virtual reality-based bilateral upper-extremity training is feasible and beneficial for improving brain activation in stroke patients.

[Application of virtual reality in surgical treatment of complex head and neck carcinoma].

PubMed

Zhou, Y Q; Li, C; Shui, C Y; Cai, Y C; Sun, R H; Zeng, D F; Wang, W; Li, Q L; Huang, L; Tu, J; Jiang, J

2018-01-07

Objective: To investigate the application of virtual reality technology in the preoperative evaluation of complex head and neck carcinoma and he value of virtual reality technology in surgical treatment of head and neck carcinoma. Methods: The image data of eight patients with complex head and neck carcinoma treated from December 2016 to May 2017 was acquired. The data were put into virtual reality system to built the three-dimensional anatomical model of carcinoma and to created the surgical scene. The process of surgery was stimulated by recognizing the relationship between tumor and surrounding important structures. Finally all patients were treated with surgery. And two typical cases were reported. Results: With the help of virtual reality, surgeons could adequately assess the condition of carcinoma and the security of operation and ensured the safety of operations. Conclusions: Virtual reality can provide the surgeons with the sensory experience in virtual surgery scenes and achieve the man-computer cooperation and stereoscopic assessment, which will ensure the safety of surgery. Virtual reality has a huge impact on guiding the traditional surgical procedure of head and neck carcinoma.

Cognitive load of navigating without vision when guided by virtual sound versus spatial language.

PubMed

Klatzky, Roberta L; Marston, James R; Giudice, Nicholas A; Golledge, Reginald G; Loomis, Jack M

2006-12-01

A vibrotactile N-back task was used to generate cognitive load while participants were guided along virtual paths without vision. As participants stepped in place, they moved along a virtual path of linear segments. Information was provided en route about the direction of the next turning point, by spatial language ("left," "right," or "straight") or virtual sound (i.e., the perceived azimuth of the sound indicated the target direction). The authors hypothesized that virtual sound, being processed at direct perceptual levels, would have lower load than even simple language commands, which require cognitive mediation. As predicted, whereas the guidance modes did not differ significantly in the no-load condition, participants showed shorter distance traveled and less time to complete a path when performing the N-back task while navigating with virtual sound as guidance. Virtual sound also produced better N-back performance than spatial language. By indicating the superiority of virtual sound for guidance when cognitive load is present, as is characteristic of everyday navigation, these results have implications for guidance systems for the visually impaired and others.

[Virtual + 1] * Reality

NASA Astrophysics Data System (ADS)

Beckhaus, Steffi

Virtual Reality aims at creating an artificial environment that can be perceived as a substitute to a real setting. Much effort in research and development goes into the creation of virtual environments that in their majority are perceivable only by eyes and hands. The multisensory nature of our perception, however, allows and, arguably, also expects more than that. As long as we are not able to simulate and deliver a fully sensory believable virtual environment to a user, we could make use of the fully sensory, multi-modal nature of real objects to fill in for this deficiency. The idea is to purposefully integrate real artifacts into the application and interaction, instead of dismissing anything real as hindering the virtual experience. The term virtual reality - denoting the goal, not the technology - shifts from a core virtual reality to an “enriched” reality, technologically encompassing both the computer generated and the real, physical artifacts. Together, either simultaneously or in a hybrid way, real and virtual jointly provide stimuli that are perceived by users through their senses and are later formed into an experience by the user's mind.

Effects of decades of physical driving on body movement and motion sickness during virtual driving

PubMed Central

Chang, Chih-Hui; Chen, Fu-Chen; Zeng, Wei-Jhong

2017-01-01

We investigated relations between experience driving physical automobiles and motion sickness during the driving of virtual automobiles. Middle-aged individuals drove a virtual automobile in a driving video game. Drivers were individuals who had possessed a driver’s license for approximately 30 years, and who drove regularly, while non-drivers were individuals who had never held a driver’s license, or who had not driven for more than 15 years. During virtual driving, we monitored movement of the head and torso. During virtual driving, drivers became motion sick more rapidly than non-drivers, but the incidence and severity of motion sickness did not differ as a function of driving experience. Patterns of movement during virtual driving differed as a function of driving experience. Separately, movement differed between participants who later became motion sick and those who did not. Most importantly, physical driving experience influenced patterns of postural activity that preceded motion sickness during virtual driving. The results are consistent with the postural instability theory of motion sickness, and help to illuminate relations between the control of physical and virtual vehicles. PMID:29121059

Virtual sensors for active noise control in acoustic-structural coupled enclosures using structural sensing: robust virtual sensor design.

