WorldWideScience

Sample records for bioinformatics summer institutes

  1. Bioengineering and Bioinformatics Summer Institutes: Meeting Modern Challenges in Undergraduate Summer Research

    Science.gov (United States)

    Butler, Peter J.; Dong, Cheng; Snyder, Alan J.; Jones, A. Daniel; Sheets, Erin D.

    2008-01-01

    Summer undergraduate research programs in science and engineering facilitate research progress for faculty and provide a close-ended research experience for students, which can prepare them for careers in industry, medicine, and academia. However, ensuring these outcomes is a challenge when the students arrive ill-prepared for substantive research…

  2. 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…

  3. Summer Youth Forestry Institute

    Science.gov (United States)

    Roesch, Gabrielle E.; Neuffer, Tamara; Zobrist, Kevin

    2013-01-01

    The Summer Youth Forestry Institute (SYFI) was developed to inspire youth through experiential learning opportunities and early work experience in the field of natural resources. Declining enrollments in forestry and other natural resource careers has made it necessary to actively engage youth and provide them with exposure to careers in these…

  4. The UCI Summer Science Institute.

    Science.gov (United States)

    Taagepera, M.; And Others

    1987-01-01

    Describes a summer institute for elementary secondary science teachers held at the University of California, Irvine, which is designed to update and refine the scientific knowledge of the teachers and to build a scientific foundation for crossover teachers who are teaching without an adequate science background. (TW)

  5. GLEANINGS FROM A SUMMER INSTITUTE.

    Science.gov (United States)

    Twin City Inst. for Talented Youth, St. Paul, Minn.

    IN THIS REPORT TO THE ENGLISH TEACHING PROFESSION, THE TWIN CITY INSTITUTE STAFF DESCRIBES ITS CURRICULUM EXPERIMENTATION WITH ACADEMICALLY TALENTED HIGH SCHOOL STUDENTS DURING THE SUMMER OF 1967. THE FOLLOWING COURSES ARE BRIEFLY DISCUSSED IN THEIR REPORTS--(1) COMPOSITION AND RHETORIC, IN WHICH THEORY AND PRACTICE WERE BALANCED, AND EXPOSITION…

  6. Quartz Mountain/Oklahoma Summer Arts Institute.

    Science.gov (United States)

    Frates, Mary Y.; Madeja, Stanley S.

    1982-01-01

    Describes the Quartz Mountain Oklahoma Summer Arts Institute program. It is designed to nurture artistic talent and to provide intensive arts experiences in music, dance, theater, and the visual arts for talented students aged 14-18. (AM)

  7. 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)

  8. WU-Blast2 server at the European Bioinformatics Institute

    Science.gov (United States)

    Lopez, Rodrigo; Silventoinen, Ville; Robinson, Stephen; Kibria, Asif; Gish, Warren

    2003-01-01

    Since 1995, the WU-BLAST programs (http://blast.wustl.edu) have provided a fast, flexible and reliable method for similarity searching of biological sequence databases. The software is in use at many locales and web sites. The European Bioinformatics Institute's WU-Blast2 (http://www.ebi.ac.uk/blast2/) server has been providing free access to these search services since 1997 and today supports many features that both enhance the usability and expand on the scope of the software. PMID:12824421

  9. 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...

  10. The USDA Food and Nutrition Summer Institute

    Science.gov (United States)

    The USDA Food and Nutrition Summer Institute was sponsored by the Beltsville Human Nutrition Research Center in partnership with several USDA and non-USDA agencies between 1999 and 2007. Partners included the USDA Food and Nutrition Service, USDA Cooperative State Research and Extension Service, US...

  11. 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

  12. Bioinformatics training: selecting an appropriate learning content management system--an example from the European Bioinformatics Institute.

    Science.gov (United States)

    Wright, Victoria Ann; Vaughan, Brendan W; Laurent, Thomas; Lopez, Rodrigo; Brooksbank, Cath; Schneider, Maria Victoria

    2010-11-01

    Today's molecular life scientists are well educated in the emerging experimental tools of their trade, but when it comes to training on the myriad of resources and tools for dealing with biological data, a less ideal situation emerges. Often bioinformatics users receive no formal training on how to make the most of the bioinformatics resources and tools available in the public domain. The European Bioinformatics Institute, which is part of the European Molecular Biology Laboratory (EMBL-EBI), holds the world's most comprehensive collection of molecular data, and training the research community to exploit this information is embedded in the EBI's mission. We have evaluated eLearning, in parallel with face-to-face courses, as a means of training users of our data resources and tools. We anticipate that eLearning will become an increasingly important vehicle for delivering training to our growing user base, so we have undertaken an extensive review of Learning Content Management Systems (LCMSs). Here, we describe the process that we used, which considered the requirements of trainees, trainers and systems administrators, as well as taking into account our organizational values and needs. This review describes the literature survey, user discussions and scripted platform testing that we performed to narrow down our choice of platform from 36 to a single platform. We hope that it will serve as guidance for others who are seeking to incorporate eLearning into their bioinformatics training programmes.

