WorldWideScience

Sample records for genome lab opens

  1. OpenLabNotes

    DEFF Research Database (Denmark)

    List, Markus; Franz, Michael; Tan, Qihua

    2015-01-01

    be advantageous if an ELN was Integrated with a laboratory information management system to allow for a comprehensive documentation of experimental work including the location of samples that were used in a particular experiment. Here, we present OpenLabNotes, which adds state-of-the-art ELN capabilities to Open......LabFramework, a powerful and flexible laboratory information management system. In contrast to comparable solutions, it allows to protect the intellectual property of its users by offering data protection with digital signatures. OpenLabNotes effectively Closes the gap between research documentation and sample management...

  2. Comparative genomics of Lactobacillus and other LAB

    DEFF Research Database (Denmark)

    Wassenaar, Trudy M.; Lukjancenko, Oksana

    2014-01-01

    The genomes of 66 LABs, belonging to five different genera, were compared for genome size and gene content. The analyzed genomes included 37 Lactobacillus genomes of 17 species, six Lactococcus lactis genomes, four Leuconostoc genomes of three species, six Streptococcus genomes of two species...... that of the others, with the two Streptococcus species having the shortest genomes. The widest distribution in genome content was observed for Lactobacillus. The number of tRNA and rRNA gene copies varied considerably, with exceptional high numbers observed for Lb. delbrueckii, while these numbers were relatively...

  3. OpenLabNotes – An Electronic Laboratory Notebook Extension for OpenLabFramework

    Directory of Open Access Journals (Sweden)

    List Markus

    2015-09-01

    Full Text Available Electronic laboratory notebooks (ELNs are more accessible and reliable than their paper based alternatives and thus find widespread adoption. While a large number of commercial products is available, small- to mid-sized laboratories can often not afford the costs or are concerned about the longevity of the providers. Turning towards free alternatives, however, raises questions about data protection, which are not sufficiently addressed by available solutions. To serve as legal documents, ELNs must prevent scientific fraud through technical means such as digital signatures. It would also be advantageous if an ELN was integrated with a laboratory information management system to allow for a comprehensive documentation of experimental work including the location of samples that were used in a particular experiment. Here, we present OpenLabNotes, which adds state-of-the-art ELN capabilities to OpenLabFramework, a powerful and flexible laboratory information management system. In contrast to comparable solutions, it allows to protect the intellectual property of its users by offering data protection with digital signatures. OpenLabNotes effectively closes the gap between research documentation and sample management, thus making Open- LabFramework more attractive for laboratories that seek to increase productivity through electronic data management.

  4. Recent developments from the OPEnS Lab

    Science.gov (United States)

    Selker, J. S.; Good, S. P.; Higgins, C. W.; Sayde, C.; Buskirk, B.; Lopez, M.; Nelke, M.; Udell, C.

    2016-12-01

    The Openly Published Environmental Sensing (OPEnS) lab is a facility that is open to all from around the world to use (http://agsci.oregonstate.edu/open-sensing). With 3-D CAD, electronics benches, 3-D printers and laser cutters, and a complete precision metal shop, the lab can build just about anything. Electronic platforms such as the Arduino are combined with cutting edge sensors, and packaged in rugged housing to address critical environmental sensing needs. The results are published in GITHub and in the AGU journal Earth and Space Sciences under the special theme of "Environmental Sensing." In this poster we present advancements including: A ultra-precise isotopic sampler for rainfall; an isotopic sampler for soil gas; a data-logging wind vane that can be mounted on the tether of a balloon; a rain-gage calibrator with three rates of constant application; a sketch your idea on a white board and send it in. The conversation is started, and your prototype can be ready in a few weeks. We have a staff of three engineers ready to help, where you are working remotely, or decide to spend some time with the team in Corvallis.

  5. Genomics Education in Practice: Evaluation of a Mobile Lab Design

    Science.gov (United States)

    Van Mil, Marc H. W.; Boerwinkel, Dirk Jan; Buizer-Voskamp, Jacobine E.; Speksnijder, Annelies; Waarlo, Arend Jan

    2010-01-01

    Dutch genomics research centers have developed the "DNA labs on the road" to bridge the gap between modern genomics research practice and secondary-school curriculum in the Netherlands. These mobile DNA labs offer upper-secondary students the opportunity to experience genomics research through experiments with laboratory equipment that…

  6. Open chromatin in plant genomes.

    Science.gov (United States)

    Zhang, Wenli; Zhang, Tao; Wu, Yufeng; Jiang, Jiming

    2014-01-01

    Sensitivity to DNase I digestion is an indicator of the accessibility and configuration of chromatin in eukaryotic genomes. Open chromatin exhibits high sensitivity to DNase I cleavage. DNase I hypersensitive sites (DHSs) in eukaryotic genomes can be identified through DNase I treatment followed by sequencing (DNase-seq). DHSs are most frequently associated with various cis-regulatory DNA elements, including promoters, enhancers, and silencers in both animal and plant genomes. Genome-wide identification of DHSs provides an efficient method to interpret previously un-annotated regulatory DNA sequences. In this review, we provide an overview of the historical perspective of DHS research in eukaryotes. We summarize the main achievements of DHS research in model animal species and review the recent progress of DHS research in plants. We finally discuss possible future directions of using DHS as a tool in plant genomics research. © 2014 S. Karger AG, Basel.

  7. GeneLab: NASA's Open Access, Collaborative Platform for Systems Biology and Space Medicine

    Science.gov (United States)

    Berrios, Daniel C.; Thompson, Terri G.; Fogle, Homer W.; Rask, Jon C.; Coughlan, Joseph C.

    2015-01-01

    NASA is investing in GeneLab1 (http:genelab.nasa.gov), a multi-year effort to maximize utilization of the limited resources to conduct biological and medical research in space, principally aboard the International Space Station (ISS). High-throughput genomic, transcriptomic, proteomic or other omics analyses from experiments conducted on the ISS will be stored in the GeneLab Data Systems (GLDS), an open-science information system that will also include a biocomputation platform with collaborative science capabilities, to enable the discovery and validation of molecular networks.

  8. EHS Open House: Learning Lab and Life Safety | Poster

    Science.gov (United States)

    Attendees of the Environment, Health, and Safety Program’s (EHS’) Open House had a chance to learn self-defense techniques, as well as visit with vendors demonstrating the latest trends in laboratory safety. “Working with sharps in labs is inherently dangerous, so EHS proactively focused on featuring equipment that would promote safer techniques,” said Siobhan Tierney, program manager, EHS.

  9. Open source and DIY hardware for DNA nanotechnology labs.

    Science.gov (United States)

    Damase, Tulsi R; Stephens, Daniel; Spencer, Adam; Allen, Peter B

    A set of instruments and specialized equipment is necessary to equip a laboratory to work with DNA. Reducing the barrier to entry for DNA manipulation should enable and encourage new labs to enter the field. We present three examples of open source/DIY technology with significantly reduced costs relative to commercial equipment. This includes a gel scanner, a horizontal PAGE gel mold, and a homogenizer for generating DNA-coated particles. The overall cost savings obtained by using open source/DIY equipment was between 50 and 90%.

  10. Open source and DIY hardware for DNA nanotechnology labs

    Directory of Open Access Journals (Sweden)

    Tulsi R. Damase

    2015-08-01

    Full Text Available A set of instruments and specialized equipment is necessary to equip a laboratory to work with DNA. Reducing the barrier to entry for DNA manipulation should enable and encourage new labs to enter the field. We present three examples of open source/DIY technology with significantly reduced costs relative to commercial equipment. This includes a gel scanner, a horizontal PAGE gel mold, and a homogenizer for generating DNA-coated particles. The overall cost savings obtained by using open source/DIY equipment was between 50 and 90%.

  11. Open Labware: 3-D printing your own lab equipment.

    Directory of Open Access Journals (Sweden)

    Tom Baden

    2015-03-01

    Full Text Available The introduction of affordable, consumer-oriented 3-D printers is a milestone in the current "maker movement," which has been heralded as the next industrial revolution. Combined with free and open sharing of detailed design blueprints and accessible development tools, rapid prototypes of complex products can now be assembled in one's own garage--a game-changer reminiscent of the early days of personal computing. At the same time, 3-D printing has also allowed the scientific and engineering community to build the "little things" that help a lab get up and running much faster and easier than ever before.

  12. Open Labware: 3-D printing your own lab equipment.

    Science.gov (United States)

    Baden, Tom; Chagas, Andre Maia; Gage, Gregory J; Gage, Greg; Marzullo, Timothy C; Marzullo, Timothy; Prieto-Godino, Lucia L; Euler, Thomas

    2015-03-01

    The introduction of affordable, consumer-oriented 3-D printers is a milestone in the current "maker movement," which has been heralded as the next industrial revolution. Combined with free and open sharing of detailed design blueprints and accessible development tools, rapid prototypes of complex products can now be assembled in one's own garage--a game-changer reminiscent of the early days of personal computing. At the same time, 3-D printing has also allowed the scientific and engineering community to build the "little things" that help a lab get up and running much faster and easier than ever before.

  13. Open Access Data Sharing in Genomic Research

    Directory of Open Access Journals (Sweden)

    Stacey Pereira

    2014-08-01

    Full Text Available The current emphasis on broad sharing of human genomic data generated in research in order to maximize utility and public benefit is a significant legacy of the Human Genome Project. Concerns about privacy and discrimination have led to policy responses that restrict access to genomic data as the means for protecting research participants. Our research and experience show, however, that a considerable number of research participants agree to open access sharing of their genomic data when given the choice. General policies that limit access to all genomic data fail to respect the autonomy of these participants and, at the same time, unnecessarily limit the utility of the data. We advocate instead a more balanced approach that allows for individual choice and encourages informed decision making, while protecting against the misuse of genomic data through enhanced legislation.

  14. PySeqLab: an open source Python package for sequence labeling and segmentation.

    Science.gov (United States)

    Allam, Ahmed; Krauthammer, Michael

    2017-11-01

    Text and genomic data are composed of sequential tokens, such as words and nucleotides that give rise to higher order syntactic constructs. In this work, we aim at providing a comprehensive Python library implementing conditional random fields (CRFs), a class of probabilistic graphical models, for robust prediction of these constructs from sequential data. Python Sequence Labeling (PySeqLab) is an open source package for performing supervised learning in structured prediction tasks. It implements CRFs models, that is discriminative models from (i) first-order to higher-order linear-chain CRFs, and from (ii) first-order to higher-order semi-Markov CRFs (semi-CRFs). Moreover, it provides multiple learning algorithms for estimating model parameters such as (i) stochastic gradient descent (SGD) and its multiple variations, (ii) structured perceptron with multiple averaging schemes supporting exact and inexact search using 'violation-fixing' framework, (iii) search-based probabilistic online learning algorithm (SAPO) and (iv) an interface for Broyden-Fletcher-Goldfarb-Shanno (BFGS) and the limited-memory BFGS algorithms. Viterbi and Viterbi A* are used for inference and decoding of sequences. Using PySeqLab, we built models (classifiers) and evaluated their performance in three different domains: (i) biomedical Natural language processing (NLP), (ii) predictive DNA sequence analysis and (iii) Human activity recognition (HAR). State-of-the-art performance comparable to machine-learning based systems was achieved in the three domains without feature engineering or the use of knowledge sources. PySeqLab is available through https://bitbucket.org/A_2/pyseqlab with tutorials and documentation. ahmed.allam@yale.edu or michael.krauthammer@yale.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  15. Screensaver: an open source lab information management system (LIMS) for high throughput screening facilities.

    Science.gov (United States)

    Tolopko, Andrew N; Sullivan, John P; Erickson, Sean D; Wrobel, David; Chiang, Su L; Rudnicki, Katrina; Rudnicki, Stewart; Nale, Jennifer; Selfors, Laura M; Greenhouse, Dara; Muhlich, Jeremy L; Shamu, Caroline E

    2010-05-18

    Shared-usage high throughput screening (HTS) facilities are becoming more common in academe as large-scale small molecule and genome-scale RNAi screening strategies are adopted for basic research purposes. These shared facilities require a unique informatics infrastructure that must not only provide access to and analysis of screening data, but must also manage the administrative and technical challenges associated with conducting numerous, interleaved screening efforts run by multiple independent research groups. We have developed Screensaver, a free, open source, web-based lab information management system (LIMS), to address the informatics needs of our small molecule and RNAi screening facility. Screensaver supports the storage and comparison of screening data sets, as well as the management of information about screens, screeners, libraries, and laboratory work requests. To our knowledge, Screensaver is one of the first applications to support the storage and analysis of data from both genome-scale RNAi screening projects and small molecule screening projects. The informatics and administrative needs of an HTS facility may be best managed by a single, integrated, web-accessible application such as Screensaver. Screensaver has proven useful in meeting the requirements of the ICCB-Longwood/NSRB Screening Facility at Harvard Medical School, and has provided similar benefits to other HTS facilities.

  16. Screensaver: an open source lab information management system (LIMS for high throughput screening facilities

    Directory of Open Access Journals (Sweden)

    Nale Jennifer

    2010-05-01

    Full Text Available Abstract Background Shared-usage high throughput screening (HTS facilities are becoming more common in academe as large-scale small molecule and genome-scale RNAi screening strategies are adopted for basic research purposes. These shared facilities require a unique informatics infrastructure that must not only provide access to and analysis of screening data, but must also manage the administrative and technical challenges associated with conducting numerous, interleaved screening efforts run by multiple independent research groups. Results We have developed Screensaver, a free, open source, web-based lab information management system (LIMS, to address the informatics needs of our small molecule and RNAi screening facility. Screensaver supports the storage and comparison of screening data sets, as well as the management of information about screens, screeners, libraries, and laboratory work requests. To our knowledge, Screensaver is one of the first applications to support the storage and analysis of data from both genome-scale RNAi screening projects and small molecule screening projects. Conclusions The informatics and administrative needs of an HTS facility may be best managed by a single, integrated, web-accessible application such as Screensaver. Screensaver has proven useful in meeting the requirements of the ICCB-Longwood/NSRB Screening Facility at Harvard Medical School, and has provided similar benefits to other HTS facilities.

  17. Usage Patterns of Open Genomic Data

    Science.gov (United States)

    Xia, Jingfeng; Liu, Ying

    2013-01-01

    This paper uses Genome Expression Omnibus (GEO), a data repository in biomedical sciences, to examine the usage patterns of open data repositories. It attempts to identify the degree of recognition of data reuse value and understand how e-science has impacted a large-scale scholarship. By analyzing a list of 1,211 publications that cite GEO data…

  18. Exploring business models for open innovation in rural living labs

    CSIR Research Space (South Africa)

    Schaffers, H

    2007-06-01

    Full Text Available identifies critical aspects of business models and pre-conditions for business models design. These first findings are relevant to understand how to arrive at successful business models for open collaborative innovation fostering rural and regional...

  19. Open Innovation Labs for Physics Undergraduate Independent Research

    Science.gov (United States)

    Carlsmith, Duncan

    2014-03-01

    The open undergraduate laboratory Garage Physics at the University of Wisconsin-Madison is home to a variety of independent physics and multidisciplinary research projects. Its maker-style environment encourages innovation and entrepreneurship. Experience establishing and staffing the laboratory will be described.

  20. Genome Annotation in a Community College Cell Biology Lab

    Science.gov (United States)

    Beagley, C. Timothy

    2013-01-01

    The Biology Department at Salt Lake Community College has used the IMG-ACT toolbox to introduce a genome mapping and annotation exercise into the laboratory portion of its Cell Biology course. This project provides students with an authentic inquiry-based learning experience while introducing them to computational biology and contemporary learning…

  1. How to Cope with Working in an Open-space Lab?

    NARCIS (Netherlands)

    Pautasso, Marco; Werf, van der Wopke

    2017-01-01

    Open-space labs and research environments are increasingly common worldwide. They are supposed to facilitate interactions among researchers, but can be disruptive to those who need to be in a quiet environment in order to concentrate. This problem is increasingly felt across the natural, medical

  2. MetaLIMS, a simple open-source laboratory information management system for small metagenomic labs.

    Science.gov (United States)

    Heinle, Cassie Elizabeth; Gaultier, Nicolas Paul Eugène; Miller, Dana; Purbojati, Rikky Wenang; Lauro, Federico M

    2017-06-01

    As the cost of sequencing continues to fall, smaller groups increasingly initiate and manage larger sequencing projects and take on the complexity of data storage for high volumes of samples. This has created a need for low-cost laboratory information management systems (LIMS) that contain flexible fields to accommodate the unique nature of individual labs. Many labs do not have a dedicated information technology position, so LIMS must also be easy to setup and maintain with minimal technical proficiency. MetaLIMS is a free and open-source web-based application available via GitHub. The focus of MetaLIMS is to store sample metadata prior to sequencing and analysis pipelines. Initially designed for environmental metagenomics labs, in addition to storing generic sample collection information and DNA/RNA processing information, the user can also add fields specific to the user's lab. MetaLIMS can also produce a basic sequencing submission form compatible with the proprietary Clarity LIMS system used by some sequencing facilities. To help ease the technical burden associated with web deployment, MetaLIMS options the use of commercial web hosting combined with MetaLIMS bash scripts for ease of setup. MetaLIMS overcomes key challenges common in LIMS by giving labs access to a low-cost and open-source tool that also has the flexibility to meet individual lab needs and an option for easy deployment. By making the web application open source and hosting it on GitHub, we hope to encourage the community to build upon MetaLIMS, making it more robust and tailored to the needs of more researchers. © The Authors 2017. Published by Oxford University Press.

  3. Project-based physics labs using low-cost open-source hardware

    Science.gov (United States)

    Bouquet, F.; Bobroff, J.; Fuchs-Gallezot, M.; Maurines, L.

    2017-03-01

    We describe a project-based physics lab, which we proposed to third-year university students. These labs are based on new open-source low-cost equipment (Arduino microcontrollers and compatible sensors). Students are given complete autonomy: they develop their own experimental setup and study the physics topic of their choice. The goal of these projects is to let students to discover the reality of experimental physics. Technical specifications of the acquisition material and case studies are presented for practical implementation in other universities.

  4. Genome annotation in a community college cell biology lab.

    Science.gov (United States)

    Beagley, C Timothy

    2013-01-01

    The Biology Department at Salt Lake Community College has used the IMG-ACT toolbox to introduce a genome mapping and annotation exercise into the laboratory portion of its Cell Biology course. This project provides students with an authentic inquiry-based learning experience while introducing them to computational biology and contemporary learning skills. Additionally, the project strengthens student understanding of the scientific method and contributes to student learning gains in curricular objectives centered around basic molecular biology, specifically, the Central Dogma. Importantly, inclusion of this project in the laboratory course provides students with a positive learning environment and allows for the use of cooperative learning strategies to increase overall student success. Copyright © 2012 International Union of Biochemistry and Molecular Biology, Inc.

  5. HTC Vive MeVisLab integration via OpenVR for medical applications.

    Science.gov (United States)

    Egger, Jan; Gall, Markus; Wallner, Jürgen; Boechat, Pedro; Hann, Alexander; Li, Xing; Chen, Xiaojun; Schmalstieg, Dieter

    2017-01-01

    Virtual Reality, an immersive technology that replicates an environment via computer-simulated reality, gets a lot of attention in the entertainment industry. However, VR has also great potential in other areas, like the medical domain, Examples are intervention planning, training and simulation. This is especially of use in medical operations, where an aesthetic outcome is important, like for facial surgeries. Alas, importing medical data into Virtual Reality devices is not necessarily trivial, in particular, when a direct connection to a proprietary application is desired. Moreover, most researcher do not build their medical applications from scratch, but rather leverage platforms like MeVisLab, MITK, OsiriX or 3D Slicer. These platforms have in common that they use libraries like ITK and VTK, and provide a convenient graphical interface. However, ITK and VTK do not support Virtual Reality directly. In this study, the usage of a Virtual Reality device for medical data under the MeVisLab platform is presented. The OpenVR library is integrated into the MeVisLab platform, allowing a direct and uncomplicated usage of the head mounted display HTC Vive inside the MeVisLab platform. Medical data coming from other MeVisLab modules can directly be connected per drag-and-drop to the Virtual Reality module, rendering the data inside the HTC Vive for immersive virtual reality inspection.

  6. HTC Vive MeVisLab integration via OpenVR for medical applications.

    Directory of Open Access Journals (Sweden)

    Jan Egger

    Full Text Available Virtual Reality, an immersive technology that replicates an environment via computer-simulated reality, gets a lot of attention in the entertainment industry. However, VR has also great potential in other areas, like the medical domain, Examples are intervention planning, training and simulation. This is especially of use in medical operations, where an aesthetic outcome is important, like for facial surgeries. Alas, importing medical data into Virtual Reality devices is not necessarily trivial, in particular, when a direct connection to a proprietary application is desired. Moreover, most researcher do not build their medical applications from scratch, but rather leverage platforms like MeVisLab, MITK, OsiriX or 3D Slicer. These platforms have in common that they use libraries like ITK and VTK, and provide a convenient graphical interface. However, ITK and VTK do not support Virtual Reality directly. In this study, the usage of a Virtual Reality device for medical data under the MeVisLab platform is presented. The OpenVR library is integrated into the MeVisLab platform, allowing a direct and uncomplicated usage of the head mounted display HTC Vive inside the MeVisLab platform. Medical data coming from other MeVisLab modules can directly be connected per drag-and-drop to the Virtual Reality module, rendering the data inside the HTC Vive for immersive virtual reality inspection.

  7. IRootLab: a free and open-source MATLAB toolbox for vibrational biospectroscopy data analysis.

    Science.gov (United States)

    Trevisan, Júlio; Angelov, Plamen P; Scott, Andrew D; Carmichael, Paul L; Martin, Francis L

    2013-04-15

    IRootLab is a free and open-source MATLAB toolbox for vibrational biospectroscopy (VBS) data analysis. It offers an object-oriented programming class library, graphical user interfaces (GUIs) and automatic MATLAB code generation. The class library contains a large number of methods, concepts and visualizations for VBS data analysis, some of which are introduced in the toolbox. The GUIs provide an interface to the class library, including a module to merge several spectral files into a dataset. Automatic code allows developers to quickly write VBS data analysis scripts and is a unique resource among tools for VBS. Documentation includes a manual, tutorials, Doxygen-generated reference and a demonstration showcase. IRootLab can handle some of the most popular file formats used in VBS. License: GNU-LGPL. Official website: http://irootlab.googlecode.com/. Supplementary data are available at Bioinformatics online.

  8. Droplet-based Biosensing for Lab-on-a-Chip, Open Microfluidics Platforms.

    Science.gov (United States)

    Dak, Piyush; Ebrahimi, Aida; Swaminathan, Vikhram; Duarte-Guevara, Carlos; Bashir, Rashid; Alam, Muhammad A

    2016-04-14

    Low cost, portable sensors can transform health care by bringing easily available diagnostic devices to low and middle income population, particularly in developing countries. Sample preparation, analyte handling and labeling are primary cost concerns for traditional lab-based diagnostic systems. Lab-on-a-chip (LoC) platforms based on droplet-based microfluidics promise to integrate and automate these complex and expensive laboratory procedures onto a single chip; the cost will be further reduced if label-free biosensors could be integrated onto the LoC platforms. Here, we review some recent developments of label-free, droplet-based biosensors, compatible with "open" digital microfluidic systems. These low-cost droplet-based biosensors overcome some of the fundamental limitations of the classical sensors, enabling timely diagnosis. We identify the key challenges that must be addressed to make these sensors commercially viable and summarize a number of promising research directions.

  9. LabKey Server: An open source platform for scientific data integration, analysis and collaboration

    Science.gov (United States)

    2011-01-01

    Background Broad-based collaborations are becoming increasingly common among disease researchers. For example, the Global HIV Enterprise has united cross-disciplinary consortia to speed progress towards HIV vaccines through coordinated research across the boundaries of institutions, continents and specialties. New, end-to-end software tools for data and specimen management are necessary to achieve the ambitious goals of such alliances. These tools must enable researchers to organize and integrate heterogeneous data early in the discovery process, standardize processes, gain new insights into pooled data and collaborate securely. Results To meet these needs, we enhanced the LabKey Server platform, formerly known as CPAS. This freely available, open source software is maintained by professional engineers who use commercially proven practices for software development and maintenance. Recent enhancements support: (i) Submitting specimens requests across collaborating organizations (ii) Graphically defining new experimental data types, metadata and wizards for data collection (iii) Transitioning experimental results from a multiplicity of spreadsheets to custom tables in a shared database (iv) Securely organizing, integrating, analyzing, visualizing and sharing diverse data types, from clinical records to specimens to complex assays (v) Interacting dynamically with external data sources (vi) Tracking study participants and cohorts over time (vii) Developing custom interfaces using client libraries (viii) Authoring custom visualizations in a built-in R scripting environment. Diverse research organizations have adopted and adapted LabKey Server, including consortia within the Global HIV Enterprise. Atlas is an installation of LabKey Server that has been tailored to serve these consortia. It is in production use and demonstrates the core capabilities of LabKey Server. Atlas now has over 2,800 active user accounts originating from approximately 36 countries and 350

  10. Long conduction time plasma opening switch experiments at Sandia National Labs

    Science.gov (United States)

    Savage, M. E.; Simpson, W. W.; Cooper, G. W.; Usher, M. A.

    1992-01-01

    Sandia National Labs has undertaken an ambitious program to reduce the size and cost of large pulsed power drivers. The program basis is inductive energy storage and Plasma Opening Switches (POS). Inductive energy storage has well known advantages, including increased efficiency and reduced stress on the vacuum interface. The Sandia approach is to retain the reliable and efficient Marx generator and the temporal pulse compression of the water dielectric capacitor. A triggered closing switch, developed at Sandia, transfers the capacitor charge into the energy storage inductor. This approach has several advantages, including relaxed requirements on Marx jitter and inductance, and must faster current risetime in the energy storage inductor. The POS itself is the key to the Sandia program. The switch design uses an auxiliary magnetic field to inject the plasma and hold it in place during conduction. After opening begins, the self magnetic field of the power pulse pushes on the plasma to increase the opened gap. We use magnetic pressure because we desire POS gaps of several cm. Erosion POS devices typically open much less than that. Improved opening allows more efficient energy transfer to loads.

  11. Human genome and open source: balancing ethics and business.

    Science.gov (United States)

    Marturano, Antonio

    2011-01-01

    The Human Genome Project has been completed thanks to a massive use of computer techniques, as well as the adoption of the open-source business and research model by the scientists involved. This model won over the proprietary model and allowed a quick propagation and feedback of research results among peers. In this paper, the author will analyse some ethical and legal issues emerging by the use of such computer model in the Human Genome property rights. The author will argue that the Open Source is the best business model, as it is able to balance business and human rights perspectives.

  12. Chemotion ELN: an Open Source electronic lab notebook for chemists in academia.

    Science.gov (United States)

    Tremouilhac, Pierre; Nguyen, An; Huang, Yu-Chieh; Kotov, Serhii; Lütjohann, Dominic Sebastian; Hübsch, Florian; Jung, Nicole; Bräse, Stefan

    2017-09-25

    The development of an electronic lab notebook (ELN) for researchers working in the field of chemical sciences is presented. The web based application is available as an Open Source software that offers modern solutions for chemical researchers. The Chemotion ELN is equipped with the basic functionalities necessary for the acquisition and processing of chemical data, in particular the work with molecular structures and calculations based on molecular properties. The ELN supports planning, description, storage, and management for the routine work of organic chemists. It also provides tools for communicating and sharing the recorded research data among colleagues. Meeting the requirements of a state of the art research infrastructure, the ELN allows the search for molecules and reactions not only within the user's data but also in conventional external sources as provided by SciFinder and PubChem. The presented development makes allowance for the growing dependency of scientific activity on the availability of digital information by providing Open Source instruments to record and reuse research data. The current version of the ELN has been using for over half of a year in our chemistry research group, serves as a common infrastructure for chemistry research and enables chemistry researchers to build their own databases of digital information as a prerequisite for the detailed, systematic investigation and evaluation of chemical reactions and mechanisms.

  13. Open web system of Virtual labs for nuclear and applied physics

    Science.gov (United States)

    Saldikov, I. S.; Afanasyev, V. V.; Petrov, V. I.; Ternovykh, M. Yu

    2017-01-01

    An example of virtual lab work on unique experimental equipment is presented. The virtual lab work is software based on a model of real equipment. Virtual labs can be used for educational process in nuclear safety and analysis field. As an example it includes the virtual lab called “Experimental determination of the material parameter depending on the pitch of a uranium-water lattice”. This paper included general description of this lab. A description of a database on the support of laboratory work on unique experimental equipment which is included this work, its concept development are also presented.

  14. CompaGB: An open framework for genome browsers comparison

    Directory of Open Access Journals (Sweden)

    Chiapello Hélène

    2011-05-01

    Full Text Available Abstract Background Tools to visualize and explore genomes hold a central place in genomics and the diversity of genome browsers has increased dramatically over the last few years. It often turns out to be a daunting task to compare and choose a well-adapted genome browser, as multidisciplinary knowledge is required to carry out this task and the number of tools, functionalities and features are overwhelming. Findings To assist in this task, we propose a community-based framework based on two cornerstones: (i the implementation of industry promoted software qualification method (QSOS adapted for genome browser evaluations, and (ii a web resource providing numerous facilities either for visualizing comparisons or performing new evaluations. We formulated 60 criteria specifically for genome browsers, and incorporated another 65 directly from QSOS's generic section. Those criteria aim to answer versatile needs, ranging from a biologist whose interest primarily lies into user-friendly and informative functionalities, a bioinformatician who wants to integrate the genome browser into a wider framework, or a computer scientist who might choose a software according to more technical features. We developed a dedicated web application to enrich the existing QSOS functionalities (weighting of criteria, user profile with features of interest to a community-based framework: easy management of evolving data, user comments... Conclusions The framework is available at http://genome.jouy.inra.fr/CompaGB. It is open to anyone who wishes to participate in the evaluations. It helps the scientific community to (1 choose a genome browser that would better fit their particular project, (2 visualize features comparatively with easily accessible formats, such as tables or radar plots and (3 perform their own evaluation against the defined criteria. To illustrate the CompaGB functionalities, we have evaluated seven genome browsers according to the implemented methodology

  15. Open sharing of genomic data: Who does it and why?

    Science.gov (United States)

    Haeusermann, Tobias; Greshake, Bastian; Blasimme, Alessandro; Irdam, Darja; Richards, Martin; Vayena, Effy

    2017-01-01

    We explored the characteristics and motivations of people who, having obtained their genetic or genomic data from Direct-To-Consumer genetic testing (DTC-GT) companies, voluntarily decide to share them on the publicly accessible web platform openSNP. The study is the first attempt to describe open data sharing activities undertaken by individuals without institutional oversight. In the paper we provide a detailed overview of the distribution of the demographic characteristics and motivations of people engaged in genetic or genomic open data sharing. The geographical distribution of the respondents showed the USA as dominant. There was no significant gender divide, the age distribution was broad, educational background varied and respondents with and without children were equally represented. Health, even though prominent, was not the respondents' primary or only motivation to be tested. As to their motivations to openly share their data, 86.05% indicated wanting to learn about themselves as relevant, followed by contributing to the advancement of medical research (80.30%), improving the predictability of genetic testing (76.02%) and considering it fun to explore genotype and phenotype data (75.51%). Whereas most respondents were well aware of the privacy risks of their involvement in open genetic data sharing and considered the possibility of direct, personal repercussions troubling, they estimated the risk of this happening to be negligible. Our findings highlight the diversity of DTC-GT consumers who decide to openly share their data. Instead of focusing exclusively on health-related aspects of genetic testing and data sharing, our study emphasizes the importance of taking into account benefits and risks that stretch beyond the health spectrum. Our results thus lend further support to the call for a broader and multi-faceted conceptualization of genomic utility.

  16. Open sharing of genomic data: Who does it and why?

    Directory of Open Access Journals (Sweden)

    Tobias Haeusermann

    Full Text Available We explored the characteristics and motivations of people who, having obtained their genetic or genomic data from Direct-To-Consumer genetic testing (DTC-GT companies, voluntarily decide to share them on the publicly accessible web platform openSNP. The study is the first attempt to describe open data sharing activities undertaken by individuals without institutional oversight. In the paper we provide a detailed overview of the distribution of the demographic characteristics and motivations of people engaged in genetic or genomic open data sharing. The geographical distribution of the respondents showed the USA as dominant. There was no significant gender divide, the age distribution was broad, educational background varied and respondents with and without children were equally represented. Health, even though prominent, was not the respondents' primary or only motivation to be tested. As to their motivations to openly share their data, 86.05% indicated wanting to learn about themselves as relevant, followed by contributing to the advancement of medical research (80.30%, improving the predictability of genetic testing (76.02% and considering it fun to explore genotype and phenotype data (75.51%. Whereas most respondents were well aware of the privacy risks of their involvement in open genetic data sharing and considered the possibility of direct, personal repercussions troubling, they estimated the risk of this happening to be negligible. Our findings highlight the diversity of DTC-GT consumers who decide to openly share their data. Instead of focusing exclusively on health-related aspects of genetic testing and data sharing, our study emphasizes the importance of taking into account benefits and risks that stretch beyond the health spectrum. Our results thus lend further support to the call for a broader and multi-faceted conceptualization of genomic utility.

  17. Map of open and closed chromatin domains in Drosophila genome.

    Science.gov (United States)

    Milon, Beatrice; Sun, Yezhou; Chang, Weizhong; Creasy, Todd; Mahurkar, Anup; Shetty, Amol; Nurminsky, Dmitry; Nurminskaya, Maria

    2014-11-18

    Chromatin compactness has been considered a major determinant of gene activity and has been associated with specific chromatin modifications in studies on a few individual genetic loci. At the same time, genome-wide patterns of open and closed chromatin have been understudied, and are at present largely predicted from chromatin modification and gene expression data. However the universal applicability of such predictions is not self-evident, and requires experimental verification. We developed and implemented a high-throughput analysis for general chromatin sensitivity to DNase I which provides a comprehensive epigenomic assessment in a single assay. Contiguous domains of open and closed chromatin were identified by computational analysis of the data, and correlated to other genome annotations including predicted chromatin "states", individual chromatin modifications, nuclear lamina interactions, and gene expression. While showing that the widely trusted predictions of chromatin structure are correct in the majority of cases, we detected diverse "exceptions" from the conventional rules. We found a profound paucity of chromatin modifications in a major fraction of closed chromatin, and identified a number of loci where chromatin configuration is opposite to that expected from modification and gene expression patterns. Further, we observed that chromatin of large introns tends to be closed even when the genes are expressed, and that a significant proportion of active genes including their promoters are located in closed chromatin. These findings reveal limitations of the existing predictive models, indicate novel mechanisms of epigenetic regulation, and provide important insights into genome organization and function.

  18. Using OpenTarget to Generate Potential Countermeasures for Long-Term Space Exposure from Data Available on GeneLab

    Science.gov (United States)

    Beheshti, Afshin

    2018-01-01

    GeneLab as a general tool for the scientific community; Utilizing GeneLab datasets to generate hypothesis and determining potential biological targets against health risks due to long-term space missions; How can OpenTarget be used to discover novel drugs to test as countermeasures that can be utilized by astronauts.

  19. Droplet-based Biosensing for Lab-on-a-Chip, Open Microfluidics Platforms

    Directory of Open Access Journals (Sweden)

    Piyush Dak

    2016-04-01

    Full Text Available Low cost, portable sensors can transform health care by bringing easily available diagnostic devices to low and middle income population, particularly in developing countries. Sample preparation, analyte handling and labeling are primary cost concerns for traditional lab-based diagnostic systems. Lab-on-a-chip (LoC platforms based on droplet-based microfluidics promise to integrate and automate these complex and expensive laboratory procedures onto a single chip; the cost will be further reduced if label-free biosensors could be integrated onto the LoC platforms. Here, we review some recent developments of label-free, droplet-based biosensors, compatible with “open” digital microfluidic systems. These low-cost droplet-based biosensors overcome some of the fundamental limitations of the classical sensors, enabling timely diagnosis. We identify the key challenges that must be addressed to make these sensors commercially viable and summarize a number of promising research directions.

  20. ExpressionDB: An open source platform for distributing genome-scale datasets.

    Directory of Open Access Journals (Sweden)

    Laura D Hughes

    Full Text Available RNA-sequencing (RNA-seq and microarrays are methods for measuring gene expression across the entire transcriptome. Recent advances have made these techniques practical and affordable for essentially any laboratory with experience in molecular biology. A variety of computational methods have been developed to decrease the amount of bioinformatics expertise necessary to analyze these data. Nevertheless, many barriers persist which discourage new labs from using functional genomics approaches. Since high-quality gene expression studies have enduring value as resources to the entire research community, it is of particular importance that small labs have the capacity to share their analyzed datasets with the research community. Here we introduce ExpressionDB, an open source platform for visualizing RNA-seq and microarray data accommodating virtually any number of different samples. ExpressionDB is based on Shiny, a customizable web application which allows data sharing locally and online with customizable code written in R. ExpressionDB allows intuitive searches based on gene symbols, descriptions, or gene ontology terms, and it includes tools for dynamically filtering results based on expression level, fold change, and false-discovery rates. Built-in visualization tools include heatmaps, volcano plots, and principal component analysis, ensuring streamlined and consistent visualization to all users. All of the scripts for building an ExpressionDB with user-supplied data are freely available on GitHub, and the Creative Commons license allows fully open customization by end-users. We estimate that a demo database can be created in under one hour with minimal programming experience, and that a new database with user-supplied expression data can be completed and online in less than one day.

  1. Analysis of Whole-Genome Data in a Public Health Lab

    Centers for Disease Control (CDC) Podcasts

    2017-10-17

    Dr. Kelly Oakeson, a bioinformatics and genomics research analyst with the Utah Department of Health, discusses bioinformatics and genomics research.  Created: 10/17/2017 by National Center for Emerging and Zoonotic Infectious Diseases (NCEZID).   Date Released: 10/17/2017.

  2. The Udall Lab

    Data.gov (United States)

    Federal Laboratory Consortium — The Udall lab is interested in genome evolution and cotton genomics.The cotton genus ( Gossypium) is an extraordinarily diverse group with approximately 50 species...

  3. Design and Evaluation of an Open Web Platform Cartography Lab Curriculum

    Science.gov (United States)

    Sack, Carl M.; Roth, Robert E.

    2017-01-01

    Recent shifts in web map technology away from proprietary software and toward development on the Open Web Platform have increased the number and complexity of technical skills needed to do cartography on the Web. Web-based cartography curricula likewise must be adapted to prepare geography, cartography, and GIS students with the skills needed to…

  4. A LabVIEW model incorporating an open-loop arterial impedance and a closed-loop circulatory system.

    Science.gov (United States)

    Cole, R T; Lucas, C L; Cascio, W E; Johnson, T A

    2005-11-01

    While numerous computer models exist for the circulatory system, many are limited in scope, contain unwanted features or incorporate complex components specific to unique experimental situations. Our purpose was to develop a basic, yet multifaceted, computer model of the left heart and systemic circulation in LabVIEW having universal appeal without sacrificing crucial physiologic features. The program we developed employs Windkessel-type impedance models in several open-loop configurations and a closed-loop model coupling a lumped impedance and ventricular pressure source. The open-loop impedance models demonstrate afterload effects on arbitrary aortic pressure/flow inputs. The closed-loop model catalogs the major circulatory waveforms with changes in afterload, preload, and left heart properties. Our model provides an avenue for expanding the use of the ventricular equations through closed-loop coupling that includes a basic coronary circuit. Tested values used for the afterload components and the effects of afterload parameter changes on various waveforms are consistent with published data. We conclude that this model offers the ability to alter several circulatory factors and digitally catalog the most salient features of the pressure/flow waveforms employing a user-friendly platform. These features make the model a useful instructional tool for students as well as a simple experimental tool for cardiovascular research.

  5. Didactical contract: An analytical concept to facilitate successful implementation of open-ended physics labs

    DEFF Research Database (Denmark)

    Jacobsen, Lærke Bang; Johannsen, Bjørn Friis; Rump, Camilla Østerberg

    What seems straightforward on paper might turn out to be complex in reality. This is a lesson often learned by educational designers when implementing variations of open-ended alternatives to traditional education and disappointedly reviewing the outcome. Based on observations of discouraging...... of the traditional laboratory learning environment that would lead to resistance from those involved if faced with alternatives. We conclude that both teachers and students lean heavily on a type of algorithm that ensures an appearance of having successfully completed the assigned tasks. This algorithmic didactical...... outcomes of alternative laboratory work in secondary and tertiary physics education we decided to approach the underlying cause of the problem. Framed in the theory of Didactical Situations in mathematics we adapt the concept of the didactical contract to the physics education context to locate aspects...

  6. Open versus Controlled-Access Data | Office of Cancer Genomics

    Science.gov (United States)

    OCG employs stringent human subjects’ protection and data access policies to protect the privacy and confidentiality of the research participants. Depending on the risk of patient identification, OCG programs data are available to the scientific community in two tiers: open or controlled access. Both types of data can be accessed through its corresponding OCG program-specific data matrix or portal. Open-access Data

  7. BUILDING A COMPLETE FREE AND OPEN SOURCE GIS INFRASTRUCTURE FOR HYDROLOGICAL COMPUTING AND DATA PUBLICATION USING GIS.LAB AND GISQUICK PLATFORMS

    Directory of Open Access Journals (Sweden)

    M. Landa

    2017-07-01

    Full Text Available Building a complete free and open source GIS computing and data publication platform can be a relatively easy task. This paper describes an automated deployment of such platform using two open source software projects – GIS.lab and Gisquick. GIS.lab (http: //web.gislab.io is a project for rapid deployment of a complete, centrally managed and horizontally scalable GIS infrastructure in the local area network, data center or cloud. It provides a comprehensive set of free geospatial software seamlessly integrated into one, easy-to-use system. A platform for GIS computing (in our case demonstrated on hydrological data processing requires core components as a geoprocessing server, map server, and a computation engine as eg. GRASS GIS, SAGA, or other similar GIS software. All these components can be rapidly, and automatically deployed by GIS.lab platform. In our demonstrated solution PyWPS is used for serving WPS processes built on the top of GRASS GIS computation platform. GIS.lab can be easily extended by other components running in Docker containers. This approach is shown on Gisquick seamless integration. Gisquick (http://gisquick.org is an open source platform for publishing geospatial data in the sense of rapid sharing of QGIS projects on the web. The platform consists of QGIS plugin, Django-based server application, QGIS server, and web/mobile clients. In this paper is shown how to easily deploy complete open source GIS infrastructure allowing all required operations as data preparation on desktop, data sharing, and geospatial computation as the service. It also includes data publication in the sense of OGC Web Services and importantly also as interactive web mapping applications.

  8. Quality control, analysis and secure sharing of Luminex® immunoassay data using the open source LabKey Server platform.

    Science.gov (United States)

    Eckels, Josh; Nathe, Cory; Nelson, Elizabeth K; Shoemaker, Sara G; Nostrand, Elizabeth Van; Yates, Nicole L; Ashley, Vicki C; Harris, Linda J; Bollenbeck, Mark; Fong, Youyi; Tomaras, Georgia D; Piehler, Britt

    2013-04-30

    Immunoassays that employ multiplexed bead arrays produce high information content per sample. Such assays are now frequently used to evaluate humoral responses in clinical trials. Integrated software is needed for the analysis, quality control, and secure sharing of the high volume of data produced by such multiplexed assays. Software that facilitates data exchange and provides flexibility to perform customized analyses (including multiple curve fits and visualizations of assay performance over time) could increase scientists' capacity to use these immunoassays to evaluate human clinical trials. The HIV Vaccine Trials Network and the Statistical Center for HIV/AIDS Research and Prevention collaborated with LabKey Software to enhance the open source LabKey Server platform to facilitate workflows for multiplexed bead assays. This system now supports the management, analysis, quality control, and secure sharing of data from multiplexed immunoassays that leverage Luminex xMAP® technology. These assays may be custom or kit-based. Newly added features enable labs to: (i) import run data from spreadsheets output by Bio-Plex Manager™ software; (ii) customize data processing, curve fits, and algorithms through scripts written in common languages, such as R; (iii) select script-defined calculation options through a graphical user interface; (iv) collect custom metadata for each titration, analyte, run and batch of runs; (v) calculate dose-response curves for titrations; (vi) interpolate unknown concentrations from curves for titrated standards; (vii) flag run data for exclusion from analysis; (viii) track quality control metrics across runs using Levey-Jennings plots; and (ix) automatically flag outliers based on expected values. Existing system features allow researchers to analyze, integrate, visualize, export and securely share their data, as well as to construct custom user interfaces and workflows. Unlike other tools tailored for Luminex immunoassays, LabKey Server

  9. Quality control, analysis and secure sharing of Luminex® immunoassay data using the open source LabKey Server platform

    Science.gov (United States)

    2013-01-01

    Background Immunoassays that employ multiplexed bead arrays produce high information content per sample. Such assays are now frequently used to evaluate humoral responses in clinical trials. Integrated software is needed for the analysis, quality control, and secure sharing of the high volume of data produced by such multiplexed assays. Software that facilitates data exchange and provides flexibility to perform customized analyses (including multiple curve fits and visualizations of assay performance over time) could increase scientists’ capacity to use these immunoassays to evaluate human clinical trials. Results The HIV Vaccine Trials Network and the Statistical Center for HIV/AIDS Research and Prevention collaborated with LabKey Software to enhance the open source LabKey Server platform to facilitate workflows for multiplexed bead assays. This system now supports the management, analysis, quality control, and secure sharing of data from multiplexed immunoassays that leverage Luminex xMAP® technology. These assays may be custom or kit-based. Newly added features enable labs to: (i) import run data from spreadsheets output by Bio-Plex Manager™ software; (ii) customize data processing, curve fits, and algorithms through scripts written in common languages, such as R; (iii) select script-defined calculation options through a graphical user interface; (iv) collect custom metadata for each titration, analyte, run and batch of runs; (v) calculate dose–response curves for titrations; (vi) interpolate unknown concentrations from curves for titrated standards; (vii) flag run data for exclusion from analysis; (viii) track quality control metrics across runs using Levey-Jennings plots; and (ix) automatically flag outliers based on expected values. Existing system features allow researchers to analyze, integrate, visualize, export and securely share their data, as well as to construct custom user interfaces and workflows. Conclusions Unlike other tools tailored for

  10. OpenADAM: an open source genome-wide association data management system for Affymetrix SNP arrays

    Directory of Open Access Journals (Sweden)

    Sham P C

    2008-12-01

    Full Text Available Abstract Background Large scale genome-wide association studies have become popular since the introduction of high throughput genotyping platforms. Efficient management of the vast array of data generated poses many challenges. Description We have developed an open source web-based data management system for the large amount of genotype data generated from the Affymetrix GeneChip® Mapping Array and Affymetrix Genome-Wide Human SNP Array platforms. The database supports genotype calling using DM, BRLMM, BRLMM-P or Birdseed algorithms provided by the Affymetrix Power Tools. The genotype and corresponding pedigree data are stored in a relational database for efficient downstream data manipulation and analysis, such as calculation of allele and genotype frequencies, sample identity checking, and export of genotype data in various file formats for analysis using commonly-available software. A novel method for genotyping error estimation is implemented using linkage disequilibrium information from the HapMap project. All functionalities are accessible via a web-based user interface. Conclusion OpenADAM provides an open source database system for management of Affymetrix genome-wide association SNP data.

  11. NRF2011-EDU001-EL001 EduLab Project Scaling-up Reflections on Using Open Source Physics

    OpenAIRE

    Wee, Loo Kang; Lim, Ai Phing; Lye, Sze Yee

    2014-01-01

    eduLab (MOE, 2012b) is a key programme under the third MasterPlan for ICT in Education (mp3) where teachers with good ideas for an ICT-enhanced lesson or curriculum (learning with computer models through inquiry, example PhET (PhET, 2011) can come together to collaborate. eduLab aims to support teachers to develop, prototype and test-bed their lesson ideas (journey in 2012-2014) while ensuring that the results, in the form of complete lesson packages (see http://edulab.moe.edu.sg/edulab-progr...

  12. Vision Lab

    Data.gov (United States)

    Federal Laboratory Consortium — The Vision Lab personnel perform research, development, testing and evaluation of eye protection and vision performance. The lab maintains and continues to develop...

  13. Next Practise Labs

    DEFF Research Database (Denmark)

    2016-01-01

    Klaus Thestrup explains what Next Practise Labs are and how that involves both participants, the researcher and teachers. He also talks about how the term builds upon the open laboratory and experimenting communities - and cultures of creativity.......Klaus Thestrup explains what Next Practise Labs are and how that involves both participants, the researcher and teachers. He also talks about how the term builds upon the open laboratory and experimenting communities - and cultures of creativity....

  14. An RNA Phage Lab: MS2 in Walter Fiers' laboratory of molecular biology in Ghent, from genetic code to gene and genome, 1963-1976.

    Science.gov (United States)

    Pierrel, Jérôme

    2012-01-01

    The importance of viruses as model organisms is well-established in molecular biology and Max Delbrück's phage group set standards in the DNA phage field. In this paper, I argue that RNA phages, discovered in the 1960s, were also instrumental in the making of molecular biology. As part of experimental systems, RNA phages stood for messenger RNA (mRNA), genes and genome. RNA was thought to mediate information transfers between DNA and proteins. Furthermore, RNA was more manageable at the bench than DNA due to the availability of specific RNases, enzymes used as chemical tools to analyse RNA. Finally, RNA phages provided scientists with a pure source of mRNA to investigate the genetic code, genes and even a genome sequence. This paper focuses on Walter Fiers' laboratory at Ghent University (Belgium) and their work on the RNA phage MS2. When setting up his Laboratory of Molecular Biology, Fiers planned a comprehensive study of the virus with a strong emphasis on the issue of structure. In his lab, RNA sequencing, now a little-known technique, evolved gradually from a means to solve the genetic code, to a tool for completing the first genome sequence. Thus, I follow the research pathway of Fiers and his 'RNA phage lab' with their evolving experimental system from 1960 to the late 1970s. This study illuminates two decisive shifts in post-war biology: the emergence of molecular biology as a discipline in the 1960s in Europe and of genomics in the 1990s.

  15. CRISPR/Cas9-mediated genome editing and gene replacement in plants: Transitioning from lab to field

    Science.gov (United States)

    The CRISPR/Cas9 genome engineering system has ignited and swept through the scientific community like wildfire. Owing largely to its efficiency, specificity, and flexibility, the CRISPR/Cas9 system has quickly become the preferred genome-editing tool of plant scientists. In plants, much of the earl...

  16. An open-source LabVIEW application toolkit for phasic heart rate analysis in psychophysiological research.

    Science.gov (United States)

    Duley, Aaron R; Janelle, Christopher M; Coombes, Stephen A

    2004-11-01

    The cardiovascular system has been extensively measured in a variety of research and clinical domains. Despite technological and methodological advances in cardiovascular science, the analysis and evaluation of phasic changes in heart rate persists as a way to assess numerous psychological concomitants. Some researchers, however, have pointed to constraints on data analysis when evaluating cardiac activity indexed by heart rate or heart period. Thus, an off-line application toolkit for heart rate analysis is presented. The program, written with National Instruments' LabVIEW, incorporates a variety of tools for off-line extraction and analysis of heart rate data. Current methods and issues concerning heart rate analysis are highlighted, and how the toolkit provides a flexible environment to ameliorate common problems that typically lead to trial rejection is discussed. Source code for this program may be downloaded from the Psychonomic Society Web archive at www.psychonomic.org/archive/.

  17. Life-cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton

    Science.gov (United States)

    von Dassow, Peter; John, Uwe; Ogata, Hiroyuki; Probert, Ian; Bendif, El Mahdi; Kegel, Jessica U; Audic, Stéphane; Wincker, Patrick; Da Silva, Corinne; Claverie, Jean-Michel; Doney, Scott; Glover, David M; Flores, Daniella Mella; Herrera, Yeritza; Lescot, Magali; Garet-Delmas, Marie-José; de Vargas, Colomban

    2015-01-01

    Emiliania huxleyi is the most abundant calcifying plankton in modern oceans with substantial intraspecific genome variability and a biphasic life cycle involving sexual alternation between calcified 2N and flagellated 1N cells. We show that high genome content variability in Emiliania relates to erosion of 1N-specific genes and loss of the ability to form flagellated cells. Analysis of 185 E. huxleyi strains isolated from world oceans suggests that loss of flagella occurred independently in lineages inhabiting oligotrophic open oceans over short evolutionary timescales. This environmentally linked physiogenomic change suggests life cycling is not advantageous in very large/diluted populations experiencing low biotic pressure and low ecological variability. Gene loss did not appear to reflect pressure for genome streamlining in oligotrophic oceans as previously observed in picoplankton. Life-cycle modifications might be common in plankton and cause major functional variability to be hidden from traditional taxonomic or molecular markers. PMID:25461969

  18. The openness of pluripotent epigenome - Defining the genomic integrity of stemness for regenerative medicine

    Directory of Open Access Journals (Sweden)

    Xuejun H Parsons

    2014-02-01

    Full Text Available This article is an editorial, and it doesn't include an abstract. Full text of this article is available in HTML and PDF.Cite this article as: Parsons XH. The openness of pluripotent epigenome - Defining the genomic Integrity of stemness for regenerative medicine. Int J Cancer Ther Oncol 2014; 2(1:020114.DOI: http://dx.doi.org/10.14319/ijcto.0201.14

  19. Open reading frames associated with cancer in the dark matter of the human genome.

    Science.gov (United States)

    Delgado, Ana Paula; Brandao, Pamela; Chapado, Maria Julia; Hamid, Sheilin; Narayanan, Ramaswamy

    2014-01-01

    The uncharacterized proteins (open reading frames, ORFs) in the human genome offer an opportunity to discover novel targets for cancer. A systematic analysis of the dark matter of the human proteome for druggability and biomarker discovery is crucial to mining the genome. Numerous data mining tools are available to mine these ORFs to develop a comprehensive knowledge base for future target discovery and validation. Using the Genetic Association Database, the ORFs of the human dark matter proteome were screened for evidence of association with neoplasms. The Phenome-Genome Integrator tool was used to establish phenotypic association with disease traits including cancer. Batch analysis of the tools for protein expression analysis, gene ontology and motifs and domains was used to characterize the ORFs. Sixty-two ORFs were identified for neoplasm association. The expression Quantitative Trait Loci (eQTL) analysis identified thirteen ORFs related to cancer traits. Protein expression, motifs and domain analysis and genome-wide association studies verified the relevance of these OncoORFs in diverse tumors. The OncoORFs are also associated with a wide variety of human diseases and disorders. Our results link the OncoORFs to diverse diseases and disorders. This suggests a complex landscape of the uncharacterized proteome in human diseases. These results open the dark matter of the proteome to novel cancer target research. Copyright© 2014, International Institute of Anticancer Research (Dr. John G. Delinasios), All rights reserved.