PubMed

Halim, Dunant; Cheng, Li; Su, Zhongqing

2011-03-01

The work was aimed to develop a robust virtual sensing design methodology for sensing and active control applications of vibro-acoustic systems. The proposed virtual sensor was designed to estimate a broadband acoustic interior sound pressure using structural sensors, with robustness against certain dynamic uncertainties occurring in an acoustic-structural coupled enclosure. A convex combination of Kalman sub-filters was used during the design, accommodating different sets of perturbed dynamic model of the vibro-acoustic enclosure. A minimax optimization problem was set up to determine an optimal convex combination of Kalman sub-filters, ensuring an optimal worst-case virtual sensing performance. The virtual sensing and active noise control performance was numerically investigated on a rectangular panel-cavity system. It was demonstrated that the proposed virtual sensor could accurately estimate the interior sound pressure, particularly the one dominated by cavity-controlled modes, by using a structural sensor. With such a virtual sensing technique, effective active noise control performance was also obtained even for the worst-case dynamics. © 2011 Acoustical Society of America

Effects of Exercise in Immersive Virtual Environments on Cortical Neural Oscillations and Mental State.

PubMed

Vogt, Tobias; Herpers, Rainer; Askew, Christopher D; Scherfgen, David; Strüder, Heiko K; Schneider, Stefan

2015-01-01

Virtual reality environments are increasingly being used to encourage individuals to exercise more regularly, including as part of treatment those with mental health or neurological disorders. The success of virtual environments likely depends on whether a sense of presence can be established, where participants become fully immersed in the virtual environment. Exposure to virtual environments is associated with physiological responses, including cortical activation changes. Whether the addition of a real exercise within a virtual environment alters sense of presence perception, or the accompanying physiological changes, is not known. In a randomized and controlled study design, moderate-intensity Exercise (i.e., self-paced cycling) and No-Exercise (i.e., automatic propulsion) trials were performed within three levels of virtual environment exposure. Each trial was 5 minutes in duration and was followed by posttrial assessments of heart rate, perceived sense of presence, EEG, and mental state. Changes in psychological strain and physical state were generally mirrored by neural activation patterns. Furthermore, these changes indicated that exercise augments the demands of virtual environment exposures and this likely contributed to an enhanced sense of presence.

Virtual terrain: a security-based representation of a computer network

NASA Astrophysics Data System (ADS)

Holsopple, Jared; Yang, Shanchieh; Argauer, Brian

2008-03-01

Much research has been put forth towards detection, correlating, and prediction of cyber attacks in recent years. As this set of research progresses, there is an increasing need for contextual information of a computer network to provide an accurate situational assessment. Typical approaches adopt contextual information as needed; yet such ad hoc effort may lead to unnecessary or even conflicting features. The concept of virtual terrain is, therefore, developed and investigated in this work. Virtual terrain is a common representation of crucial information about network vulnerabilities, accessibilities, and criticalities. A virtual terrain model encompasses operating systems, firewall rules, running services, missions, user accounts, and network connectivity. It is defined as connected graphs with arc attributes defining dynamic relationships among vertices modeling network entities, such as services, users, and machines. The virtual terrain representation is designed to allow feasible development and maintenance of the model, as well as efficacy in terms of the use of the model. This paper will describe the considerations in developing the virtual terrain schema, exemplary virtual terrain models, and algorithms utilizing the virtual terrain model for situation and threat assessment.

Virtual Embodiment of White People in a Black Virtual Body Leads to a Sustained Reduction in Their Implicit Racial Bias.

PubMed

Banakou, Domna; Hanumanthu, Parasuram D; Slater, Mel

2016-01-01

Virtual reality can be used to visually substitute a person's body by a life-sized virtual one. Such embodiment results in a perceptual illusion of body ownership over the virtual body (VB). Previous research has shown that the form of the VB can influence implicit attitudes. In particular, embodying White people in a Black virtual body is associated with an immediate decrease in their implicit racial bias against Black people. We tested whether the reduction in implicit bias lasts for at least 1 week and whether it is enhanced by multiple exposures. Two experiments were carried out with a total of 90 female participants where the virtual body was either Black or White. Participants were required to follow a virtual Tai Chi teacher who was either Asian or European Caucasian. Each participant had 1, 2, or 3 exposures separated by days. Implicit racial bias was measured 1 week before their first exposure and 1 week after their last. The results show that implicit bias decreased more for those with the Black virtual body than the White. There was also some evidence of a general decrease in bias independently of body type for which possible explanations are put forward.

