WorldWideScience

Sample records for bioinformatics summer institutes

  1. A Summer Program Designed to Educate College Students for Careers in Bioinformatics

    Science.gov (United States)

    Krilowicz, Beverly; Johnston, Wendie; Sharp, Sandra B.; Warter-Perez, Nancy; Momand, Jamil

    2007-01-01

    A summer program was created for undergraduates and graduate students that teaches bioinformatics concepts, offers skills in professional development, and provides research opportunities in academic and industrial institutions. We estimate that 34 of 38 graduates (89%) are in a career trajectory that will use bioinformatics. Evidence from…

  2. Virginia Bioinformatics Institute to expand cyberinfrastructure education and outreach project

    OpenAIRE

    Whyte, Barry James

    2008-01-01

    The National Science Foundation has awarded the Virginia Bioinformatics Institute at Virginia Tech $918,000 to expand its education and outreach program in Cyberinfrastructure - Training, Education, Advancement and Mentoring, commonly known as the CI-TEAM.

  3. The World Nuclear University Summer Institute

    International Nuclear Information System (INIS)

    Rivard, D.; McIntyre, M.

    2007-01-01

    The World Nuclear University (WNU) Summer Institute is a six weeks intensive training program aimed to develop a global leadership in the field of nuclear sciences and technologies. The topics covered include global setting, international regimes, technology innovation and nuclear industry operations. This event has been held annually since 2005. Mark McIntyre and Dominic Rivard attended this activity as a personal initiative. In this paper they will present the WNU and its Summer Institute, share their participation experience and discuss as well of some technical content covered during the Institute, highlighting the benefits this brought to their careers. (author)

  4. Bioinformatics

    DEFF Research Database (Denmark)

    Baldi, Pierre; Brunak, Søren

    , and medicine will be particularly affected by the new results and the increased understanding of life at the molecular level. Bioinformatics is the development and application of computer methods for analysis, interpretation, and prediction, as well as for the design of experiments. It has emerged...

  5. The European Bioinformatics Institute in 2017: data coordination and integration

    Science.gov (United States)

    Cochrane, Guy; Apweiler, Rolf; Birney, Ewan

    2018-01-01

    Abstract The European Bioinformatics Institute (EMBL-EBI) supports life-science research throughout the world by providing open data, open-source software and analytical tools, and technical infrastructure (https://www.ebi.ac.uk). We accommodate an increasingly diverse range of data types and integrate them, so that biologists in all disciplines can explore life in ever-increasing detail. We maintain over 40 data resources, many of which are run collaboratively with partners in 16 countries (https://www.ebi.ac.uk/services). Submissions continue to increase exponentially: our data storage has doubled in less than two years to 120 petabytes. Recent advances in cellular imaging and single-cell sequencing techniques are generating a vast amount of high-dimensional data, bringing to light new cell types and new perspectives on anatomy. Accordingly, one of our main focus areas is integrating high-quality information from bioimaging, biobanking and other types of molecular data. This is reflected in our deep involvement in Open Targets, stewarding of plant phenotyping standards (MIAPPE) and partnership in the Human Cell Atlas data coordination platform, as well as the 2017 launch of the Omics Discovery Index. This update gives a birds-eye view of EMBL-EBI’s approach to data integration and service development as genomics begins to enter the clinic. PMID:29186510

  6. 5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK--Setting the analysis frame.

    Science.gov (United States)

    Stephan, Christian; Hamacher, Michael; Blüggel, Martin; Körting, Gerhard; Chamrad, Daniel; Scheer, Christian; Marcus, Katrin; Reidegeld, Kai A; Lohaus, Christiane; Schäfer, Heike; Martens, Lennart; Jones, Philip; Müller, Michael; Auyeung, Kevin; Taylor, Chris; Binz, Pierre-Alain; Thiele, Herbert; Parkinson, David; Meyer, Helmut E; Apweiler, Rolf

    2005-09-01

    The Bioinformatics Committee of the HUPO Brain Proteome Project (HUPO BPP) meets regularly to execute the post-lab analyses of the data produced in the HUPO BPP pilot studies. On July 7, 2005 the members came together for the 5th time at the European Bioinformatics Institute (EBI) in Hinxton, UK, hosted by Rolf Apweiler. As a main result, the parameter set of the semi-automated data re-analysis of MS/MS spectra has been elaborated and the subsequent work steps have been defined.

  7. Summer institute of sustainability and energy

    Energy Technology Data Exchange (ETDEWEB)

    Crabtree, George W. [Univ. of Illinois, Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States)

    2012-08-01

    The vision for the Summer Institute on Sustainability and Energy (SISE) is to integrate advancements in basic energy sciences with innovative energy technologies to train the next generation of interdisciplinary scientists and policy makers for both government and industry. Through BES related research, these future leaders will be equipped to make educated decisions about energy at the personal, civic, and global levels in energy related fields including science, technology, entrepreneurship, economics, policy, planning, and behavior. This vision explicitly supports the 2008 report by the Department of Energy’s Basic Energy Science Advisory Committee (2), which outlines scientific opportunities and challenges to achieve energy security, lower CO2 emissions, reduce reliance on foreign oil and create enduring economic growth through discovery, development and the marketing of new technologies for sustainable energy production, delivery, and use (3).

  8. Summer Institute for Physical Science Teachers

    Science.gov (United States)

    Maheswaranathan, Ponn; Calloway, Cliff

    2007-04-01

    A summer institute for physical science teachers was conducted at Winthrop University, June 19-29, 2006. Ninth grade physical science teachers at schools within a 50-mile radius from Winthrop were targeted. We developed a graduate level physics professional development course covering selected topics from both the physics and chemistry content areas of the South Carolina Science Standards. Delivery of the material included traditional lectures and the following new approaches in science teaching: hands-on experiments, group activities, computer based data collection, computer modeling, with group discussions & presentations. Two experienced master teachers assisted us during the delivery of the course. The institute was funded by the South Carolina Department of Education. The requested funds were used for the following: faculty salaries, the University contract course fee, some of the participants' room and board, startup equipment for each teacher, and indirect costs to Winthrop University. Startup equipment included a Pasco stand-alone, portable Xplorer GLX interface with sensors (temperature, voltage, pH, pressure, motion, and sound), and modeling software (Wavefunction's Spartan Student and Odyssey). What we learned and ideas for future K-12 teacher preparation initiatives will be presented.

  9. The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

    OpenAIRE

    Bultet, Lisandra Aguilar; Aguilar Rodriguez, Jose; Ahrens, Christian H; Ahrne, Erik Lennart; Ai, Ni; Aimo, Lucila; Akalin, Altuna; Aleksiev, Tyanko; Alocci, Davide; Altenhoff, Adrian; Alves, Isabel; Ambrosini, Giovanna; Pedone, Pascale Anderle; Angelina, Paolo; Anisimova, Maria

    2016-01-01

    The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB'...

  10. An Innovative Summer Institute for Teachers: Examining the Underground Railroad

    Science.gov (United States)

    Dallmer, Denise

    2002-01-01

    In this article, the author describes the summer institute which she planned through her involvement with the Institute for Freedom Studies at Northern Kentucky University, whose purpose is to promote interdisciplinary research, teaching and community outreach grounded in the study of the Underground Railroad. The purpose of the institute was to…

  11. Aspen Global Change Institute Summer Science Sessions

    Energy Technology Data Exchange (ETDEWEB)

    Katzenberger, John; Kaye, Jack A

    2006-10-01

    The Aspen Global Change Institute (AGCI) successfully organized and convened six interdisciplinary meetings over the course of award NNG04GA21G. The topics of the meetings were consistent with a range of issues, goals and objectives as described within the NASA Earth Science Enterprise Strategic Plan and more broadly by the US Global Change Research Program/Our Changing Planet, the more recent Climate Change Program Strategic Plan and the NSF Pathways report. The meetings were chaired by two or more leaders from within the disciplinary focus of each session. 222 scholars for a total of 1097 participants-days were convened under the auspices of this award. The overall goal of each AGCI session is to further the understanding of Earth system science and global environmental change through interdisciplinary dialog. The format and structure of the meetings allows for presentation by each participant, in-depth discussion by the whole group, and smaller working group and synthesis activities. The size of the group is important in terms of the group dynamics and interaction, and the ability for each participant's work to be adequately presented and discussed within the duration of the meeting, while still allowing time for synthesis

  12. Summer Institute in Biomedical Engineering for College Teachers

    Science.gov (United States)

    Cleaver, T. G.; And Others

    1973-01-01

    Discusses the objectives, curricula, and accomplishments of an interdisciplinary summer institute designed to prepare college teachers qualified in both the life sciences and engineering. Indicates that joint educational programs between engineering, science, and medical faculties are completely feasible if each group is interested in the other…

  13. The Advanced Technology Environmental Education Center Summer Fellows Institute.

    Science.gov (United States)

    Depken, Diane E.; Zeman, Catherine L.; Lensch, Ellen Kabat; Brown, Edward J.

    2002-01-01

    Describes the background, activities, and outcomes of the Advanced Technology Environmental Education Center (ATEEC) and its Summer Fellows Institutes as a model for disciplinary and cross-disciplinary infusion of environmental science and technology content, curriculum, and methods into the classroom. Presents experiences, themes, and activities…

  14. Summer Research Institute Interfacial and Condensed Phase Chemical Physics

    Energy Technology Data Exchange (ETDEWEB)

    Barlow, Stephan E.

    2004-10-01

    Pacific Northwest National Laboratory (PNNL) hosted its first annual Summer Research Institute in Interfacial and Condensed Phase Chemical Physics from May through September 2004. During this period, fourteen PNNL scientists hosted sixteen young scientists from eleven different universities. Of the sixteen participants, fourteen were graduate students; one was transitioning to graduate school; and one was a university faculty member.

  15. Summer Institute in Engineering and Computer Applications: Learning Through Experience

    Science.gov (United States)

    Langdon, Joan S.

    1995-01-01

    The document describing the Summer Institute project is made up of the following information: Administrative procedures; Seminars/Special Courses/Tours/College fair; Facilities/ Transportation; Staff and Administration; Collaboration; Participant/Project monitoring and evaluation; Fiscal and developmental activities; Job readiness/Job internship development and placement; and Student Follow-up/Tracking. Appendices include presentations, self-evaluations; abstracts and papers developed by the students during their participation in the program.

  16. Proceedings of Summer Institute on Particle Physics: the weak interaction

    International Nuclear Information System (INIS)

    Mosher, A.

    1981-01-01

    The SLAC Summer Institute on Particle Physics held its eighth session on July 28-August 8, 1980, and the focus of the meeting was The Weak Interaction. Following the now traditional format, the first seven days of the Institute were spent with the mornings given to pedagogic lectures on the experimental and theoretical foundations of the topic. This year included a very stimulating and successful series on the physics of particle detectors. In the afternoons were seminars on the various experimental tools being designed or constructed to further probe the Weak Interaction, followed by lively discussion of the morning's lectures. Again, following the usual format, the school led into a three-day topical conference at which the most recent theoretical and experimental results were presented and discussed. Abstracts of twenty-seven items from the Institute were prepared separately for the data base

  17. 7th International Summer Institute in Surface Science

    CERN Document Server

    Howe, Russell

    1986-01-01

    This volume contains review articles which were written by the invited speak­ ers of the seventh International Summer Institute in Surface Science (ISISS), held at the University of Wisconsin - Milwaukee in July 1985. The form of ISISS is a set of tutorial review lectures presented over a one-week period by internationally recognized experts on various aspects of surface science. Each speaker is asked, in addition, to write a review article on his lecture topic. No single volume in the series Chemistry and Physics of Solid Surfaces can possibly cover the entire field of modern surface science. However, the series as a whole is intended to provide experts and students alike with a comprehensive set of reviews and literature references, particularly empha­ sizing the gas-solid interface. The collected articles from previous Summer Institutes have been published under the following titles: Surface Science: Recent Progress and Perspectives, Crit. Rev. Solid State Sci. 4, 125-559 (1974) Chemistry and Physics of ...

  18. 8th International Summer Institute in Surface Science

    CERN Document Server

    Howe, Russell

    1988-01-01

    This volume contains review articles written by the invited speakers at the eighth International Summer Institute in Surface Science (ISISS 1987), held at the University of Wisconsin-Milwaukee in August of 1987. During the course of ISISS, invited speakers, all internationally recognized experts in the various fields of surface science, present tutorial review lectures. In addition, these experts are asked to write review articles on their lecture topic. Former ISISS speakers serve as advisors concerning the selection of speakers and lecture topics. Em­ phasis is given to those areas which have not been covered in depth by recent Summer Institutes, as well as to areas which have recently gained in significance and in which important progress has been made. Because of space limitations, no individual volume of Chemistry and Physics of Solid Surfaces can possibly cover the whole area of modem surface science, or even give a complete survey of recent pro­ gress in the field. However, an attempt is made to pres...

  19. Howard University Energy Expert Systems Institute Summer Program (EESI)

    Science.gov (United States)

    Momoh, James A.; Chuku, Arunsi; Abban, Joseph

    1996-01-01

    Howard University, under the auspices of the Center for Energy Systems and Controls runs the Energy Expert Systems Institute (EESI) summer outreach program for high school/pre-college minority students. The main objectives are to introduce precollege minority students to research in the power industry using modern state-of-the-art technology such as Expert Systems, Fuzzy Logic and Artificial Neural Networks; to involve minority students in space power management, systems and failure diagnosis; to generate interest in career options in electrical engineering; and to experience problem-solving in a teamwork environment consisting of faculty, senior research associates and graduate students. For five weeks the students are exposed not only to the exciting experience of college life, but also to the inspiring field of engineering, especially electrical engineering. The program consists of lectures in the fundamentals of engineering, mathematics, communication skills and computer skills. The projects are divided into mini and major. Topics for the 1995 mini projects were Expert Systems for the Electric Bus and Breast Cancer Detection. Topics on the major projects include Hybrid Electric Vehicle, Solar Dynamics and Distribution Automation. On the final day, designated as 'EESI Day' the students did oral presentations of their projects and prizes were awarded to the best group. The program began in the summer of 1993. The reaction from the students has been very positive. The program also arranges field trips to special places of interest such as the NASA Goddard Space Center.

  20. An experience in World Nuclear University-Summer Institute 2012

    International Nuclear Information System (INIS)

    Suzilawati Mohd Sarowi

    2013-01-01

    Full-text: World Nuclear University-Summer Institute (WNU-SI) has been held annually since 2005 in Cristchurh College, Oxford, London. This six weeks course is attended by 80-90 young professionals, or fellow from 20-25 countries across the world. The WNU-SI is designed not only to discuss the full spectrum of issues surrounding nuclear energy, but also emphasis on team building, cultural awareness and the development of leadership potential in multinational environment. Interestingly, the mentors play their role base on their experience in leading the nuclear industry throughout the globe. At the end of the course, the participant could understand the most important issues address in the industry with global perspective, experience and learn from practical teamwork internationally. Finally, this course is believed to be a step in developing a worldwide network among the fellows to support each other in their careers. This paper will discuss the experience gained in WNU-SI 2012. (author)

  1. The World Nuclear University and its Summer Institute

    Energy Technology Data Exchange (ETDEWEB)

    Borysova, Irina [World Nuclear Association - WNA, Summer Institute of the World Nuclear University - WNU, 22a Saint James' s Sq., SW1Y 4JH London (United Kingdom)

    2008-07-01

    The World Nuclear University is a global partnership committed to enhancing international education and leadership in the peaceful applications of nuclear science and technology. The central elements of the WNU partnership are: - The global organizations of the nuclear industry: WNA and WANO; - The inter-governmental nuclear agencies: IAEA and OECD-NEA; - Leading institutions of nuclear learning in some thirty countries. The WNU was inaugurated in 2003 as a non-profit corporation. Operationally, the WNU is a public-private partnership. On the public side, the WNUCC's multinational secretariat is composed mainly of nuclear professionals supplied by governments; the IAEA further assists with financial support for certain WNU activities. On the private side, the nuclear industry provides administrative, logistical and financial support via the WNA. WNU activities fall into six programmatic categories: 1. Facilitate Multinational Academic Cooperation. 2. Build Nuclear Leadership. 3. Foster Policy Consensus on Institutional and Technological Innovation. 4. Enhance Public Understanding. 5. Shape Scientific and Regulatory Consensus on Issues Affecting Nuclear Operations. 6. Strengthen International Workforce Professionalism. This presentation will describe the WNU programmes addressed to young professionals. Among such programmes, the flagship of the WNU is the WNU Summer Institute. This unique six-week course occurs in a different country each year, offering an inspiring career opportunity for some 100 outstanding young nuclear professionals and academics from around the world. The WNU-SI programme combines an extensive series of 'big picture' presentations from world-class experts with daily team-building exercises. In the process, WNU Fellows become part of a global network of future nuclear leaders. Other WNU programmes for younger generation in the nuclear industry will also be briefly covered in this presentation. (author)

  2. Lecture 10: The European Bioinformatics Institute - "Big data" for biomedical sciences

    CERN Multimedia

    CERN. Geneva; Dana, Jose

    2013-01-01

    Part 1: Big data for biomedical sciences (Tom Hancocks) Ten years ago witnessed the completion of the first international 'Big Biology' project that sequenced the human genome. In the years since biological sciences, have seen a vast growth in data. In the coming years advances will come from integration of experimental approaches and the translation into applied technologies is the hospital, clinic and even at home. This talk will examine the development of infrastructure, physical and virtual, that will allow millions of life scientists across Europe better access to biological data Tom studied Human Genetics at the University of Leeds and McMaster University, before completing an MSc in Analytical Genomics at the University of Birmingham. He has worked for the UK National Health Service in diagnostic genetics and in training healthcare scientists and clinicians in bioinformatics. Tom joined the EBI in 2012 and is responsible for the scientific development and delivery of training for the BioMedBridges pr...

  3. School nurse summer institute: a model for professional development.

    Science.gov (United States)

    Neighbors, Marianne; Barta, Kathleen

    2004-06-01

    The components of a professional development model designed to empower school nurses to become leaders in school health services is described. The model was implemented during a 3-day professional development institute that included clinical and leadership components, especially coalition building, with two follow-up sessions in the fall and spring. Coalition building is an important tool to enhance the influence of the school nurse in improving the health of individuals, families, and communities. School nurses and nursing educators with expertise in the specialty of school nursing could replicate this model in their own regions.

  4. The first Summer Institute of the World Nuclear University - a personal record

    International Nuclear Information System (INIS)

    Denk, W.; Fischer, C.; Seidl, M.

    2005-01-01

    The first World Nuclear University Summer Institute was held at Idaho Falls, USA, between July 9 and August 20, 2005. The event was hosted by the Institute of Nuclear Science and Engineering of Idaho State University (ISU) and by the Idaho National Laboratory (INL), which has been planned to be the central nuclear technology research institution in the United States. The World Nuclear University (WNU) was founded in 2003 by the International Atomic Energy Agency (IAEA), the OECD Nuclear Energy Agency (OECD-NEA), the World Association of Nuclear Operators (WANO), and the World Nuclear Association (WNA) as a global association fo scientific and educational institutions in the nuclear field. The first WNU Summer Institute was designed at IAEA in Vienna in the course of the following year and planned by the WNU Coordinating Centre in London. The six weeks of lectures and presentations arranged by the World nuclear University in Idaho Falls are described in detail from the participants' perspective. (orig.)

  5. Summer Institute in Agricultural Mechanics Education, Southern Region, Proceedings (Blacksburg, Virginia, August 3-7, 1970).

    Science.gov (United States)

    Virginia Polytechnic Inst. and State Univ., Blacksburg.

    This summer institute emphasizes the establishment of minimum measurable standards of attainment in agricultural engineering phases of teacher education in agriculture. Speeches presented are: (1) "Where We Are in Agricultural Mechanics Education," by Alfred H. Krebs, (2) "Research Offerings for More Effective Teaching in Agricultural Mechanics,"…

  6. Financial Management and Job Social Skills Training Components in a Summer Business Institute

    Science.gov (United States)

    Donohue, Brad; Conway, Debbie; Beisecker, Monica; Murphy, Heather; Farley, Alisha; Waite, Melissa; Gugino, Kristin; Knatz, Danielle; Lopez-Frank, Carolina; Burns, Jack; Madison, Suzanne; Shorty, Carrie

    2005-01-01

    Ninety-two adolescents, predominantly ethnic minority high school students, participated in a structured Summer Business Institute (SBI). Participating youth were randomly assigned to receive either job social skills or financial management skills training components. Students who additionally received the job social skills training component were…

  7. 2005 Annual Report Summer Research Institute Interfacial and Condensed Phase Chemical Physics

    Energy Technology Data Exchange (ETDEWEB)

    Barlow, Stephan E.

    2005-11-15

    The Pacific Northwest National Laboratory (PNNL) hosted its second annual Summer Research Institute in Interfacial and Condensed Phase Chemical Physics from May through September 2005. During this period, sixteen PNNL scientists hosted fourteen young scientists from eleven different universities. Of the fourteen participants, twelve were graduate students; one was a postdoctoral fellow; and one was a university faculty member.

  8. 2006 Annual Report Summer Research Institute Interfacial and Condensed Phase Chemical Physics

    Energy Technology Data Exchange (ETDEWEB)

    Avery, Nikki B.; Barlow, Stephan E.

    2006-11-10

    The Pacific Northwest National Laboratory (PNNL) hosted its third annual Summer Research Institute in Interfacial and Condensed Phase Chemical Physics from May through September 2006. During this period, twenty PNNL scientists hosted twenty-seven scientists from twenty-five different universities. Of the twenty-seven participants, one was a graduating senior; twenty-one were graduate students; one was a postdoctoral fellow; and four were university faculty members.

  9. Summer camp and the AGPA Institute: what do they have in common?

    Science.gov (United States)

    Stone, Walter N

    2011-04-01

    This paper describes similarities between children's experiences when going to summer camp and experiences in the two-day Institute of AGPA. The paper focuses on the dynamics of leadership and membership, addressing tasks involved in joining, including finding the courage and taking the risks required to emotionally fully join a group. Particular resistances arising out of being a therapist-as-member and exposing one's work as a leader to colleagues are discussed.

  10. 2007 Annual Report Summer Research Institute Interfacial and Condensed Phase Chemical Physics

    Energy Technology Data Exchange (ETDEWEB)

    Beck, Kenneth M.

    2007-10-31

    The Pacific Northwest National Laboratory (PNNL) hosted its fourth annual Summer Research Institute in Interfacial and Condensed Phase Chemical Physics from April through September 2007. During this time, 21 PNNL scientists hosted 23 participants from 20 different universities. Of the 23 participants, 20 were graduate students, 1 was a postdoctoral fellow, and 2 were university faculty members. This report covers the essense of the program and the research the participants performed.

  11. The 2013 Summer Undergraduate Research Internship Program at the Pisgah Astronomical Research Institute

    Science.gov (United States)

    Castelaz, Michael W.; Cline, J. D.; Whitworth, C.; Clavier, D.; Barker, T.

    2014-01-01

    Pisgah Astronomical Research Institute (PARI) offers summer undergraduate research internships. PARI has received support for the internships from the EMC Corporation, private donations, private foundations, and through a collaboration with the Pisgah Astronomical Research and Education Center of the University of North Carolina - Asheville. The internship program began in 2001 with 4 students. This year 10 funded students participated. Mentors for the interns include PARI’s Directors of Science, Education, and Information Technology and visiting faculty who are members of the PARI Research Faculty Affiliate program. Students work with mentors on radio and optical astronomy research, electrical engineering for robotic control of instruments, software development for instrument control and and science education by developing curricula and multimedia and teaching high school students in summer programs at PARI. At the end of the summer interns write a paper about their research which is published in the PARI Summer Student Proceedings. Students are encouraged to present their research at AAS Meetings. We will present a summary of specific research conducted by the students with their mentors.

  12. The Summer Undergraduate Research Internship Program at the Pisgah Astronomical Research Institute

    Science.gov (United States)

    Cline, J. Donald; Castelaz, M.; Whitworth, C.; Clavier, D.; Owen, L.; Barker, T.

    2012-01-01

    Pisgah Astronomical Research Institute (PARI) offers summer undergraduate research internships. PARI has received support for the internships from the NC Space Grant Consortium, NSF awards for public science education, private donations, private foundations, and through a collaboration with the Pisgah Astronomical Research and Education Center of the University of North Carolina - Asheville. The internship program began in 2001 with 4 students. This year 7 funded students participated in 2011. Mentors for the interns include PARI's Science, Education, and Information Technology Directors and visiting faculty who are members of the PARI Research Affiliate Faculty program. Students work with mentors on radio and optical astronomy research, electrical engineering for robotic control of instruments, software development for instrument control and software for citizen science projects, and science education by developing curricula and multimedia and teaching high school students in summer programs at PARI. At the end of the summer interns write a paper about their research which is published in the PARI Summer Student Proceedings. Several of the students have presented their results at AAS Meetings. We will present a summary of specific research conducted by the students with their mentors, the logistics for hosting the PARI undergraduate internship program, and plans for growth based on the impact of an NSF supported renovation to the Research Building on the PARI campus.

  13. [Factors affecting the adoption of ICT tools in experiments with bioinformatics in biopharmaceutical organizations: a case study in the Brazilian Cancer Institute].

    Science.gov (United States)

    Pitassi, Claudio; Gonçalves, Antonio Augusto; Moreno Júnior, Valter de Assis

    2014-01-01

    The scope of this article is to identify and analyze the factors that influence the adoption of ICT tools in experiments with bioinformatics at the Brazilian Cancer Institute (INCA). It involves a descriptive and exploratory qualitative field study. Evidence was collected mainly based on in-depth interviews with the management team at the Research Center and the IT Division. The answers were analyzed using the categorical content method. The categories were selected from the scientific literature and consolidated in the Technology-Organization-Environment (TOE) framework created for this study. The model proposed made it possible to demonstrate how the factors selected impacted INCA´s adoption of bioinformatics systems and tools, contributing to the investigation of two critical areas for the development of the health industry in Brazil, namely technological innovation and bioinformatics. Based on the evidence collected, a research question was posed: to what extent can the alignment of the factors related to the adoption of ICT tools in experiments with bioinformatics increase the innovation capacity of a Brazilian biopharmaceutical organization?

  14. Development of human resources through the 2nd WNU Summer Institute

    International Nuclear Information System (INIS)

    Min, B. J.; Kang, H. K.; Kim, E. S.; Yun, S. K.

    2006-10-01

    WNU-SI(World Nuclear University - Summer Institute) is the six-week program designed to develop and inspire future international leaders in the field of nuclear science and technology. In 2006, three Korean young scientists had chances to participate by support of this project. There were three purposes in this project; (1) to motivate young Korean nuclear engineers, (2) to develop the human network with future nuclear leaders in the world, (3) to collect the information for successful WNU-SI 2007 Korea

  15. Proceedings of Summer Institute of Particle Physics, July 27-August 7, 1981: the strong interactions

    Energy Technology Data Exchange (ETDEWEB)

    Mosher, A. (ed.)

    1982-01-01

    The ninth SLAC Summer Institute on Particle Physics was held in the period July 27 to August 7, 1981. The central topic was the strong interactions with the first seven days spent in a pedagogic mode and the last three in a topical conference. In addition to the morning lectures on experimental and theoretical aspects of the strong interactions, three were lectures on machine physics; this year it was electron-positron colliding beam machines, both storage rings and linear colliders. Twenty-three individual items from the meeting were prepared separately for the data base. (GHT)

  16. 1992 Environmental Summer Science Camp Program evaluation. The International Environmental Institute of Westinghouse Hanford Company

    Energy Technology Data Exchange (ETDEWEB)

    1993-07-01

    This report describes the 1992 Westinghouse Hanford Company/US Department of Energy Environmental Summer Science Camp. The objective of the ``camp`` was to motivate sixth and seventh graders to pursue studies in math, science, and the environment. This objective was accomplished through hands-on fun activities while studying the present and future challenges facing our environment. The camp was funded through Technical Task Plan, 424203, from the US Department of Energy-Headquarters, Office of Environmental Restoration and Waste Management, Technology Development,to Westinghouse Hanford Company`s International Environmental Institute, Education and Internship Performance Group.

  17. Development of human resources through the 2nd WNU Summer Institute

    Energy Technology Data Exchange (ETDEWEB)

    Min, B. J.; Kang, H. K.; Kim, E. S.; Yun, S. K

    2006-10-15

    WNU-SI(World Nuclear University - Summer Institute) is the six-week program designed to develop and inspire future international leaders in the field of nuclear science and technology. In 2006, three Korean young scientists had chances to participate by support of this project. There were three purposes in this project; (1) to motivate young Korean nuclear engineers, (2) to develop the human network with future nuclear leaders in the world, (3) to collect the information for successful WNU-SI 2007 Korea.

  18. 2012 Summer Research Experiences for Undergraduates at Pisgah Astronomical Research Institute

    Science.gov (United States)

    Castelaz, Michael W.; Cline, J. D.; Whitworth, C.; Clavier, D.; Owen, L.

    2013-01-01

    Pisgah Astronomical Research Institute (PARI) offers research experiences for undergraduates (REU). PARI receives support for the internships from the NC Space Grant Consortium, NSF awards, private donations, and industry partner funding. The PARI REU program began in 2001 with 4 students and has averaged 6 students per year over the past 11 years. This year PARI hosted 8 funded REU students. Mentors for the interns include PARI’s Science, Education, and Information Technology staff and visiting faculty who are members of the PARI Research Faculty Affiliate program. Students work with mentors on radio and optical astronomy research, electrical engineering for robotic control of instruments, software development for instrument control and software for citizen science projects, and science education by developing curricula and multimedia and teaching high school students in summer programs at PARI. At the end of the summer interns write a paper about their research which is published in the annually published PARI Summer Student Proceedings. Several of the students have presented their results at AAS Meetings. We will present a summary of specific research conducted by the students with their mentors and the logistics for hosting the PARI undergraduate internship program.

  19. The Lunar and Planetary Institute Summer Intern Program in Planetary Science

    Science.gov (United States)

    Kramer, G. Y.

    2017-12-01

    Since 1977, the Lunar and Planetary Institute (LPI) Summer Intern Program brings undergraduate students from across the world to Houston for 10 weeks of their summer where they work one-on-one with a scientist at either LPI or Johnson Space Center on a cutting-edge research project in the planetary sciences. The program is geared for students finishing their sophomore and junior years, although graduating seniors may also apply. It is open to international undergraduates as well as students from the United States. Applicants must have at least 50 semester hours of credit (or equivalent sophomore status) and an interest in pursuing a career in the sciences. The application process is somewhat rigorous, requiring three letters of recommendation, official college transcripts, and a letter describing their background, interests, and career goals. The deadline for applications is in early January of that year of the internship. More information about the program and how to apply can be found on the LPI website: http://www.lpi.usra.edu/lpiintern/. Each advisor reads through the applications, looking for academically excellent students and those with scientific interest and backgrounds compatible with the advisor's specific project. Interns are selected fairly from the applicant pool - there are no pre-arranged agreements or selections based on who knows whom. The projects are different every year as new advisors come into the program, and existing ones change their research interest and directions. The LPI Summer Intern Program gives students the opportunity to participate in peer-reviewed research, learn from top-notch planetary scientists, and preview various careers in science. For many interns, this program was a defining moment in their careers - when they decided whether or not to follow an academic path, which direction they would take, and how. While past interns can be found all over the world and in a wide variety of occupations, all share the common bond of

  20. The summer institute in clinical dental research methods: still going and growing after twenty years.

    Science.gov (United States)

    Derouen, Timothy A; Wiesenbach, Carol

    2012-11-01

    The first Summer Institute in Clinical Dental Research Methods, a faculty development program at the University of Washington, was offered in the summer of 1992 for sixteen participants. The primary objective of the program was to give clinical faculty members in dentistry an introduction to and an understanding of the fundamental principles and methods used in good clinical research. In the twentieth offering of the institute in 2011, there were thirty-five participants, and over the twenty institutes, there has been a cumulative total of 463 participants who have come from thirty U.S. states as well as forty-three countries outside the United States. The curriculum has expanded from the initial offering of biostatistics, clinical epidemiology, behavioral research methods, and ethics in clinical research to now include clinical trials, grantsmanship, data analysis, an elective in molecular biology, and a team project that provides participants with hands-on experience in research proposal development as members of an interdisciplinary team. Enrollment has doubled since the first year, yet exit evaluations of the program content have remained consistently high (rated as very good to excellent). One of the indicators of program quality is that at least 50 percent of recent participants indicated that they attended because the program was recommended by colleagues who had attended. There seems to be an ever-increasing pool of dental faculty members who are eager to learn more about clinical research methodology through the institute despite the intensive demands of full-time participation in a six-week program.

  1. Energy, environment, and policy choices: Summer institutes for science and social studies educators

    Energy Technology Data Exchange (ETDEWEB)

    Marek, E.A.; Chiodo, J.J.; Gerber, B.L.

    1997-06-01

    The Center for Energy Education (CEE) is a partnership linking the University of Oklahoma, Close Up Foundation and Department of Energy. Based upon the theme of energy, environment and public policy, the CEE`s main purposes are to: (1) educate teachers on energy sources, environmental issues and decisionmaking choices regarding public policy; (2) develop interdisciplinary curricula that are interactive in nature (see attachments); (3) disseminate energy education curricula; (4) serve as a resource center for a wide variety of energy education materials; (5) provide a national support system for teachers in energy education; and (6) conduct research in energy education. The CEE conducted its first two-week experimentially-based program for educators during the summer of 1993. Beginning at the University of Oklahoma, 57 teachers from across the country examined concepts and issues related to energy and environment, and how the interdependence of energy and environment significantly influences daily life. During the second week of the institute, participants went to Washington, D.C. to examine the processes used by government officials to make critical decisions involving interrelationships among energy, environment and public policy. Similar institutes were conducted during the summers of 1994 and 1995 resulting in nearly 160 science and social studies educators who had participated in the CEE programs. Collectively the participants represented 36 states, the Pacific Territories, Puerto Rico, and Japan.

  2. 2008 Summer Research Institute Interfacial and Condensed Phase Chemical Physics Annual Report

    Energy Technology Data Exchange (ETDEWEB)

    Garrett, Bruce C.; Tonkyn, Russell G.; Avery, Nachael B.

    2008-11-01

    For the fifth year, the Pacific Northwest National Laboratory in Richland, Washington, invited graduate students, postdoctoral fellows, university faculty, and students entering graduate students from around the world to participate in the Summer Research Institute in Interfacial and Condensed Phase Chemical Physics. The institute offers participants the opportunity to gain hands-on experience in top-notch research laboratories while working along internationally respected mentors. Of the 38 applicants, 20 were accepted for the 8- to 10-week program. The participants came from universities as close as Seattle and Portland and as far away as Germany and Singapore. At Pacific Northwest National Laboratory, the 20 participants were mentored by 13 scientists. These mentors help tailor the participant’s experience to the needs of that person. Further, the mentors provide guidance on experimental and theoretical techniques, research design and completion, and other aspects of scientific careers in interfacial and condensed phase chemical physics. The research conducted at the institute can result in tangible benefits for the participants. For example, many have co-authored papers that have been published in peer-reviewed journals, including top-rated journals such as Science. Also, they have presented their research at conferences, such as the Gordon Research Conference on Dynamics at Surfaces and the AVS national meeting. Beyond that, many of the participants have started building professional connections with researchers at Pacific Northwest National Laboratory, connections that will serve them well during their careers.

  3. Proceedings of the Summer institute on particle physics: The top quark and the electroweak interaction

    Energy Technology Data Exchange (ETDEWEB)

    Burke, D.; Dixon, L.; Leith, D.W.G.S.

    1997-01-01

    The XXIII SLAC Summer Institute on Particle Physics addressed the physics of the recently discovered top quark, and its connection to the electroweak interaction and to physics beyond the Standard Model. The seven-day school portion of the Institute covered many avenues for studying the top quark, from its direct production at hadron colliders and at future electron-positron colliders, to its virtual effects in precision electroweak quantities, in heavy flavor physics, and in the renormalization of supersymmetric theories, Vertex detectors - critical for identifying the b quark decay products of the top - and Cherenkov techniques for particle identification were also reviewed. The Institute concluded with a three-day topical conference covering recent developments in theory and experiment; this year, the highlights were the CDF and D0 top quark discovery. Also featured were updated precision electroweak measurements from SLC, LEP, and the Tevatron, heavy quark results from these facilities as well as CLEO, and new photoproduction and deep-inelastic scattering data from HERA. Separate abstracts have been submitted to the energy database for articles from this proceedings.

  4. Proceedings of the Summer institute on particle physics: The top quark and the electroweak interaction

    International Nuclear Information System (INIS)

    Burke, D.; Dixon, L.; Leith, D.W.G.S.

    1997-01-01

    The XXIII SLAC Summer Institute on Particle Physics addressed the physics of the recently discovered top quark, and its connection to the electroweak interaction and to physics beyond the Standard Model. The seven-day school portion of the Institute covered many avenues for studying the top quark, from its direct production at hadron colliders and at future electron-positron colliders, to its virtual effects in precision electroweak quantities, in heavy flavor physics, and in the renormalization of supersymmetric theories, Vertex detectors - critical for identifying the b quark decay products of the top - and Cherenkov techniques for particle identification were also reviewed. The Institute concluded with a three-day topical conference covering recent developments in theory and experiment; this year, the highlights were the CDF and D0 top quark discovery. Also featured were updated precision electroweak measurements from SLC, LEP, and the Tevatron, heavy quark results from these facilities as well as CLEO, and new photoproduction and deep-inelastic scattering data from HERA. Separate abstracts have been submitted to the energy database for articles from this proceedings

  5. FCCSET/CEHR summer institutes for teacher development in science, mathematics, and technology. Final report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-05-01

    This report summarizes the profiling procedure that grantees used to carry out a formative evaluation of their summer institutes. It discusses programmatic issues identified through profiling as well as how well the profiling process worked for the grantees. The report contains recommendations on both programmatic issues and profiling for NSTC/DOE, NCISE (the technical assistance provider), and the grantees themselves. In early September NCISE held its second workshop for NSTC grantees. Data from the evaluation of this two-day event generated six recommendations for DOE and the technical assistance provider. This NCISE report summarizes the two-year process NCISE used in attempting to help the grantees establish some indicators of success. A number of indicators were identified the first year with others added the second year. Additionally, a compilation of the various measures for the indicators of success developed collaboratively by NCISE and grantees is included. Although these indicators are not mandatory, they do provide guides for grantees in assessing the impact of the institutes. Embedded in the report are several recommendations for NSTC/DOE and the technical assistance provider.

  6. Student-Athlete Perceptions of a Summer Pre-Enrollment Experience at an NCAA Division I-AAA Institution

    Science.gov (United States)

    Dalgety, Michael Franklin

    2012-01-01

    The purpose of this exploratory qualitative study was to examine student-athlete perceptions of the role of summer pre-enrollment in their adjustment and transition to college. The study focused on student-athletes who received athletically-related financial aid at a National Collegiate Athletic Association (NCAA) Division I-AAA institution. The…

  7. Proceedings of Summer Institute on particle physics: Lepton-Hadron scattering

    International Nuclear Information System (INIS)

    Hawthorne, J.

    1992-09-01

    The nineteenth annual SLAC Summer Institute on Particle Physics took place from August 5 to 16, 1991, attracting 236 participants from 10 different countries. The theme was lepton-hadron scattering, the subjects ranging from the pioneering SLAC-MIT experiments, through the new era of e-p collisions to be ushered in by HERA. Richard Taylor led off the Institute with a historical review of lepton-proton scattering experiments, from Rutherford to the 1960s, while Sid Drell laid out the theoretical framework, in terms of parton distributions and sum rules. Frank Sciulli picked up where Richard Taylor left off, at the discovery of scaling violation, and brought us up to the present. Joel Feltesse and Roberto Peccei described the physics opportunities at HERA, most notably the investigation of the low x behavior of structure functions. Traudl Hansl-Kozanecka reviewed the current experimental status of QCD, at e + e - and hadron colliders as well as in deep-inelastic lepton-hadron scattering. Bob Hollebeek lectured on techniques for electromagnetic and hadronic calorimetry. Finally, Bob Siemann gave a series of lectures on the many uses of superconductivity in particle accelerators, from bending magnets at FNAL HERA and the SSC to RF cavities at CEBAF and LEP. Following the school, the topical conference provided us with a spectrum of current experimental and theoretical developments. Lepton-hadron scattering experiments at CERN and Fermilab were well represented. The existence of the 17 0 , keV neutrino was debated in two separate talks. We heard the latest results from the CDF and UA2 hadron collider experiments; from the four LEP experiments; and from ARGUS and CLEO. Also presented were overviews of the rare K decay program at BNL, the CP violation experiments at CERN and Fermilab, B physics, neutrino masses and mixings, and precision electroweak theory

  8. Innovation in Collaboration: The Summer Institute on Youth Mentoring as a university-community partnership

    Directory of Open Access Journals (Sweden)

    Kevin R. Jones

    2011-11-01

    Full Text Available The Summer Institute on Youth Mentoring (SIYM at Portland State University is an intensive week-long seminar designed to offer a highly interactive educational opportunity for experienced professionals and leading researchers in the field of youth mentoring. The current study explores the extent to which SIYM represents an example of a successful university-community partnership and identifies ways in which SIYM innovates on established partnership models. Using grounded theory methods and typological analysis, the researchers analysed questionnaire responses from SIYM participants and research fellows to compare key characteristics of SIYM with the elements of effective partnerships described in the literature. Findings suggest that SIYM reflects many essential partnership qualities, including the presence of a shared vision; strong, mutually beneficial relationships; and a partnering process that includes communication and work for positive change. SIYM also introduces several innovations in format and structure that could inform the improvement or development of effective partnership efforts across disciplines. Implications for service providers, researchers and other stakeholders are discussed. Keywords communication, collaboration, mutually beneficial relationships, innovation

  9. Development of human resources through the 3rd WNU Summer Institute

    International Nuclear Information System (INIS)

    Min, B. J.; Kang, H. G.; Shin, J. H.; Lim, S. G.; Lee, A. R.

    2008-01-01

    WNU-SI(World Nuclear University - Summer Institute) is the six-week program designed to develop and inspire future international leaders in the field of nuclear science and technology. In 2007, three Korean young scientists had chances to participate by support of this project. The main purposes in this project are to promote abilities of young Korean nuclear professions, and to build the human network with future leaders in the world-wide nuclear field. The WNU-SI offered an intensive six-week program of lectures, group discussion, field trips, and team projects presented by some of the world's foremost authorities on the global environment and sustainable development, nuclear-related technology innovation, nuclear diplomacy, and nuclear industry operations. The programme is consisted of the following parts. -Lecture -Distinguished Speaker's Presentation -Group Discussion -Case Study -Issue Forum -Technical Tour -Cultural Events Lectures were given by 33 outstanding profession from international organizations, companies, universities and institutes around the world. It covered the wide ranges of subjects from technology to economics and politics. 11 working group were facilitated by Mentors, who are 14 from 8 different countries, to review and discuss about the each lecture subjects. Twice case studies and the issue forum were also main work in working group. The case study is the chance to find the solutions about some specific cases regarding lecture subject. The results was presented and evaluated with all the fellows, mentors and specialists in that field. In the issue forum, the participants selected the subjects they wanted to attend, and proceeded the term project for two weeks after technical tour. This program was one of the highlight in this programme. The final output was presented to the fellows, mentors, and specialists with a final summary report. The following issues were dealt with. -Options for storing radioactive waste -Advantages and

  10. Development of human resources through the 3rd WNU Summer Institute

    Energy Technology Data Exchange (ETDEWEB)

    Min, B. J.; Kang, H. G. [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of); Shin, J. H. [KAIST, Daejeon (Korea, Republic of); Lim, S. G. [Kyunghee University, Seoul (Korea, Republic of); Lee, A. R. [Hanyang University, Seoul (Korea, Republic of)

    2008-01-15

    WNU-SI(World Nuclear University - Summer Institute) is the six-week program designed to develop and inspire future international leaders in the field of nuclear science and technology. In 2007, three Korean young scientists had chances to participate by support of this project. The main purposes in this project are to promote abilities of young Korean nuclear professions, and to build the human network with future leaders in the world-wide nuclear field. The WNU-SI offered an intensive six-week program of lectures, group discussion, field trips, and team projects presented by some of the world's foremost authorities on the global environment and sustainable development, nuclear-related technology innovation, nuclear diplomacy, and nuclear industry operations. The programme is consisted of the following parts. -Lecture -Distinguished Speaker's Presentation -Group Discussion -Case Study -Issue Forum -Technical Tour -Cultural Events Lectures were given by 33 outstanding profession from international organizations, companies, universities and institutes around the world. It covered the wide ranges of subjects from technology to economics and politics. 11 working group were facilitated by Mentors, who are 14 from 8 different countries, to review and discuss about the each lecture subjects. Twice case studies and the issue forum were also main work in working group. The case study is the chance to find the solutions about some specific cases regarding lecture subject. The results was presented and evaluated with all the fellows, mentors and specialists in that field. In the issue forum, the participants selected the subjects they wanted to attend, and proceeded the term project for two weeks after technical tour. This program was one of the highlight in this programme. The final output was presented to the fellows, mentors, and specialists with a final summary report. The following issues were dealt with. -Options for storing radioactive waste -Advantages and

  11. Conference/Symposium: 2017 Princeton-Combustion Institute Summer School on Combustion

    Science.gov (United States)

    2018-02-07

    Technology (KAUST). On behalf of all the attendees, the organizers of the Summer School express their profound gratitude to the lecturers, sponsors...professors. Personally, I want to thank you, Professor Law, and express my gratitude for the tremendous arrangement, great munificence, and the new

  12. The American Indian Summer Institute in Earth System Science (AISESS) at UC Irvine: A Two-Week Residential Summer Program for High School Students

    Science.gov (United States)

    Johnson, K. R.; Polequaptewa, N.; Leon, Y.

    2012-12-01

    Native Americans remain severely underrepresented in the geosciences, despite a clear need for qualified geoscience professionals within Tribal communities to address critical issues such as natural resource and land management, water and air pollution, and climate change. In addition to the need for geoscience professionals within Tribal communities, increased participation of Native Americans in the geosciences would enhance the overall diversity of perspectives represented within the Earth science community and lead to improved Earth science literacy within Native communities. To address this need, the Department of Earth System Science and the American Indian Resource Program at the University California have organized a two-week residential American Indian Summer Institute in Earth System Science (AISESS) for high-school students (grades 9-12) from throughout the nation. The format of the AISESS program is based on the highly-successful framework of a previous NSF Funded American Indian Summer Institute in Computer Science (AISICS) at UC Irvine and involves key senior personnel from the AISICS program. The AISESS program, however, incorporates a week of camping on the La Jolla Band of Luiseño Indians reservation in Northern San Diego County, California. Following the week of camping and field projects, the students spend a week on the campus of UC Irvine participating in Earth System Science lectures, laboratory activities, and tours. The science curriculum is closely woven together with cultural activities, native studies, and communication skills programs The program culminates with a closing ceremony during which students present poster projects on environmental issues relevant to their tribal communities. The inaugural AISESS program took place from July 15th-28th, 2012. We received over 100 applications from Native American high school students from across the nation. We accepted 40 students for the first year, of which 34 attended the program. The

  13. The Minneapolis Heart Institute Foundation Summer Research Internship Program: the benefits of preprofessional experience for prospective physicians.

    Science.gov (United States)

    Willenbring, Benjamin D; McKee, Katherine C; Wilson, Betsy V; Henry, Timothy D

    2008-08-01

    There is a distinct shortage of preprofessional opportunities for undergraduate premedical students. During the last 7 summers, the Minneapolis Heart Institute Foundation Summer Research Internship Program has exposed interested students to cardiology and clinical research. The goals of the internship program are threefold: to bring students in contact with the medical profession, to offer experiences in the various disciplines of cardiology, and to introduce students to clinical research. The success of the program can be measured by its influence on participants' academic pursuits and scholarly contributions. Of the 65 internship alumni, 52 are studying to become physicians and most of the others are in health-related fields. Interns have also contributed abstracts and manuscripts to peer-reviewed journals and presented their research at major conferences.

  14. Integrating the Functions of Institutional Research, Institutional Effectiveness, and Information Management. Professional File. Number 126, Summer 2012

    Science.gov (United States)

    Posey, James T.; Pitter, Gita Wijesinghe

    2012-01-01

    The objective of this paper is to identify common essential information and data needs of colleges and universities and to suggest a model to integrate these data needs into one office or department. The paper suggests there are five major data and information foundations that are essential to the effective functioning of an institution: (a)…

  15. Enhancing the Careers of Under-Represented Junior Faculty in Biomedical Research: The Summer Institute Program to Increase Diversity (SIPID).

    Science.gov (United States)

    Rice, Treva K; Liu, Li; Jeffe, Donna B; Jobe, Jared B; Boutjdir, Mohamed; Pace, Betty S; Rao, Dabeeru C

    2014-01-01

    The Summer Institute Program to Increase Diversity (SIPID) in Health-Related Research is a career advancement opportunity sponsored by the National Heart, Lung, and Blood Institute. Three mentored programs address difficulties experienced by junior investigators in establishing independent research careers and academic advancement. Aims are to increase the number of faculty from under-represented minority groups who successfully compete for external research funding. Data were collected using a centralized data-entry system from three Summer Institutes. Outcomes include mentees' satisfaction rating about the program, grant and publications productivity and specific comments. Fifty-eight junior faculty mentees (38% male) noticeably improved their rates of preparing/submitting grant applications and publications, with a 18-23% increase in confidence levels in planning and conducting research. According to survey comments, the training received in grantsmanship skills and one-on-one mentoring were the most valuable program components. The SIPID mentoring program was highly valued by the junior faculty mentees. The program will continue in 2011-2014 as PRIDE (PRogram to Increase Diversity among individuals Engaged in health-related research). Long-term follow-up of current mentees will be indexed at five years post training (2013). In summary, these mentoring programs hope to continue increasing the diversity of the next generation of scientists in biomedical research.

  16. Online Bioinformatics Tutorials | Office of Cancer Genomics

    Science.gov (United States)

    Bioinformatics is a scientific discipline that applies computer science and information technology to help understand biological processes. The NIH provides a list of free online bioinformatics tutorials, either generated by the NIH Library or other institutes, which includes introductory lectures and "how to" videos on using various tools.

  17. Summer Teacher Enhancement Institute for Science, Mathematics, and Technology Using the Problem-Based Learning Model

    Science.gov (United States)

    Petersen, Richard H.

    1997-01-01

    The objectives of the Institute were: (a) increase participants' content knowledge about aeronautics, science, mathematics, and technology, (b) model and promote the use of scientific inquiry through problem-based learning, (c) investigate the use of instructional technologies and their applications to curricula, and (d) encourage the dissemination of TEI experiences to colleagues, students, and parents.

  18. 75 FR 14565 - NIST Summer Institute for Middle School Science Teachers; Availability of Funds

    Science.gov (United States)

    2010-03-26

    ... areas of science, technology, engineering and mathematics (STEM) at the middle school level (grades 6-8... encourage them to inspire students to pursue careers in STEM fields. DATES: Proposals must be received at... educational institutions that are teaching students in the areas of Science, Technology, Engineering and...

  19. Evaluation of the Radiography Program at Caldwell Community College and Technical Institute--Summer, 1982.

    Science.gov (United States)

    Pipes, V. David

    As part of a periodic evaluation of the occupational programs at Caldwell Community College and Technical Institute (CCC&TI), a study of the radiography program was conducted to collect information to facilitate planning, aid in program improvement, and meet accountability demands. The specific objectives of the program evaluation were to…

  20. XXII SLAC summer institute on particle physics: Proceedings. Particle physics, astrophysics and cosmology

    Energy Technology Data Exchange (ETDEWEB)

    Chan, J; DePorcel, L [eds.

    1996-02-01

    The seven-day school portion of the Institute revolved around the question of dark matter: where is it and what is it? Reviews were given of microlensing searches for baryonic dark matter, of dark matter candidates in the form of neutrinos and exotic particles, and of low-noise detection techniques used to search for the latter. The history of the universe, from the Big Bang to the role of dark matter in the formation of large-scale structure, was also covered. Other lecture series described the astrophysics that might be done with x-ray timing experiments and through the detection of gravitational radiation. As in past years, the lectures each morning were followed by stimulating afternoon discussion sessions, in which students could pursue with the lecturers the topics that most interested them. The Institute concluded with a three-day topical conference covering recent developments in theory and experiment. Highlights from the astrophysical and cosmological arenas included observations of anisotropy in the cosmic microwave background, and of the mysterious gamma-ray bursters. From terrestrial accelerators came tantalizing hints of the top quark and marked improvements in precision electroweak measurements, among many other results. Selected papers are indexed separately for inclusion in the Energy Science and Technology Database.

  1. XXII SLAC summer institute on particle physics: Proceedings. Particle physics, astrophysics and cosmology

    International Nuclear Information System (INIS)

    Chan, J.; DePorcel, L.

    1996-02-01

    The seven-day school portion of the Institute revolved around the question of dark matter: where is it and what is it? Reviews were given of microlensing searches for baryonic dark matter, of dark matter candidates in the form of neutrinos and exotic particles, and of low-noise detection techniques used to search for the latter. The history of the universe, from the Big Bang to the role of dark matter in the formation of large-scale structure, was also covered. Other lecture series described the astrophysics that might be done with x-ray timing experiments and through the detection of gravitational radiation. As in past years, the lectures each morning were followed by stimulating afternoon discussion sessions, in which students could pursue with the lecturers the topics that most interested them. The Institute concluded with a three-day topical conference covering recent developments in theory and experiment. Highlights from the astrophysical and cosmological arenas included observations of anisotropy in the cosmic microwave background, and of the mysterious gamma-ray bursters. From terrestrial accelerators came tantalizing hints of the top quark and marked improvements in precision electroweak measurements, among many other results. Selected papers are indexed separately for inclusion in the Energy Science and Technology Database

  2. Proceedings of the summer institute on particle physics: The strong interaction, from hadrons to partons

    International Nuclear Information System (INIS)

    Chan, J.; DePorcel, L.; Dixon, L.