  20. Open window: when easily identifiable genomes and traits are in the public domain.

    Directory of Open Access Journals (Sweden)

    Misha Angrist

    Full Text Available "One can't be of an enquiring and experimental nature, and still be very sensible."--Charles Fort. As the costs of personal genetic testing "self-quantification" fall, publicly accessible databases housing people's genotypic and phenotypic information are gradually increasing in number and scope. The latest entrant is openSNP, which allows participants to upload their personal genetic/genomic and self-reported phenotypic data. I believe the emergence of such open repositories of human biological data is a natural reflection of inquisitive and digitally literate people's desires to make genomic and phenotypic information more easily available to a community beyond the research establishment. Such unfettered databases hold the promise of contributing mightily to science, science education and medicine. That said, in an age of increasingly widespread governmental and corporate surveillance, we would do well to be mindful that genomic DNA is uniquely identifying. Participants in open biological databases are engaged in a real-time experiment whose outcome is unknown.

  1. Open source 3D printers: an appropriate technology for building low cost optics labs for the developing communities

    Science.gov (United States)

    Gwamuri, J.; Pearce, Joshua M.

    2017-08-01

    The recent introduction of RepRap (self-replicating rapid prototyper) 3-D printers and the resultant open source technological improvements have resulted in affordable 3-D printing, enabling low-cost distributed manufacturing for individuals. This development and others such as the rise of open source-appropriate technology (OSAT) and solar powered 3-D printing are moving 3-D printing from an industry based technology to one that could be used in the developing world for sustainable development. In this paper, we explore some specific technological improvements and how distributed manufacturing with open-source 3-D printing can be used to provide open-source 3-D printable optics components for developing world communities through the ability to print less expensive and customized products. This paper presents an open-source low cost optical equipment library which enables relatively easily adapted customizable designs with the potential of changing the way optics is taught in resource constraint communities. The study shows that this method of scientific hardware development has a potential to enables a much broader audience to participate in optical experimentation both as research and teaching platforms. Conclusions on the technical viability of 3-D printing to assist in development and recommendations on how developing communities can fully exploit this technology to improve the learning of optics through hands-on methods have been outlined.

  2. Novel Networked Remote Laboratory Architecture for Open Connectivity Based on PLC-OPC-LabVIEW-EJS Integration. Application in Remote Fuzzy Control and Sensors Data Acquisition

    Directory of Open Access Journals (Sweden)

    Isaías González

    2016-10-01

    Full Text Available In this paper the design and implementation of a network for integrating Programmable Logic Controllers (PLC, the Object-Linking and Embedding for Process Control protocol (OPC and the open-source Easy Java Simulations (EJS package is presented. A LabVIEW interface and the Java-Internet-LabVIEW (JIL server complete the scheme for data exchange. This configuration allows the user to remotely interact with the PLC. Such integration can be considered a novelty in scientific literature for remote control and sensor data acquisition of industrial plants. An experimental application devoted to remote laboratories is developed to demonstrate the feasibility and benefits of the proposed approach. The experiment to be conducted is the parameterization and supervision of a fuzzy controller of a DC servomotor. The graphical user interface has been developed with EJS and the fuzzy control is carried out by our own PLC. In fact, the distinctive features of the proposed novel network application are the integration of the OPC protocol to share information with the PLC and the application under control. The user can perform the tuning of the controller parameters online and observe in real time the effect on the servomotor behavior. The target group is engineering remote users, specifically in control- and automation-related tasks. The proposed architecture system is described and experimental results are presented.

  3. Novel Networked Remote Laboratory Architecture for Open Connectivity Based on PLC-OPC-LabVIEW-EJS Integration. Application in Remote Fuzzy Control and Sensors Data Acquisition.

    Science.gov (United States)

    González, Isaías; Calderón, Antonio José; Mejías, Andrés; Andújar, José Manuel

    2016-10-31

    In this paper the design and implementation of a network for integrating Programmable Logic Controllers (PLC), the Object-Linking and Embedding for Process Control protocol (OPC) and the open-source Easy Java Simulations (EJS) package is presented. A LabVIEW interface and the Java-Internet-LabVIEW (JIL) server complete the scheme for data exchange. This configuration allows the user to remotely interact with the PLC. Such integration can be considered a novelty in scientific literature for remote control and sensor data acquisition of industrial plants. An experimental application devoted to remote laboratories is developed to demonstrate the feasibility and benefits of the proposed approach. The experiment to be conducted is the parameterization and supervision of a fuzzy controller of a DC servomotor. The graphical user interface has been developed with EJS and the fuzzy control is carried out by our own PLC. In fact, the distinctive features of the proposed novel network application are the integration of the OPC protocol to share information with the PLC and the application under control. The user can perform the tuning of the controller parameters online and observe in real time the effect on the servomotor behavior. The target group is engineering remote users, specifically in control- and automation-related tasks. The proposed architecture system is described and experimental results are presented.

  4. Targeted Genome Sequencing Reveals Varicella-Zoster Virus Open Reading Frame 12 Deletion.

    Science.gov (United States)

    Cohrs, Randall J; Lee, Katherine S; Beach, Addilynn; Sanford, Bridget; Baird, Nicholas L; Como, Christina; Graybill, Chiharu; Jones, Dallas; Tekeste, Eden; Ballard, Mitchell; Chen, Xiaomi; Yalacki, David; Frietze, Seth; Jones, Kenneth; Lenac Rovis, Tihana; Jonjić, Stipan; Haas, Jürgen; Gilden, Don

    2017-10-15

    The neurotropic herpesvirus varicella-zoster virus (VZV) establishes a lifelong latent infection in humans following primary infection. The low abundance of VZV nucleic acids in human neurons has hindered an understanding of the mechanisms that regulate viral gene transcription during latency. To overcome this critical barrier, we optimized a targeted capture protocol to enrich VZV DNA and cDNA prior to whole-genome/transcriptome sequence analysis. Since the VZV genome is remarkably stable, it was surprising to detect that VZV32, a VZV laboratory strain with no discernible growth defect in tissue culture, contained a 2,158-bp deletion in open reading frame (ORF) 12. Consequently, ORF 12 and 13 protein expression was abolished and Akt phosphorylation was inhibited. The discovery of the ORF 12 deletion, revealed through targeted genome sequencing analysis, points to the need to authenticate the VZV genome when the virus is propagated in tissue culture. IMPORTANCE Viruses isolated from clinical samples often undergo genetic modifications when cultured in the laboratory. Historically, VZV is among the most genetically stable herpesviruses, a notion supported by more than 60 complete genome sequences from multiple isolates and following multiple in vitro passages. However, application of enrichment protocols to targeted genome sequencing revealed the unexpected deletion of a significant portion of VZV ORF 12 following propagation in cultured human fibroblast cells. While the enrichment protocol did not introduce bias in either the virus genome or transcriptome, the findings indicate the need for authentication of VZV by sequencing when the virus is propagated in tissue culture. Copyright © 2017 American Society for Microbiology.

  5. ChiMS: Open-source instrument control software platform on LabVIEW for imaging/depth profiling mass spectrometers.

    Science.gov (United States)

    Cui, Yang; Hanley, Luke

    2015-06-01

    ChiMS is an open-source data acquisition and control software program written within LabVIEW for high speed imaging and depth profiling mass spectrometers. ChiMS can also transfer large datasets from a digitizer to computer memory at high repetition rate, save data to hard disk at high throughput, and perform high speed data processing. The data acquisition mode generally simulates a digital oscilloscope, but with peripheral devices integrated for control as well as advanced data sorting and processing capabilities. Customized user-designed experiments can be easily written based on several included templates. ChiMS is additionally well suited to non-laser based mass spectrometers imaging and various other experiments in laser physics, physical chemistry, and surface science.

  6. CRISPR/Cas9-mediated genome editing and gene replacement in plants: Transitioning from lab to field.

    Science.gov (United States)

    Schaeffer, Scott M; Nakata, Paul A

    2015-11-01

    The CRISPR/Cas9 genome engineering system has ignited and swept through the scientific community like wildfire. Owing largely to its efficiency, specificity, and flexibility, the CRISPR/Cas9 system has quickly become the preferred genome-editing tool of plant scientists. In plants, much of the early CRISPR/Cas9 work has been limited to proof of concept and functional studies in model systems. These studies, along with those in other fields of biology, have led to the development of several utilities of CRISPR/Cas9 beyond single gene editing. Such utilities include multiplexing for inducing multiple cleavage events, controlling gene expression, and site specific transgene insertion. With much of the conceptual CRISPR/Cas9 work nearly complete, plant researchers are beginning to apply this gene editing technology for crop trait improvement. Before rational strategies can be designed to implement this technology to engineer a wide array of crops there is a need to expand the availability of crop-specific vectors, genome resources, and transformation protocols. We anticipate that these challenges will be met along with the continued evolution of the CRISPR/Cas9 system particularly in the areas of manipulation of large genomic regions, transgene-free genetic modification, development of breeding resources, discovery of gene function, and improvements upon CRISPR/Cas9 components. The CRISPR/Cas9 editing system appears poised to transform crop trait improvement. Published by Elsevier Ireland Ltd.

  7. Big data, open science and the brain: lessons learned from genomics.

    Science.gov (United States)

    Choudhury, Suparna; Fishman, Jennifer R; McGowan, Michelle L; Juengst, Eric T

    2014-01-01

    The BRAIN Initiative aims to break new ground in the scale and speed of data collection in neuroscience, requiring tools to handle data in the magnitude of yottabytes (10(24)). The scale, investment and organization of it are being compared to the Human Genome Project (HGP), which has exemplified "big science" for biology. In line with the trend towards Big Data in genomic research, the promise of the BRAIN Initiative, as well as the European Human Brain Project, rests on the possibility to amass vast quantities of data to model the complex interactions between the brain and behavior and inform the diagnosis and prevention of neurological disorders and psychiatric disease. Advocates of this "data driven" paradigm in neuroscience argue that harnessing the large quantities of data generated across laboratories worldwide has numerous methodological, ethical and economic advantages, but it requires the neuroscience community to adopt a culture of data sharing and open access to benefit from them. In this article, we examine the rationale for data sharing among advocates and briefly exemplify these in terms of new "open neuroscience" projects. Then, drawing on the frequently invoked model of data sharing in genomics, we go on to demonstrate the complexities of data sharing, shedding light on the sociological and ethical challenges within the realms of institutions, researchers and participants, namely dilemmas around public/private interests in data, (lack of) motivation to share in the academic community, and potential loss of participant anonymity. Our paper serves to highlight some foreseeable tensions around data sharing relevant to the emergent "open neuroscience" movement.

  8. SenseLab

    Science.gov (United States)

    Crasto, Chiquito J.; Marenco, Luis N.; Liu, Nian; Morse, Thomas M.; Cheung, Kei-Hoi; Lai, Peter C.; Bahl, Gautam; Masiar, Peter; Lam, Hugo Y.K.; Lim, Ernest; Chen, Huajin; Nadkarni, Prakash; Migliore, Michele; Miller, Perry L.; Shepherd, Gordon M.

    2009-01-01

    This article presents the latest developments in neuroscience information dissemination through the SenseLab suite of databases: NeuronDB, CellPropDB, ORDB, OdorDB, OdorMapDB, ModelDB and BrainPharm. These databases include information related to: (i) neuronal membrane properties and neuronal models, and (ii) genetics, genomics, proteomics and imaging studies of the olfactory system. We describe here: the new features for each database, the evolution of SenseLab’s unifying database architecture and instances of SenseLab database interoperation with other neuroscience online resources. PMID:17510162

  9. Opening of the TAR hairpin in the HIV-1 genome causes aberrant RNA dimerization and packaging

    Directory of Open Access Journals (Sweden)

    Das Atze T

    2012-07-01

    Full Text Available Abstract Background The TAR hairpin is present at both the 5′ and 3′ end of the HIV-1 RNA genome. The 5′ element binds the viral Tat protein and is essential for Tat-mediated activation of transcription. We recently observed that complete TAR deletion is allowed in the context of an HIV-1 variant that does not depend on this Tat-TAR axis for transcription. Mutations that open the 5′ stem-loop structure did however affect the leader RNA conformation and resulted in a severe replication defect. In this study, we set out to analyze which step of the HIV-1 replication cycle is affected by this conformational change of the leader RNA. Results We demonstrate that opening the 5′ TAR structure through a deletion in either side of the stem region caused aberrant dimerization and reduced packaging of the unspliced viral RNA genome. In contrast, truncation of the TAR hairpin through deletions in both sides of the stem did not affect RNA dimer formation and packaging. Conclusions These results demonstrate that, although the TAR hairpin is not essential for RNA dimerization and packaging, mutations in TAR can significantly affect these processes through misfolding of the relevant RNA signals.

  10. Designing inquiry learning spaces for online labs in the Go-Lab platform

    NARCIS (Netherlands)

    de Jong, Ton; Gillet, Dennis; Sotiriou, Sofoklis; Agogi, Ellinogermaniki; Zacharia, Zacharias

    2015-01-01

    The Go-Lab project (http://www.go-lab-project.eu/) aims to enable the integration of online labs through inquiry-based learning approaches into science classrooms. Through the use of an advanced plug and play technological solution the Go-Lab project opens up remote science laboratories, data

  11. Boosting Nannochloropsis oculata growth and lipid accumulation in a lab-scale open raceway pond characterized by improved light distributions employing built-in planar waveguide modules.

    Science.gov (United States)

    Sun, Yahui; Huang, Yun; Liao, Qiang; Xia, Ao; Fu, Qian; Zhu, Xun; Fu, Jingwei

    2018-02-01

    Aiming at alleviating the adverse effect of poor light penetrability on microalgae growth, planar waveguide modules functioned as diluting and redistributing the intense incident light within microalgae culture more homogeneously were introduced into a lab-scale open raceway pond (ORP) for Nannochloropsis oculata cultivation. As compared to the conventional ORP, the illumination surface area to volume ratio and effective illuminated volume percentage in the proposed ORP were respectively improved by 5.53 times and 19.68-172.72%. Consequently, the superior light distribution characteristics in the proposed ORP contributed to 193.33% and 443.71% increase in biomass concentration and lipid yield relative to those obtained in conventional ORP, respectively. Subsequently, the maximum biomass concentration (2.31 g L -1 ) and lipid yield (1258.65 mg L -1 ) was obtained when the interval between adjacent planar waveguide modules was 18 mm. The biodiesel produced in PWM-ORPs showed better properties than conventional ORP due to higher MUFA and C18:1 components proportions. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Advanced LabVIEW Labs

    International Nuclear Information System (INIS)

    Jones, Eric D.

    1999-01-01

    In the world of computer-based data acquisition and control, the graphical interface program LabVIEW from National Instruments is so ubiquitous that in many ways it has almost become the laboratory standard. To date, there have been approximately fifteen books concerning LabVIEW, but Professor Essick's treatise takes on a completely different tack than all of the previous discussions. In the more standard treatments of the ways and wherefores of LabVIEW such as LabVIEW Graphical Programming: Practical Applications in Instrumentation and Control by Gary W. Johnson (McGraw Hill, NY 1997), the emphasis has been instructing the reader how to program LabVIEW to create a Virtual Instrument (VI) on the computer for interfacing to a particular instruments. LabVIEW is written in ''G'' a graphical programming language developed by National Instruments. In the past the emphasis has been on training the experimenter to learn ''G''. Without going into details here, ''G'' incorporates the usual loops, arithmetic expressions, etc., found in many programming languages, but in an icon (graphical) environment. The net result being that LabVIEW contains all of the standard methods needed for interfacing to instruments, data acquisition, data analysis, graphics, and also methodology to incorporate programs written in other languages into LabVIEW. Historically, according to Professor Essick, he developed a series of experiments for an upper division laboratory course for computer-based instrumentation. His observation was that while many students had the necessary background in computer programming languages, there were students who had virtually no concept about writing a computer program let alone a computer- based interfacing program. Thus the beginnings of a concept for not only teaching computer- based instrumentation techniques, but aiso a method for the beginner to experience writing a com- puter program. Professor Essick saw LabVIEW as the ''perfect environment in which to

  13. Open access resources for genome-wide association mapping in rice.

    Science.gov (United States)

    McCouch, Susan R; Wright, Mark H; Tung, Chih-Wei; Maron, Lyza G; McNally, Kenneth L; Fitzgerald, Melissa; Singh, Namrata; DeClerck, Genevieve; Agosto-Perez, Francisco; Korniliev, Pavel; Greenberg, Anthony J; Naredo, Ma Elizabeth B; Mercado, Sheila Mae Q; Harrington, Sandra E; Shi, Yuxin; Branchini, Darcy A; Kuser-Falcão, Paula R; Leung, Hei; Ebana, Kowaru; Yano, Masahiro; Eizenga, Georgia; McClung, Anna; Mezey, Jason

    2016-02-04

    Increasing food production is essential to meet the demands of a growing human population, with its rising income levels and nutritional expectations. To address the demand, plant breeders seek new sources of genetic variation to enhance the productivity, sustainability and resilience of crop varieties. Here we launch a high-resolution, open-access research platform to facilitate genome-wide association mapping in rice, a staple food crop. The platform provides an immortal collection of diverse germplasm, a high-density single-nucleotide polymorphism data set tailored for gene discovery, well-documented analytical strategies, and a suite of bioinformatics resources to facilitate biological interpretation. Using grain length, we demonstrate the power and resolution of our new high-density rice array, the accompanying genotypic data set, and an expanded diversity panel for detecting major and minor effect QTLs and subpopulation-specific alleles, with immediate implications for rice improvement.

  14. The Maize TFome--development of a transcription factor open reading frame collection for functional genomics.

    Science.gov (United States)

    Burdo, Brett; Gray, John; Goetting-Minesky, Mary P; Wittler, Bettina; Hunt, Matthew; Li, Tai; Velliquette, David; Thomas, Julie; Gentzel, Irene; dos Santos Brito, Michael; Mejía-Guerra, Maria Katherine; Connolly, Layne N; Qaisi, Dalya; Li, Wei; Casas, Maria I; Doseff, Andrea I; Grotewold, Erich

    2014-10-01

    Establishing the architecture of the gene regulatory networks (GRNs) responsible for controlling the transcription of all genes in an organism is a natural development that follows elucidation of the genome sequence. Reconstruction of the GRN requires the availability of a series of molecular tools and resources that so far have been limited to a few model organisms. One such resource consists of collections of transcription factor (TF) open reading frames (ORFs) cloned into vectors that facilitate easy expression in plants or microorganisms. In this study, we describe the development of a publicly available maize TF ORF collection (TFome) of 2034 clones corresponding to 2017 unique gene models in recombination-ready vectors that make possible the facile mobilization of the TF sequences into a number of different expression vectors. The collection also includes several hundred co-regulators (CoREGs), which we classified into well-defined families, and for which we propose here a standard nomenclature, as we have previously done for TFs. We describe the strategies employed to overcome the limitations associated with cloning ORFs from a genome that remains incompletely annotated, with a partial full-length cDNA set available, and with many TF/CoREG genes lacking experimental support. In many instances this required the combination of genome-wide expression data with gene synthesis approaches. The strategies developed will be valuable for developing similar resources for other agriculturally important plants. Information on all the clones generated is available through the GRASSIUS knowledgebase (http://grassius.org/). © 2014 The Authors The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.

  15. The Maize TFome – development of a transcription factor open reading frame collection for functional genomics

    Science.gov (United States)

    Burdo, Brett; Gray, John; Goetting-Minesky, Mary P; Wittler, Bettina; Hunt, Matthew; Li, Tai; Velliquette, David; Thomas, Julie; Gentzel, Irene; Brito, Michael dos Santos; Mejía-Guerra, Maria Katherine; Connolly, Layne N; Qaisi, Dalya; Li, Wei; Casas, Maria I; Doseff, Andrea I; Grotewold, Erich

    2014-01-01

    Establishing the architecture of the gene regulatory networks (GRNs) responsible for controlling the transcription of all genes in an organism is a natural development that follows elucidation of the genome sequence. Reconstruction of the GRN requires the availability of a series of molecular tools and resources that so far have been limited to a few model organisms. One such resource consists of collections of transcription factor (TF) open reading frames (ORFs) cloned into vectors that facilitate easy expression in plants or microorganisms. In this study, we describe the development of a publicly available maize TF ORF collection (TFome) of 2034 clones corresponding to 2017 unique gene models in recombination-ready vectors that make possible the facile mobilization of the TF sequences into a number of different expression vectors. The collection also includes several hundred co-regulators (CoREGs), which we classified into well-defined families, and for which we propose here a standard nomenclature, as we have previously done for TFs. We describe the strategies employed to overcome the limitations associated with cloning ORFs from a genome that remains incompletely annotated, with a partial full-length cDNA set available, and with many TF/CoREG genes lacking experimental support. In many instances this required the combination of genome-wide expression data with gene synthesis approaches. The strategies developed will be valuable for developing similar resources for other agriculturally important plants. Information on all the clones generated is available through the GRASSIUS knowledgebase (http://grassius.org/). PMID:25053252

  16. The Precise - and Wild - Genomics Revolution: Genomics Provides Novel Treatments for Disease and Is Opening New Frontiers for Precision Medicine.

    Science.gov (United States)

    Campbell, Sarah

    2016-01-01

    In the epic endeavor to sequence the human genome, it was as though the size of the equipment and amount of effort required were inversely proportional to the microscopic materials being parsed (Figure 1). "Imagine thousands of people, many laboratories … hundreds, hundreds, hundreds of these machines just to generate that first human genome sequence over a six to eight year period," says Dr. Eric Green, director of the National Human Genome Research Institute (NHGRI) at the National Institutes of Health (NIH) (Figure 2).

  17. Stepwise Distributed Open Innovation Contests for Software Development: Acceleration of Genome-Wide Association Analysis.

    Science.gov (United States)

    Hill, Andrew; Loh, Po-Ru; Bharadwaj, Ragu B; Pons, Pascal; Shang, Jingbo; Guinan, Eva; Lakhani, Karim; Kilty, Iain; Jelinsky, Scott A

    2017-05-01

    The association of differing genotypes with disease-related phenotypic traits offers great potential to both help identify new therapeutic targets and support stratification of patients who would gain the greatest benefit from specific drug classes. Development of low-cost genotyping and sequencing has made collecting large-scale genotyping data routine in population and therapeutic intervention studies. In addition, a range of new technologies is being used to capture numerous new and complex phenotypic descriptors. As a result, genotype and phenotype datasets have grown exponentially. Genome-wide association studies associate genotypes and phenotypes using methods such as logistic regression. As existing tools for association analysis limit the efficiency by which value can be extracted from increasing volumes of data, there is a pressing need for new software tools that can accelerate association analyses on large genotype-phenotype datasets. Using open innovation (OI) and contest-based crowdsourcing, the logistic regression analysis in a leading, community-standard genetics software package (PLINK 1.07) was substantially accelerated. OI allowed us to do this in developed through distributed innovation, we achieved an end-to-end speedup of 591-fold for a data set size of 6678 subjects by 645 863 variants, compared to PLINK 1.07's logistic regression. This represents a reduction in run time from 4.8 hours to 29 seconds. Accelerated logistic regression code developed in this project has been incorporated into the PLINK2 project. Using iterative competition-based OI, we have developed a new, faster implementation of logistic regression for genome-wide association studies analysis. We present lessons learned and recommendations on running a successful OI process for bioinformatics. © The Author 2017. Published by Oxford University Press.

  18. Innovations in STEM education: the Go-Lab federation of online labs

    NARCIS (Netherlands)

    de Jong, Anthonius J.M.; Sotiriou, Sofoklis; Gillet, Dennis

    2014-01-01

    The Go-Lab federation of online labs opens up virtual laboratories (simulation), remote laboratories (real equipment accessible at distance) and data sets from physical laboratory experiments (together called “online labs”) for large-scale use in education. In this way, Go-Lab enables inquiry-based

  19. RNA Elements in Open Reading Frames of the Bluetongue Virus Genome Are Essential for Virus Replication

    NARCIS (Netherlands)

    Feenstra, F.; Gennip, van H.G.P.; Water, van de S.G.P.; Rijn, van P.A.

    2014-01-01

    Members of the Reoviridae family are non-enveloped multi-layered viruses with a double stranded RNA genome consisting of 9 to 12 genome segments. Bluetongue virus is the prototype orbivirus (family Reoviridae, genus Orbivirus), causing disease in ruminants, and is spread by Culicoides biting midges.

  20. Millstone: software for multiplex microbial genome analysis and engineering.

    Science.gov (United States)

    Goodman, Daniel B; Kuznetsov, Gleb; Lajoie, Marc J; Ahern, Brian W; Napolitano, Michael G; Chen, Kevin Y; Chen, Changping; Church, George M

    2017-05-25

    Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. We describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab.

  1. Opening plenary speaker: Human genomics, precision medicine, and advancing human health.

    Science.gov (United States)

    Green, Eric D

    2016-08-01

    Starting with the launch of the Human Genome Project in 1990, the past quarter-century has brought spectacular achievements in genomics that dramatically empower the study of human biology and disease. The human genomics enterprise is now in the midst of an important transition, as the growing foundation of genomic knowledge is being used by researchers and clinicians to tackle increasingly complex problems in biomedicine. Of particular prominence is the use of revolutionary new DNA sequencing technologies for generating prodigious amounts of DNA sequence data to elucidate the complexities of genome structure, function, and evolution, as well as to unravel the genomic bases of rare and common diseases. Together, these developments are ushering in the era of genomic medicine. Augmenting the advances in human genomics have been innovations in technologies for measuring environmental and lifestyle information, electronic health records, and data science; together, these provide opportunities of unprecedented scale and scope for investigating the underpinnings of health and disease. To capitalize on these opportunities, U.S. President Barack Obama recently announced a major new research endeavor - the U.S. Precision Medicine Initiative. This bold effort will be framed around several key aims, which include accelerating the use of genomically informed approaches to cancer care, making important policy and regulatory changes, and establishing a large research cohort of >1 million volunteers to facilitate precision medicine research. The latter will include making the partnership with all participants a centerpiece feature in the cohort's design and development. The Precision Medicine Initiative represents a broad-based research program that will allow new approaches for individualized medical care to be rigorously tested, so as to establish a new evidence base for advancing clinical practice and, eventually, human health.

  2. Reptile genomes open the frontier for comparative analysis of amniote development and regeneration.

    Science.gov (United States)

    Tollis, Marc; Hutchins, Elizabeth D; Kusumi, Kenro

    2014-01-01

    Developmental genetic studies of vertebrates have focused primarily on zebrafish, frog and mouse models, which have clear application to medicine and well-developed genomic resources. In contrast, reptiles represent the most diverse amniote group, but have only recently begun to gather the attention of genome sequencing efforts. Extant reptilian groups last shared a common ancestor ?280 million years ago and include lepidosaurs, turtles and crocodilians. This phylogenetic diversity is reflected in great morphological and behavioral diversity capturing the attention of biologists interested in mechanisms regulating developmental processes such as somitogenesis and spinal patterning, regeneration, the evolution of "snake-like" morphology, the formation of the unique turtle shell, and the convergent evolution of the four-chambered heart shared by mammals and archosaurs. The complete genome of the first non-avian reptile, the green anole lizard, was published in 2011 and has provided insights into the origin and evolution of amniotes. Since then, the genomes of multiple snakes, turtles, and crocodilians have also been completed. Here we will review the current diversity of available reptile genomes, with an emphasis on their evolutionary relationships, and will highlight how these genomes have and will continue to facilitate research in developmental and regenerative biology.

  3. Quantitative genetics theory for genomic selection and efficiency of breeding value prediction in open-pollinated populations

    Directory of Open Access Journals (Sweden)

    José Marcelo Soriano Viana

    2016-06-01

    Full Text Available ABSTRACT To date, the quantitative genetics theory for genomic selection has focused mainly on the relationship between marker and additive variances assuming one marker and one quantitative trait locus (QTL. This study extends the quantitative genetics theory to genomic selection in order to prove that prediction of breeding values based on thousands of single nucleotide polymorphisms (SNPs depends on linkage disequilibrium (LD between markers and QTLs, assuming dominance. We also assessed the efficiency of genomic selection in relation to phenotypic selection, assuming mass selection in an open-pollinated population, all QTLs of lower effect, and reduced sample size, based on simulated data. We show that the average effect of a SNP substitution is proportional to LD measure and to average effect of a gene substitution for each QTL that is in LD with the marker. Weighted (by SNP frequencies and unweighted breeding value predictors have the same accuracy. Efficiency of genomic selection in relation to phenotypic selection is inversely proportional to heritability. Accuracy of breeding value prediction is not affected by the dominance degree and the method of analysis, however, it is influenced by LD extent and magnitude of additive variance. The increase in the number of markers asymptotically improved accuracy of breeding value prediction. The decrease in the sample size from 500 to 200 did not reduce considerably accuracy of breeding value prediction.

  4. A CRISPR/Cas9 Toolbox for Multiplexed Plant Genome Editing and Transcriptional Regulation1[OPEN

    Science.gov (United States)

    Lowder, Levi G.; Zhang, Dengwei; Baltes, Nicholas J.; Paul, Joseph W.; Tang, Xu; Zheng, Xuelian; Voytas, Daniel F.; Hsieh, Tzung-Fu; Zhang, Yong; Qi, Yiping

    2015-01-01

    The relative ease, speed, and biological scope of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated Protein9 (Cas9)-based reagents for genomic manipulations are revolutionizing virtually all areas of molecular biosciences, including functional genomics, genetics, applied biomedical research, and agricultural biotechnology. In plant systems, however, a number of hurdles currently exist that limit this technology from reaching its full potential. For example, significant plant molecular biology expertise and effort is still required to generate functional expression constructs that allow simultaneous editing, and especially transcriptional regulation, of multiple different genomic loci or multiplexing, which is a significant advantage of CRISPR/Cas9 versus other genome-editing systems. To streamline and facilitate rapid and wide-scale use of CRISPR/Cas9-based technologies for plant research, we developed and implemented a comprehensive molecular toolbox for multifaceted CRISPR/Cas9 applications in plants. This toolbox provides researchers with a protocol and reagents to quickly and efficiently assemble functional CRISPR/Cas9 transfer DNA constructs for monocots and dicots using Golden Gate and Gateway cloning methods. It comes with a full suite of capabilities, including multiplexed gene editing and transcriptional activation or repression of plant endogenous genes. We report the functionality and effectiveness of this toolbox in model plants such as tobacco (Nicotiana benthamiana), Arabidopsis (Arabidopsis thaliana), and rice (Oryza sativa), demonstrating its utility for basic and applied plant research. PMID:26297141

  5. Advancing Crop Transformation in the Era of Genome Editing[OPEN

    Science.gov (United States)

    Blechl, Ann E.; Brutnell, Thomas P.; Conrad, Liza J.; Gelvin, Stanton B.; Jackson, David P.; Kausch, Albert P.; Lemaux, Peggy G.; Medford, June I.; Orozco-Cárdenas, Martha L.; Tricoli, David M.; Van Eck, Joyce; Voytas, Daniel F.

    2016-01-01

    Plant transformation has enabled fundamental insights into plant biology and revolutionized commercial agriculture. Unfortunately, for most crops, transformation and regeneration remain arduous even after more than 30 years of technological advances. Genome editing provides novel opportunities to enhance crop productivity but relies on genetic transformation and plant regeneration, which are bottlenecks in the process. Here, we review the state of plant transformation and point to innovations needed to enable genome editing in crops. Plant tissue culture methods need optimization and simplification for efficiency and minimization of time in culture. Currently, specialized facilities exist for crop transformation. Single-cell and robotic techniques should be developed for high-throughput genomic screens. Plant genes involved in developmental reprogramming, wound response, and/or homologous recombination should be used to boost the recovery of transformed plants. Engineering universal Agrobacterium tumefaciens strains and recruiting other microbes, such as Ensifer or Rhizobium, could facilitate delivery of DNA and proteins into plant cells. Synthetic biology should be employed for de novo design of transformation systems. Genome editing is a potential game-changer in crop genetics when plant transformation systems are optimized. PMID:27335450

  6. Methods for open innovation on a genome-design platform associating scientific, commercial, and educational communities in synthetic biology.

    Science.gov (United States)

    Toyoda, Tetsuro

    2011-01-01

    Synthetic biology requires both engineering efficiency and compliance with safety guidelines and ethics. Focusing on the rational construction of biological systems based on engineering principles, synthetic biology depends on a genome-design platform to explore the combinations of multiple biological components or BIO bricks for quickly producing innovative devices. This chapter explains the differences among various platform models and details a methodology for promoting open innovation within the scope of the statutory exemption of patent laws. The detailed platform adopts a centralized evaluation model (CEM), computer-aided design (CAD) bricks, and a freemium model. It is also important for the platform to support the legal aspects of copyrights as well as patent and safety guidelines because intellectual work including DNA sequences designed rationally by human intelligence is basically copyrightable. An informational platform with high traceability, transparency, auditability, and security is required for copyright proof, safety compliance, and incentive management for open innovation in synthetic biology. GenoCon, which we have organized and explained here, is a competition-styled, open-innovation method involving worldwide participants from scientific, commercial, and educational communities that aims to improve the designs of genomic sequences that confer a desired function on an organism. Using only a Web browser, a participating contributor proposes a design expressed with CAD bricks that generate a relevant DNA sequence, which is then experimentally and intensively evaluated by the GenoCon organizers. The CAD bricks that comprise programs and databases as a Semantic Web are developed, executed, shared, reused, and well stocked on the secure Semantic Web platform called the Scientists' Networking System or SciNetS/SciNeS, based on which a CEM research center for synthetic biology and open innovation should be established. Copyright © 2011 Elsevier Inc

  7. The Design:Lab as platform in participatory design research

    DEFF Research Database (Denmark)

    Binder, Thomas; Brandt, Eva

    2008-01-01

    The notion of laboratory or simply 'lab' has become popular in recent years in areas outside science and technology development. Learning Labs, Innovation Labs, Usability Labs, Media and Communication Labs and even Art Labs designate institutions or fora dedicated to change and experimentation....... Influenced by these currents we use the expression 'Design:Lab' as a shorthand description of open collaborations between many stakeholders sharing a mutual interest in design research in a particular field. Many have reacted to the term 'laboratory' or 'lab' as foreign and awkward to design, and we as well...... as others have frequently used other metaphors like workshop, studio or atelier in design research. In this article we will argue that the laboratory metaphor is particularly suitable and useful for the design:lab, and we will give examples of how we have worked with the design:lab as a platform...

  8. Open-ended Laboratory Investigations in a High School Physics Course: The difficulties and rewards of implementing inquiry-based learning in a physics lab

    Science.gov (United States)

    Szott, Aaron

    2014-01-01

    often closed-ended. The outcomes are known in advance and students replicate procedures recommended by the teacher. Over the years, I have come to appreciate the great opportunities created by allowing students investigative freedom in physics laboratories. I have realized that a laboratory environment in which students are free to conduct investigations using procedures of their own design can provide them with varied and rich opportunities for discovery. This paper describes what open-ended laboratory investigations have added to my high school physics classes. I will provide several examples of open-ended laboratories and discuss the benefits they conferred on students and teacher alike.

  9. Evolutionary Fates and Dynamic Functionalization of Young Duplicate Genes in Arabidopsis Genomes1[OPEN

    Science.gov (United States)

    Wang, Jun; Tao, Feng; Marowsky, Nicholas C.; Fan, Chuanzhu

    2016-01-01

    Gene duplication is a primary means to generate genomic novelties, playing an essential role in speciation and adaptation. Particularly in plants, a high abundance of duplicate genes has been maintained for significantly long periods of evolutionary time. To address the manner in which young duplicate genes were derived primarily from small-scale gene duplication and preserved in plant genomes and to determine the underlying driving mechanisms, we generated transcriptomes to produce the expression profiles of five tissues in Arabidopsis thaliana and the closely related species Arabidopsis lyrata and Capsella rubella. Based on the quantitative analysis metrics, we investigated the evolutionary processes of young duplicate genes in Arabidopsis. We determined that conservation, neofunctionalization, and specialization are three main evolutionary processes for Arabidopsis young duplicate genes. We explicitly demonstrated the dynamic functionalization of duplicate genes along the evolutionary time scale. Upon origination, duplicates tend to maintain their ancestral functions; but as they survive longer, they might be likely to develop distinct and novel functions. The temporal evolutionary processes and functionalization of plant duplicate genes are associated with their ancestral functions, dynamic DNA methylation levels, and histone modification abundances. Furthermore, duplicate genes tend to be initially expressed in pollen and then to gain more interaction partners over time. Altogether, our study provides novel insights into the dynamic retention processes of young duplicate genes in plant genomes. PMID:27485883

  10. The €100 lab: A 3D-printable open-source platform for fluorescence microscopy, optogenetics, and accurate temperature control during behaviour of zebrafish, Drosophila, and Caenorhabditis elegans.

    Directory of Open Access Journals (Sweden)

    Andre Maia Chagas

    2017-07-01

    Full Text Available Small, genetically tractable species such as larval zebrafish, Drosophila, or Caenorhabditis elegans have become key model organisms in modern neuroscience. In addition to their low maintenance costs and easy sharing of strains across labs, one key appeal is the possibility to monitor single or groups of animals in a behavioural arena while controlling the activity of select neurons using optogenetic or thermogenetic tools. However, the purchase of a commercial solution for these types of experiments, including an appropriate camera system as well as a controlled behavioural arena, can be costly. Here, we present a low-cost and modular open-source alternative called 'FlyPi'. Our design is based on a 3D-printed mainframe, a Raspberry Pi computer, and high-definition camera system as well as Arduino-based optical and thermal control circuits. Depending on the configuration, FlyPi can be assembled for well under €100 and features optional modules for light-emitting diode (LED-based fluorescence microscopy and optogenetic stimulation as well as a Peltier-based temperature stimulator for thermogenetics. The complete version with all modules costs approximately €200 or substantially less if the user is prepared to 'shop around'. All functions of FlyPi can be controlled through a custom-written graphical user interface. To demonstrate FlyPi's capabilities, we present its use in a series of state-of-the-art neurogenetics experiments. In addition, we demonstrate FlyPi's utility as a medical diagnostic tool as well as a teaching aid at Neurogenetics courses held at several African universities. Taken together, the low cost and modular nature as well as fully open design of FlyPi make it a highly versatile tool in a range of applications, including the classroom, diagnostic centres, and research labs.

  11. The €100 lab: A 3D-printable open-source platform for fluorescence microscopy, optogenetics, and accurate temperature control during behaviour of zebrafish, Drosophila, and Caenorhabditis elegans.

    Science.gov (United States)

    Maia Chagas, Andre; Prieto-Godino, Lucia L; Arrenberg, Aristides B; Baden, Tom

    2017-07-01

    Small, genetically tractable species such as larval zebrafish, Drosophila, or Caenorhabditis elegans have become key model organisms in modern neuroscience. In addition to their low maintenance costs and easy sharing of strains across labs, one key appeal is the possibility to monitor single or groups of animals in a behavioural arena while controlling the activity of select neurons using optogenetic or thermogenetic tools. However, the purchase of a commercial solution for these types of experiments, including an appropriate camera system as well as a controlled behavioural arena, can be costly. Here, we present a low-cost and modular open-source alternative called 'FlyPi'. Our design is based on a 3D-printed mainframe, a Raspberry Pi computer, and high-definition camera system as well as Arduino-based optical and thermal control circuits. Depending on the configuration, FlyPi can be assembled for well under €100 and features optional modules for light-emitting diode (LED)-based fluorescence microscopy and optogenetic stimulation as well as a Peltier-based temperature stimulator for thermogenetics. The complete version with all modules costs approximately €200 or substantially less if the user is prepared to 'shop around'. All functions of FlyPi can be controlled through a custom-written graphical user interface. To demonstrate FlyPi's capabilities, we present its use in a series of state-of-the-art neurogenetics experiments. In addition, we demonstrate FlyPi's utility as a medical diagnostic tool as well as a teaching aid at Neurogenetics courses held at several African universities. Taken together, the low cost and modular nature as well as fully open design of FlyPi make it a highly versatile tool in a range of applications, including the classroom, diagnostic centres, and research labs.

  12. Genomes

    National Research Council Canada - National Science Library

    Brown, T. A. (Terence A.)

    2002-01-01

    ... of genome expression and replication processes, and transcriptomics and proteomics. This text is richly illustrated with clear, easy-to-follow, full color diagrams, which are downloadable from the book's website...

  13. GeneLab: A Systems Biology Platform for Spaceflight Omics Data

    Science.gov (United States)

    Reinsch, Sigrid S.; Lai, San-Huei; Chen, Rick; Thompson, Terri; Berrios, Daniel; Fogle, Homer; Marcu, Oana; Timucin, Linda; Chakravarty, Kaushik; Coughlan, Joseph

    2015-01-01

    NASA's mission includes expanding our understanding of biological systems to improve life on Earth and to enable long-duration human exploration of space. Resources to support large numbers of spaceflight investigations are limited. NASA's GeneLab project is maximizing the science output from these experiments by: (1) developing a unique public bioinformatics database that includes space bioscience relevant "omics" data (genomics, transcriptomics, proteomics, and metabolomics) and experimental metadata; (2) partnering with NASA-funded flight experiments through bio-sample sharing or sample augmentation to expedite omics data input to the GeneLab database; and (3) developing community-driven reference flight experiments. The first database, GeneLab Data System Version 1.0, went online in April 2015. V1.0 contains numerous flight datasets and has search and download capabilities. Version 2.0 will be released in 2016 and will link to analytic tools. In 2015 Genelab partnered with two Biological Research in Canisters experiments (BBRIC-19 and BRIC-20) which examine responses of Arabidopsis thaliana to spaceflight. GeneLab also partnered with Rodent Research-1 (RR1), the maiden flight to test the newly developed rodent habitat. GeneLab developed protocols for maxiumum yield of RNA, DNA and protein from precious RR-1 tissues harvested and preserved during the SpaceX-4 mission, as well as from tissues from mice that were frozen intact during spaceflight and later dissected. GeneLab is establishing partnerships with at least three planned flights for 2016. Organism-specific nationwide Science Definition Teams (SDTs) will define future GeneLab dedicated missions and ensure the broader scientific impact of the GeneLab missions. GeneLab ensures prompt release and open access to all high-throughput omics data from spaceflight and ground-based simulations of microgravity and radiation. Overall, GeneLab will facilitate the generation and query of parallel multi-omics data, and

  14. The NEIGHBOR Consortium Primary Open Angle Glaucoma Genome-wide Association Study: Rationale, Study design and Clinical variables

    Science.gov (United States)

    Wiggs, Janey L; Hauser, Michael A; Abdrabou, Wael; Allingham, R Rand; Budenz, Donald L; DelBono, Elizabeth; Friedman, David S; Kang, Jae H; Gaasterland, Douglas; Gaasterland, Terry; Lee, Richard K; Lichter, Paul R; Loomis, Stephanie; Liu, Yutao; McCarty, Cathy; Medeiros, Felipe A; Moroi, Sayoko E; Olson, Lana M; Realini, Anthony; Richards, Julia E; Rozsa, Frank W; Schuman, Joel S; Singh, Kuldev; Stein, Joshua D; Vollrath, Douglas; Weinreb, Robert N; Wollstein, Gadi; Yaspan, Brian L; Yoneyama, Sachiko; Zack, Don; Zhang, Kang; Pericak-Vance, Margaret; Pasquale, Louis R; Haines, Jonathan L

    2012-01-01

    Primary open-angle glaucoma (POAG) is a common disease with complex inheritance. The identification of genes predisposing to POAG is an important step toward the development of novel gene-based methods of diagnosis and treatment. Genome-wide association studies (GWAS) have successfully identified genes contributing to complex traits such as POAG however, such studies frequently require very large sample sizes, and thus, collaborations and consortia have been of critical importance for the GWAS approach. In this report we describe the formation of the NEIGHBOR consortium, the harmonized case control definitions used for a POAG GWAS, the clinical features of the cases and controls and the rationale for the GWAS study design. PMID:22828004

  15. Identification of very small open reading frames in the genomes of Holmes Jungle virus, Ord River virus, and Wongabel virus of the genus , family

    Directory of Open Access Journals (Sweden)

    Aneta Gubala

    2017-07-01

    Full Text Available Viruses of the family Rhabdoviridae infect a broad range of hosts from a variety of ecological and geographical niches, including vertebrates, arthropods, and plants. The arthropod-transmitted members of this family display considerable genetic diversity and remarkable genomic flexibility that enable coding for various accessory proteins in different locations of the genome. Here, we describe the genome of Holmes Jungle virus, isolated from Culex annulirostris mosquitoes collected in northern Australia, and make detailed comparisons with the closely related Ord River and Wongabel viruses, with a focus on identifying very small open reading frames (smORFs in their genomes. This is the first systematic prediction of smORFs in rhabdoviruses, emphasising the intricacy of the rhabdovirus genome and the knowledge gaps. We speculate that these smORFs may be of importance to the life cycle of the virus in the arthropod vector.

  16. Balancing Benefits and Risks of Immortal Data: Participants' Views of Open Consent in the Personal Genome Project.

    Science.gov (United States)

    Zarate, Oscar A; Brody, Julia Green; Brown, Phil; Ramirez-Andreotta, Mónica D; Perovich, Laura; Matz, Jacob

    2016-01-01

    An individual's health, genetic, or environmental-exposure data, placed in an online repository, creates a valuable shared resource that can accelerate biomedical research and even open opportunities for crowd-sourcing discoveries by members of the public. But these data become "immortalized" in ways that may create lasting risk as well as benefit. Once shared on the Internet, the data are difficult or impossible to redact, and identities may be revealed by a process called data linkage, in which online data sets are matched to each other. Reidentification (re-ID), the process of associating an individual's name with data that were considered deidentified, poses risks such as insurance or employment discrimination, social stigma, and breach of the promises often made in informed-consent documents. At the same time, re-ID poses risks to researchers and indeed to the future of science, should re-ID end up undermining the trust and participation of potential research participants. The ethical challenges of online data sharing are heightened as so-called big data becomes an increasingly important research tool and driver of new research structures. Big data is shifting research to include large numbers of researchers and institutions as well as large numbers of participants providing diverse types of data, so the participants' consent relationship is no longer with a person or even a research institution. In addition, consent is further transformed because big data analysis often begins with descriptive inquiry and generation of a hypothesis, and the research questions cannot be clearly defined at the outset and may be unforeseeable over the long term. In this article, we consider how expanded data sharing poses new challenges, illustrated by genomics and the transition to new models of consent. We draw on the experiences of participants in an open data platform-the Personal Genome Project-to allow study participants to contribute their voices to inform ethical consent

  17. The Telecom Lab is moving

    CERN Multimedia

    IT Department

    2009-01-01

    As of 2nd March 2009, the Telecom Lab will move to Building 58 R-017. The Telecom Lab is the central point for all support questions regarding CERN mobile phone services (provision of SIM cards, requests for modifications of subscriptions, diagnostics for mobile phone problems, etc.). The opening hours as well as the contact details for the Telecom Lab remain unchanged: New location: Building 58 R-017 Opening hours: Every week day, from 11 a.m. to 12 a.m. Phone number: 72480 Email address: labo.telecom@cern.ch This change has no impact on support requests for mobile services. Users can still submit their requests concerning mobile phone subscriptions using the usual EDH form (https://edh.cern.ch/Document/GSM). The automatic message sent to inform users of their SIM card availability will be updated to indicate the new Telecom Lab location. You can find all information related to CERN mobile phone services at the following link: http://cern.ch/gsm CS Section - IT/CS group

  18. NASA's GeneLab Phase II: Federated Search and Data Discovery

    Science.gov (United States)

    Berrios, Daniel C.; Costes, Sylvain V.; Tran, Peter B.

    2017-01-01

    GeneLab is currently being developed by NASA to accelerate 'open science' biomedical research in support of the human exploration of space and the improvement of life on earth. Phase I of the four-phase GeneLab Data Systems (GLDS) project emphasized capabilities for submission, curation, search, and retrieval of genomics, transcriptomics and proteomics ('omics') data from biomedical research of space environments. The focus of development of the GLDS for Phase II has been federated data search for and retrieval of these kinds of data across other open-access systems, so that users are able to conduct biological meta-investigations using data from a variety of sources. Such meta-investigations are key to corroborating findings from many kinds of assays and translating them into systems biology knowledge and, eventually, therapeutics.

  19. NASAs GeneLab Phase II: Federated Search and Data Discovery

    Science.gov (United States)

    Berrios, Daniel C.; Costes, Sylvain; Tran, Peter

    2017-01-01

    GeneLab is currently being developed by NASA to accelerate open science biomedical research in support of the human exploration of space and the improvement of life on earth. Phase I of the four-phase GeneLab Data Systems (GLDS) project emphasized capabilities for submission, curation, search, and retrieval of genomics, transcriptomics and proteomics (omics) data from biomedical research of space environments. The focus of development of the GLDS for Phase II has been federated data search for and retrieval of these kinds of data across other open-access systems, so that users are able to conduct biological meta-investigations using data from a variety of sources. Such meta-investigations are key to corroborating findings from many kinds of assays and translating them into systems biology knowledge and, eventually, therapeutics.

  20. Genome-Wide Search for Translated Upstream Open Reading Frames in Arabidopsis Thaliana.

    Science.gov (United States)

    Hu, Qiwen; Merchante, Catharina; Stepanova, Anna N; Alonso, Jose M; Heber, Steffen

    2016-03-01

    Upstream open reading frames (uORFs) are open reading frames that occur within the 5' UTR of an mRNA. uORFs have been found in many organisms. They play an important role in gene regulation, cell development, and in various metabolic processes. It is believed that translated uORFs reduce the translational efficiency of the main coding region. However, only few uORFs are experimentally characterized. In this paper, we use ribosome footprinting together with a semi-supervised approach based on stacking classification models to identify translated uORFs in Arabidopsis thaliana. Our approach identified 5360 potentially translated uORFs in 2051 genes. GO terms enriched in genes with translated uORFs include catalytic activity, binding, transferase activity, phosphotransferase activity, kinase activity, and transcription regulator activity. The reported uORFs occur with a higher frequency in multi-isoform genes, and some uORFs are affected by alternative transcript start sites or alternative splicing events. Association rule mining revealed sequence features associated with the translation status of the uORFs. We hypothesize that uORF translation is a complex process that might be regulated by multiple factors. The identified uORFs are available online at:https://www.dropbox.com/sh/zdutupedxafhly8/AABFsdNR5zDfiozB7B4igFcja?dl=0. This paper is the extended version of our research presented at ISBRA 2015.

  1. Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae

    Science.gov (United States)

    Kastenmayer, James P.; Ni, Li; Chu, Angela; Kitchen, Lauren E.; Au, Wei-Chun; Yang, Hui; Carter, Carole D.; Wheeler, David; Davis, Ronald W.; Boeke, Jef D.; Snyder, Michael A.; Basrai, Munira A.

    2006-01-01

    Genes with small open reading frames (sORFs; molecular barcode,” bringing the total number of sORF deletion strains to 247. Phenotypic analyses of the new gene-deletion strains identified 22 sORFs required for haploid growth, growth at high temperature, growth in the presence of a nonfermentable carbon source, or growth in the presence of DNA damage and replication-arrest agents. We provide a collection of sORF deletion strains that can be integrated into the existing deletion collection as a resource for the yeast community for elucidating gene function. Moreover, our analyses of the S. cerevisiae sORFs establish that sORFs are conserved across eukaryotes and have important biological functions. PMID:16510898

  2. TERRA REF: Advancing phenomics with high resolution, open access sensor and genomics data

    Science.gov (United States)

    LeBauer, D.; Kooper, R.; Burnette, M.; Willis, C.

    2017-12-01

    Automated plant measurement has the potential to improve understanding of genetic and environmental controls on plant traits (phenotypes). The application of sensors and software in the automation of high throughput phenotyping reflects a fundamental shift from labor intensive hand measurements to drone, tractor, and robot mounted sensing platforms. These tools are expected to speed the rate of crop improvement by enabling plant breeders to more accurately select plants with improved yields, resource use efficiency, and stress tolerance. However, there are many challenges facing high throughput phenomics: sensors and platforms are expensive, currently there are few standard methods of data collection and storage, and the analysis of large data sets requires high performance computers and automated, reproducible computing pipelines. To overcome these obstacles and advance the science of high throughput phenomics, the TERRA Phenotyping Reference Platform (TERRA-REF) team is developing an open-access database of high resolution sensor data. TERRA REF is an integrated field and greenhouse phenotyping system that includes: a reference field scanner with fifteen sensors that can generate terrabytes of data each day at mm resolution; UAV, tractor, and fixed field sensing platforms; and an automated controlled-environment scanner. These platforms will enable investigation of diverse sensing modalities, and the investigation of traits under controlled and field environments. It is the goal of TERRA REF to lower the barrier to entry for academic and industry researchers by providing high-resolution data, open source software, and online computing resources. Our project is unique in that all data will be made fully public in November 2018, and is already available to early adopters through the beta-user program. We will describe the datasets and how to use them as well as the databases and computing pipeline and how these can be reused and remixed in other phenomics pipelines

  3. Virtual Reality Lab Assistant

    Science.gov (United States)

    Saha, Hrishikesh; Palmer, Timothy A.