Virtual education effect on cognitive learning and attitude of nursing students towards it.

PubMed

Borhani, Fariba; Vatanparast, Mahboubeh; Zadeh, Abbas Abbas; Ranjbar, Hadi; Pour, Reza Shojaei

2011-01-01

Along with emersion of the Internet, virtual education increasingly has been growing. Many studies discussed this method and its impact on learning. Present study investigated students' attitude towards virtual education as well as its effect on learning. This was a pretest-posttest quasi-experimental study. The nursing students, who had selected fluids and electrolyte disorders course, were randomly divided into two virtual and conventional education groups. The knowledge of students was assessed through a written exam and students' attitude towards virtual education assessed by a researcher-made questionnaire. Mean scores of students in pretest were 0.8 (0.3) and 1.1 (0.59) in virtual and conventional group respectively [mean (SD)]. At the end of the semester their scores were 15.9 (0.58) and 16.51 (0.89) respectively. Mean attitude scores at baseline were 3.19 (0.48) and 3.21 (0.33) followed by 3.55 (0.45) and 3.21 (0.46) at the end of the semester in virtual and conventional groups respectively. Although the scores of conventional group at the end of the course were higher than virtual group, both methods acted similarly in terms of increasing the knowledge. Passing a virtual education course may improve the attitude of the nurses towards it.

Use of Virtual Reality Tools for Vestibular Disorders Rehabilitation: A Comprehensive Analysis.

PubMed

Bergeron, Mathieu; Lortie, Catherine L; Guitton, Matthieu J

2015-01-01

Classical peripheral vestibular disorders rehabilitation is a long and costly process. While virtual reality settings have been repeatedly suggested to represent possible tools to help the rehabilitation process, no systematic study had been conducted so far. We systematically reviewed the current literature to analyze the published protocols documenting the use of virtual reality settings for peripheral vestibular disorders rehabilitation. There is an important diversity of settings and protocols involving virtual reality settings for the treatment of this pathology. Evaluation of the symptoms is often not standardized. However, our results unveil a clear effect of virtual reality settings-based rehabilitation of the patients' symptoms, assessed by objectives tools such as the DHI (mean decrease of 27 points), changing symptoms handicap perception from moderate to mild impact on life. Furthermore, we detected a relationship between the duration of the exposure to virtual reality environments and the magnitude of the therapeutic effects, suggesting that virtual reality treatments should last at least 150 minutes of cumulated exposure to ensure positive outcomes. Virtual reality offers a pleasant and safe environment for the patient. Future studies should standardize evaluation tools, document putative side effects further, compare virtual reality to conventional physical therapy, and evaluate economical costs/benefits of such strategies.

Stepping into the virtual unknown: feasibility study of a virtual reality-based test of ocular misalignment.

PubMed

Nesaratnam, N; Thomas, P; Vivian, A

2017-10-01

IntroductionDissociated tests of strabismus provide valuable information for diagnosis and monitoring of ocular misalignment in patients with normal retinal correspondence. However, they are vulnerable to operator error and rely on a fixed head position. Virtual reality headsets obviate the need for head fixation, while providing other clear theoretical advantages, including complete control over the illumination and targets presented for the patient's interaction.PurposeWe compared the performance of a virtual reality-based test of ocular misalignment to that of the traditional Lees screen, to establish the feasibility of using virtual reality technology in ophthalmic settings in the future.MethodsThree patients underwent a traditional Lees screen test, and a virtual reality headset-based test of ocular motility. The virtual reality headset-based programme consisted of an initial test to measure horizontal and vertical deviation, followed by a test for torsion.ResultsThe pattern of deviation obtained using the virtual reality-based test showed agreement with that obtained from the Lees screen for patients with a fourth nerve palsy, comitant esotropia, and restrictive thyroid eye disease.ConclusionsThis study reports the first use of a virtual reality headset in assessing ocular misalignment, and demonstrates that it is a feasible dissociative test of strabismus.

