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......, thus making Open-Lab Framework more attractive for laboratories that seek to increase productivity through electronic data management....

  2. Comparative genomics of Lactobacillus and other LAB

    DEFF Research Database (Denmark)

    Wassenaar, Trudy M.; Lukjancenko, Oksana

    2014-01-01

    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......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...

  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. OpenLabNotes--An Electronic Laboratory Notebook Extension for OpenLabFramework.

    Science.gov (United States)

    List, Markus; Franz, Michael; Tan, Qihua; Mollenhauer, Jan; Baumbach, Jan

    2015-10-06

    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.

  5. OpenLabNotes - An Electronic Laboratory Notebook Extension for OpenLabFramework.

    Science.gov (United States)

    List, Markus; Franz, Michael; Tan, Qihua; Mollenhauer, Jan; Baumbach, Jan

    2015-09-01

    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 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.

  6. GeneLab: Open Science For Exploration

    Science.gov (United States)

    Galazka, Jonathan

    2018-01-01

    The NASA GeneLab project capitalizes on multi-omic technologies to maximize the return on spaceflight experiments. The GeneLab project houses spaceflight and spaceflight-relevant multi-omics data in a publicly accessible data commons, and collaborates with NASA-funded principal investigators to maximize the omics data from spaceflight and spaceflight-relevant experiments. I will discuss the current status of GeneLab and give specific examples of how the GeneLab data system has been used to gain insight into how biology responds to spaceflight conditions.

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

    CSIR Research Space (South Africa)

    Schaffers, H

    2007-06-01

    Full Text Available Living Labs are user-centric environments for open innovation characterized by early and continuous involvement of users and by user-driven rapid prototyping cycles. Establishing sustainable partnerships of stakeholders with a shared set of values...

  8. 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.

  9. 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

  10. 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...... and genetically engineered cell lines. OpenLabFramework is a newly developed web-application for sample tracking, particularly laid out to fill this gap, but with an open architecture allowing it to be extended for other biological materials and functional data. Its sample tracking mechanism is fully customizable...

  11. 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%.

  12. 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.

  13. 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

  14. 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.

  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. Hands-On Open Access Broadband Wireless Technology Lab Mapping Course Outcomes to Lab Experiments

    Directory of Open Access Journals (Sweden)

    Yazan Alqudah

    2012-10-01

    Full Text Available The unprecedented growth in wireless communication is offering opportunities and challenges for educators. Thanks to technology advances and job opportunities, more and more students are interested in wireless communications courses. However, bridging the gap between classroom and real-world experience remains a challenge. Advanced undergraduate communications courses typically focus more on theory. Some courses are given online, and lack hands-on experiments. Driven by feedback from industry and students, we propose practical laboratory experiments that attempt to bridge the gap between classroom and real world. The laboratory exercises take advantage of the infrastructure of deployed wireless networks and allow students to measure, and analyze data, as well as to interact. The proposed labs can be used even in online courses. This paper describes the experiments proposed, the procedures and typical results. The experiments are tied to course objective.

  17. Predicting statistical properties of open reading frames in bacterial genomes.

    Directory of Open Access Journals (Sweden)

    Katharina Mir

    Full Text Available An analytical model based on the statistical properties of Open Reading Frames (ORFs of eubacterial genomes such as codon composition and sequence length of all reading frames was developed. This new model predicts the average length, maximum length as well as the length distribution of the ORFs of 70 species with GC contents varying between 21% and 74%. Furthermore, the number of annotated genes is predicted with high accordance. However, the ORF length distribution in the five alternative reading frames shows interesting deviations from the predicted distribution. In particular, long ORFs appear more often than expected statistically. The unexpected depletion of stop codons in these alternative open reading frames cannot completely be explained by a biased codon usage in the +1 frame. While it is unknown if the stop codon depletion has a biological function, it could be due to a protein coding capacity of alternative ORFs exerting a selection pressure which prevents the fixation of stop codon mutations. The comparison of the analytical model with bacterial genomes, therefore, leads to a hypothesis suggesting novel gene candidates which can now be investigated in subsequent wet lab experiments.

  18. 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…

  19. 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

  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 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

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

    Directory of Open Access Journals (Sweden)

    Lum Karl

    2011-03-01

    Full Text Available Abstract 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

  7. LabKey Server: an open source platform for scientific data integration, analysis and collaboration.

    Science.gov (United States)

    Nelson, Elizabeth K; Piehler, Britt; Eckels, Josh; Rauch, Adam; Bellew, Matthew; Hussey, Peter; Ramsay, Sarah; Nathe, Cory; Lum, Karl; Krouse, Kevin; Stearns, David; Connolly, Brian; Skillman, Tom; Igra, Mark

    2011-03-09

    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. 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 organizations. It tracks

  8. 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.

  9. Easy research data handling with an OpenEarth DataLab for geo-monitoring research

    Science.gov (United States)

    Vanderfeesten, Maurice; van der Kuil, Annemiek; Prinčič, Alenka; den Heijer, Kees; Rombouts, Jeroen

    2015-04-01

    OpenEarth DataLab is an open source-based collaboration and processing platform to enable streamlined research data management from raw data ingest and transformation to interoperable distribution. It enables geo-scientists to easily synchronise, share, compute and visualise the dynamic and most up-to-date research data, scripts and models in multi-stakeholder geo-monitoring programs. This DataLab is developed by the Research Data Services team of TU Delft Library and 3TU.Datacentrum together with coastal engineers of Delft University of Technology and Deltares. Based on the OpenEarth software stack an environment has been developed to orchestrate numerous geo-related open source software components that can empower researchers and increase the overall research quality by managing research data; enabling automatic and interoperable data workflows between all the components with track & trace, hit & run data transformation processing in cloud infrastructure using MatLab and Python, synchronisation of data and scripts (SVN), and much more. Transformed interoperable data products (KML, NetCDF, PostGIS) can be used by ready-made OpenEarth tools for further analyses and visualisation, and can be distributed via interoperable channels such as THREDDS (OpenDAP) and GeoServer. An example of a successful application of OpenEarth DataLab is the Sand Motor, an innovative method for coastal protection in the Netherlands. The Sand Motor is a huge volume of sand that has been applied along the coast to be spread naturally by wind, waves and currents. Different research disciplines are involved concerned with: weather, waves and currents, sand distribution, water table and water quality, flora and fauna, recreation and management. Researchers share and transform their data in the OpenEarth DataLab, that makes it possible to combine their data and to see influence of different aspects of the coastal protection on their models. During the project the data are available only for the

  10. Neue Aufgaben für wissenschaftliche Bibliotheken: Das Beispiel Open Science Lab

    Directory of Open Access Journals (Sweden)

    Lambert Heller

    2015-10-01

    Full Text Available Vor dem Hintergrund des Aufkommens vieler neuer digitaler Werkzeuge und Methoden zur Unterstützung des wissenschaftlichen Arbeitens wird seit etwa fünf Jahren unter wissenschaftlichen Bibliothekaren in Deutschland immer häufiger über Innovationsmanagement diskutiert. Wie lassen sich relevante Trends und Herausforderungen rechtzeitig erkennen und mit den begrenzten Ressourcen einer Einrichtung des öffentlichen Dienstes adäquat aufgreifen, bis hin zu einer Veränderung der Bibliotheksstrategie? Der Beitrag behandelt das Modell des an der Technischen Informationsbibliothek Hannover (TIB 2013 ins Leben gerufenen Open Science Lab. Unter Leitung des Autors werden Trends beobachtet und aufgegriffen, um in enger Zusammenarbeit mit Wissenschaftlern und Wissenschaftlerinnen neue digitale Werkzeuge und Methoden zu erproben, eine neue Informationspraxis zu kultivieren und daraus Innovationen für das Dienste-Spektrum der Bibliothek abzuleiten. Dies wird beispielhaft anhand der beiden Schwerpunktthemen kollaboratives Schreiben sowie linked-data-basierte Forschungsinformationssysteme (FIS geschildert und diskutiert. Given the rise of many new digital tools and methods for supporting scientific work, the last five years have seen a lot of discussion amongst German academic librarians about innovation management. How can we discover relevant trends and challenges in time and respond to them adequately up to the point of changing whole library strategies, despite the limited resources of a public sector institution? The paper presents the model of the Open Science Lab which was set up at the German National Library of Science and Technology (TIB Hannover in 2013. Under the direction of the author and in close collaboration with scientific communities, the lab group keeps track of trends and selects some of them in order to try out new tools and methods. The ultimate aim is to cultivate new information practices and develop new, innovative

  11. 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

  12. Using Saccharomyces cerevisiae to test the mutagenicity of household compounds: an open ended hypothesis-driven teaching lab.

    Science.gov (United States)

    Marshall, Pamela A

    2007-01-01

    In our Fundamentals of Genetics lab, students perform a wide variety of labs to reinforce and extend the topics covered in lecture. I developed an active-learning lab to augment the lecture topic of mutagenesis. In this lab exercise, students determine if a compound they bring from home is a mutagen. Students are required to read extensive background material, perform research to find a potential mutagen to test, develop a hypothesis, and bring to the lab their own suspected mutagen. This lab uses a specially developed strain of Saccharomyces cerevisiae, D7, to determine if a compound is a mutagen. Mutagenesis of the D7 genome can lead to a scorable alteration in the phenotypes of this strain. Students outline and carry out a protocol for treatment of the yeast tester strain, utilizing the concept of dose/response and positive and negative controls. Students report on their results using a PowerPoint presentation to simulate giving a scientific presentation. The students' self-assessment of their knowledge indicated that, in all cases, the students felt that they knew more about the assay, mutagenesis, and the relationship between genotype and phenotype (P exercise.

  13. 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.

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

    International Nuclear Information System (INIS)

    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. (paper)

  15. 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.

  16. Ginseng Genome Database: an open-access platform for genomics of Panax ginseng.

    Science.gov (United States)

    Jayakodi, Murukarthick; Choi, Beom-Soon; Lee, Sang-Choon; Kim, Nam-Hoon; Park, Jee Young; Jang, Woojong; Lakshmanan, Meiyappan; Mohan, Shobhana V G; Lee, Dong-Yup; Yang, Tae-Jin

    2018-04-12

    The ginseng (Panax ginseng C.A. Meyer) is a perennial herbaceous plant that has been used in traditional oriental medicine for thousands of years. Ginsenosides, which have significant pharmacological effects on human health, are the foremost bioactive constituents in this plant. Having realized the importance of this plant to humans, an integrated omics resource becomes indispensable to facilitate genomic research, molecular breeding and pharmacological study of this herb. The first draft genome sequences of P. ginseng cultivar "Chunpoong" were reported recently. Here, using the draft genome, transcriptome, and functional annotation datasets of P. ginseng, we have constructed the Ginseng Genome Database http://ginsengdb.snu.ac.kr /, the first open-access platform to provide comprehensive genomic resources of P. ginseng. The current version of this database provides the most up-to-date draft genome sequence (of approximately 3000 Mbp of scaffold sequences) along with the structural and functional annotations for 59,352 genes and digital expression of genes based on transcriptome data from different tissues, growth stages and treatments. In addition, tools for visualization and the genomic data from various analyses are provided. All data in the database were manually curated and integrated within a user-friendly query page. This database provides valuable resources for a range of research fields related to P. ginseng and other species belonging to the Apiales order as well as for plant research communities in general. Ginseng genome database can be accessed at http://ginsengdb.snu.ac.kr /.

  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. Strategic investments in non-communicable diseases (NCD) research in Africa: the GSK Africa NCD Open Lab.

    Science.gov (United States)

    Hall, Matthew D; Dufton, Ann M; Katso, Roy M; Gatsi, Sally A; Williams, Pauline M; Strange, Michael E

    2015-01-01

    In March 2014, GSK announced a number of new strategic investments in Africa. One of these included investment of up to 25 million Pounds Sterling (£25 million) to create the world's first R&D Open Lab to increase understanding of non-communicable diseases (NCDs) in Africa. The vision is to create a new global R&D effort with GSK working in partnership with major funders, academic centres and governments to share expertise and resources to conduct high-quality research. The Africa NCD Open Lab will see GSK scientists collaborate with scientific research centres across Africa. An independent advisory board of leading scientists and clinicians will provide input to develop the strategy and selection of NCD research projects within a dynamic and networked open-innovation environment. It is hoped that these research projects will inform prevention and treatment strategies in the future and will enable researchers across academia and industry to discover and develop new medicines to address the specific needs of African patients.

  20. 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.

  1. An Open Access Database of Genome-wide Association Results

    Directory of Open Access Journals (Sweden)

    Johnson Andrew D

    2009-01-01

    Full Text Available Abstract Background The number of genome-wide association studies (GWAS is growing rapidly leading to the discovery and replication of many new disease loci. Combining results from multiple GWAS datasets may potentially strengthen previous conclusions and suggest new disease loci, pathways or pleiotropic genes. However, no database or centralized resource currently exists that contains anywhere near the full scope of GWAS results. Methods We collected available results from 118 GWAS articles into a database of 56,411 significant SNP-phenotype associations and accompanying information, making this database freely available here. In doing so, we met and describe here a number of challenges to creating an open access database of GWAS results. Through preliminary analyses and characterization of available GWAS, we demonstrate the potential to gain new insights by querying a database across GWAS. Results Using a genomic bin-based density analysis to search for highly associated regions of the genome, positive control loci (e.g., MHC loci were detected with high sensitivity. Likewise, an analysis of highly repeated SNPs across GWAS identified replicated loci (e.g., APOE, LPL. At the same time we identified novel, highly suggestive loci for a variety of traits that did not meet genome-wide significant thresholds in prior analyses, in some cases with strong support from the primary medical genetics literature (SLC16A7, CSMD1, OAS1, suggesting these genes merit further study. Additional adjustment for linkage disequilibrium within most regions with a high density of GWAS associations did not materially alter our findings. Having a centralized database with standardized gene annotation also allowed us to examine the representation of functional gene categories (gene ontologies containing one or more associations among top GWAS results. Genes relating to cell adhesion functions were highly over-represented among significant associations (p -14, a finding

  2. 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.

  3. Using Saccharomyces cerevisiae to Test the Mutagenicity of Household Compounds: An Open Ended Hypothesis-Driven Teaching Lab

    OpenAIRE

    Marshall, Pamela A.

    2007-01-01

    In our Fundamentals of Genetics lab, students perform a wide variety of labs to reinforce and extend the topics covered in lecture. I developed an active-learning lab to augment the lecture topic of mutagenesis. In this lab exercise, students determine if a compound they bring from home is a mutagen. Students are required to read extensive background material, perform research to find a potential mutagen to test, develop a hypothesis, and bring to the lab their own suspected mutagen. This lab...

  4. OpenVirtualToxLab--a platform for generating and exchanging in silico toxicity data.

    Science.gov (United States)

    Vedani, Angelo; Dobler, Max; Hu, Zhenquan; Smieško, Martin

    2015-01-22

    The VirtualToxLab is an in silico technology for estimating the toxic potential--endocrine and metabolic disruption, some aspects of carcinogenicity and cardiotoxicity--of drugs, chemicals and natural products. The technology is based on an automated protocol that simulates and quantifies the binding of small molecules towards a series of currently 16 proteins, known or suspected to trigger adverse effects: 10 nuclear receptors (androgen, estrogen α, estrogen β, glucocorticoid, liver X, mineralocorticoid, peroxisome proliferator-activated receptor γ, progesterone, thyroid α, thyroid β), four members of the cytochrome P450 enzyme family (1A2, 2C9, 2D6, 3A4), a cytosolic transcription factor (aryl hydrocarbon receptor) and a potassium ion channel (hERG). The toxic potential of a compound--its ability to trigger adverse effects--is derived from its computed binding affinities toward these very proteins: the computationally demanding simulations are executed in client-server model on a Linux cluster of the University of Basel. The graphical-user interface supports all computer platforms, allows building and uploading molecular structures, inspecting and downloading the results and, most important, rationalizing any prediction at the atomic level by interactively analyzing the binding mode of a compound with its target protein(s) in real-time 3D. Access to the VirtualToxLab is available free of charge for universities, governmental agencies, regulatory bodies and non-profit organizations. Copyright © 2014 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

  5. 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...

  6. Using "Saccharomyces cerevisiae" to Test the Mutagenicity of Household Compounds: An Open Ended Hypothesis-Driven Teaching Lab

    Science.gov (United States)

    Marshall, Pamela A.

    2007-01-01

    In our Fundamentals of Genetics lab, students perform a wide variety of labs to reinforce and extend the topics covered in lecture. I developed an active-learning lab to augment the lecture topic of mutagenesis. In this lab exercise, students determine if a compound they bring from home is a mutagen. Students are required to read extensive…

  7. 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.

  8. Virtual Labs (Science Gateways) as platforms for Free and Open Source Science

    Science.gov (United States)

    Lescinsky, David; Car, Nicholas; Fraser, Ryan; Friedrich, Carsten; Kemp, Carina; Squire, Geoffrey

    2016-04-01

    The Free and Open Source Software (FOSS) movement promotes community engagement in software development, as well as provides access to a range of sophisticated technologies that would be prohibitively expensive if obtained commercially. However, as geoinformatics and eResearch tools and services become more dispersed, it becomes more complicated to identify and interface between the many required components. Virtual Laboratories (VLs, also known as Science Gateways) simplify the management and coordination of these components by providing a platform linking many, if not all, of the steps in particular scientific processes. These enable scientists to focus on their science, rather than the underlying supporting technologies. We describe a modular, open source, VL infrastructure that can be reconfigured to create VLs for a wide range of disciplines. Development of this infrastructure has been led by CSIRO in collaboration with Geoscience Australia and the National Computational Infrastructure (NCI) with support from the National eResearch Collaboration Tools and Resources (NeCTAR) and the Australian National Data Service (ANDS). Initially, the infrastructure was developed to support the Virtual Geophysical Laboratory (VGL), and has subsequently been repurposed to create the Virtual Hazards Impact and Risk Laboratory (VHIRL) and the reconfigured Australian National Virtual Geophysics Laboratory (ANVGL). During each step of development, new capabilities and services have been added and/or enhanced. We plan on continuing to follow this model using a shared, community code base. The VL platform facilitates transparent and reproducible science by providing access to both the data and methodologies used during scientific investigations. This is further enhanced by the ability to set up and run investigations using computational resources accessed through the VL. Data is accessed using registries pointing to catalogues within public data repositories (notably including the

  9. Indel Group in Genomes (IGG) Molecular Genetic Markers1[OPEN

    Science.gov (United States)

    Burkart-Waco, Diana; Kuppu, Sundaram; Britt, Anne; Chetelat, Roger

    2016-01-01

    Genetic markers are essential when developing or working with genetically variable populations. Indel Group in Genomes (IGG) markers are primer pairs that amplify single-locus sequences that differ in size for two or more alleles. They are attractive for their ease of use for rapid genotyping and their codominant nature. Here, we describe a heuristic algorithm that uses a k-mer-based approach to search two or more genome sequences to locate polymorphic regions suitable for designing candidate IGG marker primers. As input to the IGG pipeline software, the user provides genome sequences and the desired amplicon sizes and size differences. Primer sequences flanking polymorphic insertions/deletions are produced as output. IGG marker files for three sets of genomes, Solanum lycopersicum/Solanum pennellii, Arabidopsis (Arabidopsis thaliana) Columbia-0/Landsberg erecta-0 accessions, and S. lycopersicum/S. pennellii/Solanum tuberosum (three-way polymorphic) are included. PMID:27436831

  10. 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

  11. Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools.

    Science.gov (United States)

    Kisand, Veljo; Lettieri, Teresa

    2013-04-01

    De novo genome sequencing of previously uncharacterized microorganisms has the potential to open up new frontiers in microbial genomics by providing insight into both functional capabilities and biodiversity. Until recently, Roche 454 pyrosequencing was the NGS method of choice for de novo assembly because it generates hundreds of thousands of long reads (tools for processing NGS data are increasingly free and open source and are often adopted for both their high quality and role in promoting academic freedom. The error rate of pyrosequencing the Alcanivorax borkumensis genome was such that thousands of insertions and deletions were artificially introduced into the finished genome. Despite a high coverage (~30 fold), it did not allow the reference genome to be fully mapped. Reads from regions with errors had low quality, low coverage, or were missing. The main defect of the reference mapping was the introduction of artificial indels into contigs through lower than 100% consensus and distracting gene calling due to artificial stop codons. No assembler was able to perform de novo assembly comparable to reference mapping. Automated annotation tools performed similarly on reference mapped and de novo draft genomes, and annotated most CDSs in the de novo assembled draft genomes. Free and open source software (FOSS) tools for assembly and annotation of NGS data are being developed rapidly to provide accurate results with less computational effort. Usability is not high priority and these tools currently do not allow the data to be processed without manual intervention. Despite this, genome assemblers now readily assemble medium short reads into long contigs (>97-98% genome coverage). A notable gap in pyrosequencing technology is the quality of base pair calling and conflicting base pairs between single reads at the same nucleotide position. Regardless, using draft whole genomes that are not finished and remain fragmented into tens of contigs allows one to characterize

  12. 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.

  13. Open Device Lab (ODL - um movimento colaborativo para o uso de dispositivos reais em projetos para web e aplicativos (revisão da literatura.

