Sample records for genome lab opens
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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....
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OpenLabNotes--An Electronic Laboratory Notebook Extension for OpenLabFramework.
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.
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OpenLabNotes - An Electronic Laboratory Notebook Extension for OpenLabFramework.
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.
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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.
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GeneLab: NASA's Open Access, Collaborative Platform for Systems Biology and Space Medicine
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.
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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...
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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...
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Easy research data handling with an OpenEarth DataLab for geo-monitoring research
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
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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.
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Project-based physics labs using low-cost open-source hardware
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.
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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...
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Open source and DIY hardware for DNA nanotechnology labs.
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%.
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EHS Open House: Learning Lab and Life Safety | Poster
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
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How to Cope with Working in an Open-space Lab?
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
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MetaLIMS, a simple open-source laboratory information management system for small metagenomic labs.
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.
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PySeqLab: an open source Python package for sequence labeling and segmentation.
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
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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.
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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.
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GeneLab: Open Science For Exploration
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.
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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...
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NASA's GeneLab Phase II: Federated Search and Data Discovery
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.
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NASAs GeneLab Phase II: Federated Search and Data Discovery
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.
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HTC Vive MeVisLab integration via OpenVR for medical applications.
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.
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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.
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Designing inquiry learning spaces for online labs in the Go-Lab platform
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
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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.
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Innovations in STEM education: the Go-Lab federation of online labs
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
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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.
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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.
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Millstone: software for multiplex microbial genome analysis and engineering.
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.
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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.
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Human genome and open source: balancing ethics and business.
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.
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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.
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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
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Ginseng Genome Database: an open-access platform for genomics of Panax ginseng.
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 /.
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GeneLab: A Systems Biology Platform for Spaceflight Omics Data
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
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LabKey Server: An open source platform for scientific data integration, analysis and collaboration
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
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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
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LabKey Server: an open source platform for scientific data integration, analysis and collaboration.
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
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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.
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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.
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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)
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Genomics of lactic acid bacteria: Current status and potential applications.
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.
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STORMSeq: an open-source, user-friendly pipeline for processing personal genomics data in the cloud.
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.
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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.
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Living Lab voor Informatiemanagement in Agri-Food
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.
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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.
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MethLAB: a graphical user interface package for the analysis of array-based DNA methylation data.
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.
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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
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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
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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
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Teachers' Perspectives on Online Virtual Labs vs. Hands-On Labs in High School Science
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.
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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.
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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.
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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.
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Chemotion ELN: an Open Source electronic lab notebook for chemists in academia.
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.
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Map of open and closed chromatin domains in Drosophila genome.
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.
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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.
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GeneLab Phase 2: Integrated Search Data Federation of Space Biology Experimental Data
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.;
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
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STORMSeq: An Open-Source, User-Friendly Pipeline for Processing Personal Genomics Data in the Cloud
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...
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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
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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.
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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.
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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...
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Targeted Genome Sequencing Reveals Varicella-Zoster Virus Open Reading Frame 12 Deletion.
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.
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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.
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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.
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Open reading frames associated with cancer in the dark matter of the human genome.
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.
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Development of an Open Source, Air-Deployable Weather Station
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.
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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…
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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.
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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.
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The first complete genome sequences of clinical isolates of human coronavirus 229E
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
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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.
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A LabVIEW model incorporating an open-loop arterial impedance and a closed-loop circulatory system.
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.
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Arduino-Based embedded systems interfacing, simulation, and LabVIEW GUI
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.
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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...
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Lab Streaming Layer Enabled Myo Data Collection Software User Manual
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
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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.
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MarkoLAB: A simulator to study ionic channel's stochastic behavior.
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
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The Telecom Lab is moving to the Building 2, in front of the Main Building
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: ...
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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
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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.
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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.
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Evaluation of oral microbiology lab curriculum reform.
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
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Computer-based Astronomy Labs for Non-science Majors
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.
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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.
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How to re-establish Openness as default? Towards a global joint initiative
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:
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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.
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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
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Python Materials Genomics (pymatgen): A robust, open-source python library for materials analysis
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...
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Multi-color fluorescent DNA analysis in an integrated optofluidic lab-on-a-chip
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
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Multi-color fluorescent DNA analysis in an integrated optofluidic lab on a chip
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
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Craniux: a LabVIEW-based modular software framework for brain-machine interface research.
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.
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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.
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Automated ensemble assembly and validation of microbial genomes
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
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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...
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Advanced HVAC modeling with FemLab/Simulink/MatLab
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
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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.
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Genomics and privacy: implications of the new reality of closed data for the field.
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
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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
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The StratusLab cloud distribution: Use-cases and support for scientific applications
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
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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.
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Genome Annotation in a Community College Cell Biology Lab
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…
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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...
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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.)
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The community FabLab platform: applications and implications in biomedical engineering.
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.
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Overview of the Fire Lab at Missoula Experiments (FLAME)
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...
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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...
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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.
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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
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KNMI DataLab experiences in serving data-driven innovations
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.
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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.
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Open-science projects get kickstarted at CERN
Achintya Rao
2015-01-01
CERN is one of the host sites for the Mozilla Science Lab Global Sprint to be held on 4 and 5 June, which will see participants around the world work on projects to further open science and educational tools. IdeaSquare will be hosting the event at CERN. The Mozilla Science Lab Global Sprint was first held in 2014 to bring together open-science practitioners and enthusiasts to collaborate on projects designed to advance science on the open web. The sprint is a loosely federated event, and CERN is participating in the 2015 edition, hosting sprinters in the hacker-friendly IdeaSquare. Five projects have been formally proposed and CERN users and staff are invited to participate in a variety of ways. A special training session will also be held to introduce the CERN community to existing open-science and collaborative tools, including ones that have been deployed at CERN. 1. GitHub Science Badges: Sprinters will work on developing a badge-style visual representation of how open a software pro...
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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.
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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.
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User recruitment, training, and support at NOAO Data Lab
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.
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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
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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.
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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.
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Arduino: a low-cost multipurpose lab equipment.
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.
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Public Lab: Community-Based Approaches to Urban and Environmental Health and Justice.
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.
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Kinematic Labs with Mobile Devices
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.
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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
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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.
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Assessing the Impact of a Virtual Lab in an Allied Health Program.
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.
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Integration of the HTC Vive into the medical platform MeVisLab
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.
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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.
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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.
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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.
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Multi-color fluorescent DNA analysis in an integrated optofluidic lab-on-a-chip
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...
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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.
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EarthLabs - Investigating Hurricanes: Earth's Meteorological Monsters
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
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Research on OpenStack of open source cloud computing in colleges and universities’ computer room
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.
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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.
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A Lab-on-Chip Design for Miniature Autonomous Bio-Chemoprospecting Planetary Rovers
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.
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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
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Genome Variation Map: a data repository of genome variations in BIG Data Center
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...
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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/)
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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
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Multi-color fluorescent DNA analysis in an integrated optofluidic lab on a chip
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) ...
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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.
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Lab at Home: Hardware Kits for a Digital Design Lab
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…
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Labs not in a lab: A case study of instructor and student perceptions of an online biology lab class
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.
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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.
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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.
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MatLab Script and Functional Programming
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.
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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.
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Exploring linear algebra labs and projects with Mathematica
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...
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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.
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The relevance of genetic analysis to dairy bacteria: building upon our heritage
Directory of Open Access Journals (Sweden)
Moineau Sylvain
2004-12-01
Full Text Available Abstract Lactic acid bacteria (LAB are essential for the manufacture of fermented dairy products. Studies on the physiology, biochemistry and genetics of these microorganisms over the last century have contributed considerably to the improvement of fermentation processes and have resulted in better and safer products. Nevertheless, the potential of LAB is far from being maximized. The sophistication of biotechnologies and the availability of complete genome sequences have opened the door to the metabolic engineering of LAB. In this regard, the recent publication of the complete genome sequences of two Streptococcus thermophilus strains will provide a key tool to facilitate the genetic manipulation of this important dairy species.
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Improving the Quality of Lab Reports by Using Them as Lab Instructions
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
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ESIP Lab: Supporting Development of Earth Sciences Cyberinfrastructure through Innovation Commons
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.
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Out-of-plane microvalves for whole blood separation on lab-on-a-CD
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.
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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
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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...
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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)
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Open Source Initiative Powers Real-Time Data Streams
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.
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Genome Maps, a new generation genome browser.
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.
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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.
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Palmisano, Alida; Zhao, Yingdong; Li, Ming-Chung; Polley, Eric C; Simon, Richard M
2017-09-01
Trials involving genomic-driven treatment selection require the coordination of many teams interacting with a great variety of information. The need of better informatics support to manage this complex set of operations motivated the creation of OpenGeneMed. OpenGeneMed is a stand-alone and customizable version of GeneMed (Zhao et al. GeneMed: an informatics hub for the coordination of next-generation sequencing studies that support precision oncology clinical trials. Cancer Inform 2015;14(Suppl 2):45), a web-based interface developed for the National Cancer Institute Molecular Profiling-based Assignment of Cancer Therapy (NCI-MPACT) clinical trial coordinated by the NIH. OpenGeneMed streamlines clinical trial management and it can be used by clinicians, lab personnel, statisticians and researchers as a communication hub. It automates the annotation of genomic variants identified by sequencing tumor DNA, classifies the actionable mutations according to customizable rules and facilitates quality control in reviewing variants. The system generates summarized reports with detected genomic alterations that a treatment review team can use for treatment assignment. OpenGeneMed allows collaboration to happen seamlessly along the clinical pipeline; it helps reduce errors made transferring data between groups and facilitates clear documentation along the pipeline. OpenGeneMed is distributed as a stand-alone virtual machine, ready for deployment and use from a web browser; its code is customizable to address specific needs of different clinical trials and research teams. Examples on how to change the code are provided in the technical documentation distributed with the virtual machine. In summary, OpenGeneMed offers an initial set of features inspired by our experience with GeneMed, a system that has been proven to be efficient and successful for coordinating the application of next-generation sequencing in the NCI-MPACT trial. Published by Oxford University Press 2016. This
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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...
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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…
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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.
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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.
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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.
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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
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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.
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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.
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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...
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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.
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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.
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Opening plenary speaker: Human genomics, precision medicine, and advancing human health.
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.
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GenColors-based comparative genome databases for small eukaryotic genomes.
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.
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Indel Group in Genomes (IGG) Molecular Genetic Markers1[OPEN
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
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Patient-controlled encrypted genomic data: an approach to advance clinical genomics
Directory of Open Access Journals (Sweden)
Trakadis Yannis J
2012-07-01
Full Text Available Abstract Background The revolution in DNA sequencing technologies over the past decade has made it feasible to sequence an individual’s whole genome at a relatively low cost. The potential value of the information generated by genomic technologies for medicine and society is enormous. However, in order for exome sequencing, and eventually whole genome sequencing, to be implemented clinically, a number of major challenges need to be overcome. For instance, obtaining meaningful informed-consent, managing incidental findings and the great volume of data generated (including multiple findings with uncertain clinical significance, re-interpreting the genomic data and providing additional counselling to patients as genetic knowledge evolves are issues that need to be addressed. It appears that medical genetics is shifting from the present “phenotype-first” medical model to a “data-first” model which leads to multiple complexities. Discussion This manuscript discusses the different challenges associated with integrating genomic technologies into clinical practice and describes a “phenotype-first” approach, namely, “Individualized Mutation-weighed Phenotype Search”, and its benefits. The proposed approach allows for a more efficient prioritization of the genes to be tested in a clinical lab based on both the patient’s phenotype and his/her entire genomic data. It simplifies “informed-consent” for clinical use of genomic technologies and helps to protect the patient’s autonomy and privacy. Overall, this approach could potentially render widespread use of genomic technologies, in the immediate future, practical, ethical and clinically useful. Summary The “Individualized Mutation-weighed Phenotype Search” approach allows for an incremental integration of genomic technologies into clinical practice. It ensures that we do not over-medicalize genomic data but, rather, continue our current medical model which is based on serving
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Directory of Open Access Journals (Sweden)
Guillermo Nourdin-Galindo
2017-10-01
Full Text Available Piscirickettsia salmonis is the etiological agent of salmonid rickettsial septicemia, a disease that seriously affects the salmonid industry. Despite efforts to genomically characterize P. salmonis, functional information on the life cycle, pathogenesis mechanisms, diagnosis, treatment, and control of this fish pathogen remain lacking. To address this knowledge gap, the present study conducted an in silico pan-genome analysis of 19 P. salmonis strains from distinct geographic locations and genogroups. Results revealed an expected open pan-genome of 3,463 genes and a core-genome of 1,732 genes. Two marked genogroups were identified, as confirmed by phylogenetic and phylogenomic relationships to the LF-89 and EM-90 reference strains, as well as by assessments of genomic structures. Different structural configurations were found for the six identified copies of the ribosomal operon in the P. salmonis genome, indicating translocation throughout the genetic material. Chromosomal divergences in genomic localization and quantity of genetic cassettes were also found for the Dot/Icm type IVB secretion system. To determine divergences between core-genomes, additional pan-genome descriptions were compiled for the so-termed LF and EM genogroups. Open pan-genomes composed of 2,924 and 2,778 genes and core-genomes composed of 2,170 and 2,228 genes were respectively found for the LF and EM genogroups. The core-genomes were functionally annotated using the Gene Ontology, KEGG, and Virulence Factor databases, revealing the presence of several shared groups of genes related to basic function of intracellular survival and bacterial pathogenesis. Additionally, the specific pan-genomes for the LF and EM genogroups were defined, resulting in the identification of 148 and 273 exclusive proteins, respectively. Notably, specific virulence factors linked to adherence, colonization, invasion factors, and endotoxins were established. The obtained data suggest that these
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The Next Generation of Lab and Classroom Computing - The Silver Lining
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
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Beyond Classroom, Lab, Studio and Field
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.
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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.
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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.
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Genome annotation in a community college cell biology lab.
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.
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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.
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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
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Bergsveinson, Jordyn; Ziola, Barry
2017-12-01
Beer-spoilage-related lactic acid bacteria (BSR LAB) belong to multiple genera and species; however, beer-spoilage capacity is isolate-specific and partially acquired via horizontal gene transfer within the brewing environment. Thus, the extent to which genus-, species-, or environment- (i.e., brewery-) level genetic variability influences beer-spoilage phenotype is unknown. Publicly available Lactobacillus brevis genomes were analyzed via BlAst Diagnostic Gene findEr (BADGE) for BSR genes and assessed for pangenomic relationships. Also analyzed were functional coding capacities of plasmids of LAB inhabiting extreme niche environments. Considerable genetic variation was observed in L. brevis isolated from clinical samples, whereas 16 candidate genes distinguish BSR and non-BSR L. brevis genomes. These genes are related to nutrient scavenging of gluconate or pentoses, mannose, and metabolism of pectin. BSR L. brevis isolates also have higher average nucleotide identity and stronger pangenome association with one another, though isolation source (i.e., specific brewery) also appears to influence the plasmid coding capacity of BSR LAB. Finally, it is shown that niche-specific adaptation and phenotype are plasmid-encoded for both BSR and non-BSR LAB. The ultimate combination of plasmid-encoded genes dictates the ability of L. brevis to survive in the most extreme beer environment, namely, gassed (i.e., pressurized) beer.
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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
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Evans, Teri; Johnson, Andrew D; Loose, Matthew
2018-01-12
Large repeat rich genomes present challenges for assembly using short read technologies. The 32 Gb axolotl genome is estimated to contain ~19 Gb of repetitive DNA making an assembly from short reads alone effectively impossible. Indeed, this model species has been sequenced to 20× coverage but the reads could not be conventionally assembled. Using an alternative strategy, we have assembled subsets of these reads into scaffolds describing over 19,000 gene models. We call this method Virtual Genome Walking as it locally assembles whole genome reads based on a reference transcriptome, identifying exons and iteratively extending them into surrounding genomic sequence. These assemblies are then linked and refined to generate gene models including upstream and downstream genomic, and intronic, sequence. Our assemblies are validated by comparison with previously published axolotl bacterial artificial chromosome (BAC) sequences. Our analyses of axolotl intron length, intron-exon structure, repeat content and synteny provide novel insights into the genic structure of this model species. This resource will enable new experimental approaches in axolotl, such as ChIP-Seq and CRISPR and aid in future whole genome sequencing efforts. The assembled sequences and annotations presented here are freely available for download from https://tinyurl.com/y8gydc6n . The software pipeline is available from https://github.com/LooseLab/iterassemble .
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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
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HGVA: the Human Genome Variation Archive.
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.
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OpenVirtualToxLab--a platform for generating and exchanging in silico toxicity data.
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.
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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
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Open source systems security certification
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
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GeneLab Analysis Working Group Kick-Off Meeting
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
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Build your own social network laboratory with Social Lab: a tool for research in social media.
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.
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Reefgenomics.Org - a repository for marine genomics data
Liew, Yi Jin
2016-11-01
Over the last decade, technological advancements have substantially decreased the cost and time of obtaining large amounts of sequencing data. Paired with the exponentially increased computing power, individual labs are now able to sequence genomes or transcriptomes to investigate biological questions of interest. This has led to a significant increase in available sequence data. Although the bulk of data published in articles are stored in public sequence databases, very often, only raw sequencing data are available; miscellaneous data such as assembled transcriptomes, genome annotations etc. are not easily obtainable through the same means. Here, we introduce our website (http://reefgenomics.org) that aims to centralize genomic and transcriptomic data from marine organisms. Besides providing convenient means to download sequences, we provide (where applicable) a genome browser to explore available genomic features, and a BLAST interface to search through the hosted sequences. Through the interface, multiple datasets can be queried simultaneously, allowing for the retrieval of matching sequences from organisms of interest. The minimalistic, no-frills interface reduces visual clutter, making it convenient for end-users to search and explore processed sequence data.
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Reefgenomics.Org - a repository for marine genomics data
Liew, Yi Jin; Aranda, Manuel; Voolstra, Christian R.
2016-01-01
Over the last decade, technological advancements have substantially decreased the cost and time of obtaining large amounts of sequencing data. Paired with the exponentially increased computing power, individual labs are now able to sequence genomes or transcriptomes to investigate biological questions of interest. This has led to a significant increase in available sequence data. Although the bulk of data published in articles are stored in public sequence databases, very often, only raw sequencing data are available; miscellaneous data such as assembled transcriptomes, genome annotations etc. are not easily obtainable through the same means. Here, we introduce our website (http://reefgenomics.org) that aims to centralize genomic and transcriptomic data from marine organisms. Besides providing convenient means to download sequences, we provide (where applicable) a genome browser to explore available genomic features, and a BLAST interface to search through the hosted sequences. Through the interface, multiple datasets can be queried simultaneously, allowing for the retrieval of matching sequences from organisms of interest. The minimalistic, no-frills interface reduces visual clutter, making it convenient for end-users to search and explore processed sequence data.
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Primer to analysis of genomic data using R
Gondro, Cedric
2015-01-01
Through this book, researchers and students will learn to use R for analysis of large-scale genomic data and how to create routines to automate analytical steps. The philosophy behind the book is to start with real world raw datasets and perform all the analytical steps needed to reach final results. Though theory plays an important role, this is a practical book for advanced undergraduate and graduate classes in bioinformatics, genomics and statistical genetics or for use in lab sessions. This book is also designed to be used by students in computer science and statistics who want to learn the practical aspects of genomic analysis without delving into algorithmic details. The datasets used throughout the book may be downloaded from the publisher’s website. Chapters show how to handle and manage high-throughput genomic data, create automated workflows and speed up analyses in R. A wide range of R packages useful for working with genomic data are illustrated with practical examples. In recent years R has b...
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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.
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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. CDCâs laboratories play a critical role in the agencyâs ability to find, stop, and prevent disease outbreaks. This podcast provides a brief overview of what goes on inside CDCâs labs, and why this work makes a difference in Americanâs health.
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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.
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Advancing Crop Transformation in the Era of Genome Editing[OPEN
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
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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...
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Genomics-assisted breeding in fruit trees
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...
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IRB PERSPECTIVES ON THE RETURN OF INDIVIDUAL RESULTS FROM GENOMIC RESEARCH
Dressler, Lynn G.; Smolek, Sondra; Ponsaran, Roselle; Markey, Janell M.; Starks, Helene; Gerson, Nancy; Lewis, Susan; Press, Nancy; Juengst, Eric; Wiesner, Georgia L.
2012-01-01
Purpose Return of individual research results from genomic studies is a hotly debated ethical issue in genomic research. However, the perspective of key stakeholders—Institutional Review Board (IRB) reviewers—has been missing from this dialogue. This study explores the positions and experiences of IRB members and staff regarding this issue. Methods In depth interviews with 31 IRB professionals at six sites across the United States. Results IRB professionals agreed that research results should be returned to research participants when results are medically actionable but only if the participants wanted to know the result. Many respondents expected researchers to address the issue of return of results (ROR) in the IRB application and informed-consent document. Many respondents were not comfortable with their expertise in genomics research, and only a few described actual experiences in addressing ROR. Although participants agreed that guidelines would be helpful, most were reticent to develop them in isolation. Even where IRB guidance exists (e.g., CLIA lab certification required for return), in practice, the guidance has been overruled to allow return (e.g., no CLIA lab performs the assay). Conclusion An IRB-researcher partnership is needed to help inform responsible and feasible institutional approaches to returning research results. PMID:22241094
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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.
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Audit, Benjamin; Zaghloul, Lamia; Baker, Antoine; Arneodo, Alain; Chen, Chun-Long; d'Aubenton-Carafa, Yves; Thermes, Claude
2013-01-01
In higher eukaryotes, the absence of specific sequence motifs, marking the origins of replication has been a serious hindrance to the understanding of (i) the mechanisms that regulate the spatio-temporal replication program, and (ii) the links between origins activation, chromatin structure and transcription. In this chapter, we review the partitioning of the human genome into megabased-size replication domains delineated as N-shaped motifs in the strand compositional asymmetry profiles. They collectively span 28.3% of the genome and are bordered by more than 1,000 putative replication origins. We recapitulate the comparison of this partition of the human genome with high-resolution experimental data that confirms that replication domain borders are likely to be preferential replication initiation zones in the germline. In addition, we highlight the specific distribution of experimental and numerical chromatin marks along replication domains. Domain borders correspond to particular open chromatin regions, possibly encoded in the DNA sequence, and around which replication and transcription are highly coordinated. These regions also present a high evolutionary breakpoint density, suggesting that susceptibility to breakage might be linked to local open chromatin fiber state. Altogether, this chapter presents a compartmentalization of the human genome into replication domains that are landmarks of the human genome organization and are likely to play a key role in genome dynamics during evolution and in pathological situations.
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Gonzalez, Michael A; Lebrigio, Rafael F Acosta; Van Booven, Derek; Ulloa, Rick H; Powell, Eric; Speziani, Fiorella; Tekin, Mustafa; Schüle, Rebecca; Züchner, Stephan
2013-06-01
Novel genes are now identified at a rapid pace for many Mendelian disorders, and increasingly, for genetically complex phenotypes. However, new challenges have also become evident: (1) effectively managing larger exome and/or genome datasets, especially for smaller labs; (2) direct hands-on analysis and contextual interpretation of variant data in large genomic datasets; and (3) many small and medium-sized clinical and research-based investigative teams around the world are generating data that, if combined and shared, will significantly increase the opportunities for the entire community to identify new genes. To address these challenges, we have developed GEnomes Management Application (GEM.app), a software tool to annotate, manage, visualize, and analyze large genomic datasets (https://genomics.med.miami.edu/). GEM.app currently contains ∼1,600 whole exomes from 50 different phenotypes studied by 40 principal investigators from 15 different countries. The focus of GEM.app is on user-friendly analysis for nonbioinformaticians to make next-generation sequencing data directly accessible. Yet, GEM.app provides powerful and flexible filter options, including single family filtering, across family/phenotype queries, nested filtering, and evaluation of segregation in families. In addition, the system is fast, obtaining results within 4 sec across ∼1,200 exomes. We believe that this system will further enhance identification of genetic causes of human disease. © 2013 Wiley Periodicals, Inc.