  13. 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).

  14. 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.

  15. Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support.

    Science.gov (United States)

    Stockinger, Heinz; Altenhoff, Adrian M; Arnold, Konstantin; Bairoch, Amos; Bastian, Frederic; Bergmann, Sven; Bougueleret, Lydie; Bucher, Philipp; Delorenzi, Mauro; Lane, Lydie; Le Mercier, Philippe; Lisacek, Frédérique; Michielin, Olivier; Palagi, Patricia M; Rougemont, Jacques; Schwede, Torsten; von Mering, Christian; van Nimwegen, Erik; Walther, Daniel; Xenarios, Ioannis; Zavolan, Mihaela; Zdobnov, Evgeny M; Zoete, Vincent; Appel, Ron D

    2014-07-01

    The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) was created in 1998 as an institution to foster excellence in bioinformatics. It is renowned worldwide for its databases and software tools, such as UniProtKB/Swiss-Prot, PROSITE, SWISS-MODEL, STRING, etc, that are all accessible on ExPASy.org, SIB's Bioinformatics Resource Portal. This article provides an overview of the scientific and training resources SIB has consistently been offering to the life science community for more than 15 years. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. 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

  17. 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…

  18. 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.

  19. FOREWORD: Corfu Summer Institute on Elementary Particle Physics (CORFU2005)

    Science.gov (United States)

    Anagnostopoulos, Konstantinos; Antoniadis, Ignatios; Fanourakis, George; Kehagias, Alexandros; Savoy-Navarro, Aurore; Wess, Julius; Zoupanos, George

    2006-12-01

    These are the Proceedings of the Corfu Summer Institute on Elementary Particle Physics (CORFU2005) (http://corfu2005.physics.uoi.gr), which took place in Corfu, Greece from 4 - 26 September 2005. The Corfu Summer Institute has a very long, interesting and successful history, some elements of which can be found in http://www.corfu-summer-institute.gr. In short, the Corfu Meeting started as a Summer School on Elementary Particle Physics (EPP) mostly for Greek graduate students in 1982 and has developed into a leading international Summer Institute in the field of EPP, both experimental and theoretical, providing in addition a very rich outreach programme to teachers and school students. The CORFU2005 Summer Institute on EPP, although based on the general format that has been developed and established in the Corfu Meetings during previous years, is characterized by the fact that it was a full realization of a new idea, which started experimentally in the previous two Corfu Meetings. The successful new ingredient was that three European Marie Curie Research Training Networks decided to hold their Workshops in Corfu during September 2005 and they managed to coordinate the educational part of their meetings to a huge Summer School called `The 8th Hellenic School on Elementary Particle Physics' (4 - 11 September). The European Networks which joined forces to materialize this project and the corresponding dates of their own Workshops are: The Third Generation as a Probe for New Physics: Experimental and Technological Approach (4 - 11 September) The Quest for Unification Theory Confronts Experiment (11 - 18 September) Constituents Fundamental Forces and Symmetries of the Universe (20 - 26 September) To these Workshops has been added a Satellite one called `Noncommutative Geometry in Field and String Theory', and some extra speakers have been invited to complement the full programme of CORFU2005, some of whom have integrated into the Workshop's programme. The result was

  20. 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.

  1. Summer Institute for Mathematics and Science teachers (SIMS). Final report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1994-07-01

    The Summer Institute for Mathematics and Science Teachers (SIMS) was to provide training for science and mathematics educators in strategies and techniques to use for educating and motivating historically under-represented populations. The Institute featured 40 hours of training over five days, July 13-17, 1993 plus half-day follow-up training November 13, 1993 and April 30, 1994. The objective of the training was to include sensitization to cultural and gender issues, and to instruct participants in the utilization of a variety of techniques and activities for encouraging historically under-represented groups to take more advanced science and mathematics courses.

  2. 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

  3. 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...

  4. 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 ...

  5. 77 FR 38840 - Proposed Collection; Comment Request; National Institute of Nursing Research (NINR) Summer...

    Science.gov (United States)

    2012-06-29

    ... Request; National Institute of Nursing Research (NINR) Summer Genetics Institute Alumni Survey SUMMARY: In.../National Institute of Nursing Research (NINR) Summer Genetics Institute Alumni Survey. Type of Information... opportunity for public comment on proposed data collection projects, the National Institute of Nursing...