    1996-01-01

    Virtual Reality Lab Assistant (VRLA) demonstration model is aligned for engineering and material science experiments to be performed by undergraduate and graduate students in the course as a pre-lab simulation experience. This will help students to get a preview of how to use the lab equipment and run experiments without using the lab hardware/software equipment. The quality of the time available for laboratory experiments can be significantly improved through the use of virtual reality technology.

  4. Human variation database: an open-source database template for genomic discovery.

    Science.gov (United States)

    Fejes, Anthony P; Khodabakhshi, Alireza Hadj; Birol, Inanc; Jones, Steven J M

    2011-04-15

    Current public variation databases are based upon collaboratively pooling data into a single database with a single interface available to the public. This gives little control to the collaborator to mine the database and requires that they freely share their data with the owners of the repository. We aim to provide an alternative mechanism: providing the source code and application programming interface (API) of a database, enabling researchers to set up local versions without investing heavily in the development of the resource and allowing for confidential information to remain secure. We describe an open-source database that can be installed easily at any research facility for the storage and analysis of thousands of next-generation sequencing variations. This database is built using PostgreSQL 8.4 (The PostgreSQL Global Development Group. postgres 8.4: http://www.postgresql.org) and provides a novel method for collating and searching across the reported results from thousands of next-generation sequence samples, as well as rapidly accessing vital information on the origin of the samples. The schema of the database makes rapid and insightful queries simple and enables easy annotation of novel or known genetic variations. A modular and cross-platform Java API is provided to perform common functions, such as generation of standard experimental reports and graphical summaries of modifications to genes. Included libraries allow adopters of the database to quickly develop their own queries. The software is available for download through the Vancouver Short Read Analysis Package on Sourceforge, http://vancouvershortr.sourceforge.net. Instructions for use and deployment are provided on the accompanying wiki pages. afejes@bcgsc.ca.

  5. Canadian Open Genetics Repository (COGR): a unified clinical genomics database as a community resource for standardising and sharing genetic interpretations.

    Science.gov (United States)

    Lerner-Ellis, Jordan; Wang, Marina; White, Shana; Lebo, Matthew S

    2015-07-01

    The Canadian Open Genetics Repository is a collaborative effort for the collection, storage, sharing and robust analysis of variants reported by medical diagnostics laboratories across Canada. As clinical laboratories adopt modern genomics technologies, the need for this type of collaborative framework is increasingly important. A survey to assess existing protocols for variant classification and reporting was delivered to clinical genetics laboratories across Canada. Based on feedback from this survey, a variant assessment tool was made available to all laboratories. Each participating laboratory was provided with an instance of GeneInsight, a software featuring versioning and approval processes for variant assessments and interpretations and allowing for variant data to be shared between instances. Guidelines were established for sharing data among clinical laboratories and in the final outreach phase, data will be made readily available to patient advocacy groups for general use. The survey demonstrated the need for improved standardisation and data sharing across the country. A variant assessment template was made available to the community to aid with standardisation. Instances of the GeneInsight tool were provided to clinical diagnostic laboratories across Canada for the purpose of uploading, transferring, accessing and sharing variant data. As an ongoing endeavour and a permanent resource, the Canadian Open Genetics Repository aims to serve as a focal point for the collaboration of Canadian laboratories with other countries in the development of tools that take full advantage of laboratory data in diagnosing, managing and treating genetic diseases. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

  6. CrusView: A Java-Based Visualization Platform for Comparative Genomics Analyses in Brassicaceae Species[OPEN

    Science.gov (United States)

    Chen, Hao; Wang, Xiangfeng

    2013-01-01

    In plants and animals, chromosomal breakage and fusion events based on conserved syntenic genomic blocks lead to conserved patterns of karyotype evolution among species of the same family. However, karyotype information has not been well utilized in genomic comparison studies. We present CrusView, a Java-based bioinformatic application utilizing Standard Widget Toolkit/Swing graphics libraries and a SQLite database for performing visualized analyses of comparative genomics data in Brassicaceae (crucifer) plants. Compared with similar software and databases, one of the unique features of CrusView is its integration of karyotype information when comparing two genomes. This feature allows users to perform karyotype-based genome assembly and karyotype-assisted genome synteny analyses with preset karyotype patterns of the Brassicaceae genomes. Additionally, CrusView is a local program, which gives its users high flexibility when analyzing unpublished genomes and allows users to upload self-defined genomic information so that they can visually study the associations between genome structural variations and genetic elements, including chromosomal rearrangements, genomic macrosynteny, gene families, high-frequency recombination sites, and tandem and segmental duplications between related species. This tool will greatly facilitate karyotype, chromosome, and genome evolution studies using visualized comparative genomics approaches in Brassicaceae species. CrusView is freely available at http://www.cmbb.arizona.edu/CrusView/. PMID:23898041

  7. Teachers' Perspectives on Online Virtual Labs vs. Hands-On Labs in High School Science

    Science.gov (United States)

    Bohr, Teresa M.

    This study of online science teachers' opinions addressed the use of virtual labs in online courses. A growing number of schools use virtual labs that must meet mandated laboratory standards to ensure they provide learning experiences comparable to hands-on labs, which are an integral part of science curricula. The purpose of this qualitative case study was to examine teachers' perceptions of the quality and effectiveness of high school virtual labs. The theoretical foundation was constructivism, as labs provide student-centered activities for problem solving, inquiry, and exploration of phenomena. The research questions focused on experienced teachers' perceptions of the quality of virtual vs. hands-on labs. Data were collected through survey questions derived from the lab objectives of The Next Generation Science Standards . Eighteen teachers rated the degree of importance of each objective and also rated how they felt virtual labs met these objectives; these ratings were reported using descriptive statistics. Responses to open-ended questions were few and served to illustrate the numerical results. Many teachers stated that virtual labs are valuable supplements but could not completely replace hands-on experiences. Studies on the quality and effectiveness of high school virtual labs are limited despite widespread use. Comprehensive studies will ensure that online students have equal access to quality labs. School districts need to define lab requirements, and colleges need to specify the lab experience they require. This study has potential to inspire positive social change by assisting science educators, including those in the local school district, in evaluating and selecting courseware designed to promote higher order thinking skills, real-world problem solving, and development of strong inquiry skills, thereby improving science instruction for all high school students.

  8. The draft genome sequence of the American mink (Neovison vison) opens new opportunities of genomic research in mink

    DEFF Research Database (Denmark)

    Cai, Zexi; Panitz, Frank; Petersen, Bent

    2016-01-01

    of Carnivora. Here we present the draft genome sequence of American mink. In our study, a male inbred pearl mink was sequenced by Illumina paired-end and mate pair sequencing. The reads were assembled, which lead to 22,419 scaffolds with an N50 (shortest sequence length at 50% of the genome) of 646,304 bp...

  9. Crystallization Formulation Lab

    Data.gov (United States)

    Federal Laboratory Consortium — The Crystallization Formulation Lab fills a critical need in the process development and optimization of current and new explosives and energetic formulations. The...

  10. USNA DIGITAL FORENSICS LAB

    Data.gov (United States)

    Federal Laboratory Consortium — To enable Digital Forensics and Computer Security research and educational opportunities across majors and departments. Lab MissionEstablish and maintain a Digital...

  11. Fabrication and Prototyping Lab

    Data.gov (United States)

    Federal Laboratory Consortium — Purpose: The Fabrication and Prototyping Lab for composite structures provides a wide variety of fabrication capabilities critical to enabling hands-on research and...

  12. Magnetic Media Lab

    Data.gov (United States)

    Federal Laboratory Consortium — This lab specializes in tape certification and performance characterization of high density digital tape and isprepared to support the certification of standard size...

  13. Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access.

    Science.gov (United States)

    Taboada, Eduardo N; Graham, Morag R; Carriço, João A; Van Domselaar, Gary

    2017-01-01

    Public health labs and food regulatory agencies globally are embracing whole genome sequencing (WGS) as a revolutionary new method that is positioned to replace numerous existing diagnostic and microbial typing technologies with a single new target: the microbial draft genome. The ability to cheaply generate large amounts of microbial genome sequence data, combined with emerging policies of food regulatory and public health institutions making their microbial sequences increasingly available and public, has served to open up the field to the general scientific community. This open data access policy shift has resulted in a proliferation of data being deposited into sequence repositories and of novel bioinformatics software designed to analyze these vast datasets. There also has been a more recent drive for improved data sharing to achieve more effective global surveillance, public health and food safety. Such developments have heightened the need for enhanced analytical systems in order to process and interpret this new type of data in a timely fashion. In this review we outline the emergence of genomics, bioinformatics and open data in the context of food safety. We also survey major efforts to translate genomics and bioinformatics technologies out of the research lab and into routine use in modern food safety labs. We conclude by discussing the challenges and opportunities that remain, including those expected to play a major role in the future of food safety science.

  14. Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access

    Directory of Open Access Journals (Sweden)

    Eduardo N. Taboada

    2017-05-01

    Full Text Available Public health labs and food regulatory agencies globally are embracing whole genome sequencing (WGS as a revolutionary new method that is positioned to replace numerous existing diagnostic and microbial typing technologies with a single new target: the microbial draft genome. The ability to cheaply generate large amounts of microbial genome sequence data, combined with emerging policies of food regulatory and public health institutions making their microbial sequences increasingly available and public, has served to open up the field to the general scientific community. This open data access policy shift has resulted in a proliferation of data being deposited into sequence repositories and of novel bioinformatics software designed to analyze these vast datasets. There also has been a more recent drive for improved data sharing to achieve more effective global surveillance, public health and food safety. Such developments have heightened the need for enhanced analytical systems in order to process and interpret this new type of data in a timely fashion. In this review we outline the emergence of genomics, bioinformatics and open data in the context of food safety. We also survey major efforts to translate genomics and bioinformatics technologies out of the research lab and into routine use in modern food safety labs. We conclude by discussing the challenges and opportunities that remain, including those expected to play a major role in the future of food safety science.

  15. Online labs and the MARVEL experience

    Directory of Open Access Journals (Sweden)

    Dieter Mueller

    2005-06-01

    Full Text Available MARVEL is a Leonardo da Vinci project that provides a framework to analyse the pedagogic effectiveness of online labs in various heterogeneous areas that include solar energy, robotics, electronics and electro-pneumatics. It is also used as a test bench to compare the implementation of purely remote labs, where all devices are real, versus mixed-reality environments, where real devices work together with simulation models. This paper describes the basic concepts underlying the implementation of such online labs and presents two case studies (which are openly available to the public. A final section discusses the main pedagogical implications of online labs and presents the research directions that are being considered as a follow-up from this project.

  16. Guidelines for Urban Labs

    DEFF Research Database (Denmark)

    Scholl, Christian; Agger Eriksen, Mette; Baerten, Nik

    2017-01-01

    urban lab initiatives from five different European cities: Antwerp (B), Graz and Leoben (A), Maastricht (NL) and Malmö (S). We do not pretend that these guidelines touch upon all possible challenges an urban lab may be confronted with, but we have incorporated all those we encountered in our...

  17. Applying a Living Lab methodology to support innovation in education at a university in South Africa

    CSIR Research Space (South Africa)

    Gallaghan, R

    2015-07-01

    Full Text Available The Living Lab paradigm creates open and inter-disciplinary environments where participants can interrogate challenges and co-create solutions. A successful Living Lab context incorporates a clear focus/vision, strong leadership, self...

  18. The Living Labs: Innovation in Real-Life Settings

    Science.gov (United States)

    Hawk, Nathan; Bartle, Gamin; Romine, Martha

    2012-01-01

    The living lab (LL) is an open innovation ecosystem serving to provide opportunities for local stakeholders to practice research and to experiment with meaningful improvements for cities and other organizations. Living labs aim at involving the user as a cocreator. In this article the relationship between the LLs and a variety of stakeholders is…

  19. Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products

    DEFF Research Database (Denmark)

    Almeida, Mathieu; Hebert, Agnes; Abraham, Anne-Laure

    2014-01-01

    sequencing is a promising approach to characterize their genomic and functional profiles. Such analyses, however, critically depend on the availability of appropriate reference genome databases against which the sequencing reads can be aligned. Results: We built a reference genome catalog suitable for short...... Kluyvera, Luteococcus and Marinilactibacillus, still missing from public database. To demonstrate the potential of this catalog, we analysed the microbial composition of the surface of two smear cheeses and one blue-veined cheese, and showed that a significant part of the microbiota of these traditional...... cheeses was composed of microorganisms newly sequenced in our study. Conclusions: Our study provides data, which combined with publicly available genome references, represents the most expansive catalog to date of cheese-associated bacteria. Using this extended dairy catalog, we revealed the presence...

  20. LIDAR Research & Development Lab

    Data.gov (United States)

    Federal Laboratory Consortium — The LIDAR Research and Development labs are used to investigate and improve LIDAR components such as laser sources, optical signal detectors and optical filters. The...

  1. Clothing Systems Design Lab

    Data.gov (United States)

    Federal Laboratory Consortium — The Clothing Systems Design Lab houses facilities for the design and rapid prototyping of military protective apparel.Other focuses include: creation of patterns and...

  2. Secure Processing Lab

    Data.gov (United States)

    Federal Laboratory Consortium — The Secure Processing Lab is the center of excellence for new and novel processing techniques for the formation, calibration and analysis of radar. In addition, this...

  3. Guidelines for Urban Labs

    DEFF Research Database (Denmark)

    Scholl, Christian; Agger Eriksen, Mette; Baerten, Nik

    2017-01-01

    These guidelines are intended for team members and managers of urban labs and, more generally, for civil servants and facilitators in cities working with experimental processes to tackle complex challenges. They aim to support the everyday practice of collaboratively experimenting and learning ho...... the result is inspiring and instructive for all those who want to wrap their minds around experimental co-creative approaches to urban governance and city development.......These guidelines are intended for team members and managers of urban labs and, more generally, for civil servants and facilitators in cities working with experimental processes to tackle complex challenges. They aim to support the everyday practice of collaboratively experimenting and learning how...... to create more sustainable and inclusive cities. Policy-makers and urban development stakeholders may struggle to implement urban labs, and seek guidance for further development. Evidence-based guidelines and design principles are needed to decide for which types of challeng- es urban labs are most suited...

  4. Laser Research Lab

    Data.gov (United States)

    Federal Laboratory Consortium — The Laser Research lab is thecenter for the development of new laser sources, nonlinear optical materials, frequency conversion processes and laser-based sensors for...

  5. Evaluation of oral microbiology lab curriculum reform.

    Science.gov (United States)

    Nie, Min; Gao, Zhen Y; Wu, Xin Y; Jiang, Chen X; Du, Jia H

    2015-12-07

    According to the updated concept of oral microbiology, the School of Stomatology, Wuhan University, has carried out oral microbiology teaching reforms during the last 5 years. There was no lab curriculum before 2009 except for a theory course of oral microbiology. The school has implemented an innovative curriculum with oral medicine characteristics to strengthen understanding of knowledge, cultivate students' scientific interest and develop their potential, to cultivate the comprehensive ability of students. This study was designed to evaluate the oral microbiology lab curriculum by analyzing student performance and perceptions regarding the curriculum from 2009 to 2013. The lab curriculum adopted modalities for cooperative learning. Students collected dental plaque from each other and isolated the cariogenic bacteria with selective medium plates. Then they purified the enrichment culture medium and identified the cariogenic strains by Gram stain and biochemical tests. Both quantitative and qualitative data for 5 years were analysed in this study. Part One of the current study assessed student performance in the lab from 2009 to 2013. Part Two used qualitative means to assess students' perceptions by an open questionnaire. The 271 study students' grades on oral microbiology improved during the lab curriculum: "A" grades rose from 60.5 to 81.2 %, and "C" grades fell from 28.4 to 6.3 %. All students considered the lab curriculum to be interesting and helpful. Quantitative and qualitative data converge to suggest that the lab curriculum has strengthened students' grasp of important microbiology-related theory, cultivated their scientific interest, and developed their potential and comprehensive abilities. Our student performance and perception data support the continued use of the innovative teaching system. As an extension and complement of the theory course, the oral microbiology lab curriculum appears to improve the quality of oral medicine education and help to

  6. Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products.

    Science.gov (United States)

    Almeida, Mathieu; Hébert, Agnès; Abraham, Anne-Laure; Rasmussen, Simon; Monnet, Christophe; Pons, Nicolas; Delbès, Céline; Loux, Valentin; Batto, Jean-Michel; Leonard, Pierre; Kennedy, Sean; Ehrlich, Stanislas Dusko; Pop, Mihai; Montel, Marie-Christine; Irlinger, Françoise; Renault, Pierre

    2014-12-13

    Microbial communities of traditional cheeses are complex and insufficiently characterized. The origin, safety and functional role in cheese making of these microbial communities are still not well understood. Metagenomic analysis of these communities by high throughput shotgun sequencing is a promising approach to characterize their genomic and functional profiles. Such analyses, however, critically depend on the availability of appropriate reference genome databases against which the sequencing reads can be aligned. We built a reference genome catalog suitable for short read metagenomic analysis using a low-cost sequencing strategy. We selected 142 bacteria isolated from dairy products belonging to 137 different species and 67 genera, and succeeded to reconstruct the draft genome of 117 of them at a standard or high quality level, including isolates from the genera Kluyvera, Luteococcus and Marinilactibacillus, still missing from public database. To demonstrate the potential of this catalog, we analysed the microbial composition of the surface of two smear cheeses and one blue-veined cheese, and showed that a significant part of the microbiota of these traditional cheeses was composed of microorganisms newly sequenced in our study. Our study provides data, which combined with publicly available genome references, represents the most expansive catalog to date of cheese-associated bacteria. Using this extended dairy catalog, we revealed the presence in traditional cheese of dominant microorganisms not deliberately inoculated, mainly Gram-negative genera such as Pseudoalteromonas haloplanktis or Psychrobacter immobilis, that may contribute to the characteristics of cheese produced through traditional methods.

  7. xGDBvm: A Web GUI-Driven Workflow for Annotating Eukaryotic Genomes in the Cloud[OPEN

    Science.gov (United States)

    Merchant, Nirav

    2016-01-01

    Genome-wide annotation of gene structure requires the integration of numerous computational steps. Currently, annotation is arguably best accomplished through collaboration of bioinformatics and domain experts, with broad community involvement. However, such a collaborative approach is not scalable at today’s pace of sequence generation. To address this problem, we developed the xGDBvm software, which uses an intuitive graphical user interface to access a number of common genome analysis and gene structure tools, preconfigured in a self-contained virtual machine image. Once their virtual machine instance is deployed through iPlant’s Atmosphere cloud services, users access the xGDBvm workflow via a unified Web interface to manage inputs, set program parameters, configure links to high-performance computing (HPC) resources, view and manage output, apply analysis and editing tools, or access contextual help. The xGDBvm workflow will mask the genome, compute spliced alignments from transcript and/or protein inputs (locally or on a remote HPC cluster), predict gene structures and gene structure quality, and display output in a public or private genome browser complete with accessory tools. Problematic gene predictions are flagged and can be reannotated using the integrated yrGATE annotation tool. xGDBvm can also be configured to append or replace existing data or load precomputed data. Multiple genomes can be annotated and displayed, and outputs can be archived for sharing or backup. xGDBvm can be adapted to a variety of use cases including de novo genome annotation, reannotation, comparison of different annotations, and training or teaching. PMID:27020957

  8. Lab Attendance and Academic Performance

    OpenAIRE

    Adair, Kirk; Swinton, Omari H.

    2012-01-01

    The benefits from attendance of lectures have been established in the literature. This paper focuses on attendance not of the lecture, but of smaller labs. These labs are 50 minutes one-day-a-week sessions to emphasis material covered during lecture. Using a 200-student Principles of Economics class that covers microeconomics with six different labs, we investigate the effect of lab attendance on exam performance by taking into account individual characteristics. We find that lab attendance b...

  9. The chloroplast genome hidden in plain sight, open access publishing and anti-fragile distributed data sources.

    Science.gov (United States)

    McKernan, Kevin Judd

    2016-11-01

    We sequenced several cannabis genomes in 2011 of June and the first and the longest contigs to emerge were the chloroplast and mitochondrial genomes. Having been a contributor to the Human Genome Project and an eye-witness to the real benefits of immediate data release, I have first hand experience with the potential mal-investment of millions of dollars of tax payer money narrowly averted due to the adopted global rapid data release policy. The policy was vital in reducing duplication of effort and economic waste. As a result, we felt obligated to publish the Cannabis genome data in a similar spirit and placed them immediately on a cloud based Amazon server in August of 2011. While these rapid data release practices were heralded by many in the media, we still find some authors fail to find or reference said work and hope to compel the readership that this omission has more pervasive repercussions than bruised egos and is a regression for our community.

  10. The NOAO Data Lab

    Science.gov (United States)

    Fitzpatrick, M.; Olsen, K.; Stobie, E. B.; Mighell, K. J.; Norris, P.

    2015-09-01

    We describe the NOAO Data Lab to help community users take advantage of current large surveys and prepare them even larger surveys in the era of LSST. The Data Lab will allow users to efficiently utilize catalogs of billions of objects, combine traditional telescope image and spectral data with external archives, share custom results with collaborators, publish data products to other users, and experiment with analysis toolkits. Specific science cases will be used to develop a prototype framework and tools, allowing us to work directly with scientists from survey teams to ensure development remains focused on scientifically productive tasks.

  11. CDC Lab Values

    Centers for Disease Control (CDC) Podcasts

    2015-02-02

    More than fifteen hundred scientists fill the lab benches at CDC, logging more than four million hours each year. CDC’s laboratories play a critical role in the agency’s ability to find, stop, and prevent disease outbreaks. This podcast provides a brief overview of what goes on inside CDC’s labs, and why this work makes a difference in American’s health.  Created: 2/2/2015 by Office of the Associate Director for Communication (OADC).   Date Released: 2/2/2015.

  12. {OpenLabNotes} -- An Electronic Laboratory Notebook Extension for {OpenLabFramework}

    OpenAIRE

    List, M.; Franz, M.; Tan, O.; Mollenhauer, J.; Baumbach, J.

    2015-01-01

    Electronic laboratory notebooks (ELNs) are more accessible and reliable than their paper based alternatives and thus find widespread adoption. While a large number of Commercial products is available, small- to mid-sized laboratories can often not afford the costs or are concerned about the longevity of the providers. Turning towards free alternatives, however, raises questions about data protection, which are not sufficiently addressed by available solutions.To serve as legal documents, ELNs...

  13. Whole-Genome DNA Methylation Status Associated with Clinical PTSD Measures of OIF/OEF Veterans (Open Access)

    Science.gov (United States)

    2017-07-11

    OIF) veterans with PTSD and 51 age/ethnicity/ gender -matched combat-exposed PTSD-negative controls. Agilent whole-genome array detected ~ 5600...exclusion criteria were used19,20 to identify a training set comprising 48 male veterans with PTSD (PTSD+) and 51 age-/ethnicity-/ gender -matched controls...568 Doughten Drive, Fort Detrick, Frederick, MD 21702-5010, USA. E-mail: Rasha.Hammamieh1.civ@mail.mil 11These authors contributed equally to this

  14. The Crime Lab Project.

    Science.gov (United States)

    Hein, Annamae J.

    2003-01-01

    Describes the Crime Lab Project, which takes an economical, hands-on, interdisciplinary approach to studying the career of forensics in the middle or high school classroom. Includes step-by-step student requirements for the investigative procedure, a sample evidence request form, and an assessment rubric. (KHR)

  15. Physics lab in spin

    CERN Multimedia

    Hawkes, N

    1999-01-01

    RAL is fostering commerical exploitation of its research and facilities in two main ways : spin-out companies exploit work done at the lab, spin-in companies work on site taking advantage of the facilities and the expertise available (1/2 page).

  16. A Big Bang Lab

    Science.gov (United States)

    Scheider, Walter

    2005-01-01

    The February 2005 issue of The Science Teacher (TST) reminded everyone that by learning how scientists study stars, students gain an understanding of how science measures things that can not be set up in lab, either because they are too big, too far away, or happened in a very distant past. The authors of "How Far are the Stars?" show how the…

  17. Lab on paper

    NARCIS (Netherlands)

    Zhao, Weian; van den Berg, Albert

    2008-01-01

    Lab-on-a-chip (LOC) devices, which are suited to portable point-of-care (POC) diagnostics and on-site detection, hold great promise for improving global health, and other applications.1–8 While their importance and utility are widely acknowledged and extensive research has been conducted in the

  18. LAB bacteriocin applications in the last decade

    OpenAIRE

    Ma. del Rocío López-Cuellar; Adriana-Inés Rodríguez-Hernández; Norberto Chavarría-Hernández

    2016-01-01

    In the early 2000s, the expectations about bacteriocins produced by lactic acid bacteria (LABs) were aimed at food applications. However, the effectiveness of bacteriocins against undesirable micro-organisms opened endless possibilities for innovative research. In the present review, we collected a database including 429 published papers and 245 granted patents (from 2004 to 2015). Based on bibliometric analysis, the progress of bacteriocin research in the last 11 years was discussed in detai...

  19. CBS: an open platform that integrates predictive methods and epigenetics information to characterize conserved regulatory features in multiple Drosophila genomes

    Directory of Open Access Journals (Sweden)

    Blanco Enrique

    2012-12-01

    Full Text Available Abstract Background Information about the composition of regulatory regions is of great value for designing experiments to functionally characterize gene expression. The multiplicity of available applications to predict transcription factor binding sites in a particular locus contrasts with the substantial computational expertise that is demanded to manipulate them, which may constitute a potential barrier for the experimental community. Results CBS (Conserved regulatory Binding Sites, http://compfly.bio.ub.es/CBS is a public platform of evolutionarily conserved binding sites and enhancers predicted in multiple Drosophila genomes that is furnished with published chromatin signatures associated to transcriptionally active regions and other experimental sources of information. The rapid access to this novel body of knowledge through a user-friendly web interface enables non-expert users to identify the binding sequences available for any particular gene, transcription factor, or genome region. Conclusions The CBS platform is a powerful resource that provides tools for data mining individual sequences and groups of co-expressed genes with epigenomics information to conduct regulatory screenings in Drosophila.

  20. Digital Social Science Lab

    DEFF Research Database (Denmark)

    Svendsen, Michael; Lauersen, Christian Ulrich

    2015-01-01

    at the Faculty of Social Sciences. DSSL will host and facilitate an 80 m2 large mobile and intelligent study- and learning environment with a focus on academic events, teaching and collaboration. Besides the physical settings DSSL has two primary functions: 1. To implement relevant social scientific software......At the Faculty Library of Social Sciences (part of Copenhagen University Library) we are currently working intensely towards the establishment of a Digital Social Science Lab (DSSL). The purpose of the lab is to connect research, education and learning processes with the use of digital tools...... and hardware at the disposal for students and staff at The Faculty of Social Sciences along with instruction and teaching in the different types of software, e.g. Stata, Nvivo, Atlas.ti, R Studio, Zotero and GIS-software. 2. To facilitate academic events focusing on use of digital tools and analytic software...

  1. Nordic Study Labs

    DEFF Research Database (Denmark)

    Jørnø, Rasmus Leth Vergmann; Hestbech, Astrid Margrethe; Gynther, Karsten

    2016-01-01

    Denne rapport dokumenterer projektet Nordplus projektet The Nordic Study Lab. Projektet har haft til formål at udveksle eksisterende viden blandt projektdeltagerne om etablering og drift af distribueret uddannelse med særlig fokus på læringscentre. I løbet af en serie af studiebesøg har partnere...... med at skabe kvalificeret uddannelse på distancen. Nordic Study Labs projektet har afsløret et rigt reservoir af eksisterende erfaringer, med et stort transferpotentiale og både unikke og eksemplariske løsninger på uddannelses­ problematikker. Mange af de nordiske lande har mange års succesrige...

  2. GeneLab Phase 2: Integrated Search Data Federation of Space Biology Experimental Data

    Science.gov (United States)

    Tran, P. B.; Berrios, D. C.; Gurram, M. M.; Hashim, J. C. M.; Raghunandan, S.; Lin, S. Y.; Le, T. Q.; Heher, D. M.; Thai, H. T.; Welch, J. D.; hide

    2016-01-01

    The GeneLab project is a science initiative to maximize the scientific return of omics data collected from spaceflight and from ground simulations of microgravity and radiation experiments, supported by a data system for a public bioinformatics repository and collaborative analysis tools for these data. The mission of GeneLab is to maximize the utilization of the valuable biological research resources aboard the ISS by collecting genomic, transcriptomic, proteomic and metabolomic (so-called omics) data to enable the exploration of the molecular network responses of terrestrial biology to space environments using a systems biology approach. All GeneLab data are made available to a worldwide network of researchers through its open-access data system. GeneLab is currently being developed by NASA to support Open Science biomedical research in order to enable the human exploration of space and improve life on earth. Open access to Phase 1 of the GeneLab Data Systems (GLDS) was implemented in April 2015. Download volumes have grown steadily, mirroring the growth in curated space biology research data sets (61 as of June 2016), now exceeding 10 TB/month, with over 10,000 file downloads since the start of Phase 1. For the period April 2015 to May 2016, most frequently downloaded were data from studies of Mus musculus (39) followed closely by Arabidopsis thaliana (30), with the remaining downloads roughly equally split across 12 other organisms (each 10 of total downloads). GLDS Phase 2 is focusing on interoperability, supporting data federation, including integrated search capabilities, of GLDS-housed data sets with external data sources, such as gene expression data from NIHNCBIs Gene Expression Omnibus (GEO), proteomic data from EBIs PRIDE system, and metagenomic data from Argonne National Laboratory's MG-RAST. GEO and MG-RAST employ specifications for investigation metadata that are different from those used by the GLDS and PRIDE (e.g., ISA-Tab). The GLDS Phase 2 system

  3. Differential regulation of hepatitis B virus core protein expression and genome replication by a small upstream open reading frame and naturally occurring mutations in the precore region.

    Science.gov (United States)

    Zong, Li; Qin, Yanli; Jia, Haodi; Ye, Lei; Wang, Yongxiang; Zhang, Jiming; Wands, Jack R; Tong, Shuping; Li, Jisu

    2017-05-01

    Hepatitis B virus (HBV) transcribes two subsets of 3.5-kb RNAs: precore RNA for hepatitis B e antigen (HBeAg) expression, and pregenomic RNA for core and P protein translation as well as genome replication. HBeAg expression could be prevented by mutations in the precore region, while an upstream open reading frame (uORF) has been proposed as a negative regulator of core protein translation. We employed replication competent HBV DNA constructs and transient transfection experiments in Huh7 cells to verify the uORF effect and to explore the alternative function of precore RNA. Optimized Kozak sequence for the uORF or extra ATG codons as present in some HBV genotypes reduced core protein expression. G1896A nonsense mutation promoted more efficient core protein expression than mutated precore ATG, while a +1 frameshift mutation was ineffective. In conclusion, various HBeAg-negative precore mutations and mutations affecting uORF differentially regulate core protein expression and genome replication. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism.

    Directory of Open Access Journals (Sweden)

    Ahmad A Mannan

    Full Text Available An understanding of the dynamics of the metabolic profile of a bacterial cell is sought from a dynamical systems analysis of kinetic models. This modelling formalism relies on a deterministic mathematical description of enzyme kinetics and their metabolite regulation. However, it is severely impeded by the lack of available kinetic information, limiting the size of the system that can be modelled. Furthermore, the subsystem of the metabolic network whose dynamics can be modelled is faced with three problems: how to parameterize the model with mostly incomplete steady state data, how to close what is now an inherently open system, and how to account for the impact on growth. In this study we address these challenges of kinetic modelling by capitalizing on multi-'omics' steady state data and a genome-scale metabolic network model. We use these to generate parameters that integrate knowledge embedded in the genome-scale metabolic network model, into the most comprehensive kinetic model of the central carbon metabolism of E. coli realized to date. As an application, we performed a dynamical systems analysis of the resulting enriched model. This revealed bistability of the central carbon metabolism and thus its potential to express two distinct metabolic states. Furthermore, since our model-informing technique ensures both stable states are constrained by the same thermodynamically feasible steady state growth rate, the ensuing bistability represents a temporal coexistence of the two states, and by extension, reveals the emergence of a phenotypically heterogeneous population.

  5. Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism

    Science.gov (United States)

    Mannan, Ahmad A.; Toya, Yoshihiro; Shimizu, Kazuyuki; McFadden, Johnjoe; Kierzek, Andrzej M.; Rocco, Andrea

    2015-01-01

    An understanding of the dynamics of the metabolic profile of a bacterial cell is sought from a dynamical systems analysis of kinetic models. This modelling formalism relies on a deterministic mathematical description of enzyme kinetics and their metabolite regulation. However, it is severely impeded by the lack of available kinetic information, limiting the size of the system that can be modelled. Furthermore, the subsystem of the metabolic network whose dynamics can be modelled is faced with three problems: how to parameterize the model with mostly incomplete steady state data, how to close what is now an inherently open system, and how to account for the impact on growth. In this study we address these challenges of kinetic modelling by capitalizing on multi-‘omics’ steady state data and a genome-scale metabolic network model. We use these to generate parameters that integrate knowledge embedded in the genome-scale metabolic network model, into the most comprehensive kinetic model of the central carbon metabolism of E. coli realized to date. As an application, we performed a dynamical systems analysis of the resulting enriched model. This revealed bistability of the central carbon metabolism and thus its potential to express two distinct metabolic states. Furthermore, since our model-informing technique ensures both stable states are constrained by the same thermodynamically feasible steady state growth rate, the ensuing bistability represents a temporal coexistence of the two states, and by extension, reveals the emergence of a phenotypically heterogeneous population. PMID:26469081

  6. Applying a Living Lab methodology to support innovation in education at a university in South Africa

    Directory of Open Access Journals (Sweden)

    Ronel Callaghan

    2015-07-01

    Full Text Available The Living Lab paradigm creates open and inter-disciplinary environments where participants can interrogate challenges and co-create solutions. A successful Living Lab context incorporates a clear focus/vision, strong leadership, self-sustainability, a strong sense of community-owned challenges and the potential for sustainable community development. This paper discusses and outlines the elements of Living Labs, and how these have played a role in the establishment of a new Education Living Lab at a University in South Africa. Core values, stakeholders and key success factors of Living Labs are discussed. This is followed by the description of a case study of the establishment process of a Living Lab. The newly established Living Lab already shows success with collaborations and innovation between communities, industry, academia, learners and schools. This is illustrated in an application of the discussions on the Mobile Learning focus area - the first active sub-focus area within the Education Living Lab.

  7. An open source infrastructure for managing knowledge and finding potential collaborators in a domain-specific subset of PubMed, with an example from human genome epidemiology.

    Science.gov (United States)

    Yu, Wei; Yesupriya, Ajay; Wulf, Anja; Qu, Junfeng; Khoury, Muin J; Gwinn, Marta

    2007-11-09

    Identifying relevant research in an ever-growing body of published literature is becoming increasingly difficult. Establishing domain-specific knowledge bases may be a more effective and efficient way to manage and query information within specific biomedical fields. Adopting controlled vocabulary is a critical step toward data integration and interoperability in any information system. We present an open source infrastructure that provides a powerful capacity for managing and mining data within a domain-specific knowledge base. As a practical application of our infrastructure, we presented two applications - Literature Finder and Investigator Browser - as well as a tool set for automating the data curating process for the human genome published literature database. The design of this infrastructure makes the system potentially extensible to other data sources. Information retrieval and usability tests demonstrated that the system had high rates of recall and precision, 90% and 93% respectively. The system was easy to learn, easy to use, reasonably speedy and effective. The open source system infrastructure presented in this paper provides a novel approach to managing and querying information and knowledge from domain-specific PubMed data. Using the controlled vocabulary UMLS enhanced data integration and interoperability and the extensibility of the system. In addition, by using MVC-based design and Java as a platform-independent programming language, this system provides a potential infrastructure for any domain-specific knowledge base in the biomedical field.

  8. An open source infrastructure for managing knowledge and finding potential collaborators in a domain-specific subset of PubMed, with an example from human genome epidemiology

    Directory of Open Access Journals (Sweden)

    Khoury Muin J

    2007-11-01

    Full Text Available Abstract Background Identifying relevant research in an ever-growing body of published literature is becoming increasingly difficult. Establishing domain-specific knowledge bases may be a more effective and efficient way to manage and query information within specific biomedical fields. Adopting controlled vocabulary is a critical step toward data integration and interoperability in any information system. We present an open source infrastructure that provides a powerful capacity for managing and mining data within a domain-specific knowledge base. As a practical application of our infrastructure, we presented two applications – Literature Finder and Investigator Browser – as well as a tool set for automating the data curating process for the human genome published literature database. The design of this infrastructure makes the system potentially extensible to other data sources. Results Information retrieval and usability tests demonstrated that the system had high rates of recall and precision, 90% and 93% respectively. The system was easy to learn, easy to use, reasonably speedy and effective. Conclusion The open source system infrastructure presented in this paper provides a novel approach to managing and querying information and knowledge from domain-specific PubMed data. Using the controlled vocabulary UMLS enhanced data integration and interoperability and the extensibility of the system. In addition, by using MVC-based design and Java as a platform-independent programming language, this system provides a potential infrastructure for any domain-specific knowledge base in the biomedical field.

  9. Archimedes Remote Lab for Secondary Schools

    NARCIS (Netherlands)

    Garcia Zubia, J.; Angulo Martinez, I.; Martinez Pieper, G.; Lopez de Ipina Gonzalez de Artaza, D.; Hernandez Jayo, U.; Orduna Fernandez, P.; Dziabenko, O.; Rodriguez Gil, L.; van Riesen, Siswa; Anjewierden, Anjo Allert; Kamp, Ellen; de Jong, Anthonius J.M.

    2015-01-01

    This paper presents a remote lab designed for teaching the Archimedes’ principle to secondary school students, as well as an online virtual lab on the general domain of buoyancy. The Archimedes remote lab is integrated into WebLab-Deusto. Both labs are promoted for usage in frame of the Go-Lab

  10. DESY NanoLab

    Directory of Open Access Journals (Sweden)

    Andreas Stierle

    2016-06-01

    Full Text Available The DESY NanoLab is a facility providing access to nano-characterization, nano-structuring and nano-synthesis techniques which are complementary to the advanced X-ray techniques available at DESY’s light sources. It comprises state-of-the art scanning probe microscopy and focused ion beam manufacturing, as well as surface sensitive spectroscopy techniques for chemical analysis. Specialized laboratory x-ray diffraction setups are available for a successful sample pre-characterization before the precious synchrotron beamtimes. Future upgrades will include as well characterization of magnetic properties.

  11. e-Learning - Physics Labs

    Science.gov (United States)

    Mohottala, Hashini

    2014-03-01

    The general student population enrolled in any college level class is highly diverse. An increasing number of ``nontraditional'' students return to college and most of these students follow distance learning degree programs while engaging in their other commitments, work and family. However, those students tend to avoid taking science courses with labs, mostly because of the incapability of remotely completing the lab components in such courses. In order to address this issue, we have come across a method where introductory level physics labs can be taught remotely. In this process a lab kit with the critical lab components that can be easily accessible are conveniently packed into a box and distributed among students at the beginning of the semester. Once the students are given the apparatus they perform the experiments at home and gather data All communications with reference to the lab was done through an interactive user-friendly webpage - Wikispaces (WikiS). Students who create pages on WikiS can submit their lab write-ups, embed videos of the experiments they perform, post pictures and direct questions to the lab instructor. The students who are enrolled in the same lab can interact with each other through WikiS to discuss labs and even get assistance.

  12. Urban Living Labs: A living lab way of working

    OpenAIRE

    van Bueren, E.M.

    2017-01-01

    Urban living labs have become a popular phenomenon in today’s cities. The Living Lab approach would provide real life research with its multiple stakeholders in a co-innovating inclusive setting, crucial in creating metropolitan solutions with impact, that will be adopted smoothly and swiftly by all involved, and thus help achieve prosperous living environments that are more liveable, sustainable, resilient and just. With these ambitions, urban living labs are important links in the achieveme...

  13. 5 Pre-Lab and Lab Activities for Newtonian Mechanics

    Science.gov (United States)

    Mangold, James

    2010-03-01

    Key to success of a lab activity is the student's prerequisite skills. This workshop focuses on 5 pre-lab white board activities with the corresponding lab activities in Newtonian mechanics utilizing the GMLAD. The activities will cover projectile motion; kinematics, Newton's 2nd Law, Determination of Friction and its Coefficient, Conservation of Energy, Determination of the Spring Constant, and Conservation of Momentum in 2 Dimensions. Limited to 24 participants - 2 hours - Cost 5.00

  14. Tritium at Jefferson Lab

    Science.gov (United States)

    Bane, Jason; Jefferson Lab Hall A Collaboration Collaboration

    2017-09-01

    Jefferson Lab's recently upgraded accelerator will provide the perfect opportunity to increase the quality and quantity of the electron scattering world data on tritium. Tritium, the radioactive isotope of hydrogen with a half-life of 12 years, was last used in a large scale electron scattering experiment a few decades ago. This Fall Jefferson Lab will play host to a set of very exciting electron scattering experiments involving tritium. A 25 cm aluminum cell will be filled with 1 kCi of tritium with an internal pressure of approximately 200 psi at 295 kelvin. The tritium target will first see a 10.6 GeV beam to probe the deep inelastic scattering region to study the down to up quark ratio and the EMC effect. Then the beam will be set to 4.3 GeV to investigate SRCs and momentum distributions in the quasi-elastic scattering regime. If time permits, elastic scattering will be used to extract the ratio of the charge radius of tritium and helium3.

  15. Web GIS in practice IV: publishing your health maps and connecting to remote WMS sources using the Open Source UMN MapServer and DM Solutions MapLab.

    Science.gov (United States)

    Boulos, Maged N Kamel; Honda, Kiyoshi

    2006-01-18

    Open Source Web GIS software systems have reached a stage of maturity, sophistication, robustness and stability, and usability and user friendliness rivalling that of commercial, proprietary GIS and Web GIS server products. The Open Source Web GIS community is also actively embracing OGC (Open Geospatial Consortium) standards, including WMS (Web Map Service). WMS enables the creation of Web maps that have layers coming from multiple different remote servers/sources. In this article we present one easy to implement Web GIS server solution that is based on the Open Source University of Minnesota (UMN) MapServer. By following the accompanying step-by-step tutorial instructions, interested readers running mainstream Microsoft(R) Windows machines and with no prior technical experience in Web GIS or Internet map servers will be able to publish their own health maps on the Web and add to those maps additional layers retrieved from remote WMS servers. The 'digital Asia' and 2004 Indian Ocean tsunami experiences in using free Open Source Web GIS software are also briefly described.

  16. Web GIS in practice IV: publishing your health maps and connecting to remote WMS sources using the Open Source UMN MapServer and DM Solutions MapLab

    Directory of Open Access Journals (Sweden)

    Honda Kiyoshi

    2006-01-01

    Full Text Available Abstract Open Source Web GIS software systems have reached a stage of maturity, sophistication, robustness and stability, and usability and user friendliness rivalling that of commercial, proprietary GIS and Web GIS server products. The Open Source Web GIS community is also actively embracing OGC (Open Geospatial Consortium standards, including WMS (Web Map Service. WMS enables the creation of Web maps that have layers coming from multiple different remote servers/sources. In this article we present one easy to implement Web GIS server solution that is based on the Open Source University of Minnesota (UMN MapServer. By following the accompanying step-by-step tutorial instructions, interested readers running mainstream Microsoft® Windows machines and with no prior technical experience in Web GIS or Internet map servers will be able to publish their own health maps on the Web and add to those maps additional layers retrieved from remote WMS servers. The 'digital Asia' and 2004 Indian Ocean tsunami experiences in using free Open Source Web GIS software are also briefly described.

  17. How to re-establish Openness as default? Towards a global joint initiative

    NARCIS (Netherlands)

    Stracke, Christian M.

    2017-01-01

    Stracke, C. M. (2016, 14 April). How to re-establish Openness as default? Towards a global joint initiative. Results from the Action Lab at the Open Education Global Conference 2016, Krakow, Poland. More about the Action Lab:

  18. Urban Living Labs : A living lab way of working

    NARCIS (Netherlands)

    van Bueren, E.M.

    2017-01-01

    Urban living labs have become a popular phenomenon in today’s cities. The Living Lab approach would provide real life research with its multiple stakeholders in a co-innovating inclusive setting, crucial in creating metropolitan solutions with impact, that will be adopted smoothly and swiftly by all

  19. The Jefferson Lab Program

    International Nuclear Information System (INIS)

    The kW-class infrared (IR) free electron laser (FEL) at the Thomas Jefferson National Accelerator Facility (Jefferson Lab) had the capability of producing intra-cavity Thomson scattering of the IR off the electron beam thus producing high average flux, sub-picosecond x-rays. We have measured these x-rays and demonstrated the energy tunability range from 3.5 keV to 18 keV. The corresponding flux and brightness have been estimated and will be discussed. In 2002, the FEL was disassembled and has been reconfigured to produce 10 kW average power IR. We present the estimated x-ray capabilities for the new FEL and discuss potential applications

  20. The lab of fame

    CERN Multimedia

    Antonella Del Rosso

    2014-01-01

    For a third time, CERN is organising the Swiss heat of Famelab, the world’s leading science communication competition that has already gathered over 5,000 young and talented scientists and engineers from all across the planet.   Besides their degrees, the scientists who participate in Famelab have another thing in common: their passion for communicating science. Coming from a variety of scientific fields, from medicine to particle physics and microbiology, the contestants have three minutes to present a science, technology, mathematics or engineering-based talk using only the props he or she can carry onto the stage; PowerPoint presentations are not permitted. The contestants are then judged by a panel of three judges who evaluate the content, clarity and charisma of their talks. What's unique about FameLab is the fact that content is an important aspect of the performance. At the end of their presentation, contestants are often questioned about the scientific relevance of...

  1. GitLab repository management

    CERN Document Server

    Hethey, Jonathan

    2013-01-01

    A simple, easy to understand tutorial guide on how to build teams and efficiently use version control, using GitLab.If you are a system administrator in a company that writes software or are in charge of an infrastructure, this book will show you the most important features of GitLab, including how to speed up the overall process

  2. EPIC-CoGe: Managing and Analyzing Genomic Data.

    Science.gov (United States)

    Nelson, Andrew D L; Haug-Baltzell, Asher K; Davey, Sean; Gregory, Brian D; Lyons, Eric

    2018-02-20

    The EPIC-CoGe browser is a web-based genome visualization utility that integrates the GMOD JBrowse genome browser with the extensive CoGe genome database (currently containing over 30,000 genomes). In addition, the EPIC-CoGe browser boasts many additional features over basic JBrowse, including enhanced search capability and on-the-fly analyses for comparisons and analyses between all types of functional and diversity genomics data. There is no installation required and data (genome, annotation, functional genomic, and diversity data) can be loaded by following a simple point and click wizard, or using a REST API, making the browser widely accessible and easy to use by researchers of all computational skill levels. In addition, EPIC-CoGe and data tracks are easily embedded in other websites and JBrowse instances. EPIC-CoGe Browser is freely available for use online through CoGe (https://genomevolution.org). Source code (MIT open source) is available: https://github.com/LyonsLab/coge. ericlyons@email.arizona.edu. Supplementary data are available at Bioinformatics online.

  3. Thinking Outside the Lab

    Science.gov (United States)

    Colter, Tabitha

    2017-01-01

    As an undergraduate physics major who spent 2015 deep in a quantum optics lab at Oak Ridge National Laboratory, I knew my 2016 experience with the House of Representatives Energy and Commerce Committee would be a completely new challenge. I have long had a passion for the bridge of communication between the technical and non-technical worlds but it was only through my AIP Mather internship this summer that I was able to see that passion come to life in the realm of science policy. Suddenly, I went from squeezing political philosophy classes into my packed schedule to witnessing the political process first-hand. I was thrilled to find that the skills of critical thinking and communicating complex issues I have developed throughout my training as a physicist were directly applicable to my work in Congress. Overall, my experience this summer has given me insight into the inner workings of the federal policy process, deepened my appreciation for the work of government employees to keep Congressional members informed on the pressing current issues, and exposed me to a whole range of alternative careers within science. AIP and SPS

  4. Fermentation art and science at the Nordic Food Lab

    DEFF Research Database (Denmark)

    Reade, Benedict; de Valicourt, Justine; Evans, Joshua David

    2015-01-01

    The Nordic Food Lab (NFL) is a self-governed foundation based in Copenhagen, Denmark. The aim of NFL is to investigate food diversity and deliciousness and to share the results in an open-source format. We combine scientific and cultural approaches with culinary techniques from around the world...

  5. Overview of the Fire Lab at Missoula Experiments (FLAME)

    Science.gov (United States)

    S. M. Kreidenweis; J. L. Collett; H. Moosmuller; W. P. Arnott; WeiMin Hao; W. C. Malm

    2010-01-01

    The Fire Lab at Missoula Experiments (FLAME) used a series of open biomass burns, conducted in 2006 and 2007 at the Forest Service Fire Science Laboratory in Missoula, MT, to characterize the physical, chemical and optical properties of biomass combustion emissions. Fuels were selected primarily based on their projected importance for emissions from prescribed and wild...

  6. Skills Labs - High quality e-practicals Water Management with EMERGO

    NARCIS (Netherlands)

    Nadolski, Rob; Kurvers, Hub

    2009-01-01

    Nadolski, R. J., & Kurvers, H. (2009). Skills Labs - High quality e-practicals Water Management with EMERGO. Presentation of the project Skills Labs for members of the Learning Media Programme. May, 28, 2009, Heerlen, The Netherlands: Open University of the Netherlands.

  7. Installation and use of LabKey Server for proteomics.

    Science.gov (United States)

    Eckels, Joshua; Hussey, Peter; Nelson, Elizabeth K; Myers, Tamra; Rauch, Adam; Bellew, Matthew; Connolly, Brian; Law, Wendy; Eng, Jimmy K; Katz, Jonathan; McIntosh, Martin; Mallick, Parag; Igra, Mark

    2011-12-01

    LabKey Server (formerly CPAS, the Computational Proteomics Analysis System) provides a Web-based platform for mining data from liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomic experiments. This open source platform supports systematic proteomic analyses and secure data management, integration, and sharing. LabKey Server incorporates several tools currently used in proteomic analysis, including the X! Tandem search engine, the ProteoWizard toolkit, and the PeptideProphet and ProteinProphet data mining tools. These tools and others are integrated into LabKey Server, which provides an extensible architecture for developing high-throughput biological applications. The LabKey Server analysis pipeline acts on data in standardized file formats, so that researchers may use LabKey Server with other search engines, including Mascot or SEQUEST, that follow a standardized format for reporting search engine results. Supported builds of LabKey Server are freely available at http://www.labkey.com/. Documentation and source code are available under the Apache License 2.0 at http://www.labkey.org. © 2011 by John Wiley & Sons, Inc.

  8. Advanced Active Acoustics Lab (AAAL)

    Data.gov (United States)

    Federal Laboratory Consortium — The Advanced Active Acoustics Lab (AAAL) is a state-of-the-art Undersea Warfare (USW) acoustic data analysis facility capable of both active and passive underwater...

  9. An Annotated Math Lab Inventory.

    Science.gov (United States)

    Schussheim, Joan Yares

    1980-01-01

    A listing of mathematics laboratory material is organized as follows: learning kits, tape programs, manipulative learning materials, publications, math games, math lab library, and an alphabetized listing of publishers and/or companies offering materials. (MP)

  10. Pollution hazard closes neutrino lab

    CERN Multimedia

    Jones, Nicola

    2003-01-01

    "A leading astrophysics laboratory in Italy has closed down all but one of its experiments over concerns that toxic polluants could leak form the underground lab into the local water supply" (0.5 page)

  11. Common Systems Integration Lab (CSIL)

    Data.gov (United States)

    Federal Laboratory Consortium — The Common Systems Integration Lab (CSIL)supports the PMA-209 Air Combat Electronics Program Office. CSIL also supports development, test, integration and life cycle...

  12. Virtual Labs and Virtual Worlds

    Science.gov (United States)

    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

  13. El crecimiento de los open sources de fabricación digital y su implementación en el media lab. De la high-tech al do it yourself

    Directory of Open Access Journals (Sweden)

    José Manuel Ruiz Martín

    2015-12-01

    Full Text Available La aparición y el auge del movimiento maker y de los recursos abiertos u open sources, sobre todo los ligados a la fabricación digital, desde principios de siglo XXI, parece confirmar una tendencia transformadora generacional de gran relevancia en los medios y procesos creativos, hecho que se une al notable crecimiento de laboratorios donde estos perfiles desarrollan su labor. Pero ¿existe un cambio de paradigma en el uso de nuevos medios? ¿Qué características poseen? ¿Resulta este hecho sintomático de una transformación cultural relevante? ¿De qué forma se interrelacionan y retroalimentan dichos procesos con la cultura digital actual? La respuesta a estas cuestiones, tan candentes en la actualidad, nos ayudará a valorar el nivel de impacto de este movimiento en los procesos creativos y culturales actuales y la transformación sufrida por la tecnología implementada en dichos centros desde la segunda mitad del siglo pasado.

  14. Examination of mobile phones in a university forensic lab environment

    Science.gov (United States)

    Luttenberger, Silas; Kröger, Knut; Creutzburg, Reiner

    2011-06-01

    The aim of this article is to show forensic investigation methods for mobile phones to students in a university forensic lab environment. Students have to learn the usefulness of forensic procedures to ensure evidence collection, evidence preservation, forensic analysis, and reporting. Open source tools as well as commercial forensic tools for forensic investigation of modern mobile (smart) phones are used. It is demonstrated how important data stored in the mobile device are investigated. Different scenarios of investigations are presented that are well-suited for forensics lab work in university.