    Directory of Open Access Journals (Sweden)

    Raquel Paiva Godinho

    2015-08-01

    Full Text Available Este estudo apresenta os resultados da revisão da literatura realizada, em abril e maio de 2015, sobre o movimento, mundial, colaborativo dos Open Device Labs (ODLs. Uma iniciativa, recente, de profissionais da área com o objetivo de criar e compartilhar laboratórios com diferentes dispositivos móveis. Estes espaços proporcionam à um número maior de designers e desenvolvedores, de uma forma colaborativa e econômica, a possibilidade de testarem seus projetos em dispositivos reais. Esta prática aparece como uma etapa essencial para obtenção de melhores resultados no desenvolvimento de interfaces digitais para web e aplicativos em uma época de crescente fragmentação da tecnologia. Open Device Lab (ODL - a community movement for the use of real devices on web projects and applications. A literature review Abstract This study presents results from a literature review on the worldwide collaborative movement of Open Device Labs (ODLs. This is a recent initiative, started by professionals, and aimed at creating and sharing laboratories with diverse mobile devices connected to the Internet. These spaces provide a greater number of designers and developers with the possibility of testing their projects on different devices in a shared, economical way. The results show the importance of the movement to undertake tests with real devices and obtain better results in the development of web projects and applications at a time of growing technology fragmentation.  Keywords: Open Device Lab, Web, Applications, Test, Real devices.

  14. Lab architecture

    Science.gov (United States)

    Crease, Robert P.

    2008-04-01

    There are few more dramatic illustrations of the vicissitudes of laboratory architecturethan the contrast between Building 20 at the Massachusetts Institute of Technology (MIT) and its replacement, the Ray and Maria Stata Center. Building 20 was built hurriedly in 1943 as temporary housing for MIT's famous Rad Lab, the site of wartime radar research, and it remained a productive laboratory space for over half a century. A decade ago it was demolished to make way for the Stata Center, an architecturally striking building designed by Frank Gehry to house MIT's computer science and artificial intelligence labs (above). But in 2004 - just two years after the Stata Center officially opened - the building was criticized for being unsuitable for research and became the subject of still ongoing lawsuits alleging design and construction failures.

  15. 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.

  16. 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...

  17. 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.

  18. 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...

  19. 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

    2015-06-01

    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.

  20. 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.

  1. Python Materials Genomics (pymatgen): A robust, open-source python library for materials analysis

    OpenAIRE

    Ong, Shyue Ping; Richards, William Davidson; Jain, Anubhav; Hautier, Geoffroy; Kocher, Michael; Cholia, Shreyas; Gunter, Dan; Chevrier, Vincent L.; Persson, Kristin A.; Ceder, Gerbrand

    2012-01-01

    We present the Python Materials Genomics (pymatgen) library, a robust, open-source Python library for materials analysis. A key enabler in high-throughput computational materials science efforts is a robust set of software tools to perform initial setup for the calculations (e.g., generation of structures and necessary input files) and post-calculation analysis to derive useful material properties from raw calculated data. The pymatgen library aims to meet these needs by (1) defining core Pyt...

  2. 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

  3. 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.

  4. AutoLabDB: a substantial open source database schema to support a high-throughput automated laboratory.

    Science.gov (United States)

    Sparkes, Andrew; Clare, Amanda

    2012-05-15

    Modern automated laboratories need substantial data management solutions to both store and make accessible the details of the experiments they perform. To be useful, a modern Laboratory Information Management System (LIMS) should be flexible and easily extensible to support evolving laboratory requirements, and should be based on the solid foundations of a robust, well-designed database. We have developed such a database schema to support an automated laboratory that performs experiments in systems biology and high-throughput screening. We describe the design of the database schema (AutoLabDB), detailing the main features and describing why we believe it will be relevant to LIMS manufacturers or custom builders. This database has been developed to support two large automated Robot Scientist systems over the last 5 years, where it has been used as the basis of an LIMS that helps to manage both the laboratory and all the experiment data produced.

  5. 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/.

  6. 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.

  7. STORMSeq: An Open-Source, User-Friendly Pipeline for Processing Personal Genomics Data in the Cloud

    OpenAIRE

    Karczewski, Konrad J.; Fernald, Guy Haskin; Martin, Alicia R.; Snyder, Michael; Tatonetti, Nicholas P.; Dudley, Joel T.

    2014-01-01

    The increasing public availability of personal complete genome sequencing data has ushered in an era of democratized genomics. However, read mapping and variant calling software is constantly improving and individuals with personal genomic data may prefer to customize and update their variant calls. Here, we describe STORMSeq (Scalable Tools for Open-Source Read Mapping), a graphical interface cloud computing solution that does not require a parallel computing environment or extensive technic...

  8. 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.

  9. 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.

  10. 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

    2016-01-01

    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. PMID:27809229

  11. 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.

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

    Directory of Open Access Journals (Sweden)

    Suparna eChoudhury

    2014-05-01

    Full Text Available 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 (1024. 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 behaviour 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.

  13. STORMSeq: an open-source, user-friendly pipeline for processing personal genomics data in the cloud.

    Directory of Open Access Journals (Sweden)

    Konrad J Karczewski

    Full Text Available The increasing public availability of personal complete genome sequencing data has ushered in an era of democratized genomics. However, read mapping and variant calling software is constantly improving and individuals with personal genomic data may prefer to customize and update their variant calls. Here, we describe STORMSeq (Scalable Tools for Open-Source Read Mapping, a graphical interface cloud computing solution that does not require a parallel computing environment or extensive technical experience. This customizable and modular system performs read mapping, read cleaning, and variant calling and annotation. At present, STORMSeq costs approximately $2 and 5-10 hours to process a full exome sequence and $30 and 3-8 days to process a whole genome sequence. We provide this open-access and open-source resource as a user-friendly interface in Amazon EC2.

  14. STORMSeq: an open-source, user-friendly pipeline for processing personal genomics data in the cloud.

    Science.gov (United States)

    Karczewski, Konrad J; Fernald, Guy Haskin; Martin, Alicia R; Snyder, Michael; Tatonetti, Nicholas P; Dudley, Joel T

    2014-01-01

    The increasing public availability of personal complete genome sequencing data has ushered in an era of democratized genomics. However, read mapping and variant calling software is constantly improving and individuals with personal genomic data may prefer to customize and update their variant calls. Here, we describe STORMSeq (Scalable Tools for Open-Source Read Mapping), a graphical interface cloud computing solution that does not require a parallel computing environment or extensive technical experience. This customizable and modular system performs read mapping, read cleaning, and variant calling and annotation. At present, STORMSeq costs approximately $2 and 5-10 hours to process a full exome sequence and $30 and 3-8 days to process a whole genome sequence. We provide this open-access and open-source resource as a user-friendly interface in Amazon EC2.

  15. Altitude Lab

    Data.gov (United States)

    Federal Laboratory Consortium — The Altitude Lab evaluates the performance of complete oxygen systems operated in individually controlled hypobaric chambers, which duplicate pressures that would be...

  16. 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.

  17. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project : open letter

    NARCIS (Netherlands)

    Archibald, A.L.; Bottema, C.D.; Brauning, R.; Burgess, S.C.; Burt, D.W.; Casas, E.; Cheng, H.H.; Clarke, L.; Couldrey, C.; Dalrymple, B.P.; Elsik, C.G.; Foissac, S.; Giuffra, E.; Groenen, M.A.M.; Hayes, B.J.; Huang, L.S.; Khatib, H.; Kijas, J.W.; Kim, H.; Lunney, J.K.; McCarthy, F.M.; McEwan, J.; Moore, S.; Nanduri, B.; Notredame, C.; Palti, Y.; Plastow, G.S.; Reecy, J.M.; Rohrer, G.; Sarropoulou, E.; Schmidt, C.J.; Silverstein, J.; Tellam, R.L.; Tixier-Boichard, M.; Tosser-klopp, G.; Tuggle, C.K.; Vilkki, J.; White, S.N.; Zhao, S.; Zhou, H.

    2015-01-01

    We describe the organization of a nascent international effort, the Functional Annotation of Animal Genomes (FAANG) project, whose aim is to produce comprehensive maps of functional elements in the genomes of domesticated animal species.

  18. PD Lab

    NARCIS (Netherlands)

    Bilow, Marcel; Entrop, Alexis Gerardus; Lichtenberg, Jos; Stoutjesdijk, Pieter

    2015-01-01

    PD Lab explores the applications of building sector related product development. PD lab investigates and tests digital production technologies like CNC milled wood connections. It will also act as a platform in its wider meaning to investigate the effects and influences of file to factory

  19. 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

  20. 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

  1. PD Lab

    Directory of Open Access Journals (Sweden)

    Marcel Bilow

    2015-08-01

    Full Text Available PD Lab explores the applications of building sector related product development.  PD lab investigates and tests digital production technologies like CNC milled wood connections. It will also act as a platform in its wider meaning to investigate the effects and influences of file to factory production, to explore the potential in the field of sustainability, material use, logistics and the interaction of stakeholders within the chain of the building process.

  2. 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 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.

  3. TELECOM LAB

    CERN Multimedia

    IT-CS-TEL Section

    2001-01-01

    The Telecom Lab is moving from Building 104 to Building 31 S-026, with its entrance via the ramp on the side facing Restaurant n°2. The help desk will thus be closed to users on Tuesday 8 May. On May 9, the Lab will only be able to deal with problems of a technical nature at the new address and it will not be able to process any new subscription requests throughout the week from 7 to 11 May. We apologise for any inconvenience this may cause and thank you for your understanding.

  4. 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.

  5. Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines

    NARCIS (Netherlands)

    Ellrott, Kyle; Bailey, Matthew H.; Saksena, Gordon; Covington, Kyle R.; Kandoth, Cyriac; Stewart, Chip; Hess, Julian; Ma, Singer; Chiotti, Kami E.; McLellan, Michael; Sofia, Heidi J.; Hutter, Carolyn M.; Getz, Gad; Wheeler, David A.; Ding, Li; Caesar-Johnson, Samantha J.; Demchok, John A.; Felau, Ina; Kasapi, Melpomeni; Ferguson, Martin L.; Hutter, Carolyn M.; Sofia, Heidi J.; Tarnuzzer, Roy; Wang, Zhining; Yang, Liming; Zenklusen, Jean C.; Zhang, Jiashan (Julia); Chudamani, Sudha; Liu, Jia; Lolla, Laxmi; Naresh, Rashi; Pihl, Todd; Sun, Qiang; Wan, Yunhu; Wu, Ye; Cho, Juok; DeFreitas, Timothy; Frazer, Scott; Gehlenborg, Nils; Getz, Gad; Heiman, David I.; Kim, Jaegil; Lawrence, Michael S.; Lin, Pei; Meier, Sam; Noble, Michael S.; Saksena, Gordon; Voet, Doug; Zhang, Hailei; Bernard, Brady; Chambwe, Nyasha; Dhankani, Varsha; Knijnenburg, Theo; Kramer, Roger; Leinonen, Kalle; Liu, Yuexin; Miller, Michael; Reynolds, Sheila; Shmulevich, Ilya; Thorsson, Vesteinn; Zhang, Wei; Akbani, Rehan; Broom, Bradley M.; Hegde, Apurva M.; Ju, Zhenlin; Kanchi, Rupa S.; Korkut, Anil; Li, Jun; Liang, Han; Ling, Shiyun; Liu, Wenbin; Lu, Yiling; Mills, Gordon B.; Ng, Kwok Shing; Rao, Arvind; Ryan, Michael; Wang, Jing; Weinstein, John N.; Zhang, Jiexin; Abeshouse, Adam; Armenia, Joshua; Chakravarty, Debyani; Chatila, Walid K.; de Bruijn, Ino; Gao, Jianjiong; Gross, Benjamin E.; Heins, Zachary J.; Kundra, Ritika; La, Konnor; Ladanyi, Marc; Luna, Augustin; Nissan, Moriah G.; Ochoa, Angelica; Phillips, Sarah M.; Reznik, Ed; Sanchez-Vega, Francisco; Sander, Chris; Schultz, Nikolaus; Sheridan, Robert; Sumer, S. Onur; Sun, Yichao; Taylor, Barry S.; Wang, Jioajiao; Zhang, Hongxin; Anur, Pavana; Peto, Myron; Spellman, Paul; Benz, Christopher; Stuart, Joshua M.; Wong, Christopher K.; Yau, Christina; Hayes, D. Neil; Wilkerson, Matthew D.; Ally, Adrian; Balasundaram, Miruna; Bowlby, Reanne; Brooks, Denise; Carlsen, Rebecca; Chuah, Eric; Dhalla, Noreen; Holt, Robert; Jones, Steven J.M.; Kasaian, Katayoon; Lee, Darlene; Ma, Yussanne; Marra, Marco A.; Mayo, Michael; Moore, Richard A.; Mungall, Andrew J.; Mungall, Karen; Robertson, A. Gordon; Sadeghi, Sara; Schein, Jacqueline E.; Sipahimalani, Payal; Tam, Angela; Thiessen, Nina; Tse, Kane; Wong, Tina; Berger, Ashton C.; Beroukhim, Rameen; Cherniack, Andrew D.; Cibulskis, Carrie; Gabriel, Stacey B.; Gao, Galen F.; Ha, Gavin; Meyerson, Matthew; Schumacher, Steven E.; Shih, Juliann; Kucherlapati, Melanie H.; Kucherlapati, Raju S.; Baylin, Stephen; Cope, Leslie; Danilova, Ludmila; Bootwalla, Moiz S.; Lai, Phillip H.; Maglinte, Dennis T.; Van Den Berg, David J.; Weisenberger, Daniel J.; Auman, J. Todd; Balu, Saianand; Bodenheimer, Tom; Fan, Cheng; Hoadley, Katherine A.; Hoyle, Alan P.; Jefferys, Stuart R.; Jones, Corbin D.; Meng, Shaowu; Mieczkowski, Piotr A.; Mose, Lisle E.; Perou, Amy H.; Perou, Charles M.; Roach, Jeffrey; Shi, Yan; Simons, Janae V.; Skelly, Tara; Soloway, Matthew G.; Tan, Donghui; Veluvolu, Umadevi; Fan, Huihui; Hinoue, Toshinori; Laird, Peter W.; Shen, Hui; Zhou, Wanding; Bellair, Michelle; Chang, Kyle; Covington, Kyle; Creighton, Chad J.; Dinh, Huyen; Doddapaneni, Harsha Vardhan; Donehower, Lawrence A.; Drummond, Jennifer; Gibbs, Richard A.; Glenn, Robert; Hale, Walker; Han, Yi; Hu, Jianhong; Korchina, Viktoriya; Lee, Sandra; Lewis, Lora; Li, Wei; Liu, Xiuping; Morgan, Margaret; Morton, Donna; Muzny, Donna; Santibanez, Jireh; Sheth, Margi; Shinbrot, Eve; Wang, Linghua; Wang, Min; Wheeler, David A.; Xi, Liu; Zhao, Fengmei; Hess, Julian; Appelbaum, Elizabeth L.; Bailey, Matthew; Cordes, Matthew G.; Ding, Li; Fronick, Catrina C.; Fulton, Lucinda A.; Fulton, Robert S.; Kandoth, Cyriac; Mardis, Elaine R.; McLellan, Michael D.; Miller, Christopher A.; Schmidt, Heather K.; Wilson, Richard K.; Crain, Daniel; Curley, Erin; Gardner, Johanna; Lau, Kevin; Mallery, David; Morris, Scott; Paulauskis, Joseph; Penny, Robert; Shelton, Candace; Shelton, Troy; Sherman, Mark; Thompson, Eric; Yena, Peggy; Bowen, Jay; Gastier-Foster, Julie M.; Gerken, Mark; Leraas, Kristen M.; Lichtenberg, Tara M.; Ramirez, Nilsa C.; Wise, Lisa; Zmuda, Erik; Corcoran, Niall; Costello, Tony; Hovens, Christopher; Carvalho, Andre L.; de Carvalho, Ana C.; Fregnani, José H.; Longatto-Filho, Adhemar; Reis, Rui M.; Scapulatempo-Neto, Cristovam; Silveira, Henrique C.S.; Vidal, Daniel O.; Burnette, Andrew; Eschbacher, Jennifer; Hermes, Beth; Noss, Ardene; Singh, Rosy; Anderson, Matthew L.; Castro, Patricia D.; Ittmann, Michael; Huntsman, David; Kohl, Bernard; Le, Xuan; Thorp, Richard; Andry, Chris; Duffy, Elizabeth R.; Lyadov, Vladimir; Paklina, Oxana; Setdikova, Galiya; Shabunin, Alexey; Tavobilov, Mikhail; McPherson, Christopher; Warnick, Ronald; Berkowitz, Ross; Cramer, Daniel; Feltmate, Colleen; Horowitz, Neil; Kibel, Adam; Muto, Michael; Raut, Chandrajit P.; Malykh, Andrei; Barnholtz-Sloan, Jill S.; Barrett, Wendi; Devine, Karen; Fulop, Jordonna; Ostrom, Quinn T.; Shimmel, Kristen; Wolinsky, Yingli; Sloan, Andrew E.; De Rose, Agostino; Giuliante, Felice; Goodman, Marc; Karlan, Beth Y.; Hagedorn, Curt H.; Eckman, John; Harr, Jodi; Myers, Jerome; Tucker, Kelinda; Zach, Leigh Anne; Deyarmin, Brenda; Hu, Hai; Kvecher, Leonid; Larson, Caroline; Mural, Richard J.; Somiari, Stella; Vicha, Ales; Zelinka, Tomas; Bennett, Joseph; Iacocca, Mary; Rabeno, Brenda; Swanson, Patricia; Latour, Mathieu; Lacombe, Louis; Têtu, Bernard; Bergeron, Alain; McGraw, Mary; Staugaitis, Susan M.; Chabot, John; Hibshoosh, Hanina; Sepulveda, Antonia; Su, Tao; Wang, Timothy; Potapova, Olga; Voronina, Olga; Desjardins, Laurence; Mariani, Odette; Roman-Roman, Sergio; Sastre, Xavier; Stern, Marc Henri; Cheng, Feixiong; Signoretti, Sabina; Berchuck, Andrew; Bigner, Darell; Lipp, Eric; Marks, Jeffrey; McCall, Shannon; McLendon, Roger; Secord, Angeles; Sharp, Alexis; Behera, Madhusmita; Brat, Daniel J.; Chen, Amy; Delman, Keith; Force, Seth; Khuri, Fadlo; Magliocca, Kelly; Maithel, Shishir; Olson, Jeffrey J.; Owonikoko, Taofeek; Pickens, Alan; Ramalingam, Suresh; Shin, Dong M.; Sica, Gabriel; Van Meir, Erwin G.; Zhang, Hongzheng; Eijckenboom, Wil; Gillis, Ad; Korpershoek, Esther; Looijenga, Leendert; Oosterhuis, Wolter; Stoop, Hans; van Kessel, Kim E.; Zwarthoff, Ellen C.; Calatozzolo, Chiara; Cuppini, Lucia; Cuzzubbo, Stefania; DiMeco, Francesco; Finocchiaro, Gaetano; Mattei, Luca; Perin, Alessandro; Pollo, Bianca; Chen, Chu; Houck, John; Lohavanichbutr, Pawadee; Hartmann, Arndt; Stoehr, Christine; Stoehr, Robert; Taubert, Helge; Wach, Sven; Wullich, Bernd; Kycler, Witold; Murawa, Dawid; Wiznerowicz, Maciej; Chung, Ki; Edenfield, W. Jeffrey; Martin, Julie; Baudin, Eric; Bubley, Glenn; Bueno, Raphael; De Rienzo, Assunta; Richards, William G.; Kalkanis, Steven; Mikkelsen, Tom; Noushmehr, Houtan; Scarpace, Lisa; Girard, Nicolas; Aymerich, Marta; Campo, Elias; Giné, Eva; Guillermo, Armando López; Van Bang, Nguyen; Hanh, Phan Thi; Phu, Bui Duc; Tang, Yufang; Colman, Howard; Evason, Kimberley; Dottino, Peter R.; Martignetti, John A.; Gabra, Hani; Juhl, Hartmut; Akeredolu, Teniola; Stepa, Serghei; Hoon, Dave; Ahn, Keunsoo; Kang, Koo Jeong; Beuschlein, Felix; Breggia, Anne; Birrer, Michael; Bell, Debra; Borad, Mitesh; Bryce, Alan H.; Castle, Erik; Chandan, Vishal; Cheville, John; Copland, John A.; Farnell, Michael; Flotte, Thomas; Giama, Nasra; Ho, Thai; Kendrick, Michael; Kocher, Jean Pierre; Kopp, Karla; Moser, Catherine; Nagorney, David; O'Brien, Daniel; O'Neill, Brian Patrick; Patel, Tushar; Petersen, Gloria; Que, Florencia; Rivera, Michael; Roberts, Lewis; Smallridge, Robert; Smyrk, Thomas; Stanton, Melissa; Thompson, R. Houston; Torbenson, Michael; Yang, Ju Dong; Zhang, Lizhi; Brimo, Fadi; Ajani, Jaffer A.; Angulo Gonzalez, Ana Maria; Behrens, Carmen; Bondaruk, Jolanta; Broaddus, Russell; Czerniak, Bogdan; Esmaeli, Bita; Fujimoto, Junya; Gershenwald, Jeffrey; Guo, Charles; Lazar, Alexander J.; Logothetis, Christopher; Meric-Bernstam, Funda; Moran, Cesar; Ramondetta, Lois; Rice, David; Sood, Anil; Tamboli, Pheroze; Thompson, Timothy; Troncoso, Patricia; Tsao, Anne; Wistuba, Ignacio; Carter, Candace; Haydu, Lauren; Hersey, Peter; Jakrot, Valerie; Kakavand, Hojabr; Kefford, Richard; Lee, Kenneth; Long, Georgina; Mann, Graham; Quinn, Michael; Saw, Robyn; Scolyer, Richard; Shannon, Kerwin; Spillane, Andrew; Stretch, Jonathan; Synott, Maria; Thompson, John; Wilmott, James; Al-Ahmadie, Hikmat; Chan, Timothy A.; Ghossein, Ronald; Gopalan, Anuradha; Levine, Douglas A.; Reuter, Victor; Singer, Samuel; Singh, Bhuvanesh; Tien, Nguyen Viet; Broudy, Thomas; Mirsaidi, Cyrus; Nair, Praveen; Drwiega, Paul; Miller, Judy; Smith, Jennifer; Zaren, Howard; Park, Joong Won; Hung, Nguyen Phi; Kebebew, Electron; Linehan, W. Marston; Metwalli, Adam R.; Pacak, Karel; Pinto, Peter A.; Schiffman, Mark; Schmidt, Laura S.; Vocke, Cathy D.; Wentzensen, Nicolas; Worrell, Robert; Yang, Hannah; Moncrieff, Marc; Goparaju, Chandra; Melamed, Jonathan; Pass, Harvey; Botnariuc, Natalia; Caraman, Irina; Cernat, Mircea; Chemencedji, Inga; Clipca, Adrian; Doruc, Serghei; Gorincioi, Ghenadie; Mura, Sergiu; Pirtac, Maria; Stancul, Irina; Tcaciuc, Diana; Albert, Monique; Alexopoulou, Iakovina; Arnaout, Angel; Bartlett, John; Engel, Jay; Gilbert, Sebastien; Parfitt, Jeremy; Sekhon, Harman; Thomas, George; Rassl, Doris M.; Rintoul, Robert C.; Bifulco, Carlo; Tamakawa, Raina; Urba, Walter; Hayward, Nicholas; Timmers, Henri; Antenucci, Anna; Facciolo, Francesco; Grazi, Gianluca; Marino, Mirella; Merola, Roberta; de Krijger, Ronald; Gimenez-Roqueplo, Anne Paule; Piché, Alain; Chevalier, Simone; McKercher, Ginette; Birsoy, Kivanc; Barnett, Gene; Brewer, Cathy; Farver, Carol; Naska, Theresa; Pennell, Nathan A.; Raymond, Daniel; Schilero, Cathy; Smolenski, Kathy; Williams, Felicia; Morrison, Carl; Borgia, Jeffrey A.; Liptay, Michael J.; Pool, Mark; Seder, Christopher W.; Junker, Kerstin; Omberg, Larsson; Dinkin, Mikhail; Manikhas, George; Alvaro, Domenico; Bragazzi, Maria Consiglia; Cardinale, Vincenzo; Carpino, Guido; Gaudio, Eugenio; Chesla, David; Cottingham, Sandra; Dubina, Michael; Moiseenko, Fedor; Dhanasekaran, Renumathy; Becker, Karl Friedrich; Janssen, Klaus Peter; Slotta-Huspenina, Julia; Abdel-Rahman, Mohamed H.; Aziz, Dina; Bell, Sue; Cebulla, Colleen M.; Davis, Amy; Duell, Rebecca; Elder, J. Bradley; Hilty, Joe; Kumar, Bahavna; Lang, James; Lehman, Norman L.; Mandt, Randy; Nguyen, Phuong; Pilarski, Robert; Rai, Karan; Schoenfield, Lynn; Senecal, Kelly; Wakely, Paul; Hansen, Paul; Lechan, Ronald; Powers, James; Tischler, Arthur; Grizzle, William E.; Sexton, Katherine C.; Kastl, Alison; Henderson, Joel; Porten, Sima; Waldmann, Jens; Fassnacht, Martin; Asa, Sylvia L.; Schadendorf, Dirk; Couce, Marta; Graefen, Markus; Huland, Hartwig; Sauter, Guido; Schlomm, Thorsten; Simon, Ronald; Tennstedt, Pierre; Olabode, Oluwole; Nelson, Mark; Bathe, Oliver; Carroll, Peter R.; Chan, June M.; Disaia, Philip; Glenn, Pat; Kelley, Robin K.; Landen, Charles N.; Phillips, Joanna; Prados, Michael; Simko, Jeffry; Smith-McCune, Karen; VandenBerg, Scott; Roggin, Kevin; Fehrenbach, Ashley; Kendler, Ady; Sifri, Suzanne; Steele, Ruth; Jimeno, Antonio; Carey, Francis; Forgie, Ian; Mannelli, Massimo; Carney, Michael; Hernandez, Brenda; Campos, Benito; Herold-Mende, Christel; Jungk, Christin; Unterberg, Andreas; von Deimling, Andreas; Bossler, Aaron; Galbraith, Joseph; Jacobus, Laura; Knudson, Michael; Knutson, Tina; Ma, Deqin; Milhem, Mohammed; Sigmund, Rita; Godwin, Andrew K.; Madan, Rashna; Rosenthal, Howard G.; Adebamowo, Clement; Adebamowo, Sally N.; Boussioutas, Alex; Beer, David; Giordano, Thomas; Mes-Masson, Anne Marie; Saad, Fred; Bocklage, Therese; Landrum, Lisa; Mannel, Robert; Moore, Kathleen; Moxley, Katherine; Postier, Russel; Walker, Joan; Zuna, Rosemary; Feldman, Michael; Valdivieso, Federico; Dhir, Rajiv; Luketich, James; Mora Pinero, Edna M.; Quintero-Aguilo, Mario; Carlotti, Carlos Gilberto; Dos Santos, Jose Sebastião; Kemp, Rafael; Sankarankuty, Ajith; Tirapelli, Daniela; Catto, James; Agnew, Kathy; Swisher, Elizabeth; Creaney, Jenette; Robinson, Bruce; Shelley, Carl Simon; Godwin, Eryn M.; Kendall, Sara; Shipman, Cassaundra; Bradford, Carol; Carey, Thomas; Haddad, Andrea; Moyer, Jeffey; Peterson, Lisa; Prince, Mark; Rozek, Laura; Wolf, Gregory; Bowman, Rayleen; Fong, Kwun M.; Yang, Ian; Korst, Robert; Rathmell, W. Kimryn; Fantacone-Campbell, J. Leigh; Hooke, Jeffrey A.; Kovatich, Albert J.; Shriver, Craig D.; DiPersio, John; Drake, Bettina; Govindan, Ramaswamy; Heath, Sharon; Ley, Timothy; Van Tine, Brian; Westervelt, Peter; Rubin, Mark A.; Lee, Jung Il; Aredes, Natália D.; Mariamidze, Armaz