System-Level Virtualization for High Performance Computing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vallee, Geoffroy R; Naughton, III, Thomas J; Engelmann, Christian

2008-01-01

System-level virtualization has been a research topic since the 70's but regained popularity during the past few years because of the availability of efficient solution such as Xen and the implementation of hardware support in commodity processors (e.g. Intel-VT, AMD-V). However, a majority of system-level virtualization projects is guided by the server consolidation market. As a result, current virtualization solutions appear to not be suitable for high performance computing (HPC) which is typically based on large-scale systems. On another hand there is significant interest in exploiting virtual machines (VMs) within HPC for a number of other reasons. By virtualizing themore » machine, one is able to run a variety of operating systems and environments as needed by the applications. Virtualization allows users to isolate workloads, improving security and reliability. It is also possible to support non-native environments and/or legacy operating environments through virtualization. In addition, it is possible to balance work loads, use migration techniques to relocate applications from failing machines, and isolate fault systems for repair. This document presents the challenges for the implementation of a system-level virtualization solution for HPC. It also presents a brief survey of the different approaches and techniques to address these challenges.« less

Virtual Embodiment of White People in a Black Virtual Body Leads to a Sustained Reduction in Their Implicit Racial Bias

PubMed Central

Banakou, Domna; Hanumanthu, Parasuram D.; Slater, Mel

2016-01-01

Virtual reality can be used to visually substitute a person's body by a life-sized virtual one. Such embodiment results in a perceptual illusion of body ownership over the virtual body (VB). Previous research has shown that the form of the VB can influence implicit attitudes. In particular, embodying White people in a Black virtual body is associated with an immediate decrease in their implicit racial bias against Black people. We tested whether the reduction in implicit bias lasts for at least 1 week and whether it is enhanced by multiple exposures. Two experiments were carried out with a total of 90 female participants where the virtual body was either Black or White. Participants were required to follow a virtual Tai Chi teacher who was either Asian or European Caucasian. Each participant had 1, 2, or 3 exposures separated by days. Implicit racial bias was measured 1 week before their first exposure and 1 week after their last. The results show that implicit bias decreased more for those with the Black virtual body than the White. There was also some evidence of a general decrease in bias independently of body type for which possible explanations are put forward. PMID:27965555

Use of Virtual Reality Tools for Vestibular Disorders Rehabilitation: A Comprehensive Analysis

PubMed Central

Bergeron, Mathieu; Lortie, Catherine L.; Guitton, Matthieu J.

2015-01-01

Classical peripheral vestibular disorders rehabilitation is a long and costly process. While virtual reality settings have been repeatedly suggested to represent possible tools to help the rehabilitation process, no systematic study had been conducted so far. We systematically reviewed the current literature to analyze the published protocols documenting the use of virtual reality settings for peripheral vestibular disorders rehabilitation. There is an important diversity of settings and protocols involving virtual reality settings for the treatment of this pathology. Evaluation of the symptoms is often not standardized. However, our results unveil a clear effect of virtual reality settings-based rehabilitation of the patients' symptoms, assessed by objectives tools such as the DHI (mean decrease of 27 points), changing symptoms handicap perception from moderate to mild impact on life. Furthermore, we detected a relationship between the duration of the exposure to virtual reality environments and the magnitude of the therapeutic effects, suggesting that virtual reality treatments should last at least 150 minutes of cumulated exposure to ensure positive outcomes. Virtual reality offers a pleasant and safe environment for the patient. Future studies should standardize evaluation tools, document putative side effects further, compare virtual reality to conventional physical therapy, and evaluate economical costs/benefits of such strategies. PMID:26556560

Incorporating Virtual Reactions into a Logic-based Ligand-based Virtual Screening Method to Discover New Leads

PubMed Central

Reynolds, Christopher R; Muggleton, Stephen H; Sternberg, Michael J E

2015-01-01

The use of virtual screening has become increasingly central to the drug development pipeline, with ligand-based virtual screening used to screen databases of compounds to predict their bioactivity against a target. These databases can only represent a small fraction of chemical space, and this paper describes a method of exploring synthetic space by applying virtual reactions to promising compounds within a database, and generating focussed libraries of predicted derivatives. A ligand-based virtual screening tool Investigational Novel Drug Discovery by Example (INDDEx) is used as the basis for a system of virtual reactions. The use of virtual reactions is estimated to open up a potential space of 1.21×1012 potential molecules. A de novo design algorithm known as Partial Logical-Rule Reactant Selection (PLoRRS) is introduced and incorporated into the INDDEx methodology. PLoRRS uses logical rules from the INDDEx model to select reactants for the de novo generation of potentially active products. The PLoRRS method is found to increase significantly the likelihood of retrieving molecules similar to known actives with a p-value of 0.016. Case studies demonstrate that the virtual reactions produce molecules highly similar to known actives, including known blockbuster drugs. PMID:26583052