  15. The fishes of Genome 10K

    KAUST Repository

    Bernardi, Giacomo

    2012-09-01

    The Genome 10K project aims to sequence the genomes of 10,000 vertebrates, representing approximately one genome for each vertebrate genus. Since fishes (cartilaginous fishes, ray-finned fishes and lobe-finned fishes) represent more than 50% of extant vertebrates, it is planned to target 4,000 fish genomes. At present, nearly 60 fish genomes are being sequenced at various public funded labs, and under a Genome 10K and BGI pilot project. An additional 100 fishes have been identified for sequencing in the next phase of Genome 10K project. © 2012 Elsevier B.V.

  16. The Telecom Lab is moving to the Building 2, in front of the Main Building

    CERN Multimedia

    IT Department

    2011-01-01

      As of 28 September 2011, the Telecom Lab will move to the Building 2/1-046. Please note that the Telecom Lab desk will be closed on 28 of September due to the move. However, for all urgent matters, please contact the Telecom Lab by mail or by phone. The Telecom Lab is the central point for all support questions regarding CERN mobile phone services (provision of SIM cards, requests for modifications of subscriptions, diagnostics for mobile phone problems, etc.). The opening hours as well as the contact details for the Telecom Lab remain unchanged. New location:                Building 2/1-046 Opening hours:              From Monday to Friday, from 8 a.m. to 6 p.m. Phone number:      ...

  17. Status of chemistry lab safety in Nepal

    Science.gov (United States)

    Kandel, Krishna Prasad; Neupane, Bhanu Bhakta

    2017-01-01

    Chemistry labs can become a dangerous environment for students as the lab exercises involve hazardous chemicals, glassware, and equipment. Approximately one hundred thousand students take chemistry laboratory classes annually in Nepal. We conducted a survey on chemical lab safety issues across Nepal. In this paper, we assess the safety policy and equipment, protocols and procedures followed, and waste disposal in chemistry teaching labs. Significant population of the respondents believed that there is no monitoring of the lab safety in their lab (p<0.001). Even though many labs do not allow food and beverages inside lab and have first aid kits, they lack some basic safety equipment. There is no institutional mechanism to dispose lab waste and chemical waste is disposed haphazardly. Majority of the respondents believed that the safety training should be a part of educational training (p = 0.001) and they would benefit from short course and/or workshop on lab safety (p<0.001). PMID:28644869

  18. Beyond Classroom, Lab, Studio and Field

    Science.gov (United States)

    Waller, J. L.; Brey, J. A.; DeMuynck, E.; Weglarz, T. C.

    2017-12-01

    When the arts work in tandem with the sciences, the insights of these disciplines can be easily shared and teaching and learning are enriched. Our shared experiences in classroom/lab/studio instruction and in art and science based exhibitions reward all involved. Our individual disciplines cover a wide range of content- Art, Biology, Geography, Geology- yet we connect on aspects that link to the others'. We easily move from lab to studio and back again as we teach—as do our students as they learn! Art and science education can take place outside labs and studios through study abroad, international workshops, museum or gallery spaces, and in forums like the National Academies' programs. We can reach our neighbors at local public gatherings, nature centers and libraries. Our reach is extended in printed publications and in conferences. We will describe some of our activities listed above, with special focus on exhibitions: "Layers: Places in Peril"; "small problems, BIG TROUBLE" and the in-progress "River Bookends: Headwaters, Delta and the Volume of Stories In Between". Through these, learning and edification take place between the show and gallery visitors and is extended via class visits and related assignments, field trips for child and adult learners, interviews, films and panel presentations. These exhibitions offer the important opportunities for exhibit- participating scientists to find common ground with each other about their varied work. We will highlight a recent collaborative show opening a new university-based environmental research center and the rewarding activities there with art and science students and professors. We will talk about the learning enhancement added through a project that brought together a physical geography and a painting class. We will explore how students shared the form and content of their research projects with each other and then, became the educators through paintings and text of their geoscience topics on gallery walls.

  19. Advanced Physics Lab at TCU

    Science.gov (United States)

    Quarles, C. A.

    2009-04-01

    The one semester, one credit hour Modern Physics Lab is viewed as a transition between the structured Physics 1 and 2 labs and junior/senior research. The labs focus on a variety of experiments built around a multichannel analyzer, various alpha, beta and gamma ray detectors and weak radioactive sources. Experiments include radiation safety and detection with a Geiger counter and NaI detector, gamma ray spectroscopy with a germanium detector, beta spectrum, alpha energy loss, gamma ray absorption, Compton effect, nuclear and positron annihilation lifetime, speed of gamma rays. Other experiments include using the analog oscilloscope, x-ray diffraction of diamond and using an SEM/EDX. Error analysis is emphasized throughout. The semester ends with an individual project, often an extension of one of the earlier experiments, and students present their results as a paper and an APS style presentation to the department.

  20. PC/104 Embedded IOCs at Jefferson Lab

    Energy Technology Data Exchange (ETDEWEB)

    Jianxun Yan, Trent Allison, Sue Witherspoon, Anthony Cuffe

    2009-10-01

    Jefferson Lab has developed embedded IOCs based on PC/104 single board computers (SBC) for low level control systems. The PC/104 IOCs run EPICS on top of the RTEMS operating system. Two types of control system configurations are used in different applications, PC/104 SBC with commercial PC/104 I/O cards and PC/104 SBC with custom designed FPGA-based boards. RTEMS was built with CEXP shell to run on the PC/104 SBC. CEXP shell provides the function of dynamic object loading, which is similar to the widely used VxWorks operating system. Standard software configurations were setup for PC/104 IOC application development to provide a familiar format for new projects as well as ease the conversion of applications from VME based IOCs to PC/104 IOCs. Many new projects at Jefferson Lab are going to employ PC/104 SBCs as IOCs and some applications have already been running them for accelerator operations. The PC/104 - RTEMS IOC provides a free open source Real-Time Operating System (RTOS), low cost/maintenance, easily installed/ configured, flexible, and reliable solution for accelerator control and 12GeV Upgrade projects.

  1. Lab-on-fiber technology

    CERN Document Server

    Cusano, Andrea; Crescitelli, Alessio; Ricciardi, Armando

    2014-01-01

    This book focuses on a research field that is rapidly emerging as one of the most promising ones for the global optics and photonics community: the "lab-on-fiber" technology. Inspired by the well-established 'lab on-a-chip' concept, this new technology essentially envisages novel and highly functionalized devices completely integrated into a single optical fiber for both communication and sensing applications.Based on the R&D experience of some of the world's leading authorities in the fields of optics, photonics, nanotechnology, and material science, this book provides a broad and accurate de

  2. Innovation Incubator: Whisker Labs Technical Evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Sparn, Bethany F. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Frank, Stephen M. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Earle, Lieko [National Renewable Energy Lab. (NREL), Golden, CO (United States); Scheib, Jennifer G. [National Renewable Energy Lab. (NREL), Golden, CO (United States)

    2017-08-01

    The Wells Fargo Innovation Incubator (IN2) is a program to foster and accelerate startup companies with commercial building energy-efficiency and demand management technologies. The program is funded by the Wells Fargo Foundation and co-administered by the National Renewable Energy Laboratory (NREL). Whisker Labs, an Oakland, California-based company, was one of four awardees in the first IN2 cohort and was invited to participate in the program because of its novel electrical power sensing technology for circuit breakers. The stick-on Whisker meters install directly on the front face of the circuit breakers in an electrical panel using adhesive, eliminating the need to open the panel and install current transducers (CTs) on the circuit wiring.

  3. Exclusive processes at Jefferson Lab

    Indian Academy of Sciences (India)

    Exclusive processes such as proton–proton elastic scattering, meson photoproduction, and deuteron photodisintegration have been pursued extensively at many laboratories over the years in the search for such a transition, particularly at Jefferson Lab in recent years, taking the advantage of the high luminosity capability of ...

  4. A Simple, Successful Capacitor Lab

    Science.gov (United States)

    Ennis, William

    2011-01-01

    Capacitors are a fundamental component of modern electronics. They appear in myriad devices and in an enormous range of sizes. Although our students are taught the function and analysis of capacitors, few have the opportunity to use them in our labs.

  5. Efficient Sample Tracking With OpenLabFramework

    DEFF Research Database (Denmark)

    List, Markus; Schmidt, Steffen; Trojnar, Jakub

    2014-01-01

    of samples created and need to be replaced with state-of-the-art laboratory information management systems. Such systems have been developed in large numbers, but they are often limited to specific research domains and types of data. One domain so far neglected is the management of libraries of vector clones...

  6. The Case for Open Source Software: The Interactional Discourse Lab

    Science.gov (United States)

    Choi, Seongsook

    2016-01-01

    Computational techniques and software applications for the quantitative content analysis of texts are now well established, and many qualitative data software applications enable the manipulation of input variables and the visualization of complex relations between them via interactive and informative graphical interfaces. Although advances in…

  7. Open source posturography.

    Science.gov (United States)

    Rey-Martinez, Jorge; Pérez-Fernández, Nicolás

    2016-12-01

    The proposed validation goal of 0.9 in intra-class correlation coefficient was reached with the results of this study. With the obtained results we consider that the developed software (RombergLab) is a validated balance assessment software. The reliability of this software is dependent of the used force platform technical specifications. Develop and validate a posturography software and share its source code in open source terms. Prospective non-randomized validation study: 20 consecutive adults underwent two balance assessment tests, six condition posturography was performed using a clinical approved software and force platform and the same conditions were measured using the new developed open source software using a low cost force platform. Intra-class correlation index of the sway area obtained from the center of pressure variations in both devices for the six conditions was the main variable used for validation. Excellent concordance between RombergLab and clinical approved force platform was obtained (intra-class correlation coefficient =0.94). A Bland and Altman graphic concordance plot was also obtained. The source code used to develop RombergLab was published in open source terms.

  8. SuperFormLab: showing SuperFormLab

    DEFF Research Database (Denmark)

    2013-01-01

    3D-printing in clay and ceramic objects shaped by your own sounds and movements! Digital form transferred via CNC-milling to ornamental ceramic wall-cladding. Brave New World… Students and their teacher at SuperFormLab, the new ceramic workshop of the School of Design at the Royal Danish Academy...... of Fine Arts in Copenhagen, will be showing results of their investigations into the potential of combining digital technologies with ceramic materials. It is now possible to shape the most complex mathematical, virtual 3D objects through the use of advanced software-programs. And more than that – you can...... now get these objects out of the computer and be able to hold and experience them with your hands. Even made in clay. At SuperFormLab, workshop for the new education in Ceramic Design at the School of Design, the integration of digital technologies in relation to the ceramic materials and techniques...

  9. Functional genomics of probiotic Lactobacilli.

    Science.gov (United States)

    Klaenhammer, Todd R; Altermann, Eric; Pfeiler, Erika; Buck, Brock Logan; Goh, Yong-Jun; O'Flaherty, Sarah; Barrangou, Rodolphe; Duong, Tri

    2008-09-01

    Lactic acid bacteria (LAB) have been used in fermentation processes for millennia. Recent applications such as the use of living cultures as probiotics have significantly increased industrial interest. Related bacterial strains can differ significantly in their genotype and phenotype, and features from one bacterial strain or species cannot necessarily be applied to a related one. These strain or family-specific differences often represent unique and applicable traits. Since 2002, the complete genomes of 13 probiotic LABs have been published. The presentation will discuss these genomes and highlight probiotic traits that are predicted, or functionally linked to genetic content. We have conducted a comparative genomic analysis of 4 completely sequenced Lactobacillus strains versus 25 lactic acid bacterial genomes present in the public database at the time of analysis. Using Differential Blast Analysis, each genome is compared with 3 other Lactobacillus and 25 other LAB genomes. Differential Blast Analysis highlighted strain-specific genes that were not represented in any other LAB used in this analysis and also identified group-specific genes shared within lactobacilli. Lactobacillus-specific genes include mucus-binding proteins involved in cell-adhesion and several transport systems for carbohydrates and amino acids. Comparative genomic analysis has identified gene targets in Lactobacillus acidophilus for functional analysis, including adhesion to mucin and intestinal epithelial cells, acid tolerance, bile tolerance, and quorum sensing. Whole genome transcriptional profiling of L. acidophilus, and isogenic mutants thereof, has revealed the impact of varying conditions (pH, bile, carbohydrates) and food matrices on the expression of genes important to probiotic-linked mechanisms.

  10. Genomic selection needs to be carefully assessed to meet specific requirements in livestock breeding programs

    Directory of Open Access Journals (Sweden)

    Elisabeth eJonas

    2015-02-01

    Full Text Available Genomic selection is a promising development in agriculture, aiming improved production by exploiting molecular genetic markers to design novel breeding programs and to develop new markers-based models for genetic evaluation. It opens opportunities for research, as novel algorithms and lab methodologies are developed. Genomic selection can be applied in many breeds and species. Further research on the implementation of genomic selection in breeding programs is highly desirable not only for the common good, but also the private sector (breeding companies. It has been projected that this approach will improve selection routines, especially in species with long reproduction cycles, late or sex-limited or expensive trait recording and for complex traits. The task of integrating genomic selection into existing breeding programs is, however, not straightforward. Despite successful integration into breeding programs for dairy cattle, it has yet to be shown how much emphasis can be given to the genomic information and how much additional phenotypic information is needed from new selection candidates. Genomic selection is already part of future planning in many breeding companies of pigs and beef cattle among others, but further research is needed to fully estimate how effective the use of genomic information will be for the prediction of the performance of future breeding stock. Genomic prediction of production in crossbreeding and across-breed schemes, costs and choice of individuals for genotyping are reasons for a reluctance to fully rely on genomic information for selection decisions. Breeding objectives are highly dependent on the industry and the additional gain when using genomic information has to be considered carefully. This review synthesizes some of the suggested approaches in selected livestock species including cattle, pig, chicken and fish. It outlines tasks to help understanding possible consequences when applying genomic information in

  11. An Approach for WebLabs Analysis

    Directory of Open Access Journals (Sweden)

    Javier García Zubia

    2007-05-01

    Full Text Available The Faculty of Engineering of University of Deusto has a WebLab oriented to Microelectronics available since 2001. The first part of this paper shows several requirements that a WebLab should meet and the following sections present the WebLab-Deusto.

  12. Recent results from Jefferson Lab

    International Nuclear Information System (INIS)

    Smith, E.

    2000-01-01

    Precision measurements of the structure of nucleons and nuclei in the regime of strong interaction QCD are now possible with the availability of high current polarized electron beams, polarized targets, and recoil polarimeters, in conjunction with modern spectrometers and detector instrumentation. The authors present some recent results from the Jefferson Lab on the charge and current distributions of nucleons and nuclei. They also review measurements which relate physics at small distances to the regime where strong interaction QCD is the relevant theory

  13. Openly Published Environmental Sensing (OPEnS) | Advancing Open-Source Research, Instrumentation, and Dissemination

    Science.gov (United States)

    Udell, C.; Selker, J. S.

    2017-12-01

    The increasing availability and functionality of Open-Source software and hardware along with 3D printing, low-cost electronics, and proliferation of open-access resources for learning rapid prototyping are contributing to fundamental transformations and new technologies in environmental sensing. These tools invite reevaluation of time-tested methodologies and devices toward more efficient, reusable, and inexpensive alternatives. Building upon Open-Source design facilitates community engagement and invites a Do-It-Together (DIT) collaborative framework for research where solutions to complex problems may be crowd-sourced. However, barriers persist that prevent researchers from taking advantage of the capabilities afforded by open-source software, hardware, and rapid prototyping. Some of these include: requisite technical skillsets, knowledge of equipment capabilities, identifying inexpensive sources for materials, money, space, and time. A university MAKER space staffed by engineering students to assist researchers is one proposed solution to overcome many of these obstacles. This presentation investigates the unique capabilities the USDA-funded Openly Published Environmental Sensing (OPEnS) Lab affords researchers, within Oregon State and internationally, and the unique functions these types of initiatives support at the intersection of MAKER spaces, Open-Source academic research, and open-access dissemination.

  14. LAB bacteriocin applications in the last decade

    Directory of Open Access Journals (Sweden)

    Ma. del Rocío López-Cuellar

    2016-11-01

    Full Text Available In the early 2000s, the expectations about bacteriocins produced by lactic acid bacteria (LABs were aimed at food applications. However, the effectiveness of bacteriocins against undesirable micro-organisms opened endless possibilities for innovative research. In the present review, we collected a database including 429 published papers and 245 granted patents (from 2004 to 2015. Based on bibliometric analysis, the progress of bacteriocin research in the last 11 years was discussed in detail. It was found that 164 patents were granted in 2010–2015, which is equivalent to 60% in comparison with previous years (i.e. only 81 patents were granted in 2004–2009. Currently, the research on bacteriocins is still gaining importance. In the realm of therapeutic strategies, about a 37% of the published research was focused on biomedical applications in the last decade. This vein of research is currently seeking for alternative solutions to problems such as cancer, systemic infections, oral-care, vaginal infections, contraception and skincare. On the other hand, food preservation, bio-nanomaterial and veterinary applications represent 29%, 25% and 9%, respectively. All this technology is being applied and will surely grow in the future, since about 31% of the patents granted since 2004 are focused on the biomedical area, 29% on food preservation, 5% on veterinary use; whereas 13% and 16% correspond to patents granted on production–purification systems and recombinant proteins or molecular modifications in the producer strains. This review contributes to the analysis of recent LAB bacteriocin applications and their role in safety, quality and improvement of human health.

  15. Arduino-Based embedded systems interfacing, simulation, and LabVIEW GUI

    CERN Document Server

    Singh, Rajesh; Singh, Bhupendra; Choudhury, Sushabhan

    2018-01-01

    Arduino is an open-source electronics platform based on easy-to-use hardware and software while LabVIEW is a graphical programming telling how to connect functions and work with a variety of datatypes when constructing applications.This book will help beginners to get started with Arduino-based embedded systems including essential know-how of the programming and interfacing of the devices. Book includes programming and simulation of Arduino-based projects and interfacing with LabVIEW, based on practical case studies. The book comprises of total twenty five chapters with description, working model of LabVIEW and programming with Arduino IDE.

  16. LabVIEW 8 student edition

    CERN Document Server

    Bishop, Robert H

    2007-01-01

    For courses in Measurement and Instrumentation, Electrical Engineering lab, and Physics and Chemistry lab. This revised printing has been updated to include new LabVIEW 8.2 Student Edition. National Instruments' LabVIEW is the defacto industry standard for test, measurement, and automation software solutions. With the Student Edition of LabVIEW, students can design graphical programming solutions to their classroom problems and laboratory experiments with software that delivers the graphical programming capabilites of the LabVIEW professional version. . The Student Edition is also compatible with all National Instruments data acquisition and instrument control hardware. Note: The LabVIEW Student Edition is available to students, faculty, and staff for personal educational use only. It is not intended for research, institutional, or commercial use. For more information about these licensing options, please visit the National Instruments website at (http:www.ni.com/academic/)

  17. Automated ensemble assembly and validation of microbial genomes

    Science.gov (United States)

    2014-01-01

    Background The continued democratization of DNA sequencing has sparked a new wave of development of genome assembly and assembly validation methods. As individual research labs, rather than centralized centers, begin to sequence the majority of new genomes, it is important to establish best practices for genome assembly. However, recent evaluations such as GAGE and the Assemblathon have concluded that there is no single best approach to genome assembly. Instead, it is preferable to generate multiple assemblies and validate them to determine which is most useful for the desired analysis; this is a labor-intensive process that is often impossible or unfeasible. Results To encourage best practices supported by the community, we present iMetAMOS, an automated ensemble assembly pipeline; iMetAMOS encapsulates the process of running, validating, and selecting a single assembly from multiple assemblies. iMetAMOS packages several leading open-source tools into a single binary that automates parameter selection and execution of multiple assemblers, scores the resulting assemblies based on multiple validation metrics, and annotates the assemblies for genes and contaminants. We demonstrate the utility of the ensemble process on 225 previously unassembled Mycobacterium tuberculosis genomes as well as a Rhodobacter sphaeroides benchmark dataset. On these real data, iMetAMOS reliably produces validated assemblies and identifies potential contamination without user intervention. In addition, intelligent parameter selection produces assemblies of R. sphaeroides comparable to or exceeding the quality of those from the GAGE-B evaluation, affecting the relative ranking of some assemblers. Conclusions Ensemble assembly with iMetAMOS provides users with multiple, validated assemblies for each genome. Although computationally limited to small or mid-sized genomes, this approach is the most effective and reproducible means for generating high-quality assemblies and enables users to

  18. Genome Maps, a new generation genome browser

    Science.gov (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-01-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org. PMID:23748955

  19. Genome Maps, a new generation genome browser.

    Science.gov (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-07-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

  20. Multi-color fluorescent DNA analysis in an integrated optofluidic lab on a chip

    NARCIS (Netherlands)

    Dongre, C.

    2010-01-01

    Abstract: Sorting and sizing of DNA molecules within the human genome project has enabled the genetic mapping of various illnesses. Furthermore by employing tiny lab-on-a-chip device, integrated DNA sequencing and genetic diagnostics have become feasible. We present the combination of capillary

  1. Double success for neutrino lab

    CERN Multimedia

    2010-01-01

    "The Gran Sasso National Laboratory in Italy is celebrating two key developments in the field of neutrino physics. Number one is the first ever detection, by the OPERA experiement, of possible tau neutrino that has switched its identity from a muon neutrino as it travelled form its origins at CERN in Switzerland to the Italian lab. Number two is the successful start-up of the ICARUS detector, which, like OPERA, is designed to study neutrinos that "oscillate" between types" (0.5 pages)

  2. Remote Lab for Robotics Applications

    Directory of Open Access Journals (Sweden)

    Robinson Jiménez

    2018-01-01

    Full Text Available This article describes the development of a remote lab environment used to test and training sessions for robotics tasks. This environment is made up of the components and devices based on two robotic arms, a network link, Arduino card and Arduino shield for Ethernet, as well as an IP camera. The remote laboratory is implemented to perform remote control of the robotic arms with visual feedback by camera, of the robots actions, where, with a group of test users, it was possible to obtain performance ranges in tasks of telecontrol of up to 92%.

  3. Laser safety in the lab

    CERN Document Server

    Barat, Ken L

    2012-01-01

    There is no more challenging setting for laser use than a research environment. In almost every other setting the laser controls count on engineering controls, and human exposure is kept to a minimum. In research, however, the user often manipulates the optical layout and thereby places him or herself in peril, but this does not mean that accidents and injury are unavoidable. On the contrary, laser accidents can be avoided by following a number of simple approaches. [i]Laser Safety in the Lab[/i] provides the laser user and laser safety officer with practical guidelines from housekeeping to ey

  4. Digital media labs in libraries

    CERN Document Server

    Goodman, Amanda L

    2014-01-01

    Families share stories with each other and veterans reconnect with their comrades, while teens edit music videos and then upload them to the web: all this and more can happen in the digital media lab (DML), a gathering of equipment with which people create digital content or convert content that is in analog formats. Enabling community members to create digital content was identified by The Edge Initiative, a national coalition of leading library and local government organizations, as a library technology benchmark. Surveying academic and public libraries in a variety of settings and sharing a

  5. Recent results from Jefferson Lab

    International Nuclear Information System (INIS)

    Volker D. Burkert

    1999-01-01

    Recent results on studies of the structure of nucleons and nuclei in the regime of strong interaction QCD are discussed. Use of high current polarized electron beams, polarized targets, and recoil polarimeters, in conjunction with modern spectrometers and detector instrumentation allow much more detailed studies of nucleon and nuclear structure than has been possible in the past. The CEBAF accelerator at Jefferson Lab was build to study the internal structure of hadrons in a regime where confinement is important and strong interaction QCD is the relevant theory. They author discusses how the first experiments already make significant contributions towards an improved understanding of hadronic structure

  6. Recent Results from Jefferson Lab

    International Nuclear Information System (INIS)

    Volker Burkert

    2000-03-01

    Recent results on studies of the structure of nucleons and nuclei in the regime of strong interaction QCD are discussed. Use of high current polarized electron beams, polarized targets, and recoil polarimeters, in conjunction with modern spectrometers and detector instrumentation allow much more detailed studies of nucleon and nuclear structure than has been possible in the past. The CEBAF accelerator at Jefferson Lab was built to study the internal structure of hadrons in a regime where confinement is important and strong interaction QCD is the relevant theory. I discuss how the first experiments already make significant contributions towards an improved understanding of hadronic structure

  7. A green chemistry lab course

    International Nuclear Information System (INIS)

    Rank, J.; Lenoir, D.; Bahadir, M.; Koning, B.

    2006-01-01

    The traditional course content of chemistry classes must change to achieve better awareness of the important issues of sustainability in chemistry within the next generation of professional chemists. To provide the necessary material for the organic chemistry teaching lab course, which is part of almost all study programs in chemistry, material was developed and collected (http://www.oc-praktikum.de/en) that allows students and teachers to assess reactions beyond the experimental set up, reaction mechanism and chemical yield. Additional parameters like atom economy of chemical transformations, energy efficiency, and questions of waste, renewable feed stocks, toxicity and ecotoxicity, as well as the safety measures for the chemicals used are discussed. (author)

  8. Fully On-line Introductory Physics with a Lab

    Science.gov (United States)

    Schatz, Michael

    We describe the development and implementation of a college-level introductory physics (mechanics) course and laboratory that is suited for both on-campus and on-line environments. The course emphasizes a ``Your World is Your Lab'' approach whereby students first examine and capture on video (using cellphones) motion in their immediate surroundings, and then use free, open-source software both to extract data from the video and to apply physics principles to build models that describe, predict, and visualize the observations. Each student reports findings by creating a video lab report and posting it online; these video lab reports are then distributed to the rest of the class for peer review. In this talk, we will discuss the student and instructor experiences in courses offered to three distinct audiences in different venues: (1) a Massively Open On-line Course (MOOC) for off-campus participants, (2) a flipped/blended course for on-campus students, and, most recently, (3) a fully-online course for off-campus students.

  9. Genomics and privacy: implications of the new reality of closed data for the field.

    Directory of Open Access Journals (Sweden)

    Dov Greenbaum

    2011-12-01

    Full Text Available Open source and open data have been driving forces in bioinformatics in the past. However, privacy concerns may soon change the landscape, limiting future access to important data sets, including personal genomics data. Here we survey this situation in some detail, describing, in particular, how the large scale of the data from personal genomic sequencing makes it especially hard to share data, exacerbating the privacy problem. We also go over various aspects of genomic privacy: first, there is basic identifiability of subjects having their genome sequenced. However, even for individuals who have consented to be identified, there is the prospect of very detailed future characterization of their genotype, which, unanticipated at the time of their consent, may be more personal and invasive than the release of their medical records. We go over various computational strategies for dealing with the issue of genomic privacy. One can "slice" and reformat datasets to allow them to be partially shared while securing the most private variants. This is particularly applicable to functional genomics information, which can be largely processed without variant information. For handling the most private data there are a number of legal and technological approaches-for example, modifying the informed consent procedure to acknowledge that privacy cannot be guaranteed, and/or employing a secure cloud computing environment. Cloud computing in particular may allow access to the data in a more controlled fashion than the current practice of downloading and computing on large datasets. Furthermore, it may be particularly advantageous for small labs, given that the burden of many privacy issues falls disproportionately on them in comparison to large corporations and genome centers. Finally, we discuss how education of future genetics researchers will be important, with curriculums emphasizing privacy and data security. However, teaching personal genomics with

  10. Jefferson Lab, a status report

    International Nuclear Information System (INIS)

    Thomas Jefferson National Accelerator Facility (Jefferson Lab; formerly known as CEBAF), operates a 4 GeV, 200 microA continuous wave (CW) electron accelerator that re-circulates the beam five times through two superconducting 400 MeV linacs. Electrons can be extracted from any of the five recirculation passes and beam can be simultaneously delivered to the three experimental halls. As the commissioning stage nears completion, the accelerator is becoming a fully operational machine. Experiments in Hall C have been underway since November 1995 with beam powers of over 300 kW at various energies. Hall A has received beam for spectrometer commissioning, while Hall B is expected to receive its first beam in the fall of 1996. Accelerator availability of greater than 70% during physics runs and excellent beam quality have contributed to making Jefferson Lab a world class laboratory for accelerator-based electromagnetic nuclear physics. With the high performance of the superconducting RF cavities, machine upgrades to 6 GeV, and eventually 8 to 10 GeV are now in the planning stages. Operational and commissioning details concerning all aspects of the machine will be discussed

  11. Jefferson Lab, a status report

    International Nuclear Information System (INIS)

    Dunham, B.M.

    1996-01-01

    Thomas Jefferson National Accelerator Facility (Jefferson Lab; formerly known as CEBAF), operates a 4 GeV, 200 μA continuous wave (CW) electron accelerator that re-circulates the beam five times through two superconducting 400 MeV linacs. Electrons can be extracted from any of the five recirculation passes and beam can be simultaneously delivered to the three experimental halls. As the commissioning stage nears completion, the accelerator is becoming a fully operational machine. Experiments in Hall C have been underway since November 1995 with beam powers of over 300 kW at various energies. Hall A has received beam for spectrometer commissioning, while Hall B is expected to receive its first beam in the fall of 1996. Accelerator availability of greater than 70% during physics runs and excellent beam quality have contributed to making Jefferson Lab a world class laboratory for accelerator-based electromagnetic nuclear physics. With the high performance of the superconducting RF cavities, machine upgrades to 6 GeV, and eventually 8 to 10 GeV are now in the planning stages. Operational and commissioning details concerning all aspects of the machine will be discussed. (author)

  12. Jefferson Lab, a status report

    International Nuclear Information System (INIS)

    Dunham, B.M.

    1996-01-01

    Thomas Jefferson National Accelerator Facility (Jefferson Lab; formerly known as CEBAF), operates a 4 GeV, 200 microA continuous wave (CW) electron accelerator that re-circulates the beam five times through two superconducting 400 MeV linacs. Electrons can be extracted from any of the five recirculation passes and beam can be simultaneously delivered to the three experimental halls. As the commissioning stage nears completion, the accelerator is becoming a fully operational machine. Experiments in Hall C have been underway since November 1995 with beam powers of over 300 kW at various energies. Hall A has received beam for spectrometer commissioning, while Hall B is expected to receive its first beam in the fall of 1996. Accelerator availability of greater than 70% during physics runs and excellent beam quality have contributed to making Jefferson Lab a world class laboratory for accelerator-based electromagnetic nuclear physics. With the high performance of the superconducting RF cavities, machine upgrades to 6 GeV, and eventually 8 to 10 GeV are now in the planning stages. Operational and commissioning details concerning all aspects of the machine will be discussed

  13. Arduino: a low-cost multipurpose lab equipment.

    Science.gov (United States)

    D'Ausilio, Alessandro

    2012-06-01

    Typical experiments in psychological and neurophysiological settings often require the accurate control of multiple input and output signals. These signals are often generated or recorded via computer software and/or external dedicated hardware. Dedicated hardware is usually very expensive and requires additional software to control its behavior. In the present article, I present some accuracy tests on a low-cost and open-source I/O board (Arduino family) that may be useful in many lab environments. One of the strengths of Arduinos is the possibility they afford to load the experimental script on the board's memory and let it run without interfacing with computers or external software, thus granting complete independence, portability, and accuracy. Furthermore, a large community has arisen around the Arduino idea and offers many hardware add-ons and hundreds of free scripts for different projects. Accuracy tests show that Arduino boards may be an inexpensive tool for many psychological and neurophysiological labs.

  14. Genomic Testing

    Science.gov (United States)

    ... Events and Multimedia Implementation Genetics 101 Family Health History Genomics and Diseases Genetic Counseling Genomic Testing Epidemiology Pathogen Genomics Resources Genomic Testing Recommend on Facebook Tweet Share Compartir Fact Sheet: Identifying Opportunities to ...

  15. StagLab: Post-Processing and Visualisation in Geodynamics

    Science.gov (United States)

    Crameri, Fabio

    2017-04-01

    Despite being simplifications of nature, today's Geodynamic numerical models can, often do, and sometimes have to become very complex. Additionally, a steadily-increasing amount of raw model data results from more elaborate numerical codes and the still continuously-increasing computational power available for their execution. The current need for efficient post-processing and sensible visualisation is thus apparent. StagLab (www.fabiocrameri.ch/software) provides such much-needed strongly-automated post-processing in combination with state-of-the-art visualisation. Written in MatLab, StagLab is simple, flexible, efficient and reliable. It produces figures and movies that are both fully-reproducible and publication-ready. StagLab's post-processing capabilities include numerous diagnostics for plate tectonics and mantle dynamics. Featured are accurate plate-boundary identification, slab-polarity recognition, plate-bending derivation, mantle-plume detection, and surface-topography component splitting. These and many other diagnostics are derived conveniently from only a few parameter fields thanks to powerful image processing tools and other capable algorithms. Additionally, StagLab aims to prevent scientific visualisation pitfalls that are, unfortunately, still too common in the Geodynamics community. Misinterpretation of raw data and exclusion of colourblind people introduced with the continuous use of the rainbow (a.k.a. jet) colour scheme is just one, but a dramatic example (e.g., Rogowitz and Treinish, 1998; Light and Bartlein, 2004; Borland and Ii, 2007). StagLab is currently optimised for binary StagYY output (e.g., Tackley 2008), but is adjustable for the potential use with other Geodynamic codes. Additionally, StagLab's post-processing routines are open-source. REFERENCES Borland, D., and R. M. T. Ii (2007), Rainbow color map (still) considered harmful, IEEE Computer Graphics and Applications, 27(2), 14-17. Light, A., and P. J. Bartlein (2004), The end of

  16. MatLab Script and Functional Programming

    Science.gov (United States)

    Shaykhian, Gholam Ali

    2007-01-01

    MatLab Script and Functional Programming: MatLab is one of the most widely used very high level programming languages for scientific and engineering computations. It is very user-friendly and needs practically no formal programming knowledge. Presented here are MatLab programming aspects and not just the MatLab commands for scientists and engineers who do not have formal programming training and also have no significant time to spare for learning programming to solve their real world problems. Specifically provided are programs for visualization. The MatLab seminar covers the functional and script programming aspect of MatLab language. Specific expectations are: a) Recognize MatLab commands, script and function. b) Create, and run a MatLab function. c) Read, recognize, and describe MatLab syntax. d) Recognize decisions, loops and matrix operators. e) Evaluate scope among multiple files, and multiple functions within a file. f) Declare, define and use scalar variables, vectors and matrices.

  17. Famed lab seeks big grid

    CERN Document Server

    Lillington, K

    2001-01-01

    DUBLIN, Ireland -- CERN, the famed Swiss high-energy particle physics lab, has a problem. It's about to start generating more data than any computer or network anywhere in the world is able to analyze. That prospect has led CERN to drive a major European project to create a vast "grid" research network of computers across Europe. When completed, the 10 million euro, Linux-based endeavor called DataGRID, will become a principal European computing resource for researchers of many disciplines. "I believe grid computing will revolutionize the way we compute, in much the same way as the World Wide Web and Internet changed the way we communicate," said John Ellis, a theoretical physicist and adviser to the director general of CERN.

  18. Gramene database: navigating plant comparative genomics resources

    Science.gov (United States)

    Gramene (http://www.gramene.org) is an online, open source, curated resource for plant comparative genomics and pathway analysis designed to support researchers working in plant genomics, breeding, evolutionary biology, system biology, and metabolic engineering. It exploits phylogenetic relationship...

  19. Renewed lab banks on experience

    International Nuclear Information System (INIS)

    Herzig, Janine

    2007-01-01

    South Australia has huge uranium resources, Amdel has opened a new mineral processing facility in Wingfield, Adelaide. The facility originally was focused solely on mineral processing activities, that included crushing, screening, flotation and leaching. There are plans to open a dedicated uranium processing materials facility in Wingfield. A unique part of Amdel's geo-analytical business is the x-ray diffraction (XRD), and asbestos identification capability

  20. Encouraging entrepreneurship in university labs: Research activities, research outputs, and early doctorate careers

    Science.gov (United States)

    2017-01-01

    This paper investigates how the encouragement of entrepreneurship within university research labs relates with research activities, research outputs, and early doctorate careers. Utilizing a panel survey of 6,840 science & engineering doctoral students at 39 R1 research universities, this study shows that entrepreneurship is widely encouraged across university research labs, ranging from 54% in biomedical engineering to 18% in particle physics, while only a small share of labs openly discourage entrepreneurship, from approximately 3% in engineering to approximately 12% in the life sciences. Within fields, there is no difference between labs that encourage entrepreneurship and those that do not with respect to basic research activity and the number of publications. At the same time, labs that encourage entrepreneurship are significantly more likely to report invention disclosures, particularly in engineering where such labs are 41% more likely to disclose inventions. With respect to career pathways, PhDs students in labs that encourage entrepreneurship do not differ from other PhDs in their interest in academic careers, but they are 87% more likely to be interested in careers in entrepreneurship and 44% more likely to work in a startup after graduation. These results persist even when accounting for individuals’ pre-PhD interest in entrepreneurship and the encouragement of other non-academic industry careers. PMID:28178270

  1. Encouraging entrepreneurship in university labs: Research activities, research outputs, and early doctorate careers.

    Directory of Open Access Journals (Sweden)

    Michael Roach

    Full Text Available This paper investigates how the encouragement of entrepreneurship within university research labs relates with research activities, research outputs, and early doctorate careers. Utilizing a panel survey of 6,840 science & engineering doctoral students at 39 R1 research universities, this study shows that entrepreneurship is widely encouraged across university research labs, ranging from 54% in biomedical engineering to 18% in particle physics, while only a small share of labs openly discourage entrepreneurship, from approximately 3% in engineering to approximately 12% in the life sciences. Within fields, there is no difference between labs that encourage entrepreneurship and those that do not with respect to basic research activity and the number of publications. At the same time, labs that encourage entrepreneurship are significantly more likely to report invention disclosures, particularly in engineering where such labs are 41% more likely to disclose inventions. With respect to career pathways, PhDs students in labs that encourage entrepreneurship do not differ from other PhDs in their interest in academic careers, but they are 87% more likely to be interested in careers in entrepreneurship and 44% more likely to work in a startup after graduation. These results persist even when accounting for individuals' pre-PhD interest in entrepreneurship and the encouragement of other non-academic industry careers.

  2. The community FabLab platform: applications and implications in biomedical engineering.

    Science.gov (United States)

    Stephenson, Makeda K; Dow, Douglas E

    2014-01-01

    Skill development in science, technology, engineering and math (STEM) education present one of the most formidable challenges of modern society. The Community FabLab platform presents a viable solution. Each FabLab contains a suite of modern computer numerical control (CNC) equipment, electronics and computing hardware and design, programming, computer aided design (CAD) and computer aided machining (CAM) software. FabLabs are community and educational resources and open to the public. Development of STEM based workforce skills such as digital fabrication and advanced manufacturing can be enhanced using this platform. Particularly notable is the potential of the FabLab platform in STEM education. The active learning environment engages and supports a diversity of learners, while the iterative learning that is supported by the FabLab rapid prototyping platform facilitates depth of understanding, creativity, innovation and mastery. The product and project based learning that occurs in FabLabs develops in the student a personal sense of accomplishment, self-awareness, command of the material and technology. This helps build the interest and confidence necessary to excel in STEM and throughout life. Finally the introduction and use of relevant technologies at every stage of the education process ensures technical familiarity and a broad knowledge base needed for work in STEM based fields. Biomedical engineering education strives to cultivate broad technical adeptness, creativity, interdisciplinary thought, and an ability to form deep conceptual understanding of complex systems. The FabLab platform is well designed to enhance biomedical engineering education.

  3. Encouraging entrepreneurship in university labs: Research activities, research outputs, and early doctorate careers.

    Science.gov (United States)

    Roach, Michael

    2017-01-01

    This paper investigates how the encouragement of entrepreneurship within university research labs relates with research activities, research outputs, and early doctorate careers. Utilizing a panel survey of 6,840 science & engineering doctoral students at 39 R1 research universities, this study shows that entrepreneurship is widely encouraged across university research labs, ranging from 54% in biomedical engineering to 18% in particle physics, while only a small share of labs openly discourage entrepreneurship, from approximately 3% in engineering to approximately 12% in the life sciences. Within fields, there is no difference between labs that encourage entrepreneurship and those that do not with respect to basic research activity and the number of publications. At the same time, labs that encourage entrepreneurship are significantly more likely to report invention disclosures, particularly in engineering where such labs are 41% more likely to disclose inventions. With respect to career pathways, PhDs students in labs that encourage entrepreneurship do not differ from other PhDs in their interest in academic careers, but they are 87% more likely to be interested in careers in entrepreneurship and 44% more likely to work in a startup after graduation. These results persist even when accounting for individuals' pre-PhD interest in entrepreneurship and the encouragement of other non-academic industry careers.

  4. [Probiotics: from the lab to the consumer].

    Science.gov (United States)

    Rodríguez, J M

    2015-02-07

    In the last years, the field of probiotics has grown notably. However, out of the thousands of strains isolated each year in the labs around the world, very few enter in a phase of industrial development and even a lower number go to the market. In this article, the main aspects that have to be taken into account in the, usually, long and winding road that a strain must follow from isolation to the market are reviewed Results and conclusions: A probiotic microorganism has to be correctly identified at the species and strain levels. The genome sequence is the gold identification standard and provides valuable information on the safety, functionality and technological properties of a strain. The cases in which a link between a probiotic and an adverse effect has been established are scarce and have involved people with underlying pathologies. There is a wide variety of in vitro, ex vivo and animal model assays for the screening of probiotics, which provide useful information throughout the selection process; however, correctly designed clinical trials are the only way to obtain direct results on the safety and efficacy of a probiotic to the target population. Probiotic companies have the need to obtain a very high bacterial biomass in an economically viable manner while preserving the concentration of live bacteria required for exerting the expected beneficial effect until the end of the probiotic's shelf life. Finally, commercial aspects play a key role in the decision of starting an industrial development and, eventually, to place a probiotic in the market. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

  5. Innovation - A view from the Lab

    Science.gov (United States)

    The USDA Ag Lab in Peoria helps bridge the gap between agricultural producers and commercial manufacturers. In 2015, the Ag Lab, officially known as the Agricultural Research Service (ARS) National Center for Agricultural Utilization Research (NCAUR), is celebrating 75 years of research in Peoria. T...

  6. Latest results from FROST at Jefferson Lab

    Directory of Open Access Journals (Sweden)

    Ritchie B.G.

    2014-06-01

    Full Text Available The spectrum of broad and overlapping nucleon excitations can be greatly clarified by use of a polarized photon beam incident on a polarized target in meson photoproduction experiments. At Jefferson Lab, a program of such measurements has made use of the Jefferson Lab FROzen Spin Target (FROST. An overview of preliminary results are presented.

  7. Latest results from FROST at Jefferson Lab

    Energy Technology Data Exchange (ETDEWEB)

    Ritchie, Barry G. [Arizona State University

    2014-06-01

    The spectrum of broad and overlapping nucleon excitations can be greatly clarified by use of a polarized photon beam incident on a polarized target in meson photoproduction experiments. At Jefferson Lab, a program of such measurements has made use of the Jefferson Lab FROzen Spin Target (FROST). An overview of preliminary results are presented.

  8. Programming Arduino with LabVIEW

    CERN Document Server

    Schwartz, Marco

    2015-01-01

    If you already have some experience with LabVIEW and want to apply your skills to control physical objects and make measurements using the Arduino sensor, this book is for you. Prior knowledge of Arduino and LabVIEW is essential to fully understand the projects detailed in this book.

  9. Supercharging Lessons with a Virtual Lab

    Science.gov (United States)

    Stewart, Jefferson; Vincent, Daniel

    2013-01-01

    The authors describes their experiences incorporating the virtual lab into a simple circuit lesson during an energy unit in a sixth-grade class. The lesson included a hands-on group experiment using wire, batteries, and light bulbs to make a circuit and an online simulation, using a virtual lab. Class discussions, student inquiries, and the study…

  10. Exploring linear algebra labs and projects with Mathematica

    CERN Document Server

    Arangala, Crista

    2014-01-01

    Matrix Operations Lab 0: An Introduction to Mathematica Lab 1: Matrix Basics and Operations Lab 2: A Matrix Representation of Linear Systems Lab 3: Powers, Inverses, and Special Matrices Lab 4: Graph Theory and Adjacency Matrices Lab 5: Permutations and Determinants Lab 6: 4 x 4 Determinants and Beyond Project Set 1 Invertibility Lab 7: Singular or Nonsingular? Why Singularity Matters Lab 8: Mod It Out, Matrices with Entries in ZpLab 9: It's a Complex World Lab 10: Declaring Independence: Is It Linear? Project Set 2 Vector Spaces Lab 11: Vector Spaces and SubspacesLab 12: Basing It All on Just a Few Vectors Lab 13: Linear Transformations Lab 14: Eigenvalues and Eigenspaces Lab 15: Markov Chains, An Application of Eigenvalues Project Set 3 Orthogonality Lab 16: Inner Product Spaces Lab 17: The Geometry of Vector and Inner Product SpacesLab 18: Orthogonal Matrices, QR Decomposition, and Least Squares Regression Lab 19: Symmetric Matrices and Quadratic Forms Project Set 4 Matrix Decomposition with Applications L...

  11. Setting Up a Veterinary Medicine Skills Lab in Germany

    Science.gov (United States)

    Dilly, Marc; Tipold, Andrea; Schaper, Elisabeth; Ehlers, Jan P.

    2014-01-01

    The amendments introduced to the current Veterinary Licensing Ordinance (TAppV) by the Veterinary Licensing Regulation (TAppO) have brought a high degree of skills orientation to fill the gap between academic study and preparing for a wide range of professional skills. In order to improve the veterinary skills of students while conveying fundamental methods in a structured and reproducible way, the University of Veterinary Medicine Hannover, Foundation, has set up the first central veterinary skills lab in Germany. Practical training is provided by means of a three-tier delivery approach. This involves around 40 simulators on an area of approx. 800 m² under the guidance of 6-8 staff members, along with supplementary resources such as posters, text instructions and YouTube videos. Since it opened in March 2013, there have been 769 visits to the skills lab and 30,734 hits on YouTube. Initial results show that the skills lab helps to maintain student motivation by teaching them practical skills at an early stage of the basic study-based acquisition of knowledge, whilst reinforcing skills acquisition per se in competence-based teaching. It enables veterinary students to prepare for their first examinations and treatments of live patients in a manner compliant with animal welfare. PMID:24872855

  12. Etablierung eines Skills Labs in der Tiermedizin in Deutschland

    Directory of Open Access Journals (Sweden)

    Dilly, Marc

    2014-05-01

    Full Text Available [english] The amendments introduced to the current Veterinary Licensing Ordinance (TAppV by the Veterinary Licensing Regulation (TAppO have brought a high degree of skills orientation to fill the gap between academic study and preparing for a wide range of professional skills. In order to improve the veterinary skills of students while conveying fundamental methods in a structured and reproducible way, the University of Veterinary Medicine Hannover, Foundation, has set up the first central veterinary skills lab in Germany.Practical training is provided by means of a three-tier delivery approach. This involves around 40 simulators on an area of approx. 800 m² under the guidance of 6-8 staff members, along with supplementary resources such as posters, text instructions and YouTube videos. Since it opened in March 2013, there have been 769 visits to the skills lab and 30,734 hits on YouTube.Initial results show that the skills lab helps to maintain student motivation by teaching them practical skills at an early stage of the basic study-based acquisition of knowledge, whilst reinforcing skills acquisition per se in competence-based teaching. It enables veterinary students to prepare for their first examinations and treatments of live patients in a manner compliant with animal welfare.

  13. Setting up a veterinary medicine skills lab in Germany.

    Science.gov (United States)

    Dilly, Marc; Tipold, Andrea; Schaper, Elisabeth; Ehlers, Jan P

    2014-01-01

    The amendments introduced to the current Veterinary Licensing Ordinance (TAppV) by the Veterinary Licensing Regulation (TAppO) have brought a high degree of skills orientation to fill the gap between academic study and preparing for a wide range of professional skills. In order to improve the veterinary skills of students while conveying fundamental methods in a structured and reproducible way, the University of Veterinary Medicine Hannover, Foundation, has set up the first central veterinary skills lab in Germany. Practical training is provided by means of a three-tier delivery approach. This involves around 40 simulators on an area of approx. 800 m(2) under the guidance of 6-8 staff members, along with supplementary resources such as posters, text instructions and YouTube videos. Since it opened in March 2013, there have been 769 visits to the skills lab and 30,734 hits on YouTube. Initial results show that the skills lab helps to maintain student motivation by teaching them practical skills at an early stage of the basic study-based acquisition of knowledge, whilst reinforcing skills acquisition per se in competence-based teaching. It enables veterinary students to prepare for their first examinations and treatments of live patients in a manner compliant with animal welfare.

  14. The complete integration of MissionLab and CARMEN

    Directory of Open Access Journals (Sweden)

    FJ Serrano Rodriguez

    2017-05-01

    Full Text Available Nowadays, a major challenge in the development of advanced robotic systems is the creation of complex missions for groups of robots, with two main restrictions: complex programming activities not needed and the mission configuration time should be short (e.g. Urban Search And Rescue. With these ideas in mind, we analysed several robotic development environments, such as Robot Operating System (ROS, Open Robot Control Software (OROCOS, MissionLab, Carnegie Mellon Robot Navigation Toolkit (CARMEN and Player/Stage, which are helpful when creating autonomous robots. MissionLab provides high-level features (automatic mission creation, code generation and a graphical mission editor that are unavailable in other significant robotic development environments. It has however some weaknesses regarding its map-based capabilities. Creating, managing and taking advantage of maps for localization and navigation tasks are among CARMEN’s most significant features. This fact makes the integration of MissionLab with CARMEN both possible and interesting. This article describes the resulting robotic development environment, which makes it possible to work with several robots, and makes use of their map-based navigation capabilities. It will be shown that the proposed platform solves the proposed goal, that is, it simplifies the programmer’s job when developing control software for robot teams, and it further facilitates multi-robot deployment task in mission-critical situations.

  15. Lab-on-a-Chip

    Science.gov (United States)

    2004-01-01

    Labs on chips are manufactured in many shapes and sizes and can be used for numerous applications, from medical tests to water quality monitoring to detecting the signatures of life on other planets. The eight holes on this chip are actually ports that can be filled with fluids or chemicals. Tiny valves control the chemical processes by mixing fluids that move in the tiny channels that look like lines, connecting the ports. Scientists at NASA's Marshall Space Flight Center (MSFC) in Huntsville, Alabama designed this chip to grow biological crystals on the International Space Station. Through this research, they discovered that this technology is ideally suited for solving the challenges of the Vision for Space Exploration. For example, thousands of chips the size of dimes could be loaded on a Martian rover looking for biosignatures of past or present life. Other types of chips could be placed in handheld devices used to monitor microbes in water or to quickly conduct medical tests on astronauts. (NASA/MSFC/D.Stoffer)

  16. How to speak the same language with European innovation-policy in terms of living labs? Kuidas innovatsioonipoliitikas eluslaborite (living labs kontekstis Euroopaga sama keelt rääkida?

    Directory of Open Access Journals (Sweden)

    Ave Lepik

    2013-01-01

    Full Text Available A Living Lab is a user driven open innovation ecosystem, which combines consumers, firms and public sector. It is a rather new innovation methodology, which steadily gains stronger acceptance and becomes a significant innovation policy’s instrument in many countries. This article provides suggestions and conceptual framework for the applying living lab as the innovation policy instrument in the framework of national innovation-system in small countries. In the countries with the total lack or very limited experience about using the living labs the introduction of living lab approach requires answering several important questions. The paper is focused on the identification of potential areas of using living labs approach as well highlighting also potential obstacles in the process of its application in Estonia

  17. Open Chemistry: Realizing Open Data, Open Standards, and Open Source

    OpenAIRE

    Hanwell, Marcus; Harris, Chris; Lonie, David; Lutz, Kyle; Cole, David

    2012-01-01

    The Blue Obelisk has brought together the computational chemistry community and those who are passionate about Open Chemistry and realizing the promise of Open Data, Open Standards, and Open Software (ODOSOS); the three pillars the group promotes. We will present current work that has taken place over the past five years, which is inspired by these pillars, and present plans for future work.The group is actively engaged in multiple open source projects that rely on and promote open standards ...

  18. Designing Viable Business Models for Living Labs

    Directory of Open Access Journals (Sweden)

    Bernhard R. Katzy

    2012-09-01

    Full Text Available Over 300 regions have integrated the concept of living labs into their economic development strategy since 2006, when the former Finnish Prime Minister Esko Aho launched the living lab innovation policy initiative during his term of European presidency. Despite motivating initial results, however, success cases of turning research into usable new products and services remain few and uncertainty remains on what living labs actually do and contribute. This practitioner-oriented article presents a business excellence model that shows processes of idea creation and team mobilization, new product development, user involvement, and entrepreneurship through which living labs deliver high-potential investment opportunities. Customers of living labs are identified as investors such as venture capitalists or industrial firms because living labs can generate revenue from them to create their own sustainable business model. The article concludes that living labs provide extensive support “lab” infrastructure and that it remains a formidable challenge to finance it, which calls for a more intensive debate.

  19. Baseball Physics: A New Mechanics Lab

    Science.gov (United States)

    Wagoner, Kasey; Flanagan, Daniel

    2018-05-01

    The game of baseball provides an interesting laboratory for experimenting with mechanical phenomena (there are many good examples in The Physics Teacher, available on Professor Alan Nathan's website, and discussed in Physics of Baseball & Softball). We have developed a lab, for an introductory-level physics course, that investigates many of these phenomena. The lab uses inexpensive, readily available equipment such as wooden baseball bats, baseballs, and actual Major League Baseball data. By the end of the lab, students have revisited many concepts they learned earlier in the semester and come away with an understanding of how to put seemingly disparate ideas together to analyze a fun sport.