    2018-01-01

    The Cancer Genome Atlas (TCGA) cancer genomics dataset includes over 10,000 tumor-normal exome pairs across 33 different cancer types, in total >400 TB of raw data files requiring analysis. Here we describe the Multi-Center Mutation Calling in Multiple Cancers project, our effort to generate a

  6. 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

  7. 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.

  8. Public data and open source tools for multi-assay genomic investigation of disease.

    Science.gov (United States)

    Kannan, Lavanya; Ramos, Marcel; Re, Angela; El-Hachem, Nehme; Safikhani, Zhaleh; Gendoo, Deena M A; Davis, Sean; Gomez-Cabrero, David; Castelo, Robert; Hansen, Kasper D; Carey, Vincent J; Morgan, Martin; Culhane, Aedín C; Haibe-Kains, Benjamin; Waldron, Levi

    2016-07-01

    Molecular interrogation of a biological sample through DNA sequencing, RNA and microRNA profiling, proteomics and other assays, has the potential to provide a systems level approach to predicting treatment response and disease progression, and to developing precision therapies. Large publicly funded projects have generated extensive and freely available multi-assay data resources; however, bioinformatic and statistical methods for the analysis of such experiments are still nascent. We review multi-assay genomic data resources in the areas of clinical oncology, pharmacogenomics and other perturbation experiments, population genomics and regulatory genomics and other areas, and tools for data acquisition. Finally, we review bioinformatic tools that are explicitly geared toward integrative genomic data visualization and analysis. This review provides starting points for accessing publicly available data and tools to support development of needed integrative methods. © The Author 2015. Published by Oxford University Press.

  9. 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.

  10. Living Lab voor Informatiemanagement in Agri-Food

    NARCIS (Netherlands)

    Wolfert, J.

    2010-01-01

    Het Living Lab is een specifieke open innovatie aanpak waarbij in feite het laboratorium naar de praktijk wordt gebracht. het Agri-Food Living lab is een informatiemanagementsysteem specifiek voor de agri-food sector.

  11. 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

  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. 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

  14. Cytoplasmic male sterility-associated chimeric open reading frames identified by mitochondrial genome sequencing of four Cajanus genotypes.

    Science.gov (United States)

    Tuteja, Reetu; Saxena, Rachit K; Davila, Jaime; Shah, Trushar; Chen, Wenbin; Xiao, Yong-Li; Fan, Guangyi; Saxena, K B; Alverson, Andrew J; Spillane, Charles; Town, Christopher; Varshney, Rajeev K

    2013-10-01

    The hybrid pigeonpea (Cajanus cajan) breeding technology based on cytoplasmic male sterility (CMS) is currently unique among legumes and displays major potential for yield increase. CMS is defined as a condition in which a plant is unable to produce functional pollen grains. The novel chimeric open reading frames (ORFs) produced as a results of mitochondrial genome rearrangements are considered to be the main cause of CMS. To identify these CMS-related ORFs in pigeonpea, we sequenced the mitochondrial genomes of three C. cajan lines (the male-sterile line ICPA 2039, the maintainer line ICPB 2039, and the hybrid line ICPH 2433) and of the wild relative (Cajanus cajanifolius ICPW 29). A single, circular-mapping molecule of length 545.7 kb was assembled and annotated for the ICPA 2039 line. Sequence annotation predicted 51 genes, including 34 protein-coding and 17 RNA genes. Comparison of the mitochondrial genomes from different Cajanus genotypes identified 31 ORFs, which differ between lines within which CMS is present or absent. Among these chimeric ORFs, 13 were identified by comparison of the related male-sterile and maintainer lines. These ORFs display features that are known to trigger CMS in other plant species and to represent the most promising candidates for CMS-related mitochondrial rearrangements in pigeonpea.

  15. Genome-wide linkage scan for primary open angle glaucoma: influences of ancestry and age at diagnosis.

    Directory of Open Access Journals (Sweden)

    Kristy R Crooks

    Full Text Available Primary open-angle glaucoma (POAG is the most common form of glaucoma and one of the leading causes of vision loss worldwide. The genetic etiology of POAG is complex and poorly understood. The purpose of this work is to identify genomic regions of interest linked to POAG. This study is the largest genetic linkage study of POAG performed to date: genomic DNA samples from 786 subjects (538 Caucasian ancestry, 248 African ancestry were genotyped using either the Illumina GoldenGate Linkage 4 Panel or the Illumina Infinium Human Linkage-12 Panel. A total of 5233 SNPs was analyzed in 134 multiplex POAG families (89 Caucasian ancestry, 45 African ancestry. Parametric and non-parametric linkage analyses were performed on the overall dataset and within race-specific datasets (Caucasian ancestry and African ancestry. Ordered subset analysis was used to stratify the data on the basis of age of glaucoma diagnosis. Novel linkage regions were identified on chromosomes 1 and 20, and two previously described loci-GLC1D on chromosome 8 and GLC1I on chromosome 15--were replicated. These data will prove valuable in the context of interpreting results from genome-wide association studies for POAG.

  16. 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

  17. 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.

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

    Science.gov (United States)

    Gubala, Aneta; Walsh, Susan; McAllister, Jane; Weir, Richard; Davis, Steven; Melville, Lorna; Mitchell, Ian; Bulach, Dieter; Gauci, Penny; Skvortsov, Alex; Boyle, David

    2017-01-01

    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.

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

    Science.gov (United States)

    Gubala, Aneta; Walsh, Susan; McAllister, Jane; Weir, Richard; Davis, Steven; Melville, Lorna; Mitchell, Ian; Bulach, Dieter; Gauci, Penny; Skvortsov, Alex; Boyle, David

    2017-01-01

    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. PMID:28747815

  20. 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.

  1. 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.

  2. From the Bench to the Clinic Part 1: Martin McIntosh, Ph.D., Introduces His Lab's Immunotherapy Research | Office of Cancer Genomics

    Science.gov (United States)

    The field of immunotherapy is rapidly advancing and genomics techniques are being incorporated to add a “precision” approach. OCG spoke with two CTD2 investigators from the Fred Hutchinson Cancer Research Center (FHCRC) about new advances in immunotherapy. For the first article of this two-part series, we interviewed Martin McIntosh, Ph.D., member of the Fred Hutchinson Translational Research program and previously Program Head in Computational Biology at FHCRC/University of Washington Comprehensive Cancer Center.

  3. 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

  4. 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

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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

  10. CoNekT: an open-source framework for comparative genomic and transcriptomic network analyses.

    Science.gov (United States)

    Proost, Sebastian; Mutwil, Marek

    2018-05-01

    The recent accumulation of gene expression data in the form of RNA sequencing creates unprecedented opportunities to study gene regulation and function. Furthermore, comparative analysis of the expression data from multiple species can elucidate which functional gene modules are conserved across species, allowing the study of the evolution of these modules. However, performing such comparative analyses on raw data is not feasible for many biologists. Here, we present CoNekT (Co-expression Network Toolkit), an open source web server, that contains user-friendly tools and interactive visualizations for comparative analyses of gene expression data and co-expression networks. These tools allow analysis and cross-species comparison of (i) gene expression profiles; (ii) co-expression networks; (iii) co-expressed clusters involved in specific biological processes; (iv) tissue-specific gene expression; and (v) expression profiles of gene families. To demonstrate these features, we constructed CoNekT-Plants for green alga, seed plants and flowering plants (Picea abies, Chlamydomonas reinhardtii, Vitis vinifera, Arabidopsis thaliana, Oryza sativa, Zea mays and Solanum lycopersicum) and thus provide a web-tool with the broadest available collection of plant phyla. CoNekT-Plants is freely available from http://conekt.plant.tools, while the CoNekT source code and documentation can be found at https://github.molgen.mpg.de/proost/CoNekT/.

  11. 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.

  12. 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

  13. 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.

  14. 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

    The American mink (Neovison vison) is a semiaquatic mustelid native to North America. It is an important animal for the fur industry. Although many efforts have been made to locate genes influencing fur quality and color, the lack of a reference genome impedes the search. American mink has...... 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...

  15. 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...

  16. 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...

  17. 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...

  18. 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...

  19. 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.

  20. Reforming Cookbook Labs

    Science.gov (United States)

    Peters, Erin

    2005-01-01

    Deconstructing cookbook labs to require the students to be more thoughtful could break down perceived teacher barriers to inquiry learning. Simple steps that remove or disrupt the direct transfer of step-by-step procedures in cookbook labs make students think more critically about their process. Through trials in the author's middle school…

  1. Payments to the Lab

    Science.gov (United States)

    Goals Recycling Green Purchasing Pollution Prevention Reusing Water Resources Environmental Management the Lab Make payments for event registrations, sponsorships, insurance, travel, other fees. Contact Treasury Team (505) 667-4090 Email If you need to make a payment to the Lab for an event registration

  2. 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...

  3. Kinematic Labs with Mobile Devices

    Science.gov (United States)

    Kinser, Jason M.

    2015-07-01

    This book provides 13 labs spanning the common topics in the first semester of university-level physics. Each lab is designed to use only the student's smartphone, laptop and items easily found in big-box stores or a hobby shop. Each lab contains theory, set-up instructions and basic analysis techniques. All of these labs can be performed outside of the traditional university lab setting and initial costs averaging less than 8 per student, per lab.

  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. 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...

  6. 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...

  7. 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.

  8. CDC Lab Values

    Centers for Disease Control (CDC) Podcasts

    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.

  9. 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

  10. 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

  11. MethLAB: a graphical user interface package for the analysis of array-based DNA methylation data.

    Science.gov (United States)

    Kilaru, Varun; Barfield, Richard T; Schroeder, James W; Smith, Alicia K; Conneely, Karen N

    2012-03-01

    Recent evidence suggests that DNA methylation changes may underlie numerous complex traits and diseases. The advent of commercial, array-based methods to interrogate DNA methylation has led to a profusion of epigenetic studies in the literature. Array-based methods, such as the popular Illumina GoldenGate and Infinium platforms, estimate the proportion of DNA methylated at single-base resolution for thousands of CpG sites across the genome. These arrays generate enormous amounts of data, but few software resources exist for efficient and flexible analysis of these data. We developed a software package called MethLAB (http://genetics.emory.edu/conneely/MethLAB) using R, an open source statistical language that can be edited to suit the needs of the user. MethLAB features a graphical user interface (GUI) with a menu-driven format designed to efficiently read in and manipulate array-based methylation data in a user-friendly manner. MethLAB tests for association between methylation and relevant phenotypes by fitting a separate linear model for each CpG site. These models can incorporate both continuous and categorical phenotypes and covariates, as well as fixed or random batch or chip effects. MethLAB accounts for multiple testing by controlling the false discovery rate (FDR) at a user-specified level. Standard output includes a spreadsheet-ready text file and an array of publication-quality figures. Considering the growing interest in and availability of DNA methylation data, there is a great need for user-friendly open source analytical tools. With MethLAB, we present a timely resource that will allow users with no programming experience to implement flexible and powerful analyses of DNA methylation data.

  12. 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.

  13. Introduction to Metagenomics at DOE JGI (Opening Remarks for the Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    Energy Technology Data Exchange (ETDEWEB)

    Kyrpides, Nikos [DOE JGI

    2011-10-12

    After a quick introduction by DOE JGI Director Eddy Rubin, DOE JGI's Nikos Kyrpides delivers the opening remarks at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011

  14. 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

  15. 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.

  16. {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...

  17. 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).

  18. Modifying Cookbook Labs.

    Science.gov (United States)

    Clark, Robert, L.; Clough, Michael P.; Berg, Craig A.

    2000-01-01

    Modifies an extended lab activity from a cookbook approach for determining the percent mass of water in copper sulfate pentahydrate crystals to one which incorporates students' prior knowledge, engenders active mental struggling with prior knowledge and new experiences, and encourages metacognition. (Contains 12 references.) (ASK)

  19. 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…

  20. Advanced HVAC modeling with FemLab/Simulink/MatLab

    NARCIS (Netherlands)

    Schijndel, van A.W.M.

    2003-01-01

    The combined MatLab toolboxes FemLab and Simulink are evaluated as solvers for HVAC problems based on partial differential equations (PDEs). The FemLab software is designed to simulate systems of coupled PDEs, 1-D, 2-D or 3-D, nonlinear and time dependent. In order to show how the program works, a

  1. Implementation of the Realized Genomic Relationship Matrix to Open-Pollinated White Spruce Family Testing for Disentangling Additive from Nonadditive Genetic Effects

    Directory of Open Access Journals (Sweden)

    Omnia Gamal El-Dien

    2016-03-01

    Full Text Available The open-pollinated (OP family testing combines the simplest known progeny evaluation and quantitative genetics analyses as candidates’ offspring are assumed to represent independent half-sib families. The accuracy of genetic parameter estimates is often questioned as the assumption of “half-sibling” in OP families may often be violated. We compared the pedigree- vs. marker-based genetic models by analysing 22-yr height and 30-yr wood density for 214 white spruce [Picea glauca (Moench Voss] OP families represented by 1694 individuals growing on one site in Quebec, Canada. Assuming half-sibling, the pedigree-based model was limited to estimating the additive genetic variances which, in turn, were grossly overestimated as they were confounded by very minor dominance and major additive-by-additive epistatic genetic variances. In contrast, the implemented genomic pairwise realized relationship models allowed the disentanglement of additive from all nonadditive factors through genetic variance decomposition. The marker-based models produced more realistic narrow-sense heritability estimates and, for the first time, allowed estimating the dominance and epistatic genetic variances from OP testing. In addition, the genomic models showed better prediction accuracies compared to pedigree models and were able to predict individual breeding values for new individuals from untested families, which was not possible using the pedigree-based model. Clearly, the use of marker-based relationship approach is effective in estimating the quantitative genetic parameters of complex traits even under simple and shallow pedigree structure.

  2. Digital Social Science Lab

    DEFF Research Database (Denmark)

    Svendsen, Michael; Lauersen, Christian Ulrich

    2015-01-01

    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...... 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...... 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...

  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....