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Particle physicists want to expand open access
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)
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Particle physicists want to expand open access
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)
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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...
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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...
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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
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Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium.
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.
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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
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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…
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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
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CRISPR/Cas9-mediated genome editing and gene replacement in plants: Transitioning from lab to field
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...
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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
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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.
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The role of wet lab in thoracic surgery.
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.
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RoboLab and virtual environments
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.
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DStat: A Versatile, Open-Source Potentiostat for Electroanalysis and Integration.
Dryden, Michael D M; Wheeler, Aaron R
2015-01-01
Most electroanalytical techniques require the precise control of the potentials in an electrochemical cell using a potentiostat. Commercial potentiostats function as "black boxes," giving limited information about their circuitry and behaviour which can make development of new measurement techniques and integration with other instruments challenging. Recently, a number of lab-built potentiostats have emerged with various design goals including low manufacturing cost and field-portability, but notably lacking is an accessible potentiostat designed for general lab use, focusing on measurement quality combined with ease of use and versatility. To fill this gap, we introduce DStat (http://microfluidics.utoronto.ca/dstat), an open-source, general-purpose potentiostat for use alone or integrated with other instruments. DStat offers picoampere current measurement capabilities, a compact USB-powered design, and user-friendly cross-platform software. DStat is easy and inexpensive to build, may be modified freely, and achieves good performance at low current levels not accessible to other lab-built instruments. In head-to-head tests, DStat's voltammetric measurements are much more sensitive than those of "CheapStat" (a popular open-source potentiostat described previously), and are comparable to those of a compact commercial "black box" potentiostat. Likewise, in head-to-head tests, DStat's potentiometric precision is similar to that of a commercial pH meter. Most importantly, the versatility of DStat was demonstrated through integration with the open-source DropBot digital microfluidics platform. In sum, we propose that DStat is a valuable contribution to the "open source" movement in analytical science, which is allowing users to adapt their tools to their experiments rather than alter their experiments to be compatible with their tools.
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DStat: A Versatile, Open-Source Potentiostat for Electroanalysis and Integration.
Directory of Open Access Journals (Sweden)
Michael D M Dryden
Full Text Available Most electroanalytical techniques require the precise control of the potentials in an electrochemical cell using a potentiostat. Commercial potentiostats function as "black boxes," giving limited information about their circuitry and behaviour which can make development of new measurement techniques and integration with other instruments challenging. Recently, a number of lab-built potentiostats have emerged with various design goals including low manufacturing cost and field-portability, but notably lacking is an accessible potentiostat designed for general lab use, focusing on measurement quality combined with ease of use and versatility. To fill this gap, we introduce DStat (http://microfluidics.utoronto.ca/dstat, an open-source, general-purpose potentiostat for use alone or integrated with other instruments. DStat offers picoampere current measurement capabilities, a compact USB-powered design, and user-friendly cross-platform software. DStat is easy and inexpensive to build, may be modified freely, and achieves good performance at low current levels not accessible to other lab-built instruments. In head-to-head tests, DStat's voltammetric measurements are much more sensitive than those of "CheapStat" (a popular open-source potentiostat described previously, and are comparable to those of a compact commercial "black box" potentiostat. Likewise, in head-to-head tests, DStat's potentiometric precision is similar to that of a commercial pH meter. Most importantly, the versatility of DStat was demonstrated through integration with the open-source DropBot digital microfluidics platform. In sum, we propose that DStat is a valuable contribution to the "open source" movement in analytical science, which is allowing users to adapt their tools to their experiments rather than alter their experiments to be compatible with their tools.
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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...
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Reefgenomics.Org - a repository for marine genomics data.
Liew, Yi Jin; Aranda, Manuel; Voolstra, Christian R
2016-01-01
Over the last decade, technological advancements have substantially decreased the cost and time of obtaining large amounts of sequencing data. Paired with the exponentially increased computing power, individual labs are now able to sequence genomes or transcriptomes to investigate biological questions of interest. This has led to a significant increase in available sequence data. Although the bulk of data published in articles are stored in public sequence databases, very often, only raw sequencing data are available; miscellaneous data such as assembled transcriptomes, genome annotations etc. are not easily obtainable through the same means. Here, we introduce our website (http://reefgenomics.org) that aims to centralize genomic and transcriptomic data from marine organisms. Besides providing convenient means to download sequences, we provide (where applicable) a genome browser to explore available genomic features, and a BLAST interface to search through the hosted sequences. Through the interface, multiple datasets can be queried simultaneously, allowing for the retrieval of matching sequences from organisms of interest. The minimalistic, no-frills interface reduces visual clutter, making it convenient for end-users to search and explore processed sequence data. DATABASE URL: http://reefgenomics.org. © The Author(s) 2016. Published by Oxford University Press.
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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. CDCâs laboratories play a critical role in the agencyâs ability to find, stop, and prevent disease outbreaks. This podcast provides a brief overview of what goes on inside CDCâs labs, and why this work makes a difference in Americanâs health. Created: 2/2/2015 by Office of the Associate Director for Communication (OADC). Date Released: 2/2/2015.
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Qin, Qi-Long; Xie, Bin-Bin; Yu, Yong; Shu, Yan-Li; Rong, Jin-Cheng; Zhang, Yan-Jiao; Zhao, Dian-Li; Chen, Xiu-Lan; Zhang, Xi-Ying; Chen, Bo; Zhou, Bai-Cheng; Zhang, Yu-Zhong
2014-06-01
To what extent the genomes of different species belonging to one genus can be diverse and the relationship between genomic differentiation and environmental factor remain unclear for oceanic bacteria. With many new bacterial genera and species being isolated from marine environments, this question warrants attention. In this study, we sequenced all the type strains of the published species of Glaciecola, a recently defined cold-adapted genus with species from diverse marine locations, to study the genomic diversity and cold-adaptation strategy in this genus.The genome size diverged widely from 3.08 to 5.96 Mb, which can be explained by massive gene gain and loss events. Horizontal gene transfer and new gene emergence contributed substantially to the genome size expansion. The genus Glaciecola had an open pan-genome. Comparative genomic research indicated that species of the genus Glaciecola had high diversity in genome size, gene content and genetic relatedness. This may be prevalent in marine bacterial genera considering the dynamic and complex environments of the ocean. Species of Glaciecola had some common genomic features related to cold adaptation, which enable them to thrive and play a role in biogeochemical cycle in the cold marine environments.
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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
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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.
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Awakening interest in the natural sciences - BASF's Kids' Labs.
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.
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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
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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.
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Incorporating lab experience into computer security courses
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
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Heinzen, Mareike; Cacciatori, Eugenia; Zoller, Frank A; Boutellier, Roman
2018-04-13
Although several studies have examined the impact of open workspaces, there is still an on-going debate about its advantages and disadvantages. Our paper contributes to this debate by shedding light on three issues: the effect of open workspaces on (1) the flow of communication along and across hierarchical lines; (2) the content of communication; and (3) the specificities of open integrated laboratories. Our findings derive from a longitudinal case in a large pharmaceutical company that has relocated some R&D teams from enclosed to multi-space offices and labs. The relocation has resulted in (a) increased interdisciplinary communication, particularly at lower hierarchical levels, (b) a shift of the location of discussions and the content of conversations and (c) an improved knowledge about expertise distribution. Practitioner Summary: Communication is essential in knowledge-driven organisations. This article examines the impact of a relocation of R&D employees from enclosed to multi-space offices and labs on communication patterns. We explain how the new environment fosters interdisciplinary communication, shifts the location of discussions and increases the knowledge of expertise distribution.
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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....
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Chromatin structure and evolution in the human genome
Directory of Open Access Journals (Sweden)
Dunlop Malcolm G
2007-05-01
Full Text Available Abstract Background Evolutionary rates are not constant across the human genome but genes in close proximity have been shown to experience similar levels of divergence and selection. The higher-order organisation of chromosomes has often been invoked to explain such phenomena but previously there has been insufficient data on chromosome structure to investigate this rigorously. Using the results of a recent genome-wide analysis of open and closed human chromatin structures we have investigated the global association between divergence, selection and chromatin structure for the first time. Results In this study we have shown that, paradoxically, synonymous site divergence (dS at non-CpG sites is highest in regions of open chromatin, primarily as a result of an increased number of transitions, while the rates of other traditional measures of mutation (intergenic, intronic and ancient repeat divergence as well as SNP density are highest in closed regions of the genome. Analysis of human-chimpanzee divergence across intron-exon boundaries indicates that although genes in relatively open chromatin generally display little selection at their synonymous sites, those in closed regions show markedly lower divergence at their fourfold degenerate sites than in neighbouring introns and intergenic regions. Exclusion of known Exonic Splice Enhancer hexamers has little affect on the divergence observed at fourfold degenerate sites across chromatin categories; however, we show that closed chromatin is enriched with certain classes of ncRNA genes whose RNA secondary structure may be particularly important. Conclusion We conclude that, overall, non-CpG mutation rates are lowest in open regions of the genome and that regions of the genome with a closed chromatin structure have the highest background mutation rate. This might reflect lower rates of DNA damage or enhanced DNA repair processes in regions of open chromatin. Our results also indicate that dS is a poor
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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...
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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.
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Future{at}Labs.Prosperity Game{trademark}
Energy Technology Data Exchange (ETDEWEB)
Beck, D.F.; Boyack, K.W.; Berman, M. [Sandia National Labs., Albuquerque, NM (United States). Innovative Alliances Dept.
1996-10-01
Prosperity Games{trademark} are an outgrowth and adaptation of move/countermove and seminar War Games, Prosperity Games{trademark} are simulations that explore complex issues in a variety of areas including economics, politics, sociology, environment, education, and research. These issues can be examined from a variety of perspectives ranging from global, macroeconomic and geopolitical viewpoint down to the details of customer/supplier/market interactions specific industries. All Prosperity Games{trademark} are unique in that both the game format and the player contributions vary from game to game. This report documents the Future{at}Labs.Prosperity Game{trademark} conducted under the sponsorship of the Industry Advisory Boards of the national labs, the national labs, Lockheed Martin Corporation, and the University of California. Players were drawn from all stakeholders involved including government, industry, labs, and academia. The primary objectives of this game were to: (1) explore ways to optimize the role of the multidisciplinary labs in serving national missions and needs; (2) explore ways to increase collaboration and partnerships among government, laboratories, universities, and industry; and (3) create a network of partnership champions to promote findings and policy options. The deliberations and recommendations of these players provided valuable insights as to the views of this diverse group of decision makers concerning the future of the labs.
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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.
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Open science versus commercialization: a modern research conflict?
Caulfield, Timothy; Harmon, Shawn He; Joly, Yann
2012-02-27
Efforts to improve research outcomes have resulted in genomic researchers being confronted with complex and seemingly contradictory instructions about how to perform their tasks. Over the past decade, there has been increasing pressure on university researchers to commercialize their work. Concurrently, they are encouraged to collaborate, share data and disseminate new knowledge quickly (that is, to adopt an open science model) in order to foster scientific progress, meet humanitarian goals, and to maximize the impact of their research. We present selected guidelines from three countries (Canada, United States, and United Kingdom) situated at the forefront of genomics to illustrate this potential policy conflict. Examining the innovation ecosystem and the messages conveyed by the different policies surveyed, we further investigate the inconsistencies between open science and commercialization policies. Commercialization and open science are not necessarily irreconcilable and could instead be envisioned as complementary elements of a more holistic innovation framework. Given the exploratory nature of our study, we wish to point out the need to gather additional evidence on the coexistence of open science and commercialization policies and on its impact, both positive and negative, on genomics academic research.
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Programming Arduino with LabVIEW
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.
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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
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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.
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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.
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Blazier, J. Chris; Ruhlman, Tracey A.; Weng, Mao-Lun; Rehman, Sumaiyah K.; Sabir, Jamal S. M.; Jansen, Robert K.
2016-01-01
Genes for the plastid-encoded RNA polymerase (PEP) persist in the plastid genomes of all photosynthetic angiosperms. However, three unrelated lineages (Annonaceae, Passifloraceae and Geraniaceae) have been identified with unusually divergent open reading frames (ORFs) in the conserved region of rpoA, the gene encoding the PEP ? subunit. We used sequence-based approaches to evaluate whether these genes retain function. Both gene sequences and complete plastid genome sequences were assembled an...
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Successes and Challenges in Transitioning to Large Enrollment NEXUS/Physics IPLS Labs
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.
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Behind the scenes at FameLab, the international competition for young scientists
CERN Bulletin
2012-01-01
FameLab is an international science communication competition for young researchers and science teachers aged 18 to 35. At CERN, preparations are under way to recruit participants, advertise the event to the public and organise the regional semi-finals for Suisse Romande, which will take place on Saturday, 4 February 2012 in the Globe of Science and Innovation. The Bulletin looks ahead to the forthcoming event… As you might have read in the 5 December 2011 issue of the Bulletin, Switzerland is one of the 20 countries participating in the FameLab 2012 competition, and the regional finals for French-speaking Switzerland will take place at CERN in the Globe of Science and Innovation on Saturday, 4 February 2012. “At the moment we’re still recruiting participants through various channels (registration is open till 31 January) and organising the one-day programme of events in the Globe,” says project coordinator Paola Catapano of the CERN Communication ...
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From Genomics to Gene Therapy: Induced Pluripotent Stem Cells Meet Genome Editing.
Hotta, Akitsu; Yamanaka, Shinya
2015-01-01
The advent of induced pluripotent stem (iPS) cells has opened up numerous avenues of opportunity for cell therapy, including the initiation in September 2014 of the first human clinical trial to treat dry age-related macular degeneration. In parallel, advances in genome-editing technologies by site-specific nucleases have dramatically improved our ability to edit endogenous genomic sequences at targeted sites of interest. In fact, clinical trials have already begun to implement this technology to control HIV infection. Genome editing in iPS cells is a powerful tool and enables researchers to investigate the intricacies of the human genome in a dish. In the near future, the groundwork laid by such an approach may expand the possibilities of gene therapy for treating congenital disorders. In this review, we summarize the exciting progress being made in the utilization of genomic editing technologies in pluripotent stem cells and discuss remaining challenges toward gene therapy applications.
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An Inexpensive, Open-Source USB Arduino Data Acquisition Device for Chemical Instrumentation.
Grinias, James P; Whitfield, Jason T; Guetschow, Erik D; Kennedy, Robert T
2016-07-12
Many research and teaching labs rely on USB data acquisition devices to collect voltage signals from instrumentation. However, these devices can be cost-prohibitive (especially when large numbers are needed for teaching labs) and require software to be developed for operation. In this article, we describe the development and use of an open-source USB data acquisition device (with 16-bit acquisition resolution) built using simple electronic components and an Arduino Uno that costs under $50. Additionally, open-source software written in Python is included so that data can be acquired using nearly any PC or Mac computer with a simple USB connection. Use of the device was demonstrated for a sophomore-level analytical experiment using GC and a CE-UV separation on an instrument used for research purposes.
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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.
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PatternLab for proteomics: a tool for differential shotgun proteomics
Directory of Open Access Journals (Sweden)
Yates John R
2008-07-01
Full Text Available Abstract Background A goal of proteomics is to distinguish between states of a biological system by identifying protein expression differences. Liu et al. demonstrated a method to perform semi-relative protein quantitation in shotgun proteomics data by correlating the number of tandem mass spectra obtained for each protein, or "spectral count", with its abundance in a mixture; however, two issues have remained open: how to normalize spectral counting data and how to efficiently pinpoint differences between profiles. Moreover, Chen et al. recently showed how to increase the number of identified proteins in shotgun proteomics by analyzing samples with different MS-compatible detergents while performing proteolytic digestion. The latter introduced new challenges as seen from the data analysis perspective, since replicate readings are not acquired. Results To address the open issues above, we present a program termed PatternLab for proteomics. This program implements existing strategies and adds two new methods to pinpoint differences in protein profiles. The first method, ACFold, addresses experiments with less than three replicates from each state or having assays acquired by different protocols as described by Chen et al. ACFold uses a combined criterion based on expression fold changes, the AC test, and the false-discovery rate, and can supply a "bird's-eye view" of differentially expressed proteins. The other method addresses experimental designs having multiple readings from each state and is referred to as nSVM (natural support vector machine because of its roots in evolutionary computing and in statistical learning theory. Our observations suggest that nSVM's niche comprises projects that select a minimum set of proteins for classification purposes; for example, the development of an early detection kit for a given pathology. We demonstrate the effectiveness of each method on experimental data and confront them with existing strategies
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Reptile genomes open the frontier for comparative analysis of amniote development and regeneration.
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.
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Ensembl 2002: accommodating comparative genomics.
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.
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The Ensembl genome database project.
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.
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Treangen, Todd J; Ondov, Brian D; Koren, Sergey; Phillippy, Adam M
2014-01-01
Whole-genome sequences are now available for many microbial species and clades, however existing whole-genome alignment methods are limited in their ability to perform sequence comparisons of multiple sequences simultaneously. Here we present the Harvest suite of core-genome alignment and visualization tools for the rapid and simultaneous analysis of thousands of intraspecific microbial strains. Harvest includes Parsnp, a fast core-genome multi-aligner, and Gingr, a dynamic visual platform. Together they provide interactive core-genome alignments, variant calls, recombination detection, and phylogenetic trees. Using simulated and real data we demonstrate that our approach exhibits unrivaled speed while maintaining the accuracy of existing methods. The Harvest suite is open-source and freely available from: http://github.com/marbl/harvest.
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Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.
Thorvaldsdóttir, Helga; Robinson, James T; Mesirov, Jill P
2013-03-01
Data visualization is an essential component of genomic data analysis. However, the size and diversity of the data sets produced by today's sequencing and array-based profiling methods present major challenges to visualization tools. The Integrative Genomics Viewer (IGV) is a high-performance viewer that efficiently handles large heterogeneous data sets, while providing a smooth and intuitive user experience at all levels of genome resolution. A key characteristic of IGV is its focus on the integrative nature of genomic studies, with support for both array-based and next-generation sequencing data, and the integration of clinical and phenotypic data. Although IGV is often used to view genomic data from public sources, its primary emphasis is to support researchers who wish to visualize and explore their own data sets or those from colleagues. To that end, IGV supports flexible loading of local and remote data sets, and is optimized to provide high-performance data visualization and exploration on standard desktop systems. IGV is freely available for download from http://www.broadinstitute.org/igv, under a GNU LGPL open-source license.
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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.
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Towards a Manifesto for Living Lab Co-creation
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.
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Open source Modeling and optimization tools for Planning
Energy Technology Data Exchange (ETDEWEB)
Peles, S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2017-02-10
Open source modeling and optimization tools for planning The existing tools and software used for planning and analysis in California are either expensive, difficult to use, or not generally accessible to a large number of participants. These limitations restrict the availability of participants for larger scale energy and grid studies in the state. The proposed initiative would build upon federal and state investments in open source software, and create and improve open source tools for use in the state planning and analysis activities. Computational analysis and simulation frameworks in development at national labs and universities can be brought forward to complement existing tools. An open source platform would provide a path for novel techniques and strategies to be brought into the larger community and reviewed by a broad set of stakeholders.
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LabVIEW A Developer's Guide to Real World Integration
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
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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.
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Diversity, Equity, & Inclusion at Berkeley Lab
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
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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...
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Crystallization Formulation Lab
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...
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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...
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Complete genome sequence of pronghorn virus, a pestivirus
The complete genome sequence of Pronghorn virus, a member of the Pestivirus genus of the Flaviviridae, was determined. The virus, originally isolated from a pronghorn antelope, had a genome of 12,287 nucleotides with a single open reading frame of 11,694 bases encoding 3898 amino acids....
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LAB building a home for scientists
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.
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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.
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77 FR 64816 - National Human Genome Research Institute; Notice of Meeting
2012-10-23
... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome..., National Human Genome Research Institute. The meeting will be open to the public as indicated below, with... invasion of personal privacy. Name of Committee: Board of Scientific Counselors, National Human Genome...
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75 FR 2147 - National Human Genome Research Institute; Notice of Meetings
2010-01-14
... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... Council for Human Genome Research. The meetings will be open to the public as indicated below, with... Extramural Research, National Human Genome Research Institute, 5635 Fishers Lane, Suite 4076, MSC 9305...
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76 FR 65204 - National Human Genome Research Institute; Notice of Meeting
2011-10-20
... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome..., National Human Genome Research Institute. The meeting will be open to the public as indicated below, with... invasion of personal privacy. Name of Committee: Board of Scientific Counselors, National Human Genome...
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75 FR 60467 - National Human Genome Research Institute; Notice of Meeting
2010-09-30
... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome..., National Human Genome Research Institute. The meeting will be open to the public as indicated below, with... invasion of personal privacy. Name of Committee: Board of Scientific Counselors, National Human Genome...
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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
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GeneLab for High Schools: Data Mining for the Next Generation
Blaber, Elizabeth A.; Ly, Diana; Sato, Kevin Y.; Taylor, Elizabeth
2016-01-01
Modern biological sciences have become increasingly based on molecular biology and high-throughput molecular techniques, such as genomics, transcriptomics, and proteomics. NASA Scientists and the NASA Space Biology Program have aimed to examine the fundamental building blocks of life (RNA, DNA and protein) in order to understand the response of living organisms to space and aid in fundamental research discoveries on Earth. In an effort to enable NASA funded science to be available to everyone, NASA has collected the data from omics studies and curated them in a data system called GeneLab. Whilst most college-level interns, academics and other scientists have had some interaction with omics data sets and analysis tools, high school students often have not. Therefore, the Space Biology Program is implementing a new Summer Program for high-school students that aims to inspire the next generation of scientists to learn about and get involved in space research using GeneLabs Data System. The program consists of three main components core learning modules, focused on developing students knowledge on the Space Biology Program and Space Biology research, Genelab and the data system, and previous research conducted on model organisms in space; networking and team work, enabling students to interact with guest lecturers from local universities and their fellow peers, and also enabling them to visit local universities and genomics centers around the Bay area; and finally an independent learning project, whereby students will be required to form small groups, analyze a dataset on the Genelab platform, generate a hypothesis and develop a research plan to test their hypothesis. This program will not only help inspire high-school students to become involved in space-based research but will also help them develop key critical thinking and bioinformatics skills required for most college degrees and furthermore, will enable them to establish networks with their peers and connections
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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
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Innovation - A view from the Lab
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...
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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.
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A Semi-Open Learning Environment for Mobile Robotics
Directory of Open Access Journals (Sweden)
Enrique Sucar
2007-05-01
Full Text Available We have developed a semi-open learning environment for mobile robotics, to learn through free exploration, but with specific performance criteria that guides the learning process. The environment includes virtual and remote robotics laboratories, and an intelligent virtual assistant the guides the students using the labs. A series of experiments in the virtual and remote labs are designed to gradually learn the basics of mobile robotics. Each experiment considers exploration and performance aspects, which are evaluated by the virtual assistant, giving feedback to the user. The virtual laboratory has been incorporated to a course in mobile robotics and used by a group of students. A preliminary evaluation shows that the intelligent tutor combined with the virtual laboratory can improve the learning process.
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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
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A computational genomics pipeline for prokaryotic sequencing projects.