  6. 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.

  7. 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)

  8. 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...

  9. Evaluation of the General Electric Foundation Summer Institutes on Career Education and Guidance.

    Science.gov (United States)

    Gray, Kenney E.; Pierson, Terrence K.

    An evaluation was conducted to determine the effects of the General Electric Foundation Summer Institutes on Career Education and Guidance over a one to two year period in participating school districts and communities. The study evaluated the team-oriented institutes held in 1976 and 1977 at the University of South Carolina and Indiana…

  10. 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.)

  11. A Profile of the Characteristics, Needs and Counseling Preferences of Talent Search Summer Institute Participants.

    Science.gov (United States)

    Strop, Jean M.; Hultgren, Holly M.

    The Rocky Mountain Talent Search 1984 Summer Institute participants, consisting of 12 through 15-year-old, highly able, high achieving students, are described in this study. The Harter Perceived Competence Scale for Children was used to measure feelings in the areas of cognitive, social, and physical competence and general self-esteem. An…

  12. Work Papers of the Summer Institute of Linguistics, University of North Dakota Session, Volume 30, 1986.

    Science.gov (United States)

    Derbyshire, Desmond C., Ed.

    Working papers resulting from the 1986 University of North Dakota Summer Institute of Linguistics include: "Orthographic Reform in Kope" (John M. Clifton); "Ternarity and Obligatory Branching in Piraha" (Daniel Everett); "Reduplication in Majang" (Pete Unseth); "Indirect Objects and Incorporation in Mazatec"…

  13. Summer Institute at Indiana U. Uses Immersion to Teach Hard-to-Learn East Asian Languages.

    Science.gov (United States)

    Oberlander, Susan

    1989-01-01

    As East Asian countries continue to develop into major powers in the economic world, students come to Indiana University's East Asian Summer Language Institute to improve their chances for careers in those countries in international law, teaching, and business. Advice on proper etiquette is also included. (MLW)

  14. 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,"…

  15. 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.

  16. Contemporary Art and the Role of Interpretation: Reflections from Tate Modern's Summer Institute for Teachers

    Science.gov (United States)

    Charman, Helen; Ross, Michaela

    2006-01-01

    Recent research indicates that the taught curriculum in art and design secondary school education pays scant attention to meaning-making in visual art. This article explores possibilities for teaching interpretation through a report on an action-research project based on Tate Modern's Summer Institute for Teachers. In doing so it argues for the…

  17. 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.

  18. 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.

  19. EVALUATIONS OF SUMMER 1965 NDEA INSTITUTES, A REPORT EVALUATING NDEA INSTITUTES FOR ADVANCED STUDY FOR EDUCATIONAL MEDIA SPECIALISTS AND SCHOOL LIBRARY PERSONNEL.

    Science.gov (United States)

    BROWN, JAMES W.

    APPROXIMATELY 500 NATIONAL DEFENSE EDUCATION ACT INSTITUTES FOR ELEMENTARY AND SECONDARY SCHOOL TEACHERS WERE EVALUATED DURING THE SUMMER OF 1965. THE EDUCATION MEDIA INSTITUTE EVALUATION (EMIE) PROJECT EVALUATED (1) EDUCATIONAL MEDIA SPECIALIST INSTITUTES, (2) SCHOOL LIBRARIANSHIP INSTITUTES THAT EMPHASIZED THE INSTRUCTIONAL MATERIALS CENTER…

  20. 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.

  1. 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.

  2. 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

  3. 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)

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. Aptamer Bioinformatics

    Directory of Open Access Journals (Sweden)

    Andrew B. Kinghorn

    2017-11-01

    Full Text Available Aptamers are short nucleic acid sequences capable of specific, high-affinity molecular binding. They are isolated via SELEX (Systematic Evolution of Ligands by Exponential Enrichment, an evolutionary process that involves iterative rounds of selection and amplification before sequencing and aptamer characterization. As aptamers are genetic in nature, bioinformatic approaches have been used to improve both aptamers and their selection. This review will discuss the advancements made in several enclaves of aptamer bioinformatics, including simulation of aptamer selection, fragment-based aptamer design, patterning of libraries, identification of lead aptamers from high-throughput sequencing (HTS data and in silico aptamer optimization.

  13. 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.