  4. 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

  5. Lab Streaming Layer Enabled Myo Data Collection Software User Manual

    Science.gov (United States)

    2017-06-07

    SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT UU 18. NUMBER OF PAGES 32 19a. NAME OF RESPONSIBLE PERSON...www.tumsenahopayga.com/ wp-content/uploads/2015/12/Myo- By-Thalmic-Labs-Gesture-Sensor-Controller-Armbad-For-iPhone- Android -Mac-and-PC.jpg...uploads/2015/12/Myo-By-Thalmic-Labs- Gesture-Sensor-Controller-Armbad-For-iPhone- Android -Mac-and-PC.jpg) LSL is an open source system for transmitting

  6. Computer-based Astronomy Labs for Non-science Majors

    Science.gov (United States)

    Smith, A. B. E.; Murray, S. D.; Ward, R. A.

    1998-12-01

    We describe and demonstrate two laboratory exercises, Kepler's Third Law and Stellar Structure, which are being developed for use in an astronomy laboratory class aimed at non-science majors. The labs run with Microsoft's Excel 98 (Macintosh) or Excel 97 (Windows). They can be run in a classroom setting or in an independent learning environment. The intent of the labs is twofold; first and foremost, students learn the subject matter through a series of informational frames. Next, students enhance their understanding by applying their knowledge in lab procedures, while also gaining familiarity with the use and power of a widely-used software package and scientific tool. No mathematical knowledge beyond basic algebra is required to complete the labs or to understand the computations in the spreadsheets, although the students are exposed to the concepts of numerical integration. The labs are contained in Excel workbook files. In the files are multiple spreadsheets, which contain either a frame with information on how to run the lab, material on the subject, or one or more procedures. Excel's VBA macro language is used to automate the labs. The macros are accessed through button interfaces positioned on the spreadsheets. This is done intentionally so that students can focus on learning the subject matter and the basic spreadsheet features without having to learn advanced Excel features all at once. Students open the file and progress through the informational frames to the procedures. After each procedure, student comments and data are automatically recorded in a preformatted Lab Report spreadsheet. Once all procedures have been completed, the student is prompted for a filename in which to save their Lab Report. The lab reports can then be printed or emailed to the instructor. The files will have full worksheet and workbook protection, and will have a "redo" feature at the end of the lab for students who want to repeat a procedure.

  7. 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.

  8. Genome-wide analysis of central corneal thickness in primary open-angle glaucoma cases in the NEIGHBOR and GLAUGEN consortia.

    Science.gov (United States)

    Ulmer, Megan; Li, Jun; Yaspan, Brian L; Ozel, Ayse Bilge; Richards, Julia E; Moroi, Sayoko E; Hawthorne, Felicia; Budenz, Donald L; Friedman, David S; Gaasterland, Douglas; Haines, Jonathan; Kang, Jae H; Lee, Richard; Lichter, Paul; Liu, Yutao; Pasquale, Louis R; Pericak-Vance, Margaret; Realini, Anthony; Schuman, Joel S; Singh, Kuldev; Vollrath, Douglas; Weinreb, Robert; Wollstein, Gadi; Zack, Donald J; Zhang, Kang; Young, Terri; Allingham, R Rand; Wiggs, Janey L; Ashley-Koch, Allison; Hauser, Michael A

    2012-07-03

    To investigate the effects of central corneal thickness (CCT)-associated variants on primary open-angle glaucoma (POAG) risk using single nucleotide polymorphisms (SNP) data from the Glaucoma Genes and Environment (GLAUGEN) and National Eye Institute (NEI) Glaucoma Human Genetics Collaboration (NEIGHBOR) consortia. A replication analysis of previously reported CCT SNPs was performed in a CCT dataset (n = 1117) and these SNPs were then tested for association with POAG using a larger POAG dataset (n = 6470). Then a CCT genome-wide association study (GWAS) was performed. Top SNPs from this analysis were selected and tested for association with POAG. cDNA libraries from fetal and adult brain and ocular tissue samples were generated and used for candidate gene expression analysis. Association with one of 20 previously published CCT SNPs was replicated: rs12447690, near the ZNF469 gene (P = 0.001; β = -5.08 μm/allele). None of these SNPs were significantly associated with POAG. In the CCT GWAS, no SNPs reached genome-wide significance. After testing 50 candidate SNPs for association with POAG, one SNP was identified, rs7481514 within the neurotrimin (NTM) gene, that was significantly associated with POAG in a low-tension subset (P = 0.00099; Odds Ratio [OR] = 1.28). Additionally, SNPs in the CNTNAP4 gene showed suggestive association with POAG (top SNP = rs1428758; P = 0.018; OR = 0.84). NTM and CNTNAP4 were shown to be expressed in ocular tissues. The results suggest previously reported CCT loci are not significantly associated with POAG susceptibility. By performing a quantitative analysis of CCT and a subsequent analysis of POAG, SNPs in two cell adhesion molecules, NTM and CNTNAP4, were identified and may increase POAG susceptibility in a subset of cases.

  9. Increasing Students’ Interest by Encouraging them to Create Original Lab Projects

    Directory of Open Access Journals (Sweden)

    Petre Lucian Ogrutan

    2017-11-01

    Full Text Available Sometimes traditional lab projects based on standard kits and modules fail to stimulate students’ interest and creativity. This paper presents a novel laboratory concept which allows students to develop their own lab projects using open-source resources. The lab experiment includes competition aspects allowing every student to come up with ideas of which the best are selected. The lab projects include both hard and software components using Arduino-compatible systems and interfaces. Before starting the practical activities as well as after the completion of the lab session, the students were asked to fill in an anonymous questionnaire.

  10. 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.

  11. ERLN Technical Support for Labs

    Science.gov (United States)

    The Environmental Response Laboratory Network provides policies and guidance on lab and data requirements, Standardized Analytical Methods, and technical support for water and radiological sampling and analysis

  12. Aircraft Lighting and Transparency Lab

    Data.gov (United States)

    Federal Laboratory Consortium — The Advanced Lighting and Transparencies with Night Combat Lab performs radiometric and photometric measurements of cockpit lighting and displays. Evaluates the day,...

  13. 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:

  14. Lab at Home: Hardware Kits for a Digital Design Lab

    Science.gov (United States)

    Oliver, J. P.; Haim, F.

    2009-01-01

    An innovative laboratory methodology for an introductory digital design course is presented. Instead of having traditional lab experiences, where students have to come to school classrooms, a "lab at home" concept is proposed. Students perform real experiments in their own homes, using hardware kits specially developed for this purpose. They…

  15. RemoteLabs Platform

    Directory of Open Access Journals (Sweden)

    Nils Crabeel

    2012-03-01

    Full Text Available This paper reports on a first step towards the implementation of a framework for remote experimentation of electric machines – the RemoteLabs platform. This project was focused on the development of two main modules: the user Web-based and the electric machines interfaces. The Web application provides the user with a front-end and interacts with the back-end – the user and experiment persistent data. The electric machines interface is implemented as a distributed client server application where the clients, launched by the Web application, interact with the server modules located in platforms physically connected the electric machines drives. Users can register and authenticate, schedule, specify and run experiments and obtain results in the form of CSV, XML and PDF files. These functionalities were successfully tested with real data, but still without including the electric machines. This inclusion is part of another project scheduled to start soon.

  16. 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...

  17. 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

  18. Report from the banding lab

    Science.gov (United States)

    Tautin, J.

    1995-01-01

    Mr. Tautin reported on the seemingly everchanging structure of biological science units within the Interior Department. Current Congressional proposals would either change the name of the Bird Banding Lab's parent agency or make it part of the Geological Survey. The current Congress has not looked favorably on science budgets within the Interior Department, and the Banding Lab's budget is being squeezed ever tighter.

  19. Ntal/Lab/Lat2

    DEFF Research Database (Denmark)

    Iwaki, Shoko; Jensen, Bettina M; Gilfillan, Alasdair M

    2007-01-01

    T cells. As demonstrated in monocytes and B cells, phosphorylated NTAL/LAB/LAT2 recruits signaling molecules such as Grb2, Gab1 and c-Cbl into receptor-signaling complexes. Although gene knock out and knock down studies have indicated that NTAL/LAB/LAT2 may function as both a positive and negative...

  20. Future Scientific Opportunities At Jefferson Lab

    International Nuclear Information System (INIS)

    Thomas, Anthony

    2007-01-01

    Nuclear physics requires at least one major facility world-wide which is capable of fully exploiting the properties of the electro-weak force to investigate precisely the structure of strongly interacting systems. At its current maximum energy of 6 GeV Jefferson Lab has provided a wealth of important information on the structure of nucleons and nuclei. However, the plans to double the energy over the next seven years promise to open new frontiers in nuclear and particle physics. We briefly describe the plans for the 12 GeV Upgrade and the associated physics opportunities.

  1. Genomics of lactic acid bacteria: Current status and potential applications.

    Science.gov (United States)

    Wu, Chongde; Huang, Jun; Zhou, Rongqing

    2017-08-01

    Lactic acid bacteria (LAB) are widely used for the production of a variety of foods and feed raw materials where they contribute to flavor and texture of the fermented products. In addition, specific LAB strains are considered as probiotic due to their health-promoting effects in consumers. Recently, the genome sequencing of LAB is booming and the increased amount of published genomics data brings unprecedented opportunity for us to reveal the important traits of LAB. This review describes the recent progress on LAB genomics and special emphasis is placed on understanding the industry-related physiological features based on genomics analysis. Moreover, strategies to engineer metabolic capacity and stress tolerance of LAB with improved industrial performance are also discussed.

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

    OpenAIRE

    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 discoura...

  3. 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.

  4. The fishes of Genome 10K

    KAUST Repository

    Bernardi, Giacomo; Wiley, Edward O.; Mansour, Hicham; Miller, Michael R.; Ortí , Guillermo; Haussler, David H.; O'Brien, Stephen J O; Ryder, Oliver A.; Venkatesh, Byrappa

    2012-01-01

    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.

  5. 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...

  6. 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...

  7. 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...

  8. 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)

  9. 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)

  10. 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...

  11. 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.

  12. 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:      ...

  13. 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.

  14. PC/104 Embedded IOCs at Jefferson Lab

    International Nuclear Information System (INIS)

    Yan, Jianxun; Allison, Trent; Witherspoon, Sue; Cuffe, Anthony

    2009-01-01

    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.

  15. 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

  16. 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.

  17. 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

  18. 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.

  19. The first draft genome of the aquatic model plant Lemna minor opens the route for future stress physiology research and biotechnological applications.

    Science.gov (United States)

    Van Hoeck, Arne; Horemans, Nele; Monsieurs, Pieter; Cao, Hieu Xuan; Vandenhove, Hildegarde; Blust, Ronny

    2015-01-01

    Freshwater duckweed, comprising the smallest, fastest growing and simplest macrophytes has various applications in agriculture, phytoremediation and energy production. Lemna minor, the so-called common duckweed, is a model system of these aquatic plants for ecotoxicological bioassays, genetic transformation tools and industrial applications. Given the ecotoxic relevance and high potential for biomass production, whole-genome information of this cosmopolitan duckweed is needed. The 472 Mbp assembly of the L. minor genome (2n = 40; estimated 481 Mbp; 98.1 %) contains 22,382 protein-coding genes and 61.5 % repetitive sequences. The repeat content explains 94.5 % of the genome size difference in comparison with the greater duckweed, Spirodela polyrhiza (2n = 40; 158 Mbp; 19,623 protein-coding genes; and 15.79 % repetitive sequences). Comparison of proteins from other monocot plants, protein ortholog identification, OrthoMCL, suggests 1356 duckweed-specific groups (3367 proteins, 15.0 % total L. minor proteins) and 795 Lemna-specific groups (2897 proteins, 12.9 % total L. minor proteins). Interestingly, proteins involved in biosynthetic processes in response to various stimuli and hydrolase activities are enriched in the Lemna proteome in comparison with the Spirodela proteome. The genome sequence and annotation of L. minor protein-coding genes provide new insights in biological understanding and biomass production applications of Lemna species.

  20. 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…

  1. OpenLabs Security Laboratory - The Online Security Experiment Platform

    OpenAIRE

    Johan Zackrisson; Charlie Svahnberg

    2008-01-01

    For experiments to be reproducible, it is important to have a known and controlled environment. This requires isolation from the surroundings. For security experiments, e.g. with hostile software, this is even more important as the experiment can affect the environment in adverse ways. In a normal campus laboratory, isolation can be achieved by network separation. For an online environment, where remote control is essential, separation and isolation are still needed, and therefore the securit...

  2. 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.

  3. Formalising Living Labs to achieve organisational objectives in emerging economies

    CSIR Research Space (South Africa)

    Smit, D

    2011-05-01

    Full Text Available Conference Proceedings Paul Cunningham and Miriam Cunningham (Eds) IIMC International Information Management Corporation, 2011 ISBN: 978-1-905824-24-3 Formalising Living Labs to Achieve Organisational Objectives in Emerging Economies Danie SMIT1... organisation, a university) in the innovation process. In contrast to closed- innovation where firms only use internal sources, open-innovation suggests the companies use both external and internal sources. This shift in innovation paradigm becomes more...

  4. Flexible HVAC System for Lab or Classroom.

    Science.gov (United States)

    Friedan, Jonathan

    2001-01-01

    Discusses an effort to design a heating, ventilation, and air conditioning system flexible enough to accommodate an easy conversion of classrooms to laboratories and dry labs to wet labs. The design's energy efficiency and operations and maintenance are examined. (GR)

  5. 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

  6. 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.

  7. The first draft genome of the aquatic model plant Lemna minor opens the route for future stress physiology research and biotechnological applications

    OpenAIRE

    Van Hoeck, Arne; Horemans, Nele; Monsieurs, Pieter; Cao, Hieu Xuan; Vandenhove, Hildegarde; Blust, Ronny

    2015-01-01

    Background: Freshwater duckweed, comprising the smallest, fastest growing and simplest macrophytes has various applications in agriculture, phytoremediation and energy production. Lemna minor, the so-called common duckweed, is a model system of these aquatic plants for ecotoxicological bioassays, genetic transformation tools and industrial applications. Given the ecotoxic relevance and high potential for biomass production, whole-genome information of this cosmopolitan duckweed is needed. Res...

  8. Incorporating lab experience into computer security courses

    NARCIS (Netherlands)

    Ben Othmane, L.; Bhuse, V.; Lilien, L.T.

    2013-01-01

    We describe our experience with teaching computer security labs at two different universities. We report on the hardware and software lab setups, summarize lab assignments, present the challenges encountered, and discuss the lessons learned. We agree with and emphasize the viewpoint that security

  9. Safety Protocols at MAT Lab

    International Nuclear Information System (INIS)

    Wadawale, A.; Chopade, S.; Chaudhury, K.; Pal, M.K.; Kushwah, N.; Shah, A.Y.; Kedarnath, G.; Priyadarsini, K.I.; Jain, V.K.

    2017-01-01

    MAT Lab of Chemistry Division, BARC (A Class 10000 Clean room laboratory) has been in operation since 2004 for process development of ultra-purification of several strategically important materials (Ga, As, Sb, In, CsI and Ge) and synthesis of their organometallic compounds. Of these, work related to purification of As, Sb, and In, has been discontinued. Due to high toxicity and pyrophoric nature of some of the compounds, stringent safety regulations were formulated and subsequently implemented by the division

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

    Science.gov (United States)

    Jonas, Elisabeth; de Koning, Dirk-Jan

    2015-01-01

    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 (GS) 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 GS 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 breeding scenarios.

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

    Science.gov (United States)

    Greenbaum, Dov; Sboner, Andrea; Mu, Xinmeng Jasmine; Gerstein, Mark

    2011-12-01

    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 identifiable subjects in the

  12. 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

  13. The first complete genome sequences of clinical isolates of human coronavirus 229E

    NARCIS (Netherlands)

    Farsani, Seyed Mohammad Jazaeri; Dijkman, Ronald; Jebbink, Maarten F.; Goossens, Herman; Ieven, Margareta; Deijs, Martin; Molenkamp, Richard; van der Hoek, Lia

    2012-01-01

    Human coronavirus 229E has been identified in the mid-1960s, yet still only one full-genome sequence is available. This full-length sequence has been determined from the cDNA-clone Inf-1 that is based on the lab-adapted strain VR-740. Lab-adaptation might have resulted in genomic changes, due to

  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. Genomics using the Assembly of the Mink Genome

    DEFF Research Database (Denmark)

    Guldbrandtsen, Bernt; Cai, Zexi; Sahana, Goutam

    2018-01-01

    The American Mink’s (Neovison vison) genome has recently been sequenced. This opens numerous avenues of research both for studying the basic genetics and physiology of the mink as well as genetic improvement in mink. Using genotyping-by-sequencing (GBS) generated marker data for 2,352 Danish farm...... mink runs of homozygosity (ROH) were detect in mink genomes. Detectable ROH made up on average 1.7% of the genome indicating the presence of at most a moderate level of genomic inbreeding. The fraction of genome regions found in ROH varied. Ten percent of the included regions were never found in ROH....... The ability to detect ROH in the mink genome also demonstrates the general reliability of the new mink genome assembly. Keywords: american mink, run of homozygosity, genome, selection, genomic inbreeding...

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

    NARCIS (Netherlands)

    Dongre, C.; van Weerd, J.; van Weeghel, R.; Martinez-Vazquez, R.; Osellame, R.; Cerullo, G.; Besselink, G.A.J.; van den Vlekkert, H.H.; Hoekstra, Hugo; Pollnau, Markus

    Sorting and sizing of DNA molecules within the human genome project has enabled the genetic mapping of various illnesses. By employing tiny lab-on-a-chip devices for such DNA analysis, integrated DNA sequencing and genetic diagnostics have become feasible. However, such diagnostic chips typically

  17. 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

  18. 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/)

  19. 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.

  20. EarthLabs - Investigating Hurricanes: Earth's Meteorological Monsters

    Science.gov (United States)

    McDaris, J. R.; Dahlman, L.; Barstow, D.

    2007-12-01

    Earth science is one of the most important tools that the global community needs to address the pressing environmental, social, and economic issues of our time. While, at times considered a second-rate science at the high school level, it is currently undergoing a major revolution in the depth of content and pedagogical vitality. As part of this revolution, labs in Earth science courses need to shift their focus from cookbook-like activities with known outcomes to open-ended investigations that challenge students to think, explore and apply their learning. We need to establish a new model for Earth science as a rigorous lab science in policy, perception, and reality. As a concerted response to this need, five states, a coalition of scientists and educators, and an experienced curriculum team are creating a national model for a lab-based high school Earth science course named EarthLabs. This lab course will comply with the National Science Education Standards as well as the states' curriculum frameworks. The content will focus on Earth system science and environmental literacy. The lab experiences will feature a combination of field work, classroom experiments, and computer access to data and visualizations, and demonstrate the rigor and depth of a true lab course. The effort is being funded by NOAA's Environmental Literacy program. One of the prototype units of the course is Investigating Hurricanes. Hurricanes are phenomena which have tremendous impact on humanity and the resources we use. They are also the result of complex interacting Earth systems, making them perfect objects for rigorous investigation of many concepts commonly covered in Earth science courses, such as meteorology, climate, and global wind circulation. Students are able to use the same data sets, analysis tools, and research techniques that scientists employ in their research, yielding truly authentic learning opportunities. This month-long integrated unit uses hurricanes as the story line by

  1. 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.

  2. Lab, Field, Gallery and Beyond

    DEFF Research Database (Denmark)

    Binder, Thomas; Koskinen, Ilpo; Redström, Johan

    2009-01-01

    Over the last ten years we have seen a growing number of researchers integrating design experiments in their research inquiries. Initially, this work borrowed heavily from neighboring fields, employing a dual strategy in which design experiments and their evaluation were largely treated as separate...... processes that were often carried out by different people. More recently, design researchers have developed several approaches that integrate design-specific work methods to research. This paper takes a methodological look at three such established approaches that we call Lab, Field, and Gallery. We...

  3. 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)

  4. 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)

  5. 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

  6. 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%.

  7. 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

  8. 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

  9. 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)

  10. A dedicated lab for interventional cardiology and hybrid surgery

    Energy Technology Data Exchange (ETDEWEB)

    Berger, F. [KinderSpital Zurich (Switzerland). Department of Congenital Heart Disease/Pediatric Cardiology

    2004-07-01

    Pediatric interventionalists and surgeons treating congenital heart defects at the KinderSpital children's hospital in Zurich, Switzerland, use a ''hybrid'' approach to minimize the incidence and extent of open-heart surgery. The hybrid approach combines catheterization and surgical techniques in a single procedure, performed in the same lab. The combined cardiac cath lab/surgery suite is equipped with a Philips Integris Allura BH5000 9''/9'' biplane system, designed to meet all the requirements for pediatric applications, including the need to keep the quantity of contrast agent and the radiation dose to the minimum. Wherever possible, diagnostic X-ray examinations are supplemented by MR and Ultrasound. (orig.)

  11. 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.

  12. SuperFormLab: showing SuperFormLab

    DEFF Research Database (Denmark)

    2013-01-01

    bachelor program, followed by two years of master studies. The courses are offered equally to students from other design disciplines, e.g. industrial design. Teaching is mainly in English as the program is attended by a relatively large group of non-Danish students, who seek exactly this combination......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...