  20. Lab-on-a-chip technologies for single-molecule studies.

    Science.gov (United States)

    Zhao, Yanhui; Chen, Danqi; Yue, Hongjun; French, Jarrod B; Rufo, Joseph; Benkovic, Stephen J; Huang, Tony Jun

    2013-06-21

    Recent developments on various lab-on-a-chip techniques allow miniaturized and integrated devices to perform on-chip single-molecule studies. Fluidic-based platforms that utilize unique microscale fluidic behavior are capable of conducting single-molecule experiments with high sensitivities and throughputs, while biomolecular systems can be studied on-chip using techniques such as DNA curtains, magnetic tweezers, and solid-state nanopores. The advances of these on-chip single-molecule techniques lead to next-generation lab-on-a-chip devices, such as DNA transistors, and single-molecule real-time (SMRT) technology for rapid and low-cost whole genome DNA sequencing. In this Focus article, we will discuss some recent successes in the development of lab-on-a-chip techniques for single-molecule studies and expound our thoughts on the near future of on-chip single-molecule studies.

  1. Labs not in a lab: A case study of instructor and student perceptions of an online biology lab class

    Science.gov (United States)

    Doiron, Jessica Boyce

    Distance learning is not a new phenomenon but with the advancement in technology, the different ways of delivering an education have increased. Today, many universities and colleges offer their students the option of taking courses online instead of sitting in a classroom on campus. In general students like online classes because they allow for flexibility, the comfort of sitting at home, and the potential to save money. Even though there are advantages to taking online classes, many students and instructors still debate the effectiveness and quality of education in a distant learning environment. Many universities and colleges are receiving pressure from students to offer more and more classes online. Research argues for both the advantages and disadvantages of online classes and stresses the importance of colleges and universities weighing both sides before deciding to adopt an online class. Certain classes may not be suitable for online instruction and not all instructors are suitable to teach online classes. The literature also reveals that there is a need for more research on online biology lab classes. With the lack of information on online biology labs needed by science educators who face the increasing demand for online biology labs, this case study hopes to provide insight into the use of online biology lab classes and the how students and an instructor at a community college in Virginia perceive their online biology lab experience as well as the effectiveness of the online labs.

  2. The Design:Lab as platform in participatory design research

    DEFF Research Database (Denmark)

    Binder, Thomas; Brandt, Eva

    2008-01-01

    The notion of laboratory or simply 'lab' has become popular in recent years in areas outside science and technology development. Learning Labs, Innovation Labs, Usability Labs, Media and Communication Labs and even Art Labs designate institutions or fora dedicated to change and experimentation...... as others have frequently used other metaphors like workshop, studio or atelier in design research. In this article we will argue that the laboratory metaphor is particularly suitable and useful for the design:lab, and we will give examples of how we have worked with the design:lab as a platform...

  3. MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis.

    Science.gov (United States)

    Klepper, Kjetil; Drabløs, Finn

    2013-01-16

    Traditional methods for computational motif discovery often suffer from poor performance. In particular, methods that search for sequence matches to known binding motifs tend to predict many non-functional binding sites because they fail to take into consideration the biological state of the cell. In recent years, genome-wide studies have generated a lot of data that has the potential to improve our ability to identify functional motifs and binding sites, such as information about chromatin accessibility and epigenetic states in different cell types. However, it is not always trivial to make use of this data in combination with existing motif discovery tools, especially for researchers who are not skilled in bioinformatics programming. Here we present MotifLab, a general workbench for analysing regulatory sequence regions and discovering transcription factor binding sites and cis-regulatory modules. MotifLab supports comprehensive motif discovery and analysis by allowing users to integrate several popular motif discovery tools as well as different kinds of additional information, including phylogenetic conservation, epigenetic marks, DNase hypersensitive sites, ChIP-Seq data, positional binding preferences of transcription factors, transcription factor interactions and gene expression. MotifLab offers several data-processing operations that can be used to create, manipulate and analyse data objects, and complete analysis workflows can be constructed and automatically executed within MotifLab, including graphical presentation of the results. We have developed MotifLab as a flexible workbench for motif analysis in a genomic context. The flexibility and effectiveness of this workbench has been demonstrated on selected test cases, in particular two previously published benchmark data sets for single motifs and modules, and a realistic example of genes responding to treatment with forskolin. MotifLab is freely available at http://www.motiflab.org.

  4. Virtual labs in Leonardo da Vinci

    Directory of Open Access Journals (Sweden)

    Stanislaw Nagy

    2006-10-01

    Full Text Available This paper discusses the problem of virtual lab capabilities in the e-learning. Using combination of web conferencing and "virtual labs" capabilities, a new quality distance learning teaching is now in preparation and will be included in the course teaching to produce interactive, online simulations for the natural gas engineering studies. The activities are designed to enhance the existing curriculum and to include online assessments. A special care is devoted to the security problem between a server and a client computer. Several examples of the virtual labs related to the PVT thermodynamics, fluid flow, the natural gas well-testing, and thev gas network flow are prepared and tested. A major challenge for the 'CELGAS' system is in managing the delicate balance between the student collaboration and the isolation. Students may be encouraged to collaborate and work with each other, simulating their exploration of the lab material.

  5. LAB building a home for scientists

    CERN Document Server

    Fishman, Mark C

    2017-01-01

    Laboratories are both monasteries and space stations, redolent of the great ideas of generations past and of technologies to propel the future. Yet standard lab design has changed only little over recent years. Here Mark Fishman describes how to build labs as homes for scientists, to accommodate not just their fancy tools, but also their personalities. This richly illustrated book explores the roles of labs through history, from the alchemists of the Middle Ages to the chemists of the 19th and 20th centuries, and to the geneticists and structural biologists of today, and then turns to the special features of the laboratories Fishman helped to design in Cambridge, Shanghai, and Basel. Anyone who works in, or plans to build a lab, will enjoy this book, which will encourage them to think about how this special environment drives or impedes their important work.

  6. Jefferson Lab physics overview: Recent results

    International Nuclear Information System (INIS)

    I review highlights of the Jefferson Lab nucleon structure program. I shall emphasize recent results from experiments exploring the spin structure of the nucleon and from dedicated experiments aimed at accessing the generalized parton distributions (GPDs).

  7. Cockle Temperature Exposure Lab Experiment (2016)

    Data.gov (United States)

    U.S. Environmental Protection Agency — We carried out a lab experiment in which we exposed cockles to a range of air temperatures to simulate the physiological rigors of exposure to sunlight and air at...

  8. GeoLab Sample Handling System

    Data.gov (United States)

    National Aeronautics and Space Administration — This work builds upon the successes in developing and field testing GeoLab as part of the 2010 and 2011 Habitat Demonstration Unit (HDU) and Desert RATS activities....

  9. Photonics and Fiber Optics Processor Lab

    Data.gov (United States)

    Federal Laboratory Consortium — The Photonics and Fiber Optics Processor Lab develops, tests and evaluates high speed fiber optic network components as well as network protocols. In addition, this...

  10. Airborne Low-Frequency Sonar (ALFS) Lab

    Data.gov (United States)

    Federal Laboratory Consortium — The ALFS lab is dedicated to support acoustic data analysis and processing software support to the AN/AQS-22 dipping sonar system. It includes stand-alone Software...

  11. Berkeley Lab Laser Accelerator (BELLA) facility

    Data.gov (United States)

    Federal Laboratory Consortium — The Berkeley Lab Laser Accelerator (BELLA) facility (formerly LOASIS) develops advanced accelerators and radiation sources. High gradient (1-100 GV/m) laser-plasma...

  12. European labs fight back against cuts

    CERN Multimedia

    König, R

    1997-01-01

    Germany's 1997 budget contains cuts amounting to 3.7% in funding of domestic research programs and in contributions to international labs. Contributions will be cut to the European Space Agency, the European Synchrotron facility and CERN.

  13. Generator Inspection Report: Bio - Lab, Inc.

    Science.gov (United States)

    Contains report from Georgia Department of Natural Resources of July 21, 1999 inspection of the Bio - Lab Incorporated Plant 4 in Conyers, Rockdale County, Georgia, reporting that no violations were observed.

  14. Thanatology for Everyone: Developmental Labs and Workshops

    Science.gov (United States)

    O'Connell, Walter E.; And Others

    1977-01-01

    In an effort to "treat" the growing death concerns of many medical staffs, an experiential death and dying lab was created. Its evolution to meet changing needs is discussed, as well as future potential for work in this area. (Author)

  15. PLC Support Software at Jefferson Lab

    Energy Technology Data Exchange (ETDEWEB)

    P. Chevtsov; S. Higgins; S. Schaffner; D. Seidman

    2002-10-01

    Several Automation Direct (DirectNet) Programmable Logic Controllers (PLCs) have been integrated into the accelerator control system at Jefferson Lab. The integration is based on new software that consists of three main parts: a PLC driver with a state machine control block, a device support module, and a common serial driver. The components of new software and experience gained with the use of this software for beam dump systems at Jefferson Lab are presented.

  16. German lab wins linear collider contest

    CERN Multimedia

    Cartlidge, Edwin

    2004-01-01

    Particle physicists have chosen to base the proposed International Linear Collider on superconducting technology developed by an international collaboration centred on the DESY lab in Germany. The superconducting approach was chosen by an internatinal panel ahead of a rival technology developed at Stanford in the US and the KEK lab in Japan. The eagerly-awaited decision was announced at the International Conference on High Energy Physics in Beijing today (½ page)

  17. S'Cool LAB Summer CAMP 2017

    CERN Multimedia

    Woithe, Julia

    2017-01-01

    The S’Cool LAB Summer CAMP is an opportunity for high-school students (aged 16-19) from all around the world to spend 2 weeks exploring the fascinating world of particle physics. The 24 selected participants spend their summer at S’Cool LAB, CERN’s hands-on particle physics learning laboratory, for an epic programme of lectures and tutorials, team research projects, visits of CERN’s research installations, and social activities.

  18. Technology Roadmap: Lab-on-a-Chip

    OpenAIRE

    Pattharaporn Suntharasaj; Tugrul U Daim

    2010-01-01

    With the integration of microfluidic and MEMS technologies, biochips such as the lab-on-a-chip (LOC) devices are at the brink of revolutionizing the medical disease diagnostics industries. Remarkable advancements in the biochips industry are making products resembling Star Trek.s "tricorder" and handheld medical scanners a reality. Soon, doctors can screen for cancer at the molecular level without costly and cumbersome equipments, and discuss treatment plans based on immediate lab results. Th...

  19. LabVIEW Support at CERN

    CERN Multimedia

    HR Department

    2010-01-01

    Since the beginning of 2009, due to the CERN restructuring, LabVIEW support moved from the IT to the EN department, joining the Industrial Controls and Electronics Group (ICE). LabVIEW support has been merged with the Measurement, Test and Analysis (MTA) section which, using LabVIEW, has developed most of the measurement systems to qualify the LHC magnets and components over the past 10 years. The post mortem analysis for the LHC hardware commissioning has also been fully implemented using LabVIEW, customised into a framework, called RADE, for CERN needs. The MTA section has started with a proactive approach sharing its tools and experience with the CERN LabVIEW community. Its framework (RADE) for CERN integrated application development has been made available to the users. Courses on RADE have been integrated into the standard National Instruments training program at CERN. RADE and LabVIEW support were merged together in 2010 on a single email address:labview.support@cern.ch For more information please...

  20. Scaffolding students’ reflective dialogues in the chemistry lab: challenging the cookbook

    DEFF Research Database (Denmark)

    Nielsen, Birgitte Lund; Hougaard, Rikke Frøhlich

    -scaffolding of students’ activities and dialogues, in order to stimulate them to work at higher cognitive levels. A specific lab-exercise in the course Macroscopic Physical Chemistry was redesigned with the aim of stimulating students’ metacognition both before and during the experimental work. The redesign included...... a prelab task, related to planning experimental work and explaining theory, and a definite level of openness in relation to the choice of data points. The analysis of activities and dialogue in the laboratory indicated that this rather simple redesign of a lab exercise successfully macro-scaffolded student...

  1. Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium.

    Science.gov (United States)

    Machado, Henrique; Gram, Lone

    2017-01-01

    Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur , amino-acid usage, ANI), which allowed us to identify two misidentified strains. Genome analyses also revealed occurrence of higher and lower GC content clades, correlating with phylogenetic clusters. Pan- and core-genome analysis revealed the conservation of 25% of the genome throughout the genus, with a large and open pan-genome. The major source of genomic diversity could be traced to the smaller chromosome and plasmids. Several of the physiological traits studied in the genus did not correlate with phylogenetic data. Since horizontal gene transfer (HGT) is often suggested as a source of genetic diversity and a potential driver of genomic evolution in bacterial species, we looked into evidence of such in Photobacterium genomes. Genomic islands were the source of genomic differences between strains of the same species. Also, we found transposase genes and CRISPR arrays that suggest multiple encounters with foreign DNA. Presence of genomic exchange traits was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.

  2. Genomic research perspectives in Kazakhstan

    Directory of Open Access Journals (Sweden)

    Ainur Akilzhanova

    2014-01-01

    Full Text Available Introduction: Technological advancements rapidly propel the field of genome research. Advances in genetics and genomics such as the sequence of the human genome, the human haplotype map, open access databases, cheaper genotyping and chemical genomics, have transformed basic and translational biomedical research. Several projects in the field of genomic and personalized medicine have been conducted at the Center for Life Sciences in Nazarbayev University. The prioritized areas of research include: genomics of multifactorial diseases, cancer genomics, bioinformatics, genetics of infectious diseases and population genomics. At present, DNA-based risk assessment for common complex diseases, application of molecular signatures for cancer diagnosis and prognosis, genome-guided therapy, and dose selection of therapeutic drugs are the important issues in personalized medicine. Results: To further develop genomic and biomedical projects at Center for Life Sciences, the development of bioinformatics research and infrastructure and the establishment of new collaborations in the field are essential. Widespread use of genetic tools will allow the identification of diseases before the onset of clinical symptoms, the individualization of drug treatment, and could induce individual behavioral changes on the basis of calculated disease risk. However, many challenges remain for the successful translation of genomic knowledge and technologies into health advances, such as medicines and diagnostics. It is important to integrate research and education in the fields of genomics, personalized medicine, and bioinformatics, which will be possible with opening of the new Medical Faculty at Nazarbayev University. People in practice and training need to be educated about the key concepts of genomics and engaged so they can effectively apply their knowledge in a matter that will bring the era of genomic medicine to patient care. This requires the development of well

  3. Assessing Usage and Maximizing Finance Lab Impact: A Case Exploration

    Science.gov (United States)

    Noguera, Magdy; Budden, Michael Craig; Silva, Alberto

    2011-01-01

    This paper reports the results of a survey conducted to assess students' usage and perceptions of a finance lab. Finance labs differ from simple computer labs as they typically contain data boards, streaming market quotes, terminals and software that allow for real-time financial analyses. Despite the fact that such labs represent significant and…

  4. Genomics and fish adaptation

    Directory of Open Access Journals (Sweden)

    Agostinho Antunes

    2015-12-01

    Full Text Available The completion of the human genome sequencing in 2003 opened a new perspective into the importance of whole genome sequencing projects, and currently multiple species are having their genomes completed sequenced, from simple organisms, such as bacteria, to more complex taxa, such as mammals. This voluminous sequencing data generated across multiple organisms provides also the framework to better understand the genetic makeup of such species and related ones, allowing to explore the genetic changes underlining the evolution of diverse phenotypic traits. Here, recent results from our group retrieved from comparative evolutionary genomic analyses of varied fish species will be considered to exemplify how gene novelty and gene enhancement by positive selection might have been determinant in the success of adaptive radiations into diverse habitats and lifestyles.

  5. GeneLab Analysis Working Group Kick-Off Meeting

    Science.gov (United States)

    Costes, Sylvain V.

    2018-01-01

    Goals to achieve for GeneLab AWG - GL vision - Review of GeneLab AWG charter Timeline and milestones for 2018 Logistics - Monthly Meeting - Workshop - Internship - ASGSR Introduction of team leads and goals of each group Introduction of all members Q/A Three-tier Client Strategy to Democratize Data Physiological changes, pathway enrichment, differential expression, normalization, processing metadata, reproducibility, Data federation/integration with heterogeneous bioinformatics external databases The GLDS currently serves over 100 omics investigations to the biomedical community via open access. In order to expand the scope of metadata record searches via the GLDS, we designed a metadata warehouse that collects and updates metadata records from external systems housing similar data. To demonstrate the capabilities of federated search and retrieval of these data, we imported metadata records from three open-access data systems into the GLDS metadata warehouse: NCBI's Gene Expression Omnibus (GEO), EBI's PRoteomics IDEntifications (PRIDE) repository, and the Metagenomics Analysis server (MG-RAST). Each of these systems defines metadata for omics data sets differently. One solution to bridge such differences is to employ a common object model (COM) to which each systems' representation of metadata can be mapped. Warehoused metadata records are then transformed at ETL to this single, common representation. Queries generated via the GLDS are then executed against the warehouse, and matching records are shown in the COM representation (Fig. 1). While this approach is relatively straightforward to implement, the volume of the data in the omics domain presents challenges in dealing with latency and currency of records. Furthermore, the lack of a coordinated has been federated data search for and retrieval of these kinds of data across other open-access systems, so that users are able to conduct biological meta-investigations using data from a variety of sources. Such meta

  6. Particle physicists want to expand open access

    CERN Multimedia

    Kaiser, Jocelyn

    2006-01-01

    "Particle physicists have come up with a novel way to promote free, immediate access to journal articles. Led by CERN, the giant lab near Geneva, Switzerland, thay want to raise at lesat $6 million a year to begin buying open access to all published papers in their field." (1/2 page)

  7. Particle physicists want to expand open access

    CERN Document Server

    Kaiser, Jocelyn

    2006-01-01

    "Particle physicists have come up with a novel way to promote free, immediate access to journal articles. Led by CERN, the gian lab near Geneva, Switzerland, they want to raise at least $6 million a year to begin buying open access to all published papers in their field." (1 page)

  8. eLabEL: Technology-supported living labs in primary care

    NARCIS (Netherlands)

    Vermeulen, Joan; Huygens, Martine; de Witte, Luc P.; Oude Nijeweme-d'Hollosy, Wendeline; Swinkels, Ilse; van Velsen, Lex Stefan; Jansen, Yvonne

    2015-01-01

    Telecare technologies and eHealth applications can support patients and care professionals. However, these technologies are currently not being implemented in primary care. The eLabEL project aims to contribute to a solution for this problem by establishing Living Labs in which patients, healthcare

  9. Are Virtual Labs as Effective as Hands-on Labs for Undergraduate Physics? A Comparative Study at Two Major Universities

    Science.gov (United States)

    Darrah, Marjorie; Humbert, Roxann; Finstein, Jeanne; Simon, Marllin; Hopkins, John

    2014-01-01

    Most physics professors would agree that the lab experiences students have in introductory physics are central to the learning of the concepts in the course. It is also true that these physics labs require time and money for upkeep, not to mention the hours spent setting up and taking down labs. Virtual physics lab experiences can provide an…

  10. Are Remote Labs Worth the Cost? Insights From a Study of Student Perceptions of Remote Labs

    Directory of Open Access Journals (Sweden)

    David Uttal

    2011-05-01

    Full Text Available Remote online laboratories enable students to conduct scientific investigations using real experimental equipment. However, scaling up remote labs may require significant costs in purchasing and maintaining expensive equipment compared to scaling simulated labs. While these costs are a consequence of using physical equipment, we argue that there are unique educational advantages to remote labs. This paper presents the results of a preliminary study of student perceptions of a remote lab in comparison to an identical lab experience with simulated data. The findings reveal several intriguing themes that highlight the pedagogical value of remote laboratories. In addition, we provide recommendations for the design and pedagogy of online laboratory experiences based on our findings.

  11. Co-Governing Smart Cities Through Living Labs. Top Evidences From EU

    Directory of Open Access Journals (Sweden)

    Francesco BIFULCO

    2017-02-01

    Full Text Available Our purpose is to identify the relevance of participative governance in urban areas characterized by smart cities projects, especially those implementing Living Labs initiatives as real-life settings to develop services innovation and enhance engagement of all urban stakeholders. A research on the three top smart cities in Europe – i.e. Amsterdam, Barcelona and Helsinki – is proposed through a content analysis with NVivo on the offi cial documents issued by the project partners (2012-2015 to investigate their Living Lab initiatives. The results show the increasing usefulness of Living Labs for the development of more inclusive smart cities projects in which public and private actors, and people, collaborate in innovation processes and governance for the co-creation of new services, underlining the importance of the open and ecosystem-oriented approach for smart cities.

  12. Swabs to genomes: a comprehensive workflow

    Directory of Open Access Journals (Sweden)

    Madison I. Dunitz

    2015-05-01

    Full Text Available The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become much easier for research labs with access to standard molecular biology and computational tools. However, there are a confusing variety of options available for DNA library preparation and sequencing, and inexperience with bioinformatics can pose a significant barrier to entry for many who may be interested in microbial genomics. The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab to a published microbial genome; empowering even a lab or classroom with limited resources and bioinformatics experience to perform it.

  13. Genelab: Scientific Partnerships and an Open-Access Database to Maximize Usage of Omics Data from Space Biology Experiments

    Science.gov (United States)

    Reinsch, S. S.; Galazka, J..; Berrios, D. C; Chakravarty, K.; Fogle, H.; Lai, S.; Bokyo, V.; Timucin, L. R.; Tran, P.; Skidmore, M.

    2016-01-01

    NASA's mission includes expanding our understanding of biological systems to improve life on Earth and to enable long-duration human exploration of space. The GeneLab Data System (GLDS) is NASA's premier open-access omics data platform for biological experiments. GLDS houses standards-compliant, high-throughput sequencing and other omics data from spaceflight-relevant experiments. The GeneLab project at NASA-Ames Research Center is developing the database, and also partnering with spaceflight projects through sharing or augmentation of experiment samples to expand omics analyses on precious spaceflight samples. The partnerships ensure that the maximum amount of data is garnered from spaceflight experiments and made publically available as rapidly as possible via the GLDS. GLDS Version 1.0, went online in April 2015. Software updates and new data releases occur at least quarterly. As of October 2016, the GLDS contains 80 datasets and has search and download capabilities. Version 2.0 is slated for release in September of 2017 and will have expanded, integrated search capabilities leveraging other public omics databases (NCBI GEO, PRIDE, MG-RAST). Future versions in this multi-phase project will provide a collaborative platform for omics data analysis. Data from experiments that explore the biological effects of the spaceflight environment on a wide variety of model organisms are housed in the GLDS including data from rodents, invertebrates, plants and microbes. Human datasets are currently limited to those with anonymized data (e.g., from cultured cell lines). GeneLab ensures prompt release and open access to high-throughput genomics, transcriptomics, proteomics, and metabolomics data from spaceflight and ground-based simulations of microgravity, radiation or other space environment factors. The data are meticulously curated to assure that accurate experimental and sample processing metadata are included with each data set. GLDS download volumes indicate strong

  14. Environment monitoring using LabVIEW

    International Nuclear Information System (INIS)

    Hawtree, J.

    1995-01-01

    A system has been developed for electronically recording and monitoring temperature, humidity, and other environmental variables at the Silicon Detector Facility located in Lab D. The data is collected by LabVIEW software, which runs in the background on an Apple Macintosh. The software is completely portable between Macintosh, MS Windows, and Sun platforms. The hardware includes a Macintosh with 8 MB of RAM; an external ADC-1 analog-to-digital converter that uses a serial port; LabVIEW software; temperature sensors; humidity sensors; and other voltage/current sensing devices. ADC values are converted to ASCII strings and entered into files which are read over Ethernet. Advantages include automatic logging, automatic recovery after power interruptions, and the availability of stand-alone applications for other locations with inexpensive software and hardware

  15. A Moodle extension to book online labs

    Directory of Open Access Journals (Sweden)

    Antonio C. Cardoso

    2005-11-01

    Full Text Available The social constructivist philosophy of Moodle makes it an excellent choice to deliver e-learning contents that require collaborative activities, such as those that are associated with online labs. In the case of online labs that enable web access to real devices (remote workbenches, access time should be reserved beforehand. A booking tool will avoid access conflicts and at the same time will help the students to organise their time and activities. This paper presents a Moodle extension that was developed within the Leonardo da Vinci MARVEL project, with the objective of meeting this requirement. The booking tool presented enables resource sharing in general and may be used to organise access to any type of scarce resources, such as to online labs and to the videoconferencing rooms that are needed to support collaborative activities.

  16. Collaborative Creation of a Lab Rubric

    Directory of Open Access Journals (Sweden)

    Carrie Miller-DeBoer

    2011-03-01

    Full Text Available While there are a number of tested rubrics in circulation, our task was to intervene in a particular situation: the lead professor was concerned because her graduate teaching assistants held negative views about student performance on the lab reports. GTAs found poor products frustrating, and admitted that their grading was thus superficial and provided no feedback to students. Specifically, GTAs did not feel equipped to evaluate writing and, as a result, simply graded on steps completed in the lab process.We have a rubric now for an Introduction to Zoology lab that could be submitted here as a pretty darn good rubric for other instructors to use. But the intent of our “Tips and Tools” is to describe the actual creation of the rubric. We believe the active “real time” development of the rubric carried as much or more value than the finished product.

  17. LabVIEW Real-Time

    CERN Multimedia

    CERN. Geneva; Flockhart, Ronald Bruce; Seppey, P

    2003-01-01

    With LabVIEW Real-Time, you can choose from a variety of RT Series hardware. Add a real-time data acquisition component into a larger measurement and automation system or create a single stand-alone real-time solution with data acquisition, signal conditioning, motion control, RS-232, GPIB instrumentation, and Ethernet connectivity. With the various hardware options, you can create a system to meet your precise needs today, while the modularity of the system means you can add to the solution as your system requirements grow. If you are interested in Reliable and Deterministic systems for Measurement and Automation, you will profit from this seminar. Agenda: Real-Time Overview LabVIEW RT Hardware Platforms - Linux on PXI Programming with LabVIEW RT Real-Time Operating Systems concepts Timing Applications Data Transfer

  18. Open Content in Open Context

    Science.gov (United States)

    Kansa, Sarah Whitcher; Kansa, Eric C.

    2007-01-01

    This article presents the challenges and rewards of sharing research content through a discussion of Open Context, a new open access data publication system for field sciences and museum collections. Open Context is the first data repository of its kind, allowing self-publication of research data, community commentary through tagging, and clear…

  19. Genomics-assisted breeding in fruit trees

    OpenAIRE

    Iwata, Hiroyoshi; Minamikawa, Mai F.; Kajiya-Kanegae, Hiromi; Ishimori, Motoyuki; Hayashi, Takeshi

    2016-01-01

    Recent advancements in genomic analysis technologies have opened up new avenues to promote the efficiency of plant breeding. Novel genomics-based approaches for plant breeding and genetics research, such as genome-wide association studies (GWAS) and genomic selection (GS), are useful, especially in fruit tree breeding. The breeding of fruit trees is hindered by their long generation time, large plant size, long juvenile phase, and the necessity to wait for the physiological maturity of the pl...

  20. Out-of-plane microvalves for whole blood separation on lab-on-a-CD

    International Nuclear Information System (INIS)

    Li, Tingjie; Zhang, Limin; Leung, Kar Man; Yang, Jun

    2010-01-01

    The emergence of lab-on-a-CD technology provides a centrifugal and compact platform for high throughput blood analysis in point-of-care (POC) diagnostics. Blood separation of the whole blood is the first step for clinical blood diagnosis. This paper describes a novel design of an out-of-plane microvalve that enables high performance of whole blood separation on lab-on-a-CD centrifugal devices. In our lab-on-a-CD design, blood cells and plasma are redistributed into a downstream sedimentation reservoir and an upstream supernatant reservoir, respectively, when the device spins. By tuning the rotational speed, the 'close' or 'open' status of an out-of-plane microvalve embedded in the lab-on-a-CD device is controlled to isolate these two reservoirs. Compared with a similar design but without the out-of-plane microvalve, this novel microvalve structure can effectively prevent blood cells from diffusing back to the supernatant reservoir containing pure plasma, and thus improve the performance of blood separation as well as subsequent blood analysis. We demonstrate that the lab-on-a-CD device with out-of-plane microvalves can achieve 99.9% plasma purity and 96 ± 0.5% plasma yield for the whole blood. Because of its simple structure and easily controlled working mechanism, the out-of-plane microvalve not only leads to high performance of whole blood separation, but also makes the manufacturing of this type of lab-on-a-CD device easy and inexpensive. If integrated into some existing lab-on-a-CD devices, the out-of-plane microvalve may also help improve their performance

  1. Out-of-plane microvalves for whole blood separation on lab-on-a-CD

    Science.gov (United States)

    Li, Tingjie; Zhang, Limin; Leung, Kar Man; Yang, Jun

    2010-10-01

    The emergence of lab-on-a-CD technology provides a centrifugal and compact platform for high throughput blood analysis in point-of-care (POC) diagnostics. Blood separation of the whole blood is the first step for clinical blood diagnosis. This paper describes a novel design of an out-of-plane microvalve that enables high performance of whole blood separation on lab-on-a-CD centrifugal devices. In our lab-on-a-CD design, blood cells and plasma are redistributed into a downstream sedimentation reservoir and an upstream supernatant reservoir, respectively, when the device spins. By tuning the rotational speed, the 'close' or 'open' status of an out-of-plane microvalve embedded in the lab-on-a-CD device is controlled to isolate these two reservoirs. Compared with a similar design but without the out-of-plane microvalve, this novel microvalve structure can effectively prevent blood cells from diffusing back to the supernatant reservoir containing pure plasma, and thus improve the performance of blood separation as well as subsequent blood analysis. We demonstrate that the lab-on-a-CD device with out-of-plane microvalves can achieve 99.9% plasma purity and 96 ± 0.5% plasma yield for the whole blood. Because of its simple structure and easily controlled working mechanism, the out-of-plane microvalve not only leads to high performance of whole blood separation, but also makes the manufacturing of this type of lab-on-a-CD device easy and inexpensive. If integrated into some existing lab-on-a-CD devices, the out-of-plane microvalve may also help improve their performance.

  2. Digital Design with KP-Lab

    Directory of Open Access Journals (Sweden)

    D. Ponta

    2007-08-01

    Full Text Available KP-Lab is an EU Integrated Project envisioning a learning system that facilitates innovative practices of sharing, creating and working with knowledge in education and workplaces. The project exploits a novel pedagogical view, the knowledge-creation metaphor of learning. According to such “trialogical” approach, cognition arises through collaborative work in systematically developing shared “knowledge artefacts”, such as concepts, plans, material products, or social practices. The paper presents the plan of a pilot course to test the KP-Lab methodologies and tools in the field of Digital Design.

  3. [Semiotic Studies Lab for Patient Care Interactions].

    Science.gov (United States)

    Nunes, Dulce Maria; Portella, Jean Cristtus; Bianchi e Silva, Laura

    2011-12-01

    The aim of this experience report is to present the Semiotic Studies Lab for Patient Care Interactions (Laboratório de Estudos Semióticos nas Interações de Cuidado - LESIC). The lab was set up at the Nursing School of the Federal University of Rio Grande do Sul (UFRGS), Brazil in 2010. It has the purpose of providing didactic and pedagogical updates, based on the Theory developed by the Paris School of Semiotics, that enable the increase of knowledge and interactive/observational skills regarding the nature and mastery of human care.

  4. Boosting Big National Lab Data

    Energy Technology Data Exchange (ETDEWEB)

    Kleese van Dam, Kerstin [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2013-02-21

    Introduction: Big data. Love it or hate it, solving the world’s most intractable problems requires the ability to make sense of huge and complex sets of data and do it quickly. Speeding up the process – from hours to minutes or from weeks to days – is key to our success. One major source of such big data are physical experiments. As many will know, these physical experiments are commonly used to solve challenges in fields such as energy security, manufacturing, medicine, pharmacology, environmental protection and national security. Experiments use different instruments and sensor types to research for example the validity of new drugs, the base cause for diseases, more efficient energy sources, new materials for every day goods, effective methods for environmental cleanup, the optimal ingredients composition for chocolate or determine how to preserve valuable antics. This is done by experimentally determining the structure, properties and processes that govern biological systems, chemical processes and materials. The speed and quality at which we can acquire new insights from experiments directly influences the rate of scientific progress, industrial innovation and competitiveness. And gaining new groundbreaking insights, faster, is key to the economic success of our nations. Recent years have seen incredible advances in sensor technologies, from house size detector systems in large experiments such as the Large Hadron Collider and the ‘Eye of Gaia’ billion pixel camera detector to high throughput genome sequencing. These developments have led to an exponential increase in data volumes, rates and variety produced by instruments used for experimental work. This increase is coinciding with a need to analyze the experimental results at the time they are collected. This speed is required to optimize the data taking and quality, and also to enable new adaptive experiments, where the sample is manipulated as it is observed, e.g. a substance is injected into a

  5. Integration of the HTC Vive into the medical platform MeVisLab

    Science.gov (United States)

    Egger, Jan; Gall, Markus; Wallner, Jürgen; de Almeida Germano Boechat, Pedro; Hann, Alexander; Li, Xing; Chen, Xiaojun; Schmalstieg, Dieter

    2017-03-01

    Virtual Reality (VR) is an immersive technology that replicates an environment via computer-simulated reality. VR gets a lot of attention in computer games but has also great potential in other areas, like the medical domain. Examples are planning, simulations and training of medical interventions, like for facial surgeries where an aesthetic outcome is important. However, importing medical data into VR devices is not trivial, especially when a direct connection and visualization from your own application is needed. Furthermore, most researcher don't build their medical applications from scratch, rather they use platforms, like MeVisLab, Slicer or MITK. The platforms have in common that they integrate and build upon on libraries like ITK and VTK, further providing a more convenient graphical interface to them for the user. In this contribution, we demonstrate the usage of a VR device for medical data under MeVisLab. Therefore, we integrated the OpenVR library into MeVisLab as an own module. This enables the direct and uncomplicated usage of head mounted displays, like the HTC Vive under MeVisLab. Summarized, medical data from other MeVisLab modules can directly be connected per drag-and-drop to our VR module and will be rendered inside the HTC Vive for an immersive inspection.

  6. Weak openness and almost openness

    Directory of Open Access Journals (Sweden)

    David A. Rose

    1984-01-01

    Full Text Available Weak openness and almost openness for arbitrary functions between topological spaces are defined as duals to the weak continuity of Levine and the almost continuity of Husain respectively. Independence of these two openness conditions is noted and comparison is made between these and the almost openness of Singal and Singal. Some results dual to those known for weak continuity and almost continuity are obtained. Nearly almost openness is defined and used to obtain an improved link from weak continuity to almost continuity.

  7. Genotyping-By-Sequencing for Plant Genetic Diversity Analysis: A Lab Guide for SNP Genotyping

    Directory of Open Access Journals (Sweden)

    Gregory W. Peterson

    2014-10-01

    Full Text Available Genotyping-by-sequencing (GBS has recently emerged as a promising genomic approach for exploring plant genetic diversity on a genome-wide scale. However, many uncertainties and challenges remain in the application of GBS, particularly in non-model species. Here, we present a GBS protocol we developed and use for plant genetic diversity analysis. It uses two restriction enzymes to reduce genome complexity, applies Illumina multiplexing indexes for barcoding and has a custom bioinformatics pipeline for genotyping. This genetic diversity-focused GBS (gd-GBS protocol can serve as an easy-to-follow lab guide to assist a researcher through every step of a GBS application with five main components: sample preparation, library assembly, sequencing, SNP calling and diversity analysis. Specifically, in this presentation, we provide a brief overview of the GBS approach, describe the gd-GBS procedures, illustrate it with an application to analyze genetic diversity in 20 flax (Linum usitatissimum L. accessions and discuss related issues in GBS application. Following these lab bench procedures and using the custom bioinformatics pipeline, one could generate genome-wide SNP genotype data for a conventional genetic diversity analysis of a non-model plant species.

  8. Plantagora: modeling whole genome sequencing and assembly of plant genomes.

    Directory of Open Access Journals (Sweden)

    Roger Barthelson

    Full Text Available BACKGROUND: Genomics studies are being revolutionized by the next generation sequencing technologies, which have made whole genome sequencing much more accessible to the average researcher. Whole genome sequencing with the new technologies is a developing art that, despite the large volumes of data that can be produced, may still fail to provide a clear and thorough map of a genome. The Plantagora project was conceived to address specifically the gap between having the technical tools for genome sequencing and knowing precisely the best way to use them. METHODOLOGY/PRINCIPAL FINDINGS: For Plantagora, a platform was created for generating simulated reads from several different plant genomes of different sizes. The resulting read files mimicked either 454 or Illumina reads, with varying paired end spacing. Thousands of datasets of reads were created, most derived from our primary model genome, rice chromosome one. All reads were assembled with different software assemblers, including Newbler, Abyss, and SOAPdenovo, and the resulting assemblies were evaluated by an extensive battery of metrics chosen for these studies. The metrics included both statistics of the assembly sequences and fidelity-related measures derived by alignment of the assemblies to the original genome source for the reads. The results were presented in a website, which includes a data graphing tool, all created to help the user compare rapidly the feasibility and effectiveness of different sequencing and assembly strategies prior to testing an approach in the lab. Some of our own conclusions regarding the different strategies were also recorded on the website. CONCLUSIONS/SIGNIFICANCE: Plantagora provides a substantial body of information for comparing different approaches to sequencing a plant genome, and some conclusions regarding some of the specific approaches. Plantagora also provides a platform of metrics and tools for studying the process of sequencing and assembly

  9. Invariants of DNA genomic signals

    Science.gov (United States)

    Cristea, Paul Dan A.

    2005-02-01

    For large scale analysis purposes, the conversion of genomic sequences into digital signals opens the possibility to use powerful signal processing methods for handling genomic information. The study of complex genomic signals reveals large scale features, maintained over the scale of whole chromosomes, that would be difficult to find by using only the symbolic representation. Based on genomic signal methods and on statistical techniques, the paper defines parameters of DNA sequences which are invariant to transformations induced by SNPs, splicing or crossover. Re-orienting concatenated coding regions in the same direction, regularities shared by the genomic material in all exons are revealed, pointing towards the hypothesis of a regular ancestral structure from which the current chromosome structures have evolved. This property is not found in non-nuclear genomic material, e.g., plasmids.

  10. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines when...

  11. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

  12. Open Innovation

    OpenAIRE

    Gassmann, Oliver; Enkel, Ellen

    2006-01-01

    In the past 10 years, numerous interesting articles, book chapters, and books have been written on open innovation strategies in mainly large companies. While closed innovation models have resulted in important breakthrough innovations, many large companies have abandoned vertical integration strategies in recent years and have moved toward a combination of both closed and open innovation models that are used for reaching different sets of innovative goals. The definition of open innovation a...

  13. The Portuguese Contribution for lab2go - pt.lab2go

    Directory of Open Access Journals (Sweden)

    Maria Teresa Restivo

    2013-01-01

    Full Text Available Online experimentation provides innovative and valuable tools for use in academy, in high schools, in industry and in medical areas. It has also become a precious tool for educational and training purposes in any of those areas. Looking at online experimentation as a pure distance learning tool it represents a very efficient way of sharing hands-on capabilities, for example with developing countries. In Portugal a new consortium of online experimentation was created for fostering the national potential, using the Portuguese version of lab2go web platform, pt.lab2go. The authors pretend to demonstrate some of capabilities of the consortium in sharing online labs.

  14. LabVIEW Task Manager v. 1.10.0

    Energy Technology Data Exchange (ETDEWEB)

    2016-12-21

    LabVIEW Task Manager is a debugging tool for use during code development in the National Instruments (NI) LabVIEW® IDE. While providing a dynamic & big-picture view of running code, an expandable/collapsible tree diagram displays detailed information (both static and dynamic) on all VIs in memory, belonging to a selected project/target. It allows for interacting with single or multiple selected VIs at a time, providing significant benefits while troubleshooting, and has the following features: Look & Feel similar to Windows® Task Manager; Selection of project/target; Lists all VIs in memory, grouped by class/library; Searches for and enumerates clones in memory; DropIn VI for including dynamically referenced clones (Clone Beacon); 'Refresh Now' (F5) re-reads all VIs in memory and adds new ones to the tree; Displays VI name, owning class/library, state, path, data size & code size; Displays VI FP Behavior, Reentrant?, Reentrancy Type, Paused? & Highlight?; Sort by any column, including by library name; Filter by item types vi, ctl, and vit/ctt; Filter out vi.lib and global VIs; Tracking of, and ability to toggle, execution highlighting on multiple selected VIs; Tracking of paused VIs with ability to Pause/Resume/TogglePause multiple selected VIs; DropIn VI for pausing on a condition; If a clone initiates a pause, a different pause symbol is used for all clones of that same reentrant original VI; Select multiple VIs and open or close their FPs or BDs; Double Click a VI from the tree to bring the BD (first choice) or FP to front, if already open; and Select multiple top-level VIs and Abort them.

  15. Open innovation

    DEFF Research Database (Denmark)

    Bogers, Marcel; Chesbrough, Henry; Moedas, Carlos

    2018-01-01

    Open innovation is now a widely used concept in academia, business, and policy making. This article describes the state of open innovation at the intersection of research, practice, and policy. It discusses some key trends (e.g., digital transformation), challenges (e.g., uncertainty......), and potential solutions (e.g., EU funding programs) in the context of open innovation and innovation policy. With this background, the authors introduce select papers published in this Special Section of California Management Review that were originally presented at the second annual World Open Innovation...

  16. Open Source Initiative Powers Real-Time Data Streams

    Science.gov (United States)

    2014-01-01

    Under an SBIR contract with Dryden Flight Research Center, Creare Inc. developed a data collection tool called the Ring Buffered Network Bus. The technology has now been released under an open source license and is hosted by the Open Source DataTurbine Initiative. DataTurbine allows anyone to stream live data from sensors, labs, cameras, ocean buoys, cell phones, and more.

  17. Electronics Lab Instructors' Approaches to Troubleshooting Instruction

    Science.gov (United States)

    Dounas-Frazer, Dimitri R.; Lewandowski, H. J.

    2017-01-01

    In this exploratory qualitative study, we describe instructors' self-reported practices for teaching and assessing students' ability to troubleshoot in electronics lab courses. We collected audio data from interviews with 20 electronics instructors from 18 institutions that varied by size, selectivity, and other factors. In addition to describing…

  18. Encouraging Creativity in the Science Lab

    Science.gov (United States)

    Eyster, Linda

    2010-01-01

    Although science is a creative endeavor (NRC 1996, p. 46), many students think they are not encouraged--or even allowed--to be creative in the laboratory. When students think there is only one correct way to do a lab, their creativity is inhibited. Park and Seung (2008) argue for the importance of creativity in science classrooms and for the…

  19. FameLab - Swiss Semi Finals

    CERN Multimedia

    Corinne Pralavorio

    2012-01-01

    Twenty-two young scientists participated in the FameLab semi-final at CERN's Globe of Science and Innovation on 4 February, supported by a large audience and by more than 100 fans following via webcast. A panel of judges chose Lemmer and four other candidates to join five other semi-finalists at the national finals in Zurich on 30 March.

  20. mQoL smart lab

    DEFF Research Database (Denmark)

    De Masi, Alexandre; Ciman, Matteo; Gustarini, Mattia

    2016-01-01

    As a base for hypothesis formulation and testing, accurate, timely and reproducible data collection is a challenge for all researchers. Data collection is especially challenging in uncontrolled environments, outside of the lab and when it involves many collaborating disciplines, where the data mu...

  1. Information at a Cost: A Lab Experiment

    NARCIS (Netherlands)

    P. Robalo (Pedro); R.S. Sayag (Rei)

    2012-01-01

    textabstractThe supposed irrelevance of historical costs for rational decision making has been the subject of much interest in the economic literature. In this paper we explore whether individual decision making under risk is affected by the cost of the supplied information. Outside of the lab, it

  2. Nonverbal Communication and Writing Lab Tutorials.

    Science.gov (United States)

    Claywell, Gina

    Writing labs should utilize the knowledge gained from a variety of fields to enhance further their programs, particularly with regard to the study of nonverbal communication. Regardless of the sincerity and importance of the tutor's suggestions, nonverbal messages often are sent to the student which undermine the session. Various channels of…

  3. Design Lab 2005 : pilk steriilsesse elektrotulevikku

    Index Scriptorium Estoniae

    2005-01-01

    Design Lab kutsub disainereid ja üliõpilasi üle terve maailma tegelema kaugemale tulevikku suunatud visioonidega. 2005. a. konkurss otsis nutikaid ja säästlikke lahendusi, mis võiksid 2020. a. kodudes olla juba juurdunud, keskenduti kodutehnikale

  4. Carleton to oversee $40 million lab grant

    CERN Multimedia

    Singer, Zev

    2003-01-01

    "Carleton University got a major gift yesterday, as the federal government announced the university will oversee a $40-million grant to run the world's deepest underground lab at the Sudbury Neutrino Observatory. Five other universities are partners in the project" (1/2 page).

  5. Displacing Media: LCD LAB Artistic Residency

    Directory of Open Access Journals (Sweden)

    Filipe Pais

    2012-12-01

    Full Text Available This review refers to an artistic residency which took place at LCD LAB -  CAAA at Guimarães, in March, exploring a strategy for media art called Media Displacement. The text introduces the strategy very briefly and describes the residency's organization, structure, processses and the results produced.

  6. Surfactant Adsorption: A Revised Physical Chemistry Lab

    Science.gov (United States)

    Bresler, Marc R.; Hagen, John P.

    2008-01-01

    Many physical chemistry lab courses include an experiment in which students measure surface tension as a function of surfactant concentration. In the traditional experiment, the data are fit to the Gibbs isotherm to determine the molar area for the surfactant, and the critical micelle concentration is used to calculate the Gibbs energy of micelle…

  7. A Hardware Lab Anywhere At Any Time

    Directory of Open Access Journals (Sweden)

    Tobias Schubert

    2004-12-01

    Full Text Available Scientific technical courses are an important component in any student's education. These courses are usually characterised by the fact that the students execute experiments in special laboratories. This leads to extremely high costs and a reduction in the maximum number of possible participants. From this traditional point of view, it doesn't seem possible to realise the concepts of a Virtual University in the context of sophisticated technical courses since the students must be "on the spot". In this paper we introduce the so-called Mobile Hardware Lab which makes student participation possible at any time and from any place. This lab nevertheless transfers a feeling of being present in a laboratory. This is accomplished with a special Learning Management System in combination with hardware components which correspond to a fully equipped laboratory workstation that are lent out to the students for the duration of the lab. The experiments are performed and solved at home, then handed in electronically. Judging and marking are also both performed electronically. Since 2003 the Mobile Hardware Lab is now offered in a completely web based form.

  8. Lab-on a-Chip

    Science.gov (United States)

    2003-01-01

    Helen Cole, the project manager for the Lab-on-a-Chip Applications Development program, and Lisa Monaco, the project scientist for the program, insert a lab on a chip into the Caliper 42 which is specialized equipment that controls processes on commercial chips to support development of lab-on-a-chip applications. The system has special microscopes and imaging systems, so scientists can process and study different types of fluid, chemical, and medical tests conducted on chips. For example, researchers have examined fluorescent bacteria as it flows through the chips' fluid channels or microfluidic capillaries. Researchers at NASA's Marshall Space Flight Center (MSFC) in Huntsville, Alabama, have been studying how the lab-on-a-chip technology can be used for microbial detection, water quality monitoring, and detecting biosignatures of past or present life on Mars. The Marshall Center team is also collaborating with scientists at other NASA centers and at universities to develop custom chip designs for not only space applications, but for many Earth applications, such as for detecting deadly microbes in heating and air systems. (NASA/MSFC/D.Stoffer)

  9. How the genome folds

    Science.gov (United States)

    Lieberman Aiden, Erez

    2012-02-01

    I describe Hi-C, a novel technology for probing the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. Working with collaborators at the Broad Institute and UMass Medical School, we used Hi-C to construct spatial proximity maps of the human genome at a resolution of 1Mb. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes.

  10. LabVIEW A Developer's Guide to Real World Integration

    CERN Document Server

    Fairweather, Ian

    2011-01-01

    LabVIEW(t) has become one of the preeminent platforms for the development of data acquisition and data analysis programs. LabVIEW(t): A Developer's Guide to Real World Integration explains how to integrate LabVIEW into real-life applications. Written by experienced LabVIEW developers and engineers, the book describes how LabVIEW has been pivotal in solving real-world challenges. Each chapter is self-contained and demonstrates the power and simplicity of LabVIEW in various applications, from image processing to solar tracking systems. Many of the chapters explore how exciting new technologies c

  11. Development of an Open Source, Air-Deployable Weather Station

    Science.gov (United States)

    Krejci, A.; Lopez Alcala, J. M.; Nelke, M.; Wagner, J.; Udell, C.; Higgins, C. W.; Selker, J. S.

    2017-12-01

    We created a packaged weather station intended to be deployed in the air on tethered systems. The device incorporates lightweight sensors and parts and runs for up to 24 hours off of lithium polymer batteries, allowing the entire package to be supported by a thin fiber. As the fiber does not provide a stable platform, additional data (pitch and roll) from typical weather parameters (e.g. temperature, pressure, humidity, wind speed, and wind direction) are determined using an embedded inertial motion unit. All designs are open sourced including electronics, CAD drawings, and descriptions of assembly and can be found on the OPEnS lab website at http://www.open-sensing.org/lowcost-weather-station/. The Openly Published Environmental Sensing Lab (OPEnS: Open-Sensing.org) expands the possibilities of scientific observation of our Earth, transforming the technology, methods, and culture by combining open-source development and cutting-edge technology. New OPEnS labs are now being established in India, France, Switzerland, the Netherlands, and Ghana.

  12. In praise of open software

    CERN Multimedia

    2000-01-01

    Much scientific software is proprietary and beyond the reach of poorer scientific communities. This issue will become critical as companies build bioinformatics tools for genomics. The principal of open-source software needs to be defended by academic research institutions (1/2 p).

  13. Open hardware for open science

    CERN Document Server

    CERN Bulletin

    2011-01-01

    Inspired by the open source software movement, the Open Hardware Repository was created to enable hardware developers to share the results of their R&D activities. The recently published CERN Open Hardware Licence offers the legal framework to support this knowledge and technology exchange.   Two years ago, a group of electronics designers led by Javier Serrano, a CERN engineer, working in experimental physics laboratories created the Open Hardware Repository (OHR). This project was initiated in order to facilitate the exchange of hardware designs across the community in line with the ideals of “open science”. The main objectives include avoiding duplication of effort by sharing results across different teams that might be working on the same need. “For hardware developers, the advantages of open hardware are numerous. For example, it is a great learning tool for technologies some developers would not otherwise master, and it avoids unnecessary work if someone ha...

  14. Recent lab-on-chip developments for novel drug discovery.

    Science.gov (United States)

    Khalid, Nauman; Kobayashi, Isao; Nakajima, Mitsutoshi

    2017-07-01

    Microelectromechanical systems (MEMS) and micro total analysis systems (μTAS) revolutionized the biochemical and electronic industries, and this miniaturization process became a key driver for many markets. Now, it is a driving force for innovations in life sciences, diagnostics, analytical sciences, and chemistry, which are called 'lab-on-a-chip, (LOC)' devices. The use of these devices allows the development of fast, portable, and easy-to-use systems with a high level of functional integration for applications such as point-of-care diagnostics, forensics, the analysis of biomolecules, environmental or food analysis, and drug development. In this review, we report on the latest developments in fabrication methods and production methodologies to tailor LOC devices. A brief overview of scale-up strategies is also presented together with their potential applications in drug delivery and discovery. The impact of LOC devices on drug development and discovery has been extensively reviewed in the past. The current research focuses on fast and accurate detection of genomics, cell mutations and analysis, drug delivery, and discovery. The current research also differentiates the LOC devices into new terminology of microengineering, like organ-on-a-chip, stem cells-on-a-chip, human-on-a-chip, and body-on-a-chip. Key challenges will be the transfer of fabricated LOC devices from lab-scale to industrial large-scale production. Moreover, extensive toxicological studies are needed to justify the use of microfabricated drug delivery vehicles in biological systems. It will also be challenging to transfer the in vitro findings to suitable and promising in vivo models. WIREs Syst Biol Med 2017, 9:e1381. doi: 10.1002/wsbm.1381 For further resources related to this article, please visit the WIREs website. © 2017 Wiley Periodicals, Inc.

  15. Open Revolution.

    Directory of Open Access Journals (Sweden)

    Sean R Eddy

    2009-03-01

    Full Text Available Sean Eddy reviews "Opening Up Education," a collection of essays that explores how leaders in the "open education movement" intend to exploit digital communications technology, develop innovative and freely redistributable educational methods and resources, and improve education on a global level.

  16. Open Access

    Science.gov (United States)

    Suber, Peter

    2012-01-01

    The Internet lets us share perfect copies of our work with a worldwide audience at virtually no cost. We take advantage of this revolutionary opportunity when we make our work "open access": digital, online, free of charge, and free of most copyright and licensing restrictions. Open access is made possible by the Internet and copyright-holder…

  17. Awakening interest in the natural sciences - BASF's Kids' Labs.

    Science.gov (United States)

    Lang, Cinthia

    2012-01-01

    At BASF's Ludwigshafen headquarters, kids and young adults in grades 1-13 can learn about chemistry in the Kids' Labs. Different programs exist for different levels of knowledge. In the two 'Hands-on Lab H(2)O & Co.' Kids' Labs, students from grades 1-6 explore the secrets of chemistry. BASF Kids' Labs have now been set up in over 30 countries. In Switzerland alone, almost 2,000 students have taken part in the 'Water Loves Chemistry' Kids' Lab since it was started in 2011. In Alsace, 600 students have participated to date. In the Teens' Lab 'Xplore Middle School', middle school students explore five different programs with the themes 'substance labyrinth', 'nutrition', 'coffee, caffeine & co.', 'cosmetics' and 'energy'. Biotechnological methods are the focus of the Teens' Lab 'Xplore Biotech' for students taking basic and advanced biology courses. In the 'Xplore High School' Teens' Lab, chemistry teachers present their own experimental lab instruction for students in basic and advanced chemistry courses. The Virtual Lab has been expanding the offerings of the BASF Kids' Labs since 2011. The online lab was developed by the company for the International Year Of Chemistry and gives kids and young adults the opportunity to do interactive experiments outside of the lab.