    1997-06-01

    This conference explored the role of the strong interaction in the physics of hadrons and partons. The Institute attracted 239 physicists from 16 countries to hear lectures on the underlying theory of Quantum Chromodynamics, modern theoretical calculational techniques, and experimental investigation of the strong interaction as it appears in various phenomena. Different regimes in which one can calculate reliably in QCD were addressed in series of lectures on perturbation theory, lattice gauge theories, and heavy quark expansions. Studies of QCD in hadron-hadron collisions, electron-positron annihilation, and electron-proton collisions all give differing perspectives on the strong interaction--from low-x to high-Q 2 . Experimental understanding of the production and decay of heavy quarks as well as the lighter meson states has continued to evolve over the past years, and these topics were also covered at the School. Selected papers have been indexed separately for inclusion in the Energy Science and Technology Database

  3. Development of a Web-based International Education and Training Course Management System for World Nuclear University Summer Institute

    International Nuclear Information System (INIS)

    Ahn, S. K.; Min, B. J.; Lee, E. J.; Han, K. W.; Hwang, I. A.; Nam, Y. M.; Kwon, S. J.

    2007-12-01

    For the efficient management of the course, web-based management system is needed especially for international education and training course. The analysis on the essential condition for management system is the first step, considering the applicability for the various education and training courses. Especially, efforts were focused on the management system for user's database and schedule, evaluation system, and various contents for foreign participants. The developed management system has been applied to the World Nuclear University(WNU) Summer Institute. The distinctive feature is that participants' database and program schedule are combined and used for course evaluation function automatically. 170 users had used this system for 3 months and the operating result was successful including the performance of the evaluation. The advantages of the system are simple database management and schedule updating, easy sharing of the training materials, effective activation of interaction between participants, systematic evaluation with a high record of response, and publicity of Korea to foreign participants by various contents. As a weak point, some errors were reported by Mackintosh users, and the input process for the evaluation comments has some limitation for the special characters and some formula text by word processor. These drawbacks could be updated for the future application with additional efforts if needed. The system will offer the cost-effective high performance of the management for the international education and training course

  4. Development of a Web-based International Education and Training Course Management System for World Nuclear University Summer Institute

    Energy Technology Data Exchange (ETDEWEB)

    Ahn, S K; Min, B J; Lee, E J; Han, K W; Hwang, I A; Nam, Y M; Kwon, S J

    2007-12-15

    For the efficient management of the course, web-based management system is needed especially for international education and training course. The analysis on the essential condition for management system is the first step, considering the applicability for the various education and training courses. Especially, efforts were focused on the management system for user's database and schedule, evaluation system, and various contents for foreign participants. The developed management system has been applied to the World Nuclear University(WNU) Summer Institute. The distinctive feature is that participants' database and program schedule are combined and used for course evaluation function automatically. 170 users had used this system for 3 months and the operating result was successful including the performance of the evaluation. The advantages of the system are simple database management and schedule updating, easy sharing of the training materials, effective activation of interaction between participants, systematic evaluation with a high record of response, and publicity of Korea to foreign participants by various contents. As a weak point, some errors were reported by Mackintosh users, and the input process for the evaluation comments has some limitation for the special characters and some formula text by word processor. These drawbacks could be updated for the future application with additional efforts if needed. The system will offer the cost-effective high performance of the management for the international education and training course.

  5. Development of a Web-based International Education and Training Course Management System for World Nuclear University Summer Institute

    Energy Technology Data Exchange (ETDEWEB)

    Ahn, S. K.; Min, B. J.; Lee, E. J.; Han, K. W.; Hwang, I. A.; Nam, Y. M.; Kwon, S. J

    2007-12-15

    For the efficient management of the course, web-based management system is needed especially for international education and training course. The analysis on the essential condition for management system is the first step, considering the applicability for the various education and training courses. Especially, efforts were focused on the management system for user's database and schedule, evaluation system, and various contents for foreign participants. The developed management system has been applied to the World Nuclear University(WNU) Summer Institute. The distinctive feature is that participants' database and program schedule are combined and used for course evaluation function automatically. 170 users had used this system for 3 months and the operating result was successful including the performance of the evaluation. The advantages of the system are simple database management and schedule updating, easy sharing of the training materials, effective activation of interaction between participants, systematic evaluation with a high record of response, and publicity of Korea to foreign participants by various contents. As a weak point, some errors were reported by Mackintosh users, and the input process for the evaluation comments has some limitation for the special characters and some formula text by word processor. These drawbacks could be updated for the future application with additional efforts if needed. The system will offer the cost-effective high performance of the management for the international education and training course.

  6. Computational biology and bioinformatics in Nigeria.

    Science.gov (United States)

    Fatumo, Segun A; Adoga, Moses P; Ojo, Opeolu O; Oluwagbemi, Olugbenga; Adeoye, Tolulope; Ewejobi, Itunuoluwa; Adebiyi, Marion; Adebiyi, Ezekiel; Bewaji, Clement; Nashiru, Oyekanmi

    2014-04-01

    Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in the biological data generated by the scientific community. The critical need to process and analyze such a deluge of data and turn it into useful knowledge has caused bioinformatics to gain prominence and importance. Bioinformatics is an interdisciplinary research area that applies techniques, methodologies, and tools in computer and information science to solve biological problems. In Nigeria, bioinformatics has recently played a vital role in the advancement of biological sciences. As a developing country, the importance of bioinformatics is rapidly gaining acceptance, and bioinformatics groups comprised of biologists, computer scientists, and computer engineers are being constituted at Nigerian universities and research institutes. In this article, we present an overview of bioinformatics education and research in Nigeria. We also discuss professional societies and academic and research institutions that play central roles in advancing the discipline in Nigeria. Finally, we propose strategies that can bolster bioinformatics education and support from policy makers in Nigeria, with potential positive implications for other developing countries.

  7. Computational biology and bioinformatics in Nigeria.

    Directory of Open Access Journals (Sweden)

    Segun A Fatumo

    2014-04-01

    Full Text Available Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in the biological data generated by the scientific community. The critical need to process and analyze such a deluge of data and turn it into useful knowledge has caused bioinformatics to gain prominence and importance. Bioinformatics is an interdisciplinary research area that applies techniques, methodologies, and tools in computer and information science to solve biological problems. In Nigeria, bioinformatics has recently played a vital role in the advancement of biological sciences. As a developing country, the importance of bioinformatics is rapidly gaining acceptance, and bioinformatics groups comprised of biologists, computer scientists, and computer engineers are being constituted at Nigerian universities and research institutes. In this article, we present an overview of bioinformatics education and research in Nigeria. We also discuss professional societies and academic and research institutions that play central roles in advancing the discipline in Nigeria. Finally, we propose strategies that can bolster bioinformatics education and support from policy makers in Nigeria, with potential positive implications for other developing countries.

  8. Biggest challenges in bioinformatics.

    Science.gov (United States)

    Fuller, Jonathan C; Khoueiry, Pierre; Dinkel, Holger; Forslund, Kristoffer; Stamatakis, Alexandros; Barry, Joseph; Budd, Aidan; Soldatos, Theodoros G; Linssen, Katja; Rajput, Abdul Mateen

    2013-04-01

    The third Heidelberg Unseminars in Bioinformatics (HUB) was held on 18th October 2012, at Heidelberg University, Germany. HUB brought together around 40 bioinformaticians from academia and industry to discuss the 'Biggest Challenges in Bioinformatics' in a 'World Café' style event.

  9. Biggest challenges in bioinformatics

    OpenAIRE

    Fuller, Jonathan C; Khoueiry, Pierre; Dinkel, Holger; Forslund, Kristoffer; Stamatakis, Alexandros; Barry, Joseph; Budd, Aidan; Soldatos, Theodoros G; Linssen, Katja; Rajput, Abdul Mateen

    2013-01-01

    The third Heidelberg Unseminars in Bioinformatics (HUB) was held in October at Heidelberg University in Germany. HUB brought together around 40 bioinformaticians from academia and industry to discuss the ‘Biggest Challenges in Bioinformatics' in a ‘World Café' style event.

  10. A bioinformatics potpourri.

    Science.gov (United States)

    Schönbach, Christian; Li, Jinyan; Ma, Lan; Horton, Paul; Sjaugi, Muhammad Farhan; Ranganathan, Shoba

    2018-01-19

    The 16th International Conference on Bioinformatics (InCoB) was held at Tsinghua University, Shenzhen from September 20 to 22, 2017. The annual conference of the Asia-Pacific Bioinformatics Network featured six keynotes, two invited talks, a panel discussion on big data driven bioinformatics and precision medicine, and 66 oral presentations of accepted research articles or posters. Fifty-seven articles comprising a topic assortment of algorithms, biomolecular networks, cancer and disease informatics, drug-target interactions and drug efficacy, gene regulation and expression, imaging, immunoinformatics, metagenomics, next generation sequencing for genomics and transcriptomics, ontologies, post-translational modification, and structural bioinformatics are the subject of this editorial for the InCoB2017 supplement issues in BMC Genomics, BMC Bioinformatics, BMC Systems Biology and BMC Medical Genomics. New Delhi will be the location of InCoB2018, scheduled for September 26-28, 2018.

  11. Challenge: A Multidisciplinary Degree Program in Bioinformatics

    Directory of Open Access Journals (Sweden)

    Mudasser Fraz Wyne

    2006-06-01

    Full Text Available Bioinformatics is a new field that is poorly served by any of the traditional science programs in Biology, Computer science or Biochemistry. Known to be a rapidly evolving discipline, Bioinformatics has emerged from experimental molecular biology and biochemistry as well as from the artificial intelligence, database, pattern recognition, and algorithms disciplines of computer science. While institutions are responding to this increased demand by establishing graduate programs in bioinformatics, entrance barriers for these programs are high, largely due to the significant prerequisite knowledge which is required, both in the fields of biochemistry and computer science. Although many schools currently have or are proposing graduate programs in bioinformatics, few are actually developing new undergraduate programs. In this paper I explore the blend of a multidisciplinary approach, discuss the response of academia and highlight challenges faced by this emerging field.

  12. Bioinformatics and Cancer

    Science.gov (United States)

    Researchers take on challenges and opportunities to mine "Big Data" for answers to complex biological questions. Learn how bioinformatics uses advanced computing, mathematics, and technological platforms to store, manage, analyze, and understand data.

  13. Deep learning in bioinformatics.

    Science.gov (United States)

    Min, Seonwoo; Lee, Byunghan; Yoon, Sungroh

    2017-09-01

    In the era of big data, transformation of biomedical big data into valuable knowledge has been one of the most important challenges in bioinformatics. Deep learning has advanced rapidly since the early 2000s and now demonstrates state-of-the-art performance in various fields. Accordingly, application of deep learning in bioinformatics to gain insight from data has been emphasized in both academia and industry. Here, we review deep learning in bioinformatics, presenting examples of current research. To provide a useful and comprehensive perspective, we categorize research both by the bioinformatics domain (i.e. omics, biomedical imaging, biomedical signal processing) and deep learning architecture (i.e. deep neural networks, convolutional neural networks, recurrent neural networks, emergent architectures) and present brief descriptions of each study. Additionally, we discuss theoretical and practical issues of deep learning in bioinformatics and suggest future research directions. We believe that this review will provide valuable insights and serve as a starting point for researchers to apply deep learning approaches in their bioinformatics studies. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  14. Scientists from all over the world attend the ''Frederic Joliot/Otto Hahn Summer School 2009'' at the Karlsruhe Institute of Technology (KIT)

    International Nuclear Information System (INIS)

    Sanchez Espinoza, Victor Hugo; Fischer, Ulrich

    2009-01-01

    The ''Frederic Joliot/Otto Hahn Summer School'' is organized each year alternately by the Karlsruhe Institute of Technology and the Commissariat a l'Energie Atomique (CEA), Cadarache. This year's Summer School, the 15th since its foundation, was run at the Advanced Training Center (FTU) of KIT Campus Nord on August 26 to September 4. The key topic this year was ''The Challenges in Implementing Fast Reactor Technology.'' These are the items discussed: Principles and challenges of future fast reactor designs, Fuels, fuel cycle, and recycling of minor actinides, Innovative cladding tube and structural materials, Special aspects of coolants and the challenges they pose, Fast reactor safety. Experts from 8 leading international research establishments and universities presented and discussed with the 58 participants from 16 countries the current state of the art and the latest development trends in the topics listed above. (orig.)

  15. Introduction to bioinformatics.

    Science.gov (United States)

    Can, Tolga

    2014-01-01

    Bioinformatics is an interdisciplinary field mainly involving molecular biology and genetics, computer science, mathematics, and statistics. Data intensive, large-scale biological problems are addressed from a computational point of view. The most common problems are modeling biological processes at the molecular level and making inferences from collected data. A bioinformatics solution usually involves the following steps: Collect statistics from biological data. Build a computational model. Solve a computational modeling problem. Test and evaluate a computational algorithm. This chapter gives a brief introduction to bioinformatics by first providing an introduction to biological terminology and then discussing some classical bioinformatics problems organized by the types of data sources. Sequence analysis is the analysis of DNA and protein sequences for clues regarding function and includes subproblems such as identification of homologs, multiple sequence alignment, searching sequence patterns, and evolutionary analyses. Protein structures are three-dimensional data and the associated problems are structure prediction (secondary and tertiary), analysis of protein structures for clues regarding function, and structural alignment. Gene expression data is usually represented as matrices and analysis of microarray data mostly involves statistics analysis, classification, and clustering approaches. Biological networks such as gene regulatory networks, metabolic pathways, and protein-protein interaction networks are usually modeled as graphs and graph theoretic approaches are used to solve associated problems such as construction and analysis of large-scale networks.

  16. Scientists from all over the world attended the 'Frederic Joliot/Otto Hahn Summer School 2011' at the Karlsruhe Institute of Technology (KIT)

    International Nuclear Information System (INIS)

    Sanchez, Victor H.; Fischer, Ulrich

    2011-01-01

    The Karlsruhe Institute of Technology (KIT) and the Commissariat r leEnergie Atomique et Aux Energies Alternatives (CEA), Cadarache, alternate in organizing the annual 'Frederic Joliot/Otto Hahn Summer School.' This year's event, the 17th since its inception, was held in Karlsruhe, Germany on August 25 to September 3. Its topic was 'High-fidelity Modeling for Nuclear Reactors: Challenges and Prospects.' Here is a list of the subjects covered: - Status and perspectives of modeling and its role in design, operation, and safety. - Thermal hydraulics of nuclear reactors and simulation of 2 phase flows. - Structural mechanics, structure? fluid interaction, and seismic safety. - Advanced simulation in neutronics and reactor physics. - Progress in simulating fuel and materials behavior. - Multiphysics and uncertainty analysis methods. Experts from eight leading international research institutions and universities presented, and discussed with the 59 participants from 19 countries, the current state of the art and most recent development trends in the subjects listed above. (orig.)

  17. Applying Instructional Design Theories to Bioinformatics Education in Microarray Analysis and Primer Design Workshops

    Science.gov (United States)

    Shachak, Aviv; Ophir, Ron; Rubin, Eitan

    2005-01-01

    The need to support bioinformatics training has been widely recognized by scientists, industry, and government institutions. However, the discussion of instructional methods for teaching bioinformatics is only beginning. Here we report on a systematic attempt to design two bioinformatics workshops for graduate biology students on the basis of…

  18. The Impact of a Summer Institute on Inservice Early Childhood Teachers' Knowledge of Earth and Space Science Concepts

    Science.gov (United States)

    Sackes, Mesut; Trundle, Kathy Cabe; Krissek, Lawrence A.

    2011-01-01

    This study investigated inservice PreK to Grade two teachers' knowledge of some earth and space science concepts before and after a short-term teacher institute. A one-group pre-test-post-test design was used in the current study. Earth science concepts targeted during the professional development included properties of rocks and soils, and the…

  19. Bioinformatics for Exploration

    Science.gov (United States)

    Johnson, Kathy A.

    2006-01-01

    For the purpose of this paper, bioinformatics is defined as the application of computer technology to the management of biological information. It can be thought of as the science of developing computer databases and algorithms to facilitate and expedite biological research. This is a crosscutting capability that supports nearly all human health areas ranging from computational modeling, to pharmacodynamics research projects, to decision support systems within autonomous medical care. Bioinformatics serves to increase the efficiency and effectiveness of the life sciences research program. It provides data, information, and knowledge capture which further supports management of the bioastronautics research roadmap - identifying gaps that still remain and enabling the determination of which risks have been addressed.

  20. Proceedings of the 25th SLAC Summer Institute on Particle Physics: Physics of Leptons (SSI97) , Stanford, CA, August 4-15, 1997

    International Nuclear Information System (INIS)

    Deporcel, Lilian

    1998-01-01

    One hundred ninety-eight physicists from 16 countries gathered at SLAC from August 4 to 15, 1997 to attend the XXV SLAC Summer Institute on Particle Physics. The theme of the school was ''The Physics of Leptons'', commemorating a century since the electron, the first lepton, was discovered. We heard about the electron's role as a probe of the structure of matter, as well as the beautifully precise tests of charged-lepton universality in Z 0 decays. The focus of the school then shifted from the charged leptons to their weak partners, the neutrinos. Summer Institute attendees were not surprised in early 1998 by Super-Kamiokande's announcement of evidence for neutrino mass. After all, they had already seen the mounting evidence, both solar and atmospheric, the preceding August, in a comprehensive review of all nonaccelerator-based neutrino oscillation experiments, as well as a topical conference report from Super-Kamiokande. We also heard about the past, present, and future of reactor- and accelerator-based oscillation experiments, including the prospects for terrestrial tests of the atmospheric neutrino anomaly. Leptons in cosmology and as harbingers of physics beyond the Standard Model were the subject of two more lecture series. The three-day topical conference concluding the Institute was highlighted by the Super-Kamiokande neutrino results, and Beppo-Sax's report on the cosmological origin of gamma-ray bursters. As for terrestrial accelerators, SLC, LEP, and the Tevatron put increasing pressure on the electroweak sector through precision measurements, but all direct searches for new phenomena still came up empty

  1. Advance in structural bioinformatics

    CERN Document Server

    Wei, Dongqing; Zhao, Tangzhen; Dai, Hao

    2014-01-01

    This text examines in detail mathematical and physical modeling, computational methods and systems for obtaining and analyzing biological structures, using pioneering research cases as examples. As such, it emphasizes programming and problem-solving skills. It provides information on structure bioinformatics at various levels, with individual chapters covering introductory to advanced aspects, from fundamental methods and guidelines on acquiring and analyzing genomics and proteomics sequences, the structures of protein, DNA and RNA, to the basics of physical simulations and methods for conform

  2. Crowdsourcing for bioinformatics.

    Science.gov (United States)

    Good, Benjamin M; Su, Andrew I

    2013-08-15

    Bioinformatics is faced with a variety of problems that require human involvement. Tasks like genome annotation, image analysis, knowledge-base population and protein structure determination all benefit from human input. In some cases, people are needed in vast quantities, whereas in others, we need just a few with rare abilities. Crowdsourcing encompasses an emerging collection of approaches for harnessing such distributed human intelligence. Recently, the bioinformatics community has begun to apply crowdsourcing in a variety of contexts, yet few resources are available that describe how these human-powered systems work and how to use them effectively in scientific domains. Here, we provide a framework for understanding and applying several different types of crowdsourcing. The framework considers two broad classes: systems for solving large-volume 'microtasks' and systems for solving high-difficulty 'megatasks'. Within these classes, we discuss system types, including volunteer labor, games with a purpose, microtask markets and open innovation contests. We illustrate each system type with successful examples in bioinformatics and conclude with a guide for matching problems to crowdsourcing solutions that highlights the positives and negatives of different approaches.

  3. Phylogenetic trees in bioinformatics

    Energy Technology Data Exchange (ETDEWEB)

    Burr, Tom L [Los Alamos National Laboratory

    2008-01-01

    Genetic data is often used to infer evolutionary relationships among a collection of viruses, bacteria, animal or plant species, or other operational taxonomic units (OTU). A phylogenetic tree depicts such relationships and provides a visual representation of the estimated branching order of the OTUs. Tree estimation is unique for several reasons, including: the types of data used to represent each OTU; the use ofprobabilistic nucleotide substitution models; the inference goals involving both tree topology and branch length, and the huge number of possible trees for a given sample of a very modest number of OTUs, which implies that fmding the best tree(s) to describe the genetic data for each OTU is computationally demanding. Bioinformatics is too large a field to review here. We focus on that aspect of bioinformatics that includes study of similarities in genetic data from multiple OTUs. Although research questions are diverse, a common underlying challenge is to estimate the evolutionary history of the OTUs. Therefore, this paper reviews the role of phylogenetic tree estimation in bioinformatics, available methods and software, and identifies areas for additional research and development.

  4. NATO Advanced Study Institute on International Summer School on Chaotic Dynamics and Transport in Classical and Quantum Systems

    CERN Document Server

    Collet, P; Métens, S; Neishtadt, A; Zaslavsky, G; Chaotic Dynamics and Transport in Classical and Quantum Systems

    2005-01-01

    This book offers a modern updated review on the most important activities in today dynamical systems and statistical mechanics by some of the best experts in the domain. It gives a contemporary and pedagogical view on theories of classical and quantum chaos and complexity in hamiltonian and ergodic systems and their applications to anomalous transport in fluids, plasmas, oceans and atom-optic devices and to control of chaotic transport. The book is issued from lecture notes of the International Summer School on "Chaotic Dynamics and Transport in Classical and Quantum Systems" held in Cargèse (Corsica) 18th to the 30th August 2003. It reflects the spirit of the School to provide lectures at the post-doctoral level on basic concepts and tools. The first part concerns ergodicity and mixing, complexity and entropy functions, SRB measures, fractal dimensions and bifurcations in hamiltonian systems. Then, models of dynamical evolutions of transport processes in classical and quantum systems have been largely expla...

  5. Data mining for bioinformatics applications

    CERN Document Server

    Zengyou, He

    2015-01-01

    Data Mining for Bioinformatics Applications provides valuable information on the data mining methods have been widely used for solving real bioinformatics problems, including problem definition, data collection, data preprocessing, modeling, and validation. The text uses an example-based method to illustrate how to apply data mining techniques to solve real bioinformatics problems, containing 45 bioinformatics problems that have been investigated in recent research. For each example, the entire data mining process is described, ranging from data preprocessing to modeling and result validation. Provides valuable information on the data mining methods have been widely used for solving real bioinformatics problems Uses an example-based method to illustrate how to apply data mining techniques to solve real bioinformatics problems Contains 45 bioinformatics problems that have been investigated in recent research.

  6. Financial management and job social skills training components in a summer business institute: a controlled evaluation in high achieving predominantly ethnic minority youth.

    Science.gov (United States)

    Donohue, Brad; Conway, Debbie; Beisecker, Monica; Murphy, Heather; Farley, Alisha; Waite, Melissa; Gugino, Kristin; Knatz, Danielle; Lopez-Frank, Carolina; Burns, Jack; Madison, Suzanne; Shorty, Carrie

    2005-07-01

    Ninety-two adolescents, predominantly ethnic minority high school students, participated in a structured Summer Business Institute (SBI). Participating youth were randomly assigned to receive either job social skills or financial management skills training components. Students who additionally received the job social skills training component were more likely to recommend their employment agency to others than were youth who received the financial management component, rated their overall on-the-job work experience more favorably, and demonstrated higher scores in areas that were relevant to the skills that were taught in the job social skills workshops. The financial management component also appeared to be relatively effective, as youth who received this intervention improved their knowledge of financial management issues more than youth who received job social skills, and rated their workshops as more helpful in financial management, as well as insurance management. Future directions are discussed in light of these results.

  7. Scientists from all over the world attend the ''Frederic Joliot/Otto Hahn Summer School 2009'' at the Karlsruhe Institute of Technology (KIT); Wissenschaftler aus aller Welt bei der ''Frederic Joliot/Otto Hahn Summer School 2009'' am Karlsruhe Institute of Technologie (KIT)

    Energy Technology Data Exchange (ETDEWEB)

    Sanchez Espinoza, Victor Hugo; Fischer, Ulrich [Karlsruhe Inst. of Tech. (KIT), Campus Nord/Inst. for Neutron Physics and Reactor Tech. (INR), Eggenstein-Leopoldshafen (Germany)

    2009-11-15

    The ''Frederic Joliot/Otto Hahn Summer School'' is organized each year alternately by the Karlsruhe Institute of Technology and the Commissariat a l'Energie Atomique (CEA), Cadarache. This year's Summer School, the 15th since its foundation, was run at the Advanced Training Center (FTU) of KIT Campus Nord on August 26 to September 4. The key topic this year was ''The Challenges in Implementing Fast Reactor Technology.'' These are the items discussed: Principles and challenges of future fast reactor designs, Fuels, fuel cycle, and recycling of minor actinides, Innovative cladding tube and structural materials, Special aspects of coolants and the challenges they pose, Fast reactor safety. Experts from 8 leading international research establishments and universities presented and discussed with the 58 participants from 16 countries the current state of the art and the latest development trends in the topics listed above. (orig.)

  8. Proceedings of the 24. SLAC summer institute on particle physics: The strong interaction, from hadrons to partons

    Energy Technology Data Exchange (ETDEWEB)

    Chan, J.; DePorcel, L.; Dixon, L. [eds.

    1997-06-01

    This conference explored the role of the strong interaction in the physics of hadrons and partons. The Institute attracted 239 physicists from 16 countries to hear lectures on the underlying theory of Quantum Chromodynamics, modern theoretical calculational techniques, and experimental investigation of the strong interaction as it appears in various phenomena. Different regimes in which one can calculate reliably in QCD were addressed in series of lectures on perturbation theory, lattice gauge theories, and heavy quark expansions. Studies of QCD in hadron-hadron collisions, electron-positron annihilation, and electron-proton collisions all give differing perspectives on the strong interaction--from low-x to high-Q{sup 2}. Experimental understanding of the production and decay of heavy quarks as well as the lighter meson states has continued to evolve over the past years, and these topics were also covered at the School. Selected papers have been indexed separately for inclusion in the Energy Science and Technology Database.

  9. COMPARISON OF POPULAR BIOINFORMATICS DATABASES

    OpenAIRE

    Abdulganiyu Abdu Yusuf; Zahraddeen Sufyanu; Kabir Yusuf Mamman; Abubakar Umar Suleiman

    2016-01-01

    Bioinformatics is the application of computational tools to capture and interpret biological data. It has wide applications in drug development, crop improvement, agricultural biotechnology and forensic DNA analysis. There are various databases available to researchers in bioinformatics. These databases are customized for a specific need and are ranged in size, scope, and purpose. The main drawbacks of bioinformatics databases include redundant information, constant change, data spread over m...

  10. Bioinformatics-Aided Venomics

    Directory of Open Access Journals (Sweden)

    Quentin Kaas

    2015-06-01

    Full Text Available Venomics is a modern approach that combines transcriptomics and proteomics to explore the toxin content of venoms. This review will give an overview of computational approaches that have been created to classify and consolidate venomics data, as well as algorithms that have helped discovery and analysis of toxin nucleic acid and protein sequences, toxin three-dimensional structures and toxin functions. Bioinformatics is used to tackle specific challenges associated with the identification and annotations of toxins. Recognizing toxin transcript sequences among second generation sequencing data cannot rely only on basic sequence similarity because toxins are highly divergent. Mass spectrometry sequencing of mature toxins is challenging because toxins can display a large number of post-translational modifications. Identifying the mature toxin region in toxin precursor sequences requires the prediction of the cleavage sites of proprotein convertases, most of which are unknown or not well characterized. Tracing the evolutionary relationships between toxins should consider specific mechanisms of rapid evolution as well as interactions between predatory animals and prey. Rapidly determining the activity of toxins is the main bottleneck in venomics discovery, but some recent bioinformatics and molecular modeling approaches give hope that accurate predictions of toxin specificity could be made in the near future.

  11. Emergent Computation Emphasizing Bioinformatics

    CERN Document Server

    Simon, Matthew

    2005-01-01

    Emergent Computation is concerned with recent applications of Mathematical Linguistics or Automata Theory. This subject has a primary focus upon "Bioinformatics" (the Genome and arising interest in the Proteome), but the closing chapter also examines applications in Biology, Medicine, Anthropology, etc. The book is composed of an organized examination of DNA, RNA, and the assembly of amino acids into proteins. Rather than examine these areas from a purely mathematical viewpoint (that excludes much of the biochemical reality), the author uses scientific papers written mostly by biochemists based upon their laboratory observations. Thus while DNA may exist in its double stranded form, triple stranded forms are not excluded. Similarly, while bases exist in Watson-Crick complements, mismatched bases and abasic pairs are not excluded, nor are Hoogsteen bonds. Just as there are four bases naturally found in DNA, the existence of additional bases is not ignored, nor amino acids in addition to the usual complement of...

  12. Bioinformatics and moonlighting proteins

    Directory of Open Access Journals (Sweden)

    Sergio eHernández

    2015-06-01

    Full Text Available Multitasking or moonlighting is the capability of some proteins to execute two or more biochemical functions. Usually, moonlighting proteins are experimentally revealed by serendipity. For this reason, it would be helpful that Bioinformatics could predict this multifunctionality, especially because of the large amounts of sequences from genome projects. In the present work, we analyse and describe several approaches that use sequences, structures, interactomics and current bioinformatics algorithms and programs to try to overcome this problem. Among these approaches are: a remote homology searches using Psi-Blast, b detection of functional motifs and domains, c analysis of data from protein-protein interaction databases (PPIs, d match the query protein sequence to 3D databases (i.e., algorithms as PISITE, e mutation correlation analysis between amino acids by algorithms as MISTIC. Programs designed to identify functional motif/domains detect mainly the canonical function but usually fail in the detection of the moonlighting one, Pfam and ProDom being the best methods. Remote homology search by Psi-Blast combined with data from interactomics databases (PPIs have the best performance. Structural information and mutation correlation analysis can help us to map the functional sites. Mutation correlation analysis can only be used in very specific situations –it requires the existence of multialigned family protein sequences - but can suggest how the evolutionary process of second function acquisition took place. The multitasking protein database MultitaskProtDB (http://wallace.uab.es/multitask/, previously published by our group, has been used as a benchmark for the all of the analyses.

  13. Interdisciplinary Introductory Course in Bioinformatics

    Science.gov (United States)

    Kortsarts, Yana; Morris, Robert W.; Utell, Janine M.

    2010-01-01

    Bioinformatics is a relatively new interdisciplinary field that integrates computer science, mathematics, biology, and information technology to manage, analyze, and understand biological, biochemical and biophysical information. We present our experience in teaching an interdisciplinary course, Introduction to Bioinformatics, which was developed…

  14. Virtual Bioinformatics Distance Learning Suite

    Science.gov (United States)

    Tolvanen, Martti; Vihinen, Mauno

    2004-01-01

    Distance learning as a computer-aided concept allows students to take courses from anywhere at any time. In bioinformatics, computers are needed to collect, store, process, and analyze massive amounts of biological and biomedical data. We have applied the concept of distance learning in virtual bioinformatics to provide university course material…

  15. Staff Scientist - RNA Bioinformatics | Center for Cancer Research

    Science.gov (United States)

    The newly established RNA Biology Laboratory (RBL) at the Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH) in Frederick, Maryland is recruiting a Staff Scientist with strong expertise in RNA bioinformatics to join the Intramural Research Program’s mission of high impact, high reward science. The RBL is the equivalent of an

  16. Summer School organized by the International Centre for Theoretical Physics, Trieste, and the Institute for Information Sciences, University of Tübingen

    CERN Document Server

    Güttinger, Werner; Cin, Mario

    1974-01-01

    This volume is the record and product of the Summer School on the Physics and Mathematics of the Nervous System, held at the International Centre for Theoretical Physics in Trieste from August 21-31, 1973, and jointly organized by the Institute for Information Sciences, University of Tlibingen and by the Centre. The school served to bring biologists, physicists and mathemati­ cians together to exchange ideas about the nervous system and brain, and also to introduce young scientists to the field. The program, attended by more than a hundred scientists, was interdisciplinary both in character and participation. The primary support for the school was provided by the Volkswagen Foundation of West Germany. We are particularly indebted to Drs. G. Gambke, M. -L Zarnitz, and H. Penschuck of the Foundation for their in­ terest in and help with the project. The school also received major support from the International Centre for Theoretical Physics in Trieste and its sponsoring agencies, including the use of its exce...

  17. Summer Biomedical Engineering Institute 1972

    Science.gov (United States)

    Deloatch, E. M.

    1973-01-01

    The five problems studied for biomedical applications of NASA technology are reported. The studies reported are: design modification of electrophoretic equipment, operating room environment control, hematological viscometry, handling system for iridium, and indirect blood pressure measuring device.

  18. Bioinformatics Education in Pathology Training: Current Scope and Future Direction

    Directory of Open Access Journals (Sweden)

    Michael R Clay

    2017-04-01

    Full Text Available Training anatomic and clinical pathology residents in the principles of bioinformatics is a challenging endeavor. Most residents receive little to no formal exposure to bioinformatics during medical education, and most of the pathology training is spent interpreting histopathology slides using light microscopy or focused on laboratory regulation, management, and interpretation of discrete laboratory data. At a minimum, residents should be familiar with data structure, data pipelines, data manipulation, and data regulations within clinical laboratories. Fellowship-level training should incorporate advanced principles unique to each subspecialty. Barriers to bioinformatics education include the clinical apprenticeship training model, ill-defined educational milestones, inadequate faculty expertise, and limited exposure during medical training. Online educational resources, case-based learning, and incorporation into molecular genomics education could serve as effective educational strategies. Overall, pathology bioinformatics training can be incorporated into pathology resident curricula, provided there is motivation to incorporate, institutional support, educational resources, and adequate faculty expertise.

  19. Microbial bioinformatics 2020.

    Science.gov (United States)

    Pallen, Mark J

    2016-09-01

    Microbial bioinformatics in 2020 will remain a vibrant, creative discipline, adding value to the ever-growing flood of new sequence data, while embracing novel technologies and fresh approaches. Databases and search strategies will struggle to cope and manual curation will not be sustainable during the scale-up to the million-microbial-genome era. Microbial taxonomy will have to adapt to a situation in which most microorganisms are discovered and characterised through the analysis of sequences. Genome sequencing will become a routine approach in clinical and research laboratories, with fresh demands for interpretable user-friendly outputs. The "internet of things" will penetrate healthcare systems, so that even a piece of hospital plumbing might have its own IP address that can be integrated with pathogen genome sequences. Microbiome mania will continue, but the tide will turn from molecular barcoding towards metagenomics. Crowd-sourced analyses will collide with cloud computing, but eternal vigilance will be the price of preventing the misinterpretation and overselling of microbial sequence data. Output from hand-held sequencers will be analysed on mobile devices. Open-source training materials will address the need for the development of a skilled labour force. As we boldly go into the third decade of the twenty-first century, microbial sequence space will remain the final frontier! © 2016 The Author. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  20. Engineering bioinformatics: building reliability, performance and productivity into bioinformatics software.

    Science.gov (United States)

    Lawlor, Brendan; Walsh, Paul

    2015-01-01

    There is a lack of software engineering skills in bioinformatic contexts. We discuss the consequences of this lack, examine existing explanations and remedies to the problem, point out their shortcomings, and propose alternatives. Previous analyses of the problem have tended to treat the use of software in scientific contexts as categorically different from the general application of software engineering in commercial settings. In contrast, we describe bioinformatic software engineering as a specialization of general software engineering, and examine how it should be practiced. Specifically, we highlight the difference between programming and software engineering, list elements of the latter and present the results of a survey of bioinformatic practitioners which quantifies the extent to which those elements are employed in bioinformatics. We propose that the ideal way to bring engineering values into research projects is to bring engineers themselves. We identify the role of Bioinformatic Engineer and describe how such a role would work within bioinformatic research teams. We conclude by recommending an educational emphasis on cross-training software engineers into life sciences, and propose research on Domain Specific Languages to facilitate collaboration between engineers and bioinformaticians.

  1. Engineering bioinformatics: building reliability, performance and productivity into bioinformatics software

    Science.gov (United States)

    Lawlor, Brendan; Walsh, Paul

    2015-01-01

    There is a lack of software engineering skills in bioinformatic contexts. We discuss the consequences of this lack, examine existing explanations and remedies to the problem, point out their shortcomings, and propose alternatives. Previous analyses of the problem have tended to treat the use of software in scientific contexts as categorically different from the general application of software engineering in commercial settings. In contrast, we describe bioinformatic software engineering as a specialization of general software engineering, and examine how it should be practiced. Specifically, we highlight the difference between programming and software engineering, list elements of the latter and present the results of a survey of bioinformatic practitioners which quantifies the extent to which those elements are employed in bioinformatics. We propose that the ideal way to bring engineering values into research projects is to bring engineers themselves. We identify the role of Bioinformatic Engineer and describe how such a role would work within bioinformatic research teams. We conclude by recommending an educational emphasis on cross-training software engineers into life sciences, and propose research on Domain Specific Languages to facilitate collaboration between engineers and bioinformaticians. PMID:25996054

  2. Designing XML schemas for bioinformatics.

    Science.gov (United States)

    Bruhn, Russel Elton; Burton, Philip John

    2003-06-01

    Data interchange bioinformatics databases will, in the future, most likely take place using extensible markup language (XML). The document structure will be described by an XML Schema rather than a document type definition (DTD). To ensure flexibility, the XML Schema must incorporate aspects of Object-Oriented Modeling. This impinges on the choice of the data model, which, in turn, is based on the organization of bioinformatics data by biologists. Thus, there is a need for the general bioinformatics community to be aware of the design issues relating to XML Schema. This paper, which is aimed at a general bioinformatics audience, uses examples to describe the differences between a DTD and an XML Schema and indicates how Unified Modeling Language diagrams may be used to incorporate Object-Oriented Modeling in the design of schema.

  3. When process mining meets bioinformatics

    NARCIS (Netherlands)

    Jagadeesh Chandra Bose, R.P.; Aalst, van der W.M.P.; Nurcan, S.

    2011-01-01

    Process mining techniques can be used to extract non-trivial process related knowledge and thus generate interesting insights from event logs. Similarly, bioinformatics aims at increasing the understanding of biological processes through the analysis of information associated with biological

  4. Scientists from all over the world attended the 'Frederic Joliot/Otto Hahn Summer School 2011' at the Karlsruhe Institute of Technology (KIT); Wissenschaftler aus aller Welt bei der 'Frederic Joliot/Otto Hahn Summer School 2011' am Karlsruhe Institute of Technology (KIT)

    Energy Technology Data Exchange (ETDEWEB)

    Sanchez, Victor H.; Fischer, Ulrich [Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen (DE). Inst. for Neutron Physics and Reactor Technology (INR)

    2011-12-15

    The Karlsruhe Institute of Technology (KIT) and the Commissariat r leEnergie Atomique et Aux Energies Alternatives (CEA), Cadarache, alternate in organizing the annual 'Frederic Joliot/Otto Hahn Summer School.' This year's event, the 17th since its inception, was held in Karlsruhe, Germany on August 25 to September 3. Its topic was 'High-fidelity Modeling for Nuclear Reactors: Challenges and Prospects.' Here is a list of the subjects covered: - Status and perspectives of modeling and its role in design, operation, and safety. - Thermal hydraulics of nuclear reactors and simulation of 2 phase flows. - Structural mechanics, structure? fluid interaction, and seismic safety. - Advanced simulation in neutronics and reactor physics. - Progress in simulating fuel and materials behavior. - Multiphysics and uncertainty analysis methods. Experts from eight leading international research institutions and universities presented, and discussed with the 59 participants from 19 countries, the current state of the art and most recent development trends in the subjects listed above. (orig.)

  5. Taking Bioinformatics to Systems Medicine.

    Science.gov (United States)

    van Kampen, Antoine H C; Moerland, Perry D

    2016-01-01

    Systems medicine promotes a range of approaches and strategies to study human health and disease at a systems level with the aim of improving the overall well-being of (healthy) individuals, and preventing, diagnosing, or curing disease. In this chapter we discuss how bioinformatics critically contributes to systems medicine. First, we explain the role of bioinformatics in the management and analysis of data. In particular we show the importance of publicly available biological and clinical repositories to support systems medicine studies. Second, we discuss how the integration and analysis of multiple types of omics data through integrative bioinformatics may facilitate the determination of more predictive and robust disease signatures, lead to a better understanding of (patho)physiological molecular mechanisms, and facilitate personalized medicine. Third, we focus on network analysis and discuss how gene networks can be constructed from omics data and how these networks can be decomposed into smaller modules. We discuss how the resulting modules can be used to generate experimentally testable hypotheses, provide insight into disease mechanisms, and lead to predictive models. Throughout, we provide several examples demonstrating how bioinformatics contributes to systems medicine and discuss future challenges in bioinformatics that need to be addressed to enable the advancement of systems medicine.

  6. Generalized Centroid Estimators in Bioinformatics

    Science.gov (United States)

    Hamada, Michiaki; Kiryu, Hisanori; Iwasaki, Wataru; Asai, Kiyoshi

    2011-01-01

    In a number of estimation problems in bioinformatics, accuracy measures of the target problem are usually given, and it is important to design estimators that are suitable to those accuracy measures. However, there is often a discrepancy between an employed estimator and a given accuracy measure of the problem. In this study, we introduce a general class of efficient estimators for estimation problems on high-dimensional binary spaces, which represent many fundamental problems in bioinformatics. Theoretical analysis reveals that the proposed estimators generally fit with commonly-used accuracy measures (e.g. sensitivity, PPV, MCC and F-score) as well as it can be computed efficiently in many cases, and cover a wide range of problems in bioinformatics from the viewpoint of the principle of maximum expected accuracy (MEA). It is also shown that some important algorithms in bioinformatics can be interpreted in a unified manner. Not only the concept presented in this paper gives a useful framework to design MEA-based estimators but also it is highly extendable and sheds new light on many problems in bioinformatics. PMID:21365017

  7. Implementing a Web-Based Introductory Bioinformatics Course for Non-Bioinformaticians That Incorporates Practical Exercises

    Science.gov (United States)

    Vincent, Antony T.; Bourbonnais, Yves; Brouard, Jean-Simon; Deveau, Hélène; Droit, Arnaud; Gagné, Stéphane M.; Guertin, Michel; Lemieux, Claude; Rathier, Louis; Charette, Steve J.; Lagüe, Patrick

    2018-01-01

    A recent scientific discipline, bioinformatics, defined as using informatics for the study of biological problems, is now a requirement for the study of biological sciences. Bioinformatics has become such a powerful and popular discipline that several academic institutions have created programs in this field, allowing students to become…

  8. Bioinformatics in Middle East Program Curricula--A Focus on the Arabian Gulf

    Science.gov (United States)

    Loucif, Samia

    2014-01-01

    The purpose of this paper is to investigate the inclusion of bioinformatics in program curricula in the Middle East, focusing on educational institutions in the Arabian Gulf. Bioinformatics is a multidisciplinary field which has emerged in response to the need for efficient data storage and retrieval, and accurate and fast computational and…

  9. Influenza research database: an integrated bioinformatics resource for influenza virus research

    Science.gov (United States)

    The Influenza Research Database (IRD) is a U.S. National Institute of Allergy and Infectious Diseases (NIAID)-sponsored Bioinformatics Resource Center dedicated to providing bioinformatics support for influenza virus research. IRD facilitates the research and development of vaccines, diagnostics, an...

  10. Developing library bioinformatics services in context: the Purdue University Libraries bioinformationist program.

    Science.gov (United States)

    Rein, Diane C

    2006-07-01

    Purdue University is a major agricultural, engineering, biomedical, and applied life science research institution with an increasing focus on bioinformatics research that spans multiple disciplines and campus academic units. The Purdue University Libraries (PUL) hired a molecular biosciences specialist to discover, engage, and support bioinformatics needs across the campus. After an extended period of information needs assessment and environmental scanning, the specialist developed a week of focused bioinformatics instruction (Bioinformatics Week) to launch system-wide, library-based bioinformatics services. The specialist employed a two-tiered approach to assess user information requirements and expectations. The first phase involved careful observation and collection of information needs in-context throughout the campus, attending laboratory meetings, interviewing department chairs and individual researchers, and engaging in strategic planning efforts. Based on the information gathered during the integration phase, several survey instruments were developed to facilitate more critical user assessment and the recovery of quantifiable data prior to planning. Given information gathered while working with clients and through formal needs assessments, as well as the success of instructional approaches used in Bioinformatics Week, the specialist is developing bioinformatics support services for the Purdue community. The specialist is also engaged in training PUL faculty librarians in bioinformatics to provide a sustaining culture of library-based bioinformatics support and understanding of Purdue's bioinformatics-related decision and policy making.

  11. A Prototype Two-tier Mentoring Program for Undergraduate Summer Interns from Minority-Serving Institutions at the University of Alaska Fairbanks

    Science.gov (United States)

    Gens, R.; Prakash, A.; Ozbay, G.; Sriharan, S.; Balazs, M. S.; Chittambakkam, A.; Starkenburg, D. P.; Waigl, C.; Cook, S.; Ferguson, A.; Foster, K.; Jones, E.; Kluge, A.; Stilson, K.

    2013-12-01

    The University of Alaska Fairbanks (UAF) is partnering with Delaware State University, Virginia State University, Elizabeth City State University, Bethune-Cookman University, and Morgan State University on a U.S. Department of Agriculture - National Institute for Food and Agriculture funded grant for ';Enhancing Geographic Information System Education and Delivery through Collaboration: Curricula Design, Faculty, Staff, and Student Training and Development, and Extension Services'. As a part of this grant, in summer 2013, UAF hosted a week long workshop followed by an intense two week undergraduate internship program. Six undergraduate students from partnering Universities worked with UAF graduate students as their direct mentors. This cohort of undergraduate mentees and graduate student mentors were in-turn counseled by the two UAF principal investigators who served as ';super-mentors'. The role of each person in the two-tier mentoring system was well defined. The super-mentors ensured that there was consistency in the way the internship was setup and resources were allocated. They also ensured that there were no technical glitches in the research projects and that there was healthy communication and interaction among participants. Mentors worked with the mentees ahead of time in outlining a project that aligned with the mentees research interest, provided basic reading material to the interns to get oriented, prepared the datasets required to start the project, and guided the undergraduates throughout the internship. Undergraduates gained hands-on experience in geospatial data collection and application of tools in their projects related to mapping geomorphology, landcover, geothermal sites, fires, and meteorological conditions. Further, they shared their research results and experiences with a broad university-wide audience at the end of the internship period. All participants met at lunch-time for a daily science talk from external speakers. The program offered

  12. A BIOINFORMATIC STRATEGY TO RAPIDLY CHARACTERIZE CDNA LIBRARIES

    Science.gov (United States)

    A Bioinformatic Strategy to Rapidly Characterize cDNA LibrariesG. Charles Ostermeier1, David J. Dix2 and Stephen A. Krawetz1.1Departments of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, & Institute for Scientific Computing, Wayne State Univer...

  13. Bioinformatics in translational drug discovery.

    Science.gov (United States)

    Wooller, Sarah K; Benstead-Hume, Graeme; Chen, Xiangrong; Ali, Yusuf; Pearl, Frances M G

    2017-08-31

    Bioinformatics approaches are becoming ever more essential in translational drug discovery both in academia and within the pharmaceutical industry. Computational exploitation of the increasing volumes of data generated during all phases of drug discovery is enabling key challenges of the process to be addressed. Here, we highlight some of the areas in which bioinformatics resources and methods are being developed to support the drug discovery pipeline. These include the creation of large data warehouses, bioinformatics algorithms to analyse 'big data' that identify novel drug targets and/or biomarkers, programs to assess the tractability of targets, and prediction of repositioning opportunities that use licensed drugs to treat additional indications. © 2017 The Author(s).

  14. Summer Appendicitis

    African Journals Online (AJOL)

    hanumantp

    The increasing number of “fast food” restaurants where mainly high‑carbohydrate ... factors, food culture and the effect of migration for touristic purposes during the summer. .... Lal A, Hales S, French N, Baker MG. Seasonality in human.

  15. Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers

    DEFF Research Database (Denmark)

    Schneider, Maria V.; Walter, Peter; Blatter, Marie-Claude

    2012-01-01

    and clearly tagged in relation to target audiences, learning objectives, etc. Ideally, they would also be peer reviewed, and easily and efficiently accessible for downloading. Here, we present the Bioinformatics Training Network (BTN), a new enterprise that has been initiated to address these needs and review...

  16. Peer Mentoring for Bioinformatics presentation

    OpenAIRE

    Budd, Aidan

    2014-01-01

    A handout used in a HUB (Heidelberg Unseminars in Bioinformatics) meeting focused on career development for bioinformaticians. It describes an activity for use to help introduce the idea of peer mentoring, potnetially acting as an opportunity to create peer-mentoring groups.

  17. Reproducible Bioinformatics Research for Biologists

    Science.gov (United States)

    This book chapter describes the current Big Data problem in Bioinformatics and the resulting issues with performing reproducible computational research. The core of the chapter provides guidelines and summaries of current tools/techniques that a noncomputational researcher would need to learn to pe...

  18. Taking Bioinformatics to Systems Medicine

    NARCIS (Netherlands)

    van Kampen, Antoine H. C.; Moerland, Perry D.

    2016-01-01

    Systems medicine promotes a range of approaches and strategies to study human health and disease at a systems level with the aim of improving the overall well-being of (healthy) individuals, and preventing, diagnosing, or curing disease. In this chapter we discuss how bioinformatics critically

  19. Bioinformatics and the Undergraduate Curriculum

    Science.gov (United States)

    Maloney, Mark; Parker, Jeffrey; LeBlanc, Mark; Woodard, Craig T.; Glackin, Mary; Hanrahan, Michael

    2010-01-01

    Recent advances involving high-throughput techniques for data generation and analysis have made familiarity with basic bioinformatics concepts and programs a necessity in the biological sciences. Undergraduate students increasingly need training in methods related to finding and retrieving information stored in vast databases. The rapid rise of…

  20. Bioinformatics of genomic association mapping

    NARCIS (Netherlands)

    Vaez Barzani, Ahmad

    2015-01-01

    In this thesis we present an overview of bioinformatics-based approaches for genomic association mapping, with emphasis on human quantitative traits and their contribution to complex diseases. We aim to provide a comprehensive walk-through of the classic steps of genomic association mapping

  1. A review of bioinformatics training applied to research in molecular medicine, agriculture and biodiversity in Costa Rica and Central America.

    Science.gov (United States)

    Orozco, Allan; Morera, Jessica; Jiménez, Sergio; Boza, Ricardo

    2013-09-01

    Today, Bioinformatics has become a scientific discipline with great relevance for the Molecular Biosciences and for the Omics sciences in general. Although developed countries have progressed with large strides in Bioinformatics education and research, in other regions, such as Central America, the advances have occurred in a gradual way and with little support from the Academia, either at the undergraduate or graduate level. To address this problem, the University of Costa Rica's Medical School, a regional leader in Bioinformatics in Central America, has been conducting a series of Bioinformatics workshops, seminars and courses, leading to the creation of the region's first Bioinformatics Master's Degree. The recent creation of the Central American Bioinformatics Network (BioCANET), associated to the deployment of a supporting computational infrastructure (HPC Cluster) devoted to provide computing support for Molecular Biology in the region, is providing a foundational stone for the development of Bioinformatics in the area. Central American bioinformaticians have participated in the creation of as well as co-founded the Iberoamerican Bioinformatics Society (SOIBIO). In this article, we review the most recent activities in education and research in Bioinformatics from several regional institutions. These activities have resulted in further advances for Molecular Medicine, Agriculture and Biodiversity research in Costa Rica and the rest of the Central American countries. Finally, we provide summary information on the first Central America Bioinformatics International Congress, as well as the creation of the first Bioinformatics company (Indromics Bioinformatics), spin-off the Academy in Central America and the Caribbean.

  2. GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training.

    Science.gov (United States)

    Attwood, Teresa K; Atwood, Teresa K; Bongcam-Rudloff, Erik; Brazas, Michelle E; Corpas, Manuel; Gaudet, Pascale; Lewitter, Fran; Mulder, Nicola; Palagi, Patricia M; Schneider, Maria Victoria; van Gelder, Celia W G

    2015-04-01

    In recent years, high-throughput technologies have brought big data to the life sciences. The march of progress has been rapid, leaving in its wake a demand for courses in data analysis, data stewardship, computing fundamentals, etc., a need that universities have not yet been able to satisfy--paradoxically, many are actually closing "niche" bioinformatics courses at a time of critical need. The impact of this is being felt across continents, as many students and early-stage researchers are being left without appropriate skills to manage, analyse, and interpret their data with confidence. This situation has galvanised a group of scientists to address the problems on an international scale. For the first time, bioinformatics educators and trainers across the globe have come together to address common needs, rising above institutional and international boundaries to cooperate in sharing bioinformatics training expertise, experience, and resources, aiming to put ad hoc training practices on a more professional footing for the benefit of all.

  3. Bioinformatics for cancer immunotherapy target discovery

    DEFF Research Database (Denmark)

    Olsen, Lars Rønn; Campos, Benito; Barnkob, Mike Stein

    2014-01-01

    therapy target discovery in a bioinformatics analysis pipeline. We describe specialized bioinformatics tools and databases for three main bottlenecks in immunotherapy target discovery: the cataloging of potentially antigenic proteins, the identification of potential HLA binders, and the selection epitopes...

  4. EURASIP journal on bioinformatics & systems biology

    National Research Council Canada - National Science Library

    2006-01-01

    "The overall aim of "EURASIP Journal on Bioinformatics and Systems Biology" is to publish research results related to signal processing and bioinformatics theories and techniques relevant to a wide...