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. Magnetic Viscous Drag for Friction Labs

    Science.gov (United States)

    Gaffney, Chris; Catching, Adam

    2016-01-01

    The typical friction lab performed in introductory mechanics courses is usually not the favorite of either the student or the instructor. The measurements are not all that easy to make, and reproducibility is usually a troublesome issue. This paper describes the augmentation of such a friction lab with a study of the viscous drag on a magnet…

  20. Hydrogel Beads: The New Slime Lab?

    Science.gov (United States)

    Brockway, Debra; Libera, Matthew; Welner, Heidi

    2011-01-01

    Creating slime fascinates students. Unfortunately, though intrigue is at its peak, the educational aspect of this activity is often minimal. This article describes a chemistry lab that closely relates to the slime lab and allows high school students to explore the concepts of chemical bonding, properties, and replacement reactions. It involves the…

  1. 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...

  2. mQoL smart lab

    DEFF Research Database (Denmark)

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

    2016-01-01

    serve quality research in all of them. In this paper, we present own "mQoL Smart Lab" for interdisciplinary research efforts on individuals' "Quality of Life" improvement. We present an evolution of our current in-house living lab platform enabling continuous, pervasive data collection from individuals...

  3. 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.

  4. Diversity, Equity, & Inclusion at Berkeley Lab

    Science.gov (United States)

    Berkeley Lab A-Z Index Directory Search Diversity, Equity, & Inclusion at Berkeley Lab Home Diversity & Inclusion Council Women Scientists & Engineers Council Employee Resource Groups -and culture of inclusion are key to attracting and engaging the brightest minds and furthering our

  5. 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...

  6. 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.

  7. 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.

  8. User recruitment, training, and support at NOAO Data Lab

    Science.gov (United States)

    Nikutta, Robert; Fitzpatrick, Michael J.; NOAO Data Lab

    2018-06-01

    The NOAO Data Lab (datalab.noao.edu) is a fully-fledged science data & analysis platform. However, simply building a science platform is notenough to declare it a success. Like any such system built for users, it needs actual users who see enough value in it to be willing toovercome the inertia of registering an account, studying the documentation, working through examples, and ultimately attempting tosolve their own science problems using the platform. The NOAO Data Lab has been open to users since June 2016. In this past year we haveregistered hundreds of users and improved the system, not least through the interaction with and feedback from our users. The posterwill delineate our efforts to recruit new users through conference presentations, platform demos and user workshops, and what we do toassure that users experience their first steps and their learning process with Data Lab as easy, competent, and inspiring. It will alsopresent our efforts in user retention and user support, from a human-staffed helpdesk, to one-on-one sessions, to regular"bring-your-own-problem (BYOP)" in-house sessions with interested users.

  9. Jefferson Lab's Distributed Data Acquisition

    International Nuclear Information System (INIS)

    Trent Allison; Thomas Powers

    2006-01-01

    Jefferson Lab's Continuous Electron Beam Accelerator Facility (CEBAF) occasionally experiences fast intermittent beam instabilities that are difficult to isolate and result in downtime. The Distributed Data Acquisition (Dist DAQ) system is being developed to detect and quickly locate such instabilities. It will consist of multiple Ethernet based data acquisition chassis distributed throughout the seven-eights of a mile CEBAF site. Each chassis will monitor various control system signals that are only available locally and/or monitored by systems with small bandwidths that cannot identify fast transients. The chassis will collect data at rates up to 40 Msps in circular buffers that can be frozen and unrolled after an event trigger. These triggers will be derived from signals such as periodic timers or accelerator faults and be distributed via a custom fiber optic event trigger network. This triggering scheme will allow all the data acquisition chassis to be triggered simultaneously and provide a snapshot of relevant CEBAF control signals. The data will then be automatically analyzed for frequency content and transients to determine if and where instabilities exist

  10. 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.

  11. 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.

  12. Genome Variation Map: a data repository of genome variations in BIG Data Center

    OpenAIRE

    Song, Shuhui; Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang; Zhang, Zhang

    2017-01-01

    Abstract The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research a...

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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...

  18. Microspectroscopy At Beamline 73 MAX-lab

    International Nuclear Information System (INIS)

    Engdahl, Anders

    2010-01-01

    Presentation of some projects at the infrared microspectroscopy experimental station at beamline 73 MAX-lab. Among the subjects are found identification of organic residues in fossil material and examination of the chemistry in an old oak wood wreck.

  19. 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.

  20. 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...

  1. 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...

  2. 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...

  3. Los Alamos National Lab: National Security Science

    Science.gov (United States)

    SKIP TO PAGE CONTENT Los Alamos National Laboratory Delivering science and technology to protect Museum New Hires Publications Research Library Mission Science & Innovation Science & Innovation Facilities Science Pillars Research Library Science Briefs Science News Lab Organizations Science Programs

  4. The Jefferson Lab Trigger Supervisor System

    International Nuclear Information System (INIS)

    Ed Jastrzembsi; David Abbott; Graham Heyes; R.W. MacLeod; Carl Timmer; Elliott Wolin

    2000-01-01

    We discuss the design and performance of a Trigger Supervisor System for use in nuclear physics experiments at Jefferson Lab. We also discuss the enhanced features of a new Trigger Supervisor Module now under construction

  5. The Jefferson Lab Trigger Supervisor System

    International Nuclear Information System (INIS)

    Jastrzembski, E.; Abbott, D.J.; Heyes, W.G.; MacLeod, R.W.; Timmer, C.; Wolin, E.

    1999-01-01

    The authors discuss the design and performance of a Trigger Supervisor System for use in nuclear physics experiments at Jefferson Lab. They also discuss the enhanced features of a new Trigger Supervisor Module now under construction

  6. 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.

  7. 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.

  8. 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...

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

    OpenAIRE

    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 electrophoresis with laser-induced fluorescence for optofluidic integration toward an on-chip bio-analysis tool. Integrated optical fluorescence excitation allows for a high spatial resolution (12 μm) ...

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

    OpenAIRE

    Dongre, C.; van Weerd, J.; van Weeghel, R.; Martinez-Vazquez, R.; Osellame, R.; Cerullo, G.; Besselink, G.A.J.; van den Vlekkert, H.H.; Hoekstra, Hugo; Pollnau, Markus

    2010-01-01

    Sorting and sizing of DNA molecules within the human genome project has enabled the genetic mapping of various illnesses. By employing tiny lab-on-a-chip devices for such DNA analysis, integrated DNA sequencing and genetic diagnostics have become feasible. However, such diagnostic chips typically lack integrated sensing capability. We address this issue by combining microfluidic capillary electrophoresis with laser-induced fluorescence detection resulting in optofluidic integration towards an...

  11. 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...

  12. 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)

  13. Fifteen years experience: Egyptian metabolic lab

    Directory of Open Access Journals (Sweden)

    Ekram M. Fateen

    2014-10-01

    Conclusion: This study illustrates the experience of the reference metabolic lab in Egypt over 15 years. The lab began metabolic disorder screening by using simple diagnostic techniques like thin layer chromatography and colored tests in urine which by time updated and upgraded the methods to diagnose a wide range of disorders. This study shows the most common diagnosed inherited inborn errors of metabolism among the Egyptian population.

  14. 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.

  15. 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...

  16. A comparative study on real lab and simulation lab in communication engineering from students' perspectives

    Science.gov (United States)

    Balakrishnan, B.; Woods, P. C.

    2013-05-01

    Over the years, rapid development in computer technology has engendered simulation-based laboratory (lab) in addition to the traditional hands-on (physical) lab. Many higher education institutions adopt simulation lab, replacing some existing physical lab experiments. The creation of new systems for conducting engineering lab activities has raised concerns among educators on the merits and shortcomings of both physical and simulation labs; at the same time, many arguments have been raised on the differences of both labs. Investigating the effectiveness of both labs is complicated, as there are multiple factors that should be considered. In view of this challenge, a study on students' perspectives on their experience related to key aspects on engineering laboratory exercise was conducted. In this study, the Visual Auditory Read and Kinetic model was utilised to measure the students' cognitive styles. The investigation was done through a survey among participants from Multimedia University, Malaysia. The findings revealed that there are significant differences for most of the aspects in physical and simulation labs.

  17. 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...

  18. 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.

  19. Extreme genomes

    OpenAIRE

    DeLong, Edward F

    2000-01-01

    The complete genome sequence of Thermoplasma acidophilum, an acid- and heat-loving archaeon, has recently been reported. Comparative genomic analysis of this 'extremophile' is providing new insights into the metabolic machinery, ecology and evolution of thermophilic archaea.

  20. Grass genomes

    OpenAIRE

    Bennetzen, Jeffrey L.; SanMiguel, Phillip; Chen, Mingsheng; Tikhonov, Alexander; Francki, Michael; Avramova, Zoya

    1998-01-01

    For the most part, studies of grass genome structure have been limited to the generation of whole-genome genetic maps or the fine structure and sequence analysis of single genes or gene clusters. We have investigated large contiguous segments of the genomes of maize, sorghum, and rice, primarily focusing on intergenic spaces. Our data indicate that much (>50%) of the maize genome is composed of interspersed repetitive DNAs, primarily nested retrotransposons that in...

  1. Open source systems security certification

    CERN Document Server

    Damiani, Ernesto; El Ioini, Nabil

    2009-01-01

    Open Source Advances in Computer Applications book series provides timely technological and business information for: Enabling Open Source Systems (OSS) to become an integral part of systems and devices produced by technology companies; Inserting OSS in the critical path of complex network development and embedded products, including methodologies and tools for domain-specific OSS testing (lab code available), plus certification of security, dependability and safety properties for complex systems; Ensuring integrated systems, including OSS, meet performance and security requirements as well as achieving the necessary certifications, according to the overall strategy of OSS usage on the part of the adopter

  2. 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...

  3. Ensembl 2002: accommodating comparative genomics.

    Science.gov (United States)

    Clamp, M; Andrews, D; Barker, D; Bevan, P; Cameron, G; Chen, Y; Clark, L; Cox, T; Cuff, J; Curwen, V; Down, T; Durbin, R; Eyras, E; Gilbert, J; Hammond, M; Hubbard, T; Kasprzyk, A; Keefe, D; Lehvaslaiho, H; Iyer, V; Melsopp, C; Mongin, E; Pettett, R; Potter, S; Rust, A; Schmidt, E; Searle, S; Slater, G; Smith, J; Spooner, W; Stabenau, A; Stalker, J; Stupka, E; Ureta-Vidal, A; Vastrik, I; Birney, E

    2003-01-01

    The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of human, mouse and other genome sequences, available as either an interactive web site or as flat files. Ensembl also integrates manually annotated gene structures from external sources where available. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. These range from sequence analysis to data storage and visualisation and installations exist around the world in both companies and at academic sites. With both human and mouse genome sequences available and more vertebrate sequences to follow, many of the recent developments in Ensembl have focusing on developing automatic comparative genome analysis and visualisation.

  4. The Ensembl genome database project.

    Science.gov (United States)

    Hubbard, T; Barker, D; Birney, E; Cameron, G; Chen, Y; Clark, L; Cox, T; Cuff, J; Curwen, V; Down, T; Durbin, R; Eyras, E; Gilbert, J; Hammond, M; Huminiecki, L; Kasprzyk, A; Lehvaslaiho, H; Lijnzaad, P; Melsopp, C; Mongin, E; Pettett, R; Pocock, M; Potter, S; Rust, A; Schmidt, E; Searle, S; Slater, G; Smith, J; Spooner, W; Stabenau, A; Stalker, J; Stupka, E; Ureta-Vidal, A; Vastrik, I; Clamp, M

    2002-01-01

    The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of the human genome sequence, with confirmed gene predictions that have been integrated with external data sources, and is available as either an interactive web site or as flat files. It is also an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements from sequence analysis to data storage and visualisation. The Ensembl site is one of the leading sources of human genome sequence annotation and provided much of the analysis for publication by the international human genome project of the draft genome. The Ensembl system is being installed around the world in both companies and academic sites on machines ranging from supercomputers to laptops.

  5. 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

  6. RoboLab and virtual environments

    Science.gov (United States)

    Giarratano, Joseph C.

    1994-01-01

    A useful adjunct to the manned space station would be a self-contained free-flying laboratory (RoboLab). This laboratory would have a robot operated under telepresence from the space station or ground. Long duration experiments aboard RoboLab could be performed by astronauts or scientists using telepresence to operate equipment and perform experiments. Operating the lab by telepresence would eliminate the need for life support such as food, water and air. The robot would be capable of motion in three dimensions, have binocular vision TV cameras, and two arms with manipulators to simulate hands. The robot would move along a two-dimensional grid and have a rotating, telescoping periscope section for extension in the third dimension. The remote operator would wear a virtual reality type headset to allow the superposition of computer displays over the real-time video of the lab. The operators would wear exoskeleton type arms to facilitate the movement of objects and equipment operation. The combination of video displays, motion, and the exoskeleton arms would provide a high degree of telepresence, especially for novice users such as scientists doing short-term experiments. The RoboLab could be resupplied and samples removed on other space shuttle flights. A self-contained RoboLab module would be designed to fit within the cargo bay of the space shuttle. Different modules could be designed for specific applications, i.e., crystal-growing, medicine, life sciences, chemistry, etc. This paper describes a RoboLab simulation using virtual reality (VR). VR provides an ideal simulation of telepresence before the actual robot and laboratory modules are constructed. The easy simulation of different telepresence designs will produce a highly optimum design before construction rather than the more expensive and time consuming hardware changes afterwards.

  7. 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…

  8. University of Washington Lab Report to SNEAP, 1999

    International Nuclear Information System (INIS)

    Amsbaugh, J.F.; Harper, G.C.; Linder, C.E.; Myers, A.W.; Storns, D.W.; Wechel, T.D. van; Will, D.I.

    2000-01-01

    OAK-B135 University of Washington Lab Report to SNEAP, 1999. The NPL tandem Van de Graaff accelerator chains ran 1869 hours between 9/1/98 and 8/31/99. The DEIS ran 356 hours and the SpIS ran 667. There were 28 experiment-days in which the LINAC and tandem were used together and seven days when the tandem was used, with one of the external ion sources, as a tandem. Four of these were with light ions and three with heavy ions. There were 68 days of Tandem Terminal Ion Source (TIS) development or repair, and 46 days of TIS installation or removal or changing TIS ion species. The TIS/tandem was used a total of 70 days to deliver p, d, 3 He, or 4 He beams for use by an experimenter. There were 47 experiment-days during which the injector deck was used to generate C 60 or LiF 3 clusters, which were then investigated without further acceleration. They had 25 tank openings over the year. There were three scheduled openings for the installation or removal of the TIS, and seven to change the TIS ion species. There were 10 openings for 4 He ion source and column resistor gradient development. There were four openings for various repairs other than ion source, and one to replace the LE grid, which was found undamaged after all

  9. 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

  10. 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…

  11. The role of wet lab in thoracic surgery.

    Science.gov (United States)

    Bedetti, Benedetta; Schnorr, Philipp; Schmidt, Joachim; Scarci, Marco

    2017-01-01

    During the last three decades, minimally invasive surgery has become common practice in all kinds of surgical disciplines and, in Thoracic Surgery, the minimally invasive approach is recommended as the treatment of choice for early-stage non-small cell lung cancer. Nevertheless, all over the world a large number of lobectomies is still performed by conventional open thoracotomy and not as video-assisted thoracic surgery (VATS), which shows the need of a proper training for this technique. Development and improvement of surgical skills are not only challenging and time-consuming components of the training curriculum for resident or fellow surgeons, but also for more experienced consultants learning new techniques. The rapid evolution of medical technologies like VATS or robotic surgery requires an evolution of the existing educational models to improve cognitive and procedural skills before reaching the operating room in order to increase patient safety. Nowadays, in the Thoracic Surgery field, there is a wide range of simulation-based training methods for surgeons starting or wanting to improve their learning curve in VATS. Aim is to overcome the learning curve required to successfully master this new technique in a brief time. In general, the basic difference between the various learning techniques is the distinction between "dry" and "wet" lab modules, which mainly reflects the use of synthetic or animal-model-based materials. Wet lab trainings can be further sub-divided into in vivo modules, where living anaesthetized animals are used, and ex vivo modules, where only animal tissues serve as basis of the simulation-based training method. In the literature, the role of wet lab in Thoracic Surgery is still debated.

  12. Esophagectomy - open

    Science.gov (United States)

    ... Lewis esophagectomy, Blunt esophagectomy; Esophageal cancer - esophagectomy - open; Cancer of the esophagus - esophagectomy - open ... lining of the esophagus that can lead to cancer ( Barrett esophagus ) Severe trauma Destroyed esophagus Severely damaged stomach

  13. 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.

  14. Low Cost Implementation of Remote Lab with Large Number of Configurations for a BJT Amplifier

    Directory of Open Access Journals (Sweden)

    Olaf H. Graven

    2011-09-01

    Full Text Available This paper demonstrate how to construct an advanced yet low cost remote lab for experiments for an module in analogue electronics at an electrical engineering course at second year bachelor level. The remote lab is designed for running experiments on a normal BJT common emitter amplifier circuit, while maintaining the possibility for the students to use a wide range of different setups. The main reasons for using remote lab are the opportunity to give the students the chance to focus on the theory for the laboratory and not setup problems, in addition the availability of the exercise is 24/7 and not dependent on the opening hours of the physical laboratory.

  15. 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 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)

  16. 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)

  17. 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.

  18. 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

  19. 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.

  20. eComLab: remote laboratory platform

    Science.gov (United States)

    Pontual, Murillo; Melkonyan, Arsen; Gampe, Andreas; Huang, Grant; Akopian, David

    2011-06-01

    Hands-on experiments with electronic devices have been recognized as an important element in the field of engineering to help students get familiar with theoretical concepts and practical tasks. The continuing increase the student number, costly laboratory equipment, and laboratory maintenance slow down the physical lab efficiency. As information technology continues to evolve, the Internet has become a common media in modern education. Internetbased remote laboratory can solve a lot of restrictions, providing hands-on training as they can be flexible in time and the same equipment can be shared between different students. This article describes an on-going remote hands-on experimental radio modulation, network and mobile applications lab project "eComLab". Its main component is a remote laboratory infrastructure and server management system featuring various online media familiar with modern students, such as chat rooms and video streaming.

  1. 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

  2. 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

  3. Open access

    NARCIS (Netherlands)

    Valkenburg, P.M.

    2015-01-01

    Open access week Van 19 tot en met 25 oktober 2015 vond wereldwijd de Open Access Week plaats. Tijdens deze week werden er over de hele wereld evenementen georganiseerd waar open access een rol speelt. Ook in Nederland zijn er diverse symposia, workshops en debatten georganiseerd zoals het debat in

  4. 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.

  5. Fossil Groups as Cosmological Labs

    Science.gov (United States)

    D'Onghia, Elena

    Optical and X-ray measurements of fossil groups (FGs) suggest that they are old and relaxed systems. If FGs are assembled at higher redshift, there is enough time for intermediate-luminosity galaxies to merge, resulting in the formation of the brightest group galaxy (BGG). We carry out the first, systematic study of a large sample of FGs, the "FOssil Group Origins'' (FOGO) based on an International Time Project at the Roque de los Muchachos Observatory. For ten FOGO FGs we have been awarded time at SUZAKU Telescope to measure the temperature of the hot intragroup gas (IGM). For these systems we plan to evaluate and correlate their X-ray luminosity and X-ray temperature, Lx-Tx, optical luminosity and X-ray temperature, Lopt-Tx, and group velocity dispersion with their X-ray temperature, sigma V-Tx, as compared to the non fossil systems. By combining these observations with state-of-art cosmological hydrodynamical simulations we will open a new window into the study of the IGM and the nature of fossil systems. Our proposed work will be of direct relevance for the understanding and interpretation of data from several NASA science missions. Specifically, the scaling relations obtained from these data combined with our predictions obtained using state-of-the-art hydrodynamical simulation numerical adopting a new hydrodynamical scheme will motivate new proposal on CHANDRA X-ray telescope for fossil groups and clusters. We will additionally create a public Online Planetarium Show. This will be an educational site, containing an interactive program called: "A Voyage to our Universe''. In the show we will provide observed images of fossil groups and similar images and movies obtained from the numerical simulations showing their evolution. The online planetarium show will be a useful reference and an interactive educational tool for both students and the public.

  6. Study Labs Kortlægningsrapport UCSJ

    DEFF Research Database (Denmark)

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

    2015-01-01

    Rapporten er en delleverance i det regionale forprojekt S​tudy Labs,​der udføres som et samarbejde mellem Holbæk, Odsherred og Kalundborg kommune og University College Sjælland (UCSJ). Samarbejdet er delvist medfinansieret af Region Sjælland. Rapporten behandler projektets etableringsfase...... for at nå de kommunale målsætninger. De potentielle målgrupper er blevet kortlagt. Samtidig er undersøgelser i brugergrupperne blevet gjort håndgribelige i form af Personaer. Kommunerne har, faciliteret af Educationlab, gennemført designworkshops og er fremkommet med designs for Study Labs, der som...

  7. 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.

  8. 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

  9. 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.