  18. Molluscan Evolutionary Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Simison, W. Brian; Boore, Jeffrey L.

    2005-12-01

    In the last 20 years there have been dramatic advances in techniques of high-throughput DNA sequencing, most recently accelerated by the Human Genome Project, a program that has determined the three billion base pair code on which we are based. Now this tremendous capability is being directed at other genome targets that are being sampled across the broad range of life. This opens up opportunities as never before for evolutionary and organismal biologists to address questions of both processes and patterns of organismal change. We stand at the dawn of a new 'modern synthesis' period, paralleling that of the early 20th century when the fledgling field of genetics first identified the underlying basis for Darwin's theory. We must now unite the efforts of systematists, paleontologists, mathematicians, computer programmers, molecular biologists, developmental biologists, and others in the pursuit of discovering what genomics can teach us about the diversity of life. Genome-level sampling for mollusks to date has mostly been limited to mitochondrial genomes and it is likely that these will continue to provide the best targets for broad phylogenetic sampling in the near future. However, we are just beginning to see an inroad into complete nuclear genome sequencing, with several mollusks and other eutrochozoans having been selected for work about to begin. Here, we provide an overview of the state of molluscan mitochondrial genomics, highlight a few of the discoveries from this research, outline the promise of broadening this dataset, describe upcoming projects to sequence whole mollusk nuclear genomes, and challenge the community to prepare for making the best use of these data.

  19. Differences between Lab Completion and Non-Completion on Student Performance in an Online Undergraduate Environmental Science Program

    Science.gov (United States)

    Corsi, Gianluca

    2011-12-01

    Web-based technology has revolutionized the way education is delivered. Although the advantages of online learning appeal to large numbers of students, some concerns arise. One major concern in online science education is the value that participation in labs has on student performance. The purpose of this study was to assess the relationships between lab completion and student academic success as measured by test grades, scientific self-confidence, scientific skills, and concept mastery. A random sample of 114 volunteer undergraduate students, from an online Environmental Science program at the American Public University System, was tested. The study followed a quantitative, non-experimental research design. Paired sample t-tests were used for statistical comparison between pre-lab and post-lab test grades, two scientific skills quizzes, and two scientific self-confidence surveys administered at the beginning and at the end of the course. The results of the paired sample t-tests revealed statistically significant improvements on all post-lab test scores: Air Pollution lab, t(112) = 6.759, p gender were available, regression models were developed. The results indicated weak multiple correlation coefficients and were not statistically significant at alpha = .05. Evidence suggests that labs play a positive role in a student's academic success. It is recommended that lab experiences be included in all online Environmental Science programs, with emphasis on open-ended inquiries, and adoption of online tools to enhance hands-on experiences, such as virtual reality platforms and digital animations. Future research is encouraged to investigate possible correlations between socio-demographic attributes and academic success of students enrolled in online science programs in reference to lab completion.

  20. Ultrafiltration Lactic Acid Bacteria (LAB in mung Beans Broth by Mixed LAB Culture

    Directory of Open Access Journals (Sweden)

    Aspiyanto Aspiyanto

    2014-06-01

    Full Text Available Increasing Lactic Acid Bacteria (LAB concentration in fermented broth of mung beans by mixed culture of Lactobacillus sp. and Streptococcus thermophillus through ultrafiltration (UF (20,000 MWCO at flow rate of ~8.87 L/min, room temperature and pressure 5 and 7 bars for 0, 30, 60, 90 and 120 minutes was performed. The results showed that pressure and time affected on UF performance, total solids, total protein and total number of LAB. Optimal time at pressure 5 bar was reached 60 minutes with flux 11.94 L/m2.hour, total solids 13.9423%, total protein 8.95%, total LAB 6.18 log CFU/mL, Robs of total solids 3.45%, total protein  58.67%, LAB 100% and DC 1.38 folds. The best time at 7 bar was reached 30 minutes with flux 16.16 L/m2.hour, total solids 12.2879%, total protein 4.41%, total LAB 6.04 Log CFU/mL, Robs of total solids 11.98%, total protein 45.76%, LAB 99.5 and DC 1.16 folds.

  1. Vortex-Concept for Radioactivity Release Prevention at NPP: Development of Computational Model of Lab-Scale Experimental Setup

    Energy Technology Data Exchange (ETDEWEB)

    Ullah, Sana; Sung, Yim Man; Park, Jin Soo; Sung Hyung Jin [KAERI, Daejeon (Korea, Republic of)

    2016-05-15

    The experimental validation of the vortex-like air curtain concept and use of an appropriate CFD modelling approach for analyzing the problem becomes crucial. A lab-scale experimental setup is designed to validate the proposed concept and CFD modeling approach as a part of validation process. In this study, a computational model of this lab-scale experiment setup is developed using open source CFD code OpenFOAM. The computational results will be compared with experimental data for validation purposes in future, when experimental data is available. 1) A computation model of a lab-scale experimental setup, designed to validate the concept of artificial vortex-like airflow generation for application to radioactivity dispersion prevention in the event of severe accident, was developed. 2) The mesh sensitivity study was performed and a mesh of about 2 million cells was found to be sufficient for this setup.

  2. CELSTEC Learning Labs: Mobile App Development for Education and Training

    NARCIS (Netherlands)

    Specht, Marcus

    2011-01-01

    Specht, M. (2011). CELSTEC Learning Labs: Mobile App Development for Education and Training. Presentation given in Workshop at CELSTEC Learning Lab for Bluetea. February, 21, 2011, Heerlen, The Netherlands.

  3. Open Source and Open Standards

    NARCIS (Netherlands)

    Koper, Rob

    2006-01-01

    Publication reference: Koper, R. (2008). Open Source and Open Standards. In J. M. Spector, M. Merrill, J. van Merriënboer & M. P. Driscol (Eds.), Handbook of Research on Educational Communications and Technology (3rd ed., pp. 355-368). New York: Routledge.

  4. MarkoLAB: A simulator to study ionic channel's stochastic behavior.

    Science.gov (United States)

    da Silva, Robson Rodrigues; Goroso, Daniel Gustavo; Bers, Donald M; Puglisi, José Luis

    2017-08-01

    Mathematical models of the cardiac cell have started to include markovian representations of the ionic channels instead of the traditional Hodgkin & Huxley formulations. There are many reasons for this: Markov models are not restricted to the idea of independent gates defining the channel, they allow more complex description with specific transitions between open, closed or inactivated states, and more importantly those states can be closely related to the underlying channel structure and conformational changes. We used the LabVIEW ® and MATLAB ® programs to implement the simulator MarkoLAB that allow a dynamical 3D representation of the markovian model of the channel. The Monte Carlo simulation was used to implement the stochastic transitions among states. The user can specify the voltage protocol by setting the holding potential, the step-to voltage and the duration of the stimuli. The most studied feature of a channel is the current flowing through it. This happens when the channel stays in the open state, but most of the time, as revealed by the low open probability values, the channel remains on the inactive or closed states. By focusing only when the channel enters or leaves the open state we are missing most of its activity. MarkoLAB proved to be quite useful to visualize the whole behavior of the channel and not only when the channel produces a current. Such dynamic representation provides more complete information about channel kinetics and will be a powerful tool to demonstrate the effect of gene mutations or drugs on the channel function. MarkoLAB provides an original way of visualizing the stochastic behavior of a channel. It clarifies concepts, such as recovery from inactivation, calcium- versus voltage-dependent inactivation, and tail currents. It is not restricted to ionic channels only but it can be extended to other transporters, such as exchangers and pumps. This program is intended as a didactical tool to illustrate the dynamical behavior of a

  5. Genome Exploitation and Bioinformatics Tools

    Science.gov (United States)

    de Jong, Anne; van Heel, Auke J.; Kuipers, Oscar P.

    Bioinformatic tools can greatly improve the efficiency of bacteriocin screening efforts by limiting the amount of strains. Different classes of bacteriocins can be detected in genomes by looking at different features. Finding small bacteriocins can be especially challenging due to low homology and because small open reading frames (ORFs) are often omitted from annotations. In this chapter, several bioinformatic tools/strategies to identify bacteriocins in genomes are discussed.

  6. ESIP Lab: Supporting Development of Earth Sciences Cyberinfrastructure through Innovation Commons

    Science.gov (United States)

    Burgess, A. B.; Robinson, E.

    2017-12-01

    The Earth Science Information Partners (ESIP) is an open, networked community that brings together science, data and information technology practitioners from across sectors. Participation in ESIP is beneficial because it provides an intellectual commons to expose, gather and enhance in-house capabilities in support of an organization's own mandate. Recently, ESIP has begun to explore piloting activities that have worked in the U.S. in other countries as a way to facilitate international collaboration and cross-pollination. The newly formed ESIP Lab realizes the commons concept by providing a virtual place to come up with with new solutions through facilitated ideation, take that idea to a low stakes development environment and potentially fail, but if successful, expose developing technology to domain experts through a technology evaluation process. The Lab does this by supporting and funding solution-oriented projects that have discrete development periods and associated budgets across organizations and agencies. In addition, the Lab provides access to AWS cloud computing resources, travel support, virtual and in-person collaborative platform for distributed groups and exposure to the ESIP community as an expert pool. This cycle of ideation to incubation to evaluation and ultimately adoption or infusion of Earth sciences cyberinfrastructure empowers the scientific community and has spawned a variety of developments like community-led ontology portals, ideas for W3C prov standard improvement and an evaluation framework that pushes technology forward and aides in infusion. The Lab is one of these concepts that could be implemented in other countries and the outputs of the Lab would be shared as a commons and available across traditional borders. This presentation will share the methods and the outcomes of the Lab and seed ideas for adoption internationally.

  7. Needsfinding in living labs : A structured research approach

    NARCIS (Netherlands)

    Savelkoul, L.E.M.; Peutz, M.

    Living labs enable innovations to be facilitated and implemented quickly and efficiently. A key element of the living lab approach is the active involvement of users. In this article, we examine a structured needsfinding phase of a living lab infrastructure project within the context of bicycle

  8. Experiential Learning of Digital Communication Using LabVIEW

    Science.gov (United States)

    Zhan, Wei; Porter, Jay R.; Morgan, Joseph A.

    2014-01-01

    This paper discusses the design and implementation of laboratories and course projects using LabVIEW in an instrumentation course. The pedagogical challenge is to enhance students' learning of digital communication using LabVIEW. LabVIEW was extensively used in the laboratory sessions, which better prepared students for the course projects. Two…

  9. Introduction to Computing: Lab Manual. Faculty Guide [and] Student Guide.

    Science.gov (United States)

    Frasca, Joseph W.

    This lab manual is designed to accompany a college course introducing students to computing. The exercises are designed to be completed by the average student in a supervised 2-hour block of time at a computer lab over 15 weeks. The intent of each lab session is to introduce a topic and have the student feel comfortable with the use of the machine…

  10. Cassandra - WP400 - final report of living lab 2

    NARCIS (Netherlands)

    Engler, M.; Klievink, A.J.

    2014-01-01

    This CASSANDRA LL2 final deliverable contains all information regarding the CASSANDRA Living Lab Europe – USA via Bremerhaven including information from two intermediate reports (CASSANDRA D4.21 and D4.22) about the very same Living Lab handed in during runtime of the Living Lab. CASSANDRA Living

  11. The NOAO Data Lab PHAT Photometry Database

    Science.gov (United States)

    Olsen, Knut; Williams, Ben; Fitzpatrick, Michael; PHAT Team

    2018-01-01

    We present a database containing both the combined photometric object catalog and the single epoch measurements from the Panchromatic Hubble Andromeda Treasury (PHAT). This database is hosted by the NOAO Data Lab (http://datalab.noao.edu), and as such exposes a number of data services to the PHAT photometry, including access through a Table Access Protocol (TAP) service, direct PostgreSQL queries, web-based and programmatic query interfaces, remote storage space for personal database tables and files, and a JupyterHub-based Notebook analysis environment, as well as image access through a Simple Image Access (SIA) service. We show how the Data Lab database and Jupyter Notebook environment allow for straightforward and efficient analyses of PHAT catalog data, including maps of object density, depth, and color, extraction of light curves of variable objects, and proper motion exploration.

  12. New mission for the national labs

    International Nuclear Information System (INIS)

    Weisman, J.

    1995-01-01

    As a testing moratorium takes hold, the future of the weapons laboratories may lie in a $3 billion package of science projects meant to keep the arsenal reliable-and weapons-designing talents sharp. When President Clinton declared an end to all nuclear testing a month ago, he offered the nation's three weapons laboratories an enormous, expensive pacifier-a $3 billion package of scientific projects to replace testing. The labs swallowed hard, choked back their conviction that explosive testing is the best and cheapest means of ensuring the reliability of the nation's nuclear stockpile, and took the bait. The lab directors duly issued statements embracing the test ban-providing the new program materializes

  13. New mission for the national labs

    Energy Technology Data Exchange (ETDEWEB)

    Weisman, J.

    1995-10-06

    As a testing moratorium takes hold, the future of the weapons laboratories may lie in a $3 billion package of science projects meant to keep the arsenal reliable-and weapons-designing talents sharp. When President Clinton declared an end to all nuclear testing a month ago, he offered the nation`s three weapons laboratories an enormous, expensive pacifier-a $3 billion package of scientific projects to replace testing. The labs swallowed hard, choked back their conviction that explosive testing is the best and cheapest means of ensuring the reliability of the nation`s nuclear stockpile, and took the bait. The lab directors duly issued statements embracing the test ban-providing the new program materializes.

  14. Implementation of a Mobile Accessible Remote Lab

    Directory of Open Access Journals (Sweden)

    Danilo Garbi Zutin

    2008-07-01

    Full Text Available The purpose of the proposed research is to designand implement a LabVIEW-based remote lab client to runon a TCP/IP enabled PDA (Personal Digital Assistantdevice, thus teaching using this wireless m-learning systemwill not be limited by time and location. In addition,resources and equipments can be integrated and shared tothe extent that critically events can be monitored andhandled in time. An environment will be created to trainstudents to handle factory automation, data acquisition,data management, and manufacturing processes usingmobile devices. Furthermore, the integration and sharing oflab equipments via the Internet is a kind of teachingenvironment which promotes learning interests andefficiency using mobile devices.

  15. Technology Roadmap: Lab-on-a-Chip

    Directory of Open Access Journals (Sweden)

    Pattharaporn Suntharasaj

    2010-04-01

    Full Text Available With the integration of microfluidic and MEMS technologies, biochips such as the lab-on-a-chip (LOC devices are at the brink of revolutionizing the medical disease diagnostics industries. Remarkable advancements in the biochips industry are making products resembling Star Trek.s "tricorder" and handheld medical scanners a reality. Soon, doctors can screen for cancer at the molecular level without costly and cumbersome equipments, and discuss treatment plans based on immediate lab results. This paper develops a roadmap for a hypothetical company (XI which is seeking to be successful in this market. The roadmapping process starts with gathering data through literature research and expert opinions, and progress through defining the market/product/technology layers, linking and integrating these layers, and finally creating a labon-a-chip for disease diagnostics technology roadmap.

  16. Lab-on-a-Chip Multiplex Assays.

    Science.gov (United States)

    Peter, Harald; Wienke, Julia; Bier, Frank F

    2017-01-01

    Lab-on-a-chip multiplex assays allow a rapid identification of multiple parameters in an automated manner. Here we describe a lab-based preparation followed by a rapid and fully automated DNA microarray hybridization and readout in less than 10 min using the Fraunhofer in vitro diagnostics (ivD) platform to enable rapid identification of bacterial species and detection of antibiotic resistance. The use of DNA microarrays allows a fast adaptation of new biomarkers enabling the identification of different genes as well as single-nucleotide-polymorphisms (SNPs) within these genes. In this protocol we describe a DNA microarray developed for identification of Staphylococcus aureus and the mecA resistance gene.

  17. Tools for open geospatial science

    Science.gov (United States)

    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.

  18. Open IS

    DEFF Research Database (Denmark)

    Germonprez, Matt; Crowston, Kevin; Avital, Michel

    2013-01-01

    The collective intelligence and collective action of “open” communities have produced a variety of complex knowledge goods and radical social change. The Information Systems (IS) community has invested significant effort into researching open communities and the ecosystems in which they operate...... therefore seeks to stimulate a thoughtful and dynamic discussion around the proposition that becoming a more open community will enhance the IS discipline’s scholarly inquiry and global impact....

  19. co_LAB @ Web We Want

    OpenAIRE

    Thayne, Martyn; Cooper, Graham; Field, James; McCarthy, Clive; Vickers, Richard; Lawlor, Louise; West, Andrew

    2015-01-01

    co_LAB projects typically involve working with interdisciplinary groups of students, using discovery-based learning methods to explore questions, concerns and issues within digital culture and the incorporation of digital media into aspects of everyday life. Most recently the group participated in the 'Web We Want Festival' at the Southbank Arts Centre in London, which was part of Sir Tim Berners-Lee's campaign to develop a 'Magna Carta for the digital age'. In the week leading up to the fest...

  20. Report to Lincoln Labs on TWPAs

    Energy Technology Data Exchange (ETDEWEB)

    Dubois, J. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Carosi, G. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Woollett, N. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Holland, E. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Horsley, M. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Qu, D. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Materise, N. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Drury, O. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Chapline, G. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Friedrich, S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2017-09-26

    This past spring LLNL’s Quantum Sensor’s team received two TWPA amplifiers from Lincoln Labs along with a data-sheet explaining handling, operations and expected performance. Here we will outline some of the initial tests performed on this amplifiers as part of LLNL’s Quantum Sensors Strategic Initiative (QSSI). Initial testing confirmed that both amplifiers worked and provided gain and SNR improvement similar to that called out in the data-sheets provided.

  1. Berkeley's Advanced Labs for Undergraduate Astronomy Majors

    Science.gov (United States)

    Heiles, C.

    1998-12-01

    We currently offer three advanced laboratory courses for undergraduate majors: optical, IR, and radio. These courses contain both intellectual and practical content; in this talk we focus on the radio lab as a representative example. The first half of the semester concentrates on fundamentals of microwave electronics and radio astronomy techniques in four formal laboratory exercises which emphasize hands-on use of microwave devices, laboratory instruments, and computer-controlled data taking. The second half of the course emphasizes astronomy, using a horn with ~ 1 m(2) aperture to map the HI in the Galaxy and a two-element interferometer composed of ~ 1 m diameter dishes on a ~ 10 m baseline to measure accurate positions of radio sources and accurate diameters for the Sun and Moon. These experiments and observations offer ideal opportunities for teaching coordinates, time, rotation matrices, data reduction techniques, least squares, signal processing, image processing, Fourier transforms, and laboratory and astronomical instrumentation. The students can't get along without using computers as actually used by astronomers. We stay away from packaged software such as IRAF, which are ``black boxes''; rather, students learn far more by writing their own software, usually for the first time. They use the IDL language to take and reduce data and prepare them for the lab reports. We insist on quality reports---including tables, postscript graphs and images, correct grammar, spelling, and all the rest---and we strongly urge (successfully!) the students to use LATEX. The other two lab courses have the same emphasis: the guiding spirit is to place the students in a real-life research-like situation. There is too much to do, so students perform the work in small groups of 3 or 4 and groups are encouraged to share their knowledge. Lab reports are written individually. These courses are very demanding, requiring an average of 20 hours per week from the students (and probably

  2. Berkeley Lab Computing Sciences: Accelerating Scientific Discovery

    International Nuclear Information System (INIS)

    Hules, John A.

    2008-01-01

    Scientists today rely on advances in computer science, mathematics, and computational science, as well as large-scale computing and networking facilities, to increase our understanding of ourselves, our planet, and our universe. Berkeley Lab's Computing Sciences organization researches, develops, and deploys new tools and technologies to meet these needs and to advance research in such areas as global climate change, combustion, fusion energy, nanotechnology, biology, and astrophysics

  3. Towards personalized agriculture: What chemical genomics can bring to plant biotechnology

    Directory of Open Access Journals (Sweden)

    Michael E Stokes

    2014-07-01

    Full Text Available In contrast to the dominant drug paradigm in which compounds were developed to fit all, new models focused around personalized medicine are appearing where treatments are customized for individual patients. The agricultural biotechnology industry should also think about these new personalized models. For example, most common herbicides are generic in action, which led to the development of genetically modified crops to add specificity. The ease and accessibility of modern genomic analysis should facilitate the discovery of chemicals that are more selective in their utility. Is it possible to develop species-selective herbicides and growth regulators? More generally put, is plant research at a stage where chemicals can be developed that streamline plant development and growth to various environments? We believe the advent of chemical genomics now opens up these and other opportunities to personalize agriculture. Furthermore, chemical genomics does not necessarily require genetically tractable plant models, which in principle should allow quick translation to practical applications. For this to happen, however, will require collaboration between the Ag-biotech industry and academic labs for early-stage research and development.

  4. Research on OpenStack of open source cloud computing in colleges and universities’ computer room

    Science.gov (United States)

    Wang, Lei; Zhang, Dandan

    2017-06-01

    In recent years, the cloud computing technology has a rapid development, especially open source cloud computing. Open source cloud computing has attracted a large number of user groups by the advantages of open source and low cost, have now become a large-scale promotion and application. In this paper, firstly we briefly introduced the main functions and architecture of the open source cloud computing OpenStack tools, and then discussed deeply the core problems of computer labs in colleges and universities. Combining with this research, it is not that the specific application and deployment of university computer rooms with OpenStack tool. The experimental results show that the application of OpenStack tool can efficiently and conveniently deploy cloud of university computer room, and its performance is stable and the functional value is good.

  5. Tele-Lab IT-Security: an Architecture for an online virtual IT Security Lab

    Directory of Open Access Journals (Sweden)

    Christoph Meinel

    2008-05-01

    Full Text Available Recently, Awareness Creation in terms of IT security has become a big thing – not only for enterprises. Campaigns for pupils try to highlight the importance of IT security even in the user’s early years. Common practices in security education – as seen in computer science courses at universities – mainly consist of literature and lecturing. In the best case, the teaching facility offers practical courses in a dedicated isolated computer lab. Additionally, there are some more or less interactive e-learning applications around. Most existing offers can do nothing more than impart theoretical knowledge or basic information. They all lack of possibilities to provide practical experience with security software or even hacker tools in a realistic environment. The only exceptions are the expensive and hard-to-maintain dedicated computer security labs. Those can only be provided by very few organizations. Tele-Lab IT-Security was designed to offer hands-on experience exercises in IT security without the need of additional hardware or maintenance expenses. The existing implementation of Tele-Lab even provides access to the learning environment over the Internet – and thus can be used anytime and anywhere. The present paper describes the extended architecture on which the current version of the Tele-Lab server is built.

  6. Model to Implement Virtual Computing Labs via Cloud Computing Services

    Directory of Open Access Journals (Sweden)

    Washington Luna Encalada

    2017-07-01

    Full Text Available In recent years, we have seen a significant number of new technological ideas appearing in literature discussing the future of education. For example, E-learning, cloud computing, social networking, virtual laboratories, virtual realities, virtual worlds, massive open online courses (MOOCs, and bring your own device (BYOD are all new concepts of immersive and global education that have emerged in educational literature. One of the greatest challenges presented to e-learning solutions is the reproduction of the benefits of an educational institution’s physical laboratory. For a university without a computing lab, to obtain hands-on IT training with software, operating systems, networks, servers, storage, and cloud computing similar to that which could be received on a university campus computing lab, it is necessary to use a combination of technological tools. Such teaching tools must promote the transmission of knowledge, encourage interaction and collaboration, and ensure students obtain valuable hands-on experience. That, in turn, allows the universities to focus more on teaching and research activities than on the implementation and configuration of complex physical systems. In this article, we present a model for implementing ecosystems which allow universities to teach practical Information Technology (IT skills. The model utilizes what is called a “social cloud”, which utilizes all cloud computing services, such as Software as a Service (SaaS, Platform as a Service (PaaS, and Infrastructure as a Service (IaaS. Additionally, it integrates the cloud learning aspects of a MOOC and several aspects of social networking and support. Social clouds have striking benefits such as centrality, ease of use, scalability, and ubiquity, providing a superior learning environment when compared to that of a simple physical lab. The proposed model allows students to foster all the educational pillars such as learning to know, learning to be, learning

  7. Open-market innovation.

    Science.gov (United States)

    Rigby, Darrell; Zook, Chris

    2002-10-01

    Companies in many industries are feeling immense pressure to improve their ability to innovate. Even in these tough economic times, executives have pushed innovation initiatives to the top of their priority lists, but they know that the best ideas aren't always coming out of their own R&D labs. That's why a growing number of companies are exploring the idea of open-market innovation--an approach that uses tools such as licensing, joint ventures, and strategic alliances to bring the benefits of free trade to the flow of new ideas. For instance, when faced with the unanticipated anthrax scare last fall, Pitney Bowes had nothing in its R&D pipeline to help its customers combat the deadly spores. So it sought help from outside innovators to come up with scanning and imaging technologies that could alert its customers to tainted letters and packages. And Dow Chemical and Cargill jointly produced a new form of plastic derived from plant starches--a breakthrough product that neither company could have created on its own. In this article, Bain consultants Darrell Rigby and Chris Zook describe the advantages and disadvantages of open-market innovation and the ways some companies are using it to gain competitive advantage. By importing ideas from the outside, the authors say, companies can collect more and better ideas from different kinds of experts. Creative types within a company will stick around longer if they know their ideas will eventually find a home--as internal R&D projects or as concepts licensed to outside buyers. Exporting ideas also gives companies a way to measure an innovation's real value. However, the authors warn against entering into open-market innovation without properly structuring deals: Xerox and TRW virtually gave away their innovations and had to stand by while other companies capitalized on them.

  8. The StratusLab cloud distribution: Use-cases and support for scientific applications

    Science.gov (United States)

    Floros, E.

    2012-04-01

    The StratusLab project is integrating an open cloud software distribution that enables organizations to setup and provide their own private or public IaaS (Infrastructure as a Service) computing clouds. StratusLab distribution capitalizes on popular infrastructure virtualization solutions like KVM, the OpenNebula virtual machine manager, Claudia service manager and SlipStream deployment platform, which are further enhanced and expanded with additional components developed within the project. The StratusLab distribution covers the core aspects of a cloud IaaS architecture, namely Computing (life-cycle management of virtual machines), Storage, Appliance management and Networking. The resulting software stack provides a packaged turn-key solution for deploying cloud computing services. The cloud computing infrastructures deployed using StratusLab can support a wide range of scientific and business use cases. Grid computing has been the primary use case pursued by the project and for this reason the initial priority has been the support for the deployment and operation of fully virtualized production-level grid sites; a goal that has already been achieved by operating such a site as part of EGI's (European Grid Initiative) pan-european grid infrastructure. In this area the project is currently working to provide non-trivial capabilities like elastic and autonomic management of grid site resources. Although grid computing has been the motivating paradigm, StratusLab's cloud distribution can support a wider range of use cases. Towards this direction, we have developed and currently provide support for setting up general purpose computing solutions like Hadoop, MPI and Torque clusters. For what concerns scientific applications the project is collaborating closely with the Bioinformatics community in order to prepare VM appliances and deploy optimized services for bioinformatics applications. In a similar manner additional scientific disciplines like Earth Science can take

  9. Open access

    CERN Document Server

    Suber, Peter

    2012-01-01

    The Internet lets us share perfect copies of our work with a worldwide audience at virtually no cost. We take advantage of this revolutionary opportunity when we make our work "open access": digital, online, free of charge, and free of most copyright and licensing restrictions. Open access is made possible by the Internet and copyright-holder consent, and many authors, musicians, filmmakers, and other creators who depend on royalties are understandably unwilling to give their consent. But for 350 years, scholars have written peer-reviewed journal articles for impact, not for money, and are free to consent to open access without losing revenue. In this concise introduction, Peter Suber tells us what open access is and isn't, how it benefits authors and readers of research, how we pay for it, how it avoids copyright problems, how it has moved from the periphery to the mainstream, and what its future may hold. Distilling a decade of Suber's influential writing and thinking about open access, this is the indispe...

  10. Comparative Genomics

    Indian Academy of Sciences (India)

    An important hallmark of biological research is the aspect of 'comparisons'. As the complete genome sequences of numerous organisms have become available, the emphasis in biology has shifted to comparisons at the genome level. Indeed, the last few years have witnessed an exponential rise in the number of ...

  11. Comparative Genomics

    Indian Academy of Sciences (India)

    structions of the tree of life, drug discovery programs, func- tion predictions of hypothetical proteins and genes, regula- tory motifs and other non-coding DNA motifs, and genome ... expertise in assembling sequences. Beginning with the complete genome sequence of the bacterial pathogen Haemophilus influenzae that was ...

  12. The Dynamics and Facilitation of a Living Lab Construct

    DEFF Research Database (Denmark)

    Brønnum, Louise; Nielsen, Louise Møller

    2013-01-01

    During the last decade Living Labs have established itself as an attractive innovation approach. Living Labs are an interesting construction because it offers a collaboration platform for dynamic interaction with users in all the project phases. Living Labs frame knowledge about actors in their own...... settings, in which new opportunities for innovation can be discovered. However, the practical management of a Living Lab is often a great challenge. It involves managing several actors, who are working with different agendas and within very different development traditions. The managing of a Living Lab...... and the different actors, processes and methods are therefore interesting to put into perspective as it contains opportunities for staging a well‐functioning Living Lab. This paper contributes to unfolding and discussing some of the main challenges in managing a Living Lab while keeping the different actors engaged...

  13. Remote monitoring of vacuum and valve status using LabVIEW

    International Nuclear Information System (INIS)

    Rozario, C.; Pal, S.; Nanal, V.; Pillay, R.G.

    2015-01-01

    For remote monitoring of vacuum status in LINAC and associated beam transport lines, a LabVIEW based interface through RS232 communication is developed. All vacuum stations in LINAC are equipped with Pfeiffer pressure measurement units, namely, TPQ 262 (for 2 no.s) and TPG256 (for 6 no.s). The communication to the unit is done via RS232 with the Serial Device Server. The electro-pneumatic gate valves separating beam line sections and cryostats are fitted with limit switches for indicating open/close status. A modular unit based on PIC 18F4520 microcontroller is developed to read the limit switch positions of up to 10 valves. Both the vacuum readout unit and the gate valve monitor unit act as a server to the client PC on the console. Each unit is assigned a unique IP address and connected to the TCP/IP Ethernet bus. The LabVIEW Virtual Instrument based TCP/IP is used for communication through the distributed LAN. It is possible to connect additional client PCs using the LabVIEW Remote Console features. During the accelerator operation the vacuum reading of the gauge and the status of valves can be monitored from the control room console. All the vacuum parameters like gauge value and status at different physical locations are scanned and logged approximately every second. The LabVIEW GUI has helped in making the system user friendly and can be expanded easily. (author)

  14. Changes in Urban Youths' Attitude Towards Science and Perception of a Mobile Science Lab Experience

    Science.gov (United States)

    Fox, Jared

    This dissertation examined changes in urban youth's attitude towards science as well as their perception of the informal science education setting and third space opportunity provided by the BioBus, a mobile science lab. Science education researchers have often suggested that informal science education settings provide one possible way to positively influence student attitude towards science and engage marginalized urban youth within the traditional science classroom (Banks et al., 2007; Hofstein & Rosenfeld, 1996; National Research Council, 2009; Schwarz & Stolow, 2006; Stocklmayer, Rennie, & Gilbert, 2010). However, until now, this possibility has not been explored within the setting of a mobile science lab nor examined using a theoretical framework intent on analyzing how affective outcomes may occur. The merits of this analytical stance were evaluated via observation, attitudinal survey, open-response questionnaire, and interview data collected before and after a mobile science lab experience from a combination of 239 students in Grades 6, 8, 9, 11, and 12 from four different schools within a major Northeastern metropolitan area. Findings from this study suggested that urban youth's attitude towards science changed both positively and negatively in statistically significant ways after a BioBus visit and that the experience itself was highly enjoyable. Furthermore, implications for how to construct a third space within the urban science classroom and the merits of utilizing the theoretical framework developed to analyze cultural tensions between urban youth and school science are discussed. Key Words: Attitude towards science, third space, mobile science lab, urban science education.

  15. KNMI DataLab experiences in serving data-driven innovations

    Science.gov (United States)

    Noteboom, Jan Willem; Sluiter, Raymond

    2016-04-01

    Climate change research and innovations in weather forecasting rely more and more on (Big) data. Besides increasing data from traditional sources (such as observation networks, radars and satellites), the use of open data, crowd sourced data and the Internet of Things (IoT) is emerging. To deploy these sources of data optimally in our services and products, KNMI has established a DataLab to serve data-driven innovations in collaboration with public and private sector partners. Big data management, data integration, data analytics including machine learning and data visualization techniques are playing an important role in the DataLab. Cross-domain data-driven innovations that arise from public-private collaborative projects and research programmes can be explored, experimented and/or piloted by the KNMI DataLab. Furthermore, advice can be requested on (Big) data techniques and data sources. In support of collaborative (Big) data science activities, scalable environments are offered with facilities for data integration, data analysis and visualization. In addition, Data Science expertise is provided directly or from a pool of internal and external experts. At the EGU conference, gained experiences and best practices are presented in operating the KNMI DataLab to serve data-driven innovations for weather and climate applications optimally.

  16. Fungal Genomics for Energy and Environment

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.

    2013-03-11

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). One of its projects, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts) by means of genome sequencing and analysis. New chapters of the Encyclopedia can be opened with user proposals to the JGI Community Sequencing Program (CSP). Another JGI project, the 1000 fungal genomes, explores fungal diversity on genome level at scale and is open for users to nominate new species for sequencing. Over 200 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  17. Open Education and the Open Science Economy

    Science.gov (United States)

    Peters, Michael A.

    2009-01-01

    Openness as a complex code word for a variety of digital trends and movements has emerged as an alternative mode of "social production" based on the growing and overlapping complexities of open source, open access, open archiving, open publishing, and open science. This paper argues that the openness movement with its reinforcing structure of…

  18. Open data

    DEFF Research Database (Denmark)

    Bodum, Lars

    2017-01-01

    Everyone wants open data, but the road towards it can be both difficult and long. Implementation of data portals and ICT solutions for support of the data infrastructure can be initiated from the central government through legislation, regulation and public procurement. This is what you would cal...

  19. opened capsule

    African Journals Online (AJOL)

    The accuracy of the off-label opened capsule dosing method for stavudine is acceptable. There is no need to instruct caregivers to include sediment in the aliquot given to the infant. However, studies that confirm adequate bioavailability and efficacy are needed. In addition, it is important to avoid supplying generic capsules ...

  20. Opening Address

    Science.gov (United States)

    Garbers, C. F.

    1987-09-01

    Ladies and gentlemen, it is indeed a great privilege and pleasure for me to present the opening address at this, the 17th International Congress on High Speed Photograpy and Photonics. Before turning to the business of the Congress, I would like to briefly introduce you to South Africa: its scientific past and its research challenges for the future.

  1. Open Images

    DEFF Research Database (Denmark)

    Sanderhoff, Merete

    2013-01-01

    Museums around the world hold enormous troves of public domain artworks. In digitized form, they can be powerful tools for research and learning, as well as building blocks, in the hands of students, teachers, scholars, developers, and creative people. By opening up their digitized assets for reuse...

  2. E-Labs - Learning with Authentic Data

    Energy Technology Data Exchange (ETDEWEB)

    Bardeen, Marjorie G. [Fermilab; Wayne, Mitchell [Notre Dame U.

    2016-01-01

    the success teachers have had providing an opportunity for students to: • Organize and conduct authentic research. • Experience the environment of scientific collaborations. • Possibly make real contributions to a burgeoning scientific field. We've created projects that are problem-based, student driven and technology dependent. Students reach beyond classroom walls to explore data with other students and experts and share results, publishing original work to a worldwide audience. Students can discover and extend the research of other students, modeling the processes of modern, large-scale research projects. From start to finish e-Labs are student-led, teacher-guided projects. Students need only a Web browser to access computing techniques employed by professional researchers. A Project Map with milestones allows students to set the research plan rather than follow a step-by-step process common in other online projects. Most importantly, e-Labs build the learning experience around the students' own questions and let them use the very tools that scientists use. Students contribute to and access shared data, most derived from professional research databases. They use common analysis tools, store their work and use metadata to discover, replicate and confirm the research of others. This is where real scientific collaboration begins. Using online tools, students correspond with other research groups, post comments and questions, prepare summary reports, and in general participate in the part of scientific research that is often left out of classroom experiments. Teaching tools such as student and teacher logbooks, pre- and post-tests and an assessment rubric aligned with learner outcomes help teachers guide student work. Constraints on interface designs and administrative tools such as registration databases give teachers the "one-stop-shopping" they seek for multiple e-Labs. Teaching and administrative tools also allow us to track usage and assess the

  3. Opening Reproducible Research

    Science.gov (United States)

    Nüst, Daniel; Konkol, Markus; Pebesma, Edzer; Kray, Christian; Klötgen, Stephanie; Schutzeichel, Marc; Lorenz, Jörg; Przibytzin, Holger; Kussmann, Dirk

    2016-04-01

    Open access is not only a form of publishing such that research papers become available to the large public free of charge, it also refers to a trend in science that the act of doing research becomes more open and transparent. When science transforms to open access we not only mean access to papers, research data being collected, or data being generated, but also access to the data used and the procedures carried out in the research paper. Increasingly, scientific results are generated by numerical manipulation of data that were already collected, and may involve simulation experiments that are completely carried out computationally. Reproducibility of research findings, the ability to repeat experimental procedures and confirm previously found results, is at the heart of the scientific method (Pebesma, Nüst and Bivand, 2012). As opposed to the collection of experimental data in labs or nature, computational experiments lend themselves very well for reproduction. Some of the reasons why scientists do not publish data and computational procedures that allow reproduction will be hard to change, e.g. privacy concerns in the data, fear for embarrassment or of losing a competitive advantage. Others reasons however involve technical aspects, and include the lack of standard procedures to publish such information and the lack of benefits after publishing them. We aim to resolve these two technical aspects. We propose a system that supports the evolution of scientific publications from static papers into dynamic, executable research documents. The DFG-funded experimental project Opening Reproducible Research (ORR) aims for the main aspects of open access, by improving the exchange of, by facilitating productive access to, and by simplifying reuse of research results that are published over the Internet. Central to the project is a new form for creating and providing research results, the executable research compendium (ERC), which not only enables third parties to

  4. Genome editing in cardiovascular diseases.

    Science.gov (United States)

    Strong, Alanna; Musunuru, Kiran

    2017-01-01

    Genome-editing tools, which include zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) systems, have emerged as an invaluable technology to achieve somatic and germline genomic manipulation in cells and model organisms for multiple applications, including the creation of knockout alleles, introducing desired mutations into genomic DNA, and inserting novel transgenes. Genome editing is being rapidly adopted into all fields of biomedical research, including the cardiovascular field, where it has facilitated a greater understanding of lipid metabolism, electrophysiology, cardiomyopathies, and other cardiovascular disorders, has helped to create a wider variety of cellular and animal models, and has opened the door to a new class of therapies. In this Review, we discuss the applications of genome-editing technology throughout cardiovascular disease research and the prospect of in vivo genome-editing therapies in the future. We also describe some of the existing limitations of genome-editing tools that will need to be addressed if cardiovascular genome editing is to achieve its full scientific and therapeutic potential.

  5. Charpy V, an application in Mat lab

    International Nuclear Information System (INIS)

    Castillo M, J.A.; Torres V, M.

    2003-01-01

    The obtained results with the system Charpy V V 1 designed in Mat lab for the estimate of parameters of three mathematical models are shown. The adjustment of data is used to determine the fracture energy, the lateral expansion and the percentage of ductility of steels coming from the reactor vessels of Laguna Verde, Veracruz. The data come from test tubes type Charpy V of irradiated material and not irradiated. To verify our results they were compared with those obtained by General Electric of data coming from the Laguna Verde nuclear power plant. (Author)

  6. CompTIA Network+ Lab Manual

    CERN Document Server

    Skandier, Toby

    2012-01-01

    Gain street-smart skills in network administration Think of the most common and challenging tasks that network administrators face, then read this book and find out how to perform those tasks, step by step. CompTIA Network + Lab Manual provides an inside look into the field of network administration as though you were actually on the job. You'll find a variety of scenarios and potential roadblocks, as well as clearly mapped sections to help you prepare for the CompTIA Network+ Exam N10-005. Learn how to design, implement, configure, maintain, secure, and troubleshoot a network with this street

  7. DOSAR/CalLab Operations Manual

    Energy Technology Data Exchange (ETDEWEB)

    Bogard, J.S.

    2000-03-01

    The Life Sciences Division (LSD) of Oak Ridge National Laboratory (ORNL) has a long record of radiation dosimetry research, primarily using the Health Physics Research Reactor (HPRR) and the Dosimetry Applications Research (DOSAR) Program Calibration Laboratory (CalLab), referred to formerly as the Radiation Calibration Laboratory. These facilities have been used by a broad segment of the research community to perform a variety of experiments in areas including, but not limited to, radiobiology, radiation dosimeter and instrumentation development and calibration, and the testing of materials in a variety of radiation environments.

  8. Quark Hadron Duality - Recent Jefferson Lab Results

    Energy Technology Data Exchange (ETDEWEB)

    Niculescu, Maria Ioana [James Madison Univ., Harrisonburg, VA (United States); Thomas Jefferson National Accelerator Facility (TJNAF), Newport News, VA (United States)

    2016-08-01

    The duality between the partonic and hadronic descriptions of electron--nucleon scattering is a remarkable feature of nuclear interactions. When averaged over appropriate energy intervals the cross section at low energy which is dominated by nucleon resonances resembles the smooth behavior expected from perturbative QCD. Recent Jefferson Lab results indicate that quark-hadron duality is present in a variety of observables, not just the proton F2 structure function. An overview of recent results, especially local quark-hadron duality on the neutron, are presented here.

  9. Cardiovascular genomics.

    Science.gov (United States)

    Wung, Shu-Fen; Hickey, Kathleen T; Taylor, Jacquelyn Y; Gallek, Matthew J

    2013-03-01

    This article provides an update on cardiovascular genomics using three clinically relevant exemplars, including myocardial infarction (MI) and coronary artery disease (CAD), stroke, and sudden cardiac death (SCD). ORGANIZATIONAL CONSTRUCT: Recent advances in cardiovascular genomic research, testing, and clinical implications are presented. Genomic nurse experts reviewed and summarized recent salient literature to provide updates on three selected cardiovascular genomic conditions. Research is ongoing to discover comprehensive genetic markers contributing to many common forms of cardiovascular disease (CVD), including MI and stroke. However, genomic technologies are increasingly being used clinically, particularly in patients with long QT syndrome (LQTS) or hypertrophic cardiomyopathy (HCM) who are at risk for SCD. Currently, there are no clinically recommended genetic tests for many common forms of CVD even though direct-to-consumer genetic tests are being marketed to healthcare providers and the general public. On the other hand, genetic testing for patients with certain single gene conditions, including channelopathies (e.g., LQTS) and cardiomyopathies (e.g., HCM), is recommended clinically. Nurses play a pivotal role in cardiogenetics and are actively engaged in direct clinical care of patients and families with a wide variety of heritable conditions. It is important for nurses to understand current development of cardiovascular genomics and be prepared to translate the new genomic knowledge into practice. © 2013 Sigma Theta Tau International.

  10. Craniux: A LabVIEW-Based Modular Software Framework for Brain-Machine Interface Research

    Directory of Open Access Journals (Sweden)

    Alan D. Degenhart

    2011-01-01

    Full Text Available This paper presents “Craniux,” an open-access, open-source software framework for brain-machine interface (BMI research. Developed in LabVIEW, a high-level graphical programming environment, Craniux offers both out-of-the-box functionality and a modular BMI software framework that is easily extendable. Specifically, it allows researchers to take advantage of multiple features inherent to the LabVIEW environment for on-the-fly data visualization, parallel processing, multithreading, and data saving. This paper introduces the basic features and system architecture of Craniux and describes the validation of the system under real-time BMI operation using simulated and real electrocorticographic (ECoG signals. Our results indicate that Craniux is able to operate consistently in real time, enabling a seamless work flow to achieve brain control of cursor movement. The Craniux software framework is made available to the scientific research community to provide a LabVIEW-based BMI software platform for future BMI research and development.

  11. Genome-based polymorphic microsatellite development and validation in the mosquito Aedes aegypti and application to population genetics in Haiti

    Directory of Open Access Journals (Sweden)

    Streit Thomas G

    2009-12-01

    Full Text Available Abstract Background Microsatellite markers have proven useful in genetic studies in many organisms, yet microsatellite-based studies of the dengue and yellow fever vector mosquito Aedes aegypti have been limited by the number of assayable and polymorphic loci available, despite multiple independent efforts to identify them. Here we present strategies for efficient identification and development of useful microsatellites with broad coverage across the Aedes aegypti genome, development of multiplex-ready PCR groups of microsatellite loci, and validation of their utility for population analysis with field collections from Haiti. Results From 79 putative microsatellite loci representing 31 motifs identified in 42 whole genome sequence supercontig assemblies in the Aedes aegypti genome, 33 microsatellites providing genome-wide coverage amplified as single copy sequences in four lab strains, with a range of 2-6 alleles per locus. The tri-nucleotide motifs represented the majority (51% of the polymorphic single copy loci, and none of these was located within a putative open reading frame. Seven groups of 4-5 microsatellite loci each were developed for multiplex-ready PCR. Four multiplex-ready groups were used to investigate population genetics of Aedes aegypti populations sampled in Haiti. Of the 23 loci represented in these groups, 20 were polymorphic with a range of 3-24 alleles per locus (mean = 8.75. Allelic polymorphic information content varied from 0.171 to 0.867 (mean = 0.545. Most loci met Hardy-Weinberg expectations across populations and pairwise FST comparisons identified significant genetic differentiation between some populations. No evidence for genetic isolation by distance was observed. Conclusion Despite limited success in previous reports, we demonstrate that the Aedes aegypti genome is well-populated with single copy, polymorphic microsatellite loci that can be uncovered using the strategy developed here for rapid and efficient

  12. Theory of microbial genome evolution

    Science.gov (United States)

    Koonin, Eugene

    Bacteria and archaea have small genomes tightly packed with protein-coding genes. This compactness is commonly perceived as evidence of adaptive genome streamlining caused by strong purifying selection in large microbial populations. In such populations, even the small cost incurred by nonfunctional DNA because of extra energy and time expenditure is thought to be sufficient for this extra genetic material to be eliminated by selection. However, contrary to the predictions of this model, there exists a consistent, positive correlation between the strength of selection at the protein sequence level, measured as the ratio of nonsynonymous to synonymous substitution rates, and microbial genome size. By fitting the genome size distributions in multiple groups of prokaryotes to predictions of mathematical models of population evolution, we show that only models in which acquisition of additional genes is, on average, slightly beneficial yield a good fit to genomic data. Thus, the number of genes in prokaryotic genomes seems to reflect the equilibrium between the benefit of additional genes that diminishes as the genome grows and deletion bias. New genes acquired by microbial genomes, on average, appear to be adaptive. Evolution of bacterial and archaeal genomes involves extensive horizontal gene transfer and gene loss. Many microbes have open pangenomes, where each newly sequenced genome contains more than 10% `ORFans', genes without detectable homologues in other species. A simple, steady-state evolutionary model reveals two sharply distinct classes of microbial genes, one of which (ORFans) is characterized by effectively instantaneous gene replacement, whereas the other consists of genes with finite, distributed replacement rates. These findings imply a conservative estimate of at least a billion distinct genes in the prokaryotic genomic universe.

  13. Three pedagogical approaches to introductory physics labs and their effects on student learning outcomes

    Science.gov (United States)

    Chambers, Timothy

    This dissertation presents the results of an experiment that measured the learning outcomes associated with three different pedagogical approaches to introductory physics labs. These three pedagogical approaches presented students with the same apparatus and covered the same physics content, but used different lab manuals to guide students through distinct cognitive processes in conducting their laboratory investigations. We administered post-tests containing multiple-choice conceptual questions and free-response quantitative problems one week after students completed these laboratory investigations. In addition, we collected data from the laboratory practical exam taken by students at the end of the semester. Using these data sets, we compared the learning outcomes for the three curricula in three dimensions of ability: conceptual understanding, quantitative problem-solving skill, and laboratory skills. Our three pedagogical approaches are as follows. Guided labs lead students through their investigations via a combination of Socratic-style questioning and direct instruction, while students record their data and answers to written questions in the manual during the experiment. Traditional labs provide detailed written instructions, which students follow to complete the lab objectives. Open labs provide students with a set of apparatus and a question to be answered, and leave students to devise and execute an experiment to answer the question. In general, we find that students performing Guided labs perform better on some conceptual assessment items, and that students performing Open labs perform significantly better on experimental tasks. Combining a classical test theory analysis of post-test results with in-lab classroom observations allows us to identify individual components of the laboratory manuals and investigations that are likely to have influenced the observed differences in learning outcomes associated with the different pedagogical approaches. Due to

  14. Open Source, Open Access, Open Review, Open Data. Initiativen zu mehr Offenheit in der digitalen Welt

    OpenAIRE

    Herb, Ulrich

    2011-01-01

    The article discusses the principles of openess, open access and open availability of information based on the examples of open access to scientific information, open government data, open geographical data and open source software.

  15. The Design of NetSecLab: A Small Competition-Based Network Security Lab

    Science.gov (United States)

    Lee, C. P.; Uluagac, A. S.; Fairbanks, K. D.; Copeland, J. A.

    2011-01-01

    This paper describes a competition-style of exercise to teach system and network security and to reinforce themes taught in class. The exercise, called NetSecLab, is conducted on a closed network with student-formed teams, each with their own Linux system to defend and from which to launch attacks. Students are expected to learn how to: 1) install…

  16. Tools for application management at Jefferson Lab

    International Nuclear Information System (INIS)

    The Software Controls Group at Thomas Jefferson National Accelerator Facility (Jefferson Lab) is responsible for slow controls for many Jefferson Lab facilities. The Experimental Physics and Industrial Control System (EPICS) is used as the basis of these control systems. The Controls Group developed and maintains over 150 control applications running on over 100 I/O controllers (IOCs). With so many applications, it becomes increasingly difficult to maintain and upgrade older applications and still produce new applications. The difficulties became especially apparent this year as a major effort was undertaken to upgrade all control system applications to the newest versions of EPICS and VxWorks. Over the past few years, the Controls Group has worked on constructing a framework within which to develop and maintain applications more efficiently. As the framework has matured and applications have been structured to fit the framework, a number of tools have been developed to help with software maintenance and upgrades. This paper will describe some of these tools and how they are used to enhance the maintainability and reliability of the control system

  17. Control system reliability at Jefferson Lab

    International Nuclear Information System (INIS)

    At Thomas Jefferson National Accelerator Facility (Jefferson Lab), the availability of the control system is crucial to the operation of the accelerator for experimental programs. Jefferson Lab's control system, uses 68040 based microprocessors running VxWorks, Unix workstations, and a variety of VME, CAMAC. GPIB, and serial devices. The software consists of control system toolkit software, commercial packages, and over 200 custom and generic applications, some of which are highly complex. The challenge is to keep this highly diverse and still growing system, with over 162,000 control points, operating reliably, while managing changes and upgrades to both the hardware and software. Downtime attributable to the control system includes the time to troubleshoot and repair problems and the time to restore the machine to operation of the scheduled program. This paper describes the availability of the control system during the last year, the heaviest contributors to downtime and the response to problems. Strategies for improving the robustness of the control system am detailed and include changes in hardware, software, procedures and processes. The improvements range from the routine preventive hardware maintenance, to improving their ability to detect, predict and prevent problems. This paper also describes the software tools used to assist in control system troubleshooting, maintenance and failure recovery processes

  18. The evolution of Jefferson Lab's control system

    International Nuclear Information System (INIS)

    K. S. White; M. Bickley; W. Watson

    1999-01-01

    Thomas Jefferson National Accelerator Facility's (Jefferson Lab) accelerator controls were initially implemented as a proprietary in-house system. During machine commissioning, problems were encountered leading to a decision to migrate to the Experimental Physics and Industrial Controls System (EPICS). Since then, the accelerator and all other laboratory controls have been successfully converted. In addition to implementing Jefferson Lab's controls using EPICS, new data visualization tools have been developed and existing programs have been enhanced with new capabilities. In order to provide a more generic interface for high level applications development, a device abstraction layer, called Common DEVice (CDEV), was implemented. These additions have been made available to other laboratories and are in use at many sites, including some that do not use EPICS. Control System development is not limited to computer scientists; operators, engineers and physicists frequently add capabilities using EPICS, CDEV, Tel/tk, and other tools. These contributions have tailored the control system for many different types of customers. For the future, the authors envision more intelligent processing and more capable tools for data storage, retrieval and visualization

  19. Quality of Lab Appliances in Orthodontic Offices.

    Science.gov (United States)

    Pruzansky, D P; Park, J H

    Lab appliances are an integral part of orthodontics, from active treatment to retention. The quality and fit of an appliance can affect the treatment result and stability. This study aims to determine common points of failure in orthodontic appliances, and suggest methods to reduce this rate. A survey consisting of 23 questions was distributed to active members of the American Association of Orthodontists (AAO) via Survey Monkey. The most common appliance to need an adjustment was the wrap-around retainer, with the Hawley retainer as a close second. The least common appliance needing adjustment was the Essix/clear retainer. Respondents were asked which component of each appliance was most commonly responsible for an ill-fit. For Hawley and wrap-around retainers, clasps were the most common problem at 50%, whereas spring aligners had two components - clasps and labial bows, both at 38%. Ill-fitting Essix/clear retainers had gingival impingement (52%) closely followed by poor posterior seating (43%). Communication between the orthodontist and lab technician can be improved by establishing a quality assurance protocol for outgoing and incoming cases. The labial bow of Hawley's, wrap-arounds and spring aligners should be clearly demarcated on the casts. Impressions should be free of distortion and casts should be inspected for accuracy. Clear retainers and positioner should be trimmed to avoid gingival impingement. The type of clasp should be selected based on the anatomy of the teeth, and bands should be checked for accuracy of fit.