Kislyuk, Andrey O; Katz, Lee S; Agrawal, Sonia; Hagen, Matthew S; Conley, Andrew B; Jayaraman, Pushkala; Nelakuditi, Viswateja; Humphrey, Jay C; Sammons, Scott A; Govil, Dhwani; Mair, Raydel D; Tatti, Kathleen M; Tondella, Maria L; Harcourt, Brian H; Mayer, Leonard W; Jordan, I King
2010-08-01
New sequencing technologies have accelerated research on prokaryotic genomes and have made genome sequencing operations outside major genome sequencing centers routine. However, no off-the-shelf solution exists for the combined assembly, gene prediction, genome annotation and data presentation necessary to interpret sequencing data. The resulting requirement to invest significant resources into custom informatics support for genome sequencing projects remains a major impediment to the accessibility of high-throughput sequence data. We present a self-contained, automated high-throughput open source genome sequencing and computational genomics pipeline suitable for prokaryotic sequencing projects. The pipeline has been used at the Georgia Institute of Technology and the Centers for Disease Control and Prevention for the analysis of Neisseria meningitidis and Bordetella bronchiseptica genomes. The pipeline is capable of enhanced or manually assisted reference-based assembly using multiple assemblers and modes; gene predictor combining; and functional annotation of genes and gene products. Because every component of the pipeline is executed on a local machine with no need to access resources over the Internet, the pipeline is suitable for projects of a sensitive nature. Annotation of virulence-related features makes the pipeline particularly useful for projects working with pathogenic prokaryotes. The pipeline is licensed under the open-source GNU General Public License and available at the Georgia Tech Neisseria Base (http://nbase.biology.gatech.edu/). The pipeline is implemented with a combination of Perl, Bourne Shell and MySQL and is compatible with Linux and other Unix systems.
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Changes in Urban Youths' Attitude Towards Science and Perception of a Mobile Science Lab Experience
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.
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Experiential Learning of Digital Communication Using LabVIEW
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…
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Public data and open source tools for multi-assay genomic investigation of disease.
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.
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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.
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The Saccharomyces Genome Database Variant Viewer.
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.
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Black, Christopher; Voigts, Jakob; Agrawal, Uday; Ladow, Max; Santoyo, Juan; Moore, Christopher; Jones, Stephanie
2017-06-01
Electroencephalography (EEG) offers a unique opportunity to study human neural activity non-invasively with millisecond resolution using minimal equipment in or outside of a lab setting. EEG can be combined with a number of techniques for closed-loop experiments, where external devices are driven by specific neural signals. However, reliable, commercially available EEG systems are expensive, often making them impractical for individual use and research development. Moreover, by design, a majority of these systems cannot be easily altered to the specification needed by the end user. We focused on mitigating these issues by implementing open-source tools to develop a new EEG platform to drive down research costs and promote collaboration and innovation. Here, we present methods to expand the open-source electrophysiology system, Open Ephys (www.openephys.org), to include human EEG recordings. We describe the equipment and protocol necessary to interface various EEG caps with the Open Ephys acquisition board, and detail methods for processing data. We present applications of Open Ephys + EEG as a research tool and discuss how this innovative EEG technology lays a framework for improved closed-loop paradigms and novel brain-computer interface experiments. The Open Ephys + EEG system can record reliable human EEG data, as well as human EMG data. A side-by-side comparison of eyes closed 8-14 Hz activity between the Open Ephys + EEG system and the Brainvision ActiCHamp EEG system showed similar average power and signal to noise. Open Ephys + EEG enables users to acquire high-quality human EEG data comparable to that of commercially available systems, while maintaining the price point and extensibility inherent to open-source systems.
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Black, Christopher; Voigts, Jakob; Agrawal, Uday; Ladow, Max; Santoyo, Juan; Moore, Christopher; Jones, Stephanie
2017-06-01
Objective. Electroencephalography (EEG) offers a unique opportunity to study human neural activity non-invasively with millisecond resolution using minimal equipment in or outside of a lab setting. EEG can be combined with a number of techniques for closed-loop experiments, where external devices are driven by specific neural signals. However, reliable, commercially available EEG systems are expensive, often making them impractical for individual use and research development. Moreover, by design, a majority of these systems cannot be easily altered to the specification needed by the end user. We focused on mitigating these issues by implementing open-source tools to develop a new EEG platform to drive down research costs and promote collaboration and innovation. Approach. Here, we present methods to expand the open-source electrophysiology system, Open Ephys (www.openephys.org), to include human EEG recordings. We describe the equipment and protocol necessary to interface various EEG caps with the Open Ephys acquisition board, and detail methods for processing data. We present applications of Open Ephys + EEG as a research tool and discuss how this innovative EEG technology lays a framework for improved closed-loop paradigms and novel brain-computer interface experiments. Main results. The Open Ephys + EEG system can record reliable human EEG data, as well as human EMG data. A side-by-side comparison of eyes closed 8-14 Hz activity between the Open Ephys + EEG system and the Brainvision ActiCHamp EEG system showed similar average power and signal to noise. Significance. Open Ephys + EEG enables users to acquire high-quality human EEG data comparable to that of commercially available systems, while maintaining the price point and extensibility inherent to open-source systems.
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Baseball Physics: A New Mechanics Lab
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.
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Genome Variation Map: a data repository of genome variations in BIG Data Center.
Song, Shuhui; Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang; Zhang, Zhang
2018-01-04
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 activities. Unlike existing related databases, GVM features integration of a large number of genome variations for a broad diversity of species including human, cultivated plants and domesticated animals. Specifically, the current implementation of GVM not only houses a total of ∼4.9 billion variants for 19 species including chicken, dog, goat, human, poplar, rice and tomato, but also incorporates 8669 individual genotypes and 13 262 manually curated high-quality genotype-to-phenotype associations for non-human species. In addition, GVM provides friendly intuitive web interfaces for data submission, browse, search and visualization. Collectively, GVM serves as an important resource for archiving genomic variation data, helpful for better understanding population genetic diversity and deciphering complex mechanisms associated with different phenotypes. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.
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Genome Variation Map: a data repository of genome variations in BIG Data Center
Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang
2018-01-01
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 activities. Unlike existing related databases, GVM features integration of a large number of genome variations for a broad diversity of species including human, cultivated plants and domesticated animals. Specifically, the current implementation of GVM not only houses a total of ∼4.9 billion variants for 19 species including chicken, dog, goat, human, poplar, rice and tomato, but also incorporates 8669 individual genotypes and 13 262 manually curated high-quality genotype-to-phenotype associations for non-human species. In addition, GVM provides friendly intuitive web interfaces for data submission, browse, search and visualization. Collectively, GVM serves as an important resource for archiving genomic variation data, helpful for better understanding population genetic diversity and deciphering complex mechanisms associated with different phenotypes. PMID:29069473
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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).
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Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes.
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.
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Hydrogel Beads: The New Slime Lab?
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…
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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...
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Savant Genome Browser 2: visualization and analysis for population-scale genomics.
Fiume, Marc; Smith, Eric J M; Brook, Andrew; Strbenac, Dario; Turner, Brian; Mezlini, Aziz M; Robinson, Mark D; Wodak, Shoshana J; Brudno, Michael
2012-07-01
High-throughput sequencing (HTS) technologies are providing an unprecedented capacity for data generation, and there is a corresponding need for efficient data exploration and analysis capabilities. Although most existing tools for HTS data analysis are developed for either automated (e.g. genotyping) or visualization (e.g. genome browsing) purposes, such tools are most powerful when combined. For example, integration of visualization and computation allows users to iteratively refine their analyses by updating computational parameters within the visual framework in real-time. Here we introduce the second version of the Savant Genome Browser, a standalone program for visual and computational analysis of HTS data. Savant substantially improves upon its predecessor and existing tools by introducing innovative visualization modes and navigation interfaces for several genomic datatypes, and synergizing visual and automated analyses in a way that is powerful yet easy even for non-expert users. We also present a number of plugins that were developed by the Savant Community, which demonstrate the power of integrating visual and automated analyses using Savant. The Savant Genome Browser is freely available (open source) at www.savantbrowser.com.
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Open versus Controlled-Access Data | Office of Cancer Genomics
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
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Clarke, Laura; Fairley, Susan; Zheng-Bradley, Xiangqun; Streeter, Ian; Perry, Emily; Lowy, Ernesto; Tassé, Anne-Marie; Flicek, Paul
2017-01-04
The International Genome Sample Resource (IGSR; http://www.internationalgenome.org) expands in data type and population diversity the resources from the 1000 Genomes Project. IGSR represents the largest open collection of human variation data and provides easy access to these resources. IGSR was established in 2015 to maintain and extend the 1000 Genomes Project data, which has been widely used as a reference set of human variation and by researchers developing analysis methods. IGSR has mapped all of the 1000 Genomes sequence to the newest human reference (GRCh38), and will release updated variant calls to ensure maximal usefulness of the existing data. IGSR is collecting new structural variation data on the 1000 Genomes samples from long read sequencing and other technologies, and will collect relevant functional data into a single comprehensive resource. IGSR is extending coverage with new populations sequenced by collaborating groups. Here, we present the new data and analysis that IGSR has made available. We have also introduced a new data portal that increases discoverability of our data-previously only browseable through our FTP site-by focusing on particular samples, populations or data sets of interest. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.
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GeoLab: A Geological Workstation for Future Missions
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
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Development and design of a late-model fitness test instrument based on LabView
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.
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CERN Technical Training 2006: LabVIEW Course Sessions (September-December 2006)
2006-01-01
The following LabVIEW course sessions are currently scheduled in the framework of the CERN Technical Training Programme 2006, and in collaboration with National Instruments (CH): LabVIEW Basics 1 (course in English): 11-13.9.2006 (3 days, only 3 places available) LabVIEW Basics 2 (course in English): 14-15.9.2006 (2 days) LabVIEW: Working efficiently with LabVIEW 8 (course in English): 18.9.2006 (1 day) **NEW COURSE** LabVIEW Application Development (course in English): 13-15.11.2006 (3 days. Pre-requisite: LabVIEW Basics I ans II, or equivalent experience) LabVIEW Advanced Programming (course in English): 16-17.11.2006 (2 days. Pre-requisite: LabVIEW Application Development, or equivalent experience) LabVIEW Base 1 (course in French): 4-6.12.2006 (3 days, only 1 place available) LabVIEW Base 2 (course in French): 7-8.12.2006 (2 days) If you are interested in attending any of the above course sessions, please discuss with your supervisor and/or your DTO, and apply electronically via EDH from the cour...
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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.
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The catfish genome database cBARBEL: an informatic platform for genome biology of ictalurid catfish.
Lu, Jianguo; Peatman, Eric; Yang, Qing; Wang, Shaolin; Hu, Zhiliang; Reecy, James; Kucuktas, Huseyin; Liu, Zhanjiang
2011-01-01
The catfish genome database, cBARBEL (abbreviated from catfish Breeder And Researcher Bioinformatics Entry Location) is an online open-access database for genome biology of ictalurid catfish (Ictalurus spp.). It serves as a comprehensive, integrative platform for all aspects of catfish genetics, genomics and related data resources. cBARBEL provides BLAST-based, fuzzy and specific search functions, visualization of catfish linkage, physical and integrated maps, a catfish EST contig viewer with SNP information overlay, and GBrowse-based organization of catfish genomic data based on sequence similarity with zebrafish chromosomes. Subsections of the database are tightly related, allowing a user with a sequence or search string of interest to navigate seamlessly from one area to another. As catfish genome sequencing proceeds and ongoing quantitative trait loci (QTL) projects bear fruit, cBARBEL will allow rapid data integration and dissemination within the catfish research community and to interested stakeholders. cBARBEL can be accessed at http://catfishgenome.org.
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ABrowse - a customizable next-generation genome browser framework
Directory of Open Access Journals (Sweden)
Kong Lei
2012-01-01
Full Text Available Abstract Background With the rapid growth of genome sequencing projects, genome browser is becoming indispensable, not only as a visualization system but also as an interactive platform to support open data access and collaborative work. Thus a customizable genome browser framework with rich functions and flexible configuration is needed to facilitate various genome research projects. Results Based on next-generation web technologies, we have developed a general-purpose genome browser framework ABrowse which provides interactive browsing experience, open data access and collaborative work support. By supporting Google-map-like smooth navigation, ABrowse offers end users highly interactive browsing experience. To facilitate further data analysis, multiple data access approaches are supported for external platforms to retrieve data from ABrowse. To promote collaborative work, an online user-space is provided for end users to create, store and share comments, annotations and landmarks. For data providers, ABrowse is highly customizable and configurable. The framework provides a set of utilities to import annotation data conveniently. To build ABrowse on existing annotation databases, data providers could specify SQL statements according to database schema. And customized pages for detailed information display of annotation entries could be easily plugged in. For developers, new drawing strategies could be integrated into ABrowse for new types of annotation data. In addition, standard web service is provided for data retrieval remotely, providing underlying machine-oriented programming interface for open data access. Conclusions ABrowse framework is valuable for end users, data providers and developers by providing rich user functions and flexible customization approaches. The source code is published under GNU Lesser General Public License v3.0 and is accessible at http://www.abrowse.org/. To demonstrate all the features of ABrowse, a live demo for
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ABrowse--a customizable next-generation genome browser framework.
Kong, Lei; Wang, Jun; Zhao, Shuqi; Gu, Xiaocheng; Luo, Jingchu; Gao, Ge
2012-01-05
With the rapid growth of genome sequencing projects, genome browser is becoming indispensable, not only as a visualization system but also as an interactive platform to support open data access and collaborative work. Thus a customizable genome browser framework with rich functions and flexible configuration is needed to facilitate various genome research projects. Based on next-generation web technologies, we have developed a general-purpose genome browser framework ABrowse which provides interactive browsing experience, open data access and collaborative work support. By supporting Google-map-like smooth navigation, ABrowse offers end users highly interactive browsing experience. To facilitate further data analysis, multiple data access approaches are supported for external platforms to retrieve data from ABrowse. To promote collaborative work, an online user-space is provided for end users to create, store and share comments, annotations and landmarks. For data providers, ABrowse is highly customizable and configurable. The framework provides a set of utilities to import annotation data conveniently. To build ABrowse on existing annotation databases, data providers could specify SQL statements according to database schema. And customized pages for detailed information display of annotation entries could be easily plugged in. For developers, new drawing strategies could be integrated into ABrowse for new types of annotation data. In addition, standard web service is provided for data retrieval remotely, providing underlying machine-oriented programming interface for open data access. ABrowse framework is valuable for end users, data providers and developers by providing rich user functions and flexible customization approaches. The source code is published under GNU Lesser General Public License v3.0 and is accessible at http://www.abrowse.org/. To demonstrate all the features of ABrowse, a live demo for Arabidopsis thaliana genome has been built at http://arabidopsis.cbi.edu.cn/.
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ABrowse - a customizable next-generation genome browser framework
2012-01-01
Background With the rapid growth of genome sequencing projects, genome browser is becoming indispensable, not only as a visualization system but also as an interactive platform to support open data access and collaborative work. Thus a customizable genome browser framework with rich functions and flexible configuration is needed to facilitate various genome research projects. Results Based on next-generation web technologies, we have developed a general-purpose genome browser framework ABrowse which provides interactive browsing experience, open data access and collaborative work support. By supporting Google-map-like smooth navigation, ABrowse offers end users highly interactive browsing experience. To facilitate further data analysis, multiple data access approaches are supported for external platforms to retrieve data from ABrowse. To promote collaborative work, an online user-space is provided for end users to create, store and share comments, annotations and landmarks. For data providers, ABrowse is highly customizable and configurable. The framework provides a set of utilities to import annotation data conveniently. To build ABrowse on existing annotation databases, data providers could specify SQL statements according to database schema. And customized pages for detailed information display of annotation entries could be easily plugged in. For developers, new drawing strategies could be integrated into ABrowse for new types of annotation data. In addition, standard web service is provided for data retrieval remotely, providing underlying machine-oriented programming interface for open data access. Conclusions ABrowse framework is valuable for end users, data providers and developers by providing rich user functions and flexible customization approaches. The source code is published under GNU Lesser General Public License v3.0 and is accessible at http://www.abrowse.org/. To demonstrate all the features of ABrowse, a live demo for Arabidopsis thaliana genome
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Tools for open geospatial science
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.
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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.
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Magnetic Viscous Drag for Friction Labs
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…
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Wojtczyk, Martin; Panin, Giorgio; Röder, Thorsten; Lenz, Claus; Nair, Suraj; Heidemann, Rüdiger; Goudar, Chetan; Knoll, Alois
2010-01-01
After utilizing robots for more than 30 years for classic industrial automation applications, service robots form a constantly increasing market, although the big breakthrough is still awaited. Our approach to service robots was driven by the idea of supporting lab personnel in a biotechnology laboratory. After initial development in Germany, a mobile robot platform extended with an industrial manipulator and the necessary sensors for indoor localization and object manipulation, has been shipped to Bayer HealthCare in Berkeley, CA, USA, a global player in the sector of biopharmaceutical products, located in the San Francisco bay area. The determined goal of the mobile manipulator is to support the off-shift staff to carry out completely autonomous or guided, remote controlled lab walkthroughs, which we implement utilizing a recent development of our computer vision group: OpenTL - an integrated framework for model-based visual tracking.
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Automatic creation of LabVIEW network shared variables
International Nuclear Information System (INIS)
Kluge, T.; Schroeder, H.
2012-01-01
We are in the process of preparing the LabVIEW controlled system components of our Solid State Direct Drive experiments for the integration into a Supervisory Control And Data Acquisition (SCADA) or distributed control system. The predetermined route to this is the generation of LabVIEW network shared variables that can easily be exported by LabVIEW to the SCADA system using OLE for Process Control (OPC) or other means. Many repetitive tasks are associated with the creation of the shared variables and the required code. We are introducing an efficient and inexpensive procedure that automatically creates shared variable libraries and sets default values for the shared variables. Furthermore, LabVIEW controls are created that are used for managing the connection to the shared variable inside the LabVIEW code operating on the shared variables. The procedure takes as input an XML spread-sheet defining the required input. The procedure utilizes XSLT and LabVIEW scripting. In a later state of the project the code generation can be expanded to also create code and configuration files that will become necessary in order to access the shared variables from the SCADA system of choice. (authors)
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Microstructural characterization of LaB6-ZrB2 eutectic composites
International Nuclear Information System (INIS)
Wang Shengchang; Wei, W.J.; Zhang Litong
2003-01-01
Detail microstructure of LaB 6 -ZrB 2 composites has been characterized by TEM and HRTEM. The directionally solidified ZrB 2 fibers in LaB 6 matrix near LaB 6 -ZrB 2 eutectics present at least three growing relationship systems. In addition to previous report of [001]LaB 6 / [0001]ZrB 2 relationship, [0 anti 11]LaB 6 / [0001]ZrB 2 and [1 anti 20]LaB 6 / [0001]ZrB 2 . were identified. Different with [001]LaB 6 / [0001]ZrB 2 system, the interfaces of [0 anti 11]LaB 6 / [0001]ZrB 2 and [1 anti 20]LaB 6 / [0001]ZrB 2 . show non-coherent and clean interfaces. There is neither glassy phase nor reaction products found at the interfaces (orig.)
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Functional annotation of the genome unravels probiotic potential of Bacillus coagulans HS243.
Kapse, N G; Engineer, A S; Gowdaman, V; Wagh, S; Dhakephalkar, P K
2018-05-30
Spore forming Bacillus species are widely used as probiotics for human dietary supplements and in animal feeds. However, information on genetic basis of their probiotic action is obscure. Therefore, the present investigation was undertaken to elucidate probiotic traits of B. coagulans HS243 through its genome analysis. Genome mining revealed the presence of an arsenal of marker genes attributed to genuine probiotic traits. In silico analysis of HS243 genome revealed the presence of multi subunit ATPases, ADI pathway genes, chologlycine hydrolase, adhesion proteins for surviving and colonizing harsh gastric transit. HS243 genome harbored vitamin and essential amino acid biosynthetic genes, suggesting the use of HS243 as a nutrient supplement. Bacteriocin producing genes highlighted the disease preventing potential of HS243. Thus, this work established that HS243 possessed the genetic repertoire required for surviving harsh gastric transit and conferring health benefits to the host which were further validated by wet lab evidences. Copyright © 2018. Published by Elsevier Inc.
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HpBase: A genome database of a sea urchin, Hemicentrotus pulcherrimus.
Kinjo, Sonoko; Kiyomoto, Masato; Yamamoto, Takashi; Ikeo, Kazuho; Yaguchi, Shunsuke
2018-04-01
To understand the mystery of life, it is important to accumulate genomic information for various organisms because the whole genome encodes the commands for all the genes. Since the genome of Strongylocentrotus purpratus was sequenced in 2006 as the first sequenced genome in echinoderms, the genomic resources of other North American sea urchins have gradually been accumulated, but no sea urchin genomes are available in other areas, where many scientists have used the local species and reported important results. In this manuscript, we report a draft genome of the sea urchin Hemincentrotus pulcherrimus because this species has a long history as the target of developmental and cell biology in East Asia. The genome of H. pulcherrimus was assembled into 16,251 scaffold sequences with an N50 length of 143 kbp, and approximately 25,000 genes were identified in the genome. The size of the genome and the sequencing coverage were estimated to be approximately 800 Mbp and 100×, respectively. To provide these data and information of annotation, we constructed a database, HpBase (http://cell-innovation.nig.ac.jp/Hpul/). In HpBase, gene searches, genome browsing, and blast searches are available. In addition, HpBase includes the "recipes" for experiments from each lab using H. pulcherrimus. These recipes will continue to be updated according to the circumstances of individual scientists and can be powerful tools for experimental biologists and for the community. HpBase is a suitable dataset for evolutionary, developmental, and cell biologists to compare H. pulcherrimus genomic information with that of other species and to isolate gene information. © 2018 Japanese Society of Developmental Biologists.
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Whole genome amplification - Review of applications and advances
Energy Technology Data Exchange (ETDEWEB)
Hawkins, Trevor L.; Detter, J.C.; Richardson, Paul
2001-11-15
The concept of Whole Genome Amplification is something that has arisen in the past few years as modifications to the polymerase chain reaction (PCR) have been adapted to replicate regions of genomes which are of biological interest. The applications here are many--forensics, embryonic disease diagnosis, bio terrorism genome detection, ''imoralization'' of clinical samples, microbial diversity, and genotyping. The key question is if DNA can be replicated a genome at a time without bias or non random distribution of the target. Several papers published in the last year and currently in preparation may lead to the conclusion that whole genome amplification may indeed be possible and therefore open up a new avenue to molecular biology.
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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.
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Flexible HVAC System for Lab or Classroom.
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)
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The Human Genome Project: big science transforms biology and medicine.
Hood, Leroy; Rowen, Lee
2013-01-01
The Human Genome Project has transformed biology through its integrated big science approach to deciphering a reference human genome sequence along with the complete sequences of key model organisms. The project exemplifies the power, necessity and success of large, integrated, cross-disciplinary efforts - so-called 'big science' - directed towards complex major objectives. In this article, we discuss the ways in which this ambitious endeavor led to the development of novel technologies and analytical tools, and how it brought the expertise of engineers, computer scientists and mathematicians together with biologists. It established an open approach to data sharing and open-source software, thereby making the data resulting from the project accessible to all. The genome sequences of microbes, plants and animals have revolutionized many fields of science, including microbiology, virology, infectious disease and plant biology. Moreover, deeper knowledge of human sequence variation has begun to alter the practice of medicine. The Human Genome Project has inspired subsequent large-scale data acquisition initiatives such as the International HapMap Project, 1000 Genomes, and The Cancer Genome Atlas, as well as the recently announced Human Brain Project and the emerging Human Proteome Project.
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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...