  10. 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

  11. Assessing the Impact of a Virtual Lab in an Allied Health Program.

    Science.gov (United States)

    Kay, Robin; Goulding, Helene; Li, Jia

    2018-01-01

    Competency-based education in health care requires rigorous standards to ensure professional proficiency. Demonstrating competency in hands-on laboratories calls for effective preparation, knowledge, and experience, all of which can be difficult to achieve using traditional teaching methods. Virtual laboratories are an alternative, cost-effective approach to providing students with sufficient preparatory information. Research on the use of virtual labs in allied health education is limited. The current study investigated the benefits, challenges, and perceived impact of a virtual lab in an allied health program. The sample consisted of 64 students (55 females, 9 males) enrolled in a university medical laboratory science program. A convergent mixed-methods approach (Likert survey, open-ended questions, think-aloud protocol data) revealed that students had positive attitudes towards visual learning, authenticity, learner control, organization, and scaffolding afforded by the virtual lab. Challenges reported included navigational difficulties, an absence of control over content selection, and lack of understanding for certain concepts. Over 90% of students agreed that the virtual lab helped them prepare for hands-on laboratory sessions and that they would use this format of instruction again. Overall, 84% of the students agreed that the virtual lab helped them to achieve greater success in learning.

  12. Institutional transparency improves public perception of lab animal technicians and support for animal research.

    Science.gov (United States)

    Mills, Katelyn E; Han, Zetta; Robbins, Jesse; Weary, Daniel M

    2018-01-01

    The use of animals in research is controversial and often takes place under a veil of secrecy. Lab animal technicians responsible for the care of animals at research institutions are sometimes described as performing 'dirty work' (i.e. professions that are viewed as morally tainted), and may be stigmatized by negative perceptions of their job. This study assessed if transparency affects public perceptions of lab animal technicians and support for animal research. Participants (n = 550) were randomly assigned to one of six scenarios (using a 3x2 design) that described identical research varying only the transparency of the facility (low, high) and the species used (mice, dogs, cows). Participants provided Likert-type and open-ended responses to questions about the personal characteristics (warmth, competence) of a hypothetical lab technician 'Cathy' and their support for the described research. Quantitative analysis showed participants in the low-transparency condition perceived Cathy to be less warm and were less supportive of the research regardless of animal species. Qualitative responses varied greatly, with some participants expressing support for both Cathy and the research. These results suggest that increasing transparency in lab animal institutions could result in a more positive perception of lab animal researchers and the work that they do.

  13. 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.

  14. 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…

  15. 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.

  16. Improving the Quality of Lab Reports by Using Them as Lab Instructions

    Science.gov (United States)

    Haagen-Schuetzenhoefer, Claudia

    2012-10-01

    Lab exercises are quite popular in teaching science. Teachers have numerous goals in mind when teaching science laboratories. Nevertheless, empirical research draws a heterogeneous picture of the benefits of lab work. Research has shown that it does not necessarily contribute to the enhancement of practical abilities or content knowledge. Lab activities are frequently based on recipe-like, step-by-step instructions ("cookbook style"), which do not motivate students to engage cognitively. Consequently, students put the emphasis on "task completion" or "manipulating equipment."2

  17. 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.

  18. Special Report: Hazardous Wastes in Academic Labs.

    Science.gov (United States)

    Sanders, Howard J.

    1986-01-01

    Topics and issues related to toxic wastes in academic laboratories are addressed, pointing out that colleges/universities are making efforts to dispose of hazardous wastes safely to comply with tougher federal regulations. University sites on the Environmental Protection Agency Superfund National Priorities List, costs, and use of lab packs are…

  19. 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

  20. Map Your Way to a Better Lab.

    Science.gov (United States)

    Roth, Wolff-Michael

    1990-01-01

    The use of concept maps, Vee diagrams, flow charts, and productive questions to increase student understanding of laboratory exercises and to improve student attitudes toward lab classes is discussed. Examples of each are provided. Student responses to these teaching methods are described. (CW)

  1. A New Twist on Torque Labs

    Science.gov (United States)

    Lane, W. Brian

    2014-01-01

    The traditional introductory-level meterstick-balancing lab assumes that students already know what torque is and that they readily identify it as a physical quantity of interest. We propose a modified version of this activity in which students qualitatively and quantitatively measure the amount of force required to keep the meterstick level. The…

  2. 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…

  3. Folding Inquiry into Cookbook Lab Activities

    Science.gov (United States)

    Gooding, Julia; Metz, Bill

    2012-01-01

    Cookbook labs have been a part of science programs for years, even though they serve little purpose other than to verify phenomena that have been previously presented by means other than through investigations. Cookbook science activities follow a linear path to a known outcome, telling students what procedures to follow, which materials to use,…

  4. Laboratory Accreditation Bureau (L-A-B)

    Science.gov (United States)

    2011-03-28

    to all Technical Advisors. Must agree with code of conduct, confidentiality and our mission DoD ELAP Program  ISO / IEC 17025 :2005 and DoD QSM...Additional DoD QSM requirements fit well in current 17025 process … just much, much more. Sector Specific. Outcome (L-A-B case)  83

  5. 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

  6. 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.

  7. Baseball Physics: A New Mechanics Lab

    Science.gov (United States)

    Wagoner, Kasey; Flanagan, Daniel

    2018-01-01

    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…

  8. 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.

  9. Library-Labs-for-Science Literacy Courses.

    Science.gov (United States)

    Pestel, Beverly C.; Engeldinger, Eugene A.

    1992-01-01

    Describes two library-lab exercises the authors have incorporated into their college chemistry course. The first exercise introduces students to scientific information and familiarizes them with the tools for accessing it. The second provides a framework for evaluating the reliability of that information and addresses the criteria that should be…

  10. 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.

  11. A "Language Lab" for Architectural Design.

    Science.gov (United States)

    Mackenzie, Arch; And Others

    This paper discusses a "language lab" strategy in which traditional studio learning may be supplemented by language lessons using computer graphics techniques to teach architectural grammar, a body of elements and principles that govern the design of buildings belonging to a particular architectural theory or style. Two methods of…

  12. 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).

  13. Virtual Lab for Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    PICOVICI, D.

    2008-06-01

    Full Text Available This article details an experimental system developed to enhance the education and research in the area of wireless networks technologies. The system referred, as Virtual Lab (VL is primarily targeting first time users or users with limited experience in programming and using wireless sensor networks. The VL enables a set of predefined sensor networks to be remotely accessible and controlled for constructive and time-efficient experimentation. In order to facilitate the user's wireless sensor applications, the VL is using three main components: a a Virtual Lab Motes (VLM, representing the wireless sensor, b a Virtual Lab Client (VLC, representing the user's tool to interact with the VLM and c a Virtual Lab Server (VLS representing the software link between the VLM and VLC. The concept has been proven using the moteiv produced Tmote Sky modules. Initial experimental use clearly demonstrates that the VL approach reduces dramatically the learning curve involved in programming and using the associated wireless sensor nodes. In addition the VL allows the user's focus to be directed towards the experiment and not towards the software programming challenges.

  14. 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.

  15. 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

  16. 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).

  17. 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.

  18. 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.

  19. Genome Imprinting

    Indian Academy of Sciences (India)

    the cell nucleus (mitochondrial and chloroplast genomes), and. (3) traits governed ... tively good embryonic development but very poor development of membranes and ... Human homologies for the type of situation described above are naturally ..... imprint; (b) New modifications of the paternal genome in germ cells of each ...

  20. Baculovirus Genomics

    NARCIS (Netherlands)

    Oers, van M.M.; Vlak, J.M.

    2007-01-01

    Baculovirus genomes are covalently closed circles of double stranded-DNA varying in size between 80 and 180 kilobase-pair. The genomes of more than fourty-one baculoviruses have been sequenced to date. The majority of these (37) are pathogenic to lepidopteran hosts; three infect sawflies

  1. Genomic Testing

    Science.gov (United States)

    ... this database. Top of Page Evaluation of Genomic Applications in Practice and Prevention (EGAPP™) In 2004, the Centers for Disease Control and Prevention launched the EGAPP initiative to establish and test a ... and other applications of genomic technology that are in transition from ...

  2. Ancient genomes

    OpenAIRE

    Hoelzel, A Rus

    2005-01-01

    Ever since its invention, the polymerase chain reaction has been the method of choice for work with ancient DNA. In an application of modern genomic methods to material from the Pleistocene, a recent study has instead undertaken to clone and sequence a portion of the ancient genome of the cave bear.

  3. 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.

  4. Open hardware for open science

    CERN Multimedia

    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...

  5. 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.

  6. 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

    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...... but also offer input that can stimulate new innovations and give consumers more power and influence....

  7. The Next Generation of Lab and Classroom Computing - The Silver Lining

    Science.gov (United States)

    2016-12-01

    Figure 2.  Basic Client Server Network. Source: Dean (2012, p. 6). .........................14  Figure 3.  The OSI Model . Source: Rivero (2015...connection is ended. Communications among multiple computers on a network was accomplished through the open systems interconnection ( OSI ) model (see Figure...architecture, which is currently in use in most networks including the labs and classrooms at NPS. Figure 3. The OSI Model . Source: Rivero (2015

  8. 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.

  9. 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…

  10. 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...

  11. Jefferson Lab: A Long Decade of Physics

    International Nuclear Information System (INIS)

    Montgomery, Hugh

    2011-01-01

    Jefferson Lab was created in 1984 and started operating in about 1996. 2011 is an appropriate time to try to take a look at the results that have appeared, what has been learned, and what has been exciting for our scientific community. Rather than attempt to construct a coherent view with a single author or at least a small number, we have, instead, invited small groups of people who have been intimately involved in the work itself to make contributions. These people are accelerator experts, experimentalists and theorists, staff and users. We have, in the main, sought reviews of the actual sub-fields. The primary exception is the first paper, which sets the scene as it was, in one person's view, at the beginning of Jefferson Lab. In reviewing the material as it appeared, I was impressed by the breadth of the material. Major advances are documented from form factors to structure functions, from spectroscopy to physics beyond the standard model of nuclear and particle physics. Recognition of the part played by spin, the helicities of the beams, the polarizations of the targets, and the polarizations of final state particles, is inescapable. Access to the weak interaction amplitudes through measurements of the parity violating asymmetries has led to quantification of the strange content of the nucleon and the neutron radius of lead, and to measurements of the electroweak mixing angle. Lattice QCD calculations flourished and are setting the platform for understanding of the spectroscopy of baryons and mesons. But the star of the game was the accelerator. Its performance enabled the physics and also the use of the technology to generate a powerful free electron laser. These important pieces of Jefferson Lab physics are given their place. As the third Director of Jefferson Lab, and on behalf of the other physicists and others presently associated with the lab, I would like to express my admiration and gratitude for the efforts of the directors, chief scientists

  12. 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.

  13. Towards a Manifesto for Living Lab Co-creation

    Science.gov (United States)

    Følstad, Asbjørn; Brandtzæg, Petter Bae; Gulliksen, Jan; Börjeson, Mikael; Näkki, Pirjo

    There is a growing interest in Living Labs for innovation and development in the field of information and communication technology. In particular there seem to be a tendency that current Living Labs aim to involve users for co-creative purposes. However, the current literature on Living Lab co-creation is severely limited. Therefore an Interact workshop is arranged as a first step towards a manifesto for Living Lab co-creation.

  14. 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

  15. 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

  16. Constructing the Components of a Lab Report Using Peer Review

    Science.gov (United States)

    Berry, David E.; Fawkes, Kelli L.

    2010-01-01

    A protocol that emphasizes lab report writing using a piecemeal approach coupled with peer review is described. As the lab course progresses, the focus of the report writing changes sequentially through the abstract and introduction, the discussion, and the procedure. Two styles of lab programs are presented. One style rotates the students through…

  17. 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…

  18. 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 o...

  19. 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…

  20. 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.

  1. Jefferson Lab Data Acquisition Run Control System

    International Nuclear Information System (INIS)

    Vardan Gyurjyan; Carl Timmer; David Abbott; William Heyes; Edward Jastrzembski; David Lawrence; Elliott Wolin

    2004-01-01

    A general overview of the Jefferson Lab data acquisition run control system is presented. This run control system is designed to operate the configuration, control, and monitoring of all Jefferson Lab experiments. It controls data-taking activities by coordinating the operation of DAQ sub-systems, online software components and third-party software such as external slow control systems. The main, unique feature which sets this system apart from conventional systems is its incorporation of intelligent agent concepts. Intelligent agents are autonomous programs which interact with each other through certain protocols on a peer-to-peer level. In this case, the protocols and standards used come from the domain-independent Foundation for Intelligent Physical Agents (FIPA), and the implementation used is the Java Agent Development Framework (JADE). A lightweight, XML/RDF-based language was developed to standardize the description of the run control system for configuration purposes

  2. 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.

  3. Bringing optics to Fab Labs in Europe

    Science.gov (United States)

    Adam, Aurèle; Zuidwijk, Thim; Urbach, Paul

    2017-08-01

    The Optics Group of Delft University of Technology plays a major role in teaching optics to bachelor and master students. In addition, the group has a long record of introducing, demonstrating and teaching optics to quite diverse groups of people from outside of the university. We will describe some of these activities and focus on a recently started project funded by the European Commission called Phablabs 4.0, which aims to bring photonics to European Fab labs.

  4. 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

  5. Chemical engineering and thermodynamics using Mat lab

    International Nuclear Information System (INIS)

    Kim Heon; Kim, Moon Gap; Lee, Hak Yeong; Yeo, Yeong Gu; Ham, Seong Won

    2002-02-01

    This book consists of twelve chapters and four appendixes about chemical engineering and thermodynamics using Mat lab, which deals with introduction, energy budget, entropy, thermodynamics process, generalization on any fluid, engineering equation of state for PVT properties, deviation of the function, phase equilibrium of pure fluid, basic of multicomponent, phase equilibrium of compound by state equation, activity model and reaction system. The appendixes is about summary of computer program, related mathematical formula and material property of pure component.

  6. 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.

  7. Electronics lab instructors' approaches to troubleshooting instruction

    Science.gov (United States)

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

    2017-06-01

    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 participants' instructional practices, we characterize their perceptions about the role of troubleshooting in electronics, the importance of the ability to troubleshoot more generally, and what it means for students to be competent troubleshooters. One major finding of this work is that, while almost all instructors in our study said that troubleshooting is an important learning outcome for students in electronics lab courses, only half of instructors said they directly assessed students' ability to troubleshoot. Based on our findings, we argue that there is a need for research-based instructional materials that attend to both cognitive and noncognitive aspects of troubleshooting proficiency. We also identify several areas for future investigation related to troubleshooting instruction in electronics lab courses.

  8. 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.

  9. Herbarium genomics

    DEFF Research Database (Denmark)

    Bakker, Freek T.; Lei, Di; Yu, Jiaying

    2016-01-01

    Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens...... up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organelle Genome Assembly, that assembles paired-end reads into a series of candidate assemblies, the best one of which is selected based on likelihood estimation. We used 93 specimens from 12 different...... correlation between plastome coverage and nuclear genome size (C value) in our samples, but the range of C values included is limited. Finally, we conclude that routine plastome sequencing from herbarium specimens is feasible and cost-effective (compared with Sanger sequencing or plastome...

  10. Open Bibliography

    OpenAIRE

    Murray-Rust, Peter; Pollock, Rufus; MacGillivray, Mark; O'Steen, Ben; Waites, William

    2011-01-01

    Poster presented at the VSMF Symposium held at the Unilever Centre on 2011-01-17. More research is published currently than can be understood or followed by a researcher without the aid of a computer. We need Open shareable information on research publications, an Open Bibliography, to build the services that enable researchers to explore their field and discover the research they need. Producers of bibliographic data such as libraries, publishers, universities, scholars or social referenc...

  11. 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....

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. Gallbladder removal - open

    Science.gov (United States)

    Cholecystectomy - open; Gallbladder - open cholecystectomy; Cholecystitis - open cholecystectomy; Gallstones - open cholecystectomy ... a medical instrument called a laparoscope ( laparoscopic ... Open gallbladder surgery is used when laparoscopic surgery cannot ...

  17. 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

  18. 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.

  19. 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.

  20. 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)

  1. Build your own social network laboratory with Social Lab: a tool for research in social media.

    Science.gov (United States)

    Garaizar, Pablo; Reips, Ulf-Dietrich

    2014-06-01

    Social networking has surpassed e-mail and instant messaging as the dominant form of online communication (Meeker, Devitt, & Wu, 2010). Currently, all large social networks are proprietary, making it difficult to impossible for researchers to make changes to such networks for the purpose of study design and access to user-generated data from the networks. To address this issue, the authors have developed and present Social Lab, an Internet-based free and open-source social network software system available from http://www.sociallab.es . Having full availability of navigation and communication data in Social Lab allows researchers to investigate behavior in social media on an individual and group level. Automated artificial users ("bots") are available to the researcher to simulate and stimulate social networking situations. These bots respond dynamically to situations as they unfold. The bots can easily be configured with scripts and can be used to experimentally manipulate social networking situations in Social Lab. Examples for setting up, configuring, and using Social Lab as a tool for research in social media are provided.

  2. 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.

  3. 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.

  4. 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...

  5. 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

  6. 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...... by small, new, and not-for-profit organizations, as well as the linkage of individual actions and motivations to open innovation. Other opportunities include better measuring the costs, benefits, antecedents, mediators and moderators of the effects of OI on performance, and understanding why and how OI...

  7. DOSAR/CalLab Operations Manual

    International Nuclear Information System (INIS)

    Bogard, J.S.

    2000-01-01

    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. 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)

  9. Recent skyshine calculations at Jefferson Lab

    International Nuclear Information System (INIS)

    Degtyarenko, P.

    1997-01-01

    New calculations of the skyshine dose distribution of neutrons and secondary photons have been performed at Jefferson Lab using the Monte Carlo method. The dose dependence on neutron energy, distance to the neutron source, polar angle of a source neutron, and azimuthal angle between the observation point and the momentum direction of a source neutron have been studied. The azimuthally asymmetric term in the skyshine dose distribution is shown to be important in the dose calculations around high-energy accelerator facilities. A parameterization formula and corresponding computer code have been developed which can be used for detailed calculations of the skyshine dose maps

  10. 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

  11. Lab RTVE. Transmedia Storytelling in fiction series

    OpenAIRE

    Ivars-Nicolás, Begoña; Zaragoza-Fuster, Teresa

    2017-01-01

    El creciente consumo multipantalla de contenidos de ficción es clave en la transformación de los medios audiovisuales. La búsqueda de estrategias de comunicación no lineal para captar la audiencia a través de múltiples plataformas fomenta el mensaje transmedia. La transmedialidad no se limita a la forma de narrar, sino también al modo de producir y difundir una historia. El Laboratorio de Radio Televisión Española, Lab RTVE, destaca en España por su impulso innovador en la producción de conte...

  12. Craniux: a LabVIEW-based modular software framework for brain-machine interface research.

    Science.gov (United States)

    Degenhart, Alan D; Kelly, John W; Ashmore, Robin C; Collinger, Jennifer L; Tyler-Kabara, Elizabeth C; Weber, Douglas J; Wang, Wei

    2011-01-01

    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.

  13. 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.

  14. 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 (Austria......, 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...... active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described...

  15. 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…

  16. GenColors-based comparative genome databases for small eukaryotic genomes.

    Science.gov (United States)

    Felder, Marius; Romualdi, Alessandro; Petzold, Andreas; Platzer, Matthias; Sühnel, Jürgen; Glöckner, Gernot

    2013-01-01

    Many sequence data repositories can give a quick and easily accessible overview on genomes and their annotations. Less widespread is the possibility to compare related genomes with each other in a common database environment. We have previously described the GenColors database system (http://gencolors.fli-leibniz.de) and its applications to a number of bacterial genomes such as Borrelia, Legionella, Leptospira and Treponema. This system has an emphasis on genome comparison. It combines data from related genomes and provides the user with an extensive set of visualization and analysis tools. Eukaryote genomes are normally larger than prokaryote genomes and thus pose additional challenges for such a system. We have, therefore, adapted GenColors to also handle larger datasets of small eukaryotic genomes and to display eukaryotic gene structures. Further recent developments include whole genome views, genome list options and, for bacterial genome browsers, the display of horizontal gene transfer predictions. Two new GenColors-based databases for two fungal species (http://fgb.fli-leibniz.de) and for four social amoebas (http://sacgb.fli-leibniz.de) were set up. Both new resources open up a single entry point for related genomes for the amoebozoa and fungal research communities and other interested users. Comparative genomics approaches are greatly facilitated by these resources.

  17. 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

  18. Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes.