  20. Temperature quenching in LAB based liquid scintillator

    Science.gov (United States)

    Sörensen, A.; Hans, S.; Junghans, A. R.; Krosigk, B. v.; Kögler, T.; Lozza, V.; Wagner, A.; Yeh, M.; Zuber, K.

    2018-01-01

    The effect of temperature changes on the light output of LAB based liquid scintillator is investigated in a range from -5 to 30°C with α -particles and electrons in a small scale setup. Two PMTs observe the scintillator liquid inside a cylindrically shaped aluminum cuvette that is heated or cooled and the temperature dependent PMT sensitivity is monitored and corrected. The α -emitting isotopes in dissolved radon gas and in natural Samarium (bound to a LAB solution) excite the liquid scintillator mixtures and changes in light output with temperature variation are observed by fitting light output spectra. Furthermore, also changes in light output by compton electrons, which are generated from external calibration γ -ray sources, is analysed with varying temperature. Assuming a linear behaviour, a combined negative temperature coefficient of {(-0.29 ± 0.01)}{ %/°}C is found. Considering hints for a particle type dependency, electrons show {(-0.17 ± 0.02)}{ %/°}C, whereas the temperature dependency seems stronger for α -particles, with {(-0.35 ± 0.03)}{ %/°}C. Due to a high sampling rate, a pulse shape analysis can be performed and shows an enhanced slow decay component at lower temperatures, pointing to reduced non-radiative triplet state de-excitations.

  1. Control system reliability at Jefferson Lab

    International Nuclear Information System (INIS)

    White, K.S.; Areti, H.; Garza, O.

    1997-01-01

    At Thomas Jefferson National Accelerator Facility (Jefferson Lab), the availability of the control system is crucial to the operation of the accelerator for experimental programs. Jefferson Lab's control system, uses 68040 based microprocessors running VxWorks, Unix workstations, and a variety of VME, CAMAC. GPIB, and serial devices. The software consists of control system toolkit software, commercial packages, and over 200 custom and generic applications, some of which are highly complex. The challenge is to keep this highly diverse and still growing system, with over 162,000 control points, operating reliably, while managing changes and upgrades to both the hardware and software. Downtime attributable to the control system includes the time to troubleshoot and repair problems and the time to restore the machine to operation of the scheduled program. This paper describes the availability of the control system during the last year, the heaviest contributors to downtime and the response to problems. Strategies for improving the robustness of the control system am detailed and include changes in hardware, software, procedures and processes. The improvements range from the routine preventive hardware maintenance, to improving their ability to detect, predict and prevent problems. This paper also describes the software tools used to assist in control system troubleshooting, maintenance and failure recovery processes

  2. Open areas and open access

    International Nuclear Information System (INIS)

    Thorndike, A.M.

    1979-01-01

    The main objective of the two open areas in the present ISABELLE design has been to provide flexibility with respect to the size and shape of experimental equipment that would eventually be installed there. No permanent building would be installed initially. One possibility would be to enclose each experiment in a temporary structure that would provide weatherproofing and shielding; another possibility would be to erect a permanent building at a later time, when experience has made the needs clearer than they are at present. The secondary objective of the design of open areas has been to keep initial costs as low as practicable. Another objective might be added, however, which we indicate by the term ''open access.'' This note will explore this idea and some design concepts based on it. In the ISABELLE 1977 summer workshop there was considerable discussion of the importance of techniques for inserting large pieces of experimental equipment quickly and removing them with equal ease and speed. Since enclosed halls have certain restrictions in this respect, open areas may be helpful in providing this feature. If the mechanical and electrical aspects could be handled quickly, one might even attempt to reduce the time spent on bureaucratic procedures in order to expedite the introduction of new experiments and new ideas in these areas

  3. Genomic Imprinting

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 5; Issue 9. Genomic Imprinting - Some Interesting Implications for the Evolution of Social Behaviour. Raghavendra Gadagkar. General Article Volume 5 Issue 9 September 2000 pp 58-68 ...

  4. The Nostoc punctiforme Genome

    Energy Technology Data Exchange (ETDEWEB)

    John C. Meeks

    2001-12-31

    Nostoc punctiforme is a filamentous cyanobacterium with extensive phenotypic characteristics and a relatively large genome, approaching 10 Mb. The phenotypic characteristics include a photoautotrophic, diazotrophic mode of growth, but N. punctiforme is also facultatively heterotrophic; its vegetative cells have multiple development alternatives, including terminal differentiation into nitrogen-fixing heterocysts and transient differentiation into spore-like akinetes or motile filaments called hormogonia; and N. punctiforme has broad symbiotic competence with fungi and terrestrial plants, including bryophytes, gymnosperms and an angiosperm. The shotgun-sequencing phase of the N. punctiforme strain ATCC 29133 genome has been completed by the Joint Genome Institute. Annotation of an 8.9 Mb database yielded 7432 open reading frames, 45% of which encode proteins with known or probable known function and 29% of which are unique to N. punctiforme. Comparative analysis of the sequence indicates a genome that is highly plastic and in a state of flux, with numerous insertion sequences and multilocus repeats, as well as genes encoding transposases and DNA modification enzymes. The sequence also reveals the presence of genes encoding putative proteins that collectively define almost all characteristics of cyanobacteria as a group. N. punctiforme has an extensive potential to sense and respond to environmental signals as reflected by the presence of more than 400 genes encoding sensor protein kinases, response regulators and other transcriptional factors. The signal transduction systems and any of the large number of unique genes may play essential roles in the cell differentiation and symbiotic interaction properties of N. punctiforme.

  5. Open innovation

    DEFF Research Database (Denmark)

    West, Joel; Bogers, Marcel

    2017-01-01

    Interest in open innovation (OI) as a field of research has grown exponentially since the phrase was coined by Chesbrough in his 2003 book, with numerous articles, special issues, books, and conference sessions. Various reviews of the literature have summarized prior work, offered new frameworks......, and identified opportunities for future research. Here we summarize these opportunities, which include more research on outbound OI, the role of open innovation in services, and network forms of collaboration such as consortia, communities, ecosystems, and platforms. Research should also examine the use of OI...... is rejected, abandoned, or fails. Finally, we consider how OI can be better linked to prior theoretical research, including topics such as absorptive capacity, user innovation, resources, dynamic capabilities, business models, and the definition of the firm....

  6. Development and design of a late-model fitness test instrument based on LabView

    Science.gov (United States)

    Xie, Ying; Wu, Feiqing

    2010-12-01

    Undergraduates are pioneers of China's modernization program and undertake the historic mission of rejuvenating our nation in the 21st century, whose physical fitness is vital. A smart fitness test system can well help them understand their fitness and health conditions, thus they can choose more suitable approaches and make practical plans for exercising according to their own situation. following the future trends, a Late-model fitness test Instrument based on LabView has been designed to remedy defects of today's instruments. The system hardware consists of fives types of sensors with their peripheral circuits, an acquisition card of NI USB-6251 and a computer, while the system software, on the basis of LabView, includes modules of user register, data acquisition, data process and display, and data storage. The system, featured by modularization and an open structure, is able to be revised according to actual needs. Tests results have verified the system's stability and reliability.

  7. OpenAPC. Open-Access-Publikationskosten als Open Data

    OpenAIRE

    Tullney, Marco

    2015-01-01

    Präsentationsfolien zum Vortrag „OpenAPC. Open-Access-Publikationskosten als Open Data“ in der Session „Ausgestaltung eines wissenschaftsadäquaten APC-Marktes: Grundsätze, Finanzierungsansätze und Management“ der Open-Access-Tage 2015 in Zürich (https://www.open-access.net/community/open-access-tage/open-access-tage-2015-zuerich/programm/#c1974)

  8. Opening remarks

    International Nuclear Information System (INIS)

    Kyd, D.R.

    1993-11-01

    In his opening remarks Mr. David R. Kyd briefly described the IAEA mission. Then he outlined main aim of the seminar which is bring together journalists, educators, officials and other specialists to let them hear and put questions to experts on various aspects of nuclear energy and techniques. Further he analyzed problems and prospects of energy development in Asia and particularly in China, including environmental considerations. The final part of the remarks was devoted comparative evaluation of different energy production technologies

  9. Opening address

    International Nuclear Information System (INIS)

    Ianko, L.

    1993-01-01

    This short talk was the opening remarks to the attendees at this conference, presented by the Scientific Secretary, IWG-LMNPP, of the IAEA. This meeting is an effort to aid research on problems related to the general area of nuclear plant aging and life management. In particular it addresses fracture properties of reactor materials and components, both as installed, and at end of service condition. A major concern is relating measurements made on laboratory samples to properties displayed by actual reactor components

  10. Opening education.

    Science.gov (United States)

    Smith, Marshall S

    2009-01-02

    Spurred by the publication of Massachusetts Institute of Technology OpenCourseWare in 2002, the open educational resources (OER) movement, which has rapidly expanded and captured the imagination and energy of millions of creators and users throughout the world, now faces many opportunities and substantial challenges as it moves to become an integral part of the world's educational environment. The confluence of the Web and a spirit of sharing intellectual property have fueled a worldwide movement to make knowledge and education materials open to all for use. OER are content (courses, books, lesson plans, articles, etc.), tools (virtual laboratories, simulations, and games), and software that support learning and educational practice. OER are free on the Web, and most have licenses that allow copyright holders to retain ownership while providing specified rights for use in original and modified forms. At the least, OER have helped to level the distribution of knowledge across the world. A second promise of OER is to help transform educational practices. This article explores the history of and promises and challenges for OER.

  11. Innovative Educational Practice: Using Virtual Labs in the Secondary Classroom

    Directory of Open Access Journals (Sweden)

    Marcel Satsky Kerr, PhD

    2004-07-01

    Full Text Available Two studies investigated the effectiveness of teaching science labs online to secondary students. Study 1 compared achievement among students instructed using hands-on Chemistry labs versus those instructed using virtual Chemistry labs (eLabs. Study 2 compared the same groups of students again while both teachers instructed using hands-on Chemistry labs to determine whether teacher or student characteristics may have affected Study 1’s findings. Participants were high school Chemistry students from a Central Texas Independent School District. Results indicated that: students learn science effectively online, schools may experience cost savings from delivering labs online, and students gain valuable technology skills needed later in college and in the workplace.

  12. JAVA Implementation of the Batched iLab Shared Architecture

    Directory of Open Access Journals (Sweden)

    Lenard Payne

    2013-04-01

    Full Text Available The MIT iLab Shared Architecture is limited currently to running on the Microsoft Windows platform. A JAVA implementation of the Batched iLab Shared Architecture has been developed that can be used on other operating systems and still interoperate with the existing Microsoft .NET web services of MIT’s iLab ServiceBroker. The Batched iLab Shared Architecture has been revised and separates the Labserver into a LabServer that handles experiment management and a LabEquipment that handles experiment execution. The JAVA implementation provides a 3-tier code development model that allows code to be reused and to develop only the code that is specific to each experiment.

  13. Fueling the Future with Fungal Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.

    2014-10-27

    Genomes of fungi relevant to energy and environment are in focus of the JGI Fungal Genomic Program. One of its projects, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts and pathogens) and biorefinery processes (cellulose degradation and sugar fermentation) by means of genome sequencing and analysis. New chapters of the Encyclopedia can be opened with user proposals to the JGI Community Science Program (CSP). Another JGI project, the 1000 fungal genomes, explores fungal diversity on genome level at scale and is open for users to nominate new species for sequencing. Over 400 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics will lead to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such ‘parts’ suggested by comparative genomics and functional analysis in these areas are presented here.

  14. A Comparison of Field-Based and Lab-Based Experiments to Evaluate User Experience of Personalised Mobile Devices

    Directory of Open Access Journals (Sweden)

    Xu Sun

    2013-01-01

    Full Text Available There is a growing debate in the literature regarding the tradeoffs between lab and field evaluation of mobile devices. This paper presents a comparison of field-based and lab-based experiments to evaluate user experience of personalised mobile devices at large sports events. A lab experiment is recommended when the testing focus is on the user interface and application-oriented usability related issues. However, the results suggest that a field experiment is more suitable for investigating a wider range of factors affecting the overall acceptability of the designed mobile service. Such factors include the system function and effects of actual usage contexts aspects. Where open and relaxed communication is important (e.g., where participant groups are naturally reticent to communicate, this is more readily promoted by the use of a field study.

  15. Draft Genome Sequence of the Fungus Trametes hirsuta 072.

    Science.gov (United States)

    Pavlov, Andrey R; Tyazhelova, Tatiana V; Moiseenko, Konstantin V; Vasina, Daria V; Mosunova, Olga V; Fedorova, Tatiana V; Maloshenok, Lilya G; Landesman, Elena O; Bruskin, Sergei A; Psurtseva, Nadezhda V; Slesarev, Alexei I; Kozyavkin, Sergei A; Koroleva, Olga V

    2015-11-19

    A standard draft genome sequence of the white rot saprotrophic fungus Trametes hirsuta 072 (Basidiomycota, Polyporales) is presented. The genome sequence contains about 33.6 Mb assembled in 141 scaffolds with a G+C content of ~57.6%. The draft genome annotation predicts 14,598 putative protein-coding open reading frames (ORFs). Copyright © 2015 Pavlov et al.

  16. Respecifying lab ethnography an ethnomethodological study of experimental physics

    CERN Document Server

    Sormani, Philippe

    2014-01-01

    Respecifying Lab Ethnography delivers the first ethnomethodological study of current experimental physics in action, describing the disciplinary orientation of lab work and exploring the discipline in its social order, formal stringency and skilful performance - in situ and in vivo. In bringing together two major strands of ethnomethodological inquiry, reflexive ethnography and video analysis, which have hitherto existed in parallel, Respecifying Lab Ethnography introduces a practice-based video analysis. In doing so, the book recasts conventional distinctions to shed fresh light on methodolog

  17. Clinical training in medical students during preclinical years in the skill lab

    Directory of Open Access Journals (Sweden)

    Upadhayay N

    2017-03-01

    Full Text Available Namrata Upadhayay Department of Physiology, Gandaki Medical College Teaching Hospital and Research Center, Kaski, Nepal Background: In Nepal, medical education is a high-stakes and stressful course. To enhance learning and minimize students’ stress, the conventional method has been replaced by integrated, student-centered learning. As an approach to train effectively, colleges have started establishing skill labs.Objectives: To evaluate the effectiveness of clinical skill training on exam performance as compared with the conventional teaching practice. Further, to assess the perceptions of students of the importance of skill lab training in college.Method: Twenty students were randomly selected to participate in this cross-sectional study. On the internal examination, students showed skills on manikins, and examiners evaluated them. A sample question in the exam was “To perform cardiopulmonary resuscitation (CPR on half body human manikin.” On completion of the exam, opinions were collected from the students via a predesigned self-administered questionnaire. The questionnaire included questions regarding skill lab use and its benefits to them in developing their skills, with a few questions related to the exam pattern. The responses were expressed in frequencies.Results: We found that all (20/20 students performed CPR with confidence and without hesitation on the manikin. The practical examination performance (marks was categorized as excellent (7/20, good (8/20, average (3/20, and poor (2/20. The pass percentage after skill training was increased by 25% as compared with conventional teaching practice. The majority of the students (17/20 mentioned that skill is better learned by doing than by observing others’ performance or watching videos. A few students (6/20 said skills are better learned by observing the real disease state. They mentioned that skill lab is the better choice for learning major skills such as catheterization, opening

  18. Open access, open education resources and open data in Uganda ...

    African Journals Online (AJOL)

    As a follow up to OpenCon 2014, International Federation of Medical Students' Associations (IFMSA) students organized a 3 day workshop Open Access, Open Education Resources and Open Data in Kampala from 15-18 December 2014. One of the aims of the workshop was to engage the Open Access movement in ...

  19. Avian Disease & Oncology Lab (ADOL) Research Update

    Science.gov (United States)

    Employing Genomics, Epigenetics, and Immunogenetics to Control Diseases Induced by Avian Tumor Viruses - Gene expression is a major factor accounting for phenotypic variation. Taking advantage of allele-specific expression (ASE) screens, we found the use of genetic markers was superior to traditiona...

  20. Stream piracy in the Black Hills: A geomorphology lab exercise

    Science.gov (United States)

    Zaprowski, B.J.; Evenson, E.B.; Epstein, J.B.

    2002-01-01

    The Black Hills of South Dakota exhibits many fine examples of stream piracy that are very suitable for teaching geomorphology lab exercises. This lab goes beyond standard topographic map interpretation by using geologic maps, well logs, gravel provenance and other types of data to teach students about stream piracy. Using a step-by-step method in which the lab exercises ramp up in difficulty, students hone their skills in deductive reasoning and data assimilation. The first exercises deal with the identification of stream piracy at a variety of spatial scales and the lab culminates with an exercise on landscape evolution and drainage rearrangement.

  1. The History of Science and Technology at Bell Labs

    Science.gov (United States)

    Bishop, David

    2008-03-01

    Over the last 80 years, Bell Labs has been one of the most scientifically and technologically productive research labs in the world. Inventions such as the transistor, laser, cell phone, solar cell, negative feedback amplifier, communications satellite and many others were made there. Scientific breakthroughs such as discovery of the Big Bang, the wave nature of the electron, electron localization and the fractional quantum hall effect were also made there making Bell Labs almost unique in terms of large impacts in both science and technology. In my talk, I will discuss the history of the lab, talk about the present and give some suggestions for how I see it evolving into the future.

  2. EarthLabs Meet Sister Corita Kent

    Science.gov (United States)

    Quartini, E.; Ellins, K. K.; Cavitte, M. G.; Thirumalai, K.; Ledley, T. S.; Haddad, N.; Lynds, S. E.

    2013-12-01

    The EarthLabs project provides a framework to enhance high school students' climate literacy and awareness of climate change. The project provides climate science curriculum and teacher professional development, followed by research on students' learning as teachers implement EarthLabs climate modules in the classroom. The professional development targets high school teachers whose professional growth is structured around exposure to current climate science research, data observation collection and analysis. During summer workshops in Texas and Mississippi, teachers work through the laboratories, experiments, and hand-on activities developed for their students. In summer 2013, three graduate students from the University of Texas at Austin Institute for Geophysics with expertise in climate science participated in two weeklong workshops. The graduate students partnered with exemplary teacher leaders to provide scientific content and lead the EarthLabs learning activities. As an experiment, we integrated a visit to the Blanton Museum and an associated activity in order to motivate participants to think creatively, as well as analytically, about science. This exercise was inspired by the work and educational philosophy of Sister Corita Kent. During the visit to the Blanton Museum, we steered participants towards specific works of art pre-selected to emphasize aspects of the climate of Texas and to draw participants' attention to ways in which artists convey different concepts. For example, artists use of color, lines, and symbols conjure emotional responses to imagery in the viewer. The second part of the exercise asked participants to choose a climate message and to convey this through a collage. We encouraged participants to combine their experience at the museum with examples of Sister Corita Kent's artwork. We gave them simple guidelines for the project based on techniques and teaching of Sister Corita Kent. Evaluation results reveal that participants enjoyed the

  3. Jefferson Lab's Journey into the Nucleus

    International Nuclear Information System (INIS)

    Douglas Higinbotham

    2004-01-01

    The year 1969 saw the publication of the first results indicating that hard scattering centres exist deep inside protons. A collaboration between the Stanford Linear Accelerator Center (SLAC) and the Massachusetts Institute of Technology was using SLAC's new high-energy electron LINAC to pioneer a rich new field in the study of the nucleus--deep inelastic scattering. Their measurements revealed that nucleons are made up of point-like particles, which Richard Feynman dubbed ''partons''. Thirty-five years on, studies of the parton-nature of the nucleus continue, not only at the traditional high-energy centres, but also at lower-energy laboratories, and in particular at the Thomas Jefferson National Accelerator Facility (Jefferson Lab) in Virginia. Jefferson Lab is home to the Continuous Electron Beam Accelerator Facility (CEBAF). Its main mission is to explore the atomic nucleus and the fundamental building-blocks of matter. As part of this mission, researchers there study the transition from the picture of the nucleus as a bound state of neutrons and protons to its deeper structure in terms of quarks and gluons--in other words, the transition from the hadronic degrees of freedom of nuclear physics to the quark-gluon degrees of freedom of high-energy physics. In exploring this transition, a wide range of experiments has been performed, from measurements of elastic form factors at large momentum transfers to studies of deep inelastic scattering. An array of spectrometers together with electron-beam energies of up to 5.7 GeV has allowed the laboratory to make significant contributions to this field. This article describes three experiments, each aimed at improving our understanding of a different aspect of the partonic nature of matter. The first, a classic deep inelastic scattering experiment, seeks to further our understanding of the composition of nucleon spin. The second experiment studies the concept of quark-hadron duality--a link between the deep inelastic

  4. Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks.

    Science.gov (United States)

    Kelley, Dylan Z; Flam, Emily L; Izumchenko, Evgeny; Danilova, Ludmila V; Wulf, Hildegard A; Guo, Theresa; Singman, Dzov A; Afsari, Bahman; Skaist, Alyza M; Considine, Michael; Welch, Jane A; Stavrovskaya, Elena; Bishop, Justin A; Westra, William H; Khan, Zubair; Koch, Wayne M; Sidransky, David; Wheelan, Sarah J; Califano, Joseph A; Favorov, Alexander V; Fertig, Elana J; Gaykalova, Daria A

    2017-12-01

    Chromatin alterations mediate mutations and gene expression changes in cancer. Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) has been utilized to study genome-wide chromatin structure in human cancer cell lines, yet numerous technical challenges limit comparable analyses in primary tumors. Here we have developed a new whole-genome analytic pipeline to optimize ChIP-Seq protocols on patient-derived xenografts from human papillomavirus-related (HPV + ) head and neck squamous cell carcinoma (HNSCC) samples. We further associated chromatin aberrations with gene expression changes from a larger cohort of the tumor and normal samples with RNA-Seq data. We detect differential histone enrichment associated with tumor-specific gene expression variation, sites of HPV integration in the human genome, and HPV-associated histone enrichment sites upstream of cancer driver genes, which play central roles in cancer-associated pathways. These comprehensive analyses enable unprecedented characterization of the complex network of molecular changes resulting from chromatin alterations that drive HPV-related tumorigenesis. Cancer Res; 77(23); 6538-50. ©2017 AACR . ©2017 American Association for Cancer Research.

  5. Open areas and open access

    International Nuclear Information System (INIS)

    Thorndike, A.M.

    1978-01-01

    One objective of the two open areas in the present ISABELLE design is to provide flexibility with respect to the size and shape of experimental equipment that would eventually be installed there. No permanent building would be installed initially. A second objective of the design of open areas is to keep initial costs as low as practicable. Another objective is open access. This note explores this idea and some design concepts based on it. It would permit inserting large pieces of experimental equipment quickly and removing them with equal ease and speed. Entire experiments would be moved in a single piece (or a few) by building them on movable platforms with capacities of up to about 1000 tons per platform. Most experiments could be built on a single platform or on a few. The shielding must also be moved. It must also be organized into a small number of large units. A scheme using large tanks filled with water is described. It is important to make the equipment on a given platform as complete and self-contained as possible, with a minimum of interconnections for power, coolant, controls, data transmission, etc. 5 figures

  6. A Lab-on-Chip Design for Miniature Autonomous Bio-Chemoprospecting Planetary Rovers

    Science.gov (United States)

    Santoli, S.

    The performance of the so-called ` Lab-on-Chip ' devices, featuring micrometre size components and employed at present for carrying out in a very fast and economic way the extremely high number of sequence determinations required in genomic analyses, can be largely improved as to further size reduction, decrease of power consumption and reaction efficiency through development of nanofluidics and of nano-to-micro inte- grated systems. As is shown, such new technologies would lead to robotic, fully autonomous, microwatt consumption and complete ` laboratory on a chip ' units for accurate, fast and cost-effective astrobiological and planetary exploration missions. The theory and the manufacturing technologies for the ` active chip ' of a miniature bio/chemoprospecting planetary rover working on micro- and nanofluidics are investigated. The chip would include micro- and nanoreactors, integrated MEMS (MicroElectroMechanical System) components, nanoelectronics and an intracavity nanolaser for highly accurate and fast chemical analysis as an application of such recently introduced solid state devices. Nano-reactors would be able to strongly speed up reaction kinetics as a result of increased frequency of reactive collisions. The reaction dynamics may also be altered with respect to standard macroscopic reactors. A built-in miniature telemetering unit would connect a network of other similar rovers and a central, ground-based or orbiting control unit for data collection and transmission to an Earth-based unit through a powerful antenna. The development of the ` Lab-on-Chip ' concept for space applications would affect the economy of space exploration missions, as the rover's ` Lab-on-Chip ' development would link space missions with the ever growing terrestrial market and business concerning such devices, largely employed in modern genomics and bioinformatics, so that it would allow the recoupment of space mission costs.

  7. Open University

    CERN Multimedia

    Pentz,M

    1975-01-01

    Michel Pentz est née en Afrique du Sud et venu au Cern en 1957 comme physicien et président de l'associaion du personnel. Il est également fondateur du mouvement Antiapartheid de Genève et a participé à la fondation de l'Open University en Grande-Bretagne. Il nous parle des contextes pédagogiques, culturels et nationaux dans lesquels la méthode peut s'appliquer.

  8. Opening remarks

    International Nuclear Information System (INIS)

    Southwood, Richard

    1987-01-01

    General opening remarks to a conference on the effects of low-level radiation on man, exploring particularly areas where disagreements have most frequently been voiced. The author comments on two approaches: a) the study, stepwise of putative cause and effect chains, using models which are tested by comparing calculated and observed effects. b) the epidemiological approach by extensive correlative study of cause, correlations and effect. Attention is drawn to the confidence to be accorded to any quantitative theory supported by both approaches, and the need for further analysis if the approaches give different indications. (U.K.)

  9. Opening lecture

    International Nuclear Information System (INIS)

    Thomas, J.B.

    1997-01-01

    The opening lecture on the results of fifty years in the nuclear energy field, deals with the main principles underlying the CEA policy concerning the fission nuclear energy transformation, i.e. the design of a nuclear industry that is a safe, high-performance and reliable source of electric power, the development of an adaptive power generation tool with the capacity to progress according to new constraints, and the necessary anticipation for preparing to the effects of the next 50 year technological leaps

  10. RASPBERRY PI TIEDONKERUULAITTEENA : Case: Nab Labs Oy

    OpenAIRE

    Aho, Henri

    2016-01-01

    Opinnäytetyön aiheena oli Raspberry Pi-alustalle suunnitellun etäluettavan ja -hallittavan mittausjärjes-telmän toteuttaminen Nab Labs Oy:n ilmatutkimusyksikölle. Työn tavoitteena oli automatisoida mit-taustulosten keräämistä ja käsittelyä. Rinnakkain kulkeva teorian ja käytännön kuvaus jakaantuu kolmeen eri osa-alueeseen: Raspberry Pi ja siihen liitetyt laitteet, järjestelmän toiminta ja sen ohjelmointi sekä internet-käyttöliityntä ja www-ohjelmointi. Työn tuloksena syntyi mittalaitt...

  11. Making the Case for Jefferson Lab

    International Nuclear Information System (INIS)

    This chapter is a personal account of the initial planning and competition for a new laboratory, which eventually became known as the Thomas Jefferson National Accelerator Facility, with the official nickname 'Jefferson Lab'. The period covered starts as far back as 1964, with the introduction of quarks, and extends up to the late 1980s after the initial team was assembled, the superconducting design was in place, and construction was well underway. I describe some of the major experiments that were proposed to justify the laboratory, reflect on the present status of those initially proposed experiments, and very briefly outline some of the new ideas that emerged after the laboratory was constructed. The science is presented in a simple manner intended for a lay audience, with some of the ideas illustrated by cartoons that were often used in popular lectures given during this period.

  12. The SPARC-LAB Thomson source

    Energy Technology Data Exchange (ETDEWEB)

    Vaccarezza, C., E-mail: cristina.vaccarezza@lnf.infn.it [INFN-LNF, Via Enrico Fermi, 40 00044 Frascati, Rome (Italy); Alesini, D.; Anania, M.P. [INFN-LNF, Via Enrico Fermi, 40 00044 Frascati, Rome (Italy); Bacci, A. [INFN-MI, Via Celoria 16, 20133 Milan (Italy); Biagioni, A.; Bisesto, F.; Bellaveglia, M. [INFN-LNF, Via Enrico Fermi, 40 00044 Frascati, Rome (Italy); Cardarelli, P. [University of Ferrara and INFN-FE, via Saragat 1, 44122 Ferrara (Italy); Cardelli, F. [University La Sapienza and INFN-Roma1, Piazzale Aldo Moro, 2 00161 Rome (Italy); Cianchi, A. [University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome (Italy); Chiadroni, E.; Croia, M.; Curcio, A. [INFN-LNF, Via Enrico Fermi, 40 00044 Frascati, Rome (Italy); Delogu, P. [University of Pisa and INFN-PI, Largo B. Pontecorvo 3, 56127 Pisa (Italy); Giovenale, D. Di [INFN-LNF, Via Enrico Fermi, 40 00044 Frascati, Rome (Italy); Domenico, G. Di [University of Ferrara and INFN-FE, via Saragat 1, 44122 Ferrara (Italy); Pirro, G. Di [INFN-LNF, Via Enrico Fermi, 40 00044 Frascati, Rome (Italy); Drebot, I. [INFN-MI, Via Celoria 16, 20133 Milan (Italy); Ferrario, M. [INFN-LNF, Via Enrico Fermi, 40 00044 Frascati, Rome (Italy); Filippi, F. [University La Sapienza and INFN-Roma1, Piazzale Aldo Moro, 2 00161 Rome (Italy); and others

    2016-09-01

    The SPARC-LAB Thomson source is a compact X-ray source based on the Thomson backscattering process presently under its second phase of commissioning at the LNF. The electron beam energy ranges between 30 and 150 MeV, the electrons collide head-on with the Ti:Sapphire FLAME laser pulse the energy of which ranges between 1 and 5 J with pulse lengths in the 25 fs–10 ps range, this provides an X-ray energy tunability in the range of 20–500 keV, with the further capability to generate strongly non-linear phenomena and to drive diffusion processes due to multiple and plural scattering effects. The experimental results of the obtained X-ray radiation are presented.

  13. Replacing textbook problems with lab experiences

    Science.gov (United States)

    Register, Trevor

    2017-10-01

    End-of-the-chapter textbook problems are often the bread and butter of any traditional physics classroom. However, research strongly suggests that students be given the opportunity to apply their knowledge in multiple contexts as well as be provided with opportunities to do the process of science through laboratory experiences. Little correlation has been shown linking the number of textbook problems solved with conceptual understanding of topics in mechanics. Furthermore, textbook problems as the primary source of practice for students robs them of the joy and productive struggle of learning how to think like an experimental physicist. Methods such as Modeling Instruction tackle this problem head-on by starting each instructional unit with an inquiry-based lab aimed at establishing the important concepts and equations for the unit, and this article will discuss ideas and experiences for how to carry that philosophy throughout a unit.

  14. Making the Case for Jefferson Lab

    Energy Technology Data Exchange (ETDEWEB)

    Gross, Franz

    2011-06-01

    This chapter is a personal account of the initial planning and competition for a new laboratory, which eventually became known as the Thomas Jefferson National Accelerator Facility, with the official nickname "Jefferson Lab." The period covered starts as far back as 1964, with the introduction of quarks, and extends up to the late 1980s after the initial team was assembled, the superconducting design was in place, and construction was well underway. I describe some of the major experiments that were proposed to justify the laboratory, reflect on the present status of those initially proposed experiments, and very briefly outline some of the new ideas that emerged after the laboratory was constructed. The science is presented in a simple manner intended for a lay audience, with some of the ideas illustrated by cartoons that were often used in popular lectures given during this period.

  15. The Jefferson Lab Frozen Spin Target

    Energy Technology Data Exchange (ETDEWEB)

    Christopher Keith, James Brock, Christopher Carlin, Sara Comer, David Kashy, Josephine McAndrew, David Meekins, Eugene Pasyuk, Joshua Pierce, Mikell Seely

    2012-08-01

    A frozen spin polarized target, constructed at Jefferson Lab for use inside a large acceptance spectrometer, is described. The target has been utilized for photoproduction measurements with polarized tagged photons of both longitudinal and circular polarization. Protons in TEMPO-doped butanol were dynamically polarized to approximately 90% outside the spectrometer at 5 T and 200-300 mK. Photoproduction data were acquired with the target inside the spectrometer at a frozen-spin temperature of approximately 30 mK with the polarization maintained by a thin, superconducting coil installed inside the target cryostat. A 0.56 T solenoid was used for longitudinal target polarization and a 0.50 T dipole for transverse polarization. Spin relaxation times as high as 4000 hours were observed. We also report polarization results for deuterated propanediol doped with the trityl radical OX063.

  16. VPPD Lab - The Chemical Product Simulator

    DEFF Research Database (Denmark)

    Kalakul, Sawitree; Hussain, Rehan; Elbashir, Nimir

    2015-01-01

    of product performance models and product-chemical property models are used to evaluate different classes of product. The product classes are single molecular structure chemicals (lipids, solvents, aroma, etc.), blended products (gasoline, jet-fuels, lubricants, etc.), and emulsified product (hand wash......In this paper, the development of a systematic model-based framework for product design, implemented in the new product design software called VPPD-Lab is presented. This framework employs its in-house knowledge-based system to design and evaluate chemical products. The built-in libraries......, detergent, etc.). It has interface to identify workflow/data-flow for the inter-related activities between knowledge-based system and model-based calculation procedures to systematically, efficiently and robustly solve various types of product design-analysis problems. The application of the software...

  17. Tough Times Ahead for Government Labs

    International Nuclear Information System (INIS)

    Ban, Stephen; Buchanan, Michelle V.; Cheeks, Nona; Funsten, Herbert; Hawsey, Robert; Lane, Monya; Whitlow, Woodrow Jr.; Studt, Tim

    2008-01-01

    Many government R and D laboratory executives face a tough couple of months ahead. These anxieties are fueled by (1) possible management, technical direction, and budgetary changes in their agencies due to changes in the federal administration; (2) frozen operating budgets until March 2009 due to the Continuing Resolution (CR) attachment to the recent banking bailout bill; and (3) the financial fallout from the economic downturn. These and other pertinent questions regarding their R and D operations were addressed in R and D Magazine's 9th Annual Government R and D Executive Roundtable held on Oct. 16, 2008, in conjunction with the 46th Annual R and D 100 Awards at Chicago's Navy Pier. Most members of this year's government executive panel were hesitant to speculate on the changes that might occur in their labs as a result of the new administration. The exception to this stand was the National Renewable Energy Laboratory's (NREL's) Robert Hawsey. ''No matter who wins (the Roundtable was held before the Nov. 4th Presidential election), we expect to see continued support,'' says Hawsey. ''All of our cooperative research facilities are over-subscribed and we're looking at how we can expand them.'' Obviously, renewable energy is a hot button in the administration and likely to get increased financial backing to help meet our country's energy independence goals. When pressed, the panel was mostly optimistic about their future support, stating that external threats to the U.S. have not changed, and research work associated with homeland security and national defense is unlikely to see drastic change. ''We have a strong portfolio in life science and don't expect any changes,'' says Oak Ridge National Laboratory's (ORNL's) Michelle Buchanan. Ongoing federally funded work at the national labs that was started before the Oct. 1st start of the FY2009 fiscal year will continue without any changes - those funds are unaffected by the CR action. This applies as well to any

  18. Characterization of Tri-lab Tantalum Plate.

    Energy Technology Data Exchange (ETDEWEB)

    Buchheit, Thomas E.; Cerreta, Ellen K.; Deibler, Lisa Anne; Chen, Shu-Rong; Michael, Joseph R.

    2014-09-01

    This report provides a detailed characterization Tri-lab Tantalum (Ta) plate jointly purchased from HCStark Inc. by Sandia, Los Alamos and Lawrence Livermore National Laboratories. Data in this report was compiled from series of material and properties characterization experiments carried out at Sandia (SNL) and Los Alamos (LANL) Laboratories through a leveraged effort funded by the C2 campaign. Results include microstructure characterization detailing the crystallographic texture of the material and an increase in grain size near the end of the rolled plate. Mechanical properties evaluations include, compression cylinder, sub-scale tension specimen, micohardness and instrumented indentation testing. The plate was found to have vastly superior uniformity when compare with previously characterized wrought Ta material. Small but measurable variations in microstructure and properties were noted at the end, and at the top and bottom edges of the plate.

  19. The Jefferson Lab High Power Light Source

    International Nuclear Information System (INIS)

    Jefferson Lab has designed, built and operated two high average power free-electron lasers (FEL) using superconducting RF (SRF) technology and energy recovery techniques. Between 1999-2001 Jefferson Lab operated the IR Demo FEL. This device produced over 2 kW in the mid-infrared, in addition to producing world record average powers in the visible (50 W), ultraviolet (10 W) and terahertz range (50 W) for tunable, short-pulse (< ps) light. This FEL was the first high power demonstration of an accelerator configuration that is being exploited for a number of new accelerator-driven light source facilities that are currently under design or construction. The driver accelerator for the IR Demo FEL uses an Energy Recovered Linac (ERL) configuration that improves the energy efficiency and lowers both the capital and operating cost of such devices by recovering most of the power in the spent electron beam after optical power is extracted from the beam. The IR Demo FEL was de-commissioned in late 2001 for an upgraded FEL for extending the IR power to over 10 kW and the ultraviolet power to over 1 kW. The FEL Upgrade achieved 10 kW of average power in the mid-IR (6 microns) in July of 2004, and its IR operation currently is being extended down to 1 micron. In addition, we have demonstrated the capability of on/off cycling and recovering over a megawatt of electron beam power without diminishing machine performance. A complementary UV FEL will come on-line within the next year. This paper presents a summary of the FEL characteristics, user community accomplishments with the IR Demo, and planned user experiments

  20. The Jefferson Lab High Power Light Source

    Energy Technology Data Exchange (ETDEWEB)

    James R. Boyce

    2006-01-01

    Jefferson Lab has designed, built and operated two high average power free-electron lasers (FEL) using superconducting RF (SRF) technology and energy recovery techniques. Between 1999-2001 Jefferson Lab operated the IR Demo FEL. This device produced over 2 kW in the mid-infrared, in addition to producing world record average powers in the visible (50 W), ultraviolet (10 W) and terahertz range (50 W) for tunable, short-pulse (< ps) light. This FEL was the first high power demonstration of an accelerator configuration that is being exploited for a number of new accelerator-driven light source facilities that are currently under design or construction. The driver accelerator for the IR Demo FEL uses an Energy Recovered Linac (ERL) configuration that improves the energy efficiency and lowers both the capital and operating cost of such devices by recovering most of the power in the spent electron beam after optical power is extracted from the beam. The IR Demo FEL was de-commissioned in late 2001 for an upgraded FEL for extending the IR power to over 10 kW and the ultraviolet power to over 1 kW. The FEL Upgrade achieved 10 kW of average power in the mid-IR (6 microns) in July of 2004, and its IR operation currently is being extended down to 1 micron. In addition, we have demonstrated the capability of on/off cycling and recovering over a megawatt of electron beam power without diminishing machine performance. A complementary UV FEL will come on-line within the next year. This paper presents a summary of the FEL characteristics, user community accomplishments with the IR Demo, and planned user experiments.

  1. Lab-on a-Chip

    Science.gov (United States)

    1999-01-01

    Labs on chips are manufactured in many shapes and sizes and can be used for numerous applications, from medical tests to water quality monitoring to detecting the signatures of life on other planets. The eight holes on this chip are actually ports that can be filled with fluids or chemicals. Tiny valves control the chemical processes by mixing fluids that move in the tiny channels that look like lines, connecting the ports. Scientists at NASA's Marshall Space Flight Center (MSFC) in Huntsville, Alabama designed this chip to grow biological crystals on the International Space Station (ISS). Through this research, they discovered that this technology is ideally suited for solving the challenges of the Vision for Space Exploration. For example, thousands of chips the size of dimes could be loaded on a Martian rover looking for biosignatures of past or present life. Other types of chips could be placed in handheld devices used to monitor microbes in water or to quickly conduct medical tests on astronauts. The portable, handheld Lab-on-a Chip Application Development Portable Test System (LOCAD-PTS) made its debut flight aboard Discovery during the STS-116 mission launched December 9, 2006. The system allowed crew members to monitor their environment for problematic contaminants such as yeast, mold, and even E.coli, and salmonella. Once LOCAD-PTS reached the ISS, the Marshall team continued to manage the experiment, monitoring the study from a console in the Payload Operations Center at MSFC. The results of these studies will help NASA researchers refine the technology for future Moon and Mars missions. (NASA/MSFC/D.Stoffer)

  2. [Nutrition genomics].

    Science.gov (United States)

    Sedová, L; Seda, O

    2004-01-01

    The importance of nutrition for human health and its influence on the onset and course of many diseases are nowadays considered as proven. Only the recent development of molecular biology and biochemical methods allows the elucidation of the molecular mechanisms of diet constituent actions and their subsequent effect on homeostatic mechanisms in health and disease states. The availability of the draft human genome sequence as well as the genome sequences of model organisms, combined with the functional and integrative genomics approaches of systems biology, bring about the possibility to identify alleles and haplotypes responsible for specific reaction to the dietary challenge in susceptible individuals. Such complex interactions are studied within the newly conceived field, the nutrition genomics (nutrigenomics). Using the tools of highly parallel analyses of transcriptome, proteome and metabolome, the nutrition genomics pursues its ultimate goal, i.e. the individualized diet, respecting not only quantitative and qualitative nutritional needs and the actual health status, but also the genetic predispositions of an individual. This approach should lead to prevention of the onset of such diseases as obesity, hypertension or type 2 diabetes, or enhance the efficiency of their therapy.

  3. A new chapter in environmental sensing: The Open-Source Published Environmental Sensing (OPENS) laboratory

    Science.gov (United States)

    Selker, J. S.; Roques, C.; Higgins, C. W.; Good, S. P.; Hut, R.; Selker, A.

    2015-12-01

    The confluence of 3-Dimensional printing, low-cost solid-state-sensors, low-cost, low-power digital controllers (e.g., Arduinos); and open-source publishing (e.g., Github) is poised to transform environmental sensing. The Open-Source Published Environmental Sensing (OPENS) laboratory has launched and is available for all to use. OPENS combines cutting edge technologies and makes them available to the global environmental sensing community. OPENS includes a Maker lab space where people may collaborate in person or virtually via on-line forum for the publication and discussion of environmental sensing technology (Corvallis, Oregon, USA, please feel free to request a free reservation for space and equipment use). The physical lab houses a test-bed for sensors, as well as a complete classical machine shop, 3-D printers, electronics development benches, and workstations for code development. OPENS will provide a web-based formal publishing framework wherein global students and scientists can peer-review publish (with DOI) novel and evolutionary advancements in environmental sensor systems. This curated and peer-reviewed digital collection will include complete sets of "printable" parts and operating computer code for sensing systems. The physical lab will include all of the machines required to produce these sensing systems. These tools can be addressed in person or virtually, creating a truly global venue for advancement in monitoring earth's environment and agricultural systems. In this talk we will present an example of the process of design and publication the design and data from the OPENS-Permeameter. The publication includes 3-D printing code, Arduino (or other control/logging platform) operational code; sample data sets, and a full discussion of the design set in the scientific context of previous related devices. Editors for the peer-review process are currently sought - contact John.Selker@Oregonstate.edu or Clement.Roques@Oregonstate.edu.

  4. Reducing unnecessary lab testing in the ICU with artificial intelligence.

    Science.gov (United States)

    Cismondi, F; Celi, L A; Fialho, A S; Vieira, S M; Reti, S R; Sousa, J M C; Finkelstein, S N

    2013-05-01

    To reduce unnecessary lab testing by predicting when a proposed future lab test is likely to contribute information gain and thereby influence clinical management in patients with gastrointestinal bleeding. Recent studies have demonstrated that frequent laboratory testing does not necessarily relate to better outcomes. Data preprocessing, feature selection, and classification were performed and an artificial intelligence tool, fuzzy modeling, was used to identify lab tests that do not contribute an information gain. There were 11 input variables in total. Ten of these were derived from bedside monitor trends heart rate, oxygen saturation, respiratory rate, temperature, blood pressure, and urine collections, as well as infusion products and transfusions. The final input variable was a previous value from one of the eight lab tests being predicted: calcium, PTT, hematocrit, fibrinogen, lactate, platelets, INR and hemoglobin. The outcome for each test was a binary framework defining whether a test result contributed information gain or not. Predictive modeling was applied to recognize unnecessary lab tests in a real world ICU database extract comprising 746 patients with gastrointestinal bleeding. Classification accuracy of necessary and unnecessary lab tests of greater than 80% was achieved for all eight lab tests. Sensitivity and specificity were satisfactory for all the outcomes. An average reduction of 50% of the lab tests was obtained. This is an improvement from previously reported similar studies with average performance 37% by [1-3]. Reducing frequent lab testing and the potential clinical and financial implications are an important issue in intensive care. In this work we present an artificial intelligence method to predict the benefit of proposed future laboratory tests. Using ICU data from 746 patients with gastrointestinal bleeding, and eleven measurements, we demonstrate high accuracy in predicting the likely information to be gained from proposed future

  5. Reducing unnecessary lab testing in the ICU with artificial intelligence

    Science.gov (United States)

    Cismondi, F.; Celi, L.A.; Fialho, A.S.; Vieira, S.M.; Reti, S.R.; Sousa, J.M.C.; Finkelstein, S.N.

    2017-01-01

    Objectives To reduce unnecessary lab testing by predicting when a proposed future lab test is likely to contribute information gain and thereby influence clinical management in patients with gastrointestinal bleeding. Recent studies have demonstrated that frequent laboratory testing does not necessarily relate to better outcomes. Design Data preprocessing, feature selection, and classification were performed and an artificial intelligence tool, fuzzy modeling, was used to identify lab tests that do not contribute an information gain. There were 11 input variables in total. Ten of these were derived from bedside monitor trends heart rate, oxygen saturation, respiratory rate, temperature, blood pressure, and urine collections, as well as infusion products and transfusions. The final input variable was a previous value from one of the eight lab tests being predicted: calcium, PTT, hematocrit, fibrinogen, lactate, platelets, INR and hemoglobin. The outcome for each test was a binary framework defining whether a test result contributed information gain or not. Patients Predictive modeling was applied to recognize unnecessary lab tests in a real world ICU database extract comprising 746 patients with gastrointestinal bleeding. Main results Classification accuracy of necessary and unnecessary lab tests of greater than 80% was achieved for all eight lab tests. Sensitivity and specificity were satisfactory for all the outcomes. An average reduction of 50% of the lab tests was obtained. This is an improvement from previously reported similar studies with average performance 37% by [1–3]. Conclusions Reducing frequent lab testing and the potential clinical and financial implications are an important issue in intensive care. In this work we present an artificial intelligence method to predict the benefit of proposed future laboratory tests. Using ICU data from 746 patients with gastrointestinal bleeding, and eleven measurements, we demonstrate high accuracy in predicting the

  6. Marine genomics

    DEFF Research Database (Denmark)

    Oliveira Ribeiro, Ângela Maria; Foote, Andrew David; Kupczok, Anne

    2017-01-01

    evolutionary biology of non-model organisms to species of commercial relevance for fishing, aquaculture and biomedicine. Instead of providing an exhaustive list of available genomic data, we rather set to present contextualized examples that best represent the current status of the field of marine genomics.......Marine ecosystems occupy 71% of the surface of our planet, yet we know little about their diversity. Although the inventory of species is continually increasing, as registered by the Census of Marine Life program, only about 10% of the estimated two million marine species are known. This lag......-throughput sequencing approaches have been helping to improve our knowledge of marine biodiversity, from the rich microbial biota that forms the base of the tree of life to a wealth of plant and animal species. In this review, we present an overview of the applications of genomics to the study of marine life, from...

  7. Listeria Genomics

    Science.gov (United States)

    Cabanes, Didier; Sousa, Sandra; Cossart, Pascale

    The opportunistic intracellular foodborne pathogen Listeria monocytogenes has become a paradigm for the study of host-pathogen interactions and bacterial adaptation to mammalian hosts. Analysis of L. monocytogenes infection has provided considerable insight into how bacteria invade cells, move intracellularly, and disseminate in tissues, as well as tools to address fundamental processes in cell biology. Moreover, the vast amount of knowledge that has been gathered through in-depth comparative genomic analyses and in vivo studies makes L. monocytogenes one of the most well-studied bacterial pathogens. This chapter provides an overview of progress in the exploration of genomic, transcriptomic, and proteomic data in Listeria spp. to understand genome evolution and diversity, as well as physiological aspects of metabolism used by bacteria when growing in diverse environments, in particular in infected hosts.

  8. Cephalopod genomics

    DEFF Research Database (Denmark)

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austri...... in this white paper......., Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers...

  9. Ontology: A Support Structure for a V-Labs Network: Euronet-Lab

    Directory of Open Access Journals (Sweden)

    Raul Cordeiro Correia

    2012-11-01

    Full Text Available Our propose is to build a network of virtual laboratories, based in a Virtual Closet that will contain all the elements and parts that are needed to build the various experiences available in a v-labs network (that we call Euronet-Lab. To build this complex network we need to find a system that supports effectively this structure. This probably will be a enormous database of v-labs and independent elements, where will be possible sometimes to “recycle” some of the elements. This means “re-use” the same element several times in many experiences. To do this is necessary to have a structure that allows us to have several instances of the same element. It’s important that in our structure and virtual environment we can create several “images” of the same reality and this images can be used simultaneously in different circuits/experiments. This means that we can create several instances of the same element, to be used in different experiences and exercises.

  10. Biological mechanisms of bone and cartilage remodelling—genomic perspective

    OpenAIRE

    Borovecki, F.; Pecina-Slaus, N.; Vukicevic, S.

    2007-01-01

    Rapid advancements in the field of genomics, enabled by the achievements of the Human Genome Project and the complete decoding of the human genome, have opened an unimaginable set of opportunities for scientists to further unveil delicate mechanisms underlying the functional homeostasis of biological systems. The trend of applying whole-genome analysis techniques has also contributed to a better understanding of physiological and pathological processes involved in homeostasis of bone and cart...

  11. Living Labs als een Vehikel voor (Onderwijs)innovatie

    NARCIS (Netherlands)

    Ellen Sjoer

    2014-01-01

    Wereldwijd schieten ze als paddenstoelen uit de grond: living labs. Deze ‘levende laboratoria’ zijn er in alle soorten en maten. Meestal wordt het lab gezien als een onderzoeks- en ontwikkelomgeving om een probleem met verschillende partijen op een innovatieve manier op te lossen. De thema’s van de

  12. Incorporating a Career Planning Lab into a Managerial Communications Course

    Science.gov (United States)

    May, Gary L.

    2005-01-01

    This article describes how a small business school, as part of a strategic planning initiative to improve career services, added a self-directed career planning lab to an existing managerial communication course. The lab concept and the learning design are innovative because they met a student need without creating additional time demands on the…

  13. Aerial view of the water reservoirs for Lab II

    CERN Multimedia

    1974-01-01

    Two large reservoirs (5000 m3 each) were built on the Swiss part of the site (Lab I is on the left). The water was drawn from the pumping station at Le Vengeron on Lac Léman, through a 10 km long pipe to be distributed over all Lab II.

  14. The Global MRIO Lab - charting the world economy

    NARCIS (Netherlands)

    Lenzen, Manfred; Geschke, Arne; Rahman, Muhammad Daaniyall Abd; Xiao, Yanyan; Fry, Jacob; Reyes, Rachel; Dietzenbacher, Hendrikus; Inomata, Satoshi; Kanemoto, Keiichiro; Los, Bart; Moran, Daniel; Schulte in den Bäumen, Hagen; Tukker, Arnold; Walmsley, Terrie; Wiedmann, Thomas; Wood, Richard; Yamano, Norihiko

    2017-01-01

    We describe the creation of the Global Multi-Region Input-Output (MRIO) Lab, which is a cloud-computing platform offering a collaborative research environment through which participants can use each other's resources to assemble their own individual MRIO versions. The Global MRIO Lab's main purpose

  15. Macromolecules Inquiry: Transformation of a Standard Biochemistry Lab

    Science.gov (United States)

    Unsworth, Elizabeth

    2014-01-01

    Identification of macromolecules in food is a standard introductory high school biology lab. The intent of this article is to describe the conversion of this standard cookbook lab into an inquiry investigation. Instead of verifying the macromolecules found in food, students use their knowledge of the macromolecules in food to determine the…

  16. European labs brace for German cuts: international collaboration

    CERN Multimedia

    Clery, D

    1996-01-01

    Germany, the largest contributor to international European research labs, announced plans to reduce its contributions an average of 8% in the nation's latest budget. CERN and other labs are worried that the cuts will endanger ongoing projects and that other countries may follow Germany's lead.

  17. The Multisensory Sound Lab: Sounds You Can See and Feel.

    Science.gov (United States)

    Lederman, Norman; Hendricks, Paula

    1994-01-01

    A multisensory sound lab has been developed at the Model Secondary School for the Deaf (District of Columbia). A special floor allows vibrations to be felt, and a spectrum analyzer displays frequencies and harmonics visually. The lab is used for science education, auditory training, speech therapy, music and dance instruction, and relaxation…

  18. Living Labs as boundary-spanners between Triple Helix actors

    NARCIS (Netherlands)

    van Geenhuizen, M.S.