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Assessing Usage and Maximizing Finance Lab Impact: A Case Exploration
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…
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Oenococcus oeni in Chilean Red Wines: Technological and Genomic Characterization
Directory of Open Access Journals (Sweden)
Jaime Romero
2018-02-01
Full Text Available The presence and load of species of LAB at the end of the malolactic fermentation (MLF were investigated in 16 wineries from the different Chilean valleys (Limarí, Casablanca, Maipo, Rapel, and Maule Valleys during 2012 and 2013, using PCR-RFLP and qPCR. Oenococcus oeni was observed in 80% of the samples collected. Dominance of O. oeni was reflected in the bacterial load (O. oeni/total bacteria measured by qPCR, corresponding to >85% in most of the samples. A total of 178 LAB isolates were identified after sequencing molecular markers, 95 of them corresponded to O. oeni. Further genetic analyses were performed using MLST (7 genes including 10 commercial strains; the results indicated that commercial strains were grouped together, while autochthonous strains distributed among different genetic clusters. To pre-select some autochthonous O. oeni, these isolates were also characterized based on technological tests such as ethanol tolerance (12 and 15%, SO2 resistance (0 and 80 mg l−1, and pH (3.1 and 3.6 and malic acid transformation (1.5 and 4 g l−1. For comparison purposes, commercial strain VP41 was also tested. Based on their technological performance, only 3 isolates were selected for further examination (genome analysis and they were able to reduce malic acid concentration, to grow at low pH 3.1, 15% ethanol and 80 mg l−1 SO2. The genome analyses of three selected isolates were examined and compared to PSU-1 and VP41 strains to study their potential contribution to the organoleptic properties of the final product. The presence and homology of genes potentially related to aromatic profile were compared among those strains. The results indicated high conservation of malolactic enzyme (>99% and the absence of some genes related to odor such as phenolic acid decarboxylase, in autochthonous strains. Genomic analysis also revealed that these strains shared 470 genes with VP41 and PSU-1 and that autochthonous strains harbor an interesting
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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
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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.
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Designing virtual science labs for the Islamic Academy of Delaware
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
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Genomics-assisted breeding in fruit trees.
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 plant to assess the marketable product (fruit). In this article, we describe the potential of genomics-assisted breeding, which uses these novel genomics-based approaches, to break through these barriers in conventional fruit tree breeding. We first introduce the molecular marker systems and whole-genome sequence data that are available for fruit tree breeding. Next we introduce the statistical methods for biparental linkage and quantitative trait locus (QTL) mapping as well as GWAS and GS. We then review QTL mapping, GWAS, and GS studies conducted on fruit trees. We also review novel technologies for rapid generation advancement. Finally, we note the future prospects of genomics-assisted fruit tree breeding and problems that need to be overcome in the breeding.
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BGD: a database of bat genomes.
Fang, Jianfei; Wang, Xuan; Mu, Shuo; Zhang, Shuyi; Dong, Dong
2015-01-01
Bats account for ~20% of mammalian species, and are the only mammals with true powered flight. For the sake of their specialized phenotypic traits, many researches have been devoted to examine the evolution of bats. Until now, some whole genome sequences of bats have been assembled and annotated, however, a uniform resource for the annotated bat genomes is still unavailable. To make the extensive data associated with the bat genomes accessible to the general biological communities, we established a Bat Genome Database (BGD). BGD is an open-access, web-available portal that integrates available data of bat genomes and genes. It hosts data from six bat species, including two megabats and four microbats. Users can query the gene annotations using efficient searching engine, and it offers browsable tracks of bat genomes. Furthermore, an easy-to-use phylogenetic analysis tool was also provided to facilitate online phylogeny study of genes. To the best of our knowledge, BGD is the first database of bat genomes. It will extend our understanding of the bat evolution and be advantageous to the bat sequences analysis. BGD is freely available at: http://donglab.ecnu.edu.cn/databases/BatGenome/.
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BGD: a database of bat genomes.
Directory of Open Access Journals (Sweden)
Jianfei Fang
Full Text Available Bats account for ~20% of mammalian species, and are the only mammals with true powered flight. For the sake of their specialized phenotypic traits, many researches have been devoted to examine the evolution of bats. Until now, some whole genome sequences of bats have been assembled and annotated, however, a uniform resource for the annotated bat genomes is still unavailable. To make the extensive data associated with the bat genomes accessible to the general biological communities, we established a Bat Genome Database (BGD. BGD is an open-access, web-available portal that integrates available data of bat genomes and genes. It hosts data from six bat species, including two megabats and four microbats. Users can query the gene annotations using efficient searching engine, and it offers browsable tracks of bat genomes. Furthermore, an easy-to-use phylogenetic analysis tool was also provided to facilitate online phylogeny study of genes. To the best of our knowledge, BGD is the first database of bat genomes. It will extend our understanding of the bat evolution and be advantageous to the bat sequences analysis. BGD is freely available at: http://donglab.ecnu.edu.cn/databases/BatGenome/.
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Directory of Open Access Journals (Sweden)
Gao Hongmei
2011-05-01
Full Text Available Abstract Background Multiple types of assays allow sensitive detection of virus-specific neutralizing antibodies. For example, the extent of antibody neutralization of HIV-1, SIV and SHIV can be measured in the TZM-bl cell line through the degree of luciferase reporter gene expression after infection. In the past, neutralization curves and titers for this standard assay have been calculated using an Excel macro. Updating all instances of such a macro with new techniques can be unwieldy and introduce non-uniformity across multi-lab teams. Using Excel also poses challenges in centrally storing, sharing and associating raw data files and results. Results We present LabKey Server's NAb tool for organizing, analyzing and securely sharing data, files and results for neutralizing antibody (NAb assays, including the luciferase-based TZM-bl NAb assay. The customizable tool supports high-throughput experiments and includes a graphical plate template designer, allowing researchers to quickly adapt calculations to new plate layouts. The tool calculates the percent neutralization for each serum dilution based on luminescence measurements, fits a range of neutralization curves to titration results and uses these curves to estimate the neutralizing antibody titers for benchmark dilutions. Results, curve visualizations and raw data files are stored in a database and shared through a secure, web-based interface. NAb results can be integrated with other data sources based on sample identifiers. It is simple to make results public after publication by updating folder security settings. Conclusions Standardized tools for analyzing, archiving and sharing assay results can improve the reproducibility, comparability and reliability of results obtained across many labs. LabKey Server and its NAb tool are freely available as open source software at http://www.labkey.com under the Apache 2.0 license. Many members of the HIV research community can also access the Lab
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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.
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Stanley, Jacob T.; Su, Weifeng; Lewandowski, H. J.
2017-12-01
We demonstrate how students' use of modeling can be examined and assessed using student notebooks collected from an upper-division electronics lab course. The use of models is a ubiquitous practice in undergraduate physics education, but the process of constructing, testing, and refining these models is much less common. We focus our attention on a lab course that has been transformed to engage students in this modeling process during lab activities. The design of the lab activities was guided by a framework that captures the different components of model-based reasoning, called the Modeling Framework for Experimental Physics. We demonstrate how this framework can be used to assess students' written work and to identify how students' model-based reasoning differed from activity to activity. Broadly speaking, we were able to identify the different steps of students' model-based reasoning and assess the completeness of their reasoning. Varying degrees of scaffolding present across the activities had an impact on how thoroughly students would engage in the full modeling process, with more scaffolded activities resulting in more thorough engagement with the process. Finally, we identified that the step in the process with which students had the most difficulty was the comparison between their interpreted data and their model prediction. Students did not use sufficiently sophisticated criteria in evaluating such comparisons, which had the effect of halting the modeling process. This may indicate that in order to engage students further in using model-based reasoning during lab activities, the instructor needs to provide further scaffolding for how students make these types of experimental comparisons. This is an important design consideration for other such courses attempting to incorporate modeling as a learning goal.
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Cassandra - WP400 - final report of living lab 2
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
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Comunicación USB entre aplicaciones desarrolladas en LabVIEW y microcontroladores de Silicon Labs
Directory of Open Access Journals (Sweden)
Julio César Herrera Benítez
2013-06-01
Full Text Available El presente artículo trata sobre la utilización de LabVIEW para establecer comunicación USB con microcontroladores de la familia 8051 de Silicon Laboratories, utilizando un driver desarrollado por dicha compañía. En el documento se incluye una descripción de este driver, así como de las funciones principales que permiten el manejo del mismo, las cuales se encuentran en una biblioteca de enlace dinámico. El artículo contiene además una metodología básica para el uso de estas funciones y una explicación detallada a través de un ejemplo, donde se ilustra como cargar y configurar las mismas con el ambiente de desarrollo LabVIEW. Finalmente se muestran dos ejemplos de la utilización del driver a partir de una biblioteca de funciones USB creada en LabVIEW para la comunicación con un microcontrolador.
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Federal Laboratory Consortium — To enable Digital Forensics and Computer Security research and educational opportunities across majors and departments. Lab MissionEstablish and maintain a Digital...
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Fabrication and Prototyping Lab
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...
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Open-Source Wax RepRap 3-D Printer for Rapid Prototyping Paper-Based Microfluidics.
Pearce, J M; Anzalone, N C; Heldt, C L
2016-08-01
The open-source release of self-replicating rapid prototypers (RepRaps) has created a rich opportunity for low-cost distributed digital fabrication of complex 3-D objects such as scientific equipment. For example, 3-D printable reactionware devices offer the opportunity to combine open hardware microfluidic handling with lab-on-a-chip reactionware to radically reduce costs and increase the number and complexity of microfluidic applications. To further drive down the cost while improving the performance of lab-on-a-chip paper-based microfluidic prototyping, this study reports on the development of a RepRap upgrade capable of converting a Prusa Mendel RepRap into a wax 3-D printer for paper-based microfluidic applications. An open-source hardware approach is used to demonstrate a 3-D printable upgrade for the 3-D printer, which combines a heated syringe pump with the RepRap/Arduino 3-D control. The bill of materials, designs, basic assembly, and use instructions are provided, along with a completely free and open-source software tool chain. The open-source hardware device described here accelerates the potential of the nascent field of electrochemical detection combined with paper-based microfluidics by dropping the marginal cost of prototyping to nearly zero while accelerating the turnover between paper-based microfluidic designs. © 2016 Society for Laboratory Automation and Screening.
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DEFF Research Database (Denmark)
Miró, Manuel; Hansen, Elo Harald
2007-01-01
The analytical capabilities of the microminiaturised lab-on-a-valve (LOV) module integrated into a microsequential injection (muSI) fluidic system in terms of analytical chemical performance, microfluidic handling and on-line sample processing are compared to those of the micro total analysis...... and the kinetics of the chemical reactions at will, LOV allows accommodation of reactions which, at least at the present stage, are not feasible by application of microfluidic LOC systems. Thus, in LOV one may take advantage of kinetic discriminations schemes, where even subtle differences in reactions...... are utilized for analytical purposes. Furthemore, it is also feasible to handle multi-step sequential reactions of divergent kinetics; to conduct multi-parametric determinations without manifold reconfiguration by utilization of the inherent open architecture of the micromachined unit for the implementation...
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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.
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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)
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LabVIEW Library to EPICS Channel Access
Liyu, Andrei; Thompson, Dave H
2005-01-01
The Spallation Neutron Source (SNS) accelerator systems will deliver a 1.0 GeV, 1.4 MW proton beam to a liquid mercury target for neutron scattering research. The accelerator complex consists of a 1 GeV linear accelerator, an accumulator ring and associated transport lines. The SNS diagnostics platform is PC-based and will run Windows for its OS and LabVIEW as its programming language. Data acquisition hardware will be based on PCI cards. There will be about 300 rack-mounted computers. The Channel Access (CA) protocol of the Experimental Physics and Industrial Control System (EPICS) is the SNS control system communication standard. This paper describes the approaches, implementation, and features of LabVIEW library to CA for Windows, Linux, and Mac OS X. We also discuss how the library implements the asynchronous CA monitor routine using LabVIEW's occurrence mechanism instead of a callback function (which is not available in LabVIEW). The library is used to acquire accelerator data and applications have been ...
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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...
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Approaches for in silico finishing of microbial genome sequences
Directory of Open Access Journals (Sweden)
Frederico Schmitt Kremer
Full Text Available Abstract The introduction of next-generation sequencing (NGS had a significant effect on the availability of genomic information, leading to an increase in the number of sequenced genomes from a large spectrum of organisms. Unfortunately, due to the limitations implied by the short-read sequencing platforms, most of these newly sequenced genomes remained as “drafts”, incomplete representations of the whole genetic content. The previous genome sequencing studies indicated that finishing a genome sequenced by NGS, even bacteria, may require additional sequencing to fill the gaps, making the entire process very expensive. As such, several in silico approaches have been developed to optimize the genome assemblies and facilitate the finishing process. The present review aims to explore some free (open source, in many cases tools that are available to facilitate genome finishing.
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Approaches for in silico finishing of microbial genome sequences.
Kremer, Frederico Schmitt; McBride, Alan John Alexander; Pinto, Luciano da Silva
The introduction of next-generation sequencing (NGS) had a significant effect on the availability of genomic information, leading to an increase in the number of sequenced genomes from a large spectrum of organisms. Unfortunately, due to the limitations implied by the short-read sequencing platforms, most of these newly sequenced genomes remained as "drafts", incomplete representations of the whole genetic content. The previous genome sequencing studies indicated that finishing a genome sequenced by NGS, even bacteria, may require additional sequencing to fill the gaps, making the entire process very expensive. As such, several in silico approaches have been developed to optimize the genome assemblies and facilitate the finishing process. The present review aims to explore some free (open source, in many cases) tools that are available to facilitate genome finishing.
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A comprehensive crop genome research project: the Superhybrid Rice Genome Project in China.
Yu, Jun; Wong, Gane Ka-Shu; Liu, Siqi; Wang, Jian; Yang, Huanming
2007-06-29
In May 2000, the Beijing Institute of Genomics formally announced the launch of a comprehensive crop genome research project on rice genomics, the Chinese Superhybrid Rice Genome Project. SRGP is not simply a sequencing project targeted to a single rice (Oryza sativa L.) genome, but a full-swing research effort with an ultimate goal of providing inclusive basic genomic information and molecular tools not only to understand biology of the rice, both as an important crop species and a model organism of cereals, but also to focus on a popular superhybrid rice landrace, LYP9. We have completed the first phase of SRGP and provide the rice research community with a finished genome sequence of an indica variety, 93-11 (the paternal cultivar of LYP9), together with ample data on subspecific (between subspecies) polymorphisms, transcriptomes and proteomes, useful for within-species comparative studies. In the second phase, we have acquired the genome sequence of the maternal cultivar, PA64S, together with the detailed catalogues of genes uniquely expressed in the parental cultivars and the hybrid as well as allele-specific markers that distinguish parental alleles. Although SRGP in China is not an open-ended research programme, it has been designed to pave a way for future plant genomics research and application, such as to interrogate fundamentals of plant biology, including genome duplication, polyploidy and hybrid vigour, as well as to provide genetic tools for crop breeding and to carry along a social burden-leading a fight against the world's hunger. It began with genomics, the newly developed and industry-scale research field, and from the world's most populous country. In this review, we summarize our scientific goals and noteworthy discoveries that exploit new territories of systematic investigations on basic and applied biology of rice and other major cereal crops.
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Genomic treasure troves: complete genome sequencing of herbarium and insect museum specimens.
Staats, Martijn; Erkens, Roy H J; van de Vossenberg, Bart; Wieringa, Jan J; Kraaijeveld, Ken; Stielow, Benjamin; Geml, József; Richardson, James E; Bakker, Freek T
2013-01-01
Unlocking the vast genomic diversity stored in natural history collections would create unprecedented opportunities for genome-scale evolutionary, phylogenetic, domestication and population genomic studies. Many researchers have been discouraged from using historical specimens in molecular studies because of both generally limited success of DNA extraction and the challenges associated with PCR-amplifying highly degraded DNA. In today's next-generation sequencing (NGS) world, opportunities and prospects for historical DNA have changed dramatically, as most NGS methods are actually designed for taking short fragmented DNA molecules as templates. Here we show that using a standard multiplex and paired-end Illumina sequencing approach, genome-scale sequence data can be generated reliably from dry-preserved plant, fungal and insect specimens collected up to 115 years ago, and with minimal destructive sampling. Using a reference-based assembly approach, we were able to produce the entire nuclear genome of a 43-year-old Arabidopsis thaliana (Brassicaceae) herbarium specimen with high and uniform sequence coverage. Nuclear genome sequences of three fungal specimens of 22-82 years of age (Agaricus bisporus, Laccaria bicolor, Pleurotus ostreatus) were generated with 81.4-97.9% exome coverage. Complete organellar genome sequences were assembled for all specimens. Using de novo assembly we retrieved between 16.2-71.0% of coding sequence regions, and hence remain somewhat cautious about prospects for de novo genome assembly from historical specimens. Non-target sequence contaminations were observed in 2 of our insect museum specimens. We anticipate that future museum genomics projects will perhaps not generate entire genome sequences in all cases (our specimens contained relatively small and low-complexity genomes), but at least generating vital comparative genomic data for testing (phylo)genetic, demographic and genetic hypotheses, that become increasingly more horizontal
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Nakagawa, So; Takahashi, Mahoko Ueda
2016-01-01
In mammals, approximately 10% of genome sequences correspond to endogenous viral elements (EVEs), which are derived from ancient viral infections of germ cells. Although most EVEs have been inactivated, some open reading frames (ORFs) of EVEs obtained functions in the hosts. However, EVE ORFs usually remain unannotated in the genomes, and no databases are available for EVE ORFs. To investigate the function and evolution of EVEs in mammalian genomes, we developed EVE ORF databases for 20 genomes of 19 mammalian species. A total of 736,771 non-overlapping EVE ORFs were identified and archived in a database named gEVE (http://geve.med.u-tokai.ac.jp). The gEVE database provides nucleotide and amino acid sequences, genomic loci and functional annotations of EVE ORFs for all 20 genomes. In analyzing RNA-seq data with the gEVE database, we successfully identified the expressed EVE genes, suggesting that the gEVE database facilitates studies of the genomic analyses of various mammalian species.Database URL: http://geve.med.u-tokai.ac.jp. © The Author(s) 2016. Published by Oxford University Press.
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Design and Deployment of a General Purpose, Open Source LoRa to Wi-Fi Hub and Data Logger
DeBell, T. C.; Udell, C.; Kwon, M.; Selker, J. S.; Lopez Alcala, J. M.
2017-12-01
Methods and technologies facilitating internet connectivity and near-real-time status updates for in site environmental sensor data are of increasing interest in Earth Science. However, Open Source, Do-It-Yourself technologies that enable plug and play functionality for web-connected sensors and devices remain largely inaccessible for typical researchers in our community. The Openly Published Environmental Sensing Lab at Oregon State University (OPEnS Lab) constructed an Open Source 900 MHz Long Range Radio (LoRa) receiver hub with SD card data logger, Ethernet and Wi-Fi shield, and 3D printed enclosure that dynamically uploads transmissions from multiple wirelessly-connected environmental sensing devices. Data transmissions may be received from devices up to 20km away. The hub time-stamps, saves to SD card, and uploads all transmissions to a Google Drive spreadsheet to be accessed in near-real-time by researchers and GeoVisualization applications (such as Arc GIS) for access, visualization, and analysis. This research expands the possibilities of scientific observation of our Earth, transforming the technology, methods, and culture by combining open-source development and cutting edge technology. This poster details our methods and evaluates the application of using 3D printing, Arduino Integrated Development Environment (IDE), Adafruit's Open-Hardware Feather development boards, and the WIZNET5500 Ethernet shield for designing this open-source, general purpose LoRa to Wi-Fi data logger.
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LIDAR Research & Development Lab
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...
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German lab wins linear collider contest
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)
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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.
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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.
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Endogenous viral elements in animal genomes.
Directory of Open Access Journals (Sweden)
Aris Katzourakis
2010-11-01
Full Text Available Integration into the nuclear genome of germ line cells can lead to vertical inheritance of retroviral genes as host alleles. For other viruses, germ line integration has only rarely been documented. Nonetheless, we identified endogenous viral elements (EVEs derived from ten non-retroviral families by systematic in silico screening of animal genomes, including the first endogenous representatives of double-stranded RNA, reverse-transcribing DNA, and segmented RNA viruses, and the first endogenous DNA viruses in mammalian genomes. Phylogenetic and genomic analysis of EVEs across multiple host species revealed novel information about the origin and evolution of diverse virus groups. Furthermore, several of the elements identified here encode intact open reading frames or are expressed as mRNA. For one element in the primate lineage, we provide statistically robust evidence for exaptation. Our findings establish that genetic material derived from all known viral genome types and replication strategies can enter the animal germ line, greatly broadening the scope of paleovirological studies and indicating a more significant evolutionary role for gene flow from virus to animal genomes than has previously been recognized.
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Human genomics projects and precision medicine.
Carrasco-Ramiro, F; Peiró-Pastor, R; Aguado, B
2017-09-01
The completion of the Human Genome Project (HGP) in 2001 opened the floodgates to a deeper understanding of medicine. There are dozens of HGP-like projects which involve from a few tens to several million genomes currently in progress, which vary from having specialized goals or a more general approach. However, data generation, storage, management and analysis in public and private cloud computing platforms have raised concerns about privacy and security. The knowledge gained from further research has changed the field of genomics and is now slowly permeating into clinical medicine. The new precision (personalized) medicine, where genome sequencing and data analysis are essential components, allows tailored diagnosis and treatment according to the information from the patient's own genome and specific environmental factors. P4 (predictive, preventive, personalized and participatory) medicine is introducing new concepts, challenges and opportunities. This review summarizes current sequencing technologies, concentrates on ongoing human genomics projects, and provides some examples in which precision medicine has already demonstrated clinical impact in diagnosis and/or treatment.
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CERN Technical Training 2006: LabVIEW Course Sessions (September-December 2006)
2006-01-01
The following LabVIEW course sessions are currently scheduled in the framework of the CERN Technical Training Programme 2006, and in collaboration with National Instruments (CH): LabVIEW Basics 1 (course in English): 11-13.9.2006 (3 days, only 3 places available) (course in English): 14-15.9.2006 (2 days) LabVIEW: Working efficiently with LabVIEW 8 (course in English): 18.9.2006 (1 day) **NEW COURSE** LabVIEW Application Development (course in English): 13-15.11.2006 (3 days. Pre-requisite: LabVIEW Basics I ans II, or equivalent experience) LabVIEW Advanced Programming (course in English): 16-17.11.2006 (2 days. Pre-requisite: LabVIEW Application Development, or equivalent experience) LabVIEW Base 1 (course in French): 4-6.12.2006 (3 days, only 1 place available) LabVIEW Base 2 (course in French): 7-8.12.2006 (2 days) If you are interested in attending any of the above course sessions, please discuss with your supervisor and/or your DTO,...
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{OpenLabNotes} -- An Electronic Laboratory Notebook Extension for {OpenLabFramework}
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...
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Book Swap Now Open to All Employees | Poster
Not only did the year 2000 mark the start of a new millennium, the beginning of the Human Genome Project, and the opening of the International Space Station, but it was also the first year that the Scientific Library held its annual Book & Media Swap. Starting Nov. 12, the 15th annual Book Swap is open to all NCI at Frederick employees.
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Smartphones as pocketable labs: Visions for mobile brain imaging and neurofeedback
DEFF Research Database (Denmark)
Stopczynski, Arkadiusz; Stahlhut, Carsten; Petersen, Michael Kai
2014-01-01
Mobile brain imaging solutions, such as the Smartphone Brain Scanner, which combines low cost wireless EEG sensors with open source software for real-time neuroimaging, may transform neuroscience experimental paradigms. Normally subject to the physical constraints in labs, neuroscience experimental...... paradigms can be transformed into dynamic environments allowing for the capturing of brain signals in everyday contexts. Using smartphones or tablets to access text or images may enable experimental design capable of tracing emotional responses when shopping or consuming media, incorporating sensorimotor...... the Smartphone Brain Scanner, complemented by 3D reconstruction or source separation techniques may support a range of neuroimaging applications and thus become a valuable addition to high-end neuroimaging solutions....
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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
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Optimization of genome engineering approaches with the CRISPR/Cas9 system
DEFF Research Database (Denmark)
Li, Kai; Wang, Gang; Andersen, Troels
2014-01-01
Designer nucleases such as TALENS and Cas9 have opened new opportunities to scarlessly edit the mammalian genome. Here we explored several parameters that influence Cas9-mediated scarless genome editing efficiency in murine embryonic stem cells. Optimization of transfection conditions and enrichi...