Framing the magic

NASA Astrophysics Data System (ADS)

Tsoupikova, Daria

2006-02-01

This paper will explore how the aesthetics of the virtual world affects, transforms, and enhances the immersive emotional experience of the user. What we see and what we do upon entering the virtual environment influences our feelings, mental state, physiological changes and sensibility. To create a unique virtual experience the important component to design is the beauty of the virtual world based on the aesthetics of the graphical objects such as textures, models, animation, and special effects. The aesthetic potency of the images that comprise the virtual environment can make the immersive experience much stronger and more compelling. The aesthetic qualities of the virtual world as born out through images and graphics can influence the user's state of mind. Particular changes and effects on the user can be induced through the application of techniques derived from the research fields of psychology, anthropology, biology, color theory, education, art therapy, music, and art history. Many contemporary artists and developers derive much inspiration for their work from their experience with traditional arts such as painting, sculpture, design, architecture and music. This knowledge helps them create a higher quality of images and stereo graphics in the virtual world. The understanding of the close relation between the aesthetic quality of the virtual environment and the resulting human perception is the key to developing an impressive virtual experience.

Novel virtual reality system integrating online self-face viewing and mirror visual feedback for stroke rehabilitation: rationale and feasibility.

PubMed

Shiri, Shimon; Feintuch, Uri; Lorber-Haddad, Adi; Moreh, Elior; Twito, Dvora; Tuchner-Arieli, Maya; Meiner, Zeev

2012-01-01

To introduce the rationale of a novel virtual reality system based on self-face viewing and mirror visual feedback, and to examine its feasibility as a rehabilitation tool for poststroke patients. A novel motion capture virtual reality system integrating online self-face viewing and mirror visual feedback has been developed for stroke rehabilitation.The system allows the replacement of the impaired arm by a virtual arm. Upon making small movements of the paretic arm, patients view themselves virtually performing healthy full-range movements. A sample of 6 patients in the acute poststroke phase received the virtual reality treatment concomitantly with conservative rehabilitation treatment. Feasibility was assessed during 10 sessions for each participant. All participants succeeded in operating the system, demonstrating its feasibility in terms of adherence and improvement in task performance. Patients' performance within the virtual environment and a set of clinical-functional measures recorded before the virtual reality treatment, at 1 week, and after 3 months indicated neurological status and general functioning improvement. These preliminary results indicate that this newly developed virtual reality system is safe and feasible. Future randomized controlled studies are required to assess whether this system has beneficial effects in terms of enhancing upper limb function and quality of life in poststroke patients.

[Current problems in the data acquisition of digitized virtual human and the countermeasures].

PubMed

Zhong, Shi-zhen; Yuan, Lin

2003-06-01

As a relatively new field of medical science research that has attracted the attention from worldwide researchers, study of digitized virtual human still awaits long-term dedicated effort for its full development. In the full array of research projects of the integrated Virtual Chinese Human project, virtual visible human, virtual physical human, virtual physiome, and intellectualized virtual human must be included as the four essential constitutional opponents. The primary importance should be given to solving the problems concerning the data acquisition for the dataset of this immense project. Currently 9 virtual human datasets have been established worldwide, which are subjected to critical analyses in the paper with special attention given to the problems in the data storage and the techniques employed, for instance, in these datasets. On the basis of current research status of Virtual Chinese Human project, the authors propose some countermeasures for solving the problems in the data acquisition for the dataset, which include (1) giving the priority to the quality control instead of merely racing for quantity and speed, and (2) improving the setting up of the markers specific for the tissues and organs to meet the requirement from information technology, (3) with also attention to the development potential of the dataset which should have explicit pertinence to specific actual applications.

Prospective comparison of virtual fluoroscopy to fluoroscopy and plain radiographs for placement of lumbar pedicle screws.