    2016-01-01

    Living labs are an increasingly popular methodology to enhance innovation. Living labs aim to span boundaries between different organizations, among others Triple helix actors, by acting as a network organization typically in a real-life environment to foster co-creation by user-groups. This paper

  19. Engineering Students' Experiences from Physics Group Work in Learning Labs

    Science.gov (United States)

    Mellingsaeter, Magnus Strøm

    2014-01-01

    Background: This paper presents a case study from a physics course at a Norwegian university college, investigating key aspects of a group-work project, so-called learning labs, from the participating students' perspective. Purpose: In order to develop these learning labs further, the students' perspective is important. Which aspects are essential…

  20. Exploring differences between central located test and home use test in a living lab context

    DEFF Research Database (Denmark)

    Wendin, Karin Maria Elisabet; Annika, Åström; Anna, Ståhlbröst

    2015-01-01

    than in CLT. Applying the LL approach, there is a need for methods and approaches that capture a rich picture of consumers during test performance without being intrusive or obstructive of activities and context. The approach offers the opportunity for companies to have consumers not only test products......The concept of Living Labs (LLs) has evolved to support the creation of experience-based development of innovations in real-life, user-driven and open environments. Two types of consumer product tests used generally are central location tests (CLT) and home use tests (HUT) where the acceptability...

  1. The Work Smart Standards process at Jefferson Lab

    International Nuclear Information System (INIS)

    The Thomas Jefferson National Accelerator Facility (Jefferson Lab) has developed a set of Work Smart Standards for the Lab. The effort incorporated the Lab's performance-based contract into the Necessary and Sufficient (N and S) Standards identification process of the DOE. A rigorous protocol identified hazards in the workplace and standards that provide adequate protection of workers, public, and the environment at reasonable cost. The intensive process was a joint effort between the Lab and DOE and it required trained teams of knowledgeable experts in three fields: (1) actual required work conditions at Jefferson Lab; (2) laws, regulations, DOE directives and performance-based contracts; and (3) Environmental Health and Safety (EH and S), Rad Con, and QA. The criteria for selection of the teams, the database designed and used for the process, and lessons learned are discussed

  2. Use of tablets for instruction and learning in microbiology labs

    DEFF Research Database (Denmark)

    Møller, Karen Louise; Jelsbak, Vibe Alopaeus; Georgsen, Marianne

    ? The empirical part of the project has been documented through field observations in the lab (in writing and with photos). We have found the following to be characteristic of the work of the students: the students use the tablets collaboratively, take more photos than requested, use the video based instructions......In the Bachelor Programme of Biomedical Laboratory Analysis at University College VIA, the students work in a classified microbiology laboratory. This means that they are not allowed to bring their personal computers into the lab. Until now the students have used paper based lab instructions...... and taken notes by hand. Use of tablets in the lab offers new opportunities. In September 2012, nine tablets were introduced into one of the labs of the college. Groups of students use the tablets to access documents, watch video instructions, and to document results and procedures digitally. The objectives...

  3. The 12 GeV Upgrade at Jefferson Lab

    International Nuclear Information System (INIS)

    Rolf Ent

    2002-01-01

    There has been a remarkable fruitful evolution of our picture of the behavior of strongly interacting matter during the almost two decades that have passed since the parameters of the Continuous Electron Beam Accelerator Facility (CEBAF) at Jefferson Lab were defined. These advances have revealed important new experimental questions best addressed by a CEBAF-class machine at higher energy. Fortunately, favorable technical developments coupled with foresight in the design of the facility make it feasible to triple (double) CEBAF's design (achieved) beam energy from 4 (6) GeV to 12 GeV, in a cost-effective manner: the Upgrade can be realized for about 15% of the cost of the initial facility. This Upgrade would enable the worldwide community to greatly expand its physics horizons. In addition to in general improving the figure of merit and momentum transfer range of the present Jefferson Lab physics program, raising the energy of the accelerator to 12 GeV opens up two main new areas of physics: (1) It allows direct exploration of the quark-gluon structure of hadrons and nuclei in the ''valence quark region''. It is known that inclusive electron scattering at the high momentum and energy transfers available at 12 GeV is governed by elementary interactions with quarks and, indirectly, gluons. The original CEBAF energy is not adequate to study this critical region, while with continuous 12 GeV beams one can cleanly access the entire ''valence quark region'' and exploit the newly discovered Generalized Parton Distributions. In addition, a 12-GeV Jefferson Lab can essentially complete the studies of the transition from hadronic to quark-gluon degrees of freedom. (2) It allows crossing the threshold above which the origins of quark confinement can be investigated. Specifically, 12 GeV will enable the production of certain ''exotic'' mesons. Whereas in the QCD region of asymptotic freedom ample evidence for the role of gluons exist through the observation of gluon jets

  4. 3D-Lab: a collaborative web-based platform for molecular modeling.

    Science.gov (United States)

    Grebner, Christoph; Norrby, Magnus; Enström, Jonatan; Nilsson, Ingemar; Hogner, Anders; Henriksson, Jonas; Westin, Johan; Faramarzi, Farzad; Werner, Philip; Boström, Jonas

    2016-09-01

    The use of 3D information has shown impact in numerous applications in drug design. However, it is often under-utilized and traditionally limited to specialists. We want to change that, and present an approach making 3D information and molecular modeling accessible and easy-to-use 'for the people'. A user-friendly and collaborative web-based platform (3D-Lab) for 3D modeling, including a blazingly fast virtual screening capability, was developed. 3D-Lab provides an interface to automatic molecular modeling, like conformer generation, ligand alignments, molecular dockings and simple quantum chemistry protocols. 3D-Lab is designed to be modular, and to facilitate sharing of 3D-information to promote interactions between drug designers. Recent enhancements to our open-source virtual reality tool Molecular Rift are described. The integrated drug-design platform allows drug designers to instantaneously access 3D information and readily apply advanced and automated 3D molecular modeling tasks, with the aim to improve decision-making in drug design projects.

  5. Genome Imprinting

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 5; Issue 9. Genome Imprinting - The Silencing of ... General Article Volume 5 Issue 9 September 2000 pp 49-57 ... M T Tanuja1. Drosophila Stock Centre, Department of Studies in Zoology, University of Mysore Manasagangotri Mysore 570 006, India.

  6. Genome Imprinting

    Indian Academy of Sciences (India)

    ring pathological condition cystic fibrosis is due to inheritance of both copies of chromosome 7 from the mother. Similarly,. Prader-Willi syndrome in humans is due to the inheritance of both copies of chromosome 15 from the mother. Human Triploids. The triploid (Le. 3 copies of the haploid genome are present instead of the ...

  7. genome editing

    Indian Academy of Sciences (India)

    2016-02-11

    Feb 11, 2016 ... What history tells us. XL. The success story of the expression 'genome editing'. MICHEL MORANGE. Centre Cavaillès, République des Savoirs: Lettres, Sciences, Philosophie USR 3608, Ecole. Normale Supérieure, 29 Rue d'Ulm, 75230, Paris Cedex 05, France. (Fax, 33-144-323941; Email, ...

  8. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen

    2015-01-01

    The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequen...

  9. Comparative Genomics

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 11; Issue 8. Comparative Genomics - A Powerful New Tool in Biology. Anand K Bachhawat. General Article Volume 11 Issue 8 August 2006 pp 22-40. Fulltext. Click here to view fulltext PDF. Permanent link:

  10. Genomic databases as global public goods?

    Science.gov (United States)

    Chadwick, Ruth; Wilso, Sarah

    2004-01-01

    Recent discussions of genomics and international justice have adopted the concept of 'global public goods' to support both the view of genomics as a benefit and the sharing of genomics knowledge across nations. Such discussion relies on a particular interpretation of the global public goods argument, facilitated by the ambiguity of the concept itself. Our aim in this article is to demonstrate this by a close examination of the concept of global public goods with particular reference to its use in the context of genomic databases. We content that the argument for construing genomics as a global public good depends on seeing it as a natural good by focusing on features intrinsic to genomics knowledge. We shall argue that social and political arrangements are relevant and that recognising this opens the door to construing the use of global public goods language as a strategic one.

  11. Learning by Viewing - Nobel Labs 360

    Science.gov (United States)

    Mather, John C.

    2013-01-01

    First of all, my thanks to the Nobel Lindau Foundation for their inspiration and leadership in sharing the excitement of scientific discovery with the public and with future scientists! I have had the pleasure of participating twice in the Lindau meetings, and recently worked with the Nobel Labs 360 project to show how we are building the world's greatest telescope yet, the James Webb Space Telescope (JWST). For the future, I see the greatest challenges for all the sciences in continued public outreach and inspiration. Outreach, so the public knows why we are doing what we are doing, and what difference it makes for them today and in the long-term future. Who knows what our destiny may be? It could be glorious, or not, depending on how we all behave. Inspiration, so that the most creative and inquisitive minds can pursue the scientific and engineering discoveries that are at the heart of so much of human prosperity, health, and progress. And, of course, national and local security depend on those discoveries too; scientists have been working with "the government" throughout recorded history. For the Lindau Nobel experiment, we have a truly abundant supply of knowledge and excitement, through the interactions of young scientists with the Nobelists, and through the lectures and the video recordings we can now share with the whole world across the Internet. But the challenge is always to draw attention! With 7 billion inhabitants on Earth, trying to earn a living and have some fun, there are plenty of competing opportunities and demands on us all. So what will draw attention to our efforts at Lindau? These days, word of mouth has become word of (computer) mouse, and ideas propagate as viruses ( or memes) across the Internet according to the interests of the participants. So our challenge is to find and match those interests, so that the efforts of our scientists, photographers, moviemakers, and writers are rewarded by our public. The world changes every day, so there

  12. myGenomeBrowser: building and sharing your own genome browser.

    Science.gov (United States)

    Carrere, Sébastien; Gouzy, Jérôme

    2017-04-15

    myGenomeBrowser is a web-based environment that provides biologists with a way to build, query and share their genome browsers. This tool, that builds on JBrowse, is designed to give users more autonomy while simplifying and minimizing intervention from system administrators. We have extended genome browser basic features to allow users to query, analyze and share their data. myGenomeBrowser is freely available at https://bbric-pipelines.toulouse.inra.fr/myGenomeBrowser and includes tutorial screencasts. Source code and installation instructions can be found at https://framagit.org/BBRIC/myGenomeBrowser . myGenomeBrowser is open-source and mainly implemented in Perl, JavaScript, Apache and Docker. sebastien.carrere@inra.fr. © The Author 2017. Published by Oxford University Press.

  13. UniSchooLabs Toolkit: Tools and Methodologies to Support the Adoption of Universities’ Remote and Virtual Labs in Schools

    Directory of Open Access Journals (Sweden)

    Augusto Chioccariello

    2012-11-01

    Full Text Available The UniSchooLabs project aims at creating an infrastructure supporting web access to remote/virtual labs and associated educational resources to engage learners with hands-on and minds-on activities in science, technology and math in schools. The UniSchooLabs tool-kit supports the teacher in selecting a remote or virtual lab and developing a lab activity based on an inquiry model template. While working with the toolkit the teacher has access to three main features: a a catalogue of available online laboratories; b an archive of activities created by other users; c a tool for creating new activities or reusing existing ones.

  14. Opening keynote

    International Nuclear Information System (INIS)

    Rae, B.

    1997-01-01

    In his opening address, the former premier of Ontario summarized the background of the Macdonald Committee which was appointed by his government after it became increasingly apparent that the infrastructure of Hydro Ontario was far bigger than the province and the economy could afford, and that the service that had once given Ontario tremendous competitive advantage, in the form of relatively cheap electric power, had become unsustainable in an era of economic downturn and zero inflation. He stated that the debate about Hydro is part of a broader issue, and it is no longer possible to manage our electricity system as if we were a self-enclosed universe. He predicted that the North American electricity grid will become increasingly interdependent, and that Hydro will have to develop competitive price structures, both to hold its domestic market share and to compete for export sales. He outlined the most pressing issues for Hydro as being debt reduction, while pursuing internal changes to make the organization more efficient. Organizational changes such as the creation of Ontario Hydro International, Ontario Hydro Research, separation of generation operations from the grid, and establishment of separate price and efficiency targets for the autonomous organizations within the utility family, were moves in the right direction. Equally important is to make sure that however Hydro might develop in the future, it is going to be fair to customers, and that the billions of dollars invested in Hydro by Ontario taxpayers over the years, are safeguarded

  15. Openness initiative

    Energy Technology Data Exchange (ETDEWEB)

    Duncan, S.S. [Los Alamos National Lab., NM (United States)

    1995-12-31

    Although antinuclear campaigns seem to be effective, public communication and education efforts on low-level radioactive waste have mixed results. Attempts at public information programs on low-level radioactive waste still focus on influencing public opinion. A question then is: {open_quotes}Is it preferable to have a program focus on public education that will empower individuals to make informed decisions rather than trying to influence them in their decisions?{close_quotes} To address this question, a case study with both quantitative and qualitative data will be used. The Ohio Low-Level Radioactive Waste Education Program has a goal to provide people with information they want/need to make their own decisions. The program initiated its efforts by conducting a statewide survey to determine information needed by people and where they turned for that information. This presentation reports data from the survey and then explores the program development process in which programs were designed and presented using the information. Pre and post data from the programs reveal attitude and knowledge shifts.

  16. Designing virtual science labs for the Islamic Academy of Delaware

    Science.gov (United States)

    AlZahrani, Nada Saeed

    Science education is a basic part of the curriculum in modern day classrooms. Instructional approaches to science education can take many forms but hands-on application of theory via science laboratory activities for the learner is common. Not all schools have the resources to provide the laboratory environment necessary for hands-on application of science theory. Some settings rely on technology to provide a virtual laboratory experience instead. The Islamic Academy of Delaware (IAD), a typical community-based organization, was formed to support and meet the essential needs of the Muslim community of Delaware. IAD provides science education as part of the overall curriculum, but cannot provide laboratory activities as part of the science program. Virtual science labs may be a successful model for students at IAD. This study was conducted to investigate the potential of implementing virtual science labs at IAD and to develop an implementation plan for integrating the virtual labs. The literature has shown us that the lab experience is a valuable part of the science curriculum (NBPTS, 2013, Wolf, 2010, National Research Council, 1997 & 2012). The National Research Council (2012) stressed the inclusion of laboratory investigations in the science curriculum. The literature also supports the use of virtual labs as an effective substitute for classroom labs (Babateen, 2011; National Science Teachers Association, 2008). Pyatt and Simms (2011) found evidence that virtual labs were as good, if not better than physical lab experiences in some respects. Although not identical in experience to a live lab, the virtual lab has been shown to provide the student with an effective laboratory experience in situations where the live lab is not possible. The results of the IAD teacher interviews indicate that the teachers are well-prepared for, and supportive of, the implementation of virtual labs to improve the science education curriculum. The investigator believes that with the

  17. GenomeVIP: a cloud platform for genomic variant discovery and interpretation.

    Science.gov (United States)

    Mashl, R Jay; Scott, Adam D; Huang, Kuan-Lin; Wyczalkowski, Matthew A; Yoon, Christopher J; Niu, Beifang; DeNardo, Erin; Yellapantula, Venkata D; Handsaker, Robert E; Chen, Ken; Koboldt, Daniel C; Ye, Kai; Fenyö, David; Raphael, Benjamin J; Wendl, Michael C; Ding, Li

    2017-08-01

    Identifying genomic variants is a fundamental first step toward the understanding of the role of inherited and acquired variation in disease. The accelerating growth in the corpus of sequencing data that underpins such analysis is making the data-download bottleneck more evident, placing substantial burdens on the research community to keep pace. As a result, the search for alternative approaches to the traditional "download and analyze" paradigm on local computing resources has led to a rapidly growing demand for cloud-computing solutions for genomics analysis. Here, we introduce the Genome Variant Investigation Platform (GenomeVIP), an open-source framework for performing genomics variant discovery and annotation using cloud- or local high-performance computing infrastructure. GenomeVIP orchestrates the analysis of whole-genome and exome sequence data using a set of robust and popular task-specific tools, including VarScan, GATK, Pindel, BreakDancer, Strelka, and Genome STRiP, through a web interface. GenomeVIP has been used for genomic analysis in large-data projects such as the TCGA PanCanAtlas and in other projects, such as the ICGC Pilots, CPTAC, ICGC-TCGA DREAM Challenges, and the 1000 Genomes SV Project. Here, we demonstrate GenomeVIP's ability to provide high-confidence annotated somatic, germline, and de novo variants of potential biological significance using publicly available data sets. © 2017 Mashl et al.; Published by Cold Spring Harbor Laboratory Press.

  18. The NOAO Data Lab virtual storage system

    Science.gov (United States)

    Graham, Matthew J.; Fitzpatrick, Michael J.; Norris, Patrick; Mighell, Kenneth J.; Olsen, Knut; Stobie, Elizabeth B.; Ridgway, Stephen T.; Bolton, Adam S.; Saha, Abhijit; Huang, Lijuan W.

    2016-07-01

    Collaborative research/computing environments are essential for working with the next generations of large astronomical data sets. A key component of them is a distributed storage system to enable data hosting, sharing, and publication. VOSpace1 is a lightweight interface providing network access to arbitrary backend storage solutions and endorsed by the International Virtual Observatory Alliance (IVOA). Although similar APIs exist, such as Amazon S3, WebDav, and Dropbox, VOSpace is designed to be protocol agnostic, focusing on data control operations, and supports asynchronous and third-party data transfers, thereby minimizing unnecessary data transfers. It also allows arbitrary computations to be triggered as a result of a transfer operation: for example, a file can be automatically ingested into a database when put into an active directory or a data reduction task, such as Sextractor, can be run on it. In this paper, we shall describe the VOSpace implementations that we have developed for the NOAO Data Lab. These offer both dedicated remote storage, accessible as a local file system via FUSE, and a local VOSpace service to easily enable data synchronization.

  19. Featured Image: Making Dust in the Lab

    Science.gov (United States)

    Kohler, Susanna

    2017-12-01

    This remarkable photograph (which spans only 10 m across; click for a full view) reveals what happens when you form dust grains in a laboratory under conditions similar to those of interstellar space. The cosmic life cycle of dust grains is not well understood we know that in the interstellar medium (ISM), dust is destroyed at a higher rate than it is produced by stellar sources. Since the amount of dust in the ISM stays constant, however, there must be additional sources of dust production besides stars. A team of scientists led by Daniele Fulvio (Pontifical Catholic University of Rio de Janeiro and the Max Planck Institute for Astronomy at the Friedrich Schiller University Jena) have now studied formation mechanisms of dust grains in the lab by mimicking low-temperature ISM conditions and exploring how, under these conditions, carbonaceous materials condense from gas phase to form dust grains. To read more about their results and see additional images, check out the paper below.CitationDaniele Fulvio et al 2017 ApJS 233 14. doi:10.3847/1538-4365/aa9224

  20. BOREAS TE-1 SSA Soil Lab Data

    Science.gov (United States)

    Hall, Forrest G. (Editor); Knapp, David E. (Editor); Nerbas, Tim; Anderson, Darwin

    2000-01-01

    This data set was collected by TE-1 to provide a set of soil properties for BOREAS investigators in the SSA. The soil samples were collected at sets of soil pits in 1993 and 1994. Each set of soil pits was in the vicinity of one of the five flux towers in the BOREAS SSA. The collected soil samples were sent to a lab, where the major soil properties were determined. These properties include, but are not limited to, soil horizon; dry soil color; pH; bulk density; total, organic, and inorganic carbon; electric conductivity; cation exchange capacity; exchangeable sodium, potassium, calcium, magnesium, and hydrogen; water content at 0.01, 0.033, and 1.5 MPascals; nitrogen; phosphorus; particle size distribution; texture; pH of the mineral soil and of the organic soil; extractable acid; and sulfur. The data are stored in tabular ASCII text files. The data files are available on a CD-ROM (see document number 20010000884), or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).

  1. Di-hadron production at Jefferson Lab

    Energy Technology Data Exchange (ETDEWEB)

    Anefalos Pereira, Sergio [Lab. Naz. Frascati, Frascati, Italy; et. al.,

    2014-10-01

    Semi-inclusive deep inelastic scattering (SIDIS) has been used extensively in recent years as an important testing ground for QCD. Studies so far have concentrated on better determination of parton distribution functions, distinguishing between the quark and antiquark contributions, and understanding the fragmentation of quarks into hadrons. Hadron pair (di-hadron) SIDIS provides information on the nucleon structure and hadronization dynamics that complement single hadron SIDIS. Di-hadrons allow the study of low- and high-twist distribution functions and Dihadron Fragmentation Functions (DiFF). Together with the twist-2 PDFs ( f1, g1, h1), the Higher Twist (HT) e and hL functions are very interesting because they offer insights into the physics of the largely unexplored quark-gluon correlations, which provide access into the dynamics inside hadrons. The CLAS spectrometer, installed in Hall-B at Jefferson Lab, has collected data using the CEBAF 6 GeV longitudinally polarized electron beam on longitudinally polarized solid NH3 targets. Preliminary results on di-hadron beam-, target- and double-spin asymmetries will be presented.

  2. Refined Pichia pastoris reference genome sequence

    Science.gov (United States)

    Sturmberger, Lukas; Chappell, Thomas; Geier, Martina; Krainer, Florian; Day, Kasey J.; Vide, Ursa; Trstenjak, Sara; Schiefer, Anja; Richardson, Toby; Soriaga, Leah; Darnhofer, Barbara; Birner-Gruenberger, Ruth; Glick, Benjamin S.; Tolstorukov, Ilya; Cregg, James; Madden, Knut; Glieder, Anton

    2016-01-01

    Strains of the species Komagataella phaffii are the most frequently used “Pichia pastoris” strains employed for recombinant protein production as well as studies on peroxisome biogenesis, autophagy and secretory pathway analyses. Genome sequencing of several different P. pastoris strains has provided the foundation for understanding these cellular functions in recent genomics, transcriptomics and proteomics experiments. This experimentation has identified mistakes, gaps and incorrectly annotated open reading frames in the previously published draft genome sequences. Here, a refined reference genome is presented, generated with genome and transcriptome sequencing data from multiple P. pastoris strains. Twelve major sequence gaps from 20 to 6000 base pairs were closed and 5111 out of 5256 putative open reading frames were manually curated and confirmed by RNA-seq and published LC-MS/MS data, including the addition of new open reading frames (ORFs) and a reduction in the number of spliced genes from 797 to 571. One chromosomal fragment of 76 kbp between two previous gaps on chromosome 1 and another 134 kbp fragment at the end of chromosome 4, as well as several shorter fragments needed re-orientation. In total more than 500 positions in the genome have been corrected. This reference genome is presented with new chromosomal numbering, positioning ribosomal repeats at the distal ends of the four chromosomes, and includes predicted chromosomal centromeres as well as the sequence of two linear cytoplasmic plasmids of 13.1 and 9.5 kbp found in some strains of P. pastoris. PMID:27084056

  3. LOD lab : Scalable linked data processing

    NARCIS (Netherlands)

    Beek, Wouter; Rietveld, Laurens; Ilievski, F.; Schlobach, Stefan

    2017-01-01

    With tens if not hundreds of billions of logical statements, the Linked Open Data (LOD) is one of the biggest knowledge bases ever built. As such it is a gigantic source of information for applications in various domains, but also given its size an ideal test-bed for knowledge representation and

  4. Opening address

    International Nuclear Information System (INIS)

    Henrich, E.W.

    2005-01-01

    Full text: It is an honour for me to make this opening address on behalf of the European Commission which has cooperated with the International Atomic Energy Agency in organizing this Conference, and in particular on behalf of Hans Forsstroem from the Directorate-General, Research, who will arrive only later this week. Protection of the environment is, and will continue to be, an important consideration in the development and application of soundly based radiation protection standards. Current standards rest largely on the premise that, in protecting man, the environment is afforded an adequate level of protection. While this premise is broadly accepted by the radiation protection profession, it has come under increasing challenge in recent years. This challenge has not arisen because of any observable damage to the environment while operating within current standards. Rather, it has different origins including: - The robustness of the premise that protection of man affords protection of the environment, in particular the extent to which it is based on value judgements as opposed to rigorous scientific argument; - The more explicit inclusion of protection of the environment into national legislation on radiation protection and the need to demonstrate compliance; - A desire to achieve greater comparability between radiation and other pollutants. These trends were recognized by the Commission in the late 1990s and, as a result, the topic of protection of the environment was included as an important element of the European Union's 5th Research Framework Programme. Community support has been given to the FASSET project about which we will hear much during this Conference. This multinational project is providing much of the scientific basis underpinning and informing ongoing discussions on the development of a system of protection for the environment. Much, however, remains to be done to establish a well conceived and practicable system for protection of the environment

  5. A new LabVIEW interface for MDSplus

    Energy Technology Data Exchange (ETDEWEB)

    Manduchi, G., E-mail: gabriele.manduchi@igi.cnr.it [Consorzio RFX, Euratom-ENEA Association, Padova (Italy); De Marchi, E. [Department of Information Engineering, Padova University (Italy); Mandelli, A. [National Instruments (Italy)

    2013-10-15

    Highlights: ► Integration object oriented data access layer in LabVIEW. ► A new component of the MDSplus data acquisition package. ► A new approach in the graphical presentation of data acquisition systems. -- Abstract: The paper presents a new interface providing full integration of MDSplus in LabVIEW, based on the recent features of MDSplus, in particular, data streaming, multithreading and Object Oriented interface. Data streaming support fits into the data driven concept of LabVIEW and multithreading is a native concept in LabVIEW. The object oriented interface of MDSplus defines a set of classes which map specific functionality, such as Tree and TreeNode to represent pulse files and data items, respectively, and fits naturally into the LabVIEW Object Oriented programming interface (LVOOP) introduced in version 8.2. MDSplus objects have been mapped onto LabVIEW objects, which act as wrappers to the underlying MDSplus object instance. This approach allows exporting the full MDSplus functionality into LabVIEW retaining the language-independent system view provided by the MDSplus object oriented interface.

  6. A new LabVIEW interface for MDSplus

    International Nuclear Information System (INIS)

    Manduchi, G.; De Marchi, E.; Mandelli, A.

    2013-01-01

    Highlights: ► Integration object oriented data access layer in LabVIEW. ► A new component of the MDSplus data acquisition package. ► A new approach in the graphical presentation of data acquisition systems. -- Abstract: The paper presents a new interface providing full integration of MDSplus in LabVIEW, based on the recent features of MDSplus, in particular, data streaming, multithreading and Object Oriented interface. Data streaming support fits into the data driven concept of LabVIEW and multithreading is a native concept in LabVIEW. The object oriented interface of MDSplus defines a set of classes which map specific functionality, such as Tree and TreeNode to represent pulse files and data items, respectively, and fits naturally into the LabVIEW Object Oriented programming interface (LVOOP) introduced in version 8.2. MDSplus objects have been mapped onto LabVIEW objects, which act as wrappers to the underlying MDSplus object instance. This approach allows exporting the full MDSplus functionality into LabVIEW retaining the language-independent system view provided by the MDSplus object oriented interface

  7. Can Direct Measurement Videos Inspire Lab-like Learning?

    Science.gov (United States)

    Vonk, M.; Bohacek, P. H.

    2014-12-01

    Hands-on labs can offer students a rare opportunity to confront the laws of physics first hand and to gain experience using science practices. As such, hands-on labs are an important learning tool which have played a foundational role in science education since the time of Galileo. But labs also have features that make them difficult to implement in practice. They are often time consuming for the instructor to plan and setup, time consuming for students to perform, expensive to implement, and fraught with potential missteps that can send confused students into a spiral of misunderstanding. Our Direct Measurement Video team is working to create several series' of videos with an interface that allows students to interact with them in a way that (we hope) will start to feel lab-like, but with fewer of the impediments that tend to undermine lab-learning in the real world. We hope that lab-like videos will soon provide a needed complement to traditional hands-on labs in science classrooms across the nation. In this talk, I will present our vision of the pedagogical possibilities of video and highlight our progress toward the goal. This work is supported by NSF TUES award #1245268

  8. Personal genomics services: whose genomes?

    Science.gov (United States)

    Gurwitz, David; Bregman-Eschet, Yael

    2009-07-01

    New companies offering personal whole-genome information services over the internet are dynamic and highly visible players in the personal genomics field. For fees currently ranging from US$399 to US$2500 and a vial of saliva, individuals can now purchase online access to their individual genetic information regarding susceptibility to a range of chronic diseases and phenotypic traits based on a genome-wide SNP scan. Most of the companies offering such services are based in the United States, but their clients may come from nearly anywhere in the world. Although the scientific validity, clinical utility and potential future implications of such services are being hotly debated, several ethical and regulatory questions related to direct-to-consumer (DTC) marketing strategies of genetic tests have not yet received sufficient attention. For example, how can we minimize the risk of unauthorized third parties from submitting other people's DNA for testing? Another pressing question concerns the ownership of (genotypic and phenotypic) information, as well as the unclear legal status of customers regarding their own personal information. Current legislation in the US and Europe falls short of providing clear answers to these questions. Until the regulation of personal genomics services catches up with the technology, we call upon commercial providers to self-regulate and coordinate their activities to minimize potential risks to individual privacy. We also point out some specific steps, along the trustee model, that providers of DTC personal genomics services as well as regulators and policy makers could consider for addressing some of the concerns raised below.

  9. ADS Labs: Supporting Information Discovery in Science Education

    Science.gov (United States)

    Henneken, E. A.

    2013-04-01

    The SAO/NASA Astrophysics Data System (ADS) is an open access digital library portal for researchers in astronomy and physics, operated by the Smithsonian Astrophysical Observatory (SAO) under a NASA grant, successfully serving the professional science community for two decades. Currently there are about 55,000 frequent users (100+ queries per year), and up to 10 million infrequent users per year. Access by the general public now accounts for about half of all ADS use, demonstrating the vast reach of the content in our databases. The visibility and use of content in the ADS can be measured by the fact that there are over 17,000 links from Wikipedia pages to ADS content, a figure comparable to the number of links that Wikipedia has to OCLC's WorldCat catalog. The ADS, through its holdings and innovative techniques available in ADS Labs, offers an environment for information discovery that is unlike any other service currently available to the astrophysics community. Literature discovery and review are important components of science education, aiding the process of preparing for a class, project, or presentation. The ADS has been recognized as a rich source of information for the science education community in astronomy, thanks to its collaborations within the astronomy community, publishers and projects like ComPADRE. One element that makes the ADS uniquely relevant for the science education community is the availability of powerful tools to explore aspects of the astronomy literature as well as the relationship between topics, people, observations and scientific papers. The other element is the extensive repository of scanned literature, a significant fraction of which consists of historical literature.

  10. Nutritional genomics.

    Science.gov (United States)

    Ordovas, Jose M; Corella, Dolores

    2004-01-01

    Nutritional genomics has tremendous potential to change the future of dietary guidelines and personal recommendations. Nutrigenetics will provide the basis for personalized dietary recommendations based on the individual's genetic make up. This approach has been used for decades for certain monogenic diseases; however, the challenge is to implement a similar concept for common multifactorial disorders and to develop tools to detect genetic predisposition and to prevent common disorders decades before their manifestation. The preliminary results involving gene-diet interactions for cardiovascular diseases and cancer are promising, but mostly inconclusive. Success in this area will require the integration of different disciplines and investigators working on large population studies designed to adequately investigate gene-environment interactions. Despite the current difficulties, preliminary evidence strongly suggests that the concept should work and that we will be able to harness the information contained in our genomes to achieve successful aging using behavioral changes; nutrition will be the cornerstone of this endeavor.

  11. HGVA: the Human Genome Variation Archive.

    Science.gov (United States)

    Lopez, Javier; Coll, Jacobo; Haimel, Matthias; Kandasamy, Swaathi; Tarraga, Joaquin; Furio-Tari, Pedro; Bari, Wasim; Bleda, Marta; Rueda, Antonio; Gräf, Stefan; Rendon, Augusto; Dopazo, Joaquin; Medina, Ignacio

    2017-07-03

    High-profile genomic variation projects like the 1000 Genomes project or the Exome Aggregation Consortium, are generating a wealth of human genomic variation knowledge which can be used as an essential reference for identifying disease-causing genotypes. However, accessing these data, contrasting the various studies and integrating those data in downstream analyses remains cumbersome. The Human Genome Variation Archive (HGVA) tackles these challenges and facilitates access to genomic data for key reference projects in a clean, fast and integrated fashion. HGVA provides an efficient and intuitive web-interface for easy data mining, a comprehensive RESTful API and client libraries in Python, Java and JavaScript for fast programmatic access to its knowledge base. HGVA calculates population frequencies for these projects and enriches their data with variant annotation provided by CellBase, a rich and fast annotation solution. HGVA serves as a proof-of-concept of the genome analysis developments being carried out by the University of Cambridge together with UK's 100 000 genomes project and the National Institute for Health Research BioResource Rare-Diseases, in particular, deploying open-source for Computational Biology (OpenCB) software platform for storing and analyzing massive genomic datasets. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. GeoLab: A Geological Workstation for Future Missions

    Science.gov (United States)

    Evans, Cynthia; Calaway, Michael; Bell, Mary Sue; Li, Zheng; Tong, Shuo; Zhong, Ye; Dahiwala, Ravi

    2014-01-01

    The GeoLab glovebox was, until November 2012, fully integrated into NASA's Deep Space Habitat (DSH) Analog Testbed. The conceptual design for GeoLab came from several sources, including current research instruments (Microgravity Science Glovebox) used on the International Space Station, existing Astromaterials Curation Laboratory hardware and clean room procedures, and mission scenarios developed for earlier programs. GeoLab allowed NASA scientists to test science operations related to contained sample examination during simulated exploration missions. The team demonstrated science operations that enhance theThe GeoLab glovebox was, until November 2012, fully integrated into NASA's Deep Space Habitat (DSH) Analog Testbed. The conceptual design for GeoLab came from several sources, including current research instruments (Microgravity Science Glovebox) used on the International Space Station, existing Astromaterials Curation Laboratory hardware and clean room procedures, and mission scenarios developed for earlier programs. GeoLab allowed NASA scientists to test science operations related to contained sample examination during simulated exploration missions. The team demonstrated science operations that enhance the early scientific returns from future missions and ensure that the best samples are selected for Earth return. The facility was also designed to foster the development of instrument technology. Since 2009, when GeoLab design and construction began, the GeoLab team [a group of scientists from the Astromaterials Acquisition and Curation Office within the Astromaterials Research and Exploration Science (ARES) Directorate at JSC] has progressively developed and reconfigured the GeoLab hardware and software interfaces and developed test objectives, which were to 1) determine requirements and strategies for sample handling and prioritization for geological operations on other planetary surfaces, 2) assess the scientific contribution of selective in-situ sample

  13. A mobile design lab for user-driven innovation

    DEFF Research Database (Denmark)

    Christiansen, Ellen; Kanstrup, Anne Marie

    2007-01-01

    The paper presents the history and conceptual foundation for the Mobile Design Lab, ment to support both designers and users in the acts of user-driven innovation. The Mobile Design Lab is based on Vygotsky's theory of tool- and language-mediation, and was created in 2004 to support research...... to get 'into the street'. To support these moves might seem simple, but it is in practice not at all easy. As for today the Mobile Design Lab comprises tools and techniques for categorization, articulation and concretizatoin in design projects involving lead users as well as ordinary users, and invisible...

  14. Living lab: Format for rehearsing a new (service) practice

    DEFF Research Database (Denmark)

    Yndigegn, Signe; Aakjær, Marie Kirstejn

    service platforms takes place in the format of living labs. We characterize living labs as the design of experiential spaces where ‘what is’ and ‘what could be’ are explored over a longer period of engagement. The labs are staged to integrate multiple stakeholders’ issues and resources and to create new......Citizen engagement and the citizens as a resource are key concepts in rethinking the Danish welfare system to meet the challenges of delivering better services for the elderly, while simultaneously reducing the cost of healthcare. In this method paper, we address how the co-design of new digital...

  15. Visualization for genomics: the Microbial Genome Viewer.

    NARCIS (Netherlands)

    Kerkhoven, R.; Enckevort, F.H.J. van; Boekhorst, J.; Molenaar, D; Siezen, R.J.

    2004-01-01

    SUMMARY: A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a

  16. Opening Lab Doors to High School Students: Keys to a Successful Engagement

    Science.gov (United States)

    Slayton, Rebecca M.; Nelson, Keith A.

    2005-01-01

    A project to invite high school students into research laboratories to plan and carry out an investigation over several weeks, using the sophisticated equipment available there, can help to break down social barriers and enhance outreach activities.

  17. HTC Vive MeVisLab integration via OpenVR for medical applications

    OpenAIRE

    Egger, Jan; Gall, Markus; Wallner, Jürgen; Boechat, Pedro; Hann, Alexander; Li, Xing; Chen, Xiaojun; Schmalstieg, Dieter

    2017-01-01

    Virtual Reality, an immersive technology that replicates an environment via computer-simulated reality, gets a lot of attention in the entertainment industry. However, VR has also great potential in other areas, like the medical domain, Examples are intervention planning, training and simulation. This is especially of use in medical operations, where an aesthetic outcome is important, like for facial surgeries. Alas, importing medical data into Virtual Reality devices is not necessarily trivi...

  18. More than Meets the Eye--Infrared Cameras in Open-Ended University Thermodynamics Labs

    Science.gov (United States)

    Melander, Emil; Haglund, Jesper; Weiszflog, Matthias; Andersson, Staffan

    2016-01-01

    Educational research has found that students have challenges understanding thermal science. Undergraduate physics students have difficulties differentiating basic thermal concepts, such as heat, temperature, and internal energy. Engineering students have been found to have difficulties grasping surface emissivity as a thermal material property.…

  19. What did the Disruptive Media Learning Lab ever do for us?

    Directory of Open Access Journals (Sweden)

    Kirsty Kift

    2017-11-01

    Full Text Available Picture this. The Lanchester Library, Coventry University, 2014. The Disruptive Media Learning Lab (DMLL opens on the top floor amongst a flurry of raised eyebrows and unanswered questions. ‘What is it?’, ‘Why is it in the Library?’ and ‘Who designed the wooden hill?’ Our Academic Liaison Librarian team were asked to move in there alongside a DMLL team comprising educational researchers and principal project leads, each specializing in a flavour of teaching practice such as open, flipped and gamification. A learning technologist, project and admin staff and student activators add to the mix. Still not sure what that would mean for a library? Neither were we. This article will take you through the reasons behind this alien landing, past the hill and the grass and onto the plains of what the DMLL ever did for the Library and our students.

  20. Link Analysis in the Mission Planning Lab

    Science.gov (United States)

    McCarthy, Jessica A.; Cervantes, Benjamin W.; Daugherty, Sarah C.; Arroyo, Felipe; Mago, Divyang

    2011-01-01

    The legacy communications link analysis software currently used at Wallops Flight Facility involves processes that are different for command destruct, radar, and telemetry. There is a clear advantage to developing an easy-to-use tool that combines all the processes in one application. Link Analysis in the Mission Planning Lab (MPL) uses custom software and algorithms integrated with Analytical Graphics Inc. Satellite Toolkit (AGI STK). The MPL link analysis tool uses pre/post-mission data to conduct a dynamic link analysis between ground assets and the launch vehicle. Just as the legacy methods do, the MPL link analysis tool calculates signal strength and signal- to-noise according to the accepted processes for command destruct, radar, and telemetry assets. Graphs and other custom data are generated rapidly in formats for reports and presentations. STK is used for analysis as well as to depict plume angles and antenna gain patterns in 3D. The MPL has developed two interfaces with the STK software (see figure). The first interface is an HTML utility, which was developed in Visual Basic to enhance analysis for plume modeling and to offer a more user friendly, flexible tool. A graphical user interface (GUI) written in MATLAB (see figure upper right-hand corner) is also used to quickly depict link budget information for multiple ground assets. This new method yields a dramatic decrease in the time it takes to provide launch managers with the required link budgets to make critical pre-mission decisions. The software code used for these two custom utilities is a product of NASA's MPL.

  1. Pioneering CERN lab celebrates 50 years

    CERN Multimedia

    2004-01-01

    In a bid to raise local awareness and to celebrate its 50-year anniversary, CERN, a publicly-funded laboratory grouping scientists from 85 different countries, will hold a one-off open day in October for the general public. "We have added a lot to mankind's knowledge of the universe and that is what we were founded for", said CERN's chief spokesman James Gillies

  2. A New Era for Jefferson Lab

    International Nuclear Information System (INIS)

    McKeown, R. D.; Montgomery, H. E.; Pennington, M. R.

    2016-01-01

    On a cool Saturday morning in late April a seemingly endless stream of cars turned off Jefferson Avenue in Newport News, Virginia, bringing 12,000 people ages 1 to 91 to the Open House to learn more about “the new era in science” at the Thomas Jefferson National Accelerator Facility. Here, the visitors were dazzled by the complex equipment, the enthusiastic staff, and the advanced technology at the Laboratory.

  3. Lurking in the Lab: Analysis of Data from Molecular Biology Laboratory Instruments

    Directory of Open Access Journals (Sweden)

    Jen Ferguson

    2012-01-01

    Full Text Available OBJECTIVE: This project examined primary research data files found on instruments in a molecular biology teaching laboratory. Experimental data files were analyzed in order to learn more about the types of data generated by these instruments (e.g. file formats, and to evaluate current laboratory data management practices.SETTING: This project examined experimental data files from instruments in a teaching laboratory at Brandeis University.METHODOLOGY: Experimental data files and associated metadata on instrument hard drives were captured and analyzed using Xplorer2 software. Formats were categorized as proprietary or open, and characteristics such as file naming conventions were noted. Discussions with the faculty member and lab staff guided the project scope and informed the findings.RESULTS: Files in both proprietary and open formats were found on the instrument hard drives. 62% of the experimental data files were in proprietary formats. Image files in various formats accounted for the most prevalent types of data found. Instrument users varied widely in their approaches to data management tasks such as file naming conventions.CONCLUSIONS: This study found inconsistent approaches to managing data on laboratory instruments. Prevalence of proprietary file formats is a concern with this type of data. Students express frustration in working with these data, and files in these proprietary formats could pose curation and preservation challenges in the future. Teaching labs afford an opportunity for librarians interested in learning more about primary research data and data management practices.

  4. Quantitative analysis of lab-to-lab variability in Caco-2 permeability assays.

    Science.gov (United States)

    Lee, Jong Bong; Zgair, Atheer; Taha, Dhiaa A; Zang, Xiaowei; Kagan, Leonid; Kim, Tae Hwan; Kim, Min Gi; Yun, Hwi-Yeol; Fischer, Peter M; Gershkovich, Pavel

    2017-05-01

    In this study, Caco-2 permeability results from different laboratories were compared. Six different sets of apparent permeability coefficient (P app ) values reported in the literature were compared to experimental P app obtained in our laboratory. The differences were assessed by determining the root mean square error (RMSE) values between the datasets, which reached levels as high as 0.581 for the training set compounds, i.e. ten compounds with known effective human permeability (P eff ). The consequences of these differences in P app for prediction of oral drug absorption were demonstrated by introducing the P app into the absorption and pharmacokinetics simulation software application GastroPlus™ for prediction of the fraction absorbed (F a ) in humans using calibrated "user-defined permeability models". The RMSE were calculated to assess the differences between the simulated F a and experimental values reported in the literature. The RMSE for F a simulated with the permeability model calibrated using experimental P app from our laboratory was 0.128. When the calibration was performed using P app from literature datasets, the RMSE values for F a were higher in all cases except one. This study shows quantitative lab-to-lab variability of Caco-2 permeability results and the potential consequences this can have in the use of these results for predicting intestinal absorption of drugs. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Enabling miniaturised personalised diagnostics: from lab-on-a-chip to lab-in-a-drop.

    Science.gov (United States)

    Koo, Kevin M; Wee, Eugene J H; Wang, Yuling; Trau, Matt

    2017-09-26

    The concept of personalised diagnostics is to direct accurate clinical decisions based on an individual's unique disease molecular profile. Lab-on-a-chip (LOC) systems are prime personalised diagnostics examples which seek to perform an entire sample-to-outcome detection of disease nucleic acid (NA) biomarkers on a single miniaturised platform with minimal user handling. Despite the great potential of LOC devices in providing rapid, portable, and inexpensive personalised diagnosis at the point-of-care (POC), the translation of this technology into widespread use has still been hampered by the need for sophisticated and complex engineering. As an alternative miniaturised diagnostics platform free of precision fabrication, there have been recent developments towards a solution-based lab-in-a-drop (LID) system by which an entire laboratory-based diagnostics workflow could be downscaled and integrated within a singular fluid droplet for POC detection of NA biomarkers. In contrast to existing excellent reviews on miniaturised LOC fabrication and individual steps of NA biomarker sensing, we herein focus on miniaturised solution-based NA biosensing strategies suited for integrated LID personalised diagnostics development. In this review, we first evaluate the three fundamental bioassay steps for miniaturised NA biomarker detection: crude sample preparation, isothermal target amplification, and detection readout of amplicons. Then, we provide insights into research advancements towards a functional LID system which integrates all three of the above-mentioned fundamental steps. Finally, we discuss perspectives and future directions of LID diagnostic platforms in personalised medicine applications.

  6. Open Standards, Open Source, and Open Innovation: Harnessing the Benefits of Openness

    Science.gov (United States)

    Committee for Economic Development, 2006

    2006-01-01

    Digitization of information and the Internet have profoundly expanded the capacity for openness. This report details the benefits of openness in three areas--open standards, open-source software, and open innovation--and examines the major issues in the debate over whether openness should be encouraged or not. The report explains each of these…

  7. WheelerLab: An interactive program for sequence stratigraphic analysis of seismic sections, outcrops and well sections and the generation of chronostratigraphic sections and dynamic chronostratigraphic sections

    Science.gov (United States)

    Amosu, Adewale; Sun, Yuefeng

    WheelerLab is an interactive program that facilitates the interpretation of stratigraphic data (seismic sections, outcrop data and well sections) within a sequence stratigraphic framework and the subsequent transformation of the data into the chronostratigraphic domain. The transformation enables the identification of significant geological features, particularly erosional and non-depositional features that are not obvious in the original seismic domain. Although there are some software products that contain interactive environments for carrying out chronostratigraphic analysis, none of them are open-source codes. In addition to being open source, WheelerLab adds two important functionalities not present in currently available software: (1) WheelerLab generates a dynamic chronostratigraphic section and (2) WheelerLab enables chronostratigraphic analysis of older seismic data sets that exist only as images and not in the standard seismic file formats; it can also be used for the chronostratigraphic analysis of outcrop images and interpreted well sections. The dynamic chronostratigraphic section sequentially depicts the evolution of the chronostratigraphic chronosomes concurrently with the evolution of identified genetic stratal packages. This facilitates a better communication of the sequence-stratigraphic process. WheelerLab is designed to give the user both interactive and interpretational control over the transformation; this is most useful when determining the correct stratigraphic order for laterally separated genetic stratal packages. The program can also be used to generate synthetic sequence stratigraphic sections for chronostratigraphic analysis.

  8. WheelerLab: An interactive program for sequence stratigraphic analysis of seismic sections, outcrops and well sections and the generation of chronostratigraphic sections and dynamic chronostratigraphic sections

    Directory of Open Access Journals (Sweden)

    Adewale Amosu

    2017-01-01

    Full Text Available WheelerLab is an interactive program that facilitates the interpretation of stratigraphic data (seismic sections, outcrop data and well sections within a sequence stratigraphic framework and the subsequent transformation of the data into the chronostratigraphic domain. The transformation enables the identification of significant geological features, particularly erosional and non-depositional features that are not obvious in the original seismic domain. Although there are some software products that contain interactive environments for carrying out chronostratigraphic analysis, none of them are open-source codes. In addition to being open source, WheelerLab adds two important functionalities not present in currently available software: (1 WheelerLab generates a dynamic chronostratigraphic section and (2 WheelerLab enables chronostratigraphic analysis of older seismic data sets that exist only as images and not in the standard seismic file formats; it can also be used for the chronostratigraphic analysis of outcrop images and interpreted well sections. The dynamic chronostratigraphic section sequentially depicts the evolution of the chronostratigraphic chronosomes concurrently with the evolution of identified genetic stratal packages. This facilitates a better communication of the sequence-stratigraphic process. WheelerLab is designed to give the user both interactive and interpretational control over the transformation; this is most useful when determining the correct stratigraphic order for laterally separated genetic stratal packages. The program can also be used to generate synthetic sequence stratigraphic sections for chronostratigraphic analysis.

  9. Chapel Hill, NC Lab--Office of Research and Development

    Science.gov (United States)

    ORD scientists at the state-of-the-art lab in Chapel Hill conduct integrated research to improve our understanding of how social, economic, and health related factors affect an individual’s or com-munity’s health risks.

  10. Safety in the Chemical Laboratory: Hazards in a Photography Lab.

    Science.gov (United States)

    Houk, Cliff; Hart, Charles

    1987-01-01

    Described are case studies illustrating chemical hazards in a photography lab due to compounds containing cyanide. Suggestions for preventing problems including proper procedures, housekeeping, facilities, and ventilation are considered. (RH)

  11. VirexLab a Virtual Reality Educational System, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — The VirexLab, the centerpiece of this Tietronix proposal offers significant innovation to NASA and to the Marshall Space Flight Center, implementing the Biological...

  12. City Labs as Vehicles for Innovation in Urban Planning Processes

    Directory of Open Access Journals (Sweden)

    Christian Scholl

    2016-12-01

    Full Text Available This paper assesses the role of urban experiments for local planning processes through a case-based analysis of the city lab of Maastricht. In conjunction with this, the article offers three contributions, as additional elements. Firstly, the paper develops a set of defining characteristics of city labs as an analytical concept which is relevant for discussions about (collaborative planning. Secondly, it refines the literature on collaborative planning by drawing attention to experimentation and innovation. Thirdly, the paper assesses the potential of city labs to contribute to the innovation of urban governance. The work draws from the literature on experimentation and learning as well as the literature on collaborative urban planning. In the conclusions, we discuss the potential of city labs as vehicles for learning about new urban planning approaches and their limitations as spaces for small-scale experimentation. The paper is based on research for the URB@Exp research project funded by JPI Urban Europe.

  13. Lab-scale hydrogen peroxide data from ECBC

    Data.gov (United States)

    U.S. Environmental Protection Agency — Data from small lab scale tests conducted at ECBC. It contains efficacy data as well as data on env conditions such as temperature, RH, and hydrogen peroxide vapor...

  14. Establishing an intelligent transportation systems (ITS) lab at LTRC.

    Science.gov (United States)

    2008-09-30

    The primary goal of this research project is to lay the foundation for establishing a state-of-the-art Intelligent Transportation Systems (ITS) : lab at the Louisiana Transportation Research Center (LTRC), where data will be collected, analyzed, and ...

  15. In silico and wet lab approaches to study transcriptional regulation

    NARCIS (Netherlands)

    Hestand, Matthew Scott

    2010-01-01

    Gene expression is a complicated process with multiple types of regulation, including binding of proteins termed transcription factors. This thesis looks at transcription factors and transcription factor binding site discovery through computational predictions and wet lab work to better elucidate

  16. Chapter 3 – VPPD-Lab: The Chemical Product Simulator

    DEFF Research Database (Denmark)

    Kalakul, Sawitree; Cignitti, Stefano; Zhang, L.

    2017-01-01

    for computer-aided chemical product design and evaluation, implemented in the software called VPPD-Lab, is presented. In the same way a typical process simulator works, the VPPD-Lab allows users to: (1) analyze chemical-based products by performing virtual experiments (product property and performance...... calculations), (2) predict the properties of products, and (3) create new product property and product performance models when needed. However, unlike process simulators, VPPD-Lab can also be used directly for (1) design of chemicals based products using design templates for various types of products......, such as single molecule products, formulations, blends, emulsions, and devices; and (2) to create new product design templates when the needed template for a desired product is not available. VPPD-Lab employs a suite of algorithms (such as database search, molecular and mixture blend design) and toolboxes (such...

  17. VirexLab a Virtual Reality Educational System Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The VirexLab, the centerpiece of this Tietronix proposal offers significant innovation to NASA and to the Marshall Space Flight Center, implementing the Biological...

  18. Genome Editing in Sugarcane: Challenges Ahead

    OpenAIRE

    Mohan, Chakravarthi

    2016-01-01

    Genome editing opens new and unique opportunities for researchers to enhance crop production. Until 2013, the zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) were the key tools used for genome editing applications. The advent of RNA-guided engineered nucleases - the type II clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 (CRISPR-associated) system from Streptococcus pyogenes holds great potential since it is simple, effective an...

  19. Gail Harlamoff: Executive Director, Life Lab Science Program

    OpenAIRE

    Rabkin, Sarah

    2010-01-01

    Gail Harlamoff is Executive Director of the Life Lab Science Program, a nationally recognized, award-winning nonprofit science and environmental organization located on the UC Santa Cruz campus. Founded in 1979, Life Lab helps schools develop gardens and implement curricula to enhance students’ learning about science, math, and the natural world. The program has trained tens of thousands of educators in more than 1400 schools across the country. Life Lab’s specialized initiatives inc...

  20. Qualification Lab Testing on M1 Abrams Engine Oil Filters

    Science.gov (United States)

    2016-11-01

    OIL FILTERS FINAL REPORT TFLRF No. 483 by Kristi K. Rutta U.S...the originator. UNCLASSIFIED QUALIFICATION LAB TESTING ON M1 ABRAMS ENGINE OIL FILTERS FINAL REPORT TFLRF No. 483 by Kristi K...TITLE AND SUBTITLE Qualification Lab Testing on M1 Abrams Engine Oil Filter 5a. CONTRACT NUMBER W56HZV-15-C-0030 5b. GRANT NUMBER 5c.