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The value of new genome references.
Worley, Kim C; Richards, Stephen; Rogers, Jeffrey
2017-09-15
Genomic information has become a ubiquitous and almost essential aspect of biological research. Over the last 10-15 years, the cost of generating sequence data from DNA or RNA samples has dramatically declined and our ability to interpret those data increased just as remarkably. Although it is still possible for biologists to conduct interesting and valuable research on species for which genomic data are not available, the impact of having access to a high quality whole genome reference assembly for a given species is nothing short of transformational. Research on a species for which we have no DNA or RNA sequence data is restricted in fundamental ways. In contrast, even access to an initial draft quality genome (see below for definitions) opens a wide range of opportunities that are simply not available without that reference genome assembly. Although a complete discussion of the impact of genome sequencing and assembly is beyond the scope of this short paper, the goal of this review is to summarize the most common and highest impact contributions that whole genome sequencing and assembly has had on comparative and evolutionary biology. Copyright © 2016. Published by Elsevier Inc.
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Privacy preserving processing of genomic data: A survey.
Akgün, Mete; Bayrak, A Osman; Ozer, Bugra; Sağıroğlu, M Şamil
2015-08-01
Recently, the rapid advance in genome sequencing technology has led to production of huge amount of sensitive genomic data. However, a serious privacy challenge is confronted with increasing number of genetic tests as genomic data is the ultimate source of identity for humans. Lately, privacy threats and possible solutions regarding the undesired access to genomic data are discussed, however it is challenging to apply proposed solutions to real life problems due to the complex nature of security definitions. In this review, we have categorized pre-existing problems and corresponding solutions in more understandable and convenient way. Additionally, we have also included open privacy problems coming with each genomic data processing procedure. We believe our classification of genome associated privacy problems will pave the way for linking of real-life problems with previously proposed methods. Copyright © 2015 Elsevier Inc. All rights reserved.
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Gramene database: Navigating plant comparative genomics resources
Directory of Open Access Journals (Sweden)
Parul Gupta
2016-11-01
Full Text Available Gramene (http://www.gramene.org is an online, open source, curated resource for plant comparative genomics and pathway analysis designed to support researchers working in plant genomics, breeding, evolutionary biology, system biology, and metabolic engineering. It exploits phylogenetic relationships to enrich the annotation of genomic data and provides tools to perform powerful comparative analyses across a wide spectrum of plant species. It consists of an integrated portal for querying, visualizing and analyzing data for 44 plant reference genomes, genetic variation data sets for 12 species, expression data for 16 species, curated rice pathways and orthology-based pathway projections for 66 plant species including various crops. Here we briefly describe the functions and uses of the Gramene database.
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Reference-based pricing: an evidence-based solution for lab services shopping.
Melton, L Doug; Bradley, Kent; Fu, Patricia Lin; Armata, Raegan; Parr, James B
2014-01-01
To determine the effect of reference-based pricing (RBP) on the percentage of lab services utilized by members that were at or below the reference price. Retrospective, quasi-experimental, matched, case-control pilot evaluation of an RBP benefit for lab services. The study group included employees of a multinational grocery chain covered by a national health insurance carrier and subject to RBP for lab services; it had access to an online lab shopping tool and was informed about the RBP benefit through employer communications. The reference group was covered by the same insurance carrier but not subject to RBP. The primary end point was lab compliance, defined as the percentage of lab claims with total charges at or below the reference price. Difference-in-difference regression estimation evaluated changes in lab compliance between the 2 groups. Higher compliance per lab claim was evident for the study group compared with the reference group (69% vs 57%; Ponline shopping tool was used by 7% of the matched-adjusted study group prior to obtaining lab services. Lab compliance was 76% for study group members using the online tool compared with 68% among nonusers who were subject to RBP (P<.01). RBP can promote cost-conscious selection of lab services. Access to facilities that offer services below the reference price and education about RBP improve compliance. Evaluation of the effect of RBP on higher-cost medical services, including radiology, outpatient specialty, and elective inpatient procedures, is needed.
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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.
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A Well-Maintained Lab Is a Safer Lab. Safety Spotlight
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…
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MatLab Programming for Engineers Having No Formal Programming Knowledge
Shaykhian, Linda H.; Shaykhian, Gholam Ali
2007-01-01
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. Also, stated are the current limitations of the MatLab, which possibly can be taken care of by Mathworks Inc. in a future version to make MatLab more versatile.
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eComLab: remote laboratory platform
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.
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Draft genome sequence of Xylella fastidiosa pear leaf scorch strain in Taiwan
The draft genome sequence of Xylella fastidiosa pear leaf scorch strain (PLS229) isolated from pear cultivar Hengshan (Pyrus pyrifolia) in Taiwan is reported. The bacterium has a genome size of 2,733,013 bp with a G+C content of 53.1%. The PLS229 strain genome was annotated to have 3,259 open readin...
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The minimum information about a genome sequence (MIGS) specification
DEFF Research Database (Denmark)
Field, D; Garrity, G; Gray, T
2008-01-01
With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the...... that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases....... the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium (GSC). Here, we introduce the minimum information about a genome sequence (MIGS) specification with the intent of promoting participation in its development and discussing the resources...
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Technology Roadmap: Lab-on-a-Chip
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...
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Nanopuller-open data acquisition platform for AFM force spectroscopy experiments
International Nuclear Information System (INIS)
Pawlak, Konrad; Strzelecki, Janusz
2016-01-01
Atomic Force Microscope (AFM) is a widely used tool in force spectroscopy studies. Presently, this instrument is accessible from numerous vendors, albeit commercial solutions are expensive and almost always hardware and software closed. Approaches for open setups were published, as with modern low cost and readily available piezoelectric actuators, data acquisition interfaces and optoelectronic components building such force spectroscopy AFM is relatively easy. However, suitable software to control such laboratory made instrument was not released. Developing it in the lab requires significant time and effort. Our Nanopuller software described in this paper is intended to eliminate this obstacle. With only minimum adjustments this program can be used to control and acquire data with any suitable National Instruments universal digital/analog interface and piezoelectric actuator analog controller, giving significant freedom and flexibility in designing force spectroscopy experiment. Since the full code, written in a graphical LabVIEW environment is available, our Nanopuller can be easily customized. In this paper we describe the program and test its performance in controlling different setups. Successful and accurate force curve acquisition for standard samples (single molecules of I27O reference titin polyprotein and DNA as well as red blood cells) is shown. - Highlights: • We created open data acquisition software for performing Atomic Force Microscopy force measurements with custom laboratory made setups. • The software allows large flexibility in atomic force microscope design with minimum adjustment necessary. • The software is written in LabVIEW, allowing easy customization. • We successfully tested the program on two different hardware configurations by stretching single macromolecules and indenting cells.
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Nanopuller-open data acquisition platform for AFM force spectroscopy experiments
Energy Technology Data Exchange (ETDEWEB)
Pawlak, Konrad; Strzelecki, Janusz
2016-05-15
Atomic Force Microscope (AFM) is a widely used tool in force spectroscopy studies. Presently, this instrument is accessible from numerous vendors, albeit commercial solutions are expensive and almost always hardware and software closed. Approaches for open setups were published, as with modern low cost and readily available piezoelectric actuators, data acquisition interfaces and optoelectronic components building such force spectroscopy AFM is relatively easy. However, suitable software to control such laboratory made instrument was not released. Developing it in the lab requires significant time and effort. Our Nanopuller software described in this paper is intended to eliminate this obstacle. With only minimum adjustments this program can be used to control and acquire data with any suitable National Instruments universal digital/analog interface and piezoelectric actuator analog controller, giving significant freedom and flexibility in designing force spectroscopy experiment. Since the full code, written in a graphical LabVIEW environment is available, our Nanopuller can be easily customized. In this paper we describe the program and test its performance in controlling different setups. Successful and accurate force curve acquisition for standard samples (single molecules of I27O reference titin polyprotein and DNA as well as red blood cells) is shown. - Highlights: • We created open data acquisition software for performing Atomic Force Microscopy force measurements with custom laboratory made setups. • The software allows large flexibility in atomic force microscope design with minimum adjustment necessary. • The software is written in LabVIEW, allowing easy customization. • We successfully tested the program on two different hardware configurations by stretching single macromolecules and indenting cells.
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Theory of microbial genome evolution
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.
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LXI Technologies for Remote Labs: An Extension of the VISIR Project
Jaime Irurzun; Olga Dziabenko; Pablo Orduña; Diego Lopez-de-Ipiña; Ignacio Angulo; Javier García-Zubia; Unai Hernandez-Jayo
2010-01-01
Several remote labs to support analog circuits are presented in this work. They are analyzed from the software and the hardware point of view. VISIR remote lab is one of these labs. After this analysis, a new VISIR remote lab approach is presented. This extension of the VISIR project is based on LXI technologies with the aim of becoming it in a remote lab easily interchangeable with other instruments. The addition of new components and experiments is also easier and cheaper.
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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/.
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Reducing unnecessary lab testing in the ICU with artificial intelligence.
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
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Reducing unnecessary lab testing in the ICU with artificial intelligence
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
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Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines
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
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Genomic comparison of closely related Giant Viruses supports an accordion-like model of evolution
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...
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Overview of RepLab 2012: Evaluating Online Reputation Management Systems
Amigó, E.; Corujo, A.; Gonzalo, J.; Meij, E.; de Rijke, M.
2012-01-01
This paper summarizes the goals, organization and results of the first RepLab competitive evaluation campaign for Online Reputation Management Systems (RepLab 2012). RepLab focused on the reputation of companies, and asked participant systems to annotate different types of information on tweets
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LXI Technologies for Remote Labs: An Extension of the VISIR Project
Directory of Open Access Journals (Sweden)
Jaime Irurzun
2010-09-01
Full Text Available Several remote labs to support analog circuits are presented in this work. They are analyzed from the software and the hardware point of view. VISIR remote lab is one of these labs. After this analysis, a new VISIR remote lab approach is presented. This extension of the VISIR project is based on LXI technologies with the aim of becoming it in a remote lab easily interchangeable with other instruments. The addition of new components and experiments is also easier and cheaper.
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Integrating Multiple On-line Knowledge Bases for Disease-Lab Test Relation Extraction.
Zhang, Yaoyun; Soysal, Ergin; Moon, Sungrim; Wang, Jingqi; Tao, Cui; Xu, Hua
2015-01-01
A computable knowledge base containing relations between diseases and lab tests would be a great resource for many biomedical informatics applications. This paper describes our initial step towards establishing a comprehensive knowledge base of disease and lab tests relations utilizing three public on-line resources. LabTestsOnline, MedlinePlus and Wikipedia are integrated to create a freely available, computable disease-lab test knowledgebase. Disease and lab test concepts are identified using MetaMap and relations between diseases and lab tests are determined based on source-specific rules. Experimental results demonstrate a high precision for relation extraction, with Wikipedia achieving the highest precision of 87%. Combining the three sources reached a recall of 51.40%, when compared with a subset of disease-lab test relations extracted from a reference book. Moreover, we found additional disease-lab test relations from on-line resources, indicating they are complementary to existing reference books for building a comprehensive disease and lab test relation knowledge base.
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Transcription as a Threat to Genome Integrity.
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.
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The experiment editor: supporting inquiry-based learning with virtual labs
Galan, D.; Heradio, R.; de la Torre, L.; Dormido, S.; Esquembre, F.
2017-05-01
Inquiry-based learning is a pedagogical approach where students are motivated to pose their own questions when facing problems or scenarios. In physics learning, students are turned into scientists who carry out experiments, collect and analyze data, formulate and evaluate hypotheses, and so on. Lab experimentation is essential for inquiry-based learning, yet there is a drawback with traditional hands-on labs in the high costs associated with equipment, space, and maintenance staff. Virtual laboratories are helpful to reduce these costs. This paper enriches the virtual lab ecosystem by providing an integrated environment to automate experimentation tasks. In particular, our environment supports: (i) scripting and running experiments on virtual labs, and (ii) collecting and analyzing data from the experiments. The current implementation of our environment supports virtual labs created with the authoring tool Easy Java/Javascript Simulations. Since there are public repositories with hundreds of freely available labs created with this tool, the potential applicability to our environment is considerable.
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Energy Technology Data Exchange (ETDEWEB)
Denis, V.
2009-07-01
This is issue Nr. 5 of the news bulletin of MHyLab, the small-scale hydraulic laboratory in Montcherand, Switzerland. The history of MHyLab development is recalled. The objective of the laboratory is given: the laboratory development of efficient and reliable turbines for the entire small-scale hydraulic range (power: 10 to 2000 kW, flow rate: 0.01 to 10 m{sup 3}/s, hydraulic head: 1 m up to more than 700 m). The first period (1997-2001) was devoted to Pelton turbines for high heads (60 to 70 m) and the second (2001-2009) to Kaplan turbines for low and very low heads (1 to 30 m). In the third period (beginning 2008) diagonal turbines for medium heads (25 to 100 m) are being developed. MHyLab designed, modelled and tested all these different types. The small-scale hydraulic market developed unexpectedly quickly. The potential of small-scale hydraulics in the Canton of Vaud, western Switzerland is presented. Three implemented projects are reported on as examples for MHyLab activities on the market place. The MHyLab staff is presented.
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A Case Study of a High School Fab Lab
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.
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Application of LabVIEW on Ionization Chamber to Measurement Radiation
International Nuclear Information System (INIS)
Kerdchockchai, P.; Soodprasert, T.; Hoonnivathana, E.; Naemchnthara, P.; Limsuwan, P.; Naemchanthara, K.
2014-01-01
The purpose of this research was to apply LabVIEW program to control an ionization chamber. LabVIEW was used to compose a block diagram and front panel. The block diagram was programmed to be controlled by the front panel. Radiation dose of Cs -137 at 1.00, 1.50, 2.00, 2.50, 3.00 and 4.00 meter were compared from LabViEW and manual system. The results show that the different percentages of Pb filter of thickness 0, 20 and 39 mm are 0.68, 0.68 and 0.48, respectively. This experiment results indicated that the LabVIEW can be used in assisting radiation measurement. Furthermore, by controlling the ionization chamber by LabVIEW, the radiation dose received by operator is reduced.
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A Low-Cost Remote Lab for Internet Services Distance Education
Directory of Open Access Journals (Sweden)
James Sissom
2006-08-01
Full Text Available Academic departments seeking to reach students via distance education course offerings find that some on-line curricula require a traditional hands-on lab model for student evaluation and assessment. The authors solve the problem of providing distance education curriculum and supporting instruction lab components by using a low-cost remote lab. The remote lab is used to evaluate student performance in managing web services and website development, solving security problems, patch management, scripting and web server management. In addition, the authors discuss assessment and evaluation techniques that will be used to determine instructional quality and student performance. Discussed are the remote lab architecture, use of disk images and utilization of Windows 2003 Internet Information Service, and Linux Red Hat 9.0 platforms.
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The History of Science and Technology at Bell Labs
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.
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The minimum information about a genome sequence (MIGS) specification
Field, Dawn; Garrity, George; Gray, Tanya; Morrison, Norman; Selengut, Jeremy; Sterk, Peter; Tatusova, Tatiana; Thomson, Nicholas; Allen, Michael J; Angiuoli, Samuel V; Ashburner, Michael; Axelrod, Nelson; Baldauf, Sandra; Ballard, Stuart; Boore, Jeffrey; Cochrane, Guy; Cole, James; Dawyndt, Peter; De Vos, Paul; dePamphilis, Claude; Edwards, Robert; Faruque, Nadeem; Feldman, Robert; Gilbert, Jack; Gilna, Paul; Glöckner, Frank Oliver; Goldstein, Philip; Guralnick, Robert; Haft, Dan; Hancock, David; Hermjakob, Henning; Hertz-Fowler, Christiane; Hugenholtz, Phil; Joint, Ian; Kagan, Leonid; Kane, Matthew; Kennedy, Jessie; Kowalchuk, George; Kottmann, Renzo; Kolker, Eugene; Kravitz, Saul; Kyrpides, Nikos; Leebens-Mack, Jim; Lewis, Suzanna E; Li, Kelvin; Lister, Allyson L; Lord, Phillip; Maltsev, Natalia; Markowitz, Victor; Martiny, Jennifer; Methe, Barbara; Mizrachi, Ilene; Moxon, Richard; Nelson, Karen; Parkhill, Julian; Proctor, Lita; White, Owen; Sansone, Susanna-Assunta; Spiers, Andrew; Stevens, Robert; Swift, Paul; Taylor, Chris; Tateno, Yoshio; Tett, Adrian; Turner, Sarah; Ussery, David; Vaughan, Bob; Ward, Naomi; Whetzel, Trish; Gil, Ingio San; Wilson, Gareth; Wipat, Anil
2008-01-01
With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium (GSC). Here, we introduce the minimum information about a genome sequence (MIGS) specification with the intent of promoting participation in its development and discussing the resources that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the GSC also supports improving the ‘transparency’ of the information contained in existing genomic databases. PMID:18464787
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Vanwonterghem, Inka; Jensen, Paul D; Rabaey, Korneel; Tyson, Gene W
2016-09-01
Our understanding of the complex interconnected processes performed by microbial communities is hindered by our inability to culture the vast majority of microorganisms. Metagenomics provides a way to bypass this cultivation bottleneck and recent advances in this field now allow us to recover a growing number of genomes representing previously uncultured populations from increasingly complex environments. In this study, a temporal genome-centric metagenomic analysis was performed of lab-scale anaerobic digesters that host complex microbial communities fulfilling a series of interlinked metabolic processes to enable the conversion of cellulose to methane. In total, 101 population genomes that were moderate to near-complete were recovered based primarily on differential coverage binning. These populations span 19 phyla, represent mostly novel species and expand the genomic coverage of several rare phyla. Classification into functional guilds based on their metabolic potential revealed metabolic networks with a high level of functional redundancy as well as niche specialization, and allowed us to identify potential roles such as hydrolytic specialists for several rare, uncultured populations. Genome-centric analyses of complex microbial communities across diverse environments provide the key to understanding the phylogenetic and metabolic diversity of these interactive communities. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.
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2011-01-01
Background Angiosperm mitochondrial genomes are more complex than those of other organisms. Analyses of the mitochondrial genome sequences of at least 11 angiosperm species have showed several common properties; these cannot easily explain, however, how the diverse mitotypes evolved within each genus or species. We analyzed the evolutionary relationships of Brassica mitotypes by sequencing. Results We sequenced the mitotypes of cam (Brassica rapa), ole (B. oleracea), jun (B. juncea), and car (B. carinata) and analyzed them together with two previously sequenced mitotypes of B. napus (pol and nap). The sizes of whole single circular genomes of cam, jun, ole, and car are 219,747 bp, 219,766 bp, 360,271 bp, and 232,241 bp, respectively. The mitochondrial genome of ole is largest as a resulting of the duplication of a 141.8 kb segment. The jun mitotype is the result of an inherited cam mitotype, and pol is also derived from the cam mitotype with evolutionary modifications. Genes with known functions are conserved in all mitotypes, but clear variation in open reading frames (ORFs) with unknown functions among the six mitotypes was observed. Sequence relationship analysis showed that there has been genome compaction and inheritance in the course of Brassica mitotype evolution. Conclusions We have sequenced four Brassica mitotypes, compared six Brassica mitotypes and suggested a mechanism for mitochondrial genome formation in Brassica, including evolutionary events such as inheritance, duplication, rearrangement, genome compaction, and mutation. PMID:21988783
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Time Trials--An AP Physics Challenge Lab
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…
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Characterization of the North American beaver (Castor canadensis) papillomavirus genome.
Rogovskyy, Artem S; Chen, Zigui; Burk, Robert D; Bankhead, Troy
2014-01-10
The papillomaviruses comprise a large group of viruses that cause proliferations of the stratified squamous epithelium of skin and mucosa in a variety of animals. An earlier report identified a novel papillomavirus of the North American beaver, Castor canadensis (CcanPV1) that was associated with cutaneous exophytic lesions. In the current study, we determined the sequence of the complete 7435 basepair genome of CcanPV1. The genome contains an Upstream Regulatory Region located between the end of L1 and the start of E6, and seven canonical papillomavirus open reading frames encoding five early (E6, E7, E1, E2, and E4) and two late (L2 and L1) proteins. No E5 open reading frame was detected. Phylogenetic analysis of the CcanPV1 genome places the virus between the genera Kappapapillomavirus and Mupapillomavirus. Analyses of the papillomavirus genomes detected in different species of the order Rodentia indicate these viruses do not form a monophyletic clade. Copyright © 2013 Elsevier B.V. All rights reserved.
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Wang, Qingguo; Jia, Peilin; Zhao, Zhongming
2015-01-01
Fueled by widespread applications of high-throughput next generation sequencing (NGS) technologies and urgent need to counter threats of pathogenic viruses, large-scale studies were conducted recently to investigate virus integration in host genomes (for example, human tumor genomes) that may cause carcinogenesis or other diseases. A limiting factor in these studies, however, is rapid virus evolution and resulting polymorphisms, which prevent reads from aligning readily to commonly used virus reference genomes, and, accordingly, make virus integration sites difficult to detect. Another confounding factor is host genomic instability as a result of virus insertions. To tackle these challenges and improve our capability to identify cryptic virus-host fusions, we present a new approach that detects Virus intEgration sites through iterative Reference SEquence customization (VERSE). To the best of our knowledge, VERSE is the first approach to improve detection through customizing reference genomes. Using 19 human tumors and cancer cell lines as test data, we demonstrated that VERSE substantially enhanced the sensitivity of virus integration site detection. VERSE is implemented in the open source package VirusFinder 2 that is available at http://bioinfo.mc.vanderbilt.edu/VirusFinder/.
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Genomic Diversity and Evolution of the Fish Pathogen Flavobacterium psychrophilum
DEFF Research Database (Denmark)
Duchaud, Eric; Rochat, Tatiana; Habib, Christophe
2018-01-01
genome accounting for similar to 80% of the genes in each genome. The pan-genome seems nevertheless "open" according to the scaling exponent of a power-law fitted on the rate of new gene discovery when genomes are added one-by-one. Recombination is a key component of the evolutionary process...... of recombination and mutations to nucleotide-level differentiation (r/m) was estimated to similar to 13. Within CC-ST10, evolutionary distances computed on non-recombined regions and comparisons between 22 isolates sampled up to 27 years apart suggest a most recent common ancestor in the second half...
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European labs brace for German cuts: international collaboration
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.
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Can Graduate Teaching Assistants Teach Inquiry-Based Geology Labs Effectively?
Ryker, Katherine; McConnell, David
2014-01-01
This study examines the implementation of teaching strategies by graduate teaching assistants (GTAs) in inquiry-based introductory geology labs at a large research university. We assess the degree of inquiry present in each Physical Geology lab and compare and contrast the instructional practices of new and experienced GTAs teaching these labs. We…
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Constructing the Components of a Lab Report Using Peer Review
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…
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Genome Editing in Sugarcane: Challenges ahead
Directory of Open Access Journals (Sweden)
Chakravarthi Mohan
2016-10-01
Full Text Available Genome editing opens new and unique opportunities for researchers to enhance crop production. Until 2013, the zinc finger nucleases (ZFNs and transcription activator-like effector nucleases (TALENs were the key tools used for genome editing applications. The advent of RNA-guided engineered nucleases - the type II clustered regularly interspaced short palindromic repeat (CRISPR/Cas9 (CRISPR-associated system from Streptococcus pyogenes holds great potential since it is simple, effective and more versatile than ZFNs and TALENs. CRISPR/Cas9 system has already been successfully employed in several crop plants. Use of these techniques is in its infant stage in sugarcane. Jung and Altpeter (2016 have reported TALEN mediated approach for the first time to reduce lignin content in sugarcane to make it amenable for biofuel production. This is so far the only report describing genome editing in sugarcane. Large genome size, polyploidy, low transformation efficiency, transgene silencing and lack of high throughput screening techniques are certainly great challenges for genome editing in sugarcane which would be discussed in detail in this review.