PubMed

Resnick, Daniel K

2003-06-01

Fluoroscopy-based frameless stereotactic systems provide feedback to the surgeon using virtual fluoroscopic images. The real-life accuracy of these virtual images has not been compared with traditional fluoroscopy in a clinical setting. We prospectively studied 23 consecutive cases. In two cases, registration errors precluded the use of virtual fluoroscopy. Pedicle probes placed with virtual fluoroscopic imaging were imaged with traditional fluoroscopy in the remaining 21 cases. Position of the probes was judged to be ideal, acceptable but not ideal, or not acceptable based on the traditional fluoroscopic images. Virtual fluoroscopy was used to place probes in for 97 pedicles from L1 to the sacrum. Eighty-eight probes were judged to be in ideal position, eight were judged to be acceptable but not ideal, and one probe was judged to be in an unacceptable position. This probe was angled toward an adjacent disc space. Therefore, 96 of 97 probes placed using virtual fluoroscopy were found to be in an acceptable position. The positive predictive value for acceptable screw placement with virtual fluoroscopy compared with traditional fluoroscopy was 99%. A probe placed with virtual fluoroscopic guidance will be judged to be in an acceptable position when imaged with traditional fluoroscopy 99% of the time.

Image Mosaicking Approach for a Double-Camera System in the GaoFen2 Optical Remote Sensing Satellite Based on the Big Virtual Camera.

PubMed

Cheng, Yufeng; Jin, Shuying; Wang, Mi; Zhu, Ying; Dong, Zhipeng

2017-06-20

The linear array push broom imaging mode is widely used for high resolution optical satellites (HROS). Using double-cameras attached by a high-rigidity support along with push broom imaging is one method to enlarge the field of view while ensuring high resolution. High accuracy image mosaicking is the key factor of the geometrical quality of complete stitched satellite imagery. This paper proposes a high accuracy image mosaicking approach based on the big virtual camera (BVC) in the double-camera system on the GaoFen2 optical remote sensing satellite (GF2). A big virtual camera can be built according to the rigorous imaging model of a single camera; then, each single image strip obtained by each TDI-CCD detector can be re-projected to the virtual detector of the big virtual camera coordinate system using forward-projection and backward-projection to obtain the corresponding single virtual image. After an on-orbit calibration and relative orientation, the complete final virtual image can be obtained by stitching the single virtual images together based on their coordinate information on the big virtual detector image plane. The paper subtly uses the concept of the big virtual camera to obtain a stitched image and the corresponding high accuracy rational function model (RFM) for concurrent post processing. Experiments verified that the proposed method can achieve seamless mosaicking while maintaining the geometric accuracy.

An intelligent virtual human system for providing healthcare information and support.

PubMed

Rizzo, Albert A; Lange, Belinda; Buckwalter, John G; Forbell, Eric; Kim, Julia; Sagae, Kenji; Williams, Josh; Rothbaum, Barbara O; Difede, JoAnn; Reger, Greg; Parsons, Thomas; Kenny, Patrick

2011-01-01

Over the last 15 years, a virtual revolution has taken place in the use of Virtual Reality simulation technology for clinical purposes. Shifts in the social and scientific landscape have now set the stage for the next major movement in Clinical Virtual Reality with the "birth" of intelligent virtual humans. Seminal research and development has appeared in the creation of highly interactive, artificially intelligent and natural language capable virtual human agents that can engage real human users in a credible fashion. No longer at the level of a prop to add context or minimal faux interaction in a virtual world, virtual humans can be designed to perceive and act in a 3D virtual world, engage in spoken dialogues with real users and can be capable of exhibiting human-like emotional reactions. This paper will present an overview of the SimCoach project that aims to develop virtual human support agents to serve as online guides for promoting access to psychological healthcare information and for assisting military personnel and family members in breaking down barriers to initiating care. The SimCoach experience is being designed to attract and engage military Service Members, Veterans and their significant others who might not otherwise seek help with a live healthcare provider. It is expected that this experience will motivate users to take the first step--to empower themselves to seek advice and information regarding their healthcare and general personal welfare and encourage them to take the next step towards seeking more formal resources if needed.