  5. Preface to Introduction to Structural Bioinformatics

    NARCIS (Netherlands)

    Feenstra, K. Anton; Abeln, Sanne

    2018-01-01

    While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims to give an introduction into Structural Bioinformatics, which

  6. A Bioinformatics Facility for NASA

    Science.gov (United States)

    Schweighofer, Karl; Pohorille, Andrew

    2006-01-01

    Building on an existing prototype, we have fielded a facility with bioinformatics technologies that will help NASA meet its unique requirements for biological research. This facility consists of a cluster of computers capable of performing computationally intensive tasks, software tools, databases and knowledge management systems. Novel computational technologies for analyzing and integrating new biological data and already existing knowledge have been developed. With continued development and support, the facility will fulfill strategic NASA s bioinformatics needs in astrobiology and space exploration. . As a demonstration of these capabilities, we will present a detailed analysis of how spaceflight factors impact gene expression in the liver and kidney for mice flown aboard shuttle flight STS-108. We have found that many genes involved in signal transduction, cell cycle, and development respond to changes in microgravity, but that most metabolic pathways appear unchanged.

  7. Establishing bioinformatics research in the Asia Pacific

    OpenAIRE

    Ranganathan, Shoba; Tammi, Martti; Gribskov, Michael; Tan, Tin Wee

    2006-01-01

    Abstract In 1998, the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation was set up to champion the advancement of bioinformatics in the Asia Pacific. By 2002, APBioNet was able to gain sufficient critical mass to initiate the first International Conference on Bioinformatics (InCoB) bringing together scientists working in the field of bioinformatics in the region. This year, the InCoB2006 Conference was organized as the 5th annual conference of the Asia-...

  8. Center for Computing Research Summer Research Proceedings 2015.

    Energy Technology Data Exchange (ETDEWEB)

    Bradley, Andrew Michael [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Parks, Michael L. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-12-18

    The Center for Computing Research (CCR) at Sandia National Laboratories organizes a summer student program each summer, in coordination with the Computer Science Research Institute (CSRI) and Cyber Engineering Research Institute (CERI).

  9. Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum

    Energy Technology Data Exchange (ETDEWEB)

    Ditty, Jayna L.; Kvaal, Christopher A.; Goodner, Brad; Freyermuth, Sharyn K.; Bailey, Cheryl; Britton, Robert A.; Gordon, Stuart G.; Heinhorst, Sabine; Reed, Kelynne; Xu, Zhaohui; Sanders-Lorenz, Erin R.; Axen, Seth; Kim, Edwin; Johns, Mitrick; Scott, Kathleen; Kerfeld, Cheryl A.

    2011-08-01

    into courses or independent research projects requires infrastructure for organizing and assessing student work. Here, we present a new platform for faculty to keep current with the rapidly changing field of bioinformatics, the Integrated Microbial Genomes Annotation Collaboration Toolkit (IMG-ACT). It was developed by instructors from both research-intensive and predominately undergraduate institutions in collaboration with the Department of Energy-Joint Genome Institute (DOE-JGI) as a means to innovate and update undergraduate education and faculty development. The IMG-ACT program provides a cadre of tools, including access to a clearinghouse of genome sequences, bioinformatics databases, data storage, instructor course management, and student notebooks for organizing the results of their bioinformatic investigations. In the process, IMG-ACT makes it feasible to provide undergraduate research opportunities to a greater number and diversity of students, in contrast to the traditional mentor-to-student apprenticeship model for undergraduate research, which can be too expensive and time-consuming to provide for every undergraduate. The IMG-ACT serves as the hub for the network of faculty and students that use the system for microbial genome analysis. Open access of the IMG-ACT infrastructure to participating schools ensures that all types of higher education institutions can utilize it. With the infrastructure in place, faculty can focus their efforts on the pedagogy of bioinformatics, involvement of students in research, and use of this tool for their own research agenda. What the original faculty members of the IMG-ACT development team present here is an overview of how the IMG-ACT program has affected our development in terms of teaching and research with the hopes that it will inspire more faculty to get involved.

  10. iUTAH Summer Research Institutes: Supporting the STEM Pipeline Through Engagement of High School, Undergraduate and Graduate Students, Secondary Teachers, and University Faculty in Authentic, Joint Research Experiences

    Science.gov (United States)

    Stark, L. A.; Malone, M.

    2015-12-01

    Multiple types of programs are needed to support the STEM workforce pipeline from pre-college through graduate school and beyond. Short-term, intensive programs provide opportunities to participate in authentic scientific research for students who may not be sure of their interest in science and for teachers who may be unable to devote an entire summer to a research experience. The iUTAH (innovative Urban Transitions and Aridregion Hydro-Systainability) Summer Research Institute utilizes an innovative approach for a 5-day program that engages high school and undergraduate students as well as middle and high school teachers in conducting research projects led by graduate students and faculty members. Each Institute involves 3-4 half to full-day research projects. Participants collect (usually in the field) and analyze data for use in on-going research or that is related to a current research project. The participants work in groups with the graduate students to create a poster about each research project. They present their posters on the last day of the Institute at the state-wide meeting of all researchers and involved in this EPSCoR-funded program. In addition to introducing participants to research, one of the Institute's goals is to provide opportunities for meaningful near-peer interactions with students along the STEM pipeline from high school to undergraduate to graduate school. On the end-of-Institute evaluations, almost all students have reported that their discussions with other participants and with graduate students and faculty were a "Highly effective" or "Effective" part of the Institute. In response to a question about how the Institute will impact their course choices or their plans to pursue a career in science, many high school and undergraduate students have noted that they plan to take more science courses. Each year several undergraduates who were previously unsure about a career in science have indicated that they now intend to pursue a

  11. Summer Students

    CERN Multimedia

    2005-01-01

    SUMMER STUDENT LECTURE PROGRAMME Main Auditorium, bldg. 500 DATE TIME LECTURER TITLE Wednesday 6 July 09:15 - 10:00 F. CERUTTI (CERN) Presentation of the Summer Student Programme D. Heagerty (CERN) Computer rules O. ULLALAND (CERN) Workshops presentation 10:15 - 11:00 D. SCHLATTER (CERN) Introduction to CERN 11:15 Film on CERN Thursday 7 July 09:15 - 11:00 L. Di Lella (CERN) Introduction to Particle Physics (1-2/4) 11:15 - 12:00 P. Chomaz (GANIL / CERN) Introduction to Nuclear Physics (1/3) 12:00 Discussion Session 14:00 - 14:45 M. Lindroos (CERN) ISOLDE Facility 15:00 M. Lindroos (CERN) ISOLDE Visit Friday 8 July 09:15 - 10:00 L. Di Lella (CERN) Introduction to Particle Physics (3/4) 10:15 - 11:00 P. Chomaz (GANIL / CERN) Introduction to Nuclear Physics (2/3) 11:15 - 12:00 G. ROLANDI (CERN) How an experiment is designed (1/2) 12:00 Discussion Session Monday 11 July 09:15 - 10:00 L. Di Lella (CERN) Introduction to Particle Physi...

  12. Survey of Foreign Language Course Registrations and Student Contact Hours in Institutions of Higher Education, Fall 1970 and Summer 1971. Final Report.

    Science.gov (United States)

    Brod, Richard I.

    This study, the tenth in a series, presents college language registration and student contact hour data for all modern and classical language programs in the United States. The body of the report consists of 24 tables summarizing the data, and a directory of the 2,353 institutions that reported registrations in one or more foreign languages.…

  13. Establishing bioinformatics research in the Asia Pacific

    Directory of Open Access Journals (Sweden)

    Tammi Martti

    2006-12-01

    Full Text Available Abstract In 1998, the Asia Pacific Bioinformatics Network (APBioNet, Asia's oldest bioinformatics organisation was set up to champion the advancement of bioinformatics in the Asia Pacific. By 2002, APBioNet was able to gain sufficient critical mass to initiate the first International Conference on Bioinformatics (InCoB bringing together scientists working in the field of bioinformatics in the region. This year, the InCoB2006 Conference was organized as the 5th annual conference of the Asia-Pacific Bioinformatics Network, on Dec. 18–20, 2006 in New Delhi, India, following a series of successful events in Bangkok (Thailand, Penang (Malaysia, Auckland (New Zealand and Busan (South Korea. This Introduction provides a brief overview of the peer-reviewed manuscripts accepted for publication in this Supplement. It exemplifies a typical snapshot of the growing research excellence in bioinformatics of the region as we embark on a trajectory of establishing a solid bioinformatics research culture in the Asia Pacific that is able to contribute fully to the global bioinformatics community.

  14. Emerging strengths in Asia Pacific bioinformatics.

    Science.gov (United States)

    Ranganathan, Shoba; Hsu, Wen-Lian; Yang, Ueng-Cheng; Tan, Tin Wee

    2008-12-12

    The 2008 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998, was organized as the 7th International Conference on Bioinformatics (InCoB), jointly with the Bioinformatics and Systems Biology in Taiwan (BIT 2008) Conference, Oct. 20-23, 2008 at Taipei, Taiwan. Besides bringing together scientists from the field of bioinformatics in this region, InCoB is actively involving researchers from the area of systems biology, to facilitate greater synergy between these two groups. Marking the 10th Anniversary of APBioNet, this InCoB 2008 meeting followed on from a series of successful annual events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand), Busan (South Korea), New Delhi (India) and Hong Kong. Additionally, tutorials and the Workshop on Education in Bioinformatics and Computational Biology (WEBCB) immediately prior to the 20th Federation of Asian and Oceanian Biochemists and Molecular Biologists (FAOBMB) Taipei Conference provided ample opportunity for inducting mainstream biochemists and molecular biologists from the region into a greater level of awareness of the importance of bioinformatics in their craft. In this editorial, we provide a brief overview of the peer-reviewed manuscripts accepted for publication herein, grouped into thematic areas. As the regional research expertise in bioinformatics matures, the papers fall into thematic areas, illustrating the specific contributions made by APBioNet to global bioinformatics efforts.

  15. Summer 2011

    Directory of Open Access Journals (Sweden)

    Eric G. Strauss

    2011-01-01

    Full Text Available Cities and the Environment Editor, Eric Strauss, provides an introduction to the Summer 2011 issue. He discusses the journal's transition to its new home at Loyola Marymount University and the creation of the Center for Urban Resilience and Ecological Solution, while underscoring highlights of the special topics section on Urban Predators. The contributors to this section participated in the International Symposium on Urban Wildlife and the Environment hosted by the Wildlife Society at the University of Massachusetts Amherst in June of 2009. Finally, Dr. Strauss notes the breadth of our issue by mentioning the additional articles' focus on rain gardens, water quality, arthropod diversity, green roofs, and socio-ecological dynamics.

  16. The secondary metabolite bioinformatics portal

    DEFF Research Database (Denmark)

    Weber, Tilmann; Kim, Hyun Uk

    2016-01-01

    . In this context, this review gives a summary of tools and databases that currently are available to mine, identify and characterize natural product biosynthesis pathways and their producers based on ‘omics data. A web portal called Secondary Metabolite Bioinformatics Portal (SMBP at http...... analytical and chemical methods gave access to this group of compounds, nowadays genomics-based methods offer complementary approaches to find, identify and characterize such molecules. This paradigm shift also resulted in a high demand for computational tools to assist researchers in their daily work......Natural products are among the most important sources of lead molecules for drug discovery. With the development of affordable whole-genome sequencing technologies and other ‘omics tools, the field of natural products research is currently undergoing a shift in paradigms. While, for decades, mainly...

  17. Biology in 'silico': The Bioinformatics Revolution.

    Science.gov (United States)

    Bloom, Mark

    2001-01-01

    Explains the Human Genome Project (HGP) and efforts to sequence the human genome. Describes the role of bioinformatics in the project and considers it the genetics Swiss Army Knife, which has many different uses, for use in forensic science, medicine, agriculture, and environmental sciences. Discusses the use of bioinformatics in the high school…

  18. Using "Arabidopsis" Genetic Sequences to Teach Bioinformatics

    Science.gov (United States)

    Zhang, Xiaorong

    2009-01-01

    This article describes a new approach to teaching bioinformatics using "Arabidopsis" genetic sequences. Several open-ended and inquiry-based laboratory exercises have been designed to help students grasp key concepts and gain practical skills in bioinformatics, using "Arabidopsis" leucine-rich repeat receptor-like kinase (LRR…

  19. A Mathematical Optimization Problem in Bioinformatics

    Science.gov (United States)

    Heyer, Laurie J.

    2008-01-01

    This article describes the sequence alignment problem in bioinformatics. Through examples, we formulate sequence alignment as an optimization problem and show how to compute the optimal alignment with dynamic programming. The examples and sample exercises have been used by the author in a specialized course in bioinformatics, but could be adapted…

  20. Fuzzy Logic in Medicine and Bioinformatics

    Directory of Open Access Journals (Sweden)

    Angela Torres

    2006-01-01

    Full Text Available The purpose of this paper is to present a general view of the current applications of fuzzy logic in medicine and bioinformatics. We particularly review the medical literature using fuzzy logic. We then recall the geometrical interpretation of fuzzy sets as points in a fuzzy hypercube and present two concrete illustrations in medicine (drug addictions and in bioinformatics (comparison of genomes.

  1. Rising Strengths Hong Kong SAR in Bioinformatics.

    Science.gov (United States)

    Chakraborty, Chiranjib; George Priya Doss, C; Zhu, Hailong; Agoramoorthy, Govindasamy

    2017-06-01

    Hong Kong's bioinformatics sector is attaining new heights in combination with its economic boom and the predominance of the working-age group in its population. Factors such as a knowledge-based and free-market economy have contributed towards a prominent position on the world map of bioinformatics. In this review, we have considered the educational measures, landmark research activities and the achievements of bioinformatics companies and the role of the Hong Kong government in the establishment of bioinformatics as strength. However, several hurdles remain. New government policies will assist computational biologists to overcome these hurdles and further raise the profile of the field. There is a high expectation that bioinformatics in Hong Kong will be a promising area for the next generation.

  2. Bioinformatics clouds for big data manipulation

    Directory of Open Access Journals (Sweden)

    Dai Lin

    2012-11-01

    Full Text Available Abstract As advances in life sciences and information technology bring profound influences on bioinformatics due to its interdisciplinary nature, bioinformatics is experiencing a new leap-forward from in-house computing infrastructure into utility-supplied cloud computing delivered over the Internet, in order to handle the vast quantities of biological data generated by high-throughput experimental technologies. Albeit relatively new, cloud computing promises to address big data storage and analysis issues in the bioinformatics field. Here we review extant cloud-based services in bioinformatics, classify them into Data as a Service (DaaS, Software as a Service (SaaS, Platform as a Service (PaaS, and Infrastructure as a Service (IaaS, and present our perspectives on the adoption of cloud computing in bioinformatics. Reviewers This article was reviewed by Frank Eisenhaber, Igor Zhulin, and Sandor Pongor.

  3. The 2016 Bioinformatics Open Source Conference (BOSC).

    Science.gov (United States)

    Harris, Nomi L; Cock, Peter J A; Chapman, Brad; Fields, Christopher J; Hokamp, Karsten; Lapp, Hilmar; Muñoz-Torres, Monica; Wiencko, Heather

    2016-01-01

    Message from the ISCB: The Bioinformatics Open Source Conference (BOSC) is a yearly meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. BOSC has been run since 2000 as a two-day Special Interest Group (SIG) before the annual ISMB conference. The 17th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2016) took place in Orlando, Florida in July 2016. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community. The conference brought together nearly 100 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, and open and reproducible science.

  4. Bioinformatics clouds for big data manipulation

    KAUST Repository

    Dai, Lin

    2012-11-28

    As advances in life sciences and information technology bring profound influences on bioinformatics due to its interdisciplinary nature, bioinformatics is experiencing a new leap-forward from in-house computing infrastructure into utility-supplied cloud computing delivered over the Internet, in order to handle the vast quantities of biological data generated by high-throughput experimental technologies. Albeit relatively new, cloud computing promises to address big data storage and analysis issues in the bioinformatics field. Here we review extant cloud-based services in bioinformatics, classify them into Data as a Service (DaaS), Software as a Service (SaaS), Platform as a Service (PaaS), and Infrastructure as a Service (IaaS), and present our perspectives on the adoption of cloud computing in bioinformatics.This article was reviewed by Frank Eisenhaber, Igor Zhulin, and Sandor Pongor. 2012 Dai et al.; licensee BioMed Central Ltd.

  5. Bioinformatics clouds for big data manipulation.

    Science.gov (United States)

    Dai, Lin; Gao, Xin; Guo, Yan; Xiao, Jingfa; Zhang, Zhang

    2012-11-28

    As advances in life sciences and information technology bring profound influences on bioinformatics due to its interdisciplinary nature, bioinformatics is experiencing a new leap-forward from in-house computing infrastructure into utility-supplied cloud computing delivered over the Internet, in order to handle the vast quantities of biological data generated by high-throughput experimental technologies. Albeit relatively new, cloud computing promises to address big data storage and analysis issues in the bioinformatics field. Here we review extant cloud-based services in bioinformatics, classify them into Data as a Service (DaaS), Software as a Service (SaaS), Platform as a Service (PaaS), and Infrastructure as a Service (IaaS), and present our perspectives on the adoption of cloud computing in bioinformatics. This article was reviewed by Frank Eisenhaber, Igor Zhulin, and Sandor Pongor.

  6. Indian Summer

    Energy Technology Data Exchange (ETDEWEB)

    Galindo, E. [Sho-Ban High School, Fort Hall, ID (United States)

    1997-08-01

    This paper focuses on preserving and strengthening two resources culturally and socially important to the Shoshone-Bannock Indian Tribe on the Fort Hall Reservation in Idaho; their young people and the Pacific-Northwest Salmon. After learning that salmon were not returning in significant numbers to ancestral fishing waters at headwater spawning sites, tribal youth wanted to know why. As a result, the Indian Summer project was conceived to give Shoshone-Bannock High School students the opportunity to develop hands-on, workable solutions to improve future Indian fishing and help make the river healthy again. The project goals were to increase the number of fry introduced into the streams, teach the Shoshone-Bannock students how to use scientific methodologies, and get students, parents, community members, and Indian and non-Indian mentors excited about learning. The students chose an egg incubation experiment to help increase self-sustaining, natural production of steelhead trout, and formulated and carried out a three step plan to increase the hatch-rate of steelhead trout in Idaho waters. With the help of local companies, governmental agencies, scientists, and mentors students have been able to meet their project goals, and at the same time, have learned how to use scientific methods to solve real life problems, how to return what they have used to the water and land, and how to have fun and enjoy life while learning.

  7. Summer Students

    CERN Multimedia

    2005-01-01

    SUMMER STUDENT LECTURE PROGRAMME Main Auditorium, bldg. 500 Monday 8 August 09:15 - 10:00 A. Höcker CP Violation (3/4) 10:15 - 12:00 J-J. GOMEZ-CADENAS Neutrino Physics (1-2/4) 12:00 Discussion Session Tuesday 9 August 09:15 - 10:00 A. Höcker CP Violation (4/4) 10:15 - 11:00 J-J. GOMEZ-CADENAS Neutrino Physics (3/4) 11:15 - 12:00 F. GREY The GRID 12:00 Discussion Session 14:15 - 17:00 Student Sessions Wednesday 10 August 09:15 - 10:00 J-J. GOMEZ-CADENAS Neutrino Physics (4/4) 10:15 - 12:00 J. LESGOURGUES Introduction to Cosmology (1-2/5) 12:00 Discussion Session 14:15 - 17:00 Student Sessions Thursday 11 August 09:15 - 11:00 J. LESGOURGUES Introduction to Cosmology (3-4/5) 11:15 - 12:00 G. KALMUS The ILC Story 12:00 Discussion Session Friday 12 August 09:15 - 10:00 J. LESGOURGUES Introduction to Cosmology (5/5) 10:15 - 11:00 G. VENEZIANO String theory: has Einstein's dream come true? 11:00  Discussion...

  8. Summer Students

    CERN Multimedia

    2005-01-01

    SUMMER STUDENT LECTURE PROGRAMME Main Auditorium, bldg. 500 DATE TIME LECTURER TITLE Monday 1 August 09:15 - 10:00 P. WELLS The Higgs Saga at LEP 10:15 - 11:00 E. KIRITSIS Beyond the Standard Model (1/4) 11:15 - 12:00 G. COWAN Introduction to Statistics (1/3) 12:00 Discussion Session Tuesday 2 August 09:15 - 11:00 E. KIRITSIS Beyond the Standard Model (2-3/4) 11:15 - 12:00 G. COWAN Introduction to Statistics (2/3) 12:00 Discussion Session Wednesday 3 August 09:15 - 10:00 G. COWAN Introduction to Statistics (3/3) 10:15 - 11:00 E. KIRITSIS Beyond the Standard Model (4/4) 11:15 - 12:00 K. JAKOBS Physics at Hadronic Colliders (1/4) 12:00 Discussion Session Thursday 4 August 09:15 - 11:00 K. JAKOBS Physics at Hadronic Colliders (2-3/4) 11:15 - 12:00 A. WEINSTEIN Gravitation Waves 12:00 Discussion Session 16:30 - 18:00 Poster Session Friday 5 August 09:15 - 11:00 A. Höcker CP Violation (1-2/4) 11:15 - 12:00 K. JA...

  9. Summer Students

    CERN Multimedia

    2005-01-01

    SUMMER STUDENT LECTURE PROGRAMME Main Auditorium, bldg. 500 DATE TIME LECTURER TITLE Monday 18 July 09:15 - 11:00 G. ROSS Fundamental concepts in Particle Physics (1-2/6) 11:15 - 12:00 N. PALANQUE-DELABROUILLE Astroparticle Physics (1/3) 12:00 Discussion Session Tuesday 19 July 09:15 - 10:00 G. ROSS Fundamental concepts in Particle Physics (3/6) 10:15 - 12:00 N. PALANQUE-DELABROUILLE Astroparticle Physics (2-3/3) 12:00 Discussion Session Wednesday 20 July 09:15 - 10:00 G. ROSS Fundamental concepts in Particle Physics (4/6) 10:15 - 11:00 F. RADEMAKERS ROOT 11:15 - 12:00 L. ROSSI Super-conducting magnet technology for particle accelerators and detectors 12:00 Discussion Session Thursday 21 July 09:15 - 10:00 G. ROSS Fundamental concepts in Particle Physics (5/6) 10:15 - 12:00 C. DE LA TAILLE Introduction to Electronics (1-2/3) 12:00 Discussion Session Friday 22 July 09:15 - 10:00 C. DE LA TAILLE Introduction to Electronics (3/3) 10:15 -...

  10. Summer Students

    CERN Multimedia

    2005-01-01

    SUMMER STUDENT LECTURE PROGRAMME Main Auditorium, bldg. 500 DATE TIME LECTURER TITLE Monday 25 July 09:15 - 11:00 A. PICH The Standard Model (2-3/8) 11:15 - 12:00 J. STACHEL Quark Gluon Plasma Physics (1/3) 12:00 Discussion Session Tuesday 26 July 09:15 - 10:00 A. PICH The Standard Model (4/8) 10:15 - 12:00 J. STACHEL Quark Gluon Plasma Physics (2-3/3) 12:00 Discussion Session Wednesday 27 July 09:15 - 11:00 A. PICH The Standard Model (5-6/8) 11:15 - 12:00 J-P. DELAHAYE The CLIC Concept and Technology for an e+e-Collider at the Energy Frontier 11:15 - 12:00 Discussion Session Thursday 28 July 09:15 - 10:00 A. PICH The Standard Model (7/8) 10:15 - 11:00 P. SPHICAS Data Acquisition Systems (1/2) 11:15 - 12:00 R. JACOBSEN From Raw data to Physics Results (1/2) 12:00 Discussion Session Friday 29 July 09:15 - 10:00 A. PICH The Standard Model (8/8) 10:15 - 11:00 P. SPHICAS Data Acquisition Systems (2/2) 11:15 - 12:00 R. JACOBSEN Fr...

  11. Summer Students

    CERN Multimedia

    2005-01-01

    SUMMER STUDENT LECTURE PROGRAMME Main Auditorium, bldg. 500 DATE TIME LECTURER TITLE Monday 11 July 09:15 - 10:00 L. Di Lella (CERN) Introduction to Particle Physics (4/4) 10:15 - 11:00 P. Chomaz (GANIL / CERN) Introduction to Nuclear Physics (3/3) 11:15 - 12:00 G. ROLANDI (CERN) How an experiment is designed (2/2) 12:00 Discussion Session Tuesday 12 July  09:15 - 11:00 O. BrÜning (CERN) Accelerators (1-2/5) 11:15 - 12:00 O. ULLALAND (CERN) Detectors (1/5) 12:00 Discussion Session Wednesday 13 July 09:15 - 10:00 O. BrÜning (CERN) Accelerators (3/5) 10:15 - 11:00 R. LANDUA (CERN) Antimatter in the Lab (1/2) 11:15 - 12:00 O. ULLALAND (CERN) Detectors (2/5) 12:00 Discussion Session Thursday 14 July 09:15 - 10:00 O. ULLALAND (CERN) Detectors (3/5) 10:15 - 11:00 G. ROLANDI (CERN) Antimatter in the Lab (2/2) 11:15 - 12:00 O. BrÜning (CERN) Accelerators (4/5) 12:00 Discussion Session Friday 1...

  12. A Quick Guide for Building a Successful Bioinformatics Community

    Science.gov (United States)

    Budd, Aidan; Corpas, Manuel; Brazas, Michelle D.; Fuller, Jonathan C.; Goecks, Jeremy; Mulder, Nicola J.; Michaut, Magali; Ouellette, B. F. Francis; Pawlik, Aleksandra; Blomberg, Niklas

    2015-01-01

    “Scientific community” refers to a group of people collaborating together on scientific-research-related activities who also share common goals, interests, and values. Such communities play a key role in many bioinformatics activities. Communities may be linked to a specific location or institute, or involve people working at many different institutions and locations. Education and training is typically an important component of these communities, providing a valuable context in which to develop skills and expertise, while also strengthening links and relationships within the community. Scientific communities facilitate: (i) the exchange and development of ideas and expertise; (ii) career development; (iii) coordinated funding activities; (iv) interactions and engagement with professionals from other fields; and (v) other activities beneficial to individual participants, communities, and the scientific field as a whole. It is thus beneficial at many different levels to understand the general features of successful, high-impact bioinformatics communities; how individual participants can contribute to the success of these communities; and the role of education and training within these communities. We present here a quick guide to building and maintaining a successful, high-impact bioinformatics community, along with an overview of the general benefits of participating in such communities. This article grew out of contributions made by organizers, presenters, panelists, and other participants of the ISMB/ECCB 2013 workshop “The ‘How To Guide’ for Establishing a Successful Bioinformatics Network” at the 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 12th European Conference on Computational Biology (ECCB). PMID:25654371

  13. Improvement of the banana "Musa acuminata" reference sequence using NGS data and semi-automated bioinformatics methods

    Czech Academy of Sciences Publication Activity Database

    Martin, G.; Baurens, F.C.; Droc, G.; Rouard, M.; Cenci, A.; Kilian, A.; Hastie, A.; Doležel, Jaroslav; Aury, J. M.; Alberti, A.; Carreel, F.; D'Hont, A.

    2016-01-01

    Roč. 17, MAR 16 (2016), s. 243 ISSN 1471-2164 Institutional support: RVO:61389030 Keywords : Musa acuminata * Genome assembly * Bioinformatics tool Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.729, year: 2016

  14. Summer Mini Atomiade June 2016

    CERN Multimedia

    Staff Association

    2016-01-01

    The Mini Atomiade are coming to CERN! Members of Clubs supported by the CERN Staff Association and in conjunction with ASCERI (Association of the Sports Communities of the European Research Institutes) will be organising the summer games at the beginning of June. ASCERI aims to contribute to a united Europe through regular sports meetings, bringing together members of public Research Institutes at European level. The Association's members come from over 40 Research Institutes spanning 16 countries. Numerous sports and leisure activities are represented at regular events and each tournament is organised by a different research institute. Clubs in conjunction with the CERN Staff Association have sent teams to previous winter and summer games and now, the CERN Club’s Coordination Committee (CCC) has now taken on the challenge of organising a Mini Atomiade from Friday June 3rd to Monday June 6th 2016 in Divonne-les-Bains. The games are made up of four different tournaments/competitions: Small Fi...

  15. When cloud computing meets bioinformatics: a review.

    Science.gov (United States)

    Zhou, Shuigeng; Liao, Ruiqi; Guan, Jihong

    2013-10-01

    In the past decades, with the rapid development of high-throughput technologies, biology research has generated an unprecedented amount of data. In order to store and process such a great amount of data, cloud computing and MapReduce were applied to many fields of bioinformatics. In this paper, we first introduce the basic concepts of cloud computing and MapReduce, and their applications in bioinformatics. We then highlight some problems challenging the applications of cloud computing and MapReduce to bioinformatics. Finally, we give a brief guideline for using cloud computing in biology research.

  16. Application of machine learning methods in bioinformatics

    Science.gov (United States)

    Yang, Haoyu; An, Zheng; Zhou, Haotian; Hou, Yawen

    2018-05-01

    Faced with the development of bioinformatics, high-throughput genomic technology have enabled biology to enter the era of big data. [1] Bioinformatics is an interdisciplinary, including the acquisition, management, analysis, interpretation and application of biological information, etc. It derives from the Human Genome Project. The field of machine learning, which aims to develop computer algorithms that improve with experience, holds promise to enable computers to assist humans in the analysis of large, complex data sets.[2]. This paper analyzes and compares various algorithms of machine learning and their applications in bioinformatics.

  17. GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training

    Science.gov (United States)

    Atwood, Teresa K.; Bongcam-Rudloff, Erik; Brazas, Michelle E.; Corpas, Manuel; Gaudet, Pascale; Lewitter, Fran; Mulder, Nicola; Palagi, Patricia M.; Schneider, Maria Victoria; van Gelder, Celia W. G.

    2015-01-01

    In recent years, high-throughput technologies have brought big data to the life sciences. The march of progress has been rapid, leaving in its wake a demand for courses in data analysis, data stewardship, computing fundamentals, etc., a need that universities have not yet been able to satisfy—paradoxically, many are actually closing “niche” bioinformatics courses at a time of critical need. The impact of this is being felt across continents, as many students and early-stage researchers are being left without appropriate skills to manage, analyse, and interpret their data with confidence. This situation has galvanised a group of scientists to address the problems on an international scale. For the first time, bioinformatics educators and trainers across the globe have come together to address common needs, rising above institutional and international boundaries to cooperate in sharing bioinformatics training expertise, experience, and resources, aiming to put ad hoc training practices on a more professional footing for the benefit of all. PMID:25856076

  18. BIRCH: A user-oriented, locally-customizable, bioinformatics system

    Science.gov (United States)

    Fristensky, Brian

    2007-01-01

    Background Molecular biologists need sophisticated analytical tools which often demand extensive computational resources. While finding, installing, and using these tools can be challenging, pipelining data from one program to the next is particularly awkward, especially when using web-based programs. At the same time, system administrators tasked with maintaining these tools do not always appreciate the needs of research biologists. Results BIRCH (Biological Research Computing Hierarchy) is an organizational framework for delivering bioinformatics resources to a user group, scaling from a single lab to a large institution. The BIRCH core distribution includes many popular bioinformatics programs, unified within the GDE (Genetic Data Environment) graphic interface. Of equal importance, BIRCH provides the system administrator with tools that simplify the job of managing a multiuser bioinformatics system across different platforms and operating systems. These include tools for integrating locally-installed programs and databases into BIRCH, and for customizing the local BIRCH system to meet the needs of the user base. BIRCH can also act as a front end to provide a unified view of already-existing collections of bioinformatics software. Documentation for the BIRCH and locally-added programs is merged in a hierarchical set of web pages. In addition to manual pages for individual programs, BIRCH tutorials employ step by step examples, with screen shots and sample files, to illustrate both the important theoretical and practical considerations behind complex analytical tasks. Conclusion BIRCH provides a versatile organizational framework for managing software and databases, and making these accessible to a user base. Because of its network-centric design, BIRCH makes it possible for any user to do any task from anywhere. PMID:17291351

  19. Bioinformatics meets user-centred design: a perspective.

    Directory of Open Access Journals (Sweden)

    Katrina Pavelin

    Full Text Available Designers have a saying that "the joy of an early release lasts but a short time. The bitterness of an unusable system lasts for years." It is indeed disappointing to discover that your data resources are not being used to their full potential. Not only have you invested your time, effort, and research grant on the project, but you may face costly redesigns if you want to improve the system later. This scenario would be less likely if the product was designed to provide users with exactly what they need, so that it is fit for purpose before its launch. We work at EMBL-European Bioinformatics Institute (EMBL-EBI, and we consult extensively with life science researchers to find out what they need from biological data resources. We have found that although users believe that the bioinformatics community is providing accurate and valuable data, they often find the interfaces to these resources tricky to use and navigate. We believe that if you can find out what your users want even before you create the first mock-up of a system, the final product will provide a better user experience. This would encourage more people to use the resource and they would have greater access to the data, which could ultimately lead to more scientific discoveries. In this paper, we explore the need for a user-centred design (UCD strategy when designing bioinformatics resources and illustrate this with examples from our work at EMBL-EBI. Our aim is to introduce the reader to how selected UCD techniques may be successfully applied to software design for bioinformatics.

  20. BIRCH: A user-oriented, locally-customizable, bioinformatics system

    Directory of Open Access Journals (Sweden)

    Fristensky Brian

    2007-02-01

    Full Text Available Abstract Background Molecular biologists need sophisticated analytical tools which often demand extensive computational resources. While finding, installing, and using these tools can be challenging, pipelining data from one program to the next is particularly awkward, especially when using web-based programs. At the same time, system administrators tasked with maintaining these tools do not always appreciate the needs of research biologists. Results BIRCH (Biological Research Computing Hierarchy is an organizational framework for delivering bioinformatics resources to a user group, scaling from a single lab to a large institution. The BIRCH core distribution includes many popular bioinformatics programs, unified within the GDE (Genetic Data Environment graphic interface. Of equal importance, BIRCH provides the system administrator with tools that simplify the job of managing a multiuser bioinformatics system across different platforms and operating systems. These include tools for integrating locally-installed programs and databases into BIRCH, and for customizing the local BIRCH system to meet the needs of the user base. BIRCH can also act as a front end to provide a unified view of already-existing collections of bioinformatics software. Documentation for the BIRCH and locally-added programs is merged in a hierarchical set of web pages. In addition to manual pages for individual programs, BIRCH tutorials employ step by step examples, with screen shots and sample files, to illustrate both the important theoretical and practical considerations behind complex analytical tasks. Conclusion BIRCH provides a versatile organizational framework for managing software and databases, and making these accessible to a user base. Because of its network-centric design, BIRCH makes it possible for any user to do any task from anywhere.

  1. Bioinformatic tools for PCR Primer design

    African Journals Online (AJOL)

    ES

    Bioinformatics is an emerging scientific discipline that uses information ... complex biological questions. ... and computer programs for various purposes of primer ..... polymerase chain reaction: Human Immunodeficiency Virus 1 model studies.

  2. Deciphering psoriasis. A bioinformatic approach.

    Science.gov (United States)

    Melero, Juan L; Andrades, Sergi; Arola, Lluís; Romeu, Antoni

    2018-02-01

    Psoriasis is an immune-mediated, inflammatory and hyperproliferative disease of the skin and joints. The cause of psoriasis is still unknown. The fundamental feature of the disease is the hyperproliferation of keratinocytes and the recruitment of cells from the immune system in the region of the affected skin, which leads to deregulation of many well-known gene expressions. Based on data mining and bioinformatic scripting, here we show a new dimension of the effect of psoriasis at the genomic level. Using our own pipeline of scripts in Perl and MySql and based on the freely available NCBI Gene Expression Omnibus (GEO) database: DataSet Record GDS4602 (Series GSE13355), we explore the extent of the effect of psoriasis on gene expression in the affected tissue. We give greater insight into the effects of psoriasis on the up-regulation of some genes in the cell cycle (CCNB1, CCNA2, CCNE2, CDK1) or the dynamin system (GBPs, MXs, MFN1), as well as the down-regulation of typical antioxidant genes (catalase, CAT; superoxide dismutases, SOD1-3; and glutathione reductase, GSR). We also provide a complete list of the human genes and how they respond in a state of psoriasis. Our results show that psoriasis affects all chromosomes and many biological functions. If we further consider the stable and mitotically inheritable character of the psoriasis phenotype, and the influence of environmental factors, then it seems that psoriasis has an epigenetic origin. This fit well with the strong hereditary character of the disease as well as its complex genetic background. Copyright © 2017 Japanese Society for Investigative Dermatology. Published by Elsevier B.V. All rights reserved.

  3. Concepts and introduction to RNA bioinformatics

    DEFF Research Database (Denmark)

    Gorodkin, Jan; Hofacker, Ivo L.; Ruzzo, Walter L.

    2014-01-01

    RNA bioinformatics and computational RNA biology have emerged from implementing methods for predicting the secondary structure of single sequences. The field has evolved to exploit multiple sequences to take evolutionary information into account, such as compensating (and structure preserving) base...... for interactions between RNA and proteins.Here, we introduce the basic concepts of predicting RNA secondary structure relevant to the further analyses of RNA sequences. We also provide pointers to methods addressing various aspects of RNA bioinformatics and computational RNA biology....

  4. European Bioinformatics Institute: Research Infrastructure needed for Life Science

    CERN Multimedia

    CERN. Geneva

    2015-01-01

    The life science community is an ever increasing source of data from increasing diverse range of instruments and sources. EMBL-EBI has a remit to store and exploit this data, collected and made available openly across the world, for the benefit of the whole research community. The research infrastructure needed to support the big data analysis around this mission encompasses high performance networks, high-throughput computing, and a range of cloud and storage solutions - and will be described in the presentation.

  5. E-MSD: the European Bioinformatics Institute Macromolecular Structure Database.

    Science.gov (United States)

    Boutselakis, H; Dimitropoulos, D; Fillon, J; Golovin, A; Henrick, K; Hussain, A; Ionides, J; John, M; Keller, P A; Krissinel, E; McNeil, P; Naim, A; Newman, R; Oldfield, T; Pineda, J; Rachedi, A; Copeland, J; Sitnov, A; Sobhany, S; Suarez-Uruena, A; Swaminathan, J; Tagari, M; Tate, J; Tromm, S; Velankar, S; Vranken, W

    2003-01-01

    The E-MSD macromolecular structure relational database (http://www.ebi.ac.uk/msd) is designed to be a single access point for protein and nucleic acid structures and related information. The database is derived from Protein Data Bank (PDB) entries. Relational database technologies are used in a comprehensive cleaning procedure to ensure data uniformity across the whole archive. The search database contains an extensive set of derived properties, goodness-of-fit indicators, and links to other EBI databases including InterPro, GO, and SWISS-PROT, together with links to SCOP, CATH, PFAM and PROSITE. A generic search interface is available, coupled with a fast secondary structure domain search tool.

  6. Navigating the changing learning landscape: perspective from bioinformatics.ca

    OpenAIRE

    Brazas, Michelle D.; Ouellette, B. F. Francis

    2013-01-01

    With the advent of YouTube channels in bioinformatics, open platforms for problem solving in bioinformatics, active web forums in computing analyses and online resources for learning to code or use a bioinformatics tool, the more traditional continuing education bioinformatics training programs have had to adapt. Bioinformatics training programs that solely rely on traditional didactic methods are being superseded by these newer resources. Yet such face-to-face instruction is still invaluable...

  7. CERN openlab Summer Student Programme

    CERN Multimedia

    2012-01-01

    CERN openlab is currently taking applications for its summer student programme. The closing date for applications is 30 March 2012.   The openlab Summer Student Programme is open for applications from bachelor, master and PhD students in computer science and physics. Successful applicants will spend 8 weeks at CERN, during the period June to September 2012, to work with some of the latest hardware and software technologies. The programme is more than just a summer at CERN: it can lead to follow-on projects at the home institute and may even inspire the students to become entrepreneurs in cutting-edge computing technologies. A series of lectures will be given by experts in various domains of CERN related high-throughput computing. Study tours to external companies and universities as well as to CERN facilities are also part of the programme. Please visit www.cern.ch/openlab-students for more information.

  8. CERN openlab summer student programme

    CERN Multimedia

    2013-01-01

    CERN openlab is currently taking applications for its summer student programme. The closing date for applications is 31 March 2013.   The openlab summer student programme is open for applications from bachelor, master and PhD students in computer science and physics. Successful applicants will spend 9 weeks at CERN, during the period from June to September 2013, working with some of the latest hardware and software technologies. The programme is more than just a summer at CERN: it can lead to follow-on projects at the home institute and may even inspire students to become entrepreneurs in cutting-edge computing technologies. A series of lectures will be given by experts in various domains of CERN-related high-throughput computing. Study tours of external companies and universities as well as of CERN facilities are also part of the programme. Please visit the CERN openlab website for more information.

  9. The Griffiss Institute Summer Faculty Program

    Science.gov (United States)

    2013-05-01

    multicore architectures and distributed HPC Condor environment with respect to video processing algorithms such as flux tensor , morphology, connected...visualization using Kolam. Refined 3D multiview reconstruction algorithm based on a ray casting and voxel- voting scheme. Worked on initial...implementation of 3D reconstruction using a synthetic 3D scene with a few buildings incorporating a camera model and realistic flight parameters. Votes

  10. Summer Institute in Biomedical Engineering, 1973

    Science.gov (United States)

    Deloatch, E. M.; Coble, A. J.

    1974-01-01

    Bioengineering of medical equipment is detailed. Equipment described includes: an environmental control system for a surgical suite; surface potential mapping for an electrode system; the use of speech-modulated-white-noise to differentiate hearers and feelers among the profoundly deaf; the design of an automatic weight scale for an isolette; and an internal tibial torsion correction study. Graphs and charts are included with design specifications of this equipment.

  11. Development of Bioinformatics Infrastructure for Genomics Research.

    Science.gov (United States)

    Mulder, Nicola J; Adebiyi, Ezekiel; Adebiyi, Marion; Adeyemi, Seun; Ahmed, Azza; Ahmed, Rehab; Akanle, Bola; Alibi, Mohamed; Armstrong, Don L; Aron, Shaun; Ashano, Efejiro; Baichoo, Shakuntala; Benkahla, Alia; Brown, David K; Chimusa, Emile R; Fadlelmola, Faisal M; Falola, Dare; Fatumo, Segun; Ghedira, Kais; Ghouila, Amel; Hazelhurst, Scott; Isewon, Itunuoluwa; Jung, Segun; Kassim, Samar Kamal; Kayondo, Jonathan K; Mbiyavanga, Mamana; Meintjes, Ayton; Mohammed, Somia; Mosaku, Abayomi; Moussa, Ahmed; Muhammd, Mustafa; Mungloo-Dilmohamud, Zahra; Nashiru, Oyekanmi; Odia, Trust; Okafor, Adaobi; Oladipo, Olaleye; Osamor, Victor; Oyelade, Jellili; Sadki, Khalid; Salifu, Samson Pandam; Soyemi, Jumoke; Panji, Sumir; Radouani, Fouzia; Souiai, Oussama; Tastan Bishop, Özlem

    2017-06-01

    Although pockets of bioinformatics excellence have developed in Africa, generally, large-scale genomic data analysis has been limited by the availability of expertise and infrastructure. H3ABioNet, a pan-African bioinformatics network, was established to build capacity specifically to enable H3Africa (Human Heredity and Health in Africa) researchers to analyze their data in Africa. Since the inception of the H3Africa initiative, H3ABioNet's role has evolved in response to changing needs from the consortium and the African bioinformatics community. H3ABioNet set out to develop core bioinformatics infrastructure and capacity for genomics research in various aspects of data collection, transfer, storage, and analysis. Various resources have been developed to address genomic data management and analysis needs of H3Africa researchers and other scientific communities on the continent. NetMap was developed and used to build an accurate picture of network performance within Africa and between Africa and the rest of the world, and Globus Online has been rolled out to facilitate data transfer. A participant recruitment database was developed to monitor participant enrollment, and data is being harmonized through the use of ontologies and controlled vocabularies. The standardized metadata will be integrated to provide a search facility for H3Africa data and biospecimens. Because H3Africa projects are generating large-scale genomic data, facilities for analysis and interpretation are critical. H3ABioNet is implementing several data analysis platforms that provide a large range of bioinformatics tools or workflows, such as Galaxy, the Job Management System, and eBiokits. A set of reproducible, portable, and cloud-scalable pipelines to support the multiple H3Africa data types are also being developed and dockerized to enable execution on multiple computing infrastructures. In addition, new tools have been developed for analysis of the uniquely divergent African data and for

  12. Synergy between Medical Informatics and Bioinformatics: Facilitating Genomic Medicine for Future Health Care

    Czech Academy of Sciences Publication Activity Database

    Martin-Sanchez, F.; Iakovidis, I.; Norager, S.; Maojo, V.; de Groen, P.; Van der Lei, J.; Jones, T.; Abraham-Fuchs, K.; Apweiler, R.; Babic, A.; Baud, R.; Breton, V.; Cinquin, P.; Doupi, P.; Dugas, M.; Eils, R.; Engelbrecht, R.; Ghazal, P.; Jehenson, P.; Kulikowski, C.; Lampe, K.; De Moor, G.; Orphanoudakis, S.; Rossing, N.; Sarachan, B.; Sousa, A.; Spekowius, G.; Thireos, G.; Zahlmann, G.; Zvárová, Jana; Hermosilla, I.; Vicente, F. J.

    2004-01-01

    Roč. 37, - (2004), s. 30-42 ISSN 1532-0464 Institutional research plan: CEZ:AV0Z1030915 Keywords : bioinformatics * medical informatics * genomics * genomic medicine * biomedical informatics Subject RIV: BD - Theory of Information Impact factor: 1.013, year: 2004

  13. Translational Bioinformatics and Clinical Research (Biomedical) Informatics.

    Science.gov (United States)

    Sirintrapun, S Joseph; Zehir, Ahmet; Syed, Aijazuddin; Gao, JianJiong; Schultz, Nikolaus; Cheng, Donavan T

    2015-06-01

    Translational bioinformatics and clinical research (biomedical) informatics are the primary domains related to informatics activities that support translational research. Translational bioinformatics focuses on computational techniques in genetics, molecular biology, and systems biology. Clinical research (biomedical) informatics involves the use of informatics in discovery and management of new knowledge relating to health and disease. This article details 3 projects that are hybrid applications of translational bioinformatics and clinical research (biomedical) informatics: The Cancer Genome Atlas, the cBioPortal for Cancer Genomics, and the Memorial Sloan Kettering Cancer Center clinical variants and results database, all designed to facilitate insights into cancer biology and clinical/therapeutic correlations. Copyright © 2015 Elsevier Inc. All rights reserved.

  14. Planning bioinformatics workflows using an expert system

    Science.gov (United States)

    Chen, Xiaoling; Chang, Jeffrey T.

    2017-01-01

    Abstract Motivation: Bioinformatic analyses are becoming formidably more complex due to the increasing number of steps required to process the data, as well as the proliferation of methods that can be used in each step. To alleviate this difficulty, pipelines are commonly employed. However, pipelines are typically implemented to automate a specific analysis, and thus are difficult to use for exploratory analyses requiring systematic changes to the software or parameters used. Results: To automate the development of pipelines, we have investigated expert systems. We created the Bioinformatics ExperT SYstem (BETSY) that includes a knowledge base where the capabilities of bioinformatics software is explicitly and formally encoded. BETSY is a backwards-chaining rule-based expert system comprised of a data model that can capture the richness of biological data, and an inference engine that reasons on the knowledge base to produce workflows. Currently, the knowledge base is populated with rules to analyze microarray and next generation sequencing data. We evaluated BETSY and found that it could generate workflows that reproduce and go beyond previously published bioinformatics results. Finally, a meta-investigation of the workflows generated from the knowledge base produced a quantitative measure of the technical burden imposed by each step of bioinformatics analyses, revealing the large number of steps devoted to the pre-processing of data. In sum, an expert system approach can facilitate exploratory bioinformatic analysis by automating the development of workflows, a task that requires significant domain expertise. Availability and Implementation: https://github.com/jefftc/changlab Contact: jeffrey.t.chang@uth.tmc.edu PMID:28052928

  15. The GMOD Drupal Bioinformatic Server Framework

    Science.gov (United States)

    Papanicolaou, Alexie; Heckel, David G.

    2010-01-01

    Motivation: Next-generation sequencing technologies have led to the widespread use of -omic applications. As a result, there is now a pronounced bioinformatic bottleneck. The general model organism database (GMOD) tool kit (http://gmod.org) has produced a number of resources aimed at addressing this issue. It lacks, however, a robust online solution that can deploy heterogeneous data and software within a Web content management system (CMS). Results: We present a bioinformatic framework for the Drupal CMS. It consists of three modules. First, GMOD-DBSF is an application programming interface module for the Drupal CMS that simplifies the programming of bioinformatic Drupal modules. Second, the Drupal Bioinformatic Software Bench (biosoftware_bench) allows for a rapid and secure deployment of bioinformatic software. An innovative graphical user interface (GUI) guides both use and administration of the software, including the secure provision of pre-publication datasets. Third, we present genes4all_experiment, which exemplifies how our work supports the wider research community. Conclusion: Given the infrastructure presented here, the Drupal CMS may become a powerful new tool set for bioinformaticians. The GMOD-DBSF base module is an expandable community resource that decreases development time of Drupal modules for bioinformatics. The biosoftware_bench module can already enhance biologists' ability to mine their own data. The genes4all_experiment module has already been responsible for archiving of more than 150 studies of RNAi from Lepidoptera, which were previously unpublished. Availability and implementation: Implemented in PHP and Perl. Freely available under the GNU Public License 2 or later from http://gmod-dbsf.googlecode.com Contact: alexie@butterflybase.org PMID:20971988

  16. The GMOD Drupal bioinformatic server framework.

    Science.gov (United States)

    Papanicolaou, Alexie; Heckel, David G

    2010-12-15

    Next-generation sequencing technologies have led to the widespread use of -omic applications. As a result, there is now a pronounced bioinformatic bottleneck. The general model organism database (GMOD) tool kit (http://gmod.org) has produced a number of resources aimed at addressing this issue. It lacks, however, a robust online solution that can deploy heterogeneous data and software within a Web content management system (CMS). We present a bioinformatic framework for the Drupal CMS. It consists of three modules. First, GMOD-DBSF is an application programming interface module for the Drupal CMS that simplifies the programming of bioinformatic Drupal modules. Second, the Drupal Bioinformatic Software Bench (biosoftware_bench) allows for a rapid and secure deployment of bioinformatic software. An innovative graphical user interface (GUI) guides both use and administration of the software, including the secure provision of pre-publication datasets. Third, we present genes4all_experiment, which exemplifies how our work supports the wider research community. Given the infrastructure presented here, the Drupal CMS may become a powerful new tool set for bioinformaticians. The GMOD-DBSF base module is an expandable community resource that decreases development time of Drupal modules for bioinformatics. The biosoftware_bench module can already enhance biologists' ability to mine their own data. The genes4all_experiment module has already been responsible for archiving of more than 150 studies of RNAi from Lepidoptera, which were previously unpublished. Implemented in PHP and Perl. Freely available under the GNU Public License 2 or later from http://gmod-dbsf.googlecode.com.

  17. Summer Meal Capacity Builder

    Data.gov (United States)

    Department of Agriculture — Allows users to search for summer meal sites from the previous summer by zip code, adding “layers” of information, such as free and reduced-price lunch participation...

  18. Soviet Union: Summer school goes international

    Energy Technology Data Exchange (ETDEWEB)

    Anon.

    1990-09-15

    The traditional annual Soviet Summer School, held in June in Dubna on the banks of the Volga, this year had international participation for the first time. Initiated by Moscow's Physical Engineering Institute and the Joint Institute for Nuclear Research, Dubna, the school has rotating themes, with the accent this year on developments in high energy physics.

  19. Soviet Union: Summer school goes international

    International Nuclear Information System (INIS)

    Anon.

    1990-01-01

    The traditional annual Soviet Summer School, held in June in Dubna on the banks of the Volga, this year had international participation for the first time. Initiated by Moscow's Physical Engineering Institute and the Joint Institute for Nuclear Research, Dubna, the school has rotating themes, with the accent this year on developments in high energy physics

  20. Bioinformatic tools for PCR Primer design

    African Journals Online (AJOL)

    ES

    reaction (PCR), oligo hybridization and DNA sequencing. Proper primer design is actually one of the most important factors/steps in successful DNA sequencing. Various bioinformatics programs are available for selection of primer pairs from a template sequence. The plethora programs for PCR primer design reflects the.

  1. "Extreme Programming" in a Bioinformatics Class

    Science.gov (United States)

    Kelley, Scott; Alger, Christianna; Deutschman, Douglas

    2009-01-01

    The importance of Bioinformatics tools and methodology in modern biological research underscores the need for robust and effective courses at the college level. This paper describes such a course designed on the principles of cooperative learning based on a computer software industry production model called "Extreme Programming" (EP).…

  2. Bioinformatics: A History of Evolution "In Silico"

    Science.gov (United States)

    Ondrej, Vladan; Dvorak, Petr

    2012-01-01

    Bioinformatics, biological databases, and the worldwide use of computers have accelerated biological research in many fields, such as evolutionary biology. Here, we describe a primer of nucleotide sequence management and the construction of a phylogenetic tree with two examples; the two selected are from completely different groups of organisms:…

  3. Protein raftophilicity. How bioinformatics can help membranologists

    DEFF Research Database (Denmark)

    Nielsen, Henrik; Sperotto, Maria Maddalena

    )-based bioinformatics approach. The ANN was trained to recognize feature-based patterns in proteins that are considered to be associated with lipid rafts. The trained ANN was then used to predict protein raftophilicity. We found that, in the case of α-helical membrane proteins, their hydrophobic length does not affect...

  4. Bioinformatics in Undergraduate Education: Practical Examples

    Science.gov (United States)

    Boyle, John A.