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Khrustalev, Vladislav Victorovich; Ermalovich, Marina Anatolyevna; Hübschen, Judith M; Khrustaleva, Tatyana Aleksandrovna
2017-12-21
In this study we used non-overlapping parts of the two long open reading frames coding for nonstructural (NS) and capsid (VP) proteins of all available sequences of the Parvovirus B19 subgenotype 1a genome and found out that the rates of A to G, C to T and A to T mutations are higher in the first long reading frame (NS) of the virus than in the second one (VP). This difference in mutational pressure directions for two parts of the same viral genome can be explained by the fact of transcription of just the first long reading frame during the lifelong latency in nonerythroid cells. Adenine deamination (producing A to G and A to T mutations) and cytosine deamination (producing C to T mutations) occur more frequently in transcriptional bubbles formed by DNA "plus" strand of the first open reading frame. These mutations can be inherited only in case of reactivation of the infectious virus due to the help of Adenovirus that allows latent Parvovirus B19 to start transcription of the second reading frame and then to replicate its genome by the rolling circle mechanism using the specific origin. Results of this study provide evidence that the genomes reactivated from latency make significant contributions to the variability of Parvovirus B19. Copyright © 2017 Elsevier Ltd. All rights reserved.
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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.
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Optimization Strategies for Responsivity Control of Microgel Assisted Lab-On-Fiber Optrodes
Directory of Open Access Journals (Sweden)
Martino Giaquinto
2018-04-01
Full Text Available Integrating multi-responsive polymers such as microgels onto optical fiber tips, in a controlled fashion, enables unprecedented functionalities to Lab-on-fiber optrodes. The creation of a uniform microgel monolayer with a specific coverage factor is crucial for enhancing the probes responsivity to a pre-defined target parameter. Here we report a reliable fabrication strategy, based on the dip coating technique, for the controlled realization of microgel monolayer onto unconventional substrates, such as the optical fiber tip. The latter was previously covered by a plasmonic nanostructure to make it sensitive to superficial environment changes. Microgels have been prepared using specific Poly(N-isopropylacrylamide-based monomers that enable bulky size changes in response to both temperature and pH variations. The formation of the microgel monolayer is efficiently controlled through the selection of suitable operating pH, temperature and concentration of particle dispersions used during the dipping procedure. The effect of each parameter has been evaluated, and the validity of our procedure is confirmed by means of both morphological and optical characterizations. We demonstrate that when the coverage factor exceeds 90%, the probe responsivity to microgels swelling/collapsing is significantly improved. Our study opens new paradigms for the development of engineered microgels assisted Lab-on-Fiber probes for biochemical applications.
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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
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A LabVIEWTM-based detector testing system
International Nuclear Information System (INIS)
Yang Haori; Li Yuanjing; Wang Yi; Li Yulan; Li Jin
2003-01-01
The construction of a LabVIEW-based detector testing system is described in this paper. In this system, the signal of detector is magnified and digitized, so amplitude or time spectrum can be obtained. The Analog-to-Digital Converter is a peak-sensitive ADC based on VME bus. The virtual instrument constructed by LabVIEW can be used to acquire data, draw spectrum and save testing results
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Directory of Open Access Journals (Sweden)
Sun Meisheng
2006-08-01
Full Text Available Abstract Background Compelling evidence indicates that Shigella species, the etiologic agents of bacillary dysentery, as well as enteroinvasive Escherichia coli, are derived from multiple origins of Escherichia coli and form a single pathovar. To further understand the genome diversity and virulence evolution of Shigella, comparative genomic hybridization microarray analysis was employed to compare the gene content of E. coli K-12 with those of 43 Shigella strains from all lineages. Results For the 43 strains subjected to CGH microarray analyses, the common backbone of the Shigella genome was estimated to contain more than 1,900 open reading frames (ORFs, with a mean number of 726 undetectable ORFs. The mosaic distribution of absent regions indicated that insertions and/or deletions have led to the highly diversified genomes of pathogenic strains. Conclusion These results support the hypothesis that by gain and loss of functions, Shigella species became successful human pathogens through convergent evolution from diverse genomic backgrounds. Moreover, we also found many specific differences between different lineages, providing a window into understanding bacterial speciation and taxonomic relationships.
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Genome edited animals: Learning from GM crops?
Bruce, Ann
2017-06-01
Genome editing of livestock is poised to become commercial reality, yet questions remain as to appropriate regulation, potential impact on the industry sector and public acceptability of products. This paper looks at how genome editing of livestock has attempted to learn some of the lessons from commercialisation of GM crops, and takes a systemic approach to explore some of the complexity and ambiguity in incorporating genome edited animals in a food production system. Current applications of genome editing are considered, viewed from the perspective of past technological applications. The question of what is genome editing, and can it be considered natural is examined. The implications of regulation on development of different sectors of livestock production systems are studied, with a particular focus on the veterinary sector. From an EU perspective, regulation of genome edited animals, although not necessarily the same as for GM crops, is advocated from a number of different perspectives. This paper aims to open up new avenues of research on genome edited animals, extending from the current primary focus on science and regulation, to engage with a wider-range of food system actors.
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Complete Genome Sequence of Pseudomonas aeruginosa Phage AAT-1.
Andrade-Domínguez, Andrés; Kolter, Roberto
2016-08-25
Aspects of the interaction between phages and animals are of interest and importance for medical applications. Here, we report the genome sequence of the lytic Pseudomonas phage AAT-1, isolated from mammalian serum. AAT-1 is a double-stranded DNA phage, with a genome of 57,599 bp, containing 76 predicted open reading frames. Copyright © 2016 Andrade-Domínguez and Kolter.
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Genomic Evolution of Saccharomyces cerevisiae under Chinese Rice Wine Fermentation
Li, Yudong; Zhang, Weiping; Zheng, Daoqiong; Zhou, Zhan; Yu, Wenwen; Zhang, Lei; Feng, Lifang; Liang, Xinle; Guan, Wenjun; Zhou, Jingwen; Chen, Jian; Lin, Zhenguo
2014-01-01
Rice wine fermentation represents a unique environment for the evolution of the budding yeast, Saccharomyces cerevisiae. To understand how the selection pressure shaped the yeast genome and gene regulation, we determined the genome sequence and transcriptome of a S. cerevisiae strain YHJ7 isolated from Chinese rice wine (Huangjiu), a popular traditional alcoholic beverage in China. By comparing the genome of YHJ7 to the lab strain S288c, a Japanese sake strain K7, and a Chinese industrial bioethanol strain YJSH1, we identified many genomic sequence and structural variations in YHJ7, which are mainly located in subtelomeric regions, suggesting that these regions play an important role in genomic evolution between strains. In addition, our comparative transcriptome analysis between YHJ7 and S288c revealed a set of differentially expressed genes, including those involved in glucose transport (e.g., HXT2, HXT7) and oxidoredutase activity (e.g., AAD10, ADH7). Interestingly, many of these genomic and transcriptional variations are directly or indirectly associated with the adaptation of YHJ7 strain to its specific niches. Our molecular evolution analysis suggested that Japanese sake strains (K7/UC5) were derived from Chinese rice wine strains (YHJ7) at least approximately 2,300 years ago, providing the first molecular evidence elucidating the origin of Japanese sake strains. Our results depict interesting insights regarding the evolution of yeast during rice wine fermentation, and provided a valuable resource for genetic engineering to improve industrial wine-making strains. PMID:25212861
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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).
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Note: Tormenta: An open source Python-powered control software for camera based optical microscopy.
Barabas, Federico M; Masullo, Luciano A; Stefani, Fernando D
2016-12-01
Until recently, PC control and synchronization of scientific instruments was only possible through closed-source expensive frameworks like National Instruments' LabVIEW. Nowadays, efficient cost-free alternatives are available in the context of a continuously growing community of open-source software developers. Here, we report on Tormenta, a modular open-source software for the control of camera-based optical microscopes. Tormenta is built on Python, works on multiple operating systems, and includes some key features for fluorescence nanoscopy based on single molecule localization.
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Practical Clinical Training in Skills Labs: Theory and Practice
Directory of Open Access Journals (Sweden)
Bugaj, T. J.
2016-08-01
Full Text Available Today, skills laboratories or “skills labs”, i.e. specific practical skill training facilities, are a firmly established part of medical education offering the possibility of training clinical procedures in a safe and fault-forging environment prior to real life application at bedside or in the operating room. Skills lab training follows a structured teaching concept, takes place under supervision and in consideration of methodological-didactic concepts, ideally creating an atmosphere that allows the repeated, anxiety- and risk-free practice of targeted skills.In this selective literature review, the first section is devoted to (I the development and dissemination of the skills lab concept. There follows (II an outline of the underlying idea and (III an analysis of key efficacy factors. Thereafter, (IV the training method’s effectiveness and transference are illuminated, before (V the use of student tutors, in the sense of peer-assisted-learning, in skills labs is discussed separately. Finally, (VI the efficiency of the skills lab concept is analyzed, followed by an outlook on future developments and trends in the field of skills lab training.
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LabVIEW Interface for PCI-SpaceWire Interface Card
Lux, James; Loya, Frank; Bachmann, Alex
2005-01-01
This software provides a LabView interface to the NT drivers for the PCISpaceWire card, which is a peripheral component interface (PCI) bus interface that conforms to the IEEE-1355/ SpaceWire standard. As SpaceWire grows in popularity, the ability to use SpaceWire links within LabVIEW will be important to electronic ground support equipment vendors. In addition, there is a need for a high-level LabVIEW interface to the low-level device- driver software supplied with the card. The LabVIEW virtual instrument (VI) provides graphical interfaces to support all (1) SpaceWire link functions, including message handling and routing; (2) monitoring as a passive tap using specialized hardware; and (3) low-level access to satellite mission-control subsystem functions. The software is supplied in a zip file that contains LabVIEW VI files, which provide various functions of the PCI-SpaceWire card, as well as higher-link-level functions. The VIs are suitably named according to the matching function names in the driver manual. A number of test programs also are provided to exercise various functions.
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Aircraft Lighting and Transparency Lab
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,...
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Creative Science Teaching Labs: New Dimensions in CPD
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…
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Living Labs als een Vehikel voor (Onderwijs)innovatie
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
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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 ...
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10KP: A phylodiverse genome sequencing plan.
Cheng, Shifeng; Melkonian, Michael; Smith, Stephen A; Brockington, Samuel; Archibald, John M; Delaux, Pierre-Marc; Li, Fay-Wei; Melkonian, Barbara; Mavrodiev, Evgeny V; Sun, Wenjing; Fu, Yuan; Yang, Huanming; Soltis, Douglas E; Graham, Sean W; Soltis, Pamela S; Liu, Xin; Xu, Xun; Wong, Gane Ka-Shu
2018-03-01
Understanding plant evolution and diversity in a phylogenomic context is an enormous challenge due, in part, to limited availability of genome-scale data across phylodiverse species. The 10KP (10,000 Plants) Genome Sequencing Project will sequence and characterize representative genomes from every major clade of embryophytes, green algae, and protists (excluding fungi) within the next 5 years. By implementing and continuously improving leading-edge sequencing technologies and bioinformatics tools, 10KP will catalogue the genome content of plant and protist diversity and make these data freely available as an enduring foundation for future scientific discoveries and applications. 10KP is structured as an international consortium, open to the global community, including botanical gardens, plant research institutes, universities, and private industry. Our immediate goal is to establish a policy framework for this endeavor, the principles of which are outlined here.
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10KP: A phylodiverse genome sequencing plan
Cheng, Shifeng; Melkonian, Michael; Brockington, Samuel; Archibald, John M; Delaux, Pierre-Marc; Melkonian, Barbara; Mavrodiev, Evgeny V; Sun, Wenjing; Fu, Yuan; Yang, Huanming; Soltis, Douglas E; Graham, Sean W; Soltis, Pamela S; Liu, Xin; Xu, Xun
2018-01-01
Abstract Understanding plant evolution and diversity in a phylogenomic context is an enormous challenge due, in part, to limited availability of genome-scale data across phylodiverse species. The 10KP (10,000 Plants) Genome Sequencing Project will sequence and characterize representative genomes from every major clade of embryophytes, green algae, and protists (excluding fungi) within the next 5 years. By implementing and continuously improving leading-edge sequencing technologies and bioinformatics tools, 10KP will catalogue the genome content of plant and protist diversity and make these data freely available as an enduring foundation for future scientific discoveries and applications. 10KP is structured as an international consortium, open to the global community, including botanical gardens, plant research institutes, universities, and private industry. Our immediate goal is to establish a policy framework for this endeavor, the principles of which are outlined here. PMID:29618049
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The mitochondrial genomes of the ciliates Euplotes minuta and Euplotes crassus
Directory of Open Access Journals (Sweden)
Huynh Minh
2009-11-01
Full Text Available Abstract Background There are thousands of very diverse ciliate species from which only a handful mitochondrial genomes have been studied so far. These genomes are rather similar because the ciliates analysed (Tetrahymena spp. and Paramecium aurelia are closely related. Here we study the mitochondrial genomes of the hypotrichous ciliates Euplotes minuta and Euplotes crassus. These ciliates are only distantly related to Tetrahymena spp. and Paramecium aurelia, but more closely related to Nyctotherus ovalis, which possesses a hydrogenosomal (mitochondrial genome. Results The linear mitochondrial genomes of the hypotrichous ciliates Euplotes minuta and Euplotes crassus were sequenced and compared with the mitochondrial genomes of several Tetrahymena species, Paramecium aurelia and the partially sequenced mitochondrial genome of the anaerobic ciliate Nyctotherus ovalis. This study reports new features such as long 5'gene extensions of several mitochondrial genes, extremely long cox1 and cox2 open reading frames and a large repeat in the middle of the linear mitochondrial genome. The repeat separates the open reading frames into two blocks, each having a single direction of transcription, from the repeat towards the ends of the chromosome. Although the Euplotes mitochondrial gene content is almost identical to that of Paramecium and Tetrahymena, the order of the genes is completely different. In contrast, the 33273 bp (excluding the repeat region piece of the mitochondrial genome that has been sequenced in both Euplotes species exhibits no difference in gene order. Unexpectedly, many of the mitochondrial genes of E. minuta encoding ribosomal proteins possess N-terminal extensions that are similar to mitochondrial targeting signals. Conclusion The mitochondrial genomes of the hypotrichous ciliates Euplotes minuta and Euplotes crassus are rather different from the previously studied genomes. Many genes are extended in size compared to mitochondrial
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ERLN Technical Support for Labs
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
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Respecifying lab ethnography an ethnomethodological study of experimental physics
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
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Towards Multiplex Molecular Diagnosis—A Review of Microfluidic Genomics Technologies
Directory of Open Access Journals (Sweden)
Ismail Hussain Kamal Basha
2017-08-01
Full Text Available Highly sensitive and specific pathogen diagnosis is essential for correct and timely treatment of infectious diseases, especially virulent strains, in people. Point-of-care pathogen diagnosis can be a tremendous help in managing disease outbreaks as well as in routine healthcare settings. Infectious pathogens can be identified with high specificity using molecular methods. A plethora of microfluidic innovations in recent years have now made it increasingly feasible to develop portable, robust, accurate, and sensitive genomic diagnostic devices for deployment at the point of care. However, improving processing time, multiplexed detection, sensitivity and limit of detection, specificity, and ease of deployment in resource-limited settings are ongoing challenges. This review outlines recent techniques in microfluidic genomic diagnosis and devices with a focus on integrating them into a lab on a chip that will lead towards the development of multiplexed point-of-care devices of high sensitivity and specificity.
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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...
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Spradling, A C; Stern, D M; Kiss, I; Roote, J; Laverty, T; Rubin, G M
1995-01-01
Biologists require genetic as well as molecular tools to decipher genomic information and ultimately to understand gene function. The Berkeley Drosophila Genome Project is addressing these needs with a massive gene disruption project that uses individual, genetically engineered P transposable elements to target open reading frames throughout the Drosophila genome. DNA flanking the insertions is sequenced, thereby placing an extensive series of genetic markers on the physical genomic map and a...
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Genetic Indicators of Drug Resistance in the Highly Repetitive Genome of Trichomonas vaginalis.
Bradic, Martina; Warring, Sally D; Tooley, Grace E; Scheid, Paul; Secor, William E; Land, Kirkwood M; Huang, Po-Jung; Chen, Ting-Wen; Lee, Chi-Ching; Tang, Petrus; Sullivan, Steven A; Carlton, Jane M
2017-06-01
Trichomonas vaginalis, the most common nonviral sexually transmitted parasite, causes ∼283 million trichomoniasis infections annually and is associated with pregnancy complications and increased risk of HIV-1 acquisition. The antimicrobial drug metronidazole is used for treatment, but in a fraction of clinical cases, the parasites can become resistant to this drug. We undertook sequencing of multiple clinical isolates and lab derived lines to identify genetic markers and mechanisms of metronidazole resistance. Reduced representation genome sequencing of ∼100 T. vaginalis clinical isolates identified 3,923 SNP markers and presence of a bipartite population structure. Linkage disequilibrium was found to decay rapidly, suggesting genome-wide recombination and the feasibility of genetic association studies in the parasite. We identified 72 SNPs associated with metronidazole resistance, and a comparison of SNPs within several lab-derived resistant lines revealed an overlap with the clinically resistant isolates. We identified SNPs in genes for which no function has yet been assigned, as well as in functionally-characterized genes relevant to drug resistance (e.g., pyruvate:ferredoxin oxidoreductase). Transcription profiles of resistant strains showed common changes in genes involved in drug activation (e.g., flavin reductase), accumulation (e.g., multidrug resistance pump), and detoxification (e.g., nitroreductase). Finally, we identified convergent genetic changes in lab-derived resistant lines of Tritrichomonas foetus, a distantly related species that causes venereal disease in cattle. Shared genetic changes within and between T. vaginalis and Tr. foetus parasites suggest conservation of the pathways through which adaptation has occurred. These findings extend our knowledge of drug resistance in the parasite, providing a panel of markers that can be used as a diagnostic tool. © The Author 2017. Published by Oxford University Press on behalf of the Society for
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xGDBvm: A Web GUI-Driven Workflow for Annotating Eukaryotic Genomes in the Cloud[OPEN
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
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Introduction to Computing: Lab Manual. Faculty Guide [and] Student Guide.
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…
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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...
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On the total number of genes and their length distribution in complete microbial genomes
DEFF Research Database (Denmark)
Skovgaard, M; Jensen, L J; Brunak, S
2001-01-01
In sequenced microbial genomes, some of the annotated genes are actually not protein-coding genes, but rather open reading frames that occur by chance. Therefore, the number of annotated genes is higher than the actual number of genes for most of these microbes. Comparison of the length distribut......In sequenced microbial genomes, some of the annotated genes are actually not protein-coding genes, but rather open reading frames that occur by chance. Therefore, the number of annotated genes is higher than the actual number of genes for most of these microbes. Comparison of the length...... distribution of the annotated genes with the length distribution of those matching a known protein reveals that too many short genes are annotated in many genomes. Here we estimate the true number of protein-coding genes for sequenced genomes. Although it is often claimed that Escherichia coli has about 4300...... genes, we show that it probably has only approximately 3800 genes, and that a similar discrepancy exists for almost all published genomes....
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Kent, J. J.; Berger, E. L.; Fries, M. D.; Bastien, R.; McCubbin, F. M.; Pace, L.; Righter, K.; Sutter, B.; Zeigler, R. A.; Zolensky, M.
2017-01-01
On the early morning of September 15th, 2016, on the first floor of Building 31 at NASA-Johnson Space Center, the hose from a water chiller ruptured and began spraying water onto the floor. The water had been circulating though old metal pipes, and the leaked water contained rust-colored particulates. The water flooded much of the western wing of the building's ground floor before the leak was stopped, and it left behind a residue of rust across the floor, most notably in the Apollo and Meteorite Thin Section Labs and Sample Preparation Lab. No samples were damaged in the event, and the affected facilities are in the process of remediation. At the beginning of 2016, a separate leak occurred in the Cosmic Dust Lab, located in the same building. In that lab, a water leak occurred at the bottom of the sink used to clean the lab's tools and containers with ultra-pure water. Over years of use, the ultra-pure water eroded the metal sink piping and leaked water onto the inside of the lab's flow bench. This water also left behind a film of rusty material. The material was cleaned up and the metal piping was replaced with PVC pipe and sealed with Teflon plumber's tape. Samples of the rust detritus were collected from both incidents. These samples were imaged and analyzed to determine their chemical and mineralogical compositions. The purpose of these analyses is to document the nature of the detritus for future reference in the unlikely event that these materials occur as contaminants in the Cosmic Dust samples or Apollo or Meteorite thin sections.
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Managing the genomic revolution in cancer diagnostics.
Nguyen, Doreen; Gocke, Christopher D
2017-08-01
Molecular tumor profiling is now a routine part of patient care, revealing targetable genomic alterations and molecularly distinct tumor subtypes with therapeutic and prognostic implications. The widespread adoption of next-generation sequencing technologies has greatly facilitated clinical implementation of genomic data and opened the door for high-throughput multigene-targeted sequencing. Herein, we discuss the variability of cancer genetic profiling currently offered by clinical laboratories, the challenges of applying rapidly evolving medical knowledge to individual patients, and the need for more standardized population-based molecular profiling.
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Genome-scale metabolic representation of Amycolatopsis balhimycina
DEFF Research Database (Denmark)
Vongsangnak, Wanwipa; Figueiredo, L. F.; Förster, Jochen
2012-01-01
Infection caused by methicillin‐resistant Staphylococcus aureus (MRSA) is an increasing societal problem. Typically, glycopeptide antibiotics are used in the treatment of these infections. The most comprehensively studied glycopeptide antibiotic biosynthetic pathway is that of balhimycin...... to reconstruct a genome‐scale metabolic model for the organism. Here we generated an almost complete A. balhimycina genome sequence comprising 10,562,587 base pairs assembled into 2,153 contigs. The high GC‐genome (∼69%) includes 8,585 open reading frames (ORFs). We used our integrative toolbox called SEQTOR...
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Common Systems Integration Lab (CSIL)
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...
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Valx: A System for Extracting and Structuring Numeric Lab Test Comparison Statements from Text.
Hao, Tianyong; Liu, Hongfang; Weng, Chunhua
2016-05-17
To develop an automated method for extracting and structuring numeric lab test comparison statements from text and evaluate the method using clinical trial eligibility criteria text. Leveraging semantic knowledge from the Unified Medical Language System (UMLS) and domain knowledge acquired from the Internet, Valx takes seven steps to extract and normalize numeric lab test expressions: 1) text preprocessing, 2) numeric, unit, and comparison operator extraction, 3) variable identification using hybrid knowledge, 4) variable - numeric association, 5) context-based association filtering, 6) measurement unit normalization, and 7) heuristic rule-based comparison statements verification. Our reference standard was the consensus-based annotation among three raters for all comparison statements for two variables, i.e., HbA1c and glucose, identified from all of Type 1 and Type 2 diabetes trials in ClinicalTrials.gov. The precision, recall, and F-measure for structuring HbA1c comparison statements were 99.6%, 98.1%, 98.8% for Type 1 diabetes trials, and 98.8%, 96.9%, 97.8% for Type 2 diabetes trials, respectively. The precision, recall, and F-measure for structuring glucose comparison statements were 97.3%, 94.8%, 96.1% for Type 1 diabetes trials, and 92.3%, 92.3%, 92.3% for Type 2 diabetes trials, respectively. Valx is effective at extracting and structuring free-text lab test comparison statements in clinical trial summaries. Future studies are warranted to test its generalizability beyond eligibility criteria text. The open-source Valx enables its further evaluation and continued improvement among the collaborative scientific community.