    Science.gov (United States)

    Puigbò, Pere; Lobkovsky, Alexander E; Kristensen, David M; Wolf, Yuri I; Koonin, Eugene V

    2014-08-21

    Genomes of bacteria and archaea (collectively, prokaryotes) appear to exist in incessant flux, expanding via horizontal gene transfer and gene duplication, and contracting via gene loss. However, the actual rates of genome dynamics and relative contributions of different types of event across the diversity of prokaryotes are largely unknown, as are the sizes of microbial supergenomes, i.e. pools of genes that are accessible to the given microbial species. We performed a comprehensive analysis of the genome dynamics in 35 groups (34 bacterial and one archaeal) of closely related microbial genomes using a phylogenetic birth-and-death maximum likelihood model to quantify the rates of gene family gain and loss, as well as expansion and reduction. The results show that loss of gene families dominates the evolution of prokaryotes, occurring at approximately three times the rate of gain. The rates of gene family expansion and reduction are typically seven and twenty times less than the gain and loss rates, respectively. Thus, the prevailing mode of evolution in bacteria and archaea is genome contraction, which is partially compensated by the gain of new gene families via horizontal gene transfer. However, the rates of gene family gain, loss, expansion and reduction vary within wide ranges, with the most stable genomes showing rates about 25 times lower than the most dynamic genomes. For many groups, the supergenome estimated from the fraction of repetitive gene family gains includes about tenfold more gene families than the typical genome in the group although some groups appear to have vast, 'open' supergenomes. Reconstruction of evolution for groups of closely related bacteria and archaea reveals an extremely rapid and highly variable flux of genes in evolving microbial genomes, demonstrates that extensive gene loss and horizontal gene transfer leading to innovation are the two dominant evolutionary processes, and yields robust estimates of the supergenome size.

  19. The Open

    Directory of Open Access Journals (Sweden)

    Saitya Brata Das

    2009-12-01

    Full Text Available In the Open darkness and light, remembrance and oblivion, coming into existence and disappearing in death play their originary co-belonging, or co-figuration. Existence belongs to this opening and is exposed to its coming to presence: it is on the basis of this originary opening, this originary historical which is revealed to this mortal being called ‘man,’ on the basis of this revelation, man founds something like politics and history. There thus comes into existence out of this freedom, out of this “play space”2, this field called ‘polis’3 where there takes place war and festival, where historical revolutions tear apart history, brings ruptures and discontinuities in the very mode of his existence, where man seeks the foundation of his own foundation (which is his metaphysical task , where occurs the dialectics of negativity between man and man, where man puts at stake his own death, his own dissolution, and by the power of his own dissolution stands in relation to the total world that he seeks to dominate. This means that man’s attempts to metaphysically found his own political and historical existence must presuppose a far more originary non-foundation, the differentiating revealing of the open, the ungrounded spacing play, or playing space of natality and mortality.

  20. 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 call...

  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. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  3. ScalaLab and GroovyLab: Comparing Scala and Groovy for Scientific Computing

    Directory of Open Access Journals (Sweden)

    Stergios Papadimitriou

    2015-01-01

    Full Text Available ScalaLab and GroovyLab are both MATLAB-like environments for the Java Virtual Machine. ScalaLab is based on the Scala programming language and GroovyLab is based on the Groovy programming language. They present similar user interfaces and functionality to the user. They also share the same set of Java scientific libraries and of native code libraries. From the programmer's point of view though, they have significant differences. This paper compares some aspects of the two environments and highlights some of the strengths and weaknesses of Scala versus Groovy for scientific computing. The discussion also examines some aspects of the dilemma of using dynamic typing versus static typing for scientific programming. The performance of the Java platform is continuously improved at a fast pace. Today Java can effectively support demanding high-performance computing and scales well on multicore platforms. Thus, both systems can challenge the performance of the traditional C/C++/Fortran scientific code with an easier to use and more productive programming environment.

  4. A Well-Maintained Lab Is a Safer Lab. Safety Spotlight

    Science.gov (United States)

    Walls, William H.; Strimel, Greg J.

    2018-01-01

    Administration and funding can cause Engineering/Technology Education (ETE) programs to thrive or die. To administrators, the production/prototyping equipment and laboratory setting are often viewed as the features that set ETE apart from other school subjects. A lab is a unique gift as well as a responsibility. If an administrator can see that…

  5. 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…

  6. New GPIB Control Software at Jefferson Lab

    International Nuclear Information System (INIS)

    Matthew Bickley; Pavel Chevtsov

    2005-01-01

    The control of GPIB devices at Jefferson Lab is based on the GPIB device/driver library. The library is a part of the device/driver development framework. It is activated with the use of the device configuration files that define all hardware components used in the control system to communicate with GPIB devices. As soon as the software is activated, it is ready to handle any device connected to these components and only needs to know the set of commands that the device can understand. The old GPIB control software at Jefferson Lab requires the definition of these commands in the form of a device control software module written in C for each device. Though such modules are relatively simple, they have to be created, successfully compiled, and supported for all control computer platforms. In the new version of GPIB control software all device communication commands are defined in device protocol (ASCII text) files. This makes the support of GPIB devices in the control system much easier

  7. 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

  8. Temperature quenching in LAB based liquid scintillator

    Energy Technology Data Exchange (ETDEWEB)

    Soerensen, A.; Zuber, K. [Technische Universitaet Dresden, Institute for Nuclear- and Particle Physics, Dresden (Germany); Hans, S.; Yeh, M. [Brookhaven National Laboratory, Chemistry Devision, Upton, NY (United States); Junghans, A.R.; Koegler, T.; Wagner, A. [Helmholtz-Zentrum Dresden-Rossendorf, Dresden (Germany); Krosigk, B. v. [Technische Universitaet Dresden, Institute for Nuclear- and Particle Physics, Dresden (Germany); University of British Columbia, Department of Physics and Astronomy, Vancouver, BC (Canada); Lozza, V. [Technische Universitaet Dresden, Institute for Nuclear- and Particle Physics, Dresden (Germany); Laboratorio de Instrumentacao e Fisica Experimental de Particulas, Lisboa (Portugal)

    2018-01-15

    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. (orig.)

  9. On my association with Bell Labs

    Science.gov (United States)

    Sondhi, M. Mohan

    2004-05-01

    I joined the Acoustics Research department at Bell Labs in 1962, just eight days before AT&T launched the first communications satellite, Telstar. During the 39 years between 1962 and my retirement in 2001, I worked on several problems related in one way or another to the processing of speech signals. Schroeder and Flanagan are presenting talks from a broad perspective in this session, so I will confine this talk to just my own contributions and collaborations for some of the topics on which I worked, e.g., echo cancellation, inverse problems in acoustics, speech analysis, synthesis, and recognition. I will tell you about one of these contributions that fortunately turned out to yield considerable profits to AT&T. To give you a flavor of the spirit of free inquiry at Bell Labs during that period, I will tell you about the contribution that I am most proud of (which was supported for several years even though it had no monetary value). And I will also mention the contribution that is most often cited of all my papers (which was in collaboration with two mathematicians, and had nothing at all to do with acoustics).

  10. 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

  11. 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.

  12. INVESTIGATIONS INTO MOLECULAR PATHWAYS IN THE POST GENOME ERA: CROSS SPECIES COMPARATIVE GENOMICS APPROACH

    Science.gov (United States)

    Genome sequencing efforts in the past decade were aimed at generating draft sequences of many prokaryotic and eukaryotic model organisms. Successful completion of unicellular eukaryotes, worm, fly and human genome have opened up the new field of molecular biology and function...

  13. 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.

  14. Successes and Challenges in Transitioning to Large Enrollment NEXUS/Physics IPLS Labs

    Science.gov (United States)

    Moore, Kimberly

    2017-01-01

    UMd-PERG's NEXUS/Physics for Life Sciences laboratory curriculum, piloted in 2012-2013 in small test classes, has been implemented in large-enrollment environments at UMD from 2013-present. These labs address physical issues at biological scales using microscopy, image and video analysis, electrophoresis, and spectroscopy in an open, non-protocol-driven environment. We have collected a wealth of data (surveys, video analysis, etc.) that enables us to get a sense of the students' responses to this curriculum in a large-enrollment environment and with teaching assistants both `new to' and `experienced in' the labs. In this talk, we will provide a brief overview of what we have learned, including the challenges of transitioning to large N, student perception then and now, and comparisons of our large-enrollment results to the results from our pilot study. We will close with a discussion of the acculturation of teaching assistants to this novel environment and suggestions for sustainability.

  15. Size effect of added LaB6 particles on optical properties of LaB6/Polymer composites

    International Nuclear Information System (INIS)

    Yuan Yifei; Zhang Lin; Hu Lijie; Wang Wei; Min Guanghui

    2011-01-01

    Modified LaB 6 particles with sizes ranging from 50 nm to 400 nm were added into polymethyl methacrylate (PMMA) matrix in order to investigate the effect of added LaB 6 particles on optical properties of LaB 6 /PMMA composites. Method of in-situ polymerization was applied to prepare PMMA from raw material—methyl methacrylate (MMA), a process during which LaB 6 particles were dispersed in MMA. Ultraviolet–visible–near infrared (UV–vis–NIR) absorption spectrum was used to study optical properties of the as-prepared materials. The difference in particle size could apparently affect the composites' absorption of visible light around wavelength of 600 nm. Added LaB 6 particles with size of about 70 nm resulted in the best optical properties among these groups of composites. - Graphical abstract: 70 nm LaB 6 particles resulted in the best performance on absorption of VIS and NIR, which could not be apparently achieved by LaB 6 particles beyond nano-scale. Highlights: ► LaB 6 /PMMA composites were prepared using the method of in-situ polymerization. ► LaB 6 particles added in MMA prolonged the time needed for its pre-polymerization. ► Nanosized LaB 6 particles could obviously absorb much NIR but little VIS.

  16. 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.

  17. 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...

  18. 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.

  19. 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:

  20. 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

  1. 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

  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. 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.

  4. 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)

  5. Genome aliquoting with double cut and join

    Directory of Open Access Journals (Sweden)

    Sankoff David

    2008-01-01

    Full Text Available Abstract Background The genome aliquoting probem is, given an observed genome A with n copies of each gene, presumed to descend from an n-way polyploidization event from an ordinary diploid genome B, followed by a history of chromosomal rearrangements, to reconstruct the identity of the original genome B'. The idea is to construct B', containing exactly one copy of each gene, so as to minimize the number of rearrangements d(A, B' ⊕ B' ⊕ ... ⊕ B' necessary to convert the observed genome B' ⊕ B' ⊕ ... ⊕ B' into A. Results In this paper we make the first attempt to define and solve the genome aliquoting problem. We present a heuristic algorithm for the problem as well the data from our experiments demonstrating its validity. Conclusion The heuristic performs well, consistently giving a non-trivial result. The question as to the existence or non-existence of an exact solution to this problem remains open.

  6. The Saccharomyces Genome Database Variant Viewer.

    Science.gov (United States)

    Sheppard, Travis K; Hitz, Benjamin C; Engel, Stacia R; Song, Giltae; Balakrishnan, Rama; Binkley, Gail; Costanzo, Maria C; Dalusag, Kyla S; Demeter, Janos; Hellerstedt, Sage T; Karra, Kalpana; Nash, Robert S; Paskov, Kelley M; Skrzypek, Marek S; Weng, Shuai; Wong, Edith D; Cherry, J Michael

    2016-01-04

    The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is the authoritative community resource for the Saccharomyces cerevisiae reference genome sequence and its annotation. In recent years, we have moved toward increased representation of sequence variation and allelic differences within S. cerevisiae. The publication of numerous additional genomes has motivated the creation of new tools for their annotation and analysis. Here we present the Variant Viewer: a dynamic open-source web application for the visualization of genomic and proteomic differences. Multiple sequence alignments have been constructed across high quality genome sequences from 11 different S. cerevisiae strains and stored in the SGD. The alignments and summaries are encoded in JSON and used to create a two-tiered dynamic view of the budding yeast pan-genome, available at http://www.yeastgenome.org/variant-viewer. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. ALT Blood Test: MedlinePlus Lab Test Information

    Science.gov (United States)

    ... K. Brunner & Suddarth's Handbook of Laboratory and Diagnostic Tests. 2 nd Ed, Kindle. Philadelphia: Wolters Kluwer Health, Lippincott Williams & Wilkins; c2014. Alanine Aminotransferase (ALT); p. 31. Lab ...

  8. Blood in Urine: MedlinePlus Lab Test Information

    Science.gov (United States)

    ... K. Brunner & Suddarth's Handbook of Laboratory and Diagnostic Tests. 2 nd Ed, Kindle. Philadelphia: Wolters Kluwer Health, Lippincott Williams & Wilkins; c2014. Hemoglobin, Urine; p. 325. Lab Tests ...

  9. Ferritin Blood Test: MedlinePlus Lab Test Information

    Science.gov (United States)

    ... K. Brunner & Suddarth's Handbook of Laboratory and Diagnostic Tests. 2nd Ed, Kindle. Philadelphia: Wolters Kluwer Health, Lippincott Williams & Wilkins; c2014. Ferritin, Serum; 296 p. Lab Tests ...

  10. 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.

  11. 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

  12. Open Pneumothorax

    Directory of Open Access Journals (Sweden)

    Bart Paull

    2017-07-01

    Full Text Available History of present illness: A 27-year-old male was transported to the emergency department by emergency medical services after crashing his motorcycle into a guardrail. Upon presentation he was alert, normotensive, and tachypneic. Significant findings: A large chest wound was clinically obvious. A chest radiograph performed after intubation showed subcutaneous emphysema, an anterior rib fracture, and a right-sided pneumothorax. He was then taken to the operating room for further management. Discussion: Thoracic injuries are responsible for one-quarter of all trauma-related deaths. Following rib fracture, pneumothorax is the second most common thoracic injury, occurring in 30% of patients with thoracic trauma. An open pneumothorax occurs when a chest wall injury results in direct communication between the atmosphere and pleura.1-2 It is estimated that open pneumothorax occurs in 80% of all penetrating chest wounds, with stab wounds being more common than gunshot wounds or impalement. Open pneumothoraces can lead to ventilatory insufficiency and rapid respiratory decompensation.2 Advanced Trauma Life Support recommends that the initial management of an open pneumothorax is placement of an occlusive dressing taped on three sides to create a ‘flutter-valve’ mechanism. This should then be followed by tube thoracostomy and repair of the chest wall defect.3 The placement of an occlusive dressing or initial wound closure without subsequent tube thoracostomy may result in the development of a tension pneumothorax.2 The patient was intubated and mechanical ventilation was initiated without complication. Due to the large size of the wound, an occlusive dressing was not placed in the emergency department and the patient was rapidly transported to the operating room for further management. In the operating room two chest tubes were placed. Operative findings included a right hemopneumothorax, multiple rib fractures, and a manubrial fracture. After

  13. 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

  14. The SPARC-LAB Thomson source

    International Nuclear Information System (INIS)

    Vaccarezza, C.; Alesini, D.; Anania, M.P.; Bacci, A.; Biagioni, A.; Bisesto, F.; Bellaveglia, M.; Cardarelli, P.; Cardelli, F.; Cianchi, A.; Chiadroni, E.; Croia, M.; Curcio, A.; Delogu, P.; Giovenale, D. Di; Domenico, G. Di; Pirro, G. Di; Drebot, I.; Ferrario, M.; Filippi, F.

    2016-01-01

    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.

  15. RICH Detector for Jefferson Labs CLAS12

    Science.gov (United States)

    Trotta, Richard; Torisky, Ben; Benmokhtar, Fatiha

    2015-10-01

    Jefferson Lab (Jlab) is performing a large-scale upgrade to its Continuous Electron Beam Accelerator Facility (CEBAF) up to 12GeV beams. The Large Acceptance Spectrometer (CLAS12) in Hall B is being upgraded and a new hybrid Ring Imaging Cherenkov (RICH) detector is being developed to provide better kaon - pion separation throughout the 3 to 8 GeV/c momentum range. This detector will be used for a variety of Semi-Inclusive Deep Inelastic Scattering experiments. Cherenkov light can be accurately detected by a large array of sophisticated Multi-Anode Photomultiplier Tubes (MA-PMT) and heavier particles, like kaons, will span the inner radii. We are presenting our work on the creation of the RICH's geometry within the CLAS12 java framework. This development is crucial for future calibration, reconstructions and analysis of the detector.

  16. 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.

  17. Peers at work: Evidence from the lab

    Science.gov (United States)

    Oosterbeek, Hessel; Sonnemans, Joep

    2018-01-01

    This paper reports the results of a lab experiment designed to study the role of observability for peer effects in the setting of a simple production task. In our experiment, participants in the role of workers engage in a team real-effort task. We vary whether they can observe, or be observed by, one of their co-workers. In contrast to earlier findings from the field, we find no evidence that low-productivity workers perform better when they are observed by high-productivity co-workers. Instead, our results imply that peer effects in our experiment are heterogeneous, with some workers reciprocating a high-productivity co-worker but others taking the opportunity to free ride. PMID:29408863

  18. Making the Case for Jefferson Lab

    International Nuclear Information System (INIS)

    Gross, Franz

    2011-01-01

    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.

  19. Flow lab.: flow visualization and simulation

    International Nuclear Information System (INIS)

    Park, Chung Kyun; Cho, Won Jin; Hahn, Pil Soo

    2005-01-01

    The experimental setups for flow visualization and processes identification in laboratory scale (so called Flow Lab.) has developed to get ideas and answer fundamental questions of flow and migration in geologic media. The setup was made of a granite block of 50x50cm scale and a transparent acrylate plate. The tracers used in this experiments were tritiated water, anions, and sorbing cations as well as an organic dye, eosine, to visualize migration paths. The migration plumes were taken with a digital camera as a function of time and stored as digital images. A migration model was also developed to describe and identify the transport processes. Computer simulation was carried out not only for the hydraulic behavior such as distributions of pressure and flow vectors in the fracture but also for the migration plume and the elution curves

  20. 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

  1. 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.

  2. Peers at work: Evidence from the lab.

    Directory of Open Access Journals (Sweden)

    Roel van Veldhuizen

    Full Text Available This paper reports the results of a lab experiment designed to study the role of observability for peer effects in the setting of a simple production task. In our experiment, participants in the role of workers engage in a team real-effort task. We vary whether they can observe, or be observed by, one of their co-workers. In contrast to earlier findings from the field, we find no evidence that low-productivity workers perform better when they are observed by high-productivity co-workers. Instead, our results imply that peer effects in our experiment are heterogeneous, with some workers reciprocating a high-productivity co-worker but others taking the opportunity to free ride.

  3. 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.

  4. VPPD Lab - The Chemical Product Simulator

    DEFF Research Database (Denmark)

    Kalakul, Sawitree; Hussain, Rehan; Elbashir, Nimir

    2015-01-01

    , 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......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...... 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...

  5. 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)

  6. 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.

  7. 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 ...

  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. 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

  10. 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

  11. 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

  12. 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.)

  13. 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.

  14. 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

  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. Public Lab: Community-Based Approaches to Urban and Environmental Health and Justice.

    Science.gov (United States)

    Rey-Mazón, Pablo; Keysar, Hagit; Dosemagen, Shannon; D'Ignazio, Catherine; Blair, Don

    2018-05-03

    This paper explores three cases of Do-It-Yourself, open-source technologies developed within the diverse array of topics and themes in the communities around the Public Laboratory for Open Technology and Science (Public Lab). These cases focus on aerial mapping, water quality monitoring and civic science practices. The techniques discussed have in common the use of accessible, community-built technologies for acquiring data. They are also concerned with embedding collaborative and open source principles into the objects, tools, social formations and data sharing practices that emerge from these inquiries. The focus is on developing processes of collaborative design and experimentation through material engagement with technology and issues of concern. Problem-solving, here, is a tactic, while the strategy is an ongoing engagement with the problem of participation in its technological, social and political dimensions especially considering the increasing centralization and specialization of scientific and technological expertise. The authors also discuss and reflect on the Public Lab's approach to civic science in light of ideas and practices of citizen/civic veillance, or "sousveillance", by emphasizing people before data, and by investigating the new ways of seeing and doing that this shift in perspective might provide.

  17. 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.

  18. 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.

  19. 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…

  20. 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

  1. 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.

  2. Creative Science Teaching Labs: New Dimensions in CPD

    Science.gov (United States)

    Chappell, Kerry; Craft, Anna

    2009-01-01

    This paper offers analysis and evaluation of "Creative Science Teaching (CST) Labs III", a unique and immersive approach to science teachers' continuing professional development (CPD) designed and run by a London-based organisation, Performing Arts Labs (PAL), involving specialists from the arts, science and technology as integral. Articulating…

  3. 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

  4. Time Trials--An AP Physics Challenge Lab

    Science.gov (United States)

    Jones, David

    2009-01-01

    I have come to the conclusion that for high school physics classroom and laboratory experiences, simpler is better! In this paper I describe a very simple and effective lab experience that my AP students have thoroughly enjoyed year after year. I call this lab exercise "Time Trials." The experiment is simple in design and it is a lot of fun for…

  5. What Is LAB and Why Was It Renormed?

    Science.gov (United States)

    Abbott, Muriel

    A report on the Language Assessment Battery (LAB) explains, in question-and-answer form, the causes and results of some changes made in the test norms. The LAB is a test of communicative language competence, written in English and Spanish versions and used for student placement in the New York City Public Schools. The report describes the test…

  6. 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.

  7. Fifteen years experience: Egyptian metabolic lab | Fateen | Egyptian ...

    African Journals Online (AJOL)

    Those patients were classified as: 722 patients (69.4%) with lysosomal storage disorders, 302 patients (29%) with amino acid disorders and 17 patients (1.6%) with galactosemia. Conclusion: This study illustrates the experience of the reference metabolic lab in Egypt over 15 years. The lab began metabolic disorder ...