    2004-01-01

    Bioinformatics has emerged as an important research tool in recent years. The ability to mine large databases for relevant information has become increasingly central to many different aspects of biochemistry and molecular biology. It is important that undergraduates be introduced to the available information and methodologies. We present a…

  5. Implementing bioinformatic workflows within the bioextract server

    Science.gov (United States)

    Computational workflows in bioinformatics are becoming increasingly important in the achievement of scientific advances. These workflows typically require the integrated use of multiple, distributed data sources and analytic tools. The BioExtract Server (http://bioextract.org) is a distributed servi...

  6. Privacy Preserving PCA on Distributed Bioinformatics Datasets

    Science.gov (United States)

    Li, Xin

    2011-01-01

    In recent years, new bioinformatics technologies, such as gene expression microarray, genome-wide association study, proteomics, and metabolomics, have been widely used to simultaneously identify a huge number of human genomic/genetic biomarkers, generate a tremendously large amount of data, and dramatically increase the knowledge on human…

  7. Bioboxes: standardised containers for interchangeable bioinformatics software.

    Science.gov (United States)

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

    2015-01-01

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

  8. Development and implementation of a bioinformatics online ...

    African Journals Online (AJOL)

    Thus, there is the need for appropriate strategies of introducing the basic components of this emerging scientific field to part of the African populace through the development of an online distance education learning tool. This study involved the design of a bioinformatics online distance educative tool an implementation of ...

  9. SPECIES DATABASES AND THE BIOINFORMATICS REVOLUTION.

    Science.gov (United States)

    Biological databases are having a growth spurt. Much of this results from research in genetics and biodiversity, coupled with fast-paced developments in information technology. The revolution in bioinformatics, defined by Sugden and Pennisi (2000) as the "tools and techniques for...

  10. H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa

    Science.gov (United States)

    Mulder, Nicola J.; Adebiyi, Ezekiel; Alami, Raouf; Benkahla, Alia; Brandful, James; Doumbia, Seydou; Everett, Dean; Fadlelmola, Faisal M.; Gaboun, Fatima; Gaseitsiwe, Simani; Ghazal, Hassan; Hazelhurst, Scott; Hide, Winston; Ibrahimi, Azeddine; Jaufeerally Fakim, Yasmina; Jongeneel, C. Victor; Joubert, Fourie; Kassim, Samar; Kayondo, Jonathan; Kumuthini, Judit; Lyantagaye, Sylvester; Makani, Julie; Mansour Alzohairy, Ahmed; Masiga, Daniel; Moussa, Ahmed; Nash, Oyekanmi; Ouwe Missi Oukem-Boyer, Odile; Owusu-Dabo, Ellis; Panji, Sumir; Patterton, Hugh; Radouani, Fouzia; Sadki, Khalid; Seghrouchni, Fouad; Tastan Bishop, Özlem; Tiffin, Nicki; Ulenga, Nzovu

    2016-01-01

    The application of genomics technologies to medicine and biomedical research is increasing in popularity, made possible by new high-throughput genotyping and sequencing technologies and improved data analysis capabilities. Some of the greatest genetic diversity among humans, animals, plants, and microbiota occurs in Africa, yet genomic research outputs from the continent are limited. The Human Heredity and Health in Africa (H3Africa) initiative was established to drive the development of genomic research for human health in Africa, and through recognition of the critical role of bioinformatics in this process, spurred the establishment of H3ABioNet, a pan-African bioinformatics network for H3Africa. The limitations in bioinformatics capacity on the continent have been a major contributory factor to the lack of notable outputs in high-throughput biology research. Although pockets of high-quality bioinformatics teams have existed previously, the majority of research institutions lack experienced faculty who can train and supervise bioinformatics students. H3ABioNet aims to address this dire need, specifically in the area of human genetics and genomics, but knock-on effects are ensuring this extends to other areas of bioinformatics. Here, we describe the emergence of genomics research and the development of bioinformatics in Africa through H3ABioNet. PMID:26627985

  11. Navigating the changing learning landscape: perspective from bioinformatics.ca.

    Science.gov (United States)

    Brazas, Michelle D; Ouellette, B F Francis

    2013-09-01

    With the advent of YouTube channels in bioinformatics, open platforms for problem solving in bioinformatics, active web forums in computing analyses and online resources for learning to code or use a bioinformatics tool, the more traditional continuing education bioinformatics training programs have had to adapt. Bioinformatics training programs that solely rely on traditional didactic methods are being superseded by these newer resources. Yet such face-to-face instruction is still invaluable in the learning continuum. Bioinformatics.ca, which hosts the Canadian Bioinformatics Workshops, has blended more traditional learning styles with current online and social learning styles. Here we share our growing experiences over the past 12 years and look toward what the future holds for bioinformatics training programs.

  12. MOWServ: a web client for integration of bioinformatic resources

    Science.gov (United States)

    Ramírez, Sergio; Muñoz-Mérida, Antonio; Karlsson, Johan; García, Maximiliano; Pérez-Pulido, Antonio J.; Claros, M. Gonzalo; Trelles, Oswaldo

    2010-01-01

    The productivity of any scientist is affected by cumbersome, tedious and time-consuming tasks that try to make the heterogeneous web services compatible so that they can be useful in their research. MOWServ, the bioinformatic platform offered by the Spanish National Institute of Bioinformatics, was released to provide integrated access to databases and analytical tools. Since its release, the number of available services has grown dramatically, and it has become one of the main contributors of registered services in the EMBRACE Biocatalogue. The ontology that enables most of the web-service compatibility has been curated, improved and extended. The service discovery has been greatly enhanced by Magallanes software and biodataSF. User data are securely stored on the main server by an authentication protocol that enables the monitoring of current or already-finished user’s tasks, as well as the pipelining of successive data processing services. The BioMoby standard has been greatly extended with the new features included in the MOWServ, such as management of additional information (metadata such as extended descriptions, keywords and datafile examples), a qualified registry, error handling, asynchronous services and service replication. All of them have increased the MOWServ service quality, usability and robustness. MOWServ is available at http://www.inab.org/MOWServ/ and has a mirror at http://www.bitlab-es.com/MOWServ/. PMID:20525794

  13. Shared Bioinformatics Databases within the Unipro UGENE Platform

    Directory of Open Access Journals (Sweden)

    Protsyuk Ivan V.

    2015-03-01

    Full Text Available Unipro UGENE is an open-source bioinformatics toolkit that integrates popular tools along with original instruments for molecular biologists within a unified user interface. Nowadays, most bioinformatics desktop applications, including UGENE, make use of a local data model while processing different types of data. Such an approach causes an inconvenience for scientists working cooperatively and relying on the same data. This refers to the need of making multiple copies of certain files for every workplace and maintaining synchronization between them in case of modifications. Therefore, we focused on delivering a collaborative work into the UGENE user experience. Currently, several UGENE installations can be connected to a designated shared database and users can interact with it simultaneously. Such databases can be created by UGENE users and be used at their discretion. Objects of each data type, supported by UGENE such as sequences, annotations, multiple alignments, etc., can now be easily imported from or exported to a remote storage. One of the main advantages of this system, compared to existing ones, is the almost simultaneous access of client applications to shared data regardless of their volume. Moreover, the system is capable of storing millions of objects. The storage itself is a regular database server so even an inexpert user is able to deploy it. Thus, UGENE may provide access to shared data for users located, for example, in the same laboratory or institution. UGENE is available at: http://ugene.net/download.html.

  14. Promoting synergistic research and education in genomics and bioinformatics.

    Science.gov (United States)

    Yang, Jack Y; Yang, Mary Qu; Zhu, Mengxia Michelle; Arabnia, Hamid R; Deng, Youping

    2008-01-01

    Bioinformatics and Genomics are closely related disciplines that hold great promises for the advancement of research and development in complex biomedical systems, as well as public health, drug design, comparative genomics, personalized medicine and so on. Research and development in these two important areas are impacting the science and technology.High throughput sequencing and molecular imaging technologies marked the beginning of a new era for modern translational medicine and personalized healthcare. The impact of having the human sequence and personalized digital images in hand has also created tremendous demands of developing powerful supercomputing, statistical learning and artificial intelligence approaches to handle the massive bioinformatics and personalized healthcare data, which will obviously have a profound effect on how biomedical research will be conducted toward the improvement of human health and prolonging of human life in the future. The International Society of Intelligent Biological Medicine (http://www.isibm.org) and its official journals, the International Journal of Functional Informatics and Personalized Medicine (http://www.inderscience.com/ijfipm) and the International Journal of Computational Biology and Drug Design (http://www.inderscience.com/ijcbdd) in collaboration with International Conference on Bioinformatics and Computational Biology (Biocomp), touch tomorrow's bioinformatics and personalized medicine throughout today's efforts in promoting the research, education and awareness of the upcoming integrated inter/multidisciplinary field. The 2007 international conference on Bioinformatics and Computational Biology (BIOCOMP07) was held in Las Vegas, the United States of American on June 25-28, 2007. The conference attracted over 400 papers, covering broad research areas in the genomics, biomedicine and bioinformatics. The Biocomp 2007 provides a common platform for the cross fertilization of ideas, and to help shape knowledge and

  15. Component-Based Approach for Educating Students in Bioinformatics

    Science.gov (United States)

    Poe, D.; Venkatraman, N.; Hansen, C.; Singh, G.

    2009-01-01

    There is an increasing need for an effective method of teaching bioinformatics. Increased progress and availability of computer-based tools for educating students have led to the implementation of a computer-based system for teaching bioinformatics as described in this paper. Bioinformatics is a recent, hybrid field of study combining elements of…

  16. My Summer with Science Policy

    Science.gov (United States)

    Murray, Marissa

    This past summer I interned at the American Institute of Physics and helped research and write articles for the FYI Science Policy Bulletin. FYI is an objective digest of science policy developments in Washington, D.C. that impact the greater physical sciences community. Over the course of the summer, I independently attended, analyzed, and reported on a variety of science, technology, and funding related events including congressional hearings, government agency advisory committee meetings, and scientific society events. I wrote and co-wrote three articles on basic energy research legislation, the National Institute of Standards and Technology improvement act, and the National Science Foundation's big ideas for future investment. I had the opportunity to examine some challenging questions such as what is the role of government in funding applied research? How should science priorities be set? What is the right balance of funding across different agencies and programs? I learned about how science policy is a two-way street: science is used to inform policy decisions and policy is made to fund and regulate the conduct of science. I will conclude with how my summer working with FYI showed me the importance of science advocacy, being informed, and voting. Society of Physics Students.

  17. The Bioinformatics of Integrative Medical Insights: Proposals for an International PsychoSocial and Cultural Bioinformatics Project

    Directory of Open Access Journals (Sweden)

    Ernest Rossi

    2006-01-01

    Full Text Available We propose the formation of an International PsychoSocial and Cultural Bioinformatics Project (IPCBP to explore the research foundations of Integrative Medical Insights (IMI on all levels from the molecular-genomic to the psychological, cultural, social, and spiritual. Just as The Human Genome Project identified the molecular foundations of modern medicine with the new technology of sequencing DNA during the past decade, the IPCBP would extend and integrate this neuroscience knowledge base with the technology of gene expression via DNA/proteomic microarray research and brain imaging in development, stress, healing, rehabilitation, and the psychotherapeutic facilitation of existentional wellness. We anticipate that the IPCBP will require a unique international collaboration of, academic institutions, researchers, and clinical practioners for the creation of a new neuroscience of mind-body communication, brain plasticity, memory, learning, and creative processing during optimal experiential states of art, beauty, and truth. We illustrate this emerging integration of bioinformatics with medicine with a videotape of the classical 4-stage creative process in a neuroscience approach to psychotherapy.

  18. The Bioinformatics of Integrative Medical Insights: Proposals for an International Psycho-Social and Cultural Bioinformatics Project

    Directory of Open Access Journals (Sweden)

    Ernest Rossi

    2006-01-01

    Full Text Available We propose the formation of an International Psycho-Social and Cultural Bioinformatics Project (IPCBP to explore the research foundations of Integrative Medical Insights (IMI on all levels from the molecular-genomic to the psychological, cultural, social, and spiritual. Just as The Human Genome Project identified the molecular foundations of modern medicine with the new technology of sequencing DNA during the past decade, the IPCBP would extend and integrate this neuroscience knowledge base with the technology of gene expression via DNA/proteomic microarray research and brain imaging in development, stress, healing, rehabilitation, and the psychotherapeutic facilitation of existentional wellness. We anticipate that the IPCBP will require a unique international collaboration of, academic institutions, researchers, and clinical practioners for the creation of a new neuroscience of mind-body communication, brain plasticity, memory, learning, and creative processing during optimal experiential states of art, beauty, and truth. We illustrate this emerging integration of bioinformatics with medicine with a videotape of the classical 4-stage creative process in a neuroscience approach to psychotherapy.

  19. Bioinformatics and systems biology research update from the 15th International Conference on Bioinformatics (InCoB2016).

    Science.gov (United States)

    Schönbach, Christian; Verma, Chandra; Bond, Peter J; Ranganathan, Shoba

    2016-12-22

    The International Conference on Bioinformatics (InCoB) has been publishing peer-reviewed conference papers in BMC Bioinformatics since 2006. Of the 44 articles accepted for publication in supplement issues of BMC Bioinformatics, BMC Genomics, BMC Medical Genomics and BMC Systems Biology, 24 articles with a bioinformatics or systems biology focus are reviewed in this editorial. InCoB2017 is scheduled to be held in Shenzen, China, September 20-22, 2017.

  20. National Nuclear Physics Summer School

    CERN Document Server

    2016-01-01

    The 2016 National Nuclear Physics Summer School (NNPSS) will be held from Monday July 18 through Friday July 29, 2016, at the Massachusetts Institute of Technology (MIT). The summer school is open to graduate students and postdocs within a few years of their PhD (on either side) with a strong interest in experimental and theoretical nuclear physics. The program will include the following speakers: Accelerators and Detectors - Elke-Caroline Aschenauer, Brookhaven National Laboratory Data Analysis - Michael Williams, MIT Double Beta Decay - Lindley Winslow, MIT Electron-Ion Collider - Abhay Deshpande, Stony Brook University Fundamental Symmetries - Vincenzo Cirigliano, Los Alamos National Laboratory Hadronic Spectroscopy - Matthew Shepherd, Indiana University Hadronic Structure - Jianwei Qiu, Brookhaven National Laboratory Hot Dense Nuclear Matter 1 - Jamie Nagle, Colorado University Hot Dense Nuclear Matter 2 - Wilke van der Schee, MIT Lattice QCD - Sinead Ryan, Trinity College Dublin Neutrino Theory - Cecil...

  1. Bioinformatics in New Generation Flavivirus Vaccines

    Directory of Open Access Journals (Sweden)

    Penelope Koraka

    2010-01-01

    Full Text Available Flavivirus infections are the most prevalent arthropod-borne infections world wide, often causing severe disease especially among children, the elderly, and the immunocompromised. In the absence of effective antiviral treatment, prevention through vaccination would greatly reduce morbidity and mortality associated with flavivirus infections. Despite the success of the empirically developed vaccines against yellow fever virus, Japanese encephalitis virus and tick-borne encephalitis virus, there is an increasing need for a more rational design and development of safe and effective vaccines. Several bioinformatic tools are available to support such rational vaccine design. In doing so, several parameters have to be taken into account, such as safety for the target population, overall immunogenicity of the candidate vaccine, and efficacy and longevity of the immune responses triggered. Examples of how bio-informatics is applied to assist in the rational design and improvements of vaccines, particularly flavivirus vaccines, are presented and discussed.

  2. The growing need for microservices in bioinformatics

    Directory of Open Access Journals (Sweden)

    Christopher L Williams

    2016-01-01

    Full Text Available Objective: Within the information technology (IT industry, best practices and standards are constantly evolving and being refined. In contrast, computer technology utilized within the healthcare industry often evolves at a glacial pace, with reduced opportunities for justified innovation. Although the use of timely technology refreshes within an enterprise′s overall technology stack can be costly, thoughtful adoption of select technologies with a demonstrated return on investment can be very effective in increasing productivity and at the same time, reducing the burden of maintenance often associated with older and legacy systems. In this brief technical communication, we introduce the concept of microservices as applied to the ecosystem of data analysis pipelines. Microservice architecture is a framework for dividing complex systems into easily managed parts. Each individual service is limited in functional scope, thereby conferring a higher measure of functional isolation and reliability to the collective solution. Moreover, maintenance challenges are greatly simplified by virtue of the reduced architectural complexity of each constitutive module. This fact notwithstanding, rendered overall solutions utilizing a microservices-based approach provide equal or greater levels of functionality as compared to conventional programming approaches. Bioinformatics, with its ever-increasing demand for performance and new testing algorithms, is the perfect use-case for such a solution. Moreover, if promulgated within the greater development community as an open-source solution, such an approach holds potential to be transformative to current bioinformatics software development. Context: Bioinformatics relies on nimble IT framework which can adapt to changing requirements. Aims: To present a well-established software design and deployment strategy as a solution for current challenges within bioinformatics Conclusions: Use of the microservices framework

  3. The growing need for microservices in bioinformatics.

    Science.gov (United States)

    Williams, Christopher L; Sica, Jeffrey C; Killen, Robert T; Balis, Ulysses G J

    2016-01-01

    Within the information technology (IT) industry, best practices and standards are constantly evolving and being refined. In contrast, computer technology utilized within the healthcare industry often evolves at a glacial pace, with reduced opportunities for justified innovation. Although the use of timely technology refreshes within an enterprise's overall technology stack can be costly, thoughtful adoption of select technologies with a demonstrated return on investment can be very effective in increasing productivity and at the same time, reducing the burden of maintenance often associated with older and legacy systems. In this brief technical communication, we introduce the concept of microservices as applied to the ecosystem of data analysis pipelines. Microservice architecture is a framework for dividing complex systems into easily managed parts. Each individual service is limited in functional scope, thereby conferring a higher measure of functional isolation and reliability to the collective solution. Moreover, maintenance challenges are greatly simplified by virtue of the reduced architectural complexity of each constitutive module. This fact notwithstanding, rendered overall solutions utilizing a microservices-based approach provide equal or greater levels of functionality as compared to conventional programming approaches. Bioinformatics, with its ever-increasing demand for performance and new testing algorithms, is the perfect use-case for such a solution. Moreover, if promulgated within the greater development community as an open-source solution, such an approach holds potential to be transformative to current bioinformatics software development. Bioinformatics relies on nimble IT framework which can adapt to changing requirements. To present a well-established software design and deployment strategy as a solution for current challenges within bioinformatics. Use of the microservices framework is an effective methodology for the fabrication and

  4. The growing need for microservices in bioinformatics

    Science.gov (United States)

    Williams, Christopher L.; Sica, Jeffrey C.; Killen, Robert T.; Balis, Ulysses G. J.

    2016-01-01

    Objective: Within the information technology (IT) industry, best practices and standards are constantly evolving and being refined. In contrast, computer technology utilized within the healthcare industry often evolves at a glacial pace, with reduced opportunities for justified innovation. Although the use of timely technology refreshes within an enterprise's overall technology stack can be costly, thoughtful adoption of select technologies with a demonstrated return on investment can be very effective in increasing productivity and at the same time, reducing the burden of maintenance often associated with older and legacy systems. In this brief technical communication, we introduce the concept of microservices as applied to the ecosystem of data analysis pipelines. Microservice architecture is a framework for dividing complex systems into easily managed parts. Each individual service is limited in functional scope, thereby conferring a higher measure of functional isolation and reliability to the collective solution. Moreover, maintenance challenges are greatly simplified by virtue of the reduced architectural complexity of each constitutive module. This fact notwithstanding, rendered overall solutions utilizing a microservices-based approach provide equal or greater levels of functionality as compared to conventional programming approaches. Bioinformatics, with its ever-increasing demand for performance and new testing algorithms, is the perfect use-case for such a solution. Moreover, if promulgated within the greater development community as an open-source solution, such an approach holds potential to be transformative to current bioinformatics software development. Context: Bioinformatics relies on nimble IT framework which can adapt to changing requirements. Aims: To present a well-established software design and deployment strategy as a solution for current challenges within bioinformatics Conclusions: Use of the microservices framework is an effective

  5. Bioinformatics of cardiovascular miRNA biology.

    Science.gov (United States)

    Kunz, Meik; Xiao, Ke; Liang, Chunguang; Viereck, Janika; Pachel, Christina; Frantz, Stefan; Thum, Thomas; Dandekar, Thomas

    2015-12-01

    MicroRNAs (miRNAs) are small ~22 nucleotide non-coding RNAs and are highly conserved among species. Moreover, miRNAs regulate gene expression of a large number of genes associated with important biological functions and signaling pathways. Recently, several miRNAs have been found to be associated with cardiovascular diseases. Thus, investigating the complex regulatory effect of miRNAs may lead to a better understanding of their functional role in the heart. To achieve this, bioinformatics approaches have to be coupled with validation and screening experiments to understand the complex interactions of miRNAs with the genome. This will boost the subsequent development of diagnostic markers and our understanding of the physiological and therapeutic role of miRNAs in cardiac remodeling. In this review, we focus on and explain different bioinformatics strategies and algorithms for the identification and analysis of miRNAs and their regulatory elements to better understand cardiac miRNA biology. Starting with the biogenesis of miRNAs, we present approaches such as LocARNA and miRBase for combining sequence and structure analysis including phylogenetic comparisons as well as detailed analysis of RNA folding patterns, functional target prediction, signaling pathway as well as functional analysis. We also show how far bioinformatics helps to tackle the unprecedented level of complexity and systemic effects by miRNA, underlining the strong therapeutic potential of miRNA and miRNA target structures in cardiovascular disease. In addition, we discuss drawbacks and limitations of bioinformatics algorithms and the necessity of experimental approaches for miRNA target identification. This article is part of a Special Issue entitled 'Non-coding RNAs'. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. Comprehensive decision tree models in bioinformatics.

    Directory of Open Access Journals (Sweden)

    Gregor Stiglic

    Full Text Available PURPOSE: Classification is an important and widely used machine learning technique in bioinformatics. Researchers and other end-users of machine learning software often prefer to work with comprehensible models where knowledge extraction and explanation of reasoning behind the classification model are possible. METHODS: This paper presents an extension to an existing machine learning environment and a study on visual tuning of decision tree classifiers. The motivation for this research comes from the need to build effective and easily interpretable decision tree models by so called one-button data mining approach where no parameter tuning is needed. To avoid bias in classification, no classification performance measure is used during the tuning of the model that is constrained exclusively by the dimensions of the produced decision tree. RESULTS: The proposed visual tuning of decision trees was evaluated on 40 datasets containing classical machine learning problems and 31 datasets from the field of bioinformatics. Although we did not expected significant differences in classification performance, the results demonstrate a significant increase of accuracy in less complex visually tuned decision trees. In contrast to classical machine learning benchmarking datasets, we observe higher accuracy gains in bioinformatics datasets. Additionally, a user study was carried out to confirm the assumption that the tree tuning times are significantly lower for the proposed method in comparison to manual tuning of the decision tree. CONCLUSIONS: The empirical results demonstrate that by building simple models constrained by predefined visual boundaries, one not only achieves good comprehensibility, but also very good classification performance that does not differ from usually more complex models built using default settings of the classical decision tree algorithm. In addition, our study demonstrates the suitability of visually tuned decision trees for datasets

  7. Comprehensive decision tree models in bioinformatics.

    Science.gov (United States)

    Stiglic, Gregor; Kocbek, Simon; Pernek, Igor; Kokol, Peter

    2012-01-01

    Classification is an important and widely used machine learning technique in bioinformatics. Researchers and other end-users of machine learning software often prefer to work with comprehensible models where knowledge extraction and explanation of reasoning behind the classification model are possible. This paper presents an extension to an existing machine learning environment and a study on visual tuning of decision tree classifiers. The motivation for this research comes from the need to build effective and easily interpretable decision tree models by so called one-button data mining approach where no parameter tuning is needed. To avoid bias in classification, no classification performance measure is used during the tuning of the model that is constrained exclusively by the dimensions of the produced decision tree. The proposed visual tuning of decision trees was evaluated on 40 datasets containing classical machine learning problems and 31 datasets from the field of bioinformatics. Although we did not expected significant differences in classification performance, the results demonstrate a significant increase of accuracy in less complex visually tuned decision trees. In contrast to classical machine learning benchmarking datasets, we observe higher accuracy gains in bioinformatics datasets. Additionally, a user study was carried out to confirm the assumption that the tree tuning times are significantly lower for the proposed method in comparison to manual tuning of the decision tree. The empirical results demonstrate that by building simple models constrained by predefined visual boundaries, one not only achieves good comprehensibility, but also very good classification performance that does not differ from usually more complex models built using default settings of the classical decision tree algorithm. In addition, our study demonstrates the suitability of visually tuned decision trees for datasets with binary class attributes and a high number of possibly

  8. Penalized feature selection and classification in bioinformatics

    OpenAIRE

    Ma, Shuangge; Huang, Jian

    2008-01-01

    In bioinformatics studies, supervised classification with high-dimensional input variables is frequently encountered. Examples routinely arise in genomic, epigenetic and proteomic studies. Feature selection can be employed along with classifier construction to avoid over-fitting, to generate more reliable classifier and to provide more insights into the underlying causal relationships. In this article, we provide a review of several recently developed penalized feature selection and classific...

  9. Bioinformatics Training: A Review of Challenges, Actions and Support Requirements

    DEFF Research Database (Denmark)

    Schneider, M.V.; Watson, J.; Attwood, T.

    2010-01-01

    As bioinformatics becomes increasingly central to research in the molecular life sciences, the need to train non-bioinformaticians to make the most of bioinformatics resources is growing. Here, we review the key challenges and pitfalls to providing effective training for users of bioinformatics...... services, and discuss successful training strategies shared by a diverse set of bioinformatics trainers. We also identify steps that trainers in bioinformatics could take together to advance the state of the art in current training practices. The ideas presented in this article derive from the first...

  10. Adapting bioinformatics curricula for big data.

    Science.gov (United States)

    Greene, Anna C; Giffin, Kristine A; Greene, Casey S; Moore, Jason H

    2016-01-01

    Modern technologies are capable of generating enormous amounts of data that measure complex biological systems. Computational biologists and bioinformatics scientists are increasingly being asked to use these data to reveal key systems-level properties. We review the extent to which curricula are changing in the era of big data. We identify key competencies that scientists dealing with big data are expected to possess across fields, and we use this information to propose courses to meet these growing needs. While bioinformatics programs have traditionally trained students in data-intensive science, we identify areas of particular biological, computational and statistical emphasis important for this era that can be incorporated into existing curricula. For each area, we propose a course structured around these topics, which can be adapted in whole or in parts into existing curricula. In summary, specific challenges associated with big data provide an important opportunity to update existing curricula, but we do not foresee a wholesale redesign of bioinformatics training programs. © The Author 2015. Published by Oxford University Press.

  11. Bioinformatics on the Cloud Computing Platform Azure

    Science.gov (United States)

    Shanahan, Hugh P.; Owen, Anne M.; Harrison, Andrew P.

    2014-01-01

    We discuss the applicability of the Microsoft cloud computing platform, Azure, for bioinformatics. We focus on the usability of the resource rather than its performance. We provide an example of how R can be used on Azure to analyse a large amount of microarray expression data deposited at the public database ArrayExpress. We provide a walk through to demonstrate explicitly how Azure can be used to perform these analyses in Appendix S1 and we offer a comparison with a local computation. We note that the use of the Platform as a Service (PaaS) offering of Azure can represent a steep learning curve for bioinformatics developers who will usually have a Linux and scripting language background. On the other hand, the presence of an additional set of libraries makes it easier to deploy software in a parallel (scalable) fashion and explicitly manage such a production run with only a few hundred lines of code, most of which can be incorporated from a template. We propose that this environment is best suited for running stable bioinformatics software by users not involved with its development. PMID:25050811

  12. Application of Bioinformatics in Chronobiology Research

    Directory of Open Access Journals (Sweden)

    Robson da Silva Lopes

    2013-01-01

    Full Text Available Bioinformatics and other well-established sciences, such as molecular biology, genetics, and biochemistry, provide a scientific approach for the analysis of data generated through “omics” projects that may be used in studies of chronobiology. The results of studies that apply these techniques demonstrate how they significantly aided the understanding of chronobiology. However, bioinformatics tools alone cannot eliminate the need for an understanding of the field of research or the data to be considered, nor can such tools replace analysts and researchers. It is often necessary to conduct an evaluation of the results of a data mining effort to determine the degree of reliability. To this end, familiarity with the field of investigation is necessary. It is evident that the knowledge that has been accumulated through chronobiology and the use of tools derived from bioinformatics has contributed to the recognition and understanding of the patterns and biological rhythms found in living organisms. The current work aims to develop new and important applications in the near future through chronobiology research.

  13. Chapter 16: text mining for translational bioinformatics.

    Science.gov (United States)

    Cohen, K Bretonnel; Hunter, Lawrence E

    2013-04-01

    Text mining for translational bioinformatics is a new field with tremendous research potential. It is a subfield of biomedical natural language processing that concerns itself directly with the problem of relating basic biomedical research to clinical practice, and vice versa. Applications of text mining fall both into the category of T1 translational research-translating basic science results into new interventions-and T2 translational research, or translational research for public health. Potential use cases include better phenotyping of research subjects, and pharmacogenomic research. A variety of methods for evaluating text mining applications exist, including corpora, structured test suites, and post hoc judging. Two basic principles of linguistic structure are relevant for building text mining applications. One is that linguistic structure consists of multiple levels. The other is that every level of linguistic structure is characterized by ambiguity. There are two basic approaches to text mining: rule-based, also known as knowledge-based; and machine-learning-based, also known as statistical. Many systems are hybrids of the two approaches. Shared tasks have had a strong effect on the direction of the field. Like all translational bioinformatics software, text mining software for translational bioinformatics can be considered health-critical and should be subject to the strictest standards of quality assurance and software testing.

  14. Bringing Web 2.0 to bioinformatics.

    Science.gov (United States)

    Zhang, Zhang; Cheung, Kei-Hoi; Townsend, Jeffrey P

    2009-01-01

    Enabling deft data integration from numerous, voluminous and heterogeneous data sources is a major bioinformatic challenge. Several approaches have been proposed to address this challenge, including data warehousing and federated databasing. Yet despite the rise of these approaches, integration of data from multiple sources remains problematic and toilsome. These two approaches follow a user-to-computer communication model for data exchange, and do not facilitate a broader concept of data sharing or collaboration among users. In this report, we discuss the potential of Web 2.0 technologies to transcend this model and enhance bioinformatics research. We propose a Web 2.0-based Scientific Social Community (SSC) model for the implementation of these technologies. By establishing a social, collective and collaborative platform for data creation, sharing and integration, we promote a web services-based pipeline featuring web services for computer-to-computer data exchange as users add value. This pipeline aims to simplify data integration and creation, to realize automatic analysis, and to facilitate reuse and sharing of data. SSC can foster collaboration and harness collective intelligence to create and discover new knowledge. In addition to its research potential, we also describe its potential role as an e-learning platform in education. We discuss lessons from information technology, predict the next generation of Web (Web 3.0), and describe its potential impact on the future of bioinformatics studies.

  15. Adapting bioinformatics curricula for big data

    Science.gov (United States)

    Greene, Anna C.; Giffin, Kristine A.; Greene, Casey S.

    2016-01-01

    Modern technologies are capable of generating enormous amounts of data that measure complex biological systems. Computational biologists and bioinformatics scientists are increasingly being asked to use these data to reveal key systems-level properties. We review the extent to which curricula are changing in the era of big data. We identify key competencies that scientists dealing with big data are expected to possess across fields, and we use this information to propose courses to meet these growing needs. While bioinformatics programs have traditionally trained students in data-intensive science, we identify areas of particular biological, computational and statistical emphasis important for this era that can be incorporated into existing curricula. For each area, we propose a course structured around these topics, which can be adapted in whole or in parts into existing curricula. In summary, specific challenges associated with big data provide an important opportunity to update existing curricula, but we do not foresee a wholesale redesign of bioinformatics training programs. PMID:25829469

  16. An evaluation of the 1997 JPL Summer Teacher Enhancement Program

    Energy Technology Data Exchange (ETDEWEB)

    Slovacek, Simeon P.; Doyle-Nichols, Adelaide R.

    1997-10-20

    There were two major components in the Jet Propulsion Laboratory (JPL) Summer Teacher Enhancement Project (STEP). First, the Summer Institute was structured as a four-week, 4-credit-unit University course for middle school science teachers, and consisted of workshops, lectures, labs, and tours as activities. The second component consists of follow-up activities related to the summer institute's contents, and again is structured as a University credit-bearing course for participants to reinforce their summer training. Considerable information from the comments and course ratings as given by the participants is included.

  17. Your Best Summer Ever

    Science.gov (United States)

    Cleaver, Samantha

    2012-01-01

    "It must be nice to have summers off." Only other teachers know just how short summer is, with much of August devoted to planning for the new school year. This article offers 17 fresh ideas for exploring, making money, and preparing for next year. Plus, a reading list that hits all the marks!

  18. Indian Summer Arts Festival


    OpenAIRE

    Martel, Yann; Tabu; Tejpal, Tarun; Kunzru, Hari

    2011-01-01

    The SFU Woodward's Cultural Unit partnered with the Indian Summer Festival Society to kick off the inaugural Indian Summer Festival. Held at the Goldcorp Centre for the Arts, it included an interactive Literature Series with notable authors from both India and Canada, including special guests Yann Martel, Bollywood superstar Tabu, journalist Tarun Tejpal, writer Hari Kunzru, and many others.

  19. Research summer camp in photonics

    Science.gov (United States)

    Buyanovskaya, Elizaveta; Melnik, Maksim; Egorov, Vladimir; Gleim, Artur; Lukishova, Svetlana; Kozlov, Sergei; Zhang, Xi-Cheng

    2017-08-01

    ITMO University and the University of Rochester became close partners several years ago. One of the first outcomes of this mutually beneficial partnership was the creation of International Institute of Photonics and Optical Information Technologies led by Prof. Sergei Kozlov and Prof. Xi-Cheng Zhang. Universities have created a double Masters-degree program in optics in 2014, and several ITMO students have been awarded degrees from Rochester. At the same time ITMO University organizes Summer Research camp in Photonics for University of Rochester students. Students spent two weeks in the Northern Capital of Russia learning about the emerging practical applications of femtosecond optics, terahertz biomedicine and quantum information technologies.

  20. Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package.

    Science.gov (United States)

    El-Kalioby, Mohamed; Abouelhoda, Mohamed; Krüger, Jan; Giegerich, Robert; Sczyrba, Alexander; Wall, Dennis P; Tonellato, Peter

    2012-01-01

    Bioinformatics services have been traditionally provided in the form of a web-server that is hosted at institutional infrastructure and serves multiple users. This model, however, is not flexible enough to cope with the increasing number of users, increasing data size, and new requirements in terms of speed and availability of service. The advent of cloud computing suggests a new service model that provides an efficient solution to these problems, based on the concepts of "resources-on-demand" and "pay-as-you-go". However, cloud computing has not yet been introduced within bioinformatics servers due to the lack of usage scenarios and software layers that address the requirements of the bioinformatics domain. In this paper, we provide different use case scenarios for providing cloud computing based services, considering both the technical and financial aspects of the cloud computing service model. These scenarios are for individual users seeking computational power as well as bioinformatics service providers aiming at provision of personalized bioinformatics services to their users. We also present elasticHPC, a software package and a library that facilitates the use of high performance cloud computing resources in general and the implementation of the suggested bioinformatics scenarios in particular. Concrete examples that demonstrate the suggested use case scenarios with whole bioinformatics servers and major sequence analysis tools like BLAST are presented. Experimental results with large datasets are also included to show the advantages of the cloud model. Our use case scenarios and the elasticHPC package are steps towards the provision of cloud based bioinformatics services, which would help in overcoming the data challenge of recent biological research. All resources related to elasticHPC and its web-interface are available at http://www.elasticHPC.org.

  1. Modern bioinformatics meets traditional Chinese medicine.

    Science.gov (United States)

    Gu, Peiqin; Chen, Huajun

    2014-11-01

    Traditional Chinese medicine (TCM) is gaining increasing attention with the emergence of integrative medicine and personalized medicine, characterized by pattern differentiation on individual variance and treatments based on natural herbal synergism. Investigating the effectiveness and safety of the potential mechanisms of TCM and the combination principles of drug therapies will bridge the cultural gap with Western medicine and improve the development of integrative medicine. Dealing with rapidly growing amounts of biomedical data and their heterogeneous nature are two important tasks among modern biomedical communities. Bioinformatics, as an emerging interdisciplinary field of computer science and biology, has become a useful tool for easing the data deluge pressure by automating the computation processes with informatics methods. Using these methods to retrieve, store and analyze the biomedical data can effectively reveal the associated knowledge hidden in the data, and thus promote the discovery of integrated information. Recently, these techniques of bioinformatics have been used for facilitating the interactional effects of both Western medicine and TCM. The analysis of TCM data using computational technologies provides biological evidence for the basic understanding of TCM mechanisms, safety and efficacy of TCM treatments. At the same time, the carrier and targets associated with TCM remedies can inspire the rethinking of modern drug development. This review summarizes the significant achievements of applying bioinformatics techniques to many aspects of the research in TCM, such as analysis of TCM-related '-omics' data and techniques for analyzing biological processes and pharmaceutical mechanisms of TCM, which have shown certain potential of bringing new thoughts to both sides. © The Author 2013. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

  2. Multiobjective optimization in bioinformatics and computational biology.

    Science.gov (United States)

    Handl, Julia; Kell, Douglas B; Knowles, Joshua

    2007-01-01

    This paper reviews the application of multiobjective optimization in the fields of bioinformatics and computational biology. A survey of existing work, organized by application area, forms the main body of the review, following an introduction to the key concepts in multiobjective optimization. An original contribution of the review is the identification of five distinct "contexts," giving rise to multiple objectives: These are used to explain the reasons behind the use of multiobjective optimization in each application area and also to point the way to potential future uses of the technique.

  3. Robust Bioinformatics Recognition with VLSI Biochip Microsystem

    Science.gov (United States)

    Lue, Jaw-Chyng L.; Fang, Wai-Chi

    2006-01-01

    A microsystem architecture for real-time, on-site, robust bioinformatic patterns recognition and analysis has been proposed. This system is compatible with on-chip DNA analysis means such as polymerase chain reaction (PCR)amplification. A corresponding novel artificial neural network (ANN) learning algorithm using new sigmoid-logarithmic transfer function based on error backpropagation (EBP) algorithm is invented. Our results show the trained new ANN can recognize low fluorescence patterns better than the conventional sigmoidal ANN does. A differential logarithmic imaging chip is designed for calculating logarithm of relative intensities of fluorescence signals. The single-rail logarithmic circuit and a prototype ANN chip are designed, fabricated and characterized.

  4. Introducing bioinformatics, the biosciences' genomic revolution

    CERN Document Server

    Zanella, Paolo

    1999-01-01

    The general audience for these lectures is mainly physicists, computer scientists, engineers or the general public wanting to know more about what’s going on in the biosciences. What’s bioinformatics and why is all this fuss being made about it ? What’s this revolution triggered by the human genome project ? Are there any results yet ? What are the problems ? What new avenues of research have been opened up ? What about the technology ? These new developments will be compared with what happened at CERN earlier in its evolution, and it is hoped that the similiraties and contrasts will stimulate new curiosity and provoke new thoughts.

  5. Summer Mini Atomiade in June 2016

    CERN Multimedia

    2016-01-01

    The Mini Atomiade are coming to CERN! Members of Clubs supported by the CERN Staff Association and in conjunction with ASCERI (Association of the Sports Communities of the European Research Institutes) will be organising the summer games at the beginning of June.   ASCERI aims to contribute to a united Europe through regular sports meetings, bringing together members of public Research Institutes at European level. The Association's members come from over 40 Research Institutes spanning 16 countries. Numerous sports and leisure activities are represented at regular events and each tournament is organised by a different research institute.  Clubs in conjunction with the CERN Staff Association have sent teams to previous winter and summer games and now, the CERN Club’s Coordination Committee (CCC) has taken on the challenge of organising a Mini Atomiade from Friday 3 June to Monday 6 June 2016 in Divonne-les-Bains. The ga...

  6. Registration Summer Camp 2016

    CERN Multimedia

    2016-01-01

    Reminder: registration for the CERN Staff Association Summer Camp is now open for children from 4 to 6 years old.   More information on the website: http://nurseryschool.web.cern.ch/. The summer camp is open to all children. The proposed cost is 480.-CHF/week, lunch included. The camp will be open weeks 27, 28, 29 and 30, from 8:30 a.m. to 5:30 p.m. For further questions, you are welcome to contact us by email at Summer.Camp@cern.ch. CERN Staff Association

  7. A Survey of Scholarly Literature Describing the Field of Bioinformatics Education and Bioinformatics Educational Research

    Science.gov (United States)

    Magana, Alejandra J.; Taleyarkhan, Manaz; Alvarado, Daniela Rivera; Kane, Michael; Springer, John; Clase, Kari

    2014-01-01

    Bioinformatics education can be broadly defined as the teaching and learning of the use of computer and information technology, along with mathematical and statistical analysis for gathering, storing, analyzing, interpreting, and integrating data to solve biological problems. The recent surge of genomics, proteomics, and structural biology in the…

  8. Can Text Messages Mitigate Summer Melt?

    Science.gov (United States)

    Castleman, Benjamin L.; Page, Lindsay C.

    2013-01-01

    Higher education officials have long been familiar with the concept of "summer melt," where students who have paid a deposit to attend one college or university instead matriculate at a different institution, usually presumed to be of comparable quality. In previous research, drawing on longitudinal data from various urban school…

  9. 2003 SOLAS Summer School

    National Research Council Canada - National Science Library

    McGillis, Wade R

    2003-01-01

    In 2003, the United States provided support for the participation of 18 students, three research assistants, and seven lecturers in the first Surface Ocean Lower Atmosphere Study (SOLAS) Summer School...

  10. Summer Meal Sites

    Data.gov (United States)

    Allegheny County / City of Pittsburgh / Western PA Regional Data Center — Information pertaining to Summer Meal Sites, as collected by Citiparks in the City of Pittsburgh Department of Parks and Recreation. This dataset includes the...

  11. OpenHelix: bioinformatics education outside of a different box.

    Science.gov (United States)

    Williams, Jennifer M; Mangan, Mary E; Perreault-Micale, Cynthia; Lathe, Scott; Sirohi, Neeraj; Lathe, Warren C

    2010-11-01

    The amount of biological data is increasing rapidly, and will continue to increase as new rapid technologies are developed. Professionals in every area of bioscience will have data management needs that require publicly available bioinformatics resources. Not all scientists desire a formal bioinformatics education but would benefit from more informal educational sources of learning. Effective bioinformatics education formats will address a broad range of scientific needs, will be aimed at a variety of user skill levels, and will be delivered in a number of different formats to address different learning styles. Informal sources of bioinformatics education that are effective are available, and will be explored in this review.

  12. Summer Steelhead Distribution [ds341

    Data.gov (United States)

    California Natural Resource Agency — Summer Steelhead Distribution October 2009 Version This dataset depicts observation-based stream-level geographic distribution of anadromous summer-run steelhead...

  13. RISE OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY IN INDIA: A LOOK THROUGH PUBLICATIONS

    Directory of Open Access Journals (Sweden)

    Anjali Srivastava

    2017-09-01

    Full Text Available Computational biology and bioinformatics have been part and parcel of biomedical research for few decades now. However, the institutionalization of bioinformatics research took place with the establishment of Distributed Information Centres (DISCs in the research institutions of repute in various disciplines by the Department of Biotechnology, Government of India. Though, at initial stages, this endeavor was mainly focused on providing infrastructure for using information technology and internet based communication and tools for carrying out computational biology and in-silico assisted research in varied arena of research starting from disease biology to agricultural crops, spices, veterinary science and many more, the natural outcome of establishment of such facilities resulted into new experiments with bioinformatics tools. Thus, Biotechnology Information Systems (BTIS grew into a solid movement and a large number of publications started coming out of these centres. In the end of last century, bioinformatics started developing like a full-fledged research subject. In the last decade, a need was felt to actually make a factual estimation of the result of this endeavor of DBT which had, by then, established about two hundred centres in almost all disciplines of biomedical research. In a bid to evaluate the efforts and outcome of these centres, BTIS Centre at CSIR-CDRI, Lucknow was entrusted with collecting and collating the publications of these centres. However, when the full data was compiled, the DBT task force felt that the study must include Non-BTIS centres also so as to expand the report to have a glimpse of bioinformatics publications from the country.

  14. Widening participation would be key in enhancing bioinformatics and genomics research in Africa

    Directory of Open Access Journals (Sweden)

    Thomas K. Karikari

    2015-09-01

    Full Text Available Bioinformatics and genome science (BGS are gradually gaining roots in Africa, contributing to studies that are leading to improved understanding of health, disease, agriculture and food security. While a few African countries have established foundations for research and training in these areas, BGS appear to be limited to only a few institutions in specific African countries. However, improving the disciplines in Africa will require pragmatic efforts to expand training and research partnerships to scientists in yet-unreached institutions. Here, we discuss the need to expand BGS programmes in Africa, and propose mechanisms to do so.

  15. Bioinformatic Analysis of Strawberry GSTF12 Gene

    Science.gov (United States)

    Wang, Xiran; Jiang, Leiyu; Tang, Haoru

    2018-01-01

    GSTF12 has always been known as a key factor of proanthocyanins accumulate in plant testa. Through bioinformatics analysis of the nucleotide and encoded protein sequence of GSTF12, it is more advantageous to the study of genes related to anthocyanin biosynthesis accumulation pathway. Therefore, we chosen GSTF12 gene of 11 kinds species, downloaded their nucleotide and protein sequence from NCBI as the research object, found strawberry GSTF12 gene via bioinformation analyse, constructed phylogenetic tree. At the same time, we analysed the strawberry GSTF12 gene of physical and chemical properties and its protein structure and so on. The phylogenetic tree showed that Strawberry and petunia were closest relative. By the protein prediction, we found that the protein owed one proper signal peptide without obvious transmembrane regions.

  16. Bioinformatics for Next Generation Sequencing Data

    Directory of Open Access Journals (Sweden)

    Alberto Magi

    2010-09-01

    Full Text Available The emergence of next-generation sequencing (NGS platforms imposes increasing demands on statistical methods and bioinformatic tools for the analysis and the management of the huge amounts of data generated by these technologies. Even at the early stages of their commercial availability, a large number of softwares already exist for analyzing NGS data. These tools can be fit into many general categories including alignment of sequence reads to a reference, base-calling and/or polymorphism detection, de novo assembly from paired or unpaired reads, structural variant detection and genome browsing. This manuscript aims to guide readers in the choice of the available computational tools that can be used to face the several steps of the data analysis workflow.

  17. Combining multiple decisions: applications to bioinformatics

    International Nuclear Information System (INIS)

    Yukinawa, N; Ishii, S; Takenouchi, T; Oba, S

    2008-01-01

    Multi-class classification is one of the fundamental tasks in bioinformatics and typically arises in cancer diagnosis studies by gene expression profiling. This article reviews two recent approaches to multi-class classification by combining multiple binary classifiers, which are formulated based on a unified framework of error-correcting output coding (ECOC). The first approach is to construct a multi-class classifier in which each binary classifier to be aggregated has a weight value to be optimally tuned based on the observed data. In the second approach, misclassification of each binary classifier is formulated as a bit inversion error with a probabilistic model by making an analogy to the context of information transmission theory. Experimental studies using various real-world datasets including cancer classification problems reveal that both of the new methods are superior or comparable to other multi-class classification methods

  18. Data mining in bioinformatics using Weka.

    Science.gov (United States)

    Frank, Eibe; Hall, Mark; Trigg, Len; Holmes, Geoffrey; Witten, Ian H

    2004-10-12

    The Weka machine learning workbench provides a general-purpose environment for automatic classification, regression, clustering and feature selection-common data mining problems in bioinformatics research. It contains an extensive collection of machine learning algorithms and data pre-processing methods complemented by graphical user interfaces for data exploration and the experimental comparison of different machine learning techniques on the same problem. Weka can process data given in the form of a single relational table. Its main objectives are to (a) assist users in extracting useful information from data and (b) enable them to easily identify a suitable algorithm for generating an accurate predictive model from it. http://www.cs.waikato.ac.nz/ml/weka.

  19. Bioinformatic and Biometric Methods in Plant Morphology

    Directory of Open Access Journals (Sweden)

    Surangi W. Punyasena

    2014-08-01

    Full Text Available Recent advances in microscopy, imaging, and data analyses have permitted both the greater application of quantitative methods and the collection of large data sets that can be used to investigate plant morphology. This special issue, the first for Applications in Plant Sciences, presents a collection of papers highlighting recent methods in the quantitative study of plant form. These emerging biometric and bioinformatic approaches to plant sciences are critical for better understanding how morphology relates to ecology, physiology, genotype, and evolutionary and phylogenetic history. From microscopic pollen grains and charcoal particles, to macroscopic leaves and whole root systems, the methods presented include automated classification and identification, geometric morphometrics, and skeleton networks, as well as tests of the limits of human assessment. All demonstrate a clear need for these computational and morphometric approaches in order to increase the consistency, objectivity, and throughput of plant morphological studies.

  20. Academic Training - Bioinformatics: Decoding the Genome

    CERN Multimedia

    Chris Jones

    2006-01-01

    ACADEMIC TRAINING LECTURE SERIES 27, 28 February 1, 2, 3 March 2006 from 11:00 to 12:00 - Auditorium, bldg. 500 Decoding the Genome A special series of 5 lectures on: Recent extraordinary advances in the life sciences arising through new detection technologies and bioinformatics The past five years have seen an extraordinary change in the information and tools available in the life sciences. The sequencing of the human genome, the discovery that we possess far fewer genes than foreseen, the measurement of the tiny changes in the genomes that differentiate us, the sequencing of the genomes of many pathogens that lead to diseases such as malaria are all examples of completely new information that is now available in the quest for improved healthcare. New tools have allowed similar strides in the discovery of the associated protein structures, providing invaluable information for those searching for new drugs. New DNA microarray chips permit simultaneous measurement of the state of expression of tens...

  1. Evaluating an Inquiry-Based Bioinformatics Course Using Q Methodology

    Science.gov (United States)

    Ramlo, Susan E.; McConnell, David; Duan, Zhong-Hui; Moore, Francisco B.

    2008-01-01

    Faculty at a Midwestern metropolitan public university recently developed a course on bioinformatics that emphasized collaboration and inquiry. Bioinformatics, essentially the application of computational tools to biological data, is inherently interdisciplinary. Thus part of the challenge of creating this course was serving the needs and…

  2. Bioinformatics education dissemination with an evolutionary problem solving perspective.

    Science.gov (United States)

    Jungck, John R; Donovan, Samuel S; Weisstein, Anton E; Khiripet, Noppadon; Everse, Stephen J

    2010-11-01

    Bioinformatics is central to biology education in the 21st century. With the generation of terabytes of data per day, the application of computer-based tools to stored and distributed data is fundamentally changing research and its application to problems in medicine, agriculture, conservation and forensics. In light of this 'information revolution,' undergraduate biology curricula must be redesigned to prepare the next generation of informed citizens as well as those who will pursue careers in the life sciences. The BEDROCK initiative (Bioinformatics Education Dissemination: Reaching Out, Connecting and Knitting together) has fostered an international community of bioinformatics educators. The initiative's goals are to: (i) Identify and support faculty who can take leadership roles in bioinformatics education; (ii) Highlight and distribute innovative approaches to incorporating evolutionary bioinformatics data and techniques throughout undergraduate education; (iii) Establish mechanisms for the broad dissemination of bioinformatics resource materials and teaching models; (iv) Emphasize phylogenetic thinking and problem solving; and (v) Develop and publish new software tools to help students develop and test evolutionary hypotheses. Since 2002, BEDROCK has offered more than 50 faculty workshops around the world, published many resources and supported an environment for developing and sharing bioinformatics education approaches. The BEDROCK initiative builds on the established pedagogical philosophy and academic community of the BioQUEST Curriculum Consortium to assemble the diverse intellectual and human resources required to sustain an international reform effort in undergraduate bioinformatics education.

  3. Bioinformatics and its application in animal health: a review | Soetan ...

    African Journals Online (AJOL)

    Bioinformatics is an interdisciplinary subject, which uses computer application, statistics, mathematics and engineering for the analysis and management of biological information. It has become an important tool for basic and applied research in veterinary sciences. Bioinformatics has brought about advancements into ...

  4. Recent developments in life sciences research: Role of bioinformatics

    African Journals Online (AJOL)

    Life sciences research and development has opened up new challenges and opportunities for bioinformatics. The contribution of bioinformatics advances made possible the mapping of the entire human genome and genomes of many other organisms in just over a decade. These discoveries, along with current efforts to ...

  5. Generative Topic Modeling in Image Data Mining and Bioinformatics Studies

    Science.gov (United States)

    Chen, Xin

    2012-01-01

    Probabilistic topic models have been developed for applications in various domains such as text mining, information retrieval and computer vision and bioinformatics domain. In this thesis, we focus on developing novel probabilistic topic models for image mining and bioinformatics studies. Specifically, a probabilistic topic-connection (PTC) model…

  6. Assessment of a Bioinformatics across Life Science Curricula Initiative

    Science.gov (United States)

    Howard, David R.; Miskowski, Jennifer A.; Grunwald, Sandra K.; Abler, Michael L.

    2007-01-01

    At the University of Wisconsin-La Crosse, we have undertaken a program to integrate the study of bioinformatics across the undergraduate life science curricula. Our efforts have included incorporating bioinformatics exercises into courses in the biology, microbiology, and chemistry departments, as well as coordinating the efforts of faculty within…

  7. Concepts Of Bioinformatics And Its Application In Veterinary ...

    African Journals Online (AJOL)

    Bioinformatics has advanced the course of research and future veterinary vaccines development because it has provided new tools for identification of vaccine targets from sequenced biological data of organisms. In Nigeria, there is lack of bioinformatics training in the universities, expect for short training courses in which ...