Propagation of crises in the virtual water trade network

NASA Astrophysics Data System (ADS)

Tamea, Stefania; Laio, Francesco; Ridolfi, Luca

2015-04-01

The international trade of agricultural goods is associated to the displacement of the water used to produce such goods and embedded in trade as a factor of production. Water virtually exchanged from producing to consuming countries, named virtual water, defines flows across an international network of 'virtual water trade' which enable the assessment of environmental forcings and implications of trade, such as global water savings or country dependencies on foreign water resources. Given the recent expansion of commodity (and virtual water) trade, in both displaced volumes and network structure, concerns have been raised about the exposure to crises of individuals and societies. In fact, if one country had to markedly decrease its export following a socio-economical or environmental crisis, such as a war or a drought, many -if not all- countries would be affected due to a cascade effect within the trade network. The present contribution proposes a mechanistic model describing the propagation of a local crisis into the virtual water trade network, accounting for the network structure and the virtual water balance of all countries. The model, built on data-based assumptions, is tested on the real case study of the Argentinean crisis in 2008-09, when the internal agricultural production (measured as virtual water volume) decreased by 26% and the virtual water export of Argentina dropped accordingly. Crisis propagation and effects on the virtual water trade are correctly captured, showing the way forward to investigations of crises impact and country vulnerability based on the results of the model proposed.

Role of virtual bronchoscopy in children with a vegetable foreign body in the tracheobronchial tree.

PubMed

Behera, G; Tripathy, N; Maru, Y K; Mundra, R K; Gupta, Y; Lodha, M

2014-12-01

Multidetector computed tomography virtual bronchoscopy is a non-invasive diagnostic tool which provides a three-dimensional view of the tracheobronchial airway. This study aimed to evaluate the usefulness of virtual bronchoscopy in cases of vegetable foreign body aspiration in children. The medical records of patients with a history of foreign body aspiration from August 2006 to August 2010 were reviewed. Data were collected regarding their clinical presentation and chest X-ray, virtual bronchoscopy and rigid bronchoscopy findings. Cases of metallic and other non-vegetable foreign bodies were excluded from the analysis. Patients with multidetector computed tomography virtual bronchoscopy showing features of vegetable foreign body were included in the analysis. For each patient, virtual bronchoscopy findings were reviewed and compared with those of rigid bronchoscopy. A total of 60 patients; all children ranging from 1 month to 8 years of age, were included. The mean age at presentation was 2.01 years. Rigid bronchoscopy confirmed the results of multidetector computed tomography virtual bronchoscopy (i.e. presence of foreign body, site of lodgement, and size and shape) in 59 patients. In the remaining case, a vegetable foreign body identified by virtual bronchoscopy was revealed by rigid bronchoscopy to be a thick mucus plug. Thus, the positive predictive value of virtual bronchoscopy was 98.3 per cent. Multidetector computed tomography virtual bronchoscopy is a sensitive and specific diagnostic tool for identifying radiolucent vegetable foreign bodies in the tracheobronchial tree. It can also provide a useful pre-operative road map for rigid bronchoscopy. Patients suspected of having an airway foreign body or chronic unexplained respiratory symptoms should undergo multidetector computed tomography virtual bronchoscopy to rule out a vegetable foreign body in the tracheobronchial tree and avoid general anaesthesia and invasive rigid bronchoscopy.

A Second Chance at Health: How a 3D Virtual World Can Improve Health Self-Efficacy for Weight Loss Management Among Adults.

PubMed

Behm-Morawitz, Elizabeth; Lewallen, Jennifer; Choi, Grace

2016-02-01

Health self-efficacy, or the beliefs in one's capabilities to perform health behaviors, is a significant factor in eliciting health behavior change, such as weight loss. Research has demonstrated that virtual embodiment has the potential to alter one's psychology and physicality, particularly in health contexts; however, little is known about the impacts embodiment in a virtual world has on health self-efficacy. The present research is a randomized controlled trial (N = 90) examining the effectiveness of virtual embodiment and play in a social virtual world (Second Life [SL]) for increasing health self-efficacy (exercise and nutrition efficacy) among overweight adults. Participants were randomly assigned to a 3D social virtual world (avatar virtual interaction experimental condition), 2D social networking site (no avatar virtual interaction control condition), or no intervention (no virtual interaction control condition). The findings of this study provide initial evidence for the use of SL to improve exercise efficacy and to support weight loss. Results also suggest that individuals who have higher self-presence with their avatar reap more benefits. Finally, quantitative findings are triangulated with qualitative data to increase confidence in the results and provide richer insight into the perceived effectiveness and limitations of SL for meeting weight loss goals. Themes resulting from the qualitative analysis indicate that participation in SL can improve motivation and efficacy to try new physical activities; however, individuals who have a dislike for video games may not be benefitted by avatar-based virtual interventions. Implications for research on the transformative potential of virtual embodiment and self-presence in general are discussed.