  8. 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

  9. Open-ended versus guided laboratory activities:Impact on students' beliefs about experimental physics

    Science.gov (United States)

    Wilcox, Bethany R.; Lewandowski, H. J.

    2016-12-01

    Improving students' understanding of the nature of experimental physics is often an explicit or implicit goal of undergraduate laboratory physics courses. However, lab activities in traditional lab courses are typically characterized by highly structured, guided labs that often do not require or encourage students to engage authentically in the process of experimental physics. Alternatively, open-ended laboratory activities can provide a more authentic learning environment by, for example, allowing students to exercise greater autonomy in what and how physical phenomena are investigated. Engaging in authentic practices may be a critical part of improving students' beliefs around the nature of experimental physics. Here, we investigate the impact of open-ended activities in undergraduate lab courses on students' epistemologies and expectations about the nature of experimental physics, as well as their confidence and affect, as measured by the Colorado Learning Attitudes about Science Survey for Experimental Physics (E-CLASS). Using a national data set of student responses to the E-CLASS, we find that the inclusion of some open-ended lab activities in a lab course correlates with more expertlike postinstruction responses relative to courses that include only traditional guided lab activities. This finding holds when examining postinstruction E-CLASS scores while controlling for the variance associated with preinstruction scores, course level, student major, and student gender.

  10. 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

  11. Towards a Computable Data Corpus of Temporal Correlations between Drug Administration and Lab Value Changes.

    Directory of Open Access Journals (Sweden)

    Axel Newe

    Full Text Available The analysis of electronic health records for an automated detection of adverse drug reactions is an approach to solve the problems that arise from traditional methods like spontaneous reporting or manual chart review. Algorithms addressing this task should be modeled on the criteria for a standardized case causality assessment defined by the World Health Organization. One of these criteria is the temporal relationship between drug intake and the occurrence of a reaction or a laboratory test abnormality. Appropriate data that would allow for developing or validating related algorithms is not publicly available, though.In order to provide such data, retrospective routine data of drug administrations and temporally corresponding laboratory observations from a university clinic were extracted, transformed and evaluated by experts in terms of a reasonable time relationship between drug administration and lab value alteration.The result is a data corpus of 400 episodes of normalized laboratory parameter values in temporal context with drug administrations. Each episode has been manually classified whether it contains data that might indicate a temporal correlation between the drug administration and the change of the lab value course, whether such a change is not observable or whether a decision between those two options is not possible due to the data. In addition, each episode has been assigned a concordance value which indicates how difficult it is to assess. This is the first open data corpus of a computable ground truth of temporal correlations between drug administration and lab value alterations.The main purpose of this data corpus is the provision of data for further research and the provision of a ground truth which allows for comparing the outcome of other assessments of this data with the outcome of assessments made by human experts. It can serve as a contribution towards systematic, computerized ADR detection in retrospective data. With

  12. 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.

  13. 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

  14. Genome Sequencing and Analysis Conference IV

    Energy Technology Data Exchange (ETDEWEB)

    1993-12-31

    J. Craig Venter and C. Thomas Caskey co-chaired Genome Sequencing and Analysis Conference IV held at Hilton Head, South Carolina from September 26--30, 1992. Venter opened the conference by noting that approximately 400 researchers from 16 nations were present four times as many participants as at Genome Sequencing Conference I in 1989. Venter also introduced the Data Fair, a new component of the conference allowing exchange and on-site computer analysis of unpublished sequence data.

  15. Ancient genomics

    DEFF Research Database (Denmark)

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

    2015-01-01

    throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained...... by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans...

  16. Marine genomics

    DEFF Research Database (Denmark)

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

    2017-01-01

    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...

  17. 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.

  18. 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

  19. Electronic lab notebooks: can they replace paper?

    Science.gov (United States)

    Kanza, Samantha; Willoughby, Cerys; Gibbins, Nicholas; Whitby, Richard; Frey, Jeremy Graham; Erjavec, Jana; Zupančič, Klemen; Hren, Matjaž; Kovač, Katarina

    2017-05-24

    Despite the increasingly digital nature of society there are some areas of research that remain firmly rooted in the past; in this case the laboratory notebook, the last remaining paper component of an experiment. Countless electronic laboratory notebooks (ELNs) have been created in an attempt to digitise record keeping processes in the lab, but none of them have become a 'key player' in the ELN market, due to the many adoption barriers that have been identified in previous research and further explored in the user studies presented here. The main issues identified are the cost of the current available ELNs, their ease of use (or lack of it) and their accessibility issues across different devices and operating systems. Evidence suggests that whilst scientists willingly make use of generic notebooking software, spreadsheets and other general office and scientific tools to aid their work, current ELNs are lacking in the required functionality to meet the needs of the researchers. In this paper we present our extensive research and user study results to propose an ELN built upon a pre-existing cloud notebook platform that makes use of accessible popular scientific software and semantic web technologies to help overcome the identified barriers to adoption.

  20. Future of Open Source systems

    Directory of Open Access Journals (Sweden)

    Karel Charvát

    2010-02-01

    Full Text Available Software distribution strategies have many aspects and can be analysed by reviewing different incisions of a strategy. The focus of this paper is on Licensing aspect involves licensing strategy, licensing risks, licensing enforcement costs. Furthermore, by formulating licensing strategy main technical and logistical aspects are predicted also. The key issues of this paper are different business modes for FOSS software and also SWOT analysis of usage and development of FOSS software from point of view of different user groups. This analysis was provided as part of work of Humboldt IP and collaborative@rural IP. Currently this strategy are important issue of members of Czech Centre for Science and Society and WirelessInfo Living Lab, where the models based on dual licensing are key strategy.Keywords: Open Source, Licensing, FOSS base business models. SWOT analysis, Knowledge society, Knowledge economy

  1. 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

  2. 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

  3. 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.

  4. Transcription as a Threat to Genome Integrity.

    Science.gov (United States)

    Gaillard, Hélène; Aguilera, Andrés

    2016-06-02

    Genomes undergo different types of sporadic alterations, including DNA damage, point mutations, and genome rearrangements, that constitute the basis for evolution. However, these changes may occur at high levels as a result of cell pathology and trigger genome instability, a hallmark of cancer and a number of genetic diseases. In the last two decades, evidence has accumulated that transcription constitutes an important natural source of DNA metabolic errors that can compromise the integrity of the genome. Transcription can create the conditions for high levels of mutations and recombination by its ability to open the DNA structure and remodel chromatin, making it more accessible to DNA insulting agents, and by its ability to become a barrier to DNA replication. Here we review the molecular basis of such events from a mechanistic perspective with particular emphasis on the role of transcription as a genome instability determinant.

  5. 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

  6. Openness initiative

    International Nuclear Information System (INIS)

    Duncan, S.S.

    1995-01-01

    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

  7. 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.

  8. Automated assembly of microfluidic "lab-on-a-disc"

    Science.gov (United States)

    Berger, M.; Müller, T.; Voebel, T.; Baum, C.; Glennon, T.; Mishra, R.; Kinahan, D.; King, D.; Ducrée, J.; Brecher, C.

    2018-02-01

    Point-of-care (POC) testing attracts more and more attention in the medical health sector because of their specific property to perform the diagnostic close to the patient. The fast diagnosis right at the hospital or the doctor's office improves the medical reaction time and the chances for a successful healing process. One of this POC test systems is a "Lab-on-a-Disc" (LoaD) which looks like a compact disc crisscrossed with microfluidic tubes and cavities. The fluid to be analysed is placed in the LoaD and an external device then rotates the LoaD. The cavities inside the LoaD and the centrifugal force ensure a clearly defined sequence of the analysis. Furthermore, we aim for an inexpensive manufacture of the medical product without neglecting its quality and functionality. Therefore, the Fraunhofer IPT works on an assembly cell to implement dissoluble films concisely into the disc. This dissoluble film demonstrates its successful usage as a gate for the fluid, which opens after a predefined moment in the cycle. Furthermore, we investigate to integrate a laser welding process into our gantry system and demonstrate its efficiency with the welding of polymer discs. This procedure is clinically safe because no further laser absorption material is needed in the sealing process, which might pollute the LoaD. Moreover, this process allows the alignment of several discs before the welding and therefore leads to precisely manufactured LoaDs in large quantities. All these methods together enable a fast, costefficient and reliable mass production to bring POC testing among the people.

  9. Genomic comparison of closely related Giant Viruses supports an accordion-like model of evolution

    OpenAIRE

    Filée, Jonathan

    2015-01-01

    Genome gigantism occurs so far in Phycodnaviridae and Mimiviridae (order Megavirales). Origin and evolution of these Giant Viruses (GVs) remain open questions. Interestingly, availability of a collection of closely related GV genomes enabling genomic comparisons offer the opportunity to better understand the different evolutionary forces acting on these genomes. Whole genome alignment for five groups of viruses belonging to the Mimiviridae and Phycodnaviridae families show that there is no tr...

  10. An update on Lab Rover: A hospital material transporter

    Science.gov (United States)

    Mattaboni, Paul

    1994-01-01

    The development of a hospital material transporter, 'Lab Rover', is described. Conventional material transport now utilizes people power, push carts, pneumatic tubes and tracked vehicles. Hospitals are faced with enormous pressure to reduce operating costs. Cyberotics, Inc. developed an Autonomous Intelligent Vehicle (AIV). This battery operated service robot was designed specifically for health care institutions. Applications for the AIV include distribution of clinical lab samples, pharmacy drugs, administrative records, x-ray distribution, meal tray delivery, and certain emergency room applications. The first AIV was installed at Lahey Clinic in Burlington, Mass. Lab Rover was beta tested for one year and has been 'on line' for an additional 2 years.

  11. 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...... and teaching of user driven innovation. Being itself an example of user-driven innovation it has taken shape of HCI design research projekcts, in which we have been involved since 2004. The first challenge was to get 'out of the lab', the next to get 'out of the head', and finally we are currently working...

  12. Perspectives on Industrial Innovation from Agilent, HP, and Bell Labs

    Science.gov (United States)

    Hollenhorst, James

    2014-03-01

    Innovation is the life blood of technology companies. I will give perspectives gleaned from a career in research and development at Bell Labs, HP Labs, and Agilent Labs, from the point of view of an individual contributor and a manager. Physicists bring a unique set of skills to the corporate environment, including a desire to understand the fundamentals, a solid foundation in physical principles, expertise in applied mathematics, and most importantly, an attitude: namely, that hard problems can be solved by breaking them into manageable pieces. In my experience, hiring managers in industry seldom explicitly search for physicists, but they want people with those skills.

  13. 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

  14. Safety and shielding management for pulse power lab at IPR

    International Nuclear Information System (INIS)

    Upadhyay, Shweta; Faldu, Akash; Koshti, Rahul; Kumar, Rajesh

    2016-01-01

    Experiments in pulsed power lab works with very high voltage and high current regime for the nanosecond to microsecond time scale. This produces lot of electromagnetic noise, which can cause interference or malfunctioning of equipment. Laboratory Safety and protection are a very important aspect of science and engineering. Without it, practical performance could result in very serious injury, if not death. To reduce its effect electromagnetic shielding and grounding has to be enforced effectively. Pulse power lab deals with many safety issues like Radiation safety (shielding), High voltage safety, electrical and mechanical safety, etc. In this paper radiation all the safety aspects in pulse power lab is described. (author)

  15. Opening Address

    Science.gov (United States)

    Crovini, L.

    1994-01-01

    Ladies and Gentlemen To quote Mr Jean Terrien: "Physics must be one step ahead of metrology". A long-serving Director of the BIPM, he said these words when visiting the IMGC in 1970 as a member of the scientific board of our Institute. At that time it was still an open question whether the IMGC should start research work on the absolute measurement of silicon lattice spacing. Mr Terrien underlined the revolutionary character of x-ray interferometry and, eventually, he caused the balance needle to lean towards the ... right direction. Mr Terrien correctly foresaw that, like Michelson's interferometer of 1880, x-ray interferometry could have a prominent place in today's science and technology. And while, in the first case, after more than a century we can see instruments based on electromagnetic wave interaction within every one's reach in laboratories and, sometimes, in workshops, in the second case, twenty-five years since the first development of an x-ray interferometer we can witness its role in nanometrology. Today and tomorrow we meet to discuss how to go beyond the sixth decimal place in the value of the Avogadro constant. We are aware that the quest for this achievement requires the cooperation of scientists with complementary capabilities. I am sure that the present workshop is a very good opportunity to present and discuss results and to improve and extend existing cooperation. The new adjustment of fundamental constants envisaged by the CODATA Task Group is redoubling scientists' efforts to produce competitive values of NA. The results of the measurements of the silicon lattice spacing in terms of an optical wavelength, which were available for the 1986 adjustment, combined with the determination of silicon molar volume, demonstrate how such an NA determination produces a consistent set of other constants and opens the way to a possible redefinition of the kilogram. We shall see in these two days how far we have progressed along this road. For us at the

  16. 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

  17. 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.

  18. 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.

  19. 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

    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...... 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...... contract permeates through secondary education into university physics education. Our results allow for a better renegotiation of didactical contracts and thus for avoiding typical problems related to the implementation of alternative tasks. One might expect physics students to be special in their explicit...

  20. 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.

  1. Genomic Resource and Genome Guided Comparison of Twenty Type Strains of the Genus Methylobacterium

    Directory of Open Access Journals (Sweden)

    Vasvi Chaudhry

    2017-12-01

    Full Text Available Bacteria of the genus Methylobacterium are widespread in diverse habitats ranging from soil, water and plant (phyllosphere, rhizosphere and endosphere. In the present study, we in house generated genomic data resource of six type strains along with fourteen database genomes of the Methylobacterium genus to carry out phylogenomic, taxonomic, comparative and ecological studies of this genus. Overall, the genus shows high diversity and genetic variation primarily due to its ability to acquire genetic material from diverse sources through horizontal gene transfer. As majority of species identified in this study are plant associated with their genomes equipped with methylotrophy and photosynthesis related gene along with genes for plant probiotic traits. Most of the species genomes are equipped with genes for adaptation and defense for UV radiation, oxidative stress and desiccation. The genus has an open pan-genome and we predicted the role of gain/loss of prophages and CRISPR elements in diversity and evolution. Our genomic resource with annotation and analysis provides a platform for interspecies genomic comparisons in the genus Methylobacterium, and to unravel their natural genome diversity and to study how natural selection shapes their genome with the adaptive mechanisms which allow them to acquire diverse habitat lifestyles. This type strains genomic data display power of Next Generation Sequencing in rapidly creating resource paving the way for studies on phylogeny and taxonomy as well as for basic and applied research for this important genus.

  2. Open life science research, open software and the open century

    Directory of Open Access Journals (Sweden)

    Youhua Chen

    2015-05-01

    Full Text Available At the age of knowledge explosion and mass scientific information, I highlighted the importance of conducting open science in life and medical researches through the extensive usage of open software and documents. The proposal of conducting open science is to reduce the limited repeatability of researches in life science. I outlined the essential steps for conducting open life science and the necessary standards for creating, reusing and reproducing open materials. Different Creative Commons licenses were presented and compared of their usage scope and restriction. As a conclusion, I argued that open materials should be widely adopted in doing life and medical researches.

  3. The Earth is our lab: Ten years of geoscience school lab in Potsdam

    Science.gov (United States)

    Nikolaus Küppers, Andreas

    2016-04-01

    Starting in 2004, a geoscientific school lab for senior high school students was developed in the historical "Großer Refraktor" premises on the Telegraphenberg in Potsdam. Based on a one-day course architecture, laboratory days were developed covering singular themes: - Magnetic field of the Earth - Geographical Information Systems and geodata - Gravity field of the Earth - Geodynamics: seismology and seismics - Geoscience math - Geodata Brandenburg (Geological mapping with aerophotographs, remote sensing, underground data processing) With a focus on geophysical methodologies, course days generally focused on the field work around the Telegraphenberg site while introducing into the art of handling original professional equipment. Field data were afterwards compiled, analysed and interpreted in the group. Single days could be combined as clusters of up to one week and were bookable for national and international groups of max. 25 students. The courses were taught by active scientists with the assistance of student guides as the larger groups had to be split up. The paper gives an overview over the development history of the school lab and explains the course contents, the teaching methods and several employed escorting measures. Possible impact on the professional career decisions of the students is discussed.

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

    DEFF Research Database (Denmark)

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

    of this project are to develop a technological infrastructure to support students’ work in the lab and to develop teaching and learning resources. Our research question is: How is teaching and learning in the laboratory influenced by the tablets and the following multimodal teaching and learning materials...... 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......? 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...

  5. 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

  6. 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...

  7. 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 ...

  8. Living lab: Format for rehearsing a new (service) practice

    DEFF Research Database (Denmark)

    Yndigegn, Signe; Aakjær, Marie Kirstejn

    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...... 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...... technologies, concepts, or service designs. This paper unpacks the practices of living labs with questions of what is being produced, not only in terms of products, but also in terms of changes in practices, roles, and relations. To analyze and discuss this question the authors report about their engagement...

  9. Antibody Characterization Lab | Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The Antibody Characterization Lab (ACL), an intramural reference laboratory located at the Frederick National Laboratory for Cancer Research in Frederick, Maryland, thoroughly characterizes monoclonal antibodies or other renewable affinity binding reagents for use in cancer related research.

  10. Development and Interaction between LMS Services and Remote Labs

    Directory of Open Access Journals (Sweden)

    Manuel Castro

    2008-03-01

    Full Text Available Nowadays there is a great number of universities and organizations working in e-learning and i-learning solutions. One of the most well-known is the learning management system or LMS that allows displaying theoretical content in an organized and controlled way. In some jobs and studies it is necessary for the student to get a practical knowledge as well as a theoretical one. To obtain this practical knowledge, the universities and organizations are developing Virtual, Remote and Web labs. At these moments the LMS and Web labs are working independently. We are studying a new architecture allowing the integration of the LMS with different Web labs. This architecture must allow the students, teachers and administrators to use the services of LMS and virtual lab’s features as if they were working with the same software.

  11. Bilirubin in Urine: MedlinePlus Lab Test Information

    Science.gov (United States)

    ... K. Brunner & Suddarth's Handbook of Laboratory and Diagnostic Tests. 2 nd Ed, Kindle. Philadelphia: Wolters Kluwer Health, Lippincott Williams & Wilkins; c2014. Bilirubin (Urine); 86–87 p. Lab ...

  12. 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...

  13. Analysis on functions of mobile nuclear emergency monitoring lab

    International Nuclear Information System (INIS)

    Lai Yongfang; Wang Yonghong; Gao Jing; Sun Jian

    2012-01-01

    According to the fundamental purpose and mission of nuclear emergency monitoring and based on technological aspects, this paper discusses and analyses the functions and basic requirements on equipment in mobile radiation measurement lab in nuclear emergency response. (authors)

  14. 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.

  15. Ensembl Genomes 2016: more genomes, more complexity.

    Science.gov (United States)

    Kersey, Paul Julian; Allen, James E; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello-Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M; Howe, Kevin L; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M

    2016-01-04

    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. Rodent malaria parasites : genome organization & comparative genomics

    NARCIS (Netherlands)

    Kooij, Taco W.A.

    2006-01-01

    The aim of the studies described in this thesis was to investigate the genome organization of rodent malaria parasites (RMPs) and compare the organization and gene content of the genomes of RMPs and the human malaria parasite P. falciparum. The release of the complete genome sequence of P.

  17. 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.

  18. 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.

  19. Using RSpec in an introductory bright star spectroscopy lab activity

    Science.gov (United States)

    Howe, James; Sitar, David J.

    2018-01-01

    After presenting at the North Carolina Section of the American Association of Physics Teachers during the fall 2016 meeting, we were encouraged to turn our poster into a paper. This article describes the strengthening of a bright star spectroscopy lab activity for introductory astronomy lab students (AST1002) at Appalachian State University. Explanations of the tools and methods used in the activity are included, particularly the preparation of additional materials using RSpec and calibrated instrument response curves.

  20. A Case Study of a High School Fab Lab

    Science.gov (United States)

    Lacy, Jennifer E.

    This dissertation examines making and design-based STEM education in a formal makerspace. It focuses on how the design and implementation of a Fab Lab learning environment and curriculum affect how instructors and students see themselves engaging in science, and how the Fab Lab relates to the social sorting practices that already take place at North High School. While there is research examining design-based STEM education in informal and formal learning environments, we know little about how K-12 teachers define STEM in making activities when no university or museum partnership exists. This study sought to help fill this gap in the research literature. This case study of a formal makerspace followed instructors and students in one introductory Fab Lab course for one semester. Additional observations of an introductory woodworking course helped build the case and set it into the school context, and provided supplementary material to better understand the similarities and differences between the Fab Lab course and a more traditional design-based learning course. Using evidence from observational field notes, participant interviews, course materials, and student work, I found that the North Fab Lab relies on artifacts and rhetoric symbolic of science and STEM to set itself apart from other design-based courses at North High School. Secondly, the North Fab Lab instructors and students were unable to explain how what they were doing in the Fab Lab was science, and instead relied on vague and unsupported claims related to interdisciplinary STEM practices and dated descriptions of science. Lastly, the design and implementation of the Fab Lab learning environment and curriculum and its separation from North High School's low tech, design-based courses effectively reinforced social sorting practices and cultural assumptions about student work and intelligence.