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Timing properties and pulse shape discrimination of LAB-based liquid scintillator
International Nuclear Information System (INIS)
Li Xiaobo; Xiao Hualin; Cao Jun; Li Jin; Heng Yuekun; Ruan Xichao
2011-01-01
Linear Alkyl Benzene (LAB) is a promising liquid scintillator solvent in neutrino experiments because it has many appealing properties. The timing properties of LAB-based liquid scintillator have been studied through ultraviolet and ionization excitation in this study. The decay time of LAB, PPO and bis-MSB is found to be 48.6 ns, 1.55 ns and 1.5 ns, respectively. A model can describe the absorption and re-emission process between PPO and bis-MSB perfectly. The energy transfer time between LAB and PPO with different concentrations can be obtained via another model. We also show that the LAB-based liquid scintillator has good (n, γ) and (α, γ) discrimination power. (authors)
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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.
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Özdemir, Vural; Badr, Kamal F; Dove, Edward S; Endrenyi, Laszlo; Geraci, Christy Jo; Hotez, Peter J; Milius, Djims; Neves-Pereira, Maria; Pang, Tikki; Rotimi, Charles N; Sabra, Ramzi; Sarkissian, Christineh N; Srivastava, Sanjeeva; Tims, Hesther; Zgheib, Nathalie K; Kickbusch, Ilona
2013-04-01
Biomedical science in the 21(st) century is embedded in, and draws from, a digital commons and "Big Data" created by high-throughput Omics technologies such as genomics. Classic Edisonian metaphors of science and scientists (i.e., "the lone genius" or other narrow definitions of expertise) are ill equipped to harness the vast promises of the 21(st) century digital commons. Moreover, in medicine and life sciences, experts often under-appreciate the important contributions made by citizen scholars and lead users of innovations to design innovative products and co-create new knowledge. We believe there are a large number of users waiting to be mobilized so as to engage with Big Data as citizen scientists-only if some funding were available. Yet many of these scholars may not meet the meta-criteria used to judge expertise, such as a track record in obtaining large research grants or a traditional academic curriculum vitae. This innovation research article describes a novel idea and action framework: micro-grants, each worth $1000, for genomics and Big Data. Though a relatively small amount at first glance, this far exceeds the annual income of the "bottom one billion"-the 1.4 billion people living below the extreme poverty level defined by the World Bank ($1.25/day). We describe two types of micro-grants. Type 1 micro-grants can be awarded through established funding agencies and philanthropies that create micro-granting programs to fund a broad and highly diverse array of small artisan labs and citizen scholars to connect genomics and Big Data with new models of discovery such as open user innovation. Type 2 micro-grants can be funded by existing or new science observatories and citizen think tanks through crowd-funding mechanisms described herein. Type 2 micro-grants would also facilitate global health diplomacy by co-creating crowd-funded micro-granting programs across nation-states in regions facing political and financial instability, while sharing similar disease
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MUTAGEN: Multi-user tool for annotating GENomes
DEFF Research Database (Denmark)
Brugger, K.; Redder, P.; Skovgaard, Marie
2003-01-01
MUTAGEN is a free prokaryotic annotation system. It offers the advantages of genome comparison, graphical sequence browsers, search facilities and open-source for user-specific adjustments. The web-interface allows several users to access the system from standard desktop computers. The Sulfolobus...
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Advanced Active Acoustics Lab (AAAL)
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...
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Towards Third-Generation Living Lab Networks in Cities
Directory of Open Access Journals (Sweden)
Seppo Leminen
2017-11-01
Full Text Available Many cities engage in diverse experimentation, innovation, and development activities with a broad variety of environments and stakeholders to the benefit of citizens, companies, municipalities, and other organizations. Hence, this article discusses such engagement in terms of next-generation living lab networks in the city context. In so doing, the study contributes to the discussion on living labs by introducing a framework of collaborative innovation networks in cities and suggesting a typology of third-generation living labs. Our framework is characterized by diverse platforms and participation approaches, resulting in four distinctive modes of collaborative innovation networks where the city is: i a provider, ii a neighbourhood participator, iii a catalyst, or iv a rapid experimenter. The typology is based on an analysis of 118 interviews with participants in six Finnish cities and reveals various ways to organize innovation activities in the city context. In particular, cities can benefit from innovation networks by simultaneously exploiting multiple platforms such as living labs for innovation. We conclude by discussing implications to theory and practice, and suggesting directions for future research.
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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.
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International Nuclear Information System (INIS)
Ordan'yan, S.S.; Gardagina, E.N.; Barabanova, S.N.
1989-01-01
Investigation results of interaction in LaB 6 -MoSi 2 system within wide concentration and temperature ranges are presented. LaB 6 and MoSi 2 powders were preliminary squeezed out in vacuum at 1470 K. Presence of LaB 6 and MoSi 2 initial phases only is determined using X-ray pahse analysis of sintered and melted specimens of all compositions. Traces of MoB (probably, due to quick crystallization after melting and partial evaporation of silicon from the melt) are detected in some alloys exposed to melting
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Scaffolding students’ reflective dialogues in the chemistry lab: challenging the cookbook
DEFF Research Database (Denmark)
Nielsen, Birgitte Lund; Hougaard, Rikke Frøhlich
The paper reports on a cross-case analysis comparing students’ activities and dialogue during BA level laboratory exercises, applying a mixed methods research design with video-data, student questionnaires and interviews. Our analysis identified specific affordances in relation to macro and micro......-scaffolding of students’ activities and dialogues, in order to stimulate them to work at higher cognitive levels. A specific lab-exercise in the course Macroscopic Physical Chemistry was redesigned with the aim of stimulating students’ metacognition both before and during the experimental work. The redesign included......-student dialogue on course content. Furthermore, dialogues between students and teaching assistant revealed elements of micro-scaffolding exploratory talk and a dialogic approach with open questions and prompts. The students expressed that the preparatory assignments and the dialogue with the teaching assistant...
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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 Study 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...
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What Is LAB and Why Was It Renormed?
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…
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FOREWORD: Jefferson Lab: A Long Decade of Physics
Montgomery, Hugh
2011-04-01
Jefferson Lab 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
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Epigenetic regulation of open chromatin in pluripotent stem cells
Kobayashi, Hiroshi; Kikyo, Nobuaki
2014-01-01
The recent progress in pluripotent stem cell research has opened new avenues of disease modeling, drug screening, and transplantation of patient-specific tissues that had been unimaginable until a decade ago. The central mechanism underlying pluripotency is epigenetic gene regulation; the majority of cell signaling pathways, both extracellular and cytoplasmic, eventually alter the epigenetic status of their target genes during the process of activating or suppressing the genes to acquire or maintain pluripotency. It has long been thought that the chromatin of pluripotent stem cells is globally open to enable the timely activation of essentially all genes in the genome during differentiation into multiple lineages. The current article reviews descriptive observations and the epigenetic machinery relevant to what is supposed to be globally open chromatin in pluripotent stem cells. This includes microscopic appearance, permissive gene transcription, chromatin remodeling complexes, histone modifications, DNA methylation, noncoding RNAs, dynamic movement of chromatin proteins, nucleosome accessibility and positioning, and long-range chromosomal interactions. Detailed analyses of each element, however, have revealed that the globally open chromatin hypothesis is not necessarily supported by some of the critical experimental evidence, such as genome-wide nucleosome accessibility and nucleosome positioning. Further understanding of the epigenetic gene regulation is expected to determine the true nature of the so-called globally open chromatin in pluripotent stem. PMID:24695097
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Hadlich, Marcelo Souza; Oliveira, Gláucia Maria Moraes; Feijóo, Raúl A; Azevedo, Clerio F; Tura, Bernardo Rangel; Ziemer, Paulo Gustavo Portela; Blanco, Pablo Javier; Pina, Gustavo; Meira, Márcio; Souza e Silva, Nelson Albuquerque de
2012-10-01
The standardization of images used in Medicine in 1993 was performed using the DICOM (Digital Imaging and Communications in Medicine) standard. Several tests use this standard and it is increasingly necessary to design software applications capable of handling this type of image; however, these software applications are not usually free and open-source, and this fact hinders their adjustment to most diverse interests. To develop and validate a free and open-source software application capable of handling DICOM coronary computed tomography angiography images. We developed and tested the ImageLab software in the evaluation of 100 tests randomly selected from a database. We carried out 600 tests divided between two observers using ImageLab and another software sold with Philips Brilliance computed tomography appliances in the evaluation of coronary lesions and plaques around the left main coronary artery (LMCA) and the anterior descending artery (ADA). To evaluate intraobserver, interobserver and intersoftware agreements, we used simple and kappa statistics agreements. The agreements observed between software applications were generally classified as substantial or almost perfect in most comparisons. The ImageLab software agreed with the Philips software in the evaluation of coronary computed tomography angiography tests, especially in patients without lesions, with lesions 70% in the ADA was lower, but this is also observed when the anatomical reference standard is used.
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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
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Undergraduate Student Construction and Interpretation of Graphs in Physics Lab Activities
Nixon, Ryan S.; Godfrey, T. J.; Mayhew, Nicholas T.; Wiegert, Craig C.
2016-01-01
Lab activities are an important element of an undergraduate physics course. In these lab activities, students construct and interpret graphs in order to connect the procedures of the lab with an understanding of the related physics concepts. This study investigated undergraduate students' construction and interpretation of graphs with best-fit…
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Outreach Science Education: Evidence-Based Studies in a Gene Technology Lab
Scharfenberg, Franz-Josef; Bogner, Franz X.
2014-01-01
Nowadays, outreach labs are important informal learning environments in science education. After summarizing research to goals outreach labs focus on, we describe our evidence-based gene technology lab as a model of a research-driven outreach program. Evaluation-based optimizations of hands-on teaching based on cognitive load theory (additional…
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Virtual Labs in proteomics: new E-learning tools.
Ray, Sandipan; Koshy, Nicole Rachel; Reddy, Panga Jaipal; Srivastava, Sanjeeva
2012-05-17
Web-based educational resources have gained enormous popularity recently and are increasingly becoming a part of modern educational systems. Virtual Labs are E-learning platforms where learners can gain the experience of practical experimentation without any direct physical involvement on real bench work. They use computerized simulations, models, videos, animations and other instructional technologies to create interactive content. Proteomics being one of the most rapidly growing fields of the biological sciences is now an important part of college and university curriculums. Consequently, many E-learning programs have started incorporating the theoretical and practical aspects of different proteomic techniques as an element of their course work in the form of Video Lectures and Virtual Labs. To this end, recently we have developed a Virtual Proteomics Lab at the Indian Institute of Technology Bombay, which demonstrates different proteomics techniques, including basic and advanced gel and MS-based protein separation and identification techniques, bioinformatics tools and molecular docking methods, and their applications in different biological samples. This Tutorial will discuss the prominent Virtual Labs featuring proteomics content, including the Virtual Proteomics Lab of IIT-Bombay, and E-resources available for proteomics study that are striving to make proteomic techniques and concepts available and accessible to the student and research community. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 14). Details can be found at: http://www.proteomicstutorials.org/. Copyright © 2012 Elsevier B.V. All rights reserved.
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Haplotype assembly in polyploid genomes and identical by descent shared tracts.
Aguiar, Derek; Istrail, Sorin
2013-07-01
Genome-wide haplotype reconstruction from sequence data, or haplotype assembly, is at the center of major challenges in molecular biology and life sciences. For complex eukaryotic organisms like humans, the genome is vast and the population samples are growing so rapidly that algorithms processing high-throughput sequencing data must scale favorably in terms of both accuracy and computational efficiency. Furthermore, current models and methodologies for haplotype assembly (i) do not consider individuals sharing haplotypes jointly, which reduces the size and accuracy of assembled haplotypes, and (ii) are unable to model genomes having more than two sets of homologous chromosomes (polyploidy). Polyploid organisms are increasingly becoming the target of many research groups interested in the genomics of disease, phylogenetics, botany and evolution but there is an absence of theory and methods for polyploid haplotype reconstruction. In this work, we present a number of results, extensions and generalizations of compass graphs and our HapCompass framework. We prove the theoretical complexity of two haplotype assembly optimizations, thereby motivating the use of heuristics. Furthermore, we present graph theory-based algorithms for the problem of haplotype assembly using our previously developed HapCompass framework for (i) novel implementations of haplotype assembly optimizations (minimum error correction), (ii) assembly of a pair of individuals sharing a haplotype tract identical by descent and (iii) assembly of polyploid genomes. We evaluate our methods on 1000 Genomes Project, Pacific Biosciences and simulated sequence data. HapCompass is available for download at http://www.brown.edu/Research/Istrail_Lab/. Supplementary data are available at Bioinformatics online.
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Saunders, Daniel R; Bex, Peter J; Woods, Russell L
2013-05-20
Crowdsourcing has become a valuable method for collecting medical research data. This approach, recruiting through open calls on the Web, is particularly useful for assembling large normative datasets. However, it is not known how natural language datasets collected over the Web differ from those collected under controlled laboratory conditions. To compare the natural language responses obtained from a crowdsourced sample of participants with responses collected in a conventional laboratory setting from participants recruited according to specific age and gender criteria. We collected natural language descriptions of 200 half-minute movie clips, from Amazon Mechanical Turk workers (crowdsourced) and 60 participants recruited from the community (lab-sourced). Crowdsourced participants responded to as many clips as they wanted and typed their responses, whereas lab-sourced participants gave spoken responses to 40 clips, and their responses were transcribed. The content of the responses was evaluated using a take-one-out procedure, which compared responses to other responses to the same clip and to other clips, with a comparison of the average number of shared words. In contrast to the 13 months of recruiting that was required to collect normative data from 60 lab-sourced participants (with specific demographic characteristics), only 34 days were needed to collect normative data from 99 crowdsourced participants (contributing a median of 22 responses). The majority of crowdsourced workers were female, and the median age was 35 years, lower than the lab-sourced median of 62 years but similar to the median age of the US population. The responses contributed by the crowdsourced participants were longer on average, that is, 33 words compared to 28 words (Pcrowdsourced participants had more shared words (P=.004 and .01 respectively), whereas younger participants had higher numbers of shared words in the lab-sourced population (P=.01). Crowdsourcing is an effective approach
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Evolving approaches to the ethical management of genomic data.
McEwen, Jean E; Boyer, Joy T; Sun, Kathie Y
2013-06-01
The ethical landscape in the field of genomics is rapidly shifting. Plummeting sequencing costs, along with ongoing advances in bioinformatics, now make it possible to generate an enormous volume of genomic data about vast numbers of people. The informational richness, complexity, and frequently uncertain meaning of these data, coupled with evolving norms surrounding the sharing of data and samples and persistent privacy concerns, have generated a range of approaches to the ethical management of genomic information. As calls increase for the expanded use of broad or even open consent, and as controversy grows about how best to handle incidental genomic findings, these approaches, informed by normative analysis and empirical data, will continue to evolve alongside the science. Published by Elsevier Ltd.
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Simultaneous gene finding in multiple genomes.
König, Stefanie; Romoth, Lars W; Gerischer, Lizzy; Stanke, Mario
2016-11-15
As the tree of life is populated with sequenced genomes ever more densely, the new challenge is the accurate and consistent annotation of entire clades of genomes. We address this problem with a new approach to comparative gene finding that takes a multiple genome alignment of closely related species and simultaneously predicts the location and structure of protein-coding genes in all input genomes, thereby exploiting negative selection and sequence conservation. The model prefers potential gene structures in the different genomes that are in agreement with each other, or-if not-where the exon gains and losses are plausible given the species tree. We formulate the multi-species gene finding problem as a binary labeling problem on a graph. The resulting optimization problem is NP hard, but can be efficiently approximated using a subgradient-based dual decomposition approach. The proposed method was tested on whole-genome alignments of 12 vertebrate and 12 Drosophila species. The accuracy was evaluated for human, mouse and Drosophila melanogaster and compared to competing methods. Results suggest that our method is well-suited for annotation of (a large number of) genomes of closely related species within a clade, in particular, when RNA-Seq data are available for many of the genomes. The transfer of existing annotations from one genome to another via the genome alignment is more accurate than previous approaches that are based on protein-spliced alignments, when the genomes are at close to medium distances. The method is implemented in C ++ as part of Augustus and available open source at http://bioinf.uni-greifswald.de/augustus/ CONTACT: stefaniekoenig@ymail.com or mario.stanke@uni-greifswald.deSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
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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.
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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...
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Zhao, Xue Qiang; Aizawa, Tomoko; Schneider, Jessica; Wang, Chao; Shen, Ren Fang; Sunairi, Michio
2013-04-01
The complete mitochondrial genome of Rhodotorula taiwanensis RS1, an aluminum-tolerant Basidiomycota fungus, was determined and compared with the known mitochondrial genomes of 12 Basidiomycota species. The mitochondrial genome of R. taiwanensis RS1 is a circular DNA molecule of 40,392 bp and encodes the typical 15 mitochondrial proteins, 23 tRNAs, and small and large rRNAs as well as 10 intronic open reading frames. These genes are apparently transcribed in two directions and do not show syntenies in gene order with other investigated Basidiomycota species. The average G+C content (41%) of the mitochondrial genome of R. taiwanensis RS1 is the highest among the Basidiomycota species. Two introns were detected in the sequence of the atp9 gene of R. taiwanensis RS1, but not in that of other Basidiomycota species. Rhodotorula taiwanensis is the first species of the genus Rhodotorula whose full mitochondrial genome has been sequenced; and the data presented here supply valuable information for understanding the evolution of fungal mitochondrial genomes and researching the mechanism of aluminum tolerance in microorganisms. © 2013 The Authors. Published by Blackwell Publishing Ltd.
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Genomic evolution of Saccharomyces cerevisiae under Chinese rice wine fermentation.
Li, Yudong; Zhang, Weiping; Zheng, Daoqiong; Zhou, Zhan; Yu, Wenwen; Zhang, Lei; Feng, Lifang; Liang, Xinle; Guan, Wenjun; Zhou, Jingwen; Chen, Jian; Lin, Zhenguo
2014-09-10
Rice wine fermentation represents a unique environment for the evolution of the budding yeast, Saccharomyces cerevisiae. To understand how the selection pressure shaped the yeast genome and gene regulation, we determined the genome sequence and transcriptome of a S. cerevisiae strain YHJ7 isolated from Chinese rice wine (Huangjiu), a popular traditional alcoholic beverage in China. By comparing the genome of YHJ7 to the lab strain S288c, a Japanese sake strain K7, and a Chinese industrial bioethanol strain YJSH1, we identified many genomic sequence and structural variations in YHJ7, which are mainly located in subtelomeric regions, suggesting that these regions play an important role in genomic evolution between strains. In addition, our comparative transcriptome analysis between YHJ7 and S288c revealed a set of differentially expressed genes, including those involved in glucose transport (e.g., HXT2, HXT7) and oxidoredutase activity (e.g., AAD10, ADH7). Interestingly, many of these genomic and transcriptional variations are directly or indirectly associated with the adaptation of YHJ7 strain to its specific niches. Our molecular evolution analysis suggested that Japanese sake strains (K7/UC5) were derived from Chinese rice wine strains (YHJ7) at least approximately 2,300 years ago, providing the first molecular evidence elucidating the origin of Japanese sake strains. Our results depict interesting insights regarding the evolution of yeast during rice wine fermentation, and provided a valuable resource for genetic engineering to improve industrial wine-making strains. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
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Badr, Kamal F.; Dove, Edward S.; Endrenyi, Laszlo; Geraci, Christy Jo; Hotez, Peter J.; Milius, Djims; Neves-Pereira, Maria; Pang, Tikki; Rotimi, Charles N.; Sabra, Ramzi; Sarkissian, Christineh N.; Srivastava, Sanjeeva; Tims, Hesther; Zgheib, Nathalie K.; Kickbusch, Ilona
2013-01-01
Abstract Biomedical science in the 21st century is embedded in, and draws from, a digital commons and “Big Data” created by high-throughput Omics technologies such as genomics. Classic Edisonian metaphors of science and scientists (i.e., “the lone genius” or other narrow definitions of expertise) are ill equipped to harness the vast promises of the 21st century digital commons. Moreover, in medicine and life sciences, experts often under-appreciate the important contributions made by citizen scholars and lead users of innovations to design innovative products and co-create new knowledge. We believe there are a large number of users waiting to be mobilized so as to engage with Big Data as citizen scientists—only if some funding were available. Yet many of these scholars may not meet the meta-criteria used to judge expertise, such as a track record in obtaining large research grants or a traditional academic curriculum vitae. This innovation research article describes a novel idea and action framework: micro-grants, each worth $1000, for genomics and Big Data. Though a relatively small amount at first glance, this far exceeds the annual income of the “bottom one billion”—the 1.4 billion people living below the extreme poverty level defined by the World Bank ($1.25/day). We describe two types of micro-grants. Type 1 micro-grants can be awarded through established funding agencies and philanthropies that create micro-granting programs to fund a broad and highly diverse array of small artisan labs and citizen scholars to connect genomics and Big Data with new models of discovery such as open user innovation. Type 2 micro-grants can be funded by existing or new science observatories and citizen think tanks through crowd-funding mechanisms described herein. Type 2 micro-grants would also facilitate global health diplomacy by co-creating crowd-funded micro-granting programs across nation-states in regions facing political and financial instability, while
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Comparative analysis of prophages in Streptococcus mutans genomes
Fu, Tiwei; Fan, Xiangyu; Long, Quanxin; Deng, Wanyan; Song, Jinlin
2017-01-01
Prophages have been considered genetic units that have an intimate association with novel phenotypic properties of bacterial hosts, such as pathogenicity and genomic variation. Little is known about the genetic information of prophages in the genome of Streptococcus mutans, a major pathogen of human dental caries. In this study, we identified 35 prophage-like elements in S. mutans genomes and performed a comparative genomic analysis. Comparative genomic and phylogenetic analyses of prophage sequences revealed that the prophages could be classified into three main large clusters: Cluster A, Cluster B, and Cluster C. The S. mutans prophages in each cluster were compared. The genomic sequences of phismuN66-1, phismuNLML9-1, and phismu24-1 all shared similarities with the previously reported S. mutans phages M102, M102AD, and ϕAPCM01. The genomes were organized into seven major gene clusters according to the putative functions of the predicted open reading frames: packaging and structural modules, integrase, host lysis modules, DNA replication/recombination modules, transcriptional regulatory modules, other protein modules, and hypothetical protein modules. Moreover, an integrase gene was only identified in phismuNLML9-1 prophages. PMID:29158986
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CELSTEC Learning Labs: Mobile App Development for Education and Training
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.
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High-throughput automated microfluidic sample preparation for accurate microbial genomics.
Kim, Soohong; De Jonghe, Joachim; Kulesa, Anthony B; Feldman, David; Vatanen, Tommi; Bhattacharyya, Roby P; Berdy, Brittany; Gomez, James; Nolan, Jill; Epstein, Slava; Blainey, Paul C
2017-01-27
Low-cost shotgun DNA sequencing is transforming the microbial sciences. Sequencing instruments are so effective that sample preparation is now the key limiting factor. Here, we introduce a microfluidic sample preparation platform that integrates the key steps in cells to sequence library sample preparation for up to 96 samples and reduces DNA input requirements 100-fold while maintaining or improving data quality. The general-purpose microarchitecture we demonstrate supports workflows with arbitrary numbers of reaction and clean-up or capture steps. By reducing the sample quantity requirements, we enabled low-input (∼10,000 cells) whole-genome shotgun (WGS) sequencing of Mycobacterium tuberculosis and soil micro-colonies with superior results. We also leveraged the enhanced throughput to sequence ∼400 clinical Pseudomonas aeruginosa libraries and demonstrate excellent single-nucleotide polymorphism detection performance that explained phenotypically observed antibiotic resistance. Fully-integrated lab-on-chip sample preparation overcomes technical barriers to enable broader deployment of genomics across many basic research and translational applications.