  8. Current status and future perspectives of bioinformatics in Tanzania ...

    African Journals Online (AJOL)

    The main bottleneck in advancing genomics in present times is the lack of expertise in using bioinformatics tools and approaches for data mining in raw DNA sequences generated by modern high throughput technologies such as next generation sequencing. Although bioinformatics has been making major progress and ...

  9. The 2015 Bioinformatics Open Source Conference (BOSC 2015).

    Science.gov (United States)

    Harris, Nomi L; Cock, Peter J A; Lapp, Hilmar; Chapman, Brad; Davey, Rob; Fields, Christopher; Hokamp, Karsten; Munoz-Torres, Monica

    2016-02-01

    The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results, and software. BOSC is run as a two-day special interest group (SIG) before the annual Intelligent Systems in Molecular Biology (ISMB) conference. BOSC 2015 took place in Dublin, Ireland, and was attended by over 125 people, about half of whom were first-time attendees. Session topics included "Data Science;" "Standards and Interoperability;" "Open Science and Reproducibility;" "Translational Bioinformatics;" "Visualization;" and "Bioinformatics Open Source Project Updates". In addition to two keynote talks and dozens of shorter talks chosen from submitted abstracts, BOSC 2015 included a panel, titled "Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community," that provided an opportunity for open discussion about ways to increase the diversity of participants in BOSC in particular, and in open source bioinformatics in general. The complete program of BOSC 2015 is available online at http://www.open-bio.org/wiki/BOSC_2015_Schedule.

  10. Is there room for ethics within bioinformatics education?

    Science.gov (United States)

    Taneri, Bahar

    2011-07-01

    When bioinformatics education is considered, several issues are addressed. At the undergraduate level, the main issue revolves around conveying information from two main and different fields: biology and computer science. At the graduate level, the main issue is bridging the gap between biology students and computer science students. However, there is an educational component that is rarely addressed within the context of bioinformatics education: the ethics component. Here, a different perspective is provided on bioinformatics education, and the current status of ethics is analyzed within the existing bioinformatics programs. Analysis of the existing undergraduate and graduate programs, in both Europe and the United States, reveals the minimal attention given to ethics within bioinformatics education. Given that bioinformaticians speedily and effectively shape the biomedical sciences and hence their implications for society, here redesigning of the bioinformatics curricula is suggested in order to integrate the necessary ethics education. Unique ethical problems awaiting bioinformaticians and bioinformatics ethics as a separate field of study are discussed. In addition, a template for an "Ethics in Bioinformatics" course is provided.

  11. 4273π: bioinformatics education on low cost ARM hardware.

    Science.gov (United States)

    Barker, Daniel; Ferrier, David Ek; Holland, Peter Wh; Mitchell, John Bo; Plaisier, Heleen; Ritchie, Michael G; Smart, Steven D

    2013-08-12

    Teaching bioinformatics at universities is complicated by typical computer classroom settings. As well as running software locally and online, students should gain experience of systems administration. For a future career in biology or bioinformatics, the installation of software is a useful skill. We propose that this may be taught by running the course on GNU/Linux running on inexpensive Raspberry Pi computer hardware, for which students may be granted full administrator access. We release 4273π, an operating system image for Raspberry Pi based on Raspbian Linux. This includes minor customisations for classroom use and includes our Open Access bioinformatics course, 4273π Bioinformatics for Biologists. This is based on the final-year undergraduate module BL4273, run on Raspberry Pi computers at the University of St Andrews, Semester 1, academic year 2012-2013. 4273π is a means to teach bioinformatics, including systems administration tasks, to undergraduates at low cost.

  12. LXtoo: an integrated live Linux distribution for the bioinformatics community.

    Science.gov (United States)

    Yu, Guangchuang; Wang, Li-Gen; Meng, Xiao-Hua; He, Qing-Yu

    2012-07-19

    Recent advances in high-throughput technologies dramatically increase biological data generation. However, many research groups lack computing facilities and specialists. This is an obstacle that remains to be addressed. Here, we present a Linux distribution, LXtoo, to provide a flexible computing platform for bioinformatics analysis. Unlike most of the existing live Linux distributions for bioinformatics limiting their usage to sequence analysis and protein structure prediction, LXtoo incorporates a comprehensive collection of bioinformatics software, including data mining tools for microarray and proteomics, protein-protein interaction analysis, and computationally complex tasks like molecular dynamics. Moreover, most of the programs have been configured and optimized for high performance computing. LXtoo aims to provide well-supported computing environment tailored for bioinformatics research, reducing duplication of efforts in building computing infrastructure. LXtoo is distributed as a Live DVD and freely available at http://bioinformatics.jnu.edu.cn/LXtoo.

  13. The development and application of bioinformatics core competencies to improve bioinformatics training and education.

    Science.gov (United States)

    Mulder, Nicola; Schwartz, Russell; Brazas, Michelle D; Brooksbank, Cath; Gaeta, Bruno; Morgan, Sarah L; Pauley, Mark A; Rosenwald, Anne; Rustici, Gabriella; Sierk, Michael; Warnow, Tandy; Welch, Lonnie

    2018-02-01

    Bioinformatics is recognized as part of the essential knowledge base of numerous career paths in biomedical research and healthcare. However, there is little agreement in the field over what that knowledge entails or how best to provide it. These disagreements are compounded by the wide range of populations in need of bioinformatics training, with divergent prior backgrounds and intended application areas. The Curriculum Task Force of the International Society of Computational Biology (ISCB) Education Committee has sought to provide a framework for training needs and curricula in terms of a set of bioinformatics core competencies that cut across many user personas and training programs. The initial competencies developed based on surveys of employers and training programs have since been refined through a multiyear process of community engagement. This report describes the current status of the competencies and presents a series of use cases illustrating how they are being applied in diverse training contexts. These use cases are intended to demonstrate how others can make use of the competencies and engage in the process of their continuing refinement and application. The report concludes with a consideration of remaining challenges and future plans.

  14. The development and application of bioinformatics core competencies to improve bioinformatics training and education

    Science.gov (United States)

    Brooksbank, Cath; Morgan, Sarah L.; Rosenwald, Anne; Warnow, Tandy; Welch, Lonnie

    2018-01-01

    Bioinformatics is recognized as part of the essential knowledge base of numerous career paths in biomedical research and healthcare. However, there is little agreement in the field over what that knowledge entails or how best to provide it. These disagreements are compounded by the wide range of populations in need of bioinformatics training, with divergent prior backgrounds and intended application areas. The Curriculum Task Force of the International Society of Computational Biology (ISCB) Education Committee has sought to provide a framework for training needs and curricula in terms of a set of bioinformatics core competencies that cut across many user personas and training programs. The initial competencies developed based on surveys of employers and training programs have since been refined through a multiyear process of community engagement. This report describes the current status of the competencies and presents a series of use cases illustrating how they are being applied in diverse training contexts. These use cases are intended to demonstrate how others can make use of the competencies and engage in the process of their continuing refinement and application. The report concludes with a consideration of remaining challenges and future plans. PMID:29390004

  15. Summer Camp Registrations 2018

    CERN Multimedia

    Staff Association

    2018-01-01

    Registration for the CERN SA Summer camp, for children from 4 to 6 years old, is now open. The general conditions are available on the EVE and School website: http://nurseryschool.web.cern.ch For further questions, please contact us by email at  Summer.Camp@cern.ch An inscription per week is proposed, for 450.-CHF/week, lunch included. The camp will be open on weeks 27, 28, 29 and 30, from 8:30 am to 5:30 pm. This year the theme will be Vivaldi’s Four Seasons.

  16. Designing a course model for distance-based online bioinformatics training in Africa: The H3ABioNet experience

    Science.gov (United States)

    Panji, Sumir; Fernandes, Pedro L.; Judge, David P.; Ghouila, Amel; Salifu, Samson P.; Ahmed, Rehab; Kayondo, Jonathan; Ssemwanga, Deogratius

    2017-01-01

    Africa is not unique in its need for basic bioinformatics training for individuals from a diverse range of academic backgrounds. However, particular logistical challenges in Africa, most notably access to bioinformatics expertise and internet stability, must be addressed in order to meet this need on the continent. H3ABioNet (www.h3abionet.org), the Pan African Bioinformatics Network for H3Africa, has therefore developed an innovative, free-of-charge “Introduction to Bioinformatics” course, taking these challenges into account as part of its educational efforts to provide on-site training and develop local expertise inside its network. A multiple-delivery–mode learning model was selected for this 3-month course in order to increase access to (mostly) African, expert bioinformatics trainers. The content of the course was developed to include a range of fundamental bioinformatics topics at the introductory level. For the first iteration of the course (2016), classrooms with a total of 364 enrolled participants were hosted at 20 institutions across 10 African countries. To ensure that classroom success did not depend on stable internet, trainers pre-recorded their lectures, and classrooms downloaded and watched these locally during biweekly contact sessions. The trainers were available via video conferencing to take questions during contact sessions, as well as via online “question and discussion” forums outside of contact session time. This learning model, developed for a resource-limited setting, could easily be adapted to other settings. PMID:28981516

  17. A generally applicable lightweight method for calculating a value structure for tools and services in bioinformatics infrastructure projects.

    Science.gov (United States)

    Mayer, Gerhard; Quast, Christian; Felden, Janine; Lange, Matthias; Prinz, Manuel; Pühler, Alfred; Lawerenz, Chris; Scholz, Uwe; Glöckner, Frank Oliver; Müller, Wolfgang; Marcus, Katrin; Eisenacher, Martin

    2017-10-30

    Sustainable noncommercial bioinformatics infrastructures are a prerequisite to use and take advantage of the potential of big data analysis for research and economy. Consequently, funders, universities and institutes as well as users ask for a transparent value model for the tools and services offered. In this article, a generally applicable lightweight method is described by which bioinformatics infrastructure projects can estimate the value of tools and services offered without determining exactly the total costs of ownership. Five representative scenarios for value estimation from a rough estimation to a detailed breakdown of costs are presented. To account for the diversity in bioinformatics applications and services, the notion of service-specific 'service provision units' is introduced together with the factors influencing them and the main underlying assumptions for these 'value influencing factors'. Special attention is given on how to handle personnel costs and indirect costs such as electricity. Four examples are presented for the calculation of the value of tools and services provided by the German Network for Bioinformatics Infrastructure (de.NBI): one for tool usage, one for (Web-based) database analyses, one for consulting services and one for bioinformatics training events. Finally, from the discussed values, the costs of direct funding and the costs of payment of services by funded projects are calculated and compared. © The Author 2017. Published by Oxford University Press.

  18. PATRIC, the bacterial bioinformatics database and analysis resource

    Science.gov (United States)

    Wattam, Alice R.; Abraham, David; Dalay, Oral; Disz, Terry L.; Driscoll, Timothy; Gabbard, Joseph L.; Gillespie, Joseph J.; Gough, Roger; Hix, Deborah; Kenyon, Ronald; Machi, Dustin; Mao, Chunhong; Nordberg, Eric K.; Olson, Robert; Overbeek, Ross; Pusch, Gordon D.; Shukla, Maulik; Schulman, Julie; Stevens, Rick L.; Sullivan, Daniel E.; Vonstein, Veronika; Warren, Andrew; Will, Rebecca; Wilson, Meredith J.C.; Yoo, Hyun Seung; Zhang, Chengdong; Zhang, Yan; Sobral, Bruno W.

    2014-01-01

    The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org). A joint effort by two of the original National Institute of Allergy and Infectious Diseases-funded BRCs, PATRIC provides researchers with an online resource that stores and integrates a variety of data types [e.g. genomics, transcriptomics, protein–protein interactions (PPIs), three-dimensional protein structures and sequence typing data] and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes in PATRIC, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. All the data and integrated analysis and visualization tools are freely available. This manuscript describes updates to the PATRIC since its initial report in the 2007 NAR Database Issue. PMID:24225323

  19. PATRIC, the bacterial bioinformatics database and analysis resource.

    Science.gov (United States)

    Wattam, Alice R; Abraham, David; Dalay, Oral; Disz, Terry L; Driscoll, Timothy; Gabbard, Joseph L; Gillespie, Joseph J; Gough, Roger; Hix, Deborah; Kenyon, Ronald; Machi, Dustin; Mao, Chunhong; Nordberg, Eric K; Olson, Robert; Overbeek, Ross; Pusch, Gordon D; Shukla, Maulik; Schulman, Julie; Stevens, Rick L; Sullivan, Daniel E; Vonstein, Veronika; Warren, Andrew; Will, Rebecca; Wilson, Meredith J C; Yoo, Hyun Seung; Zhang, Chengdong; Zhang, Yan; Sobral, Bruno W

    2014-01-01

    The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org). A joint effort by two of the original National Institute of Allergy and Infectious Diseases-funded BRCs, PATRIC provides researchers with an online resource that stores and integrates a variety of data types [e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data] and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes in PATRIC, currently more than 10,000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. All the data and integrated analysis and visualization tools are freely available. This manuscript describes updates to the PATRIC since its initial report in the 2007 NAR Database Issue.

  20. ASHRAE Summer Meeting 1998

    DEFF Research Database (Denmark)

    Rudbeck, Claus Christian

    1998-01-01

    ASHRAE's (American Society for Heating, Refrigerating and Air- Condition Engineering) summer meeting was visited in June in Toronto. ASHRAE is an American organization dealing with American problems in HVAC, but many results can be used under Danish conditions. It is therefore essential that Danish...

  1. Summer of history

    NARCIS (Netherlands)

    Burman, Jeremy Trevelyan

    2017-01-01

    This summer, the University of Groningen will host three events—yes, three—that will be of special interest to the historically- and theoretically-inclined. The meeting of the International Society for the History of Philosophy of Science (HOPOS) will be held on July 9-12, a workshop exploring the

  2. Books for Summer Reading.

    Science.gov (United States)

    Phi Delta Kappan, 1992

    1992-01-01

    Advises administrators to use their summers to relax and recharge their intellectual batteries. Reading suggestions include Edith Wharton's "House of Mirth," Charlotte Perkins Gilman's "The Yellow Wallpaper," Amy Tan's "Joy Luck Club," China Achebe's "Things Fall Apart," Paule Marshall's "The Chosen…

  3. NEWS: AAPT Summer Meeting

    Science.gov (United States)

    Mellema, Steve

    2000-11-01

    The 2000 Summer Meeting of the American Association of Physics Teachers (AAPT) was held from 28~July-2~August at the University of Guelph in Ontario, Canada. Despite somewhat rainy weather throughout the week, the annual gathering was an enjoyable one, filled with interesting talks on the state of physics education in North America. Using a new scheduling format for the summer meeting, all of the paid workshops and tutorials were held on Saturday and Sunday 29-30 July. The invited and contributed papers for the main AAPT meeting were then presented on Monday, Tuesday and Wednesday. As had been done in 1999 in San Antonio, a two-day tandem meeting dedicated to Physics Education Research (PER) was held on Wednesday and Thursday 2-3 August, immediately after the main AAPT meeting. Over the three days of the main meeting, 60 sessions were held under the sponsorship of various AAPT committees. These included sessions (numbers in parentheses) organized by the committees on Apparatus (1), Astronomy Education (3), Awards (2), Computers (5), Graduate Education (2), High Schools (1), History and Philosophy (1), Instructional Media (3), International Education (1), Laboratories (2), Pre-High School Education (2), Programs (4), Professional Concerns (6), Research in Physics Education (8), Science Education for the Public (2), Two-Year Colleges (5), Undergraduate Education (7) and Women in Physics (4). Figure 1. Guelph Church of Our Lady. The main meeting opened on Sunday evening with an invited lecture by Dr John J Simpson from the host institution, the University of Guelph, describing the Sudbury Neutrino Observatory. At the ceremonial session that began the activities on Monday morning, recognition was given to Clifford Swartz for his almost 30 years of service as Editor of the AAPT journal, The Physics Teacher. This was followed by an invited talk by Jim Nelson from Seminole County Public School in Florida, who received the Excellence in Pre-College Teaching Award. The

  4. Bioinformatics research in the Asia Pacific: a 2007 update.

    Science.gov (United States)

    Ranganathan, Shoba; Gribskov, Michael; Tan, Tin Wee

    2008-01-01

    We provide a 2007 update on the bioinformatics research in the Asia-Pacific from the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998. From 2002, APBioNet has organized the first International Conference on Bioinformatics (InCoB) bringing together scientists working in the field of bioinformatics in the region. This year, the InCoB2007 Conference was organized as the 6th annual conference of the Asia-Pacific Bioinformatics Network, on Aug. 27-30, 2007 at Hong Kong, following a series of successful events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand), Busan (South Korea) and New Delhi (India). Besides a scientific meeting at Hong Kong, satellite events organized are a pre-conference training workshop at Hanoi, Vietnam and a post-conference workshop at Nansha, China. This Introduction provides a brief overview of the peer-reviewed manuscripts accepted for publication in this Supplement. We have organized the papers into thematic areas, highlighting the growing contribution of research excellence from this region, to global bioinformatics endeavours.

  5. Continuing Education Workshops in Bioinformatics Positively Impact Research and Careers.

    Science.gov (United States)

    Brazas, Michelle D; Ouellette, B F Francis

    2016-06-01

    Bioinformatics.ca has been hosting continuing education programs in introductory and advanced bioinformatics topics in Canada since 1999 and has trained more than 2,000 participants to date. These workshops have been adapted over the years to keep pace with advances in both science and technology as well as the changing landscape in available learning modalities and the bioinformatics training needs of our audience. Post-workshop surveys have been a mandatory component of each workshop and are used to ensure appropriate adjustments are made to workshops to maximize learning. However, neither bioinformatics.ca nor others offering similar training programs have explored the long-term impact of bioinformatics continuing education training. Bioinformatics.ca recently initiated a look back on the impact its workshops have had on the career trajectories, research outcomes, publications, and collaborations of its participants. Using an anonymous online survey, bioinformatics.ca analyzed responses from those surveyed and discovered its workshops have had a positive impact on collaborations, research, publications, and career progression.

  6. Bioinformatics approaches for identifying new therapeutic bioactive peptides in food

    Directory of Open Access Journals (Sweden)

    Nora Khaldi

    2012-10-01

    Full Text Available ABSTRACT:The traditional methods for mining foods for bioactive peptides are tedious and long. Similar to the drug industry, the length of time to identify and deliver a commercial health ingredient that reduces disease symptoms can take anything between 5 to 10 years. Reducing this time and effort is crucial in order to create new commercially viable products with clear and important health benefits. In the past few years, bioinformatics, the science that brings together fast computational biology, and efficient genome mining, is appearing as the long awaited solution to this problem. By quickly mining food genomes for characteristics of certain food therapeutic ingredients, researchers can potentially find new ones in a matter of a few weeks. Yet, surprisingly, very little success has been achieved so far using bioinformatics in mining for food bioactives.The absence of food specific bioinformatic mining tools, the slow integration of both experimental mining and bioinformatics, and the important difference between different experimental platforms are some of the reasons for the slow progress of bioinformatics in the field of functional food and more specifically in bioactive peptide discovery.In this paper I discuss some methods that could be easily translated, using a rational peptide bioinformatics design, to food bioactive peptide mining. I highlight the need for an integrated food peptide database. I also discuss how to better integrate experimental work with bioinformatics in order to improve the mining of food for bioactive peptides, therefore achieving a higher success rates.

  7. Bioinformatics in cancer therapy and drug design

    International Nuclear Information System (INIS)

    Horbach, D.Y.; Usanov, S.A.

    2005-01-01

    One of the mechanisms of external signal transduction (ionizing radiation, toxicants, stress) to the target cell is the existence of membrane and intracellular proteins with intrinsic tyrosine kinase activity. No wonder that etiology of malignant growth links to abnormalities in signal transduction through tyrosine kinases. The epidermal growth factor receptor (EGFR) tyrosine kinases play fundamental roles in development, proliferation and differentiation of tissues of epithelial, mesenchymal and neuronal origin. There are four types of EGFR: EGF receptor (ErbB1/HER1), ErbB2/Neu/HER2, ErbB3/HER3 and ErbB4/HER4. Abnormal expression of EGFR, appearance of receptor mutants with changed ability to protein-protein interactions or increased tyrosine kinase activity have been implicated in the malignancy of different types of human tumors. Bioinformatics is currently using in investigation on design and selection of drugs that can make alterations in structure or competitively bind with receptors and so display antagonistic characteristics. (authors)

  8. Bioinformatics in cancer therapy and drug design

    Energy Technology Data Exchange (ETDEWEB)

    Horbach, D Y [International A. Sakharov environmental univ., Minsk (Belarus); Usanov, S A [Inst. of bioorganic chemistry, National academy of sciences of Belarus, Minsk (Belarus)

    2005-05-15

    One of the mechanisms of external signal transduction (ionizing radiation, toxicants, stress) to the target cell is the existence of membrane and intracellular proteins with intrinsic tyrosine kinase activity. No wonder that etiology of malignant growth links to abnormalities in signal transduction through tyrosine kinases. The epidermal growth factor receptor (EGFR) tyrosine kinases play fundamental roles in development, proliferation and differentiation of tissues of epithelial, mesenchymal and neuronal origin. There are four types of EGFR: EGF receptor (ErbB1/HER1), ErbB2/Neu/HER2, ErbB3/HER3 and ErbB4/HER4. Abnormal expression of EGFR, appearance of receptor mutants with changed ability to protein-protein interactions or increased tyrosine kinase activity have been implicated in the malignancy of different types of human tumors. Bioinformatics is currently using in investigation on design and selection of drugs that can make alterations in structure or competitively bind with receptors and so display antagonistic characteristics. (authors)

  9. Bioinformatics study of the mangrove actin genes

    Science.gov (United States)

    Basyuni, M.; Wasilah, M.; Sumardi

    2017-01-01

    This study describes the bioinformatics methods to analyze eight actin genes from mangrove plants on DDBJ/EMBL/GenBank as well as predicted the structure, composition, subcellular localization, similarity, and phylogenetic. The physical and chemical properties of eight mangroves showed variation among the genes. The percentage of the secondary structure of eight mangrove actin genes followed the order of a helix > random coil > extended chain structure for BgActl, KcActl, RsActl, and A. corniculatum Act. In contrast to this observation, the remaining actin genes were random coil > extended chain structure > a helix. This study, therefore, shown the prediction of secondary structure was performed for necessary structural information. The values of chloroplast or signal peptide or mitochondrial target were too small, indicated that no chloroplast or mitochondrial transit peptide or signal peptide of secretion pathway in mangrove actin genes. These results suggested the importance of understanding the diversity and functional of properties of the different amino acids in mangrove actin genes. To clarify the relationship among the mangrove actin gene, a phylogenetic tree was constructed. Three groups of mangrove actin genes were formed, the first group contains B. gymnorrhiza BgAct and R. stylosa RsActl. The second cluster which consists of 5 actin genes the largest group, and the last branch consist of one gene, B. sexagula Act. The present study, therefore, supported the previous results that plant actin genes form distinct clusters in the tree.

  10. Parallel evolutionary computation in bioinformatics applications.

    Science.gov (United States)

    Pinho, Jorge; Sobral, João Luis; Rocha, Miguel

    2013-05-01

    A large number of optimization problems within the field of Bioinformatics require methods able to handle its inherent complexity (e.g. NP-hard problems) and also demand increased computational efforts. In this context, the use of parallel architectures is a necessity. In this work, we propose ParJECoLi, a Java based library that offers a large set of metaheuristic methods (such as Evolutionary Algorithms) and also addresses the issue of its efficient execution on a wide range of parallel architectures. The proposed approach focuses on the easiness of use, making the adaptation to distinct parallel environments (multicore, cluster, grid) transparent to the user. Indeed, this work shows how the development of the optimization library can proceed independently of its adaptation for several architectures, making use of Aspect-Oriented Programming. The pluggable nature of parallelism related modules allows the user to easily configure its environment, adding parallelism modules to the base source code when needed. The performance of the platform is validated with two case studies within biological model optimization. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  11. Bioconductor: open software development for computational biology and bioinformatics

    DEFF Research Database (Denmark)

    Gentleman, R.C.; Carey, V.J.; Bates, D.M.

    2004-01-01

    The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisci......The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry...... into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples....

  12. An Overview of Bioinformatics Tools and Resources in Allergy.

    Science.gov (United States)

    Fu, Zhiyan; Lin, Jing

    2017-01-01

    The rapidly increasing number of characterized allergens has created huge demands for advanced information storage, retrieval, and analysis. Bioinformatics and machine learning approaches provide useful tools for the study of allergens and epitopes prediction, which greatly complement traditional laboratory techniques. The specific applications mainly include identification of B- and T-cell epitopes, and assessment of allergenicity and cross-reactivity. In order to facilitate the work of clinical and basic researchers who are not familiar with bioinformatics, we review in this chapter the most important databases, bioinformatic tools, and methods with relevance to the study of allergens.

  13. Summer 2014 Pathways Report

    Science.gov (United States)

    Hand, Zachary

    2014-01-01

    Over the summer I had the exciting opportunity to work for NASA at the Kennedy Space Center as a Mission Assurance Engineering intern. When I was offered a position in mission assurance for the Safety and Mission Assurance directorate's Launch Services Division, I didn't really know what I would be doing, but I knew it would be an excellent opportunity to learn and grow professionally. In this report I will provide some background information on the Launch Services Division, as well as detail my duties and accomplishments during my time as an intern. Additionally, I will relate the significance of my work experience to my current academic work and future career goals. This report contains background information on Mission Assurance Engineering, a description of my duties and accomplishments over the summer of 2014, and relates the significance of my work experience to my school work and future career goals. It is a required document for the Pathways program.

  14. Summer season | Cafeteria closures

    CERN Multimedia

    2013-01-01

    Please note the following cafeteria closures over the summer season: Bldg. 54 closed from 29/07/2013 to 06/09/2013. Bldg. 13: closed from 13/07/2013 to 06/09/2013. Restaurant No. 2, table service (brasserie and restaurant): closed from 01/08/2013 to 06/09/2013. Bldg. 864: closed from 29/07/2013 to 06/09/2013. Bldg. 865: closed from 29/07/2013 to 06/09/2013.

  15. Summer and Autumn activities

    CERN Multimedia

    Staff Association

    2013-01-01

    Time to recharge the batteries, and much more… The summer holidays are an ideal opportunity to spend more time with the family, to discover new countries, make new friends, in other words to take time away from the daily grind. This recharging is essential to your work-life balance, and CERN, as a modern and socially responsible employer, has recognized this as a central part of its human resources policy.Nevertheless we should not forget that, while many of you enjoy a well-deserved summer break, some of our colleagues are hard at work making LS1 (first Long Shutdown) a success in order to guarantee that at the beginning of 2015 the LHC will be able to start physics in an energy range never before reached by mankind. Preparing the questionnaire and the elections to the Staff Council During this summer your delegates in the Staff Council are hard at work preparing for the upcoming five-yearly review whose content will be decided by CERN Council in June 2014. Therefore, as every five years, to ...

  16. Controls on summer low flow

    Science.gov (United States)

    Graham, C. B.; McNamara, J. P.

    2012-12-01

    Summer low flow has significant impacts on aquatic flora and fauna, municipal water use, and power generation. However, the controls on the minimum annual summer discharge are complex, including a combination of snowmelt dynamics, summer evapotranspiration demand, and spring, summer precipitation patterns and surface - groundwater interactions. This is especially true in the Rocky Mountain West of the United States, where snowpack provides the majority of water available for spring runoff and groundwater replenishment. In this study, we look at summer low flow conditions at four snow dominated catchments (26 km2 - 2200 km2) in South-central Idaho currently feeling the effects of climate change. Measures of snowmelt dynamics, summer evapotranspiration demand and spring and summer precipitation are used to determine the dominant controls on late summer low flow magnitude, timing and duration. These analyses show that the controls vary between watersheds, with significant implications for the impacts of climate change in snow dominated areas of the Rocky Mountain West.

  17. Allegheny County Summer Food Sites

    Data.gov (United States)

    Allegheny County / City of Pittsburgh / Western PA Regional Data Center — This data set shows the Summer Food Sites located within Allegheny County for children (18 years and younger) for breakfast and lunch during summer recess. OPEN...

  18. Development of a cloud-based Bioinformatics Training Platform.

    Science.gov (United States)

    Revote, Jerico; Watson-Haigh, Nathan S; Quenette, Steve; Bethwaite, Blair; McGrath, Annette; Shang, Catherine A

    2017-05-01

    The Bioinformatics Training Platform (BTP) has been developed to provide access to the computational infrastructure required to deliver sophisticated hands-on bioinformatics training courses. The BTP is a cloud-based solution that is in active use for delivering next-generation sequencing training to Australian researchers at geographically dispersed locations. The BTP was built to provide an easy, accessible, consistent and cost-effective approach to delivering workshops at host universities and organizations with a high demand for bioinformatics training but lacking the dedicated bioinformatics training suites required. To support broad uptake of the BTP, the platform has been made compatible with multiple cloud infrastructures. The BTP is an open-source and open-access resource. To date, 20 training workshops have been delivered to over 700 trainees at over 10 venues across Australia using the BTP. © The Author 2016. Published by Oxford University Press.

  19. An Adaptive Hybrid Multiprocessor technique for bioinformatics sequence alignment

    KAUST Repository

    Bonny, Talal; Salama, Khaled N.; Zidan, Mohammed A.

    2012-01-01

    Sequence alignment algorithms such as the Smith-Waterman algorithm are among the most important applications in the development of bioinformatics. Sequence alignment algorithms must process large amounts of data which may take a long time. Here, we

  20. Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond.

    Science.gov (United States)

    Hiraoka, Satoshi; Yang, Ching-Chia; Iwasaki, Wataru

    2016-09-29

    Metagenomic approaches are now commonly used in microbial ecology to study microbial communities in more detail, including many strains that cannot be cultivated in the laboratory. Bioinformatic analyses make it possible to mine huge metagenomic datasets and discover general patterns that govern microbial ecosystems. However, the findings of typical metagenomic and bioinformatic analyses still do not completely describe the ecology and evolution of microbes in their environments. Most analyses still depend on straightforward sequence similarity searches against reference databases. We herein review the current state of metagenomics and bioinformatics in microbial ecology and discuss future directions for the field. New techniques will allow us to go beyond routine analyses and broaden our knowledge of microbial ecosystems. We need to enrich reference databases, promote platforms that enable meta- or comprehensive analyses of diverse metagenomic datasets, devise methods that utilize long-read sequence information, and develop more powerful bioinformatic methods to analyze data from diverse perspectives.

  1. In silico cloning and bioinformatic analysis of PEPCK gene in ...

    African Journals Online (AJOL)

    Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. According to the relative conservation of homologous gene, a bioinformatics strategy was applied to clone Fusarium ...

  2. Best practices in bioinformatics training for life scientists.

    KAUST Repository

    Via, Allegra; Blicher, Thomas; Bongcam-Rudloff, Erik; Brazas, Michelle D; Brooksbank, Cath; Budd, Aidan; De Las Rivas, Javier; Dreyer, Jacqueline; Fernandes, Pedro L; van Gelder, Celia; Jacob, Joachim; Jimenez, Rafael C; Loveland, Jane; Moran, Federico; Mulder, Nicola; Nyrö nen, Tommi; Rother, Kristian; Schneider, Maria Victoria; Attwood, Teresa K

    2013-01-01

    concepts. Providing bioinformatics training to empower life scientists to handle and analyse their data efficiently, and progress their research, is a challenge across the globe. Delivering good training goes beyond traditional lectures and resource

  3. Microsoft Biology Initiative: .NET Bioinformatics Platform and Tools

    Science.gov (United States)

    Diaz Acosta, B.

    2011-01-01

    The Microsoft Biology Initiative (MBI) is an effort in Microsoft Research to bring new technology and tools to the area of bioinformatics and biology. This initiative is comprised of two primary components, the Microsoft Biology Foundation (MBF) and the Microsoft Biology Tools (MBT). MBF is a language-neutral bioinformatics toolkit built as an extension to the Microsoft .NET Framework—initially aimed at the area of Genomics research. Currently, it implements a range of parsers for common bioinformatics file formats; a range of algorithms for manipulating DNA, RNA, and protein sequences; and a set of connectors to biological web services such as NCBI BLAST. MBF is available under an open source license, and executables, source code, demo applications, documentation and training materials are freely downloadable from http://research.microsoft.com/bio. MBT is a collection of tools that enable biology and bioinformatics researchers to be more productive in making scientific discoveries.

  4. Bioinformatics tools for development of fast and cost effective simple ...

    African Journals Online (AJOL)

    Bioinformatics tools for development of fast and cost effective simple sequence repeat ... comparative mapping and exploration of functional genetic diversity in the ... Already, a number of computer programs have been implemented that aim at ...

  5. Skate Genome Project: Cyber-Enabled Bioinformatics Collaboration

    Science.gov (United States)

    Vincent, J.

    2011-01-01

    The Skate Genome Project, a pilot project of the North East Cyber infrastructure Consortium, aims to produce a draft genome sequence of Leucoraja erinacea, the Little Skate. The pilot project was designed to also develop expertise in large scale collaborations across the NECC region. An overview of the bioinformatics and infrastructure challenges faced during the first year of the project will be presented. Results to date and lessons learned from the perspective of a bioinformatics core will be highlighted.

  6. PubData: search engine for bioinformatics databases worldwide

    OpenAIRE

    Vand, Kasra; Wahlestedt, Thor; Khomtchouk, Kelly; Sayed, Mohammed; Wahlestedt, Claes; Khomtchouk, Bohdan

    2016-01-01

    We propose a search engine and file retrieval system for all bioinformatics databases worldwide. PubData searches biomedical data in a user-friendly fashion similar to how PubMed searches biomedical literature. PubData is built on novel network programming, natural language processing, and artificial intelligence algorithms that can patch into the file transfer protocol servers of any user-specified bioinformatics database, query its contents, retrieve files for download, and adapt to the use...

  7. An innovative approach for testing bioinformatics programs using metamorphic testing

    Directory of Open Access Journals (Sweden)

    Liu Huai

    2009-01-01

    Full Text Available Abstract Background Recent advances in experimental and computational technologies have fueled the development of many sophisticated bioinformatics programs. The correctness of such programs is crucial as incorrectly computed results may lead to wrong biological conclusion or misguide downstream experimentation. Common software testing procedures involve executing the target program with a set of test inputs and then verifying the correctness of the test outputs. However, due to the complexity of many bioinformatics programs, it is often difficult to verify the correctness of the test outputs. Therefore our ability to perform systematic software testing is greatly hindered. Results We propose to use a novel software testing technique, metamorphic testing (MT, to test a range of bioinformatics programs. Instead of requiring a mechanism to verify whether an individual test output is correct, the MT technique verifies whether a pair of test outputs conform to a set of domain specific properties, called metamorphic relations (MRs, thus greatly increases the number and variety of test cases that can be applied. To demonstrate how MT is used in practice, we applied MT to test two open-source bioinformatics programs, namely GNLab and SeqMap. In particular we show that MT is simple to implement, and is effective in detecting faults in a real-life program and some artificially fault-seeded programs. Further, we discuss how MT can be applied to test programs from various domains of bioinformatics. Conclusion This paper describes the application of a simple, effective and automated technique to systematically test a range of bioinformatics programs. We show how MT can be implemented in practice through two real-life case studies. Since many bioinformatics programs, particularly those for large scale simulation and data analysis, are hard to test systematically, their developers may benefit from using MT as part of the testing strategy. Therefore our work

  8. BOWS (bioinformatics open web services) to centralize bioinformatics tools in web services.

    Science.gov (United States)

    Velloso, Henrique; Vialle, Ricardo A; Ortega, J Miguel

    2015-06-02

    Bioinformaticians face a range of difficulties to get locally-installed tools running and producing results; they would greatly benefit from a system that could centralize most of the tools, using an easy interface for input and output. Web services, due to their universal nature and widely known interface, constitute a very good option to achieve this goal. Bioinformatics open web services (BOWS) is a system based on generic web services produced to allow programmatic access to applications running on high-performance computing (HPC) clusters. BOWS intermediates the access to registered tools by providing front-end and back-end web services. Programmers can install applications in HPC clusters in any programming language and use the back-end service to check for new jobs and their parameters, and then to send the results to BOWS. Programs running in simple computers consume the BOWS front-end service to submit new processes and read results. BOWS compiles Java clients, which encapsulate the front-end web service requisitions, and automatically creates a web page that disposes the registered applications and clients. Bioinformatics open web services registered applications can be accessed from virtually any programming language through web services, or using standard java clients. The back-end can run in HPC clusters, allowing bioinformaticians to remotely run high-processing demand applications directly from their machines.

  9. Assessment of Data Reliability of Wireless Sensor Network for Bioinformatics

    Directory of Open Access Journals (Sweden)

    Ting Dong

    2017-09-01

    Full Text Available As a focal point of biotechnology, bioinformatics integrates knowledge from biology, mathematics, physics, chemistry, computer science and information science. It generally deals with genome informatics, protein structure and drug design. However, the data or information thus acquired from the main areas of bioinformatics may not be effective. Some researchers combined bioinformatics with wireless sensor network (WSN into biosensor and other tools, and applied them to such areas as fermentation, environmental monitoring, food engineering, clinical medicine and military. In the combination, the WSN is used to collect data and information. The reliability of the WSN in bioinformatics is the prerequisite to effective utilization of information. It is greatly influenced by factors like quality, benefits, service, timeliness and stability, some of them are qualitative and some are quantitative. Hence, it is necessary to develop a method that can handle both qualitative and quantitative assessment of information. A viable option is the fuzzy linguistic method, especially 2-tuple linguistic model, which has been extensively used to cope with such issues. As a result, this paper introduces 2-tuple linguistic representation to assist experts in giving their opinions on different WSNs in bioinformatics that involve multiple factors. Moreover, the author proposes a novel way to determine attribute weights and uses the method to weigh the relative importance of different influencing factors which can be considered as attributes in the assessment of the WSN in bioinformatics. Finally, an illustrative example is given to provide a reasonable solution for the assessment.

  10. An interdepartmental Ph.D. program in computational biology and bioinformatics: the Yale perspective.

    Science.gov (United States)

    Gerstein, Mark; Greenbaum, Dov; Cheung, Kei; Miller, Perry L

    2007-02-01

    Computational biology and bioinformatics (CBB), the terms often used interchangeably, represent a rapidly evolving biological discipline. With the clear potential for discovery and innovation, and the need to deal with the deluge of biological data, many academic institutions are committing significant resources to develop CBB research and training programs. Yale formally established an interdepartmental Ph.D. program in CBB in May 2003. This paper describes Yale's program, discussing the scope of the field, the program's goals and curriculum, as well as a number of issues that arose in implementing the program. (Further updated information is available from the program's website, www.cbb.yale.edu.)

  11. ClusterControl: a web interface for distributing and monitoring bioinformatics applications on a Linux cluster.

    Science.gov (United States)

    Stocker, Gernot; Rieder, Dietmar; Trajanoski, Zlatko

    2004-03-22

    ClusterControl is a web interface to simplify distributing and monitoring bioinformatics applications on Linux cluster systems. We have developed a modular concept that enables integration of command line oriented program into the application framework of ClusterControl. The systems facilitate integration of different applications accessed through one interface and executed on a distributed cluster system. The package is based on freely available technologies like Apache as web server, PHP as server-side scripting language and OpenPBS as queuing system and is available free of charge for academic and non-profit institutions. http://genome.tugraz.at/Software/ClusterControl

  12. Next Generation Summer School

    Science.gov (United States)

    Eugenia, Marcu

    2013-04-01

    On 21.06.2010 the "Next Generation" Summer School has opened the doors for its first students. They were introduced in the astronomy world by astronomical observations, astronomy and radio-astronomy lectures, laboratory projects meant to initiate them into modern radio astronomy and radio communications. The didactic programme was structure as fallowing: 1) Astronomical elements from the visible spectrum (lectures + practical projects) 2) Radio astronomy elements (lectures + practical projects) 3) Radio communication base (didactic- recreative games) The students and professors accommodation was at the Agroturistic Pension "Popasul Iancului" situated at 800m from the Marisel Observatory. First day (summer solstice day) began with a practical activity: determination of the meridian by measurements of the shadow (the direction of one vertical alignment, when it has the smallest length). The experiment is very instructive and interesting because combines notions of physics, spatial geometry and basic astronomy elements. Next day the activities took place in four stages: the students processed the experimental data obtained on first day (on sheets of millimetre paper they represented the length of the shadow alignments according the time), each team realised its own sun quadrant, point were given considering the design and functionality of these quadrant, the four teams had to mimic important constellations on carton boards with phosphorescent sticky stars and the students, accompanied by the professors took a hiking trip to the surroundings, marking the interest point coordinates, using a GPS to establish the geographical coronations and at the end of the day the students realised a small map of central Marisel area based on the GPS data. On the third day, the students were introduced to basic notions of radio astronomy, the principal categories of artificial Earth satellites: low orbit satellites (LEO), Medium orbit satellites (MEO) and geostationary satellites (GEO

  13. Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community

    Science.gov (United States)

    2012-01-01

    Background A steep drop in the cost of next-generation sequencing during recent years has made the technology affordable to the majority of researchers, but downstream bioinformatic analysis still poses a resource bottleneck for smaller laboratories and institutes that do not have access to substantial computational resources. Sequencing instruments are typically bundled with only the minimal processing and storage capacity required for data capture during sequencing runs. Given the scale of sequence datasets, scientific value cannot be obtained from acquiring a sequencer unless it is accompanied by an equal investment in informatics infrastructure. Results Cloud BioLinux is a publicly accessible Virtual Machine (VM) that enables scientists to quickly provision on-demand infrastructures for high-performance bioinformatics computing using cloud platforms. Users have instant access to a range of pre-configured command line and graphical software applications, including a full-featured desktop interface, documentation and over 135 bioinformatics packages for applications including sequence alignment, clustering, assembly, display, editing, and phylogeny. Each tool's functionality is fully described in the documentation directly accessible from the graphical interface of the VM. Besides the Amazon EC2 cloud, we have started instances of Cloud BioLinux on a private Eucalyptus cloud installed at the J. Craig Venter Institute, and demonstrated access to the bioinformatic tools interface through a remote connection to EC2 instances from a local desktop computer. Documentation for using Cloud BioLinux on EC2 is available from our project website, while a Eucalyptus cloud image and VirtualBox Appliance is also publicly available for download and use by researchers with access to private clouds. Conclusions Cloud BioLinux provides a platform for developing bioinformatics infrastructures on the cloud. An automated and configurable process builds Virtual Machines, allowing the

  14. Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community.

    Science.gov (United States)

    Krampis, Konstantinos; Booth, Tim; Chapman, Brad; Tiwari, Bela; Bicak, Mesude; Field, Dawn; Nelson, Karen E

    2012-03-19

    A steep drop in the cost of next-generation sequencing during recent years has made the technology affordable to the majority of researchers, but downstream bioinformatic analysis still poses a resource bottleneck for smaller laboratories and institutes that do not have access to substantial computational resources. Sequencing instruments are typically bundled with only the minimal processing and storage capacity required for data capture during sequencing runs. Given the scale of sequence datasets, scientific value cannot be obtained from acquiring a sequencer unless it is accompanied by an equal investment in informatics infrastructure. Cloud BioLinux is a publicly accessible Virtual Machine (VM) that enables scientists to quickly provision on-demand infrastructures for high-performance bioinformatics computing using cloud platforms. Users have instant access to a range of pre-configured command line and graphical software applications, including a full-featured desktop interface, documentation and over 135 bioinformatics packages for applications including sequence alignment, clustering, assembly, display, editing, and phylogeny. Each tool's functionality is fully described in the documentation directly accessible from the graphical interface of the VM. Besides the Amazon EC2 cloud, we have started instances of Cloud BioLinux on a private Eucalyptus cloud installed at the J. Craig Venter Institute, and demonstrated access to the bioinformatic tools interface through a remote connection to EC2 instances from a local desktop computer. Documentation for using Cloud BioLinux on EC2 is available from our project website, while a Eucalyptus cloud image and VirtualBox Appliance is also publicly available for download and use by researchers with access to private clouds. Cloud BioLinux provides a platform for developing bioinformatics infrastructures on the cloud. An automated and configurable process builds Virtual Machines, allowing the development of highly

  15. Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting.

    Science.gov (United States)

    Ibrahim, Bashar; Arkhipova, Ksenia; Andeweg, Arno C; Posada-Céspedes, Susana; Enault, François; Gruber, Arthur; Koonin, Eugene V; Kupczok, Anne; Lemey, Philippe; McHardy, Alice C; McMahon, Dino P; Pickett, Brett E; Robertson, David L; Scheuermann, Richard H; Zhernakova, Alexandra; Zwart, Mark P; Schönhuth, Alexander; Dutilh, Bas E; Marz, Manja

    2018-05-14

    The Second Annual Meeting of the European Virus Bioinformatics Center (EVBC), held in Utrecht, Netherlands, focused on computational approaches in virology, with topics including (but not limited to) virus discovery, diagnostics, (meta-)genomics, modeling, epidemiology, molecular structure, evolution, and viral ecology. The goals of the Second Annual Meeting were threefold: (i) to bring together virologists and bioinformaticians from across the academic, industrial, professional, and training sectors to share best practice; (ii) to provide a meaningful and interactive scientific environment to promote discussion and collaboration between students, postdoctoral fellows, and both new and established investigators; (iii) to inspire and suggest new research directions and questions. Approximately 120 researchers from around the world attended the Second Annual Meeting of the EVBC this year, including 15 renowned international speakers. This report presents an overview of new developments and novel research findings that emerged during the meeting.

  16. Summer Camp, July 2016

    CERN Multimedia

    Staff Association

    2016-01-01

    During the month of July, the Staff Association’s Children’s Day-Care Centre and School EVEE held a summer camp for 4- to 6-year-olds. 24 children altogether joined in on the adventures. On the summer camp, the children got to “travel” to a different continent of the world every week. Day after day, they would pass through make-believe Customs upon arrival and get their passports stamped by a “customs officer”. For the first week, we went on a trip to Africa. In the spirit of the theme, the children got to do plenty of crafts and coloring, make their own little bindles and play various games. They even had the chance to visit the Museum of Ethnography in Geneva (MEG), learn to play the balafon and make musical instruments with Sterrenlab. For the second week, we set off to discover the Americas, exploring both the South and the North. Alongside different workshops (singing, dancing, storytelling, crafts), the children could enjoy several special ac...

  17. Institute enriching students in Africa

    CERN Multimedia

    Burton, H

    2004-01-01

    In Cape Town, South Africa, the first annual African Summer Theory Institute is being held. This is a three-week conference for university science students throughout the whole of Africa, co-sponsored by Perimeter Institute as part of international outreach initiatives (1 page).

  18. Documenting the emergence of bio-ontologies: or, why researching bioinformatics requires HPSSB.

    Science.gov (United States)

    Leonelli, Sabina

    2010-01-01

    This paper reflects on the analytic challenges emerging from the study of bioinformatic tools recently created to store and disseminate biological data, such as databases, repositories, and bio-ontologies. I focus my discussion on the Gene Ontology, a term that defines three entities at once: a classification system facilitating the distribution and use of genomic data as evidence towards new insights; an expert community specialised in the curation of those data; and a scientific institution promoting the use of this tool among experimental biologists. These three dimensions of the Gene Ontology can be clearly distinguished analytically, but are tightly intertwined in practice. I suggest that this is true of all bioinformatic tools: they need to be understood simultaneously as epistemic, social, and institutional entities, since they shape the knowledge extracted from data and at the same time regulate the organisation, development, and communication of research. This viewpoint has one important implication for the methodologies used to study these tools; that is, the need to integrate historical, philosophical, and sociological approaches. I illustrate this claim through examples of misunderstandings that may result from a narrowly disciplinary study of the Gene Ontology, as I experienced them in my own research.

  19. Bioinformatics in the Netherlands: the value of a nationwide community.

    Science.gov (United States)

    van Gelder, Celia W G; Hooft, Rob W W; van Rijswijk, Merlijn N; van den Berg, Linda; Kok, Ruben G; Reinders, Marcel; Mons, Barend; Heringa, Jaap

    2017-09-15

    This review provides a historical overview of the inception and development of bioinformatics research in the Netherlands. Rooted in theoretical biology by foundational figures such as Paulien Hogeweg (at Utrecht University since the 1970s), the developments leading to organizational structures supporting a relatively large Dutch bioinformatics community will be reviewed. We will show that the most valuable resource that we have built over these years is the close-knit national expert community that is well engaged in basic and translational life science research programmes. The Dutch bioinformatics community is accustomed to facing the ever-changing landscape of data challenges and working towards solutions together. In addition, this community is the stable factor on the road towards sustainability, especially in times where existing funding models are challenged and change rapidly. © The Author 2017. Published by Oxford University Press.

  20. A River Summer on the Hudson

    Science.gov (United States)

    Kenna, T. C.; Pfirman, S.; Selleck, B.; Son, L.; Land, M.; Cronin, J.

    2006-12-01

    River Summer is a month-long faculty development program extending from the continental shelf off New York City to the headwaters of the Hudson in the Adirondack Mountains. During the program, faculty from the Environmental Consortium of Hudson Valley Colleges and Universities teach each other about the Hudson environment, using innovative methods of teaching and learning, with a focus on incorporation of hands-on approaches from the perspective of multiple disciplines. Over four weeks, faculty from research universities, community colleges, liberal arts institutions, and middle and high schools work and live together, on board a research vessel or in a remote tent campsite, for several days at a time. Using the geology, hydrology, and landscape of the River as a foundation, River Summer focuses on understanding development of the Hudson within the context of its natural resources and cultural history. Participants conduct field sampling and analyses and consider issues through approaches that are common to many disciplines: scaling for problem solving; sampling and assessing bias and representation; observing and documenting; representing and depicting; interpretation and assessing relationships and causality; and evaluation. They also get a chance to experience, first-hand, the complexity and often open-ended nature of doing science. By allowing individuals, many of whom come from non-science disciplines, to experience these methods and processes in a safe learning environment, science is made more meaningful and accessible. The program's pedagogy is based on the principles of cognitive psychology and immersive field-, place- and inquiry-based learning. Field programs have been found to provide memorable, transformative experiences for undergraduate students, and our experience with River Summer 2005 and 2006 suggests they are equally effective with faculty. Evaluation shows that River Summer has a significant impact on its participants. Participants develop new

  1. Genomics and bioinformatics resources for translational science in Rosaceae.

    Science.gov (United States)

    Jung, Sook; Main, Dorrie

    2014-01-01

    Recent technological advances in biology promise unprecedented opportunities for rapid and sustainable advancement of crop quality. Following this trend, the Rosaceae research community continues to generate large amounts of genomic, genetic and breeding data. These include annotated whole genome sequences, transcriptome and expression data, proteomic and metabolomic data, genotypic and phenotypic data, and genetic and physical maps. Analysis, storage, integration and dissemination of these data using bioinformatics tools and databases are essential to provide utility of the data for basic, translational and applied research. This review discusses the currently available genomics and bioinformatics resources for the Rosaceae family.

  2. Naturally selecting solutions: the use of genetic algorithms in bioinformatics.

    Science.gov (United States)

    Manning, Timmy; Sleator, Roy D; Walsh, Paul

    2013-01-01

    For decades, computer scientists have looked to nature for biologically inspired solutions to computational problems; ranging from robotic control to scheduling optimization. Paradoxically, as we move deeper into the post-genomics era, the reverse is occurring, as biologists and bioinformaticians look to computational techniques, to solve a variety of biological problems. One of the most common biologically inspired techniques are genetic algorithms (GAs), which take the Darwinian concept of natural selection as the driving force behind systems for solving real world problems, including those in the bioinformatics domain. Herein, we provide an overview of genetic algorithms and survey some of the most recent applications of this approach to bioinformatics based problems.

  3. Best practices in bioinformatics training for life scientists

    DEFF Research Database (Denmark)

    Via, Allegra; Blicher, Thomas; Bongcam-Rudloff, Erik

    2013-01-01

    their data efficiently, and progress their research, is a challenge across the globe. Delivering good training goes beyond traditional lectures and resource-centric demos, using interactivity, problem-solving exercises and cooperative learning to substantially enhance training quality and learning outcomes...... to environmental researchers, a common theme is the need not just to use, and gain familiarity with, bioinformatics tools and resources but also to understand their underlying fundamental theoretical and practical concepts. Providing bioinformatics training to empower life scientists to handle and analyse...

  4. Evaluation of Summer Bridge Programs

    Science.gov (United States)

    Garcia, Lisa D.; Paz, Chiara C.

    2009-01-01

    Many colleges and universities in the United States offer summer programs for their incoming students. While programs are structured and administered in a variety of ways and target various student populations, the most common type of summer bridge program aims to serve historically underrepresented students and students of low socioeconomic…

  5. SUMMER STUDENT LECTURE PROGRAMME

    CERN Multimedia

    Françoise Benz

    2002-01-01

    SUMMER STUDENT LECTURE PROGRAMME Main Auditorium, bldg. 500   DATE TIME LECTURER TITLE Monday 29 July 09:15 - 10:00 R. RATTAZZI Beyond the Standard Model (3/3) 10:15 - 11:00 P. WELLS Experimental test of the SM - LEP (3/3) 11:15 - 12:00 P. WELLS Discussion Session 14:00 - 16:00 R. ASSMANN The CLIC Concept for a Future Particle Collider at the Energy Frontier Tuesday 30 July 09:15 - 10:00 F. ANTINORI Heavy Ions (1/2) 10:15 - 12:00 F. DYDAK Neutrino Physics (1&2/4) Wednesday 31 July  09:15 - 10:00 F. ANTINORI Heavy Ions (2/2) 10:15 - 11:00 F. DYDAK Neutrino Physics (3/4) 11:15 - 12:00 F. DYDAK / F. ANTINORI Discussion Session Thursday 1 August 09:15 - 10:00 T. NAKADA CP Violation (1/4) 10:15 - 11:00 F. DYDAK Neutrino Physics (4/4) 11:15 - 12:00 F. BEDESCHI Experimental test of the SM Tevatron (1/2) Friday 2 August 09:15 - 10:00 T. NAKADA CP Violation (2/4) 10:15 ? 11:00 F. BEDESCHI Experimental test of the SM Tevatron (2/2) 11:15 ? 12:00 F. BEDESCHI / T. NAKADA Di...