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Pollution hazard closes neutrino lab
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)
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Living Labs as boundary-spanners between Triple Helix actors
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
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Gene calling and bacterial genome annotation with BG7.
Tobes, Raquel; Pareja-Tobes, Pablo; Manrique, Marina; Pareja-Tobes, Eduardo; Kovach, Evdokim; Alekhin, Alexey; Pareja, Eduardo
2015-01-01
New massive sequencing technologies are providing many bacterial genome sequences from diverse taxa but a refined annotation of these genomes is crucial for obtaining scientific findings and new knowledge. Thus, bacterial genome annotation has emerged as a key point to investigate in bacteria. Any efficient tool designed specifically to annotate bacterial genomes sequenced with massively parallel technologies has to consider the specific features of bacterial genomes (absence of introns and scarcity of nonprotein-coding sequence) and of next-generation sequencing (NGS) technologies (presence of errors and not perfectly assembled genomes). These features make it convenient to focus on coding regions and, hence, on protein sequences that are the elements directly related with biological functions. In this chapter we describe how to annotate bacterial genomes with BG7, an open-source tool based on a protein-centered gene calling/annotation paradigm. BG7 is specifically designed for the annotation of bacterial genomes sequenced with NGS. This tool is sequence error tolerant maintaining their capabilities for the annotation of highly fragmented genomes or for annotating mixed sequences coming from several genomes (as those obtained through metagenomics samples). BG7 has been designed with scalability as a requirement, with a computing infrastructure completely based on cloud computing (Amazon Web Services).
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An Annotated Math Lab Inventory.
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)
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Connect high speed analog-digital converter with EPICS based on LabVIEW
International Nuclear Information System (INIS)
Wang Wei; Chi Yunlong
2008-01-01
This paper introduce a method to connect high speed analog-digital converter (ADC212/100) with EPICS on Windows platform using LabVIEW. We use labVIEW to communicate with the converter, then use interface sub-VIs between LabVIEW and EPICS to access the EPICS IOC by Channel Access (CA). For the easy use graph programming language of LabVIEW, this method could shorten the develop period and reduce manpower cost. (authors)
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Rebecca Leam
The CERN film-making club is organizing the second edition of the CinéGlobe International Short Film Festival and everyone is invited to attend a series of selection screenings in November to vote on which they like and think should be publicly shown in the Globe and at the Forum Meyrin in February 2010. This year over 700 short films were submitted for three competitions: the majority for the general fiction category for films up to ten minutes in length, and others for science fiction (20 minutes) and science documentary (30 minutes). “In 2007 we had just one competition open to films from any genre. We decided to add the science related competitions to the second edition to make a stronger link with CERN as a physics lab,” explained Quentin King, Chairman of the Selection Committee and member of CERN’s film-making club, Open Your Eyes Films. “The entries are extremely diverse and touch on almost every aspect of life. The creativity of short...
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Directory of Open Access Journals (Sweden)
Wayne Aubrey
Full Text Available Many advances in synthetic biology require the removal of a large number of genomic elements from a genome. Most existing deletion methods leave behind markers, and as there are a limited number of markers, such methods can only be applied a fixed number of times. Deletion methods that recycle markers generally are either imprecise (remove untargeted sequences, or leave scar sequences which can cause genome instability and rearrangements. No existing marker recycling method is automation-friendly. We have developed a novel openly available deletion tool that consists of: 1 a method for deleting genomic elements that can be repeatedly used without limit, is precise, scar-free, and suitable for automation; and 2 software to design the method's primers. Our tool is sequence agnostic and could be used to delete large numbers of coding sequences, promoter regions, transcription factor binding sites, terminators, etc in a single genome. We have validated our tool on the deletion of non-essential open reading frames (ORFs from S. cerevisiae. The tool is applicable to arbitrary genomes, and we provide primer sequences for the deletion of: 90% of the ORFs from the S. cerevisiae genome, 88% of the ORFs from S. pombe genome, and 85% of the ORFs from the L. lactis genome.
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Electronics lab instructors' approaches to troubleshooting instruction
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.
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Directory of Open Access Journals (Sweden)
Francisco Rodriguez Gomez
2014-09-01
Full Text Available Dairy products are currently the main carriers of probiotic microorganisms to the human body. However, the development of new matrices for probiotic delivery is convenient for intolerant to milk (or its derivatives and those requiring low-cholesterol diet consumers. The present work focused on the fortification of previously fermented green Spanish style olives with the autochthonous putative probiotic bacteria Lactobacillus pentosus TOMC-LAB2. The fortification was carried out by inoculating the bacteria into the packing brines using Manzanilla fruits from three different processes: i spontaneously fermented (F1, ii fermented using L. pentosus TOMC-LAB2 as starter (F2, and iii spontaneously fermented and then thermally treated (F3. Data showed that all inoculated treatments had higher population levels (5.49, 4.41 and 6.77 log10 cfu/cm2 than their respective controls (1.66, 4.33 and 0.0 log10 cfu/cm2, for F1, F2 and F3 treatments, respectively. The presence of L. pentosus TOMC-LAB2 on olive surface was confirmed by rep-PCR, with a recovery frequency at the end of the shelf life (200 days of 52.6, 57.9 and 100.0% for F1, F2 and F3 treatments, respectively. Thus, results obtained in this work show the ability of this microorganism to survive under packing conditions for long period of times as well as to colonize the olive surface which is the food finally ingested by consumers. This opens the possibility for the development of a new and simply probiotic fortified olive product.
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The Influence of Tablet PCs on Students' Use of Multiple Representations in Lab Reports
Guelman, Clarisa Bercovich; De Leone, Charles; Price, Edward
2009-11-01
This study examined how different tools influenced students' use of representations in the Physics laboratory. In one section of a lab course, every student had a Tablet PC that served as a digital-ink based lab notebook. Students could seamlessly create hand-drawn graphics and equations, and write lab reports on the same computer used for data acquisition, simulation, and analysis. In another lab section, students used traditional printed lab guides, kept paper notebooks, and then wrote lab reports on regular laptops. Analysis of the lab reports showed differences between the sections' use of multiple representations, including an increased use of diagrams and equations by the Tablet users.
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FameLab Switzerland: a CERN PhD student triumphs
Alexander Brown
2013-01-01
Would you be able to explain your work to a non-specialist in just three minutes? On Friday 24 May, the Swiss national final of FameLab saw six young researchers from CERN attempt just that. FameLab is an international competition in the style of a TV talent show, seeking out the next generation of talent in science communication. Participants in the Swiss national final of FameLab alongside Deni Subasic, presenter of the event (far left), on Friday 24 May. Having qualified from the Geneva heat held in the Globe in March, the six CERN representatives took to the stage in Moods bar in Zurich. As well as particle physics, from the fundamental building blocks (literally) of the Standard Model to medical applications, the line-up featured immunology, neurology and genetics. Although slideshows are strictly banned from FameLab, other visual props are strongly encouraged. For instance, Piotr Traczyk (CMS) represented the apparent chaos of particle collisions by throwing together two decks of ca...
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Interfacing LabVIEW With Instrumentation for Electronic Failure Analysis and Beyond
Buchanan, Randy K.; Bryan, Coleman; Ludwig, Larry
1996-01-01
The Laboratory Virtual Instrumentation Engineering Workstation (LabVIEW) software is designed such that equipment and processes related to control systems can be operationally lined and controlled by the use of a computer. Various processes within the failure analysis laboratories of NASA's Kennedy Space Center (KSC) demonstrate the need for modernization and, in some cases, automation, using LabVIEW. An examination of procedures and practices with the Failure Analaysis Laboratory resulted in the conclusion that some device was necessary to elevate the potential users of LabVIEW to an operational level in minimum time. This paper outlines the process involved in creating a tutorial application to enable personnel to apply LabVIEW to their specific projects. Suggestions for furthering the extent to which LabVIEW is used are provided in the areas of data acquisition and process control.
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Technical support for open-cycle MHD program
Energy Technology Data Exchange (ETDEWEB)
None
1978-05-01
The support program for open-cycle MHD at Argonne National Lab is developing the analytical tools needed to investigate the performance of the major components in the combined-cycle MHD/steam power system. The analytical effort is centered on the primary components of the system that are unique to MHD and also on the integration of these analytical representations into a model of the entire power producing system. The present project activities include modeling of the combustor, MHD channel, slag separator, and the high-temperature air preheater. In addition, these models are combined into a complete system model, which is at present capable of carrying out optimizations of the entire system on either thermodynamic efficiency or with less confidence, cost of electrical power. Also, in support of the open-cycle program, considerable effort has gone into the formulation of a CDIF Test Plan and a National MHD Test Program.
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Is LabTutor a helpful component of the blended learning approach to biosciences?
Swift, Amelia; Efstathiou, Nikolaos; Lameu, Paula
2016-09-01
To evaluate the use of LabTutor (a physiological data capture and e-learning package) in bioscience education for student nurses. Knowledge of biosciences is important for nurses the world over, who have to monitor and assess their patient's clinical condition, and interpret that information to determine the most appropriate course of action. Nursing students have long been known to find acquiring useable bioscience knowledge challenging. Blended learning strategies are common in bioscience teaching to address the difficulties students have. Student nurses have a preference for hands-on learning, small group sessions and are helped by close juxtaposition of theory and practice. An evaluation of a new teaching method using in-classroom voluntary questionnaire. A structured survey instrument including statements and visual analogue response format and open questions was given to students who participated in Labtutor sessions. The students provided feedback in about the equipment, the learning and the session itself. First year (n = 93) and third year (n = 36) students completed the evaluation forms. The majority of students were confident about the equipment and using it to learn although a few felt anxious about computer-based learning. They all found the equipment helpful as part of their bioscience education and they all enjoyed the sessions. This equipment provides a helpful way to encourage guided independent learning through practice and discovery and because each session is case study based and the relationship of the data to the patient is made clear. Our students helped to evaluate our initial use of LabTutor and found the sessions enjoyable and helpful. LabTutor provides an effective learning tool as part of a blended learning strategy for biosciences teaching. Improving bioscience knowledge will lead to a greater understanding of pathophysiology, treatments and interventions and monitoring. © 2016 John Wiley & Sons Ltd.
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Virtual Labs (Science Gateways) as platforms for Free and Open Source Science
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
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Characterization of Lactic Acid Bacteria (LAB) isolated from Indonesian shrimp paste (terasi)
Amalia, U.; Sumardianto; Agustini, T. W.
2018-02-01
Shrimp paste was one of fermented products, popular as a taste enhancer in many dishes. The processing of shrimp paste was natural fermentation, depends on shrimp it self and the presence of salt. The salt inhibits the growth of undesirable microorganism and allows the salt-tolerant lactic acid bacteria (LAB) to ferment the protein source to lactic acids. The objectives of this study were to characterize LAB isolated from Indonesian shrimp paste or "Terasi" with different times of fermentation (30, 60 and 90 days). Vitech analysis showed that there were four strains of the microorganism referred to as lactic acid bacteria (named: LABS1, LABS2, LABS3 and LABS4) with 95% sequence similarity. On the basis of biochemical, four isolates represented Lactobacillus, which the name Lactobacillus plantarum is proposed. L.plantarum was play role in resulting secondary metabolites, which gave umami flavor in shrimp paste.
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A Remote Direct Sequence Spread Spectrum Communications Lab Utilising the Emona DATEx
Directory of Open Access Journals (Sweden)
Cosmas Mwikirize
2012-12-01
Full Text Available Remote labs have become popular learning aids due to their versatility and considerable ease of utilisation as compared to their physical counterparts. At Makerere University, the remote labs are based on the standard Massachusetts Institute of Technology (MIT iLabs Shared Architecture (ISA - a scalable and generic platform. Presented in this paper is such a lab, addressing the key practical aspects of Direct Sequence Spread Spectrum (DSSS communication. The lab is built on the National Instruments Educational Laboratory Virtual Instrumentation Suite (NI ELVIS with the Emona Digital and Analog Telecommunications Experimenter (DATEx add-on board. It also incorporates switching hardware. The lab facilitates real-time control of the equipment, with users able to set, manipulate and observe signal parameters in both the frequency and the time domains. Simulation and data Acquisition modes of the experiment are supported to provide a richer learning experience.
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DEFF Research Database (Denmark)
Aylward, Frank O.; McDonald, Bradon R.; Adams, Sandra M.
2013-01-01
to the genus Sphingobium. Our pan-genomic analysis of sphingomonads reveals numerous species-specific open reading frames (ORFs) but few signatures of genus-specific cores. The organization and coding potential of the sphingomonad genomes appear to be highly variable, and plasmid-mediated gene transfer...... and chromosome-plasmid recombination, together with prophage- and transposon-mediated rearrangements, appear to play prominent roles in the genome evolution of this group. We find that many of the sphingomonad genomes encode numerous oxygenases and glycoside hydrolases, which are likely responsible...... a basis for understanding the ecological strategies employed by sphingomonads and their role in environmental nutrient cycling....
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Innovative Use of a Classroom Response System During Physics Lab
Walgren, Jay
2011-01-01
More and more physics instructors are making use of personal/classroom response systems or "clickers." The use of clickers to engage students with multiple-choice questions during lecture and available instructor resources for clickers have been well documented in this journal.1-4 Newer-generation clickers, which I refer to as classroom response systems (CRS), have evolved to accept numeric answers (such as 9.81) instead of just single "multiple-choice" entries (Fig. 1). This advancement is available from most major clicker companies and allows for a greater variety of engaging questions during lecture. In addition, these new "numeric ready" clickers are marketed to be used for student assessments. During a test or quiz, students' answers are entered into their clicker instead of on paper or Scantron® and immediately absorbed by wireless connection into a computer for grading and analysis. I recognize the usefulness and benefit these new-generation CRSs provide for many instructors. However, I do not use my CRS in either of the aforementioned activities. Instead, I use it in an unconventional way. I use the CRS to electronically capture students' lab data as they are performing a physics lab (Fig. 2). I set up the clickers as if I were going to use them for a test, but instead of entering answers to a test, my students enter lab data as they collect it. In this paper I discuss my use of a classroom response system during physics laboratory and three benefits that result: 1) Students are encouraged to "take ownership of" and "have integrity with" their physics lab data. 2) Students' measuring and unit conversion deficiencies are identified immediately during the lab. 3) The process of grading students' labs is simplified because the results of each student's lab calculations can be pre-calculated for the instructor using a spreadsheet. My use of clickers during lab can be implemented with most clicker systems available to instructors today. The CRS I use is the e
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Tema 2: Open Roberta - A Web Based Approach to Visually Program Real Educational Robots
Directory of Open Access Journals (Sweden)
Markus Ketterl
2016-01-01
Full Text Available The aim of the Open Roberta initiative is to support visual online programming of educational robots. The goal is to overcome technical and professional barriers for teachers and students alike at home or in the classrooms. The free to use cloud-based Open Roberta Lab consists of graphical programming tools for the browser that enable beginners to seamlessly start coding without long-winded system installations, setups or additional technology getting in the way. Open Roberta is a project within the Fraunhofer initiative ”Roberta - Learning with Robots”. A further aspect of the paper is the introduction of the NEPOR meta programming language as a core concept for coupling real educational robot systems.
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Tema 2: Open Roberta - A Web Based Approach to Visually Program Real Educational Robots
Directory of Open Access Journals (Sweden)
Markus Ketterl
2015-12-01
Full Text Available The aim of the Open Roberta initiative is to support visual online programming of educational robots. The goal is to overcome technical and professional barriers for teachers and students alike at home or in the classrooms. The free to use cloud-based Open Roberta Lab consists of graphical programming tools for the browser that enable beginners to seamlessly start coding without long-winded system installations, setups or additional technology getting in the way. Open Roberta is a project within the Fraunhofer initiative ”Roberta - Learning with Robots”. A further aspect of the paper is the introduction of the NEPOR meta programming language as a core concept for coupling real educational robot systems.
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First results on GlioLab/GlioSat Precursors Missions
Cappelletti, Chantal; Notarangelo, Angelo; Demoss, Darrin; Carella, Massimo
2012-07-01
Since 2009 GAUSS group is involved in a joint collaboration with Morehead State University (MSU) Space Science Center and IRCCS Casa Sollievo della Sofferenza (CSS) research labs with the aim to design a biomedical project in order to investigate if the combined effects of microgravity conditions and ionizing radiation increase or decrease the survival rate of cancer cells. The biological sample consists of Glioblastoma cancer cell line ANGM-CSS. Glioblastoma is a kind of cancer that can be treated after surgery only by radiotherapy using ionizing radiation. This treatment, anyway, results in a very low survival rate. This project uses different university space platforms: a CubeLab, named GlioLab, on board the International Space Station and the university microsatellite UniSat-5 designed by GAUSS. In addition a GlioLab/GlioSat precursor experiment has already flown two times with the Space Shuttle during the missions STS-134 and STS-135. The phase 0 or the precursor of GlioLab uses a COTS system, named Liquid Mixing Apparatus (LMA), to board the biological samples inside the Space Shuttle for thirty day . The LMA allows to board liquids inside a vial but is not equipped with environment control system. After landing the samples were investigated by researchers at CSS in Italy and at MSU in Kentucky. This paper deals with the experimental set up and the results obtained during the STS-134 and STS-135 missions and with the new evidences on the behavior of this kind of cancer. In particular the results obtained on the DNA analysis give a confirmation of the original idea of GLioLab/Gliosat project justifying the development of the two systems.
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Exceptionally diverse morphotypes and genomes of crenarchaeal hyperthermophilic viruses
DEFF Research Database (Denmark)
Prangishvili, D; Garrett, R A
2004-01-01
and Rudiviridae. They all have double-stranded DNA genomes and infect hyperthermophilic crenarchaea of the orders Sulfolobales and Thermoproteales. Representatives of the different viral families share a few homologous ORFs (open reading frames). However, about 90% of all ORFs in the seven sequenced genomes show...... no significant matches to sequences in public databases. This suggests that these hyperthermophilic viruses have exceptional biochemical solutions for biological functions. Specific features of genome organization, as well as strategies for DNA replication, suggest that phylogenetic relationships exist between...... crenarchaeal rudiviruses and the large eukaryal DNA viruses: poxviruses, the African swine fever virus and Chlorella viruses. Sequence patterns at the ends of the linear genome of the lipothrixvirus AFV1 are reminiscent of the telomeric ends of linear eukaryal chromosomes and suggest that a primitive telomeric...
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An update on Lab Rover: A hospital material transporter
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.
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Aerial view of the water reservoirs for Lab II
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.
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Genome editing: The efficient tool CRISPR–Cpf1
Mahfouz, Magdy M.
2017-01-01
The novel features of the CRISPR–Cpf1 RNA-guided endonuclease system facilitate precise and efficient genome engineering. Application of CRISPR–Cpf1 in plants shows promise for robust gene editing and regulation, opening exciting possibilities for targeted trait improvement in crops.
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Genome editing: The efficient tool CRISPR–Cpf1
Mahfouz, Magdy M.
2017-03-01
The novel features of the CRISPR–Cpf1 RNA-guided endonuclease system facilitate precise and efficient genome engineering. Application of CRISPR–Cpf1 in plants shows promise for robust gene editing and regulation, opening exciting possibilities for targeted trait improvement in crops.
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Observing copepods through a genomic lens
Directory of Open Access Journals (Sweden)
Johnson Stewart C
2011-09-01
provide genomics tools for copepods. Summary Genomics research on copepods is needed to extend our exploration and characterization of their fundamental biological traits, so that we can better understand how copepods function and interact in diverse environments. Availability of large scale genomics resources will also open doors to a wide range of systems biology type studies that view the organism as the fundamental system in which to address key questions in ecology and evolution.
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Observing copepods through a genomic lens
2011-01-01
copepods. Summary Genomics research on copepods is needed to extend our exploration and characterization of their fundamental biological traits, so that we can better understand how copepods function and interact in diverse environments. Availability of large scale genomics resources will also open doors to a wide range of systems biology type studies that view the organism as the fundamental system in which to address key questions in ecology and evolution. PMID:21933388
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Application of DICOM Standard in LabVIEW Environment
Directory of Open Access Journals (Sweden)
Dušan KONIAR
2008-01-01
Full Text Available DICOM is the world standard for picture archiving and communication in medicine. Development system LabVIEW based on graphical programming is primary designed for virtual instrumentation, it offers many tools and operators for image processing and analysis, but it does not directly support the work with DICOM standard. The article deals with possibility of importing native DICOM files to LabVIEW and work with them.
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PlanetLab Europe as Geographically-Distributed Testbed for Software Development and Evaluation
Directory of Open Access Journals (Sweden)
Dan Komosny
2015-01-01
Full Text Available In this paper, we analyse the use of PlanetLab Europe for development and evaluation of geographically-oriented Internet services. PlanetLab is a global research network with the main purpose to support development of new Internet services and protocols. PlanetLab is divided into several branches; one of them is PlanetLab Europe. PlanetLab Europe consists of about 350 nodes at 150 geographically different sites. The nodes are accessible by remote login, and the users can run their software on the nodes. In the paper, we study the PlanetLab's properties that are significant for its use as a geographically distributed testbed. This includes node position accuracy, services availability and stability. We find a considerable number of location inaccuracies and a number of services that cannot be considered as reliable. Based on the results we propose a simple approach to nodes selection in testbeds for geographically-oriented Internet services development and evaluation.
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78 FR 60245 - Privacy Act Systems of Records; LabWare Laboratory Information Management System
2013-10-01
... of Records; LabWare Laboratory Information Management System AGENCY: Animal and Plant Health... system of records, entitled LabWare Laboratory Information Management System (LabWare LIMS), to maintain... Affairs, OMB. Thomas J. Vilsack, Secretary. SYSTEM NAME: LabWare Laboratory Information Management System...
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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.
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Lifescience Database Archive (English)
Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods ...B link & Genome analysis methods English archive site is opened. 2012/08/08 PGDBj... Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods is opened. About This...ate History of This Database - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...
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Cost-effective cloud computing: a case study using the comparative genomics tool, roundup.
Kudtarkar, Parul; Deluca, Todd F; Fusaro, Vincent A; Tonellato, Peter J; Wall, Dennis P
2010-12-22
Comparative genomics resources, such as ortholog detection tools and repositories are rapidly increasing in scale and complexity. Cloud computing is an emerging technological paradigm that enables researchers to dynamically build a dedicated virtual cluster and may represent a valuable alternative for large computational tools in bioinformatics. In the present manuscript, we optimize the computation of a large-scale comparative genomics resource-Roundup-using cloud computing, describe the proper operating principles required to achieve computational efficiency on the cloud, and detail important procedures for improving cost-effectiveness to ensure maximal computation at minimal costs. Utilizing the comparative genomics tool, Roundup, as a case study, we computed orthologs among 902 fully sequenced genomes on Amazon's Elastic Compute Cloud. For managing the ortholog processes, we designed a strategy to deploy the web service, Elastic MapReduce, and maximize the use of the cloud while simultaneously minimizing costs. Specifically, we created a model to estimate cloud runtime based on the size and complexity of the genomes being compared that determines in advance the optimal order of the jobs to be submitted. We computed orthologous relationships for 245,323 genome-to-genome comparisons on Amazon's computing cloud, a computation that required just over 200 hours and cost $8,000 USD, at least 40% less than expected under a strategy in which genome comparisons were submitted to the cloud randomly with respect to runtime. Our cost savings projections were based on a model that not only demonstrates the optimal strategy for deploying RSD to the cloud, but also finds the optimal cluster size to minimize waste and maximize usage. Our cost-reduction model is readily adaptable for other comparative genomics tools and potentially of significant benefit to labs seeking to take advantage of the cloud as an alternative to local computing infrastructure.
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A Simple, Successful Capacitor Lab
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.