  6. Summer music festivals

    CERN Document Server

    2008-01-01

    Although July is set to be a crucial time in the working life of the Laboratory, the CERN clubs have organised musical events to make sure that there’s also a chance to chill out and relax. The group Blend at the 2007 Hardronic Festival. From left to right (on stage): Eric Pfirsch, Stephan Petit, Frédéric Lejal, Niklaus Hirt, Paulo Dos Santos with Laurent Tarrano filming.If you have a strong appetite for music the ‘Monts Jura Jazz Festival’, might tempt you this summer. Sponsored by both the CERN Administration and the Staff Association, it is an established highlight of the local arts calendar and will this year be held on 4 and 5 July in Crozet, France. For the third year running established musicians, stars of the jazz scene, and rising talent from France, Switzerland and Brazil will be joining forces to perform an exiting mixture of jazz music. A ‘master class’ in improvisation methods will also be held on Saturda...

  7. Summer student final report

    CERN Document Server

    Guzik, Jakub

    2013-01-01

    During my time spent at CERN I worked under the Technology Department of CERN, in the Machine Protection and Electrical Integrity (MPE) Group. The MPE Group supports LHC operations and maintains state of the art technology for magnet circuit protection and interlock systems for the present and future accelerators, magnet test facilities and CERN hosted experiments[1]. As a member of Magnet Powering Interlocks & Software (TE-MPE-MS) section I was involved in three different projects and used not only CERN developed tools like FESA Framework, but also open source C++ frameworks, Google Test and Google Mock. I had a chance to work with Programmable Logic Controllers and real-time devices known as Front End Computers. I was part of a software developer team, and familiarized myself with the Scrum agile software development methodology. The description and results of my work are presented in three parts of this report. Each part describes a separate project created during my participation in the CERN Summer St...

  8. Summer Student Programme

    CERN Multimedia

    2006-01-01

    Date Time Title Speaker 05/07/2006 09:15 - 10:00 Presentation of the Summer Student Programme F. CERUTTI Information on Computing Rules D. HEAGERTY Workshops presentation O. ULLALAND 10:15 - 11:00 Introduction to CERN J. ENGELEN 11:15 Film on CERN 11:00 Introduction to Particle Physics F. CLOSE 11:15 - 12:00 Accelerators (1/5) S. GILARDONI / E. METRAL 12:00 Discussion Session 7/07/2006 09:15 - 11:00 Introduction to Particle Physics F. CLOSE 11:15 - 12:00 Accelerators (2/5) S. GILARDONI / E. METRAL 12:00 Discussion Session 09:15 - 10:00 Accelerators (3/5) S. GILARDONI / E. METRAL 10:15 - 12:00 Detectors (1-2/5) O. ULLALAND 12:00 Discussion Session 11/07/2006 09:15 - 10:00 Accelerators (4/5) S. GILARDONI / E. METRAL 10:15 - 11:00 Detectors (3/5) O. ULLALAND 11:15 - 12:00 Introduction to Nuclear Physics (1/4) P. CHOMAZ P. CHOMAZ 10:15 - 11:00 Accelerators (5/5) S. GILARDONI / E. METRAL 11:15 - 12:00 Detectors (4/5) O. ULLALAND 12:00 Discus...

  9. Summer School on Spintronics

    CERN Document Server

    Wolf, Stuart; Idzerda, Yves

    2003-01-01

    Stuart Wolf This book originated as a series of lectures that were given as part of a Summer School on Spintronics in the end of August, 1998 at Lake Tahoe, Nevada. It has taken some time to get these lectures in a form suitable for this book and so the process has been an iterative one to provide current information on the topics that are covered. There are some topics that have developed in the intervening years and we have tried to at least alert the readers to them in the Introduction where a rather complete set of references is provided to the current state of the art. The field of magnetism, once thought to be dead or dying, has seen a remarkable rebirth in the last decade and promises to get even more important as we enter the new millennium. This rebirth is due to some very new insight into how the spin degree of freedom of both electrons and nucleons can play a role in a new type of electronics that utilizes the spin in addition to or in place of the charge. For this new field to mature and prosper, ...

  10. European summer temperatures since Roman times

    Czech Academy of Sciences Publication Activity Database

    Luterbacher, J.; Werner, J. P.; Smerdon, J. E.; Fernandez-Donado, L.; González-Rouco, J. F.; Barriopedro, D.; Ljungqvist, F. C.; Büntgen, Ulf; Zorita, E.; Wagner, S.; Esper, J.; McCarroll, D.; Toreti, A.; Frank, D.; Jungclaus, J.; Barriendos, M.; Bertolin, C.; Bothe, O.; Brázdil, Rudolf; Camuffo, D.; Dobrovolný, Petr; Gagen, M.; Garica-Bustamante, E.; Ge, Q.; Gomez-Navarro, J. J.; Guiot, J.; Hao, Z.; Hegerl, G.; Holmgren, K.; Klimenko, V. V.; Martin-Chivelet, J.; Pfister, C.; Roberts, N.; Schindler, A.; Schurer, A.; Solomina, O.; von Gunten, L.; Wahl, E.; Wanner, H.; Wetter, O.; Xoplaki, E.; Yuan, N.; Zanchettin, D.; Zhang, H.; Zerefos, C.

    2016-01-01

    Roč. 11, č. 2 (2016), č. článku 024001. ISSN 1748-9326 R&D Projects: GA ČR GA13-04291S Institutional support: RVO:67179843 Keywords : reconstructing climate anomalies * high-resolution paleoclimatology * northern-hemisphere temperature * tree-ring chronologies * last 1000 years * volcanic - eruptions * forcing reconstructions * bayesian algorithm * pmip simulations * past millennium * Common Era * heat waves * paleoclimatology * Bayesian hierarchical modelling * European summer temperature reconstruction * ensemble of climate model simulations * Medieval Climate Anomaly Subject RIV: DG - Athmosphere Sciences, Meteorology Impact factor: 4.404, year: 2016

  11. Bioinformatics for Precision Medicine in Oncology: principles and application to the SHIVA clinical trial

    Directory of Open Access Journals (Sweden)

    Nicolas eServant

    2014-05-01

    Full Text Available Precision medicine (PM requires the delivery of individually adapted medical care based on the genetic characteristics of each patient and his/her tumor. The last decade witnessed the development of high-throughput technologies such as microarrays and next-generation sequencing which paved the way to PM in the field of oncology. While the cost of these technologies decreases, we are facing an exponential increase in the amount of data produced. Our ability to use this information in daily practice relies strongly on the availability of an efficient bioinformatics system that assists in the translation of knowledge from the bench towards molecular targeting and diagnosis. Clinical trials and routine diagnoses constitute different approaches, both requiring a strong bioinformatics environment capable of i warranting the integration and the traceability of data, ii ensuring the correct processing and analyses of genomic data and iii applying well-defined and reproducible procedures for workflow management and decision-making. To address the issues, a seamless information system was developed at Institut Curie which facilitates the data integration and tracks in real-time the processing of individual samples. Moreover, computational pipelines were developed to identify reliably genomic alterations and mutations from the molecular profiles of each patient. After a rigorous quality control, a meaningful report is delivered to the clinicians and biologists for the therapeutic decision. The complete bioinformatics environment and the key points of its implementation are presented in the context of the SHIVA clinical trial, a multicentric randomized phase II trial comparing targeted therapy based on tumor molecular profiling versus conventional therapy in patients with refractory cancer. The numerous challenges faced in practice during the setting up and the conduct of this trial are discussed as an illustration of PM application.

  12. Intrageneric Primer Design: Bringing Bioinformatics Tools to the Class

    Science.gov (United States)

    Lima, Andre O. S.; Garces, Sergio P. S.

    2006-01-01

    Bioinformatics is one of the fastest growing scientific areas over the last decade. It focuses on the use of informatics tools for the organization and analysis of biological data. An example of their importance is the availability nowadays of dozens of software programs for genomic and proteomic studies. Thus, there is a growing field (private…

  13. Bioinformatics in the Netherlands : The value of a nationwide community

    NARCIS (Netherlands)

    van Gelder, Celia W.G.; Hooft, Rob; van Rijswijk, Merlijn; van den Berg, Linda; Kok, Ruben; Reinders, M.J.T.; Mons, Barend; Heringa, Jaap

    2017-01-01

    This review provides a historical overview of the inception and development of bioinformatics research in the Netherlands. Rooted in theoretical biology by foundational figures such as Paulien Hogeweg (at Utrecht University since the 1970s), the developments leading to organizational structures

  14. Bioinformatic tools and guideline for PCR primer design | Abd ...

    African Journals Online (AJOL)

    Bioinformatics has become an essential tool not only for basic research but also for applied research in biotechnology and biomedical sciences. Optimal primer sequence and appropriate primer concentration are essential for maximal specificity and efficiency of PCR. A poorly designed primer can result in little or no ...

  15. CROSSWORK for Glycans: Glycan Identificatin Through Mass Spectrometry and Bioinformatics

    DEFF Research Database (Denmark)

    Rasmussen, Morten; Thaysen-Andersen, Morten; Højrup, Peter

      We have developed "GLYCANthrope " - CROSSWORKS for glycans:  a bioinformatics tool, which assists in identifying N-linked glycosylated peptides as well as their glycan moieties from MS2 data of enzymatically digested glycoproteins. The program runs either as a stand-alone application or as a plug...

  16. Learning Genetics through an Authentic Research Simulation in Bioinformatics

    Science.gov (United States)

    Gelbart, Hadas; Yarden, Anat

    2006-01-01

    Following the rationale that learning is an active process of knowledge construction as well as enculturation into a community of experts, we developed a novel web-based learning environment in bioinformatics for high-school biology majors in Israel. The learning environment enables the learners to actively participate in a guided inquiry process…

  17. Hidden in the Middle: Culture, Value and Reward in Bioinformatics

    Science.gov (United States)

    Lewis, Jamie; Bartlett, Andrew; Atkinson, Paul

    2016-01-01

    Bioinformatics--the so-called shotgun marriage between biology and computer science--is an interdiscipline. Despite interdisciplinarity being seen as a virtue, for having the capacity to solve complex problems and foster innovation, it has the potential to place projects and people in anomalous categories. For example, valorised…

  18. Bioinformatics for Undergraduates: Steps toward a Quantitative Bioscience Curriculum

    Science.gov (United States)

    Chapman, Barbara S.; Christmann, James L.; Thatcher, Eileen F.

    2006-01-01

    We describe an innovative bioinformatics course developed under grants from the National Science Foundation and the California State University Program in Research and Education in Biotechnology for undergraduate biology students. The project has been part of a continuing effort to offer students classroom experiences focused on principles and…

  19. Mathematics and evolutionary biology make bioinformatics education comprehensible

    Science.gov (United States)

    Weisstein, Anton E.

    2013-01-01

    The patterns of variation within a molecular sequence data set result from the interplay between population genetic, molecular evolutionary and macroevolutionary processes—the standard purview of evolutionary biologists. Elucidating these patterns, particularly for large data sets, requires an understanding of the structure, assumptions and limitations of the algorithms used by bioinformatics software—the domain of mathematicians and computer scientists. As a result, bioinformatics often suffers a ‘two-culture’ problem because of the lack of broad overlapping expertise between these two groups. Collaboration among specialists in different fields has greatly mitigated this problem among active bioinformaticians. However, science education researchers report that much of bioinformatics education does little to bridge the cultural divide, the curriculum too focused on solving narrow problems (e.g. interpreting pre-built phylogenetic trees) rather than on exploring broader ones (e.g. exploring alternative phylogenetic strategies for different kinds of data sets). Herein, we present an introduction to the mathematics of tree enumeration, tree construction, split decomposition and sequence alignment. We also introduce off-line downloadable software tools developed by the BioQUEST Curriculum Consortium to help students learn how to interpret and critically evaluate the results of standard bioinformatics analyses. PMID:23821621

  20. The structural bioinformatics library: modeling in biomolecular science and beyond.

    Science.gov (United States)

    Cazals, Frédéric; Dreyfus, Tom

    2017-04-01

    Software in structural bioinformatics has mainly been application driven. To favor practitioners seeking off-the-shelf applications, but also developers seeking advanced building blocks to develop novel applications, we undertook the design of the Structural Bioinformatics Library ( SBL , http://sbl.inria.fr ), a generic C ++/python cross-platform software library targeting complex problems in structural bioinformatics. Its tenet is based on a modular design offering a rich and versatile framework allowing the development of novel applications requiring well specified complex operations, without compromising robustness and performances. The SBL involves four software components (1-4 thereafter). For end-users, the SBL provides ready to use, state-of-the-art (1) applications to handle molecular models defined by unions of balls, to deal with molecular flexibility, to model macro-molecular assemblies. These applications can also be combined to tackle integrated analysis problems. For developers, the SBL provides a broad C ++ toolbox with modular design, involving core (2) algorithms , (3) biophysical models and (4) modules , the latter being especially suited to develop novel applications. The SBL comes with a thorough documentation consisting of user and reference manuals, and a bugzilla platform to handle community feedback. The SBL is available from http://sbl.inria.fr. Frederic.Cazals@inria.fr. 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

  1. Rapid cloning and bioinformatic analysis of spinach Y chromosome ...

    Indian Academy of Sciences (India)

    Rapid cloning and bioinformatic analysis of spinach Y chromosome- specific EST sequences. Chuan-Liang Deng, Wei-Li Zhang, Ying Cao, Shao-Jing Wang, ... Arabidopsis thaliana mRNA for mitochondrial half-ABC transporter (STA1 gene). 389 2.31E-13. 98.96. SP3−12. Betula pendula histidine kinase 3 (HK3) mRNA, ...

  2. Mathematics and evolutionary biology make bioinformatics education comprehensible.

    Science.gov (United States)

    Jungck, John R; Weisstein, Anton E

    2013-09-01

    The patterns of variation within a molecular sequence data set result from the interplay between population genetic, molecular evolutionary and macroevolutionary processes-the standard purview of evolutionary biologists. Elucidating these patterns, particularly for large data sets, requires an understanding of the structure, assumptions and limitations of the algorithms used by bioinformatics software-the domain of mathematicians and computer scientists. As a result, bioinformatics often suffers a 'two-culture' problem because of the lack of broad overlapping expertise between these two groups. Collaboration among specialists in different fields has greatly mitigated this problem among active bioinformaticians. However, science education researchers report that much of bioinformatics education does little to bridge the cultural divide, the curriculum too focused on solving narrow problems (e.g. interpreting pre-built phylogenetic trees) rather than on exploring broader ones (e.g. exploring alternative phylogenetic strategies for different kinds of data sets). Herein, we present an introduction to the mathematics of tree enumeration, tree construction, split decomposition and sequence alignment. We also introduce off-line downloadable software tools developed by the BioQUEST Curriculum Consortium to help students learn how to interpret and critically evaluate the results of standard bioinformatics analyses.

  3. Bioclipse: an open source workbench for chemo- and bioinformatics

    Directory of Open Access Journals (Sweden)

    Wagener Johannes

    2007-02-01

    Full Text Available Abstract Background There is a need for software applications that provide users with a complete and extensible toolkit for chemo- and bioinformatics accessible from a single workbench. Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality. Existing open source projects are more focused on providing a framework for integrating existing, separately installed bioinformatics packages, rather than providing user-friendly interfaces. No open source chemoinformatics workbench has previously been published, and no sucessful attempts have been made to integrate chemo- and bioinformatics into a single framework. Results Bioclipse is an advanced workbench for resources in chemo- and bioinformatics, such as molecules, proteins, sequences, spectra, and scripts. It provides 2D-editing, 3D-visualization, file format conversion, calculation of chemical properties, and much more; all fully integrated into a user-friendly desktop application. Editing supports standard functions such as cut and paste, drag and drop, and undo/redo. Bioclipse is written in Java and based on the Eclipse Rich Client Platform with a state-of-the-art plugin architecture. This gives Bioclipse an advantage over other systems as it can easily be extended with functionality in any desired direction. Conclusion Bioclipse is a powerful workbench for bio- and chemoinformatics as well as an advanced integration platform. The rich functionality, intuitive user interface, and powerful plugin architecture make Bioclipse the most advanced and user-friendly open source workbench for chemo- and bioinformatics. Bioclipse is released under Eclipse Public License (EPL, an open source license which sets no constraints on external plugin licensing; it is totally open for both open source plugins as well as commercial ones. Bioclipse is freely available at http://www.bioclipse.net.

  4. BioWarehouse: a bioinformatics database warehouse toolkit

    Directory of Open Access Journals (Sweden)

    Stringer-Calvert David WJ

    2006-03-01

    Full Text Available Abstract Background This article addresses the problem of interoperation of heterogeneous bioinformatics databases. Results We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research. Conclusion BioWarehouse embodies significant progress on the

  5. BioWarehouse: a bioinformatics database warehouse toolkit.

    Science.gov (United States)

    Lee, Thomas J; Pouliot, Yannick; Wagner, Valerie; Gupta, Priyanka; Stringer-Calvert, David W J; Tenenbaum, Jessica D; Karp, Peter D

    2006-03-23

    This article addresses the problem of interoperation of heterogeneous bioinformatics databases. We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL) but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research. BioWarehouse embodies significant progress on the database integration problem for bioinformatics.

  6. Opportunities and challenges provided by cloud repositories for bioinformatics-enabled drug discovery.

    Science.gov (United States)

    Dalpé, Gratien; Joly, Yann

    2014-09-01

    Healthcare-related bioinformatics databases are increasingly offering the possibility to maintain, organize, and distribute DNA sequencing data. Different national and international institutions are currently hosting such databases that offer researchers website platforms where they can obtain sequencing data on which they can perform different types of analysis. Until recently, this process remained mostly one-dimensional, with most analysis concentrated on a limited amount of data. However, newer genome sequencing technology is producing a huge amount of data that current computer facilities are unable to handle. An alternative approach has been to start adopting cloud computing services for combining the information embedded in genomic and model system biology data, patient healthcare records, and clinical trials' data. In this new technological paradigm, researchers use virtual space and computing power from existing commercial or not-for-profit cloud service providers to access, store, and analyze data via different application programming interfaces. Cloud services are an alternative to the need of larger data storage; however, they raise different ethical, legal, and social issues. The purpose of this Commentary is to summarize how cloud computing can contribute to bioinformatics-based drug discovery and to highlight some of the outstanding legal, ethical, and social issues that are inherent in the use of cloud services. © 2014 Wiley Periodicals, Inc.

  7. Tools and data services registry: a community effort to document bioinformatics resources

    Science.gov (United States)

    Ison, Jon; Rapacki, Kristoffer; Ménager, Hervé; Kalaš, Matúš; Rydza, Emil; Chmura, Piotr; Anthon, Christian; Beard, Niall; Berka, Karel; Bolser, Dan; Booth, Tim; Bretaudeau, Anthony; Brezovsky, Jan; Casadio, Rita; Cesareni, Gianni; Coppens, Frederik; Cornell, Michael; Cuccuru, Gianmauro; Davidsen, Kristian; Vedova, Gianluca Della; Dogan, Tunca; Doppelt-Azeroual, Olivia; Emery, Laura; Gasteiger, Elisabeth; Gatter, Thomas; Goldberg, Tatyana; Grosjean, Marie; Grüning, Björn; Helmer-Citterich, Manuela; Ienasescu, Hans; Ioannidis, Vassilios; Jespersen, Martin Closter; Jimenez, Rafael; Juty, Nick; Juvan, Peter; Koch, Maximilian; Laibe, Camille; Li, Jing-Woei; Licata, Luana; Mareuil, Fabien; Mičetić, Ivan; Friborg, Rune Møllegaard; Moretti, Sebastien; Morris, Chris; Möller, Steffen; Nenadic, Aleksandra; Peterson, Hedi; Profiti, Giuseppe; Rice, Peter; Romano, Paolo; Roncaglia, Paola; Saidi, Rabie; Schafferhans, Andrea; Schwämmle, Veit; Smith, Callum; Sperotto, Maria Maddalena; Stockinger, Heinz; Vařeková, Radka Svobodová; Tosatto, Silvio C.E.; de la Torre, Victor; Uva, Paolo; Via, Allegra; Yachdav, Guy; Zambelli, Federico; Vriend, Gert; Rost, Burkhard; Parkinson, Helen; Løngreen, Peter; Brunak, Søren

    2016-01-01

    Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand. Here we present a community-driven curation effort, supported by ELIXIR—the European infrastructure for biological information—that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners. As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools. PMID:26538599

  8. Missing "Links" in Bioinformatics Education: Expanding Students' Conceptions of Bioinformatics Using a Biodiversity Database of Living and Fossil Reef Corals

    Science.gov (United States)

    Nehm, Ross H.; Budd, Ann F.

    2006-01-01

    NMITA is a reef coral biodiversity database that we use to introduce students to the expansive realm of bioinformatics beyond genetics. We introduce a series of lessons that have students use this database, thereby accessing real data that can be used to test hypotheses about biodiversity and evolution while targeting the "National Science …

  9. National Space Biomedical Research Institute (NSBRI) JSC Summer Projects

    Science.gov (United States)

    Dowdy, Forrest Ryan

    2014-01-01

    This project optimized the calorie content in a breakfast meal replacement bar for the Advanced Food Technology group. Use of multivariable optimization yielded the highest weight savings possible while simultaneously matching NASA Human Standards nutritional guidelines. The scope of this research included the study of shelf-life indicators such as water activity, moisture content, and texture analysis. Key metrics indicate higher protein content, higher caloric density, and greater mass savings as a result of the reformulation process. The optimization performed for this study demonstrated wide application to other food bars in the Advanced Food Technology portfolio. Recommendations for future work include shelf life studies on bar hardening and overall acceptability data over increased time frames and temperature fluctuation scenarios.

  10. Gearing up for transportation engineering, a summer institute : phase IX.

    Science.gov (United States)

    2009-02-01

    The numbers of female and minority students enrolled in engineering schools are increasing slowly, however there is still a relatively small percentage drawn to the field of transportation civil engineering. As a consequence, there is a need to educa...

  11. Gearing up for transportation engineering, a summer institute : phase 2

    Science.gov (United States)

    2001-12-31

    The numbers of female and minority students enrolled in engineering schools are increasing slowly; however, a relatively small percentage of these students are drawn to the field of transportation engineering. For this reason, there is a need to educ...

  12. Argonne National Laboratory HVEM Summer Institute lecture - kinetics II

    International Nuclear Information System (INIS)

    Westmacott, K.H.

    1982-08-01

    The purpose of this contribution is to outline some of the ways in which the High Voltage Electron Microscope can be used to study the kinetics of secondary defect shrinkage and precipitate particle growth and dissolution. In many cases, good agreement between the predictions of theory and the experimental observations are found and this provides not only insights into the mechanisms underlying the processes, but also quantitative measurement of parameters of metallurgical importance. To summarize, some of the advantages of the HVEM in kinetic studies include: (1) unlike bulk studies where only average behavior is measured, precise measurements on individual particles may be made; (2) in some systems it is useful for rapidly establishing phase boundaries, (3) anomolous behavior such as may occur by interactions with lattice defects and boundaries may be studied (4) growth and dissolution mechanisms may be established, (5) phase stability in an irradiation environment may be studied directly

  13. Report on the EMBER Project--A European Multimedia Bioinformatics Educational Resource

    Science.gov (United States)

    Attwood, Terri K.; Selimas, Ioannis; Buis, Rob; Altenburg, Ruud; Herzog, Robert; Ledent, Valerie; Ghita, Viorica; Fernandes, Pedro; Marques, Isabel; Brugman, Marc

    2005-01-01

    EMBER was a European project aiming to develop bioinformatics teaching materials on the Web and CD-ROM to help address the recognised skills shortage in bioinformatics. The project grew out of pilot work on the development of an interactive web-based bioinformatics tutorial and the desire to repackage that resource with the help of a professional…

  14. Introductory Bioinformatics Exercises Utilizing Hemoglobin and Chymotrypsin to Reinforce the Protein Sequence-Structure-Function Relationship

    Science.gov (United States)

    Inlow, Jennifer K.; Miller, Paige; Pittman, Bethany

    2007-01-01

    We describe two bioinformatics exercises intended for use in a computer laboratory setting in an upper-level undergraduate biochemistry course. To introduce students to bioinformatics, the exercises incorporate several commonly used bioinformatics tools, including BLAST, that are freely available online. The exercises build upon the students'…

  15. Vertical and Horizontal Integration of Bioinformatics Education: A Modular, Interdisciplinary Approach

    Science.gov (United States)

    Furge, Laura Lowe; Stevens-Truss, Regina; Moore, D. Blaine; Langeland, James A.

    2009-01-01

    Bioinformatics education for undergraduates has been approached primarily in two ways: introduction of new courses with largely bioinformatics focus or introduction of bioinformatics experiences into existing courses. For small colleges such as Kalamazoo, creation of new courses within an already resource-stretched setting has not been an option.…

  16. CERN Summer Student Project Report

    CERN Document Server

    Parton, Thomas

    2015-01-01

    My Summer Student project was divided between two areas: work on Thin Gap Chamber (TGC) Level-1 muon triggers for the ATLAS experiment, and data acquisition (DAQ) for an RPC muon detector at the Gamma Irradiation Facility (GIF++)

  17. The year without a summer

    Science.gov (United States)

    Luterbacher, J.; Pfister, C.

    2015-04-01

    The 1815 eruption of Tambora caused an unusually cold summer in much of Europe in 1816. The extreme weather led to poor harvests and malnutrition, but also demonstrated the capability of humans to adapt and help others in worse conditions.

  18. Summer Student Report - AV Workflow

    CERN Document Server

    Abramson, Jessie

    2014-01-01

    The AV Workflow is web application which allows cern users to publish, update and delete videos from cds. During my summer internship I implemented the backend of the new version of the AV Worklow in python using the django framework.

  19. Winter/Summer Monsoon Experiment

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Winter/Summer Monsoon Experiment (MONEX) was conducted during the First Global GARP (Global Atmospheric Research Program) Experiment (FGGE). An international...

  20. Summer Research Fellowship Programme–2015

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 19; Issue 12. Summer Research Fellowship Programme - 2015. Information and Announcements Volume 19 Issue 12 December 2014 pp 1199-1199. Fulltext. Click here to view fulltext PDF. Permanent link:

  1. Quantum Bio-Informatics II From Quantum Information to Bio-Informatics

    Science.gov (United States)

    Accardi, L.; Freudenberg, Wolfgang; Ohya, Masanori

    2009-02-01

    / H. Kamimura -- Massive collection of full-length complementary DNA clones and microarray analyses: keys to rice transcriptome analysis / S. Kikuchi -- Changes of influenza A(H5) viruses by means of entropic chaos degree / K. Sato and M. Ohya -- Basics of genome sequence analysis in bioinformatics - its fundamental ideas and problems / T. Suzuki and S. Miyazaki -- A basic introduction to gene expression studies using microarray expression data analysis / D. Wanke and J. Kilian -- Integrating biological perspectives: a quantum leap for microarray expression analysis / D. Wanke ... [et al.].

  2. Summer Final Report

    Science.gov (United States)

    Makidi, Nitou

    2012-01-01

    The summer of 2012 has been filled with many memorable events and activities. As an intern, I had responsibilities that had to be fulfilled. My tour of duty was completed as an administrative student trainee in the Information Technology and Communications Services Business Office (IT-A). In accordance with the Business Objectives and Agreement of the Business Office and my performance plan, I was to provide business office support, improve business, project management, and technical work processes. With this being stated, I supported a project called "The Big Move Project" (TBMP), which will take course over the next several years. The Big Move Project is the planning of the Information Technology (IT) Directorate's relocation to various buildings in the course of upcoming years, when designs and the building of Central Campus have been completed. Working directly with my supervisor and the project manager, I was responsible for gathering both administrative and operational area requirements for the Information Technology (IT) Directorate, along with its outsourced support and contractors, such as IMCS, NICS, and ACES. My first action was to create rubrics that will serve as a guideline for the information that should be given by each branch of IT. After receiving that information via a few KAITS actions, I was able to start the consolidation process, and begin working on a presentation. A SharePoint was created shortly after for others to view the progression of the project, which I managed. During the consolidation ofthis information, I would occasionally present to the IT Deputy Director and IT Chiefs. The draft of this presentation was shown to employees of Center Operations (T A) and stakeholders-IT Chief Officers and contractor managers-in the relocation of IT to make them aware of what requirements must be met that will enable IT to be accommodated appropriately in the design of Central Campus Phase 11-the time in which IT and its contractors are scheduled

  3. Meeting review: 2002 O'Reilly Bioinformatics Technology Conference.

    Science.gov (United States)

    Counsell, Damian

    2002-01-01

    At the end of January I travelled to the States to speak at and attend the first O'Reilly Bioinformatics Technology Conference. It was a large, well-organized and diverse meeting with an interesting history. Although the meeting was not a typical academic conference, its style will, I am sure, become more typical of meetings in both biological and computational sciences.Speakers at the event included prominent bioinformatics researchers such as Ewan Birney, Terry Gaasterland and Lincoln Stein; authors and leaders in the open source programming community like Damian Conway and Nat Torkington; and representatives from several publishing companies including the Nature Publishing Group, Current Science Group and the President of O'Reilly himself, Tim O'Reilly. There were presentations, tutorials, debates, quizzes and even a 'jam session' for musical bioinformaticists.

  4. Open discovery: An integrated live Linux platform of Bioinformatics tools.

    Science.gov (United States)

    Vetrivel, Umashankar; Pilla, Kalabharath

    2008-01-01

    Historically, live linux distributions for Bioinformatics have paved way for portability of Bioinformatics workbench in a platform independent manner. Moreover, most of the existing live Linux distributions limit their usage to sequence analysis and basic molecular visualization programs and are devoid of data persistence. Hence, open discovery - a live linux distribution has been developed with the capability to perform complex tasks like molecular modeling, docking and molecular dynamics in a swift manner. Furthermore, it is also equipped with complete sequence analysis environment and is capable of running windows executable programs in Linux environment. Open discovery portrays the advanced customizable configuration of fedora, with data persistency accessible via USB drive or DVD. The Open Discovery is distributed free under Academic Free License (AFL) and can be downloaded from http://www.OpenDiscovery.org.in.

  5. Rise and demise of bioinformatics? Promise and progress.

    Directory of Open Access Journals (Sweden)

    Christos A Ouzounis

    Full Text Available The field of bioinformatics and computational biology has gone through a number of transformations during the past 15 years, establishing itself as a key component of new biology. This spectacular growth has been challenged by a number of disruptive changes in science and technology. Despite the apparent fatigue of the linguistic use of the term itself, bioinformatics has grown perhaps to a point beyond recognition. We explore both historical aspects and future trends and argue that as the field expands, key questions remain unanswered and acquire new meaning while at the same time the range of applications is widening to cover an ever increasing number of biological disciplines. These trends appear to be pointing to a redefinition of certain objectives, milestones, and possibly the field itself.

  6. A Survey on Evolutionary Algorithm Based Hybrid Intelligence in Bioinformatics

    Directory of Open Access Journals (Sweden)

    Shan Li

    2014-01-01

    Full Text Available With the rapid advance in genomics, proteomics, metabolomics, and other types of omics technologies during the past decades, a tremendous amount of data related to molecular biology has been produced. It is becoming a big challenge for the bioinformatists to analyze and interpret these data with conventional intelligent techniques, for example, support vector machines. Recently, the hybrid intelligent methods, which integrate several standard intelligent approaches, are becoming more and more popular due to their robustness and efficiency. Specifically, the hybrid intelligent approaches based on evolutionary algorithms (EAs are widely used in various fields due to the efficiency and robustness of EAs. In this review, we give an introduction about the applications of hybrid intelligent methods, in particular those based on evolutionary algorithm, in bioinformatics. In particular, we focus on their applications to three common problems that arise in bioinformatics, that is, feature selection, parameter estimation, and reconstruction of biological networks.

  7. Bioinformatics and Microarray Data Analysis on the Cloud.

    Science.gov (United States)

    Calabrese, Barbara; Cannataro, Mario

    2016-01-01

    High-throughput platforms such as microarray, mass spectrometry, and next-generation sequencing are producing an increasing volume of omics data that needs large data storage and computing power. Cloud computing offers massive scalable computing and storage, data sharing, on-demand anytime and anywhere access to resources and applications, and thus, it may represent the key technology for facing those issues. In fact, in the recent years it has been adopted for the deployment of different bioinformatics solutions and services both in academia and in the industry. Although this, cloud computing presents several issues regarding the security and privacy of data, that are particularly important when analyzing patients data, such as in personalized medicine. This chapter reviews main academic and industrial cloud-based bioinformatics solutions; with a special focus on microarray data analysis solutions and underlines main issues and problems related to the use of such platforms for the storage and analysis of patients data.

  8. Architecture exploration of FPGA based accelerators for bioinformatics applications

    CERN Document Server

    Varma, B Sharat Chandra; Balakrishnan, M

    2016-01-01

    This book presents an evaluation methodology to design future FPGA fabrics incorporating hard embedded blocks (HEBs) to accelerate applications. This methodology will be useful for selection of blocks to be embedded into the fabric and for evaluating the performance gain that can be achieved by such an embedding. The authors illustrate the use of their methodology by studying the impact of HEBs on two important bioinformatics applications: protein docking and genome assembly. The book also explains how the respective HEBs are designed and how hardware implementation of the application is done using these HEBs. It shows that significant speedups can be achieved over pure software implementations by using such FPGA-based accelerators. The methodology presented in this book may also be used for designing HEBs for accelerating software implementations in other domains besides bioinformatics. This book will prove useful to students, researchers, and practicing engineers alike.

  9. 2nd Colombian Congress on Computational Biology and Bioinformatics

    CERN Document Server

    Cristancho, Marco; Isaza, Gustavo; Pinzón, Andrés; Rodríguez, Juan

    2014-01-01

    This volume compiles accepted contributions for the 2nd Edition of the Colombian Computational Biology and Bioinformatics Congress CCBCOL, after a rigorous review process in which 54 papers were accepted for publication from 119 submitted contributions. Bioinformatics and Computational Biology are areas of knowledge that have emerged due to advances that have taken place in the Biological Sciences and its integration with Information Sciences. The expansion of projects involving the study of genomes has led the way in the production of vast amounts of sequence data which needs to be organized, analyzed and stored to understand phenomena associated with living organisms related to their evolution, behavior in different ecosystems, and the development of applications that can be derived from this analysis.  .

  10. Bioinformatics for whole-genome shotgun sequencing of microbial communities.

    Directory of Open Access Journals (Sweden)

    Kevin Chen

    2005-07-01

    Full Text Available The application of whole-genome shotgun sequencing to microbial communities represents a major development in metagenomics, the study of uncultured microbes via the tools of modern genomic analysis. In the past year, whole-genome shotgun sequencing projects of prokaryotic communities from an acid mine biofilm, the Sargasso Sea, Minnesota farm soil, three deep-sea whale falls, and deep-sea sediments have been reported, adding to previously published work on viral communities from marine and fecal samples. The interpretation of this new kind of data poses a wide variety of exciting and difficult bioinformatics problems. The aim of this review is to introduce the bioinformatics community to this emerging field by surveying existing techniques and promising new approaches for several of the most interesting of these computational problems.

  11. Statistical modelling in biostatistics and bioinformatics selected papers

    CERN Document Server

    Peng, Defen

    2014-01-01

    This book presents selected papers on statistical model development related mainly to the fields of Biostatistics and Bioinformatics. The coverage of the material falls squarely into the following categories: (a) Survival analysis and multivariate survival analysis, (b) Time series and longitudinal data analysis, (c) Statistical model development and (d) Applied statistical modelling. Innovations in statistical modelling are presented throughout each of the four areas, with some intriguing new ideas on hierarchical generalized non-linear models and on frailty models with structural dispersion, just to mention two examples. The contributors include distinguished international statisticians such as Philip Hougaard, John Hinde, Il Do Ha, Roger Payne and Alessandra Durio, among others, as well as promising newcomers. Some of the contributions have come from researchers working in the BIO-SI research programme on Biostatistics and Bioinformatics, centred on the Universities of Limerick and Galway in Ireland and fu...

  12. Report of the Summer School of Pitch, Music & Associated Pathologies (Lyon, July 9-11, 2014)

    NARCIS (Netherlands)

    Pfeifer, J.; Asano, R.; Attina, V.; d’Errico, M.; El Boghdady, N.; Estivalet, G.; Grön, L.; Guillemard, D.; Kang, H.J.; Luckmann, A.; Mina, F.; Tabibi, S.; Viswanathan, J.

    2014-01-01

    The summer school on Pitch, Music and Associated Pathologies was held for 2½ days, July 9-11, 2014, at the Valpré conference center in Lyon. Fifty-five researchers and students from universities and research institutions from 11 countries participated in it. The summer school was organized in 2

  13. Application Deadlines - CPFP Summer Curriculum in Cancer Prevention Courses 2016 | Division of Cancer Prevention

    Science.gov (United States)

    The National Cancer Institute (NCI) Cancer Prevention Fellowship Program (CPFP) is now accepting applications for the Summer Curriculum in Cancer Prevention until February 26, 2016 for international applicants and March 15, 2016 for domestic applicants. For more information and to apply, please visit: https://cpfp.cancer.gov/summer-curriculum. |

  14. Neonatal Informatics: Transforming Neonatal Care Through Translational Bioinformatics

    Science.gov (United States)

    Palma, Jonathan P.; Benitz, William E.; Tarczy-Hornoch, Peter; Butte, Atul J.; Longhurst, Christopher A.

    2012-01-01

    The future of neonatal informatics will be driven by the availability of increasingly vast amounts of clinical and genetic data. The field of translational bioinformatics is concerned with linking and learning from these data and applying new findings to clinical care to transform the data into proactive, predictive, preventive, and participatory health. As a result of advances in translational informatics, the care of neonates will become more data driven, evidence based, and personalized. PMID:22924023

  15. Kubernetes as an approach for solving bioinformatic problems.

    OpenAIRE

    Markstedt, Olof

    2017-01-01

    The cluster orchestration tool Kubernetes enables easy deployment and reproducibility of life science research by utilizing the advantages of the container technology. The container technology allows for easy tool creation, sharing and runs on any Linux system once it has been built. The applicability of Kubernetes as an approach to run bioinformatic workflows was evaluated and resulted in some examples of how Kubernetes and containers could be used within the field of life science and how th...

  16. p3d--Python module for structural bioinformatics.

    Science.gov (United States)

    Fufezan, Christian; Specht, Michael

    2009-08-21

    High-throughput bioinformatic analysis tools are needed to mine the large amount of structural data via knowledge based approaches. The development of such tools requires a robust interface to access the structural data in an easy way. For this the Python scripting language is the optimal choice since its philosophy is to write an understandable source code. p3d is an object oriented Python module that adds a simple yet powerful interface to the Python interpreter to process and analyse three dimensional protein structure files (PDB files). p3d's strength arises from the combination of a) very fast spatial access to the structural data due to the implementation of a binary space partitioning (BSP) tree, b) set theory and c) functions that allow to combine a and b and that use human readable language in the search queries rather than complex computer language. All these factors combined facilitate the rapid development of bioinformatic tools that can perform quick and complex analyses of protein structures. p3d is the perfect tool to quickly develop tools for structural bioinformatics using the Python scripting language.

  17. p3d – Python module for structural bioinformatics

    Directory of Open Access Journals (Sweden)

    Fufezan Christian

    2009-08-01

    Full Text Available Abstract Background High-throughput bioinformatic analysis tools are needed to mine the large amount of structural data via knowledge based approaches. The development of such tools requires a robust interface to access the structural data in an easy way. For this the Python scripting language is the optimal choice since its philosophy is to write an understandable source code. Results p3d is an object oriented Python module that adds a simple yet powerful interface to the Python interpreter to process and analyse three dimensional protein structure files (PDB files. p3d's strength arises from the combination of a very fast spatial access to the structural data due to the implementation of a binary space partitioning (BSP tree, b set theory and c functions that allow to combine a and b and that use human readable language in the search queries rather than complex computer language. All these factors combined facilitate the rapid development of bioinformatic tools that can perform quick and complex analyses of protein structures. Conclusion p3d is the perfect tool to quickly develop tools for structural bioinformatics using the Python scripting language.

  18. mORCA: sailing bioinformatics world with mobile devices.

    Science.gov (United States)

    Díaz-Del-Pino, Sergio; Falgueras, Juan; Perez-Wohlfeil, Esteban; Trelles, Oswaldo

    2018-03-01

    Nearly 10 years have passed since the first mobile apps appeared. Given the fact that bioinformatics is a web-based world and that mobile devices are endowed with web-browsers, it seemed natural that bioinformatics would transit from personal computers to mobile devices but nothing could be further from the truth. The transition demands new paradigms, designs and novel implementations. Throughout an in-depth analysis of requirements of existing bioinformatics applications we designed and deployed an easy-to-use web-based lightweight mobile client. Such client is able to browse, select, compose automatically interface parameters, invoke services and monitor the execution of Web Services using the service's metadata stored in catalogs or repositories. mORCA is available at http://bitlab-es.com/morca/app as a web-app. It is also available in the App store by Apple and Play Store by Google. The software will be available for at least 2 years. ortrelles@uma.es. Source code, final web-app, training material and documentation is available at http://bitlab-es.com/morca. © The Author(s) 2017. Published by Oxford University Press.

  19. Bioinformatics analysis and detection of gelatinase encoded gene in Lysinibacillussphaericus

    Science.gov (United States)

    Repin, Rul Aisyah Mat; Mutalib, Sahilah Abdul; Shahimi, Safiyyah; Khalid, Rozida Mohd.; Ayob, Mohd. Khan; Bakar, Mohd. Faizal Abu; Isa, Mohd Noor Mat

    2016-11-01

    In this study, we performed bioinformatics analysis toward genome sequence of Lysinibacillussphaericus (L. sphaericus) to determine gene encoded for gelatinase. L. sphaericus was isolated from soil and gelatinase species-specific bacterium to porcine and bovine gelatin. This bacterium offers the possibility of enzymes production which is specific to both species of meat, respectively. The main focus of this research is to identify the gelatinase encoded gene within the bacteria of L. Sphaericus using bioinformatics analysis of partially sequence genome. From the research study, three candidate gene were identified which was, gelatinase candidate gene 1 (P1), NODE_71_length_93919_cov_158.931839_21 which containing 1563 base pair (bp) in size with 520 amino acids sequence; Secondly, gelatinase candidate gene 2 (P2), NODE_23_length_52851_cov_190.061386_17 which containing 1776 bp in size with 591 amino acids sequence; and Thirdly, gelatinase candidate gene 3 (P3), NODE_106_length_32943_cov_169.147919_8 containing 1701 bp in size with 566 amino acids sequence. Three pairs of oligonucleotide primers were designed and namely as, F1, R1, F2, R2, F3 and R3 were targeted short sequences of cDNA by PCR. The amplicons were reliably results in 1563 bp in size for candidate gene P1 and 1701 bp in size for candidate gene P3. Therefore, the results of bioinformatics analysis of L. Sphaericus resulting in gene encoded gelatinase were identified.

  20. KBWS: an EMBOSS associated package for accessing bioinformatics web services.

    Science.gov (United States)

    Oshita, Kazuki; Arakawa, Kazuharu; Tomita, Masaru

    2011-04-29

    The availability of bioinformatics web-based services is rapidly proliferating, for their interoperability and ease of use. The next challenge is in the integration of these services in the form of workflows, and several projects are already underway, standardizing the syntax, semantics, and user interfaces. In order to deploy the advantages of web services with locally installed tools, here we describe a collection of proxy client tools for 42 major bioinformatics web services in the form of European Molecular Biology Open Software Suite (EMBOSS) UNIX command-line tools. EMBOSS provides sophisticated means for discoverability and interoperability for hundreds of tools, and our package, named the Keio Bioinformatics Web Service (KBWS), adds functionalities of local and multiple alignment of sequences, phylogenetic analyses, and prediction of cellular localization of proteins and RNA secondary structures. This software implemented in C is available under GPL from http://www.g-language.org/kbws/ and GitHub repository http://github.com/cory-ko/KBWS. Users can utilize the SOAP services implemented in Perl directly via WSDL file at http://soap.g-language.org/kbws.wsdl (RPC Encoded) and http://soap.g-language.org/kbws_dl.wsdl (Document/literal).

  1. Combining medical informatics and bioinformatics toward tools for personalized medicine.

    Science.gov (United States)

    Sarachan, B D; Simmons, M K; Subramanian, P; Temkin, J M

    2003-01-01

    Key bioinformatics and medical informatics research areas need to be identified to advance knowledge and understanding of disease risk factors and molecular disease pathology in the 21 st century toward new diagnoses, prognoses, and treatments. Three high-impact informatics areas are identified: predictive medicine (to identify significant correlations within clinical data using statistical and artificial intelligence methods), along with pathway informatics and cellular simulations (that combine biological knowledge with advanced informatics to elucidate molecular disease pathology). Initial predictive models have been developed for a pilot study in Huntington's disease. An initial bioinformatics platform has been developed for the reconstruction and analysis of pathways, and work has begun on pathway simulation. A bioinformatics research program has been established at GE Global Research Center as an important technology toward next generation medical diagnostics. We anticipate that 21 st century medical research will be a combination of informatics tools with traditional biology wet lab research, and that this will translate to increased use of informatics techniques in the clinic.

  2. KBWS: an EMBOSS associated package for accessing bioinformatics web services

    Directory of Open Access Journals (Sweden)

    Tomita Masaru

    2011-04-01

    Full Text Available Abstract The availability of bioinformatics web-based services is rapidly proliferating, for their interoperability and ease of use. The next challenge is in the integration of these services in the form of workflows, and several projects are already underway, standardizing the syntax, semantics, and user interfaces. In order to deploy the advantages of web services with locally installed tools, here we describe a collection of proxy client tools for 42 major bioinformatics web services in the form of European Molecular Biology Open Software Suite (EMBOSS UNIX command-line tools. EMBOSS provides sophisticated means for discoverability and interoperability for hundreds of tools, and our package, named the Keio Bioinformatics Web Service (KBWS, adds functionalities of local and multiple alignment of sequences, phylogenetic analyses, and prediction of cellular localization of proteins and RNA secondary structures. This software implemented in C is available under GPL from http://www.g-language.org/kbws/ and GitHub repository http://github.com/cory-ko/KBWS. Users can utilize the SOAP services implemented in Perl directly via WSDL file at http://soap.g-language.org/kbws.wsdl (RPC Encoded and http://soap.g-language.org/kbws_dl.wsdl (Document/literal.

  3. A comparison of common programming languages used in bioinformatics.

    Science.gov (United States)

    Fourment, Mathieu; Gillings, Michael R

    2008-02-05

    The performance of different programming languages has previously been benchmarked using abstract mathematical algorithms, but not using standard bioinformatics algorithms. We compared the memory usage and speed of execution for three standard bioinformatics methods, implemented in programs using one of six different programming languages. Programs for the Sellers algorithm, the Neighbor-Joining tree construction algorithm and an algorithm for parsing BLAST file outputs were implemented in C, C++, C#, Java, Perl and Python. Implementations in C and C++ were fastest and used the least memory. Programs in these languages generally contained more lines of code. Java and C# appeared to be a compromise between the flexibility of Perl and Python and the fast performance of C and C++. The relative performance of the tested languages did not change from Windows to Linux and no clear evidence of a faster operating system was found. Source code and additional information are available from http://www.bioinformatics.org/benchmark/. This benchmark provides a comparison of six commonly used programming languages under two different operating systems. The overall comparison shows that a developer should choose an appropriate language carefully, taking into account the performance expected and the library availability for each language.

  4. Best practices in bioinformatics training for life scientists.

    KAUST Repository

    Via, Allegra

    2013-06-25

    The mountains of data thrusting from the new landscape of modern high-throughput biology are irrevocably changing biomedical research and creating a near-insatiable demand for training in data management and manipulation and data mining and analysis. Among life scientists, from clinicians to environmental researchers, a common theme is the need not just to use, and gain familiarity with, bioinformatics tools and resources but also to understand their underlying fundamental theoretical and practical concepts. Providing bioinformatics training to empower life scientists to handle and analyse their data efficiently, and progress their research, is a challenge across the globe. Delivering good training goes beyond traditional lectures and resource-centric demos, using interactivity, problem-solving exercises and cooperative learning to substantially enhance training quality and learning outcomes. In this context, this article discusses various pragmatic criteria for identifying training needs and learning objectives, for selecting suitable trainees and trainers, for developing and maintaining training skills and evaluating training quality. Adherence to these criteria may help not only to guide course organizers and trainers on the path towards bioinformatics training excellence but, importantly, also to improve the training experience for life scientists.

  5. Bioinformatics process management: information flow via a computational journal

    Directory of Open Access Journals (Sweden)

    Lushington Gerald

    2007-12-01

    Full Text Available Abstract This paper presents the Bioinformatics Computational Journal (BCJ, a framework for conducting and managing computational experiments in bioinformatics and computational biology. These experiments often involve series of computations, data searches, filters, and annotations which can benefit from a structured environment. Systems to manage computational experiments exist, ranging from libraries with standard data models to elaborate schemes to chain together input and output between applications. Yet, although such frameworks are available, their use is not widespread–ad hoc scripts are often required to bind applications together. The BCJ explores another solution to this problem through a computer based environment suitable for on-site use, which builds on the traditional laboratory notebook paradigm. It provides an intuitive, extensible paradigm designed for expressive composition of applications. Extensive features facilitate sharing data, computational methods, and entire experiments. By focusing on the bioinformatics and computational biology domain, the scope of the computational framework was narrowed, permitting us to implement a capable set of features for this domain. This report discusses the features determined critical by our system and other projects, along with design issues. We illustrate the use of our implementation of the BCJ on two domain-specific examples.

  6. Summer Research Program - 1996 High School Apprenticeship Program Volume 15A Wright Laboratory

    National Research Council Canada - National Science Library

    Moore, Gary

    1996-01-01

    The United States Air Force Summer Research Program (USAF-SRP) is designed to introduce university, college, and technical institute faculty members, graduate students, and high school students to Air Force research...

  7. Summer Research Program - 1996 High School Apprenticeship Program. Volume 12B, Armstrong Laboratory

    National Research Council Canada - National Science Library

    Moore, Gary

    1996-01-01

    The United States Air Force Summer Research Program (USAF-SRP) is designed to introduce university, college, and technical institute faculty members, graduate students, and high school students to Air Force research...

  8. Summer Research Program - 1998 High School Apprenticeship Program Final Reports. Volume 12, Armstrong Laboratory

    National Research Council Canada - National Science Library

    Moore, Gary

    1998-01-01

    The United States Air Force Summer Research Program (USAF-SRP) is designed to introduce university, college, and technical institute faculty members, graduate students, and high school students to Air Force research...

  9. Summer Research Program - 1996 High School Apprenticeship Program. Volume 16, Arnold Engineering Development Center

    National Research Council Canada - National Science Library

    Moore, Gary

    1996-01-01

    The United States Air Force Summer Research Program (USAF-SRP) is designed to introduce university, college, and technical institute faculty members, graduate students, and high school students to Air Force research...

  10. Summer Research Program - 1997. High School Apprenticeship Program. Final Reports, Volume 12A, Armstrong Laboratory

    National Research Council Canada - National Science Library

    Moore, Gary

    1997-01-01

    The United States Air Force Summer Research Program (USAF-SRP) is designed to introduce university, college, and technical institute faculty members, graduate students, and high school students to Air Force research...

  11. Summer Research Program - 1998 High School Apprenticeship Program. Volume 14. Phillips Laboratory

    National Research Council Canada - National Science Library

    Moore, Gary

    1998-01-01

    The United States Air Force Summer Research Program (USAF-SRP) is designed to introduce university, college, and technical institute faculty members, graduate students, and high school students to Air Force research...

  12. Summer Research Program - 1997. High School Apprenticeship Program. Final Reports Volume 15B, Wright Laboratory

    National Research Council Canada - National Science Library

    Moore, Gary

    1997-01-01

    The United States Air Force Summer Research Program (USAF-SRP) is designed to introduce university, college, and technical institute faculty members, graduate students, and high school students to Air Force research...

  13. Summer Research Program - 1996. High School Apprenticeship Program Final Reports. Volume 15B, Wright Laboratory

    National Research Council Canada - National Science Library

    Moore, Gary

    1996-01-01

    The United States Air Force Summer Research Program (USAF-SRP) is designed to introduce university, college, and technical institute faculty members, graduate students, and high school students to Air Force research...

  14. Summer Research Program - 1998 High School Apprenticeship Program Volume 15C Wright Laboratory

    National Research Council Canada - National Science Library

    Moore, Gary

    1998-01-01

    The United States Air Force Summer Research Program (USAF-SRP) is designed to introduce university, college, and technical institute faculty members, graduate students, and high school students to Air Force research...

  15. Summer Research Program - 1998 High School Apprenticeship Program Volume 13 Rome Laboratory

    National Research Council Canada - National Science Library

    Moore, Gary

    1998-01-01

    The United States Air Force Summer Research Program (USAF-SRP) is designed to introduce university, college, and technical institute faculty members, graduate students, and high school students to Air Force research...

  16. 1997 Summer Research Program (SRP), High School Apprenticeship Program (HSAP), Final Reports, Volume 13, Phillips Laboratory

    National Research Council Canada - National Science Library

    Moore, Gary

    1997-01-01

    The United States Air Force Summer Research Program (USAF-SRP) is designed to introduce university, college, and technical institute faculty members, graduate students, and high school students to Air Force research...

  17. Summer Research Program - 1997 High School Apprenticeship Program. Volume 14, Rome Laboratory

    National Research Council Canada - National Science Library

    Moore, Gary

    1997-01-01

    The United States Air Force Summer Research Program (USAF-SRP) is designed to introduce university, college, and technical institute faculty members, graduate students, and high school students to Air Force research...

  18. Summer Research Program - 1997. High School Apprenticeship Program Final Reports. Volume 15A, Wright Laboratory

    National Research Council Canada - National Science Library

    Moore, Gary

    1997-01-01

    The United States Air Force Summer Research Program (USAF-SRP) is designed to introduce university, college, and technical institute faculty members, graduate students, and high school students to Air Force research...

  19. Summer Research Program - 1998 High School Apprenticeship Program Volume 15B Wright Laboratory

    National Research Council Canada - National Science Library

    Moore, Gary

    1998-01-01

    The United States Air Force Summer Research Program (USAF-SRP) is designed to introduce university, college, and technical institute faculty members, graduate students, and high school students to Air Force research...

  20. Summer Research Program - 1997 High School Appenticeship Program Volume 16 Arnold Engineering Development Center

    National Research Council Canada - National Science Library

    Moore, Gary

    1997-01-01

    The United States Air Force Summer Research Program (USAF-SRP) is designed to introduce university, college, and technical institute faculty members, graduate students, and high school students to Air Force research...

  1. Summer Research Program - 1997. High School Apprenticeship Program. Final Reports. Volume 15C, Wright Laboratory

    National Research Council Canada - National Science Library

    Moore, Gary

    1997-01-01

    The United States Air Force Summer Research Program (USAF-SRP) is designed to introduce university, college, and technical institute faculty members, graduate students, and high school students to Air Force research...

  2. Summer Research Program - 1996 High School Apprenticeship Program Volume 13 Phillips Laboratory

    National Research Council Canada - National Science Library

    Moore, Gary

    1996-01-01

    The United States Air Force Summer Research Program (USAF-SRP) is designed to introduce university, college, and technical institute faculty members, graduate students, and high school students to Air Force research...

  3. 2nd Karlsruhe International Summer School on Fusion Technologies

    International Nuclear Information System (INIS)

    Bahm, W.; Stycz, K.

    2008-01-01

    For the second time, the Karlsruhe Research enter together with European research institutions and industries invited young scientists and engineers to its ''International Summer School on Fusion Technologies.'' Fifty participants from all over Europe attended the lectures by 35 experts preesenting contributions from their areas of competence. Ten young scientists from India and another 10 from China were connected to the events by video link. Physics student Kornelia Stycz describes her impressions as a participant in the ''2 nd International Summer School on Fusion Technologies.'' (orig.)

  4. Summer Schools In Nuclear Chemistry

    International Nuclear Information System (INIS)

    Clark, Sue; Herbert, Mieva; Mantica, Paul

    2006-01-01

    This the report for the 5 year activities for the ACS Summer Schools in Nuclear and Radiochemistry. The American Chemical Society's Summer Schools in Nuclear and Radiochemistry were held at Brookhaven National Laboratory (Upton, NY) and San Jose State University (San Jose, CA) during the award period February 1, 2002 to January 31, 2007. The Summer Schools are intensive, six-week program involving both a lecture component covering fundamental principles of nuclear chemistry and radiochemistry and a laboratory component allowing hands-on experience for the students to test many of the basic principles they learn about in lecture. Each site hosted 12 undergraduate students annually, and students received coursework credits towards their undergraduate degrees. Up to 7 student credit hours were earned at San Jose State University, and Brookhaven students received up to 6 college credits through BNL's management partner, SUNY Stony Brook. Funding from the award period covered travel, housing, educational expenses, and student stipends, for the 24 undergraduate participants. Furthermore, funding was also used to cover expenses for lecturers and staff to run the programs at the two facilities. The students were provided with nuclear and radiochemistry training equivalent to a three-hour upper-level undergraduate course along with a two-hour hands-on laboratory experience within the six-week summer period. Lectures were held 5 days per week. Students completed an extensive laboratory sequence, as well as radiation safety training at the start of the Summer Schools. The summer school curriculum was enhanced with a Guest Lecture series, as well as through several one-day symposia and organized field trips to nuclear-related research and applied science laboratories. This enrichment afforded an opportunity for students to see the broader impacts of nuclear science in today's world, and to experience some of the future challenges through formal and informal discussions with

  5. Video Bioinformatics Analysis of Human Embryonic Stem Cell Colony Growth

    Science.gov (United States)

    Lin, Sabrina; Fonteno, Shawn; Satish, Shruthi; Bhanu, Bir; Talbot, Prue

    2010-01-01

    Because video data are complex and are comprised of many images, mining information from video material is difficult to do without the aid of computer software. Video bioinformatics is a powerful quantitative approach for extracting spatio-temporal data from video images using computer software to perform dating mining and analysis. In this article, we introduce a video bioinformatics method for quantifying the growth of human embryonic stem cells (hESC) by analyzing time-lapse videos collected in a Nikon BioStation CT incubator equipped with a camera for video imaging. In our experiments, hESC colonies that were attached to Matrigel were filmed for 48 hours in the BioStation CT. To determine the rate of growth of these colonies, recipes were developed using CL-Quant software which enables users to extract various types of data from video images. To accurately evaluate colony growth, three recipes were created. The first segmented the image into the colony and background, the second enhanced the image to define colonies throughout the video sequence accurately, and the third measured the number of pixels in the colony over time. The three recipes were run in sequence on video data collected in a BioStation CT to analyze the rate of growth of individual hESC colonies over 48 hours. To verify the truthfulness of the CL-Quant recipes, the same data were analyzed manually using Adobe Photoshop software. When the data obtained using the CL-Quant recipes and Photoshop were compared, results were virtually identical, indicating the CL-Quant recipes were truthful. The method described here could be applied to any video data to measure growth rates of hESC or other cells that grow in colonies. In addition, other video bioinformatics recipes can be developed in the future for other cell processes such as migration, apoptosis, and cell adhesion. PMID:20495527

  6. Summer Student Report - Project Kryolize

    CERN Document Server

    Drozdowski, Pawel

    2016-01-01

    The purpose of this document is to describe the work and results obtained by the author during his summer student internship at CERN. The author of this document was attached to the project Kryolize as a software developer, overtaking the job from a recently departed technical student.

  7. [Pharmacogenetics II. Research molecular methods, bioinformatics and ethical concerns].

    Science.gov (United States)

    Daudén, E

    2007-01-01

    Pharmacogenetics refers to the study of the individual pharmacological response based on the genotype. Its objective is to optimize treatment in an individual basis, thereby creating a more efficient and safe personalized therapy. In the second part of this review, the molecular methods of study in pharmacogenetics, including microarray technology or DNA chips, are discussed. Among them we highlight the microarrays used to determine the gene expression that detect specific RNA sequences, and the microarrays employed to determine the genotype that detect specific DNA sequences, including polymorphisms, particularly single nucleotide polymorphisms (SNPs). The relationship between pharmacogenetics, bioinformatics and ethical concerns is reviewed.

  8. MicroRNA from tuberculosis RNA: A bioinformatics study

    OpenAIRE

    Wiwanitkit, Somsri; Wiwanitkit, Viroj

    2012-01-01

    The role of microRNA in the pathogenesis of pulmonary tuberculosis is the interesting topic in chest medicine at present. Recently, it was proposed that the microRNA can be a useful biomarker for monitoring of pulmonary tuberculosis and might be the important part in pathogenesis of disease. Here, the authors perform a bioinformatics study to assess the microRNA within known tuberculosis RNA. The microRNA part can be detected and this can be important key information in further study of the p...

  9. Biowep: a workflow enactment portal for bioinformatics applications.

    Science.gov (United States)

    Romano, Paolo; Bartocci, Ezio; Bertolini, Guglielmo; De Paoli, Flavio; Marra, Domenico; Mauri, Giancarlo; Merelli, Emanuela; Milanesi, Luciano

    2007-03-08

    The huge amount of biological information, its distribution over the Internet and the heterogeneity of available software tools makes the adoption of new data integration and analysis network tools a necessity in bioinformatics. ICT standards and tools, like Web Services and Workflow Management Systems (WMS), can support the creation and deployment of such systems. Many Web Services are already available and some WMS have been proposed. They assume that researchers know which bioinformatics resources can be reached through a programmatic interface and that they are skilled in programming and building workflows. Therefore, they are not viable to the majority of unskilled researchers. A portal enabling these to take profit from new technologies is still missing. We designed biowep, a web based client application that allows for the selection and execution of a set of predefined workflows. The system is available on-line. Biowep architecture includes a Workflow Manager, a User Interface and a Workflow Executor. The task of the Workflow Manager is the creation and annotation of workflows. These can be created by using either the Taverna Workbench or BioWMS. Enactment of workflows is carried out by FreeFluo for Taverna workflows and by BioAgent/Hermes, a mobile agent-based middleware, for BioWMS ones. Main workflows' processing steps are annotated on the basis of their input and output, elaboration type and application domain by using a classification of bioinformatics data and tasks. The interface supports users authentication and profiling. Workflows can be selected on the basis of users' profiles and can be searched through their annotations. Results can be saved. We developed a web system that support the selection and execution of predefined workflows, thus simplifying access for all researchers. The implementation of Web Services allowing specialized software to interact with an exhaustive set of biomedical databases and analysis software and the creation of

  10. Biowep: a workflow enactment portal for bioinformatics applications

    Directory of Open Access Journals (Sweden)

    Romano Paolo

    2007-03-01

    Full Text Available Abstract Background The huge amount of biological information, its distribution over the Internet and the heterogeneity of available software tools makes the adoption of new data integration and analysis network tools a necessity in bioinformatics. ICT standards and tools, like Web Services and Workflow Management Systems (WMS, can support the creation and deployment of such systems. Many Web Services are already available and some WMS have been proposed. They assume that researchers know which bioinformatics resources can be reached through a programmatic interface and that they are skilled in programming and building workflows. Therefore, they are not viable to the majority of unskilled researchers. A portal enabling these to take profit from new technologies is still missing. Results We designed biowep, a web based client application that allows for the selection and execution of a set of predefined workflows. The system is available on-line. Biowep architecture includes a Workflow Manager, a User Interface and a Workflow Executor. The task of the Workflow Manager is the creation and annotation of workflows. These can be created by using either the Taverna Workbench or BioWMS. Enactment of workflows is carried out by FreeFluo for Taverna workflows and by BioAgent/Hermes, a mobile agent-based middleware, for BioWMS ones. Main workflows' processing steps are annotated on the basis of their input and output, elaboration type and application domain by using a classification of bioinformatics data and tasks. The interface supports users authentication and profiling. Workflows can be selected on the basis of users' profiles and can be searched through their annotations. Results can be saved. Conclusion We developed a web system that support the selection and execution of predefined workflows, thus simplifying access for all researchers. The implementation of Web Services allowing specialized software to interact with an exhaustive set of biomedical

  11. Application of bioinformatics on the detection of pathogens by Pcr

    International Nuclear Information System (INIS)

    Rezig, Slim; Sakhri, Saber

    2007-01-01

    Salmonellas are the main responsible agent for the frequent food-borne gastrointestinal diseases. Their detection using classical methods are laborious and their results take a lot of time to be revealed. In this context, we tried to set up a revealing technique of the invA virulence gene, found in the majority of Salmonella species. After amplification with PCR using specific primers created and verified by bioinformatics programs, two couples of primers were set up and they appeared to be very specific and sensitive for the detection of invA gene. (Author)

  12. New Directions in Statistical Physics: Econophysics, Bioinformatics, and Pattern Recognition

    International Nuclear Information System (INIS)

    Grassberger, P

    2004-01-01

    This book contains 18 contributions from different authors. Its subtitle 'Econophysics, Bioinformatics, and Pattern Recognition' says more precisely what it is about: not so much about central problems of conventional statistical physics like equilibrium phase transitions and critical phenomena, but about its interdisciplinary applications. After a long period of specialization, physicists have, over the last few decades, found more and more satisfaction in breaking out of the limitations set by the traditional classification of sciences. Indeed, this classification had never been strict, and physicists in particular had always ventured into other fields. Helmholtz, in the middle of the 19th century, had considered himself a physicist when working on physiology, stressing that the physics of animate nature is as much a legitimate field of activity as the physics of inanimate nature. Later, Max Delbrueck and Francis Crick did for experimental biology what Schroedinger did for its theoretical foundation. And many of the experimental techniques used in chemistry, biology, and medicine were developed by a steady stream of talented physicists who left their proper discipline to venture out into the wider world of science. The development we have witnessed over the last thirty years or so is different. It started with neural networks where methods could be applied which had been developed for spin glasses, but todays list includes vehicular traffic (driven lattice gases), geology (self-organized criticality), economy (fractal stochastic processes and large scale simulations), engineering (dynamical chaos), and many others. By staying in the physics departments, these activities have transformed the physics curriculum and the view physicists have of themselves. In many departments there are now courses on econophysics or on biological physics, and some universities offer degrees in the physics of traffic or in econophysics. In order to document this change of attitude

  13. Engineering Institute

    Science.gov (United States)

    Projects Past Projects Publications NSEC » Engineering Institute Engineering Institute Multidisciplinary engineering research that integrates advanced modeling and simulations, novel sensing systems and new home of Engineering Institute Contact Institute Director Charles Farrar (505) 665-0860 Email UCSD EI

  14. SeqHound: biological sequence and structure database as a platform for bioinformatics research

    Directory of Open Access Journals (Sweden)

    Dumontier Michel

    2002-10-01

    Full Text Available Abstract Background SeqHound has been developed as an integrated biological sequence, taxonomy, annotation and 3-D structure database system. It provides a high-performance server platform for bioinformatics research in a locally-hosted environment. Results SeqHound is based on the National Center for Biotechnology Information data model and programming tools. It offers daily updated contents of all Entrez sequence databases in addition to 3-D structural data and information about sequence redundancies, sequence neighbours, taxonomy, complete genomes, functional annotation including Gene Ontology terms and literature links to PubMed. SeqHound is accessible via a web server through a Perl, C or C++ remote API or an optimized local API. It provides functionality necessary to retrieve specialized subsets of sequences, structures and structural domains. Sequences may be retrieved in FASTA, GenBank, ASN.1 and XML formats. Structures are available in ASN.1, XML and PDB formats. Emphasis has been placed on complete genomes, taxonomy, domain and functional annotation as well as 3-D structural functionality in the API, while fielded text indexing functionality remains under development. SeqHound also offers a streamlined WWW interface for simple web-user queries. Conclusions The system has proven useful in several published bioinformatics projects such as the BIND database and offers a cost-effective infrastructure for research. SeqHound will continue to develop and be provided as a service of the Blueprint Initiative at the Samuel Lunenfeld Research Institute. The source code and examples are available under the terms of the GNU public license at the Sourceforge site http://sourceforge.net/projects/slritools/ in the SLRI Toolkit.

  15. Protecting innovation in bioinformatics and in-silico biology.

    Science.gov (United States)

    Harrison, Robert

    2003-01-01

    Commercial success or failure of innovation in bioinformatics and in-silico biology requires the appropriate use of legal tools for protecting and exploiting intellectual property. These tools include patents, copyrights, trademarks, design rights, and limiting information in the form of 'trade secrets'. Potentially patentable components of bioinformatics programmes include lines of code, algorithms, data content, data structure and user interfaces. In both the US and the European Union, copyright protection is granted for software as a literary work, and most other major industrial countries have adopted similar rules. Nonetheless, the grant of software patents remains controversial and is being challenged in some countries. Current debate extends to aspects such as whether patents can claim not only the apparatus and methods but also the data signals and/or products, such as a CD-ROM, on which the programme is stored. The patentability of substances discovered using in-silico methods is a separate debate that is unlikely to be resolved in the near future.

  16. Bioinformatic prediction and functional characterization of human KIAA0100 gene

    Directory of Open Access Journals (Sweden)

    He Cui

    2017-02-01

    Full Text Available Our previous study demonstrated that human KIAA0100 gene was a novel acute monocytic leukemia-associated antigen (MLAA gene. But the functional characterization of human KIAA0100 gene has remained unknown to date. Here, firstly, bioinformatic prediction of human KIAA0100 gene was carried out using online softwares; Secondly, Human KIAA0100 gene expression was downregulated by the clustered regularly interspaced short palindromic repeats (CRISPR/CRISPR-associated (Cas 9 system in U937 cells. Cell proliferation and apoptosis were next evaluated in KIAA0100-knockdown U937 cells. The bioinformatic prediction showed that human KIAA0100 gene was located on 17q11.2, and human KIAA0100 protein was located in the secretory pathway. Besides, human KIAA0100 protein contained a signalpeptide, a transmembrane region, three types of secondary structures (alpha helix, extended strand, and random coil , and four domains from mitochondrial protein 27 (FMP27. The observation on functional characterization of human KIAA0100 gene revealed that its downregulation inhibited cell proliferation, and promoted cell apoptosis in U937 cells. To summarize, these results suggest human KIAA0100 gene possibly comes within mitochondrial genome; moreover, it is a novel anti-apoptotic factor related to carcinogenesis or progression in acute monocytic leukemia, and may be a potential target for immunotherapy against acute monocytic leukemia.

  17. Computational Lipidomics and Lipid Bioinformatics: Filling In the Blanks.

    Science.gov (United States)

    Pauling, Josch; Klipp, Edda

    2016-12-22

    Lipids are highly diverse metabolites of pronounced importance in health and disease. While metabolomics is a broad field under the omics umbrella that may also relate to lipids, lipidomics is an emerging field which specializes in the identification, quantification and functional interpretation of complex lipidomes. Today, it is possible to identify and distinguish lipids in a high-resolution, high-throughput manner and simultaneously with a lot of structural detail. However, doing so may produce thousands of mass spectra in a single experiment which has created a high demand for specialized computational support to analyze these spectral libraries. The computational biology and bioinformatics community has so far established methodology in genomics, transcriptomics and proteomics but there are many (combinatorial) challenges when it comes to structural diversity of lipids and their identification, quantification and interpretation. This review gives an overview and outlook on lipidomics research and illustrates ongoing computational and bioinformatics efforts. These efforts are important and necessary steps to advance the lipidomics field alongside analytic, biochemistry, biomedical and biology communities and to close the gap in available computational methodology between lipidomics and other omics sub-branches.

  18. jORCA: easily integrating bioinformatics Web Services.

    Science.gov (United States)

    Martín-Requena, Victoria; Ríos, Javier; García, Maximiliano; Ramírez, Sergio; Trelles, Oswaldo

    2010-02-15

    Web services technology is becoming the option of choice to deploy bioinformatics tools that are universally available. One of the major strengths of this approach is that it supports machine-to-machine interoperability over a network. However, a weakness of this approach is that various Web Services differ in their definition and invocation protocols, as well as their communication and data formats-and this presents a barrier to service interoperability. jORCA is a desktop client aimed at facilitating seamless integration of Web Services. It does so by making a uniform representation of the different web resources, supporting scalable service discovery, and automatic composition of workflows. Usability is at the top of the jORCA agenda; thus it is a highly customizable and extensible application that accommodates a broad range of user skills featuring double-click invocation of services in conjunction with advanced execution-control, on the fly data standardization, extensibility of viewer plug-ins, drag-and-drop editing capabilities, plus a file-based browsing style and organization of favourite tools. The integration of bioinformatics Web Services is made easier to support a wider range of users. .

  19. MAPI: towards the integrated exploitation of bioinformatics Web Services.

    Science.gov (United States)

    Ramirez, Sergio; Karlsson, Johan; Trelles, Oswaldo

    2011-10-27

    Bioinformatics is commonly featured as a well assorted list of available web resources. Although diversity of services is positive in general, the proliferation of tools, their dispersion and heterogeneity complicate the integrated exploitation of such data processing capacity. To facilitate the construction of software clients and make integrated use of this variety of tools, we present a modular programmatic application interface (MAPI) that provides the necessary functionality for uniform representation of Web Services metadata descriptors including their management and invocation protocols of the services which they represent. This document describes the main functionality of the framework and how it can be used to facilitate the deployment of new software under a unified structure of bioinformatics Web Services. A notable feature of MAPI is the modular organization of the functionality into different modules associated with specific tasks. This means that only the modules needed for the client have to be installed, and that the module functionality can be extended without the need for re-writing the software client. The potential utility and versatility of the software library has been demonstrated by the implementation of several currently available clients that cover different aspects of integrated data processing, ranging from service discovery to service invocation with advanced features such as workflows composition and asynchronous services calls to multiple types of Web Services including those registered in repositories (e.g. GRID-based, SOAP, BioMOBY, R-bioconductor, and others).

  20. A review of bioinformatic methods for forensic DNA analyses.

    Science.gov (United States)

    Liu, Yao-Yuan; Harbison, SallyAnn

    2018-03-01

    Short tandem repeats, single nucleotide polymorphisms, and whole mitochondrial analyses are three classes of markers which will play an important role in the future of forensic DNA typing. The arrival of massively parallel sequencing platforms in forensic science reveals new information such as insights into the complexity and variability of the markers that were previously unseen, along with amounts of data too immense for analyses by manual means. Along with the sequencing chemistries employed, bioinformatic methods are required to process and interpret this new and extensive data. As more is learnt about the use of these new technologies for forensic applications, development and standardization of efficient, favourable tools for each stage of data processing is being carried out, and faster, more accurate methods that improve on the original approaches have been developed. As forensic laboratories search for the optimal pipeline of tools, sequencer manufacturers have incorporated pipelines into sequencer software to make analyses convenient. This review explores the current state of bioinformatic methods and tools used for the analyses of forensic markers sequenced on the massively parallel sequencing (MPS) platforms currently most widely used. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Agonist Binding to Chemosensory Receptors: A Systematic Bioinformatics Analysis

    Directory of Open Access Journals (Sweden)

    Fabrizio Fierro

    2017-09-01

    Full Text Available Human G-protein coupled receptors (hGPCRs constitute a large and highly pharmaceutically relevant membrane receptor superfamily. About half of the hGPCRs' family members are chemosensory receptors, involved in bitter taste and olfaction, along with a variety of other physiological processes. Hence these receptors constitute promising targets for pharmaceutical intervention. Molecular modeling has been so far the most important tool to get insights on agonist binding and receptor activation. Here we investigate both aspects by bioinformatics-based predictions across all bitter taste and odorant receptors for which site-directed mutagenesis data are available. First, we observe that state-of-the-art homology modeling combined with previously used docking procedures turned out to reproduce only a limited fraction of ligand/receptor interactions inferred by experiments. This is most probably caused by the low sequence identity with available structural templates, which limits the accuracy of the protein model and in particular of the side-chains' orientations. Methods which transcend the limited sampling of the conformational space of docking may improve the predictions. As an example corroborating this, we review here multi-scale simulations from our lab and show that, for the three complexes studied so far, they significantly enhance the predictive power of the computational approach. Second, our bioinformatics analysis provides support to previous claims that several residues, including those at positions 1.50, 2.50, and 7.52, are involved in receptor activation.

  2. mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking.

    Science.gov (United States)

    Bokulich, Nicholas A; Rideout, Jai Ram; Mercurio, William G; Shiffer, Arron; Wolfe, Benjamin; Maurice, Corinne F; Dutton, Rachel J; Turnbaugh, Peter J; Knight, Rob; Caporaso, J Gregory

    2016-01-01

    Mock communities are an important tool for validating, optimizing, and comparing bioinformatics methods for microbial community analysis. We present mockrobiota, a public resource for sharing, validating, and documenting mock community data resources, available at http://caporaso-lab.github.io/mockrobiota/. The materials contained in mockrobiota include data set and sample metadata, expected composition data (taxonomy or gene annotations or reference sequences for mock community members), and links to raw data (e.g., raw sequence data) for each mock community data set. mockrobiota does not supply physical sample materials directly, but the data set metadata included for each mock community indicate whether physical sample materials are available. At the time of this writing, mockrobiota contains 11 mock community data sets with known species compositions, including bacterial, archaeal, and eukaryotic mock communities, analyzed by high-throughput marker gene sequencing. IMPORTANCE The availability of standard and public mock community data will facilitate ongoing method optimizations, comparisons across studies that share source data, and greater transparency and access and eliminate redundancy. These are also valuable resources for bioinformatics teaching and training. This dynamic resource is intended to expand and evolve to meet the changing needs of the omics community.

  3. Mathematics Intensive Summer Session (MISS). Final technical report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-11-01

    This final technical report appears in two parts: the report for the 1995 summer MISS program and the report for the 1996 summer MISS program. Copies of the US Department of Energy Pre-Freshman Enrichment Program 1995 Entry Form and 1996 Entry Form completed by all participants were sent to the Oak Ridge Institute for Science and Education in the fall of 1995 and 1996 respectively. Those forms are on file should they be needed. Attached also is a copy of the Summary of ideas for panel discussions, problem-solving sessions, or small group discussions presented at the Department of Energy Oak Ridge Institute for Science and Education Pre-Freshman Enrichment Program Project Directors Meeting held in San Antonio, TX, November 12--14, 1995.

  4. YPED: an integrated bioinformatics suite and database for mass spectrometry-based proteomics research.

    Science.gov (United States)

    Colangelo, Christopher M; Shifman, Mark; Cheung, Kei-Hoi; Stone, Kathryn L; Carriero, Nicholas J; Gulcicek, Erol E; Lam, TuKiet T; Wu, Terence; Bjornson, Robert D; Bruce, Can; Nairn, Angus C; Rinehart, Jesse; Miller, Perry L; Williams, Kenneth R

    2015-02-01

    We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database (YPED) that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a single laboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography-tandem mass spectrometry (LC-MS/MS) database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring (MRM)/selective reaction monitoring (SRM) assay development. We have linked YPED's database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results. Copyright © 2015 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

  5. FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes

    Directory of Open Access Journals (Sweden)

    Evelina Y. Basenko

    2018-03-01

    Full Text Available FungiDB (fungidb.org is a free online resource for data mining and functional genomics analysis for fungal and oomycete species. FungiDB is part of the Eukaryotic Pathogen Genomics Database Resource (EuPathDB, eupathdb.org platform that integrates genomic, transcriptomic, proteomic, and phenotypic datasets, and other types of data for pathogenic and nonpathogenic, free-living and parasitic organisms. FungiDB is one of the largest EuPathDB databases containing nearly 100 genomes obtained from GenBank, Aspergillus Genome Database (AspGD, The Broad Institute, Joint Genome Institute (JGI, Ensembl, and other sources. FungiDB offers a user-friendly web interface with embedded bioinformatics tools that support custom in silico experiments that leverage FungiDB-integrated data. In addition, a Galaxy-based workspace enables users to generate custom pipelines for large-scale data analysis (e.g., RNA-Seq, variant calling, etc.. This review provides an introduction to the FungiDB resources and focuses on available features, tools, and queries and how they can be used to mine data across a diverse range of integrated FungiDB datasets and records.

  6. InterAgency Journal (Volume 2, Issue 2, Summer 2011)

    Science.gov (United States)

    2011-01-01

    reintegrated to further improve policies or plans. An operational assignment exchange for USAID would be a position at a geographic combatant...Business Strategies of Informal Micro-Entrepreneurs in Lima, Peru,” International Institute for Labour Studies, Geneva, Switzerland, Discussion Paper, No...to real power. That fear is quite explicit with some people. 62 | Features InterAgency Journal Vol. 2, Issue 2, Summer 2011 Reintegration

  7. USAF/SCEEE Summer Faculty Research Program (1979). Volume 2

    Science.gov (United States)

    1979-12-01

    K. Schwarzschild , Math. Phys, Kiasse, Grottingen Nachrichten, p. 41 (1906). . 28-21 I -. 4; 1979 USAF - SCEEE SUMMER FACULTY RESEARCH PROGRAM...Wollam, 1968, p. 57. 22. Richard H. Hall, Organizations Structure and Process (New Jersey: Prentice-Hall, Inc., 2nd ed., 1978). 23. Karl E. Weick, The...The Analysis of the U.S. Army Aircraft Maintenance System, Battelle Memorial Institute, 1970. (AD703839) Weick, Karl E. The Social Psychology of

  8. Proceedings of the KIEE Summer Annual Conference 2000

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2000-07-01

    This is a collection of papers on research conducted by the participants in the 2000 KIEE Summer Annual Conference at the Muju Resort, Korea. The program was operated under the auspices of the Korean Institute of Electrical Engineers (KIEE) with sponsorship and funding from the Korea Electric Power Corporation(KEPCO) and Korea Research Foundation(KRF). There are four research categories such as electric materials, discharge and high-voltage, MEMS and photoelectron, electromagnetic wave.

  9. Summer Camp July 2017 - Registration

    CERN Multimedia

    EVE et École

    2017-01-01

    The CERN Staff Association’s Summer Camp will be open for children from 4 to 6 years old during four weeks, from 3 to 28 July. Registration is offered on a weekly basis for 450 CHF, lunch included. This year, the various activities will revolve around the theme of the Four Elements. Registration opened on 20 March 2017 for children currently attending the EVE and School of the Association. It will be open from 3 April for children of CERN Members of Personnel, and starting from 24 April for all other children. The general conditions are available on the website of the EVE and School of CERN Staff Association: http://nurseryschool.web.cern.ch. For further questions, please contact us by email at Summer.Camp@cern.ch.

  10. SNOWMASS (DPF Community Summer Study)

    Energy Technology Data Exchange (ETDEWEB)

    Cronin-Hennessy, et al, Daniel

    2013-08-06

    The 2013 Community Summer Study, known as Snowmass," brought together nearly 700 physicists to identify the critical research directions for the United States particle physics program. Commissioned by the American Physical Society, this meeting was the culmination of intense work over the past year by more than 1000 physicists that defined the most important questions for this field and identified the most promising opportunities to address them. This Snowmass study report is a key resource for setting priorities in particle physics.

  11. Artists Paint ... Summer: Grade 2

    Science.gov (United States)

    Herberholz, Barbara

    2012-01-01

    A humid summer haze covers the River Seine and the grassy bank where young men and boys go swimming on Sunday. Everything seems so quiet, still, and very hot. They wear hats to protect them from the hot sun. The artist Georges Seurat used warm tones to give viewers the feeling of the hot sun. Seurat was trying to catch the dazzle of hot sunlight…

  12. Institutional advantage

    NARCIS (Netherlands)

    Martin, Xavier

    Is there such a thing as institutional advantage—and what does it mean for the study of corporate competitive advantage? In this article, I develop the concept of institutional competitive advantage, as distinct from plain competitive advantage and from comparative institutional advantage. I first

  13. Evolutionary institutionalism.

    Science.gov (United States)

    Fürstenberg, Dr Kai

    Institutions are hard to define and hard to study. Long prominent in political science have been two theories: Rational Choice Institutionalism (RCI) and Historical Institutionalism (HI). Arising from the life sciences is now a third: Evolutionary Institutionalism (EI). Comparative strengths and weaknesses of these three theories warrant review, and the value-to-be-added by expanding the third beyond Darwinian evolutionary theory deserves consideration. Should evolutionary institutionalism expand to accommodate new understanding in ecology, such as might apply to the emergence of stability, and in genetics, such as might apply to political behavior? Core arguments are reviewed for each theory with more detailed exposition of the third, EI. Particular attention is paid to EI's gene-institution analogy; to variation, selection, and retention of institutional traits; to endogeneity and exogeneity; to agency and structure; and to ecosystem effects, institutional stability, and empirical limitations in behavioral genetics. RCI, HI, and EI are distinct but complementary. Institutional change, while amenable to rational-choice analysis and, retrospectively, to criticaljuncture and path-dependency analysis, is also, and importantly, ecological. Stability, like change, is an emergent property of institutions, which tend to stabilize after change in a manner analogous to allopatric speciation. EI is more than metaphorically biological in that institutional behaviors are driven by human behaviors whose evolution long preceded the appearance of institutions themselves.

  14. Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN.

    Science.gov (United States)

    He, Yongqun; Xiang, Zuoshuang

    2010-09-27

    Brucella spp. are Gram-negative, facultative intracellular bacteria that cause brucellosis, one of the commonest zoonotic diseases found worldwide in humans and a variety of animal species. While several animal vaccines are available, there is no effective and safe vaccine for prevention of brucellosis in humans. VIOLIN (http://www.violinet.org) is a web-based vaccine database and analysis system that curates, stores, and analyzes published data of commercialized vaccines, and vaccines in clinical trials or in research. VIOLIN contains information for 454 vaccines or vaccine candidates for 73 pathogens. VIOLIN also contains many bioinformatics tools for vaccine data analysis, data integration, and vaccine target prediction. To demonstrate the applicability of VIOLIN for vaccine research, VIOLIN was used for bioinformatics analysis of existing Brucella vaccines and prediction of new Brucella vaccine targets. VIOLIN contains many literature mining programs (e.g., Vaxmesh) that provide in-depth analysis of Brucella vaccine literature. As a result of manual literature curation, VIOLIN contains information for 38 Brucella vaccines or vaccine candidates, 14 protective Brucella antigens, and 68 host response studies to Brucella vaccines from 97 peer-reviewed articles. These Brucella vaccines are classified in the Vaccine Ontology (VO) system and used for different ontological applications. The web-based VIOLIN vaccine target prediction program Vaxign was used to predict new Brucella vaccine targets. Vaxign identified 14 outer membrane proteins that are conserved in six virulent strains from B. abortus, B. melitensis, and B. suis that are pathogenic in humans. Of the 14 membrane proteins, two proteins (Omp2b and Omp31-1) are not present in B. ovis, a Brucella species that is not pathogenic in humans. Brucella vaccine data stored in VIOLIN were compared and analyzed using the VIOLIN query system. Bioinformatics curation and ontological representation of Brucella vaccines

  15. Atlas – a data warehouse for integrative bioinformatics

    Directory of Open Access Journals (Sweden)

    Yuen Macaire MS

    2005-02-01

    Full Text Available Abstract Background We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development. Description The Atlas system is based on relational data models that we developed for each of the source data types. Data stored within these relational models are managed through Structured Query Language (SQL calls that are implemented in a set of Application Programming Interfaces (APIs. The APIs include three languages: C++, Java, and Perl. The methods in these API libraries are used to construct a set of loader applications, which parse and load the source datasets into the Atlas database, and a set of toolbox applications which facilitate data retrieval. Atlas stores and integrates local instances of GenBank, RefSeq, UniProt, Human Protein Reference Database (HPRD, Biomolecular Interaction Network Database (BIND, Database of Interacting Proteins (DIP, Molecular Interactions Database (MINT, IntAct, NCBI Taxonomy, Gene Ontology (GO, Online Mendelian Inheritance in Man (OMIM, LocusLink, Entrez Gene and HomoloGene. The retrieval APIs and toolbox applications are critical components that offer end-users flexible, easy, integrated access to this data. We present use cases that use Atlas to integrate these sources for genome annotation, inference of molecular interactions across species, and gene-disease associations. Conclusion The Atlas biological data warehouse serves as data infrastructure for bioinformatics research and development. It forms the backbone of the research activities in our laboratory and facilitates the integration of disparate, heterogeneous biological sources of data enabling new scientific inferences. Atlas achieves integration of diverse data sets at two levels. First

  16. Close the Achievement Gap with Summer Learning

    Science.gov (United States)

    Huggins, Gary

    2012-01-01

    Summer vacation from school can bring afternoons at the swimming pool, family vacations, and maybe a spirit-filled summer camp that ignites a passion for art or rock climbing. But for many children, summer also means setbacks in learning that take a tremendous toll on teaching and student performance over time. PTA leaders can make a vital…

  17. Finding Funds to Move Summer Learning Forward

    Science.gov (United States)

    Seidel, Bob

    2015-01-01

    Summer learning loss creates a permanent drag on the US education system. With the generous support of the Charles Stewart Mott Foundation, the National Summer Learning Association (NSLA) developed "Moving Summer Learning Forward: A Strategic Roadmap for Funding in Tough Times" to provide out-of-school time programs, school districts,…

  18. Bioinformatics and the Politics of Innovation in the Life Sciences

    Science.gov (United States)

    Zhou, Yinhua; Datta, Saheli; Salter, Charlotte

    2016-01-01

    The governments of China, India, and the United Kingdom are unanimous in their belief that bioinformatics should supply the link between basic life sciences research and its translation into health benefits for the population and the economy. Yet at the same time, as ambitious states vying for position in the future global bioeconomy they differ considerably in the strategies adopted in pursuit of this goal. At the heart of these differences lies the interaction between epistemic change within the scientific community itself and the apparatus of the state. Drawing on desk-based research and thirty-two interviews with scientists and policy makers in the three countries, this article analyzes the politics that shape this interaction. From this analysis emerges an understanding of the variable capacities of different kinds of states and political systems to work with science in harnessing the potential of new epistemic territories in global life sciences innovation. PMID:27546935

  19. An Adaptive Hybrid Multiprocessor technique for bioinformatics sequence alignment

    KAUST Repository

    Bonny, Talal

    2012-07-28

    Sequence alignment algorithms such as the Smith-Waterman algorithm are among the most important applications in the development of bioinformatics. Sequence alignment algorithms must process large amounts of data which may take a long time. Here, we introduce our Adaptive Hybrid Multiprocessor technique to accelerate the implementation of the Smith-Waterman algorithm. Our technique utilizes both the graphics processing unit (GPU) and the central processing unit (CPU). It adapts to the implementation according to the number of CPUs given as input by efficiently distributing the workload between the processing units. Using existing resources (GPU and CPU) in an efficient way is a novel approach. The peak performance achieved for the platforms GPU + CPU, GPU + 2CPUs, and GPU + 3CPUs is 10.4 GCUPS, 13.7 GCUPS, and 18.6 GCUPS, respectively (with the query length of 511 amino acid). © 2010 IEEE.

  20. Meta-learning framework applied in bioinformatics inference system design.

    Science.gov (United States)

    Arredondo, Tomás; Ormazábal, Wladimir

    2015-01-01

    This paper describes a meta-learner inference system development framework which is applied and tested in the implementation of bioinformatic inference systems. These inference systems are used for the systematic classification of the best candidates for inclusion in bacterial metabolic pathway maps. This meta-learner-based approach utilises a workflow where the user provides feedback with final classification decisions which are stored in conjunction with analysed genetic sequences for periodic inference system training. The inference systems were trained and tested with three different data sets related to the bacterial degradation of aromatic compounds. The analysis of the meta-learner-based framework involved contrasting several different optimisation methods with various different parameters. The obtained inference systems were also contrasted with other standard classification methods with accurate prediction capabilities observed.

  1. Achievements and challenges in structural bioinformatics and computational biophysics.

    Science.gov (United States)

    Samish, Ilan; Bourne, Philip E; Najmanovich, Rafael J

    2015-01-01

    The field of structural bioinformatics and computational biophysics has undergone a revolution in the last 10 years. Developments that are captured annually through the 3DSIG meeting, upon which this article reflects. An increase in the accessible data, computational resources and methodology has resulted in an increase in the size and resolution of studied systems and the complexity of the questions amenable to research. Concomitantly, the parameterization and efficiency of the methods have markedly improved along with their cross-validation with other computational and experimental results. The field exhibits an ever-increasing integration with biochemistry, biophysics and other disciplines. In this article, we discuss recent achievements along with current challenges within the field. © The Author 2014. Published by Oxford University Press.

  2. ISEV position paper: extracellular vesicle RNA analysis and bioinformatics

    Directory of Open Access Journals (Sweden)

    Andrew F. Hill

    2013-12-01

    Full Text Available Extracellular vesicles (EVs are the collective term for the various vesicles that are released by cells into the extracellular space. Such vesicles include exosomes and microvesicles, which vary by their size and/or protein and genetic cargo. With the discovery that EVs contain genetic material in the form of RNA (evRNA has come the increased interest in these vesicles for their potential use as sources of disease biomarkers and potential therapeutic agents. Rapid developments in the availability of deep sequencing technologies have enabled the study of EV-related RNA in detail. In October 2012, the International Society for Extracellular Vesicles (ISEV held a workshop on “evRNA analysis and bioinformatics.” Here, we report the conclusions of one of the roundtable discussions where we discussed evRNA analysis technologies and provide some guidelines to researchers in the field to consider when performing such analysis.

  3. Establishing a master's degree programme in bioinformatics: challenges and opportunities.

    Science.gov (United States)

    Sahinidis, N V; Harandi, M T; Heath, M T; Murphy, L; Snir, M; Wheeler, R P; Zukoski, C F

    2005-12-01

    The development of the Bioinformatics MS degree program at the University of Illinois, the challenges and opportunities associated with such a process, and the current structure of the program is described. This program has departed from earlier University practice in significant ways. Despite the existence of several interdisciplinary programs at the University, a few of which grant degrees, this is the first interdisciplinary program that grants degrees and formally recognises departmental specialisation areas. The program, which is not owned by any particular department but by the Graduate College itself, is operated in a franchise-like fashion via several departmental concentrations. With four different colleges and many more departments involved in establishing and operating the program, the logistics of the operation are of considerable complexity but result in significant interactions across the entire campus.

  4. The web server of IBM's Bioinformatics and Pattern Discovery group.

    Science.gov (United States)

    Huynh, Tien; Rigoutsos, Isidore; Parida, Laxmi; Platt, Daniel; Shibuya, Tetsuo

    2003-07-01

    We herein present and discuss the services and content which are available on the web server of IBM's Bioinformatics and Pattern Discovery group. The server is operational around the clock and provides access to a variety of methods that have been published by the group's members and collaborators. The available tools correspond to applications ranging from the discovery of patterns in streams of events and the computation of multiple sequence alignments, to the discovery of genes in nucleic acid sequences and the interactive annotation of amino acid sequences. Additionally, annotations for more than 70 archaeal, bacterial, eukaryotic and viral genomes are available on-line and can be searched interactively. The tools and code bundles can be accessed beginning at http://cbcsrv.watson.ibm.com/Tspd.html whereas the genomics annotations are available at http://cbcsrv.watson.ibm.com/Annotations/.

  5. Bioinformatics Tools for the Discovery of New Nonribosomal Peptides

    DEFF Research Database (Denmark)

    Leclère, Valérie; Weber, Tilmann; Jacques, Philippe

    2016-01-01

    -dimensional structure of the peptides can be compared with the structural patterns of all known NRPs. The presented workflow leads to an efficient and rapid screening of genomic data generated by high throughput technologies. The exploration of such sequenced genomes may lead to the discovery of new drugs (i......This chapter helps in the use of bioinformatics tools relevant to the discovery of new nonribosomal peptides (NRPs) produced by microorganisms. The strategy described can be applied to draft or fully assembled genome sequences. It relies on the identification of the synthetase genes...... and the deciphering of the domain architecture of the nonribosomal peptide synthetases (NRPSs). In the next step, candidate peptides synthesized by these NRPSs are predicted in silico, considering the specificity of incorporated monomers together with their isomery. To assess their novelty, the two...

  6. Single-Cell Transcriptomics Bioinformatics and Computational Challenges

    Directory of Open Access Journals (Sweden)

    Lana Garmire

    2016-09-01

    Full Text Available The emerging single-cell RNA-Seq (scRNA-Seq technology holds the promise to revolutionize our understanding of diseases and associated biological processes at an unprecedented resolution. It opens the door to reveal the intercellular heterogeneity and has been employed to a variety of applications, ranging from characterizing cancer cells subpopulations to elucidating tumor resistance mechanisms. Parallel to improving experimental protocols to deal with technological issues, deriving new analytical methods to reveal the complexity in scRNA-Seq data is just as challenging. Here we review the current state-of-the-art bioinformatics tools and methods for scRNA-Seq analysis, as well as addressing some critical analytical challenges that the field faces.

  7. A bioinformatics roadmap for the human vaccines project.

    Science.gov (United States)

    Scheuermann, Richard H; Sinkovits, Robert S; Schenkelberg, Theodore; Koff, Wayne C

    2017-06-01

    Biomedical research has become a data intensive science in which high throughput experimentation is producing comprehensive data about biological systems at an ever-increasing pace. The Human Vaccines Project is a new public-private partnership, with the goal of accelerating development of improved vaccines and immunotherapies for global infectious diseases and cancers by decoding the human immune system. To achieve its mission, the Project is developing a Bioinformatics Hub as an open-source, multidisciplinary effort with the overarching goal of providing an enabling infrastructure to support the data processing, analysis and knowledge extraction procedures required to translate high throughput, high complexity human immunology research data into biomedical knowledge, to determine the core principles driving specific and durable protective immune responses.

  8. BioRuby: bioinformatics software for the Ruby programming language.

    Science.gov (United States)

    Goto, Naohisa; Prins, Pjotr; Nakao, Mitsuteru; Bonnal, Raoul; Aerts, Jan; Katayama, Toshiaki

    2010-10-15

    The BioRuby software toolkit contains a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, written in the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO. BioRuby comes with a tutorial, documentation and an interactive environment, which can be used in the shell, and in the web browser. BioRuby is free and open source software, made available under the Ruby license. BioRuby runs on all platforms that support Ruby, including Linux, Mac OS X and Windows. And, with JRuby, BioRuby runs on the Java Virtual Machine. The source code is available from http://www.bioruby.org/. katayama@bioruby.org

  9. DNA mimic proteins: functions, structures, and bioinformatic analysis.

    Science.gov (United States)

    Wang, Hao-Ching; Ho, Chun-Han; Hsu, Kai-Cheng; Yang, Jinn-Moon; Wang, Andrew H-J

    2014-05-13

    DNA mimic proteins have DNA-like negative surface charge distributions, and they function by occupying the DNA binding sites of DNA binding proteins to prevent these sites from being accessed by DNA. DNA mimic proteins control the activities of a variety of DNA binding proteins and are involved in a wide range of cellular mechanisms such as chromatin assembly, DNA repair, transcription regulation, and gene recombination. However, the sequences and structures of DNA mimic proteins are diverse, making them difficult to predict by bioinformatic search. To date, only a few DNA mimic proteins have been reported. These DNA mimics were not found by searching for functional motifs in their sequences but were revealed only by structural analysis of their charge distribution. This review highlights the biological roles and structures of 16 reported DNA mimic proteins. We also discuss approaches that might be used to discover new DNA mimic proteins.

  10. Institutional entrepreneurship:

    DEFF Research Database (Denmark)

    Gretzinger, Susanne

    2018-01-01

    Institutional entrepreneurship pays specific attention to the process and outcomes of agents who are willing and capable of changing institutions. It has some common ground with the political entrepreneur, a concept that proposes change in norms and institutions because of commitment and activities...... of agents or organisations in the policy arena. The present chapter understands institutional entrepreneurship as the process of changing institutionalised practices. Based on a literature review, it describes the triggers, activities and potential effects of institutional entrepreneurs. The chapter...... concludes by tentatively arguing that political entrepreneurs can be institutional entrepreneurs, but institutional entrepreneurship can be considered as the broader concept that incorporates strategies and visions as well as interpretative-discursive power into the conceptual framework....

  11. Bioinformatics Database Tools in Analysis of Genetics of Neurodevelopmental Disorders

    Directory of Open Access Journals (Sweden)

    Dibyashree Mallik

    2017-10-01

    Full Text Available Bioinformatics tools are recently used in various sectors of biology. Many questions regarding Neurodevelopmental disorder which arises as a major health issue recently can be solved by using various bioinformatics databases. Schizophrenia is such a mental disorder which is now arises as a major threat in young age people because it is mostly seen in case of people during their late adolescence or early adulthood period. Databases like DISGENET, GWAS, PHARMGKB, and DRUGBANK have huge repository of genes associated with schizophrenia. We found a lot of genes are being associated with schizophrenia, but approximately 200 genes are found to be present in any of these databases. After further screening out process 20 genes are found to be highly associated with each other and are also a common genes in many other diseases also. It is also found that they all are serves as a common targeting gene in many antipsychotic drugs. After analysis of various biological properties, molecular function it is found that these 20 genes are mostly involved in biological regulation process and are having receptor activity. They are belonging mainly to receptor protein class. Among these 20 genes CYP2C9, CYP3A4, DRD2, HTR1A, HTR2A are shown to be a main targeting genes of most of the antipsychotic drugs and are associated with  more than 40% diseases. The basic findings of the present study enumerated that a suitable combined drug can be design by targeting these genes which can be used for the better treatment of schizophrenia.

  12. Bioinformatics approaches to single-cell analysis in developmental biology.

    Science.gov (United States)

    Yalcin, Dicle; Hakguder, Zeynep M; Otu, Hasan H

    2016-03-01

    Individual cells within the same population show various degrees of heterogeneity, which may be better handled with single-cell analysis to address biological and clinical questions. Single-cell analysis is especially important in developmental biology as subtle spatial and temporal differences in cells have significant associations with cell fate decisions during differentiation and with the description of a particular state of a cell exhibiting an aberrant phenotype. Biotechnological advances, especially in the area of microfluidics, have led to a robust, massively parallel and multi-dimensional capturing, sorting, and lysis of single-cells and amplification of related macromolecules, which have enabled the use of imaging and omics techniques on single cells. There have been improvements in computational single-cell image analysis in developmental biology regarding feature extraction, segmentation, image enhancement and machine learning, handling limitations of optical resolution to gain new perspectives from the raw microscopy images. Omics approaches, such as transcriptomics, genomics and epigenomics, targeting gene and small RNA expression, single nucleotide and structural variations and methylation and histone modifications, rely heavily on high-throughput sequencing technologies. Although there are well-established bioinformatics methods for analysis of sequence data, there are limited bioinformatics approaches which address experimental design, sample size considerations, amplification bias, normalization, differential expression, coverage, clustering and classification issues, specifically applied at the single-cell level. In this review, we summarize biological and technological advancements, discuss challenges faced in the aforementioned data acquisition and analysis issues and present future prospects for application of single-cell analyses to developmental biology. © The Author 2015. Published by Oxford University Press on behalf of the European

  13. BioStar: an online question & answer resource for the bioinformatics community

    Science.gov (United States)

    Although the era of big data has produced many bioinformatics tools and databases, using them effectively often requires specialized knowledge. Many groups lack bioinformatics expertise, and frequently find that software documentation is inadequate and local colleagues may be overburdened or unfamil...

  14. Comparative Proteome Bioinformatics: Identification of Phosphotyrosine Signaling Proteins in the Unicellular Protozoan Ciliate Tetrahymena

    DEFF Research Database (Denmark)

    Gammeltoft, Steen; Christensen, Søren Tvorup; Joachimiak, Marcin

    2005-01-01

    Tetrahymena, bioinformatics, cilia, evolution, signaling, TtPTK1, PTK, Grb2, SH-PTP 2, Plcy, Src, PTP, PI3K, SH2, SH3, PH......Tetrahymena, bioinformatics, cilia, evolution, signaling, TtPTK1, PTK, Grb2, SH-PTP 2, Plcy, Src, PTP, PI3K, SH2, SH3, PH...

  15. Bioinformatics Methods for Interpreting Toxicogenomics Data: The Role of Text-Mining

    NARCIS (Netherlands)

    Hettne, K.M.; Kleinjans, J.; Stierum, R.H.; Boorsma, A.; Kors, J.A.

    2014-01-01

    This chapter concerns the application of bioinformatics methods to the analysis of toxicogenomics data. The chapter starts with an introduction covering how bioinformatics has been applied in toxicogenomics data analysis, and continues with a description of the foundations of a specific

  16. Making Bioinformatics Projects a Meaningful Experience in an Undergraduate Biotechnology or Biomedical Science Programme

    Science.gov (United States)

    Sutcliffe, Iain C.; Cummings, Stephen P.

    2007-01-01

    Bioinformatics has emerged as an important discipline within the biological sciences that allows scientists to decipher and manage the vast quantities of data (such as genome sequences) that are now available. Consequently, there is an obvious need to provide graduates in biosciences with generic, transferable skills in bioinformatics. We present…

  17. Green Fluorescent Protein-Focused Bioinformatics Laboratory Experiment Suitable for Undergraduates in Biochemistry Courses

    Science.gov (United States)

    Rowe, Laura

    2017-01-01

    An introductory bioinformatics laboratory experiment focused on protein analysis has been developed that is suitable for undergraduate students in introductory biochemistry courses. The laboratory experiment is designed to be potentially used as a "stand-alone" activity in which students are introduced to basic bioinformatics tools and…

  18. Teaching Bioinformatics and Neuroinformatics by Using Free Web-Based Tools

    Science.gov (United States)

    Grisham, William; Schottler, Natalie A.; Valli-Marill, Joanne; Beck, Lisa; Beatty, Jackson

    2010-01-01

    This completely computer-based module's purpose is to introduce students to bioinformatics resources. We present an easy-to-adopt module that weaves together several important bioinformatic tools so students can grasp how these tools are used in answering research questions. Students integrate information gathered from websites dealing with…

  19. Exploring Cystic Fibrosis Using Bioinformatics Tools: A Module Designed for the Freshman Biology Course

    Science.gov (United States)

    Zhang, Xiaorong

    2011-01-01

    We incorporated a bioinformatics component into the freshman biology course that allows students to explore cystic fibrosis (CF), a common genetic disorder, using bioinformatics tools and skills. Students learn about CF through searching genetic databases, analyzing genetic sequences, and observing the three-dimensional structures of proteins…

  20. A Portable Bioinformatics Course for Upper-Division Undergraduate Curriculum in Sciences

    Science.gov (United States)

    Floraino, Wely B.

    2008-01-01

    This article discusses the challenges that bioinformatics education is facing and describes a bioinformatics course that is successfully taught at the California State Polytechnic University, Pomona, to the fourth year undergraduate students in biological sciences, chemistry, and computer science. Information on lecture and computer practice…

  1. Computer Programming and Biomolecular Structure Studies: A Step beyond Internet Bioinformatics

    Science.gov (United States)

    Likic, Vladimir A.

    2006-01-01

    This article describes the experience of teaching structural bioinformatics to third year undergraduate students in a subject titled "Biomolecular Structure and Bioinformatics." Students were introduced to computer programming and used this knowledge in a practical application as an alternative to the well established Internet bioinformatics…

  2. Incorporating a Collaborative Web-Based Virtual Laboratory in an Undergraduate Bioinformatics Course

    Science.gov (United States)

    Weisman, David

    2010-01-01

    Face-to-face bioinformatics courses commonly include a weekly, in-person computer lab to facilitate active learning, reinforce conceptual material, and teach practical skills. Similarly, fully-online bioinformatics courses employ hands-on exercises to achieve these outcomes, although students typically perform this work offsite. Combining a…

  3. Bioinformatics in High School Biology Curricula: A Study of State Science Standards

    Science.gov (United States)

    Wefer, Stephen H.; Sheppard, Keith

    2008-01-01

    The proliferation of bioinformatics in modern biology marks a modern revolution in science that promises to influence science education at all levels. This study analyzed secondary school science standards of 49 U.S. states (Iowa has no science framework) and the District of Columbia for content related to bioinformatics. The bioinformatics…

  4. Integration of Bioinformatics into an Undergraduate Biology Curriculum and the Impact on Development of Mathematical Skills

    Science.gov (United States)

    Wightman, Bruce; Hark, Amy T.

    2012-01-01

    The development of fields such as bioinformatics and genomics has created new challenges and opportunities for undergraduate biology curricula. Students preparing for careers in science, technology, and medicine need more intensive study of bioinformatics and more sophisticated training in the mathematics on which this field is based. In this…

  5. PayDIBI: Pay-as-you-go data integration for bioinformatics

    NARCIS (Netherlands)

    Wanders, B.

    2012-01-01

    Background: Scientific research in bio-informatics is often data-driven and supported by biolog- ical databases. In a growing number of research projects, researchers like to ask questions that require the combination of information from more than one database. Most bio-informatics papers do not

  6. A decade of Web Server updates at the Bioinformatics Links Directory: 2003-2012.

    Science.gov (United States)

    Brazas, Michelle D; Yim, David; Yeung, Winston; Ouellette, B F Francis

    2012-07-01

    The 2012 Bioinformatics Links Directory update marks the 10th special Web Server issue from Nucleic Acids Research. Beginning with content from their 2003 publication, the Bioinformatics Links Directory in collaboration with Nucleic Acids Research has compiled and published a comprehensive list of freely accessible, online tools, databases and resource materials for the bioinformatics and life science research communities. The past decade has exhibited significant growth and change in the types of tools, databases and resources being put forth, reflecting both technology changes and the nature of research over that time. With the addition of 90 web server tools and 12 updates from the July 2012 Web Server issue of Nucleic Acids Research, the Bioinformatics Links Directory at http://bioinformatics.ca/links_directory/ now contains an impressive 134 resources, 455 databases and 1205 web server tools, mirroring the continued activity and efforts of our field.

  7. 9th International Conference on Practical Applications of Computational Biology and Bioinformatics

    CERN Document Server

    Rocha, Miguel; Fdez-Riverola, Florentino; Paz, Juan

    2015-01-01

    This proceedings presents recent practical applications of Computational Biology and  Bioinformatics. It contains the proceedings of the 9th International Conference on Practical Applications of Computational Biology & Bioinformatics held at University of Salamanca, Spain, at June 3rd-5th, 2015. The International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB) is an annual international meeting dedicated to emerging and challenging applied research in Bioinformatics and Computational Biology. Biological and biomedical research are increasingly driven by experimental techniques that challenge our ability to analyse, process and extract meaningful knowledge from the underlying data. The impressive capabilities of next generation sequencing technologies, together with novel and ever evolving distinct types of omics data technologies, have put an increasingly complex set of challenges for the growing fields of Bioinformatics and Computational Biology. The analysis o...

  8. SAAPMB summer school and congress

    International Nuclear Information System (INIS)

    1990-01-01

    Medical and health physics are greatly stimulated by the exchange of personal experiences and research results among scientists working in their particular fields of interests. Individual contact is of exceptional importance in those rapidly developing areas of high technology which we find in hospitals and industry and therefor the social exchange of ideas at the Summer School and Congress is very important. Research in the fields of medical and health physics is covered by the papers and posters presented. 53 articles have been indexed (27 papers and 26 poster presentations), and 14 articles have been considered to be out of scope for INIS

  9. The Vulcano 1994 summer campaign

    Energy Technology Data Exchange (ETDEWEB)

    Caruso, P.; Valenza, M. [CNR, Palermo (Italy). Istituto Geochimica dei Fluidi; Graziani, G.; Martilli, A.; Mosca, S. [JRC Environment Institute, Ispra, Varese (Italy); Pareschi, M.T. [CNR, Pisa, (Italy). Centro di Studio per la Geologia Strutturale e Dinamica dell`Appennino

    1996-03-01

    A set of measurements from various sources was collected for the island of Vulcano (Aeolian archipelago, South Tyrrhenian sea) during summer 1994 with the scope of characterising the circulation pattern and the volcanic emission of the island. Ground meteorological stations were activated, wind profiles from pilot balloons were obtained, ground temperature measurements were produced. Furthermore, temperature and humidity data from satellite (Landsat TM) were also derived. A critical analysis of the data on the gathered information was performed to quantify the volcanic risk related to the toxic-volcanic-gas release in foreseeable paroxysmal events.

  10. Summer Oral Expression English course

    CERN Multimedia

    2012-01-01

    An English Oral Expression course will take place this summer from 20 August to 29 September.   Schedule: to be determined (2 sessions of 2 hours per week). Please note that this course is for learners who have a good knowledge of English (CERN level 7 upwards). If you are interested in following this course, please enroll through this link. Please be sure to indicate your planned absences in the comments field so we can schedule the course. If you need more information please send a message to English.training@cern.ch

  11. Summer Oral Expression English course

    CERN Document Server

    2012-01-01

    An English Oral Expression course will take place this summer at some time between 25 June and 28 September. The exact dates will be decided according to the preferences of the students.   Schedule: to be determined (2 sessions of 2 hours per week). Please note that this course is for learners who have a good knowledge of English (CERN level 7 upwards). If you are interested in following this course, please enroll through this link. Please be sure to indicate your planned absences in the comments field so we can schedule the course. If you need more information please send a message to English.training@cern.ch

  12. Summer Oral Expression English course

    CERN Document Server

    2013-01-01

    An English Oral Expression course will take place this summer at some time between August 19 and October 4.   Schedule: to be determined (2 sessions of 2 hours per week). Please note that this course is for learners who have a good knowledge of English (CERN level 7 upwards). If you are interested in following this course, please enroll through this link. Please be sure to indicate your planned absences in the comments field so we can schedule the course. If you need more information please send a message to English.training@cern.ch.

  13. North Carolina's Summer School Program for High-Risk Students: A Two-Year Follow-Up of Student Achievement.

    Science.gov (United States)

    Ward, Martha Szegda

    The long-term effectiveness of the North Carolina Basic Education Summer School Program (BEP) was examined. North Carolina has instituted a testing and summer remediation program for academically at-risk students at grades 3, 6, and 8. The BEP sample was obtained by a stratified random sampling of schools in North Carolina. Results were…

  14. Extending Asia Pacific bioinformatics into new realms in the "-omics" era.

    Science.gov (United States)

    Ranganathan, Shoba; Eisenhaber, Frank; Tong, Joo Chuan; Tan, Tin Wee

    2009-12-03

    The 2009 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation dating back to 1998, was organized as the 8th International Conference on Bioinformatics (InCoB), Sept. 7-11, 2009 at Biopolis, Singapore. Besides bringing together scientists from the field of bioinformatics in this region, InCoB has actively engaged clinicians and researchers from the area of systems biology, to facilitate greater synergy between these two groups. InCoB2009 followed on from a series of successful annual events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand), Busan (South Korea), New Delhi (India), Hong Kong and Taipei (Taiwan), with InCoB2010 scheduled to be held in Tokyo, Japan, Sept. 26-28, 2010. The Workshop on Education in Bioinformatics and Computational Biology (WEBCB) and symposia on Clinical Bioinformatics (CBAS), the Singapore Symposium on Computational Biology (SYMBIO) and training tutorials were scheduled prior to the scientific meeting, and provided ample opportunity for in-depth learning and special interest meetings for educators, clinicians and students. We provide a brief overview of the peer-reviewed bioinformatics manuscripts accepted for publication in this supplement, grouped into thematic areas. In order to facilitate scientific reproducibility and accountability, we have, for the first time, introduced minimum information criteria for our pubilcations, including compliance to a Minimum Information about a Bioinformatics Investigation (MIABi). As the regional research expertise in bioinformatics matures, we have delineated a minimum set of bioinformatics skills required for addressing the computational challenges of the "-omics" era.

  15. ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR.

    Science.gov (United States)

    Larcombe, L; Hendricusdottir, R; Attwood, T K; Bacall, F; Beard, N; Bellis, L J; Dunn, W B; Hancock, J M; Nenadic, A; Orengo, C; Overduin, B; Sansone, S-A; Thurston, M; Viant, M R; Winder, C L; Goble, C A; Ponting, C P; Rustici, G

    2017-01-01

    ELIXIR-UK is the UK node of ELIXIR, the European infrastructure for life science data. Since its foundation in 2014, ELIXIR-UK has played a leading role in training both within the UK and in the ELIXIR Training Platform, which coordinates and delivers training across all ELIXIR members. ELIXIR-UK contributes to the Training Platform's coordination and supports the development of training to address key skill gaps amongst UK scientists. As part of this work it acts as a conduit for nationally-important bioinformatics training resources to promote their activities to the ELIXIR community. ELIXIR-UK also leads ELIXIR's flagship Training Portal, TeSS, which collects information about a diverse range of training and makes it easily accessible to the community. ELIXIR-UK also works with others to provide key digital skills training, partnering with the Software Sustainability Institute to provide Software Carpentry training to the ELIXIR community and to establish the Data Carpentry initiative, and taking a lead role amongst national stakeholders to deliver the StaTS project - a coordinated effort to drive engagement with training in statistics.

  16. 1997 Summer Research Program (SRP), High School Apprenticeship Program (HSAP), Final Reports, Volume 12B, Armstrong Laboratory

    National Research Council Canada - National Science Library

    Moore, Gary

    1997-01-01

    The United States Air Force Summer Research Program (USAF-SRP) is designed to introduce university, college, and technical institute faculty members, graduate students, and high school students to Air Force research...

  17. Summer Research Fellowship Programme 2018

    Indian Academy of Sciences (India)

    Texas A&M), FNA, FNAE, FNASc. Date of birth: 20 September 1967. Specialization: Polymer, Supercritical Fluids, Catalysis Address: Department of Chemical Engineering, Indian Institute of Science, Bengaluru 560 012, Karnataka Contact:

  18. Summer Research Fellowship Programme 2018

    Indian Academy of Sciences (India)

    Date of birth: 25 June 1941. Specialization: Nuclear Magnetic Resonance Spectroscopy, NMR Techniques & its Applications to Biomolecules and Quantum Computing Address: Department of Physics, NMR Research Centre, Indian Institute of Science, Bengaluru 560 012, Karnataka Contact: Office: (080) 2293 2724

  19. Colonial Institutions

    DEFF Research Database (Denmark)

    McAtackney, Laura; Palmer, Russell

    2016-01-01

    and the USA which reveal that the study of colonial institutions should not be limited to the functional life of these institutions—or solely those that take the form of monumental architecture—but should include the long shadow of “imperial debris” (Stoler 2008) and immaterial institutions....

  20. Institutional upbringing

    DEFF Research Database (Denmark)

    Gulløv, Eva

    2008-01-01

    In the chapter, I discuss the role day care institutions play in the construction of the idea of proper childhood in Denmark. Drawing on findings from research on ethnic minority children in two Danish day care institutions, I begin with a discussion of how childcare institutions act as civilising...... agents, empowered with the legitimate right to define and control normality and proper ways of behaving oneself. I aim to show how institutions come to define the normal child and proper childhood in accordance with current efforts toward reinventing national culture, exemplified by legislation requiring...... current testing of Danish language fluency levels among pre-school minority children. Testing language skills marks and defines distinctions that reinforce images of deviance that, in turn, legitimize initiatives to enrol children, specifically minority children, in child care institutions....

  1. A web services choreography scenario for interoperating bioinformatics applications

    Directory of Open Access Journals (Sweden)

    Cheung David W

    2004-03-01

    Full Text Available Abstract Background Very often genome-wide data analysis requires the interoperation of multiple databases and analytic tools. A large number of genome databases and bioinformatics applications are available through the web, but it is difficult to automate interoperation because: 1 the platforms on which the applications run are heterogeneous, 2 their web interface is not machine-friendly, 3 they use a non-standard format for data input and output, 4 they do not exploit standards to define application interface and message exchange, and 5 existing protocols for remote messaging are often not firewall-friendly. To overcome these issues, web services have emerged as a standard XML-based model for message exchange between heterogeneous applications. Web services engines have been developed to manage the configuration and execution of a web services workflow. Results To demonstrate the benefit of using web services over traditional web interfaces, we compare the two implementations of HAPI, a gene expression analysis utility developed by the University of California San Diego (UCSD that allows visual characterization of groups or clusters of genes based on the biomedical literature. This utility takes a set of microarray spot IDs as input and outputs a hierarchy of MeSH Keywords that correlates to the input and is grouped by Medical Subject Heading (MeSH category. While the HTML output is easy for humans to visualize, it is difficult for computer applications to interpret semantically. To facilitate the capability of machine processing, we have created a workflow of three web services that replicates the HAPI functionality. These web services use document-style messages, which means that messages are encoded in an XML-based format. We compared three approaches to the implementation of an XML-based workflow: a hard coded Java application, Collaxa BPEL Server and Taverna Workbench. The Java program functions as a web services engine and interoperates

  2. The Summer Monsoon of 1987.

    Science.gov (United States)

    Krishnamurti, T. N.; Bedi, H. S.; Subramaniam, M.

    1989-04-01

    In this paper we have examined the evolution of a number of parameters we believe were important for our understanding of the drought over India during the summer of 1987. The list of parameters includes monthly means or anomalies of the following fields: sea surface temperatures, divergent circulations, outgoing longwave radiation, streamfunction of the lower and upper troposphere, and monthly precipitation (expressed as a percentage departure from a long-term mean). The El Niño related warm sea surface temperature anomaly and a weaker warm sea surface temperature anomaly over the equatorial Indian Ocean provide sustained convection, as reflected by the negative values of the outgoing longwave radiation. With the seasonal heating, a pronounced planetary-scale divergent circulation evolved with a center along the western Pacific Ocean. The monsoonal divergent circulation merged with that related to the El Niño, maintaining most of the heavy rainfall activity between the equatorial Pacific Ocean and east Asia. Persistent convective activity continued south of India during the entire monsoon season. Strong Hadley type overturnings with rising motions over these warm SST anomaly regions and descent roughly near 20° to 25°S was evident as early as April 1987. The subtropical high pressure areas near 20° to 25°S showed stronger than normal circulations. This was revealed by the presence of a counterclockwise streamfunction anomaly at 850 mb during April 1987. With the seasonal heating, this anomaly moved northwards and was located over the Arabian Sea and India. This countermonsoon circulation anomaly at the low levels was associated with a weaker than normal Somali jet and Arabian Sea circulation throughout this summer. The monsoon remained active along northeast India, Bangladesh, northern lndochina, and central China during the summer monsoon season. This was related to the eastward shift of the divergent circulation. An eastward shift of the upper tropospheric

  3. Bioinformatics programs are 31-fold over-represented among the highest impact scientific papers of the past two decades.

    Science.gov (United States)

    Wren, Jonathan D

    2016-09-01

    To analyze the relative proportion of bioinformatics papers and their non-bioinformatics counterparts in the top 20 most cited papers annually for the past two decades. When defining bioinformatics papers as encompassing both those that provide software for data analysis or methods underlying data analysis software, we find that over the past two decades, more than a third (34%) of the most cited papers in science were bioinformatics papers, which is approximately a 31-fold enrichment relative to the total number of bioinformatics papers published. More than half of the most cited papers during this span were bioinformatics papers. Yet, the average 5-year JIF of top 20 bioinformatics papers was 7.7, whereas the average JIF for top 20 non-bioinformatics papers was 25.8, significantly higher (P papers, bioinformatics journals tended to have higher Gini coefficients, suggesting that development of novel bioinformatics resources may be somewhat 'hit or miss'. That is, relative to other fields, bioinformatics produces some programs that are extremely widely adopted and cited, yet there are fewer of intermediate success. jdwren@gmail.com 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.

  4. Identification of key genes and molecular mechanisms associated with dedifferentiated liposarcoma based on bioinformatic methods

    Directory of Open Access Journals (Sweden)

    Yu H

    2017-06-01

    Full Text Available Hongliang Yu,1 Dong Pei,2 Longyun Chen,2 Xiaoxiang Zhou,2 Haiwen Zhu2 1Department of Radiation Oncology, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 2Department of Radiation Oncology, Yancheng Third People’s Hospital, Yancheng, Jiangsu, People’s Republic of China Background: Dedifferentiated liposarcoma (DDLPS is one of the most deadly types of soft tissue sarcoma. To date, there have been few studies dedicated to elucidating the molecular mechanisms behind the disease; therefore, the molecular mechanisms behind this malignancy remain largely unknown.Materials and methods: Microarray profiles of 46 DDLPS samples and nine normal fat controls were extracted from Gene Expression Omnibus (GEO. Quality control for these microarray profiles was performed before analysis. Hierarchical clustering and principal component analysis were used to distinguish the general differences in gene expression between DDLPS samples and the normal fat controls. Differentially expressed genes (DEGs were identified using the Limma package in R. Next, the enriched Gene Ontology (GO terms and Kyoto Encyclopedia of Genes and Genomes (KEGG pathways were obtained using the online tool DAVID (http://david.abcc.ncifcrf.gov/. A protein–protein interaction (PPI network was constructed using the STRING database and Cytoscape software. Furthermore, the hub genes within the PPI network were identified.Results: All 55 microarray profiles were confirmed to be of high quality. The gene expression pattern of DDLPS samples was significantly different from that of normal fat controls. In total, 700 DEGs were identified, and 83 enriched GO terms and three KEGG pathways were obtained. Specifically, within the DEGs of DDLPS samples, several pathways were identified as being significantly enriched, including the PPAR signaling pathway, cell cycle pathway, and pyruvate metabolism pathway

  5. Buying in to bioinformatics: an introduction to commercial sequence analysis software.

    Science.gov (United States)

    Smith, David Roy

    2015-07-01

    Advancements in high-throughput nucleotide sequencing techniques have brought with them state-of-the-art bioinformatics programs and software packages. Given the importance of molecular sequence data in contemporary life science research, these software suites are becoming an essential component of many labs and classrooms, and as such are frequently designed for non-computer specialists and marketed as one-stop bioinformatics toolkits. Although beautifully designed and powerful, user-friendly bioinformatics packages can be expensive and, as more arrive on the market each year, it can be difficult for researchers, teachers and students to choose the right software for their needs, especially if they do not have a bioinformatics background. This review highlights some of the currently available and most popular commercial bioinformatics packages, discussing their prices, usability, features and suitability for teaching. Although several commercial bioinformatics programs are arguably overpriced and overhyped, many are well designed, sophisticated and, in my opinion, worth the investment. If you are just beginning your foray into molecular sequence analysis or an experienced genomicist, I encourage you to explore proprietary software bundles. They have the potential to streamline your research, increase your productivity, energize your classroom and, if anything, add a bit of zest to the often dry detached world of bioinformatics. © The Author 2014. Published by Oxford University Press.

  6. ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis.

    Science.gov (United States)

    Römer, Michael; Eichner, Johannes; Dräger, Andreas; Wrzodek, Clemens; Wrzodek, Finja; Zell, Andreas

    2016-01-01

    Bioinformatics analysis has become an integral part of research in biology. However, installation and use of scientific software can be difficult and often requires technical expert knowledge. Reasons are dependencies on certain operating systems or required third-party libraries, missing graphical user interfaces and documentation, or nonstandard input and output formats. In order to make bioinformatics software easily accessible to researchers, we here present a web-based platform. The Center for Bioinformatics Tuebingen (ZBIT) Bioinformatics Toolbox provides web-based access to a collection of bioinformatics tools developed for systems biology, protein sequence annotation, and expression data analysis. Currently, the collection encompasses software for conversion and processing of community standards SBML and BioPAX, transcription factor analysis, and analysis of microarray data from transcriptomics and proteomics studies. All tools are hosted on a customized Galaxy instance and run on a dedicated computation cluster. Users only need a web browser and an active internet connection in order to benefit from this service. The web platform is designed to facilitate the usage of the bioinformatics tools for researchers without advanced technical background. Users can combine tools for complex analyses or use predefined, customizable workflows. All results are stored persistently and reproducible. For each tool, we provide documentation, tutorials, and example data to maximize usability. The ZBIT Bioinformatics Toolbox is freely available at https://webservices.cs.uni-tuebingen.de/.

  7. Second Multiflow Summer School on Turbulence

    Science.gov (United States)

    Jiménez, Javier

    2016-04-01

    Multiflow is a research program, funded by the European Research Council, whose goal is to improve our understanding of the multiscale dynamics of turbulence in fluids. Its second Summer School on Turbulence took place at the School of Aeronautics of the Technical University of Madrid from May 25 to June 26, 2015, with the goal of providing a meeting place for theoreticians, experimentalists and simulators, in which to develop and test new ideas on turbulence physics and structure. Around forty, mostly young, participants from twenty international groups met for five weeks of collaborative work, primarily using the computational data archived in the receiving institution but, in many cases, also contributing their own. Although the format included a few invited formal seminars and periodic plenary meetings, most of the work took place in small groups that, in many cases, changed their composition during the workshop. The papers in these proceedings reflect the results of the work of these groups which, in many cases, later continued in the form of new collaborations.

  8. CERN Summer Student Webfest: a cradle of creativity

    CERN Multimedia

    François Grey

    2015-01-01

    The CERN Summer Student Webfest has garnered a reputation for launching creative projects in fields as diverse as online games and cryptographic software, using the popular format of a hackfest. This year, the annual weekend event will celebrate its fourth year between 31 July and 2 August.   What unites Webfest projects is that they are conceived and developed by teams of CERN summer students, with some advice and guidance provided by mentors drawn from CERN and several partners. The event is organised by the Citizen Cyberscience Centre, a partnership between CERN, the UN Institute of Training and Research, and the University of Geneva. Event partners also include Mozilla Foundation, the EC Citizen Cyberlab project and THE Port hackathon. In 2014, one of the winning teams developed Particle Clicker, a spoof on a simple game called Cookie Clicker. Particle Clicker humorously illustrated the sociological aspects of the high-energy physics community through the rewards it provided players for clic...

  9. A Multidisciplinary Engineering Summer School in an Industrial Setting

    DEFF Research Database (Denmark)

    Larsen, Peter Gorm; Fernandes, Joao M.; Habel, Jacek

    2009-01-01

    Most university-level engineering studies produce technically skilled engineers. However, typically students face several difficulties when working in multidisciplinary teams when they initiate their industrial careers. In a globalised world, it becomes increasingly important that engineers...... are capable of collaborating across disciplinary boundaries and exhibit soft competencies, like communication, interpersonal and social skills, time planning, creativity, initiative, and reflection. To prepare a group of engineering and industrial design students to acquire those capabilities......, an international summer school that combined industrial design with different kinds of engineering disciplines was organised on the site of Bang & Olufsen (B&O) in Denmark. This multidisciplinary engineering summer school was attended by students from six European university-level teaching institutions...

  10. Arctic Sea Ice Charts from Danish Meteorological Institute, 1893 - 1956

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — From 1893 to 1956, the Danish Meteorological Institute (DMI) created charts of observed and inferred sea ice extent for each summer month. These charts are based on...

  11. High-throughput bioinformatics with the Cyrille2 pipeline system

    Directory of Open Access Journals (Sweden)

    de Groot Joost CW

    2008-02-01

    Full Text Available Abstract Background Modern omics research involves the application of high-throughput technologies that generate vast volumes of data. These data need to be pre-processed, analyzed and integrated with existing knowledge through the use of diverse sets of software tools, models and databases. The analyses are often interdependent and chained together to form complex workflows or pipelines. Given the volume of the data used and the multitude of computational resources available, specialized pipeline software is required to make high-throughput analysis of large-scale omics datasets feasible. Results We have developed a generic pipeline system called Cyrille2. The system is modular in design and consists of three functionally distinct parts: 1 a web based, graphical user interface (GUI that enables a pipeline operator to manage the system; 2 the Scheduler, which forms the functional core of the system and which tracks what data enters the system and determines what jobs must be scheduled for execution, and; 3 the Executor, which searches for scheduled jobs and executes these on a compute cluster. Conclusion The Cyrille2 system is an extensible, modular system, implementing the stated requirements. Cyrille2 enables easy creation and execution of high throughput, flexible bioinformatics pipelines.

  12. Progress and challenges in bioinformatics approaches for enhancer identification

    KAUST Repository

    Kleftogiannis, Dimitrios A.

    2017-02-03

    Enhancers are cis-acting DNA elements that play critical roles in distal regulation of gene expression. Identifying enhancers is an important step for understanding distinct gene expression programs that may reflect normal and pathogenic cellular conditions. Experimental identification of enhancers is constrained by the set of conditions used in the experiment. This requires multiple experiments to identify enhancers, as they can be active under specific cellular conditions but not in different cell types/tissues or cellular states. This has opened prospects for computational prediction methods that can be used for high-throughput identification of putative enhancers to complement experimental approaches. Potential functions and properties of predicted enhancers have been catalogued and summarized in several enhancer-oriented databases. Because the current methods for the computational prediction of enhancers produce significantly different enhancer predictions, it will be beneficial for the research community to have an overview of the strategies and solutions developed in this field. In this review, we focus on the identification and analysis of enhancers by bioinformatics approaches. First, we describe a general framework for computational identification of enhancers, present relevant data types and discuss possible computational solutions. Next, we cover over 30 existing computational enhancer identification methods that were developed since 2000. Our review highlights advantages, limitations and potentials, while suggesting pragmatic guidelines for development of more efficient computational enhancer prediction methods. Finally, we discuss challenges and open problems of this topic, which require further consideration.

  13. Bioinformatic approaches reveal metagenomic characterization of soil microbial community.

    Directory of Open Access Journals (Sweden)

    Zhuofei Xu

    Full Text Available As is well known, soil is a complex ecosystem harboring the most prokaryotic biodiversity on the Earth. In recent years, the advent of high-throughput sequencing techniques has greatly facilitated the progress of soil ecological studies. However, how to effectively understand the underlying biological features of large-scale sequencing data is a new challenge. In the present study, we used 33 publicly available metagenomes from diverse soil sites (i.e. grassland, forest soil, desert, Arctic soil, and mangrove sediment and integrated some state-of-the-art computational tools to explore the phylogenetic and functional characterizations of the microbial communities in soil. Microbial composition and metabolic potential in soils were comprehensively illustrated at the metagenomic level. A spectrum of metagenomic biomarkers containing 46 taxa and 33 metabolic modules were detected to be significantly differential that could be used as indicators to distinguish at least one of five soil communities. The co-occurrence associations between complex microbial compositions and functions were inferred by network-based approaches. Our results together with the established bioinformatic pipelines should provide a foundation for future research into the relation between soil biodiversity and ecosystem function.

  14. WeBIAS: a web server for publishing bioinformatics applications.

    Science.gov (United States)

    Daniluk, Paweł; Wilczyński, Bartek; Lesyng, Bogdan

    2015-11-02

    One of the requirements for a successful scientific tool is its availability. Developing a functional web service, however, is usually considered a mundane and ungratifying task, and quite often neglected. When publishing bioinformatic applications, such attitude puts additional burden on the reviewers who have to cope with poorly designed interfaces in order to assess quality of presented methods, as well as impairs actual usefulness to the scientific community at large. In this note we present WeBIAS-a simple, self-contained solution to make command-line programs accessible through web forms. It comprises a web portal capable of serving several applications and backend schedulers which carry out computations. The server handles user registration and authentication, stores queries and results, and provides a convenient administrator interface. WeBIAS is implemented in Python and available under GNU Affero General Public License. It has been developed and tested on GNU/Linux compatible platforms covering a vast majority of operational WWW servers. Since it is written in pure Python, it should be easy to deploy also on all other platforms supporting Python (e.g. Windows, Mac OS X). Documentation and source code, as well as a demonstration site are available at http://bioinfo.imdik.pan.pl/webias . WeBIAS has been designed specifically with ease of installation and deployment of services in mind. Setting up a simple application requires minimal effort, yet it is possible to create visually appealing, feature-rich interfaces for query submission and presentation of results.

  15. Bicycle: a bioinformatics pipeline to analyze bisulfite sequencing data.

    Science.gov (United States)

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

    2018-04-15

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

  16. Accurate Prediction of Coronary Artery Disease Using Bioinformatics Algorithms

    Directory of Open Access Journals (Sweden)

    Hajar Shafiee

    2016-06-01

    Full Text Available Background and Objectives: Cardiovascular disease is one of the main causes of death in developed and Third World countries. According to the statement of the World Health Organization, it is predicted that death due to heart disease will rise to 23 million by 2030. According to the latest statistics reported by Iran’s Minister of health, 3.39% of all deaths are attributed to cardiovascular diseases and 19.5% are related to myocardial infarction. The aim of this study was to predict coronary artery disease using data mining algorithms. Methods: In this study, various bioinformatics algorithms, such as decision trees, neural networks, support vector machines, clustering, etc., were used to predict coronary heart disease. The data used in this study was taken from several valid databases (including 14 data. Results: In this research, data mining techniques can be effectively used to diagnose different diseases, including coronary artery disease. Also, for the first time, a prediction system based on support vector machine with the best possible accuracy was introduced. Conclusion: The results showed that among the features, thallium scan variable is the most important feature in the diagnosis of heart disease. Designation of machine prediction models, such as support vector machine learning algorithm can differentiate between sick and healthy individuals with 100% accuracy.

  17. Exploiting graphics processing units for computational biology and bioinformatics.

    Science.gov (United States)

    Payne, Joshua L; Sinnott-Armstrong, Nicholas A; Moore, Jason H

    2010-09-01

    Advances in the video gaming industry have led to the production of low-cost, high-performance graphics processing units (GPUs) that possess more memory bandwidth and computational capability than central processing units (CPUs), the standard workhorses of scientific computing. With the recent release of generalpurpose GPUs and NVIDIA's GPU programming language, CUDA, graphics engines are being adopted widely in scientific computing applications, particularly in the fields of computational biology and bioinformatics. The goal of this article is to concisely present an introduction to GPU hardware and programming, aimed at the computational biologist or bioinformaticist. To this end, we discuss the primary differences between GPU and CPU architecture, introduce the basics of the CUDA programming language, and discuss important CUDA programming practices, such as the proper use of coalesced reads, data types, and memory hierarchies. We highlight each of these topics in the context of computing the all-pairs distance between instances in a dataset, a common procedure in numerous disciplines of scientific computing. We conclude with a runtime analysis of the GPU and CPU implementations of the all-pairs distance calculation. We show our final GPU implementation to outperform the CPU implementation by a factor of 1700.

  18. Graphics processing units in bioinformatics, computational biology and systems biology.

    Science.gov (United States)

    Nobile, Marco S; Cazzaniga, Paolo; Tangherloni, Andrea; Besozzi, Daniela

    2017-09-01

    Several studies in Bioinformatics, Computational Biology and Systems Biology rely on the definition of physico-chemical or mathematical models of biological systems at different scales and levels of complexity, ranging from the interaction of atoms in single molecules up to genome-wide interaction networks. Traditional computational methods and software tools developed in these research fields share a common trait: they can be computationally demanding on Central Processing Units (CPUs), therefore limiting their applicability in many circumstances. To overcome this issue, general-purpose Graphics Processing Units (GPUs) are gaining an increasing attention by the scientific community, as they can considerably reduce the running time required by standard CPU-based software, and allow more intensive investigations of biological systems. In this review, we present a collection of GPU tools recently developed to perform computational analyses in life science disciplines, emphasizing the advantages and the drawbacks in the use of these parallel architectures. The complete list of GPU-powered tools here reviewed is available at http://bit.ly/gputools. © The Author 2016. Published by Oxford University Press.

  19. Functional proteomics with new mass spectrometric and bioinformatics tools

    International Nuclear Information System (INIS)

    Kesners, P.W.A.

    2001-01-01

    A comprehensive range of mass spectrometric tools is required to investigate todays life science applications and a strong focus is on addressing the needs of functional proteomics. Application examples are given showing the streamlined process of protein identification from low femtomole amounts of digests. Sample preparation is achieved with a convertible robot for automated 2D gel picking, and MALDI target dispensing. MALDI-TOF or ESI-MS subsequent to enzymatic digestion. A choice of mass spectrometers including Q-q-TOF with multipass capability, MALDI-MS/MS with unsegmented PSD, Ion Trap and FT-MS are discussed for their respective strengths and applications. Bioinformatics software that allows both database work and novel peptide mass spectra interpretation is reviewed. The automated database searching uses either entire digest LC-MS n ESI Ion Trap data or MALDI MS and MS/MS spectra. It is shown how post translational modifications are interactively uncovered and de-novo sequencing of peptides is facilitated

  20. clubber: removing the bioinformatics bottleneck in big data analyses

    Science.gov (United States)

    Miller, Maximilian; Zhu, Chengsheng; Bromberg, Yana

    2018-01-01

    With the advent of modern day high-throughput technologies, the bottleneck in biological discovery has shifted from the cost of doing experiments to that of analyzing results. clubber is our automated cluster-load balancing system developed for optimizing these “big data” analyses. Its plug-and-play framework encourages re-use of existing solutions for bioinformatics problems. clubber’s goals are to reduce computation times and to facilitate use of cluster computing. The first goal is achieved by automating the balance of parallel submissions across available high performance computing (HPC) resources. Notably, the latter can be added on demand, including cloud-based resources, and/or featuring heterogeneous environments. The second goal of making HPCs user-friendly is facilitated by an interactive web interface and a RESTful API, allowing for job monitoring and result retrieval. We used clubber to speed up our pipeline for annotating molecular functionality of metagenomes. Here, we analyzed the Deepwater Horizon oil-spill study data to quantitatively show that the beach sands have not yet entirely recovered. Further, our analysis of the CAMI-challenge data revealed that microbiome taxonomic shifts do not necessarily correlate with functional shifts. These examples (21 metagenomes processed in 172 min) clearly illustrate the importance of clubber in the everyday computational biology environment. PMID:28609295

  1. Bioinformatics Analysis of MAPKKK Family Genes in Medicago truncatula

    Directory of Open Access Journals (Sweden)

    Wei Li

    2016-04-01

    Full Text Available Mitogen‐activated protein kinase kinase kinase (MAPKKK is a component of the MAPK cascade pathway that plays an important role in plant growth, development, and response to abiotic stress, the functions of which have been well characterized in several plant species, such as Arabidopsis, rice, and maize. In this study, we performed genome‐wide and systemic bioinformatics analysis of MAPKKK family genes in Medicago truncatula. In total, there were 73 MAPKKK family members identified by search of homologs, and they were classified into three subfamilies, MEKK, ZIK, and RAF. Based on the genomic duplication function, 72 MtMAPKKK genes were located throughout all chromosomes, but they cluster in different chromosomes. Using microarray data and high‐throughput sequencing‐data, we assessed their expression profiles in growth and development processes; these results provided evidence for exploring their important functions in developmental regulation, especially in the nodulation process. Furthermore, we investigated their expression in abiotic stresses by RNA‐seq, which confirmed their critical roles in signal transduction and regulation processes under stress. In summary, our genome‐wide, systemic characterization and expressional analysis of MtMAPKKK genes will provide insights that will be useful for characterizing the molecular functions of these genes in M. truncatula.

  2. Progress and challenges in bioinformatics approaches for enhancer identification

    KAUST Repository

    Kleftogiannis, Dimitrios A.; Kalnis, Panos; Bajic, Vladimir B.

    2017-01-01

    Enhancers are cis-acting DNA elements that play critical roles in distal regulation of gene expression. Identifying enhancers is an important step for understanding distinct gene expression programs that may reflect normal and pathogenic cellular conditions. Experimental identification of enhancers is constrained by the set of conditions used in the experiment. This requires multiple experiments to identify enhancers, as they can be active under specific cellular conditions but not in different cell types/tissues or cellular states. This has opened prospects for computational prediction methods that can be used for high-throughput identification of putative enhancers to complement experimental approaches. Potential functions and properties of predicted enhancers have been catalogued and summarized in several enhancer-oriented databases. Because the current methods for the computational prediction of enhancers produce significantly different enhancer predictions, it will be beneficial for the research community to have an overview of the strategies and solutions developed in this field. In this review, we focus on the identification and analysis of enhancers by bioinformatics approaches. First, we describe a general framework for computational identification of enhancers, present relevant data types and discuss possible computational solutions. Next, we cover over 30 existing computational enhancer identification methods that were developed since 2000. Our review highlights advantages, limitations and potentials, while suggesting pragmatic guidelines for development of more efficient computational enhancer prediction methods. Finally, we discuss challenges and open problems of this topic, which require further consideration.

  3. Analyzing gene expression profiles in dilated cardiomyopathy via bioinformatics methods.

    Science.gov (United States)

    Wang, Liming; Zhu, L; Luan, R; Wang, L; Fu, J; Wang, X; Sui, L

    2016-10-10

    Dilated cardiomyopathy (DCM) is characterized by ventricular dilatation, and it is a common cause of heart failure and cardiac transplantation. This study aimed to explore potential DCM-related genes and their underlying regulatory mechanism using methods of bioinformatics. The gene expression profiles of GSE3586 were downloaded from Gene Expression Omnibus database, including 15 normal samples and 13 DCM samples. The differentially expressed genes (DEGs) were identified between normal and DCM samples using Limma package in R language. Pathway enrichment analysis of DEGs was then performed. Meanwhile, the potential transcription factors (TFs) and microRNAs (miRNAs) of these DEGs were predicted based on their binding sequences. In addition, DEGs were mapped to the cMap database to find the potential small molecule drugs. A total of 4777 genes were identified as DEGs by comparing gene expression profiles between DCM and control samples. DEGs were significantly enriched in 26 pathways, such as lymphocyte TarBase pathway and androgen receptor signaling pathway. Furthermore, potential TFs (SP1, LEF1, and NFAT) were identified, as well as potential miRNAs (miR-9, miR-200 family, and miR-30 family). Additionally, small molecules like isoflupredone and trihexyphenidyl were found to be potential therapeutic drugs for DCM. The identified DEGs (PRSS12 and FOXG1), potential TFs, as well as potential miRNAs, might be involved in DCM.

  4. Analyzing gene expression profiles in dilated cardiomyopathy via bioinformatics methods

    Directory of Open Access Journals (Sweden)

    Liming Wang

    Full Text Available Dilated cardiomyopathy (DCM is characterized by ventricular dilatation, and it is a common cause of heart failure and cardiac transplantation. This study aimed to explore potential DCM-related genes and their underlying regulatory mechanism using methods of bioinformatics. The gene expression profiles of GSE3586 were downloaded from Gene Expression Omnibus database, including 15 normal samples and 13 DCM samples. The differentially expressed genes (DEGs were identified between normal and DCM samples using Limma package in R language. Pathway enrichment analysis of DEGs was then performed. Meanwhile, the potential transcription factors (TFs and microRNAs (miRNAs of these DEGs were predicted based on their binding sequences. In addition, DEGs were mapped to the cMap database to find the potential small molecule drugs. A total of 4777 genes were identified as DEGs by comparing gene expression profiles between DCM and control samples. DEGs were significantly enriched in 26 pathways, such as lymphocyte TarBase pathway and androgen receptor signaling pathway. Furthermore, potential TFs (SP1, LEF1, and NFAT were identified, as well as potential miRNAs (miR-9, miR-200 family, and miR-30 family. Additionally, small molecules like isoflupredone and trihexyphenidyl were found to be potential therapeutic drugs for DCM. The identified DEGs (PRSS12 and FOXG1, potential TFs, as well as potential miRNAs, might be involved in DCM.

  5. Learning structural bioinformatics and evolution with a snake puzzle

    Directory of Open Access Journals (Sweden)

    Gonzalo S. Nido

    2016-12-01

    Full Text Available We propose here a working unit for teaching basic concepts of structural bioinformatics and evolution through the example of a wooden snake puzzle, strikingly similar to toy models widely used in the literature of protein folding. In our experience, developed at a Master’s course at the Universidad Autónoma de Madrid (Spain, the concreteness of this example helps to overcome difficulties caused by the interdisciplinary nature of this field and its high level of abstraction, in particular for students coming from traditional disciplines. The puzzle will allow us discussing a simple algorithm for finding folded solutions, through which we will introduce the concept of the configuration space and the contact matrix representation. This is a central tool for comparing protein structures, for studying simple models of protein energetics, and even for a qualitative discussion of folding kinetics, through the concept of the Contact Order. It also allows a simple representation of misfolded conformations and their free energy. These concepts will motivate evolutionary questions, which we will address by simulating a structurally constrained model of protein evolution, again modelled on the snake puzzle. In this way, we can discuss the analogy between evolutionary concepts and statistical mechanics that facilitates the understanding of both concepts. The proposed examples and literature are accessible, and we provide supplementary material (see ‘Data Availability’ to reproduce the numerical experiments. We also suggest possible directions to expand the unit. We hope that this work will further stimulate the adoption of games in teaching practice.

  6. clubber: removing the bioinformatics bottleneck in big data analyses.

    Science.gov (United States)

    Miller, Maximilian; Zhu, Chengsheng; Bromberg, Yana

    2017-06-13

    With the advent of modern day high-throughput technologies, the bottleneck in biological discovery has shifted from the cost of doing experiments to that of analyzing results. clubber is our automated cluster-load balancing system developed for optimizing these "big data" analyses. Its plug-and-play framework encourages re-use of existing solutions for bioinformatics problems. clubber's goals are to reduce computation times and to facilitate use of cluster computing. The first goal is achieved by automating the balance of parallel submissions across available high performance computing (HPC) resources. Notably, the latter can be added on demand, including cloud-based resources, and/or featuring heterogeneous environments. The second goal of making HPCs user-friendly is facilitated by an interactive web interface and a RESTful API, allowing for job monitoring and result retrieval. We used clubber to speed up our pipeline for annotating molecular functionality of metagenomes. Here, we analyzed the Deepwater Horizon oil-spill study data to quantitatively show that the beach sands have not yet entirely recovered. Further, our analysis of the CAMI-challenge data revealed that microbiome taxonomic shifts do not necessarily correlate with functional shifts. These examples (21 metagenomes processed in 172 min) clearly illustrate the importance of clubber in the everyday computational biology environment.

  7. clubber: removing the bioinformatics bottleneck in big data analyses

    Directory of Open Access Journals (Sweden)

    Miller Maximilian

    2017-06-01

    Full Text Available With the advent of modern day high-throughput technologies, the bottleneck in biological discovery has shifted from the cost of doing experiments to that of analyzing results. clubber is our automated cluster-load balancing system developed for optimizing these “big data” analyses. Its plug-and-play framework encourages re-use of existing solutions for bioinformatics problems. clubber’s goals are to reduce computation times and to facilitate use of cluster computing. The first goal is achieved by automating the balance of parallel submissions across available high performance computing (HPC resources. Notably, the latter can be added on demand, including cloud-based resources, and/or featuring heterogeneous environments. The second goal of making HPCs user-friendly is facilitated by an interactive web interface and a RESTful API, allowing for job monitoring and result retrieval. We used clubber to speed up our pipeline for annotating molecular functionality of metagenomes. Here, we analyzed the Deepwater Horizon oil-spill study data to quantitatively show that the beach sands have not yet entirely recovered. Further, our analysis of the CAMI-challenge data revealed that microbiome taxonomic shifts do not necessarily correlate with functional shifts. These examples (21 metagenomes processed in 172 min clearly illustrate the importance of clubber in the everyday computational biology environment.

  8. E-MSD: an integrated data resource for bioinformatics.

    Science.gov (United States)

    Velankar, S; McNeil, P; Mittard-Runte, V; Suarez, A; Barrell, D; Apweiler, R; Henrick, K

    2005-01-01

    The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the worldwide Protein Data Bank (wwPDB) and to work towards the integration of various bioinformatics data resources. One of the major obstacles to the improved integration of structural databases such as MSD and sequence databases like UniProt is the absence of up to date and well-maintained mapping between corresponding entries. We have worked closely with the UniProt group at the EBI to clean up the taxonomy and sequence cross-reference information in the MSD and UniProt databases. This information is vital for the reliable integration of the sequence family databases such as Pfam and Interpro with the structure-oriented databases of SCOP and CATH. This information has been made available to the eFamily group (http://www.efamily.org.uk/) and now forms the basis of the regular interchange of information between the member databases (MSD, UniProt, Pfam, Interpro, SCOP and CATH). This exchange of annotation information has enriched the structural information in the MSD database with annotation from wider sequence-oriented resources. This work was carried out under the 'Structure Integration with Function, Taxonomy and Sequences (SIFTS)' initiative (http://www.ebi.ac.uk/msd-srv/docs/sifts) in the MSD group.

  9. Bioinformatic Prediction of WSSV-Host Protein-Protein Interaction

    Directory of Open Access Journals (Sweden)

    Zheng Sun

    2014-01-01

    Full Text Available WSSV is one of the most dangerous pathogens in shrimp aquaculture. However, the molecular mechanism of how WSSV interacts with shrimp is still not very clear. In the present study, bioinformatic approaches were used to predict interactions between proteins from WSSV and shrimp. The genome data of WSSV (NC_003225.1 and the constructed transcriptome data of F. chinensis were used to screen potentially interacting proteins by searching in protein interaction databases, including STRING, Reactome, and DIP. Forty-four pairs of proteins were suggested to have interactions between WSSV and the shrimp. Gene ontology analysis revealed that 6 pairs of these interacting proteins were classified into “extracellular region” or “receptor complex” GO-terms. KEGG pathway analysis showed that they were involved in the “ECM-receptor interaction pathway.” In the 6 pairs of interacting proteins, an envelope protein called “collagen-like protein” (WSSV-CLP encoded by an early virus gene “wsv001” in WSSV interacted with 6 deduced proteins from the shrimp, including three integrin alpha (ITGA, two integrin beta (ITGB, and one syndecan (SDC. Sequence analysis on WSSV-CLP, ITGA, ITGB, and SDC revealed that they possessed the sequence features for protein-protein interactions. This study might provide new insights into the interaction mechanisms between WSSV and shrimp.

  10. Institutional actorhood

    DEFF Research Database (Denmark)

    Madsen, Christian Uhrenholdt

    In this paper I describe the changing role of intra-organizational experts in the face of institutional complexity of their field. I do this through a qualitative investigation of the institutional and organizational roles of actors in Danish organizations who are responsible for the efforts...... to comply with the Danish work environment regulation. And by doing so I also describe how institutional complexity and organizational responses to this complexity are particular important for the changing modes of governance that characterizes contemporary welfare states....

  11. CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community.

    Science.gov (United States)

    Connor, Thomas R; Loman, Nicholas J; Thompson, Simon; Smith, Andy; Southgate, Joel; Poplawski, Radoslaw; Bull, Matthew J; Richardson, Emily; Ismail, Matthew; Thompson, Simon Elwood-; Kitchen, Christine; Guest, Martyn; Bakke, Marius; Sheppard, Samuel K; Pallen, Mark J

    2016-09-01

    The increasing availability and decreasing cost of high-throughput sequencing has transformed academic medical microbiology, delivering an explosion in available genomes while also driving advances in bioinformatics. However, many microbiologists are unable to exploit the resulting large genomics datasets because they do not have access to relevant computational resources and to an appropriate bioinformatics infrastructure. Here, we present the Cloud Infrastructure for Microbial Bioinformatics (CLIMB) facility, a shared computing infrastructure that has been designed from the ground up to provide an environment where microbiologists can share and reuse methods and data.

  12. New Link in Bioinformatics Services Value Chain: Position, Organization and Business Model

    Directory of Open Access Journals (Sweden)

    Mladen Čudanov

    2012-11-01

    Full Text Available This paper presents development in the bioinformatics services industry value chain, based on cloud computing paradigm. As genome sequencing costs per Megabase exponentially drop, industry needs to adopt. Paper has two parts: theoretical analysis and practical example of Seven Bridges Genomics Company. We are focused on explaining organizational, business and financial aspects of new business model in bioinformatics services, rather than technical side of the problem. In the light of that we present twofold business model fit for core bioinformatics research and Information and Communication Technologie (ICT support in the new environment, with higher level of capital utilization and better resistance to business risks.

  13. Summer Programming: What Do Children Say?

    Directory of Open Access Journals (Sweden)

    Nila Cobb

    2006-06-01

    Full Text Available Studies document that low-income children lose academic skills over the summer. Six years of reading achievement data collected by Energy Express, a nationally recognized summer reading and nutrition program in West Virginia, has established the efficacy of the intervention. The purpose of this study was to examine characteristics of a voluntary summer program that foster participation. Interview data indicates that children attend because they perceive the program as fun; large creative art (for example, full-body portraits, appliance box castles, wall murals seems particularly important. Energy Express gives children both the fun they want and the enrichment they need in the summer.

  14. Institutional Investors

    DEFF Research Database (Denmark)

    Birkmose, Hanne Søndergaard; Strand, Therese

    Research Question/Issue: Institutional investors are facing increased pressure and threats of legislation from the European Union to abandon passive ownership strategies. This study investigates the prerequisites for – and potential dissimilarities in the practice of, active ownership among...... institutional investors in two Scandinavian countries with diminutive legal and cultural distance in general. Research Findings/Insights: Using data on shareholder proposals from Danish and Swedish annual general meetings from 2006 throughout 2010, we find that institutional investors are approximately....../Policy Implications: Regulators should be aware of the impact by local governance mechanisms, and how shareholders react under different legal and practical prerequisites. The paper also highlights legal elements that differ between Denmark and Sweden, and which might affect institutional activism....

  15. Institutional Controls

    Data.gov (United States)

    U.S. Environmental Protection Agency — This dataset consists of institutional control data from multiple Superfund sites in U.S. EPA Region 8. These data were acquired from multiple sources at different...

  16. Institutional Assessment

    International Development Research Centre (IDRC) Digital Library (Canada)

    Many approaches can and have helped research institutions in the developing .... There are many good texts on project and program evaluation, not to ...... has challenged managers and students of organizational development for decades.

  17. STEM Summer Academy on the Navajo Reservation

    Science.gov (United States)

    Alexander, C. J.

    2012-12-01

    The US Rosetta Project is the NASA contribution to the International Rosetta Mission, an ESA cornerstone mission to comet Churyumov-Gerasimenko. While the project's outreach efforts span multi-media, and a variety of age and ethnic groups, a special emphasis has been made to find a way to provide meaningful outreach to the reservation communities. Because language preservation is an issue of urgent concern to the reservation communities, and because Rosetta, uniquely among NASA missions, has been named after the notion that keys to missing understanding of elements of the ancient past were found in the language on the original Rosetta stone, the US Rosetta Project has embarked upon outreach with a focus on STEM vocabulary in ancient US languages of the Navajo, Hopi, Ojibwe, and other tribal communities as the project expands. NASA image and science are used and described in the native language, alongside lay English and scientific English curriculum elements. Additionally, science (geology/chemistry/botany/physics) elements drawn from the reservation environment, including geomorphology, geochemistry, soil physics, are included and discussed in the native language as much as possible — with their analogs in other planetary environments (such as Mars). In this paper we will report on the most recent Summer Science Academy [2012], a four week summer course for middle school children, created in collaboration with teachers and administrators in the Chinle Unified School District. The concept of the Academy was initiated in 2011, and the first Academy was conducted shortly thereafter, in June 2011 with 14 children, 3 instructors, and a NASA teacher workshop. The community requested three topics: geology, astronomy, and botany. The 2012 Academy built on the curriculum already developed with more robust field trips, addressed to specific science topics, additional quantitative measurements and activities, with more written material for the cultural components from

  18. Pay-as-you-go data integration for bio-informatics

    NARCIS (Netherlands)

    Wanders, B.

    2012-01-01

    Scientific research in bio-informatics is often data-driven and supported by numerous biological databases. A biological database contains factual information collected from scientific experiments and computational analyses about areas including genomics, proteomics, metabolomics, microarray gene

  19. Fundamentals of bioinformatics and computational biology methods and exercises in matlab

    CERN Document Server

    Singh, Gautam B

    2015-01-01

    This book offers comprehensive coverage of all the core topics of bioinformatics, and includes practical examples completed using the MATLAB bioinformatics toolbox™. It is primarily intended as a textbook for engineering and computer science students attending advanced undergraduate and graduate courses in bioinformatics and computational biology. The book develops bioinformatics concepts from the ground up, starting with an introductory chapter on molecular biology and genetics. This chapter will enable physical science students to fully understand and appreciate the ultimate goals of applying the principles of information technology to challenges in biological data management, sequence analysis, and systems biology. The first part of the book also includes a survey of existing biological databases, tools that have become essential in today’s biotechnology research. The second part of the book covers methodologies for retrieving biological information, including fundamental algorithms for sequence compar...

  20. Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia.

    Science.gov (United States)

    Schneider, Maria Victoria; Griffin, Philippa C; Tyagi, Sonika; Flannery, Madison; Dayalan, Saravanan; Gladman, Simon; Watson-Haigh, Nathan; Bayer, Philipp E; Charleston, Michael; Cooke, Ira; Cook, Rob; Edwards, Richard J; Edwards, David; Gorse, Dominique; McConville, Malcolm; Powell, David; Wilkins, Marc R; Lonie, Andrew

    2017-06-30

    EMBL Australia Bioinformatics Resource (EMBL-ABR) is a developing national research infrastructure, providing bioinformatics resources and support to life science and biomedical researchers in Australia. EMBL-ABR comprises 10 geographically distributed national nodes with one coordinating hub, with current funding provided through Bioplatforms Australia and the University of Melbourne for its initial 2-year development phase. The EMBL-ABR mission is to: (1) increase Australia's capacity in bioinformatics and data sciences; (2) contribute to the development of training in bioinformatics skills; (3) showcase Australian data sets at an international level and (4) enable engagement in international programs. The activities of EMBL-ABR are focussed in six key areas, aligning with comparable international initiatives such as ELIXIR, CyVerse and NIH Commons. These key areas-Tools, Data, Standards, Platforms, Compute and Training-are described in this article. © The Author 2017. Published by Oxford University Press.