  14. A Novel Cross-Disciplinary Multi-Institute Approach to Translational Cancer Research: Lessons Learned from Pennsylvania Cancer Alliance Bioinformatics Consortium (PCABC

    Directory of Open Access Journals (Sweden)

    Ashokkumar A. Patel

    2007-01-01

    Full Text Available Background: The Pennsylvania Cancer Alliance Bioinformatics Consortium (PCABC, http://www.pcabc.upmc.edu is one of the first major project-based initiatives stemming from the Pennsylvania Cancer Alliance that was funded for four years by the Department of Health of the Commonwealth of Pennsylvania. The objective of this was to initiate a prototype biorepository and bioinformatics infrastructure with a robust data warehouse by developing a statewide data model (1 for bioinformatics and a repository of serum and tissue samples; (2 a data model for biomarker data storage; and (3 a public access website for disseminating research results and bioinformatics tools. The members of the Consortium cooperate closely, exploring the opportunity for sharing clinical, genomic and other bioinformatics data on patient samples in oncology, for the purpose of developing collaborative research programs across cancer research institutions in Pennsylvania. The Consortium’s intention was to establish a virtual repository of many clinical specimens residing in various centers across the state, in order to make them available for research. One of our primary goals was to facilitate the identification of cancer specific biomarkers and encourage collaborative research efforts among the participating centers.Methods: The PCABC has developed unique partnerships so that every region of the state can effectively contribute and participate. It includes over 80 individuals from 14 organizations, and plans to expand to partners outside the State. This has created a network of researchers, clinicians, bioinformaticians, cancer registrars, program directors, and executives from academic and community health systems, as well as external corporate partners - all working together to accomplish a common mission. The various sub-committees have developed a common IRB protocol template, common data elements for standardizing data collections for three organ sites, intellectual

  15. 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

  16. Work Papers of the Summer Institute of Linguistics, University of North Dakota Session, (Grand Forks, North Dakota 1985). Volume 29.

    Science.gov (United States)

    Derbyshire, Desmond C., Ed.

    Preliminary versions of the papers from the 1985 Summer Institute of Linguistics presented at the University of North Dakota session include: "Referential Distance and Discourse Structure in Yagua" (Thomas E. Payne); "A Note on Ergativity, S', and S'' in Karitiana" (Daniel Everett); "Some Aspects of Zapotecan Clausal…

  17. Teaching dairy production medicine to entry-level veterinarians: the summer dairy institute model.

    Science.gov (United States)

    Nydam, Charles W; Nydam, Daryl V; Guard, Charles L; Gilbert, Robert O

    2009-01-01

    Food supply veterinarians who intend to enter dairy cattle practice or other related career activities are in need of up-graded skills to better serve the dairy industry as it continues to evolve. The time available for students to increase their abilities within the conventional professional curriculum is scarce, especially as those with food-supply interests are a minority of students competing for time and resources. The dairy industry has need of skilled veterinarians who are not only well versed in their traditional capabilities, but who also have an understanding of the complete picture of that industry as a "farm-to-fork" experience. Society at large also stands to benefit from the presence of skilled dairy veterinarians contributing to the production of safe, affordable dairy foodstuffs in a manner deemed sustainable and humane. Veterinarians in practice can and do acquire the necessary skills to make themselves relevant to their clients and consumers; however, better preparation of entry-level veterinarians could increase their value to their employers, clients, themselves, and society in a more timely manner. Cornell University's College of Veterinary Medicine developed the Summer Dairy Institute to provide an avenue for advancing the skills of new veterinarians as a means to address the current and future needs of the dairy industry. This article describes the need for, concept of, and experience with that program.

  18. 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

  19. EVALUATIONS OF SUMMER 1966 NDEA INSTITUTES FOR EDUCATIONAL MEDIA SPECIALISTS AND SCHOOL LIBRARY PERSONNEL.

    Science.gov (United States)

    BROWN, DONALD J.; BROWN, JAMES W.

    THE PURPOSE OF THIS EVALUATION WAS TO GATHER DATA FROM 35 EDUCATIONAL MEDIA SPECIALIST INSTITUTES ON (1) PERSONAL AND PROFESSIONAL CHARACTERISTICS OF INSTITUTE PARTICIPANTS, (2) CHARACTERISTICS OF THE INSTITUTES THEMSELVES, (3) THE EFFECTIVENESS OF INSTITUTE PROGRAMS, (4) THE EFFECTIVENESS OF INSTITUTE EXPERIENCES ON PARTICIPANT INTERESTS AND…

  20. 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

  1. 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

  2. 76 FR 6172 - Bureau of Educational and Cultural Affairs (ECA) Request for Grant Proposals: Summer Institutes...

    Science.gov (United States)

    2011-02-03

    ... focus on topics such as leadership, teambuilding, collective problem-solving skills, effective communication, and management skills for diverse organizational settings. Institutes should include a community... United States, an important objective of the Institutes is to develop the participants' leadership skills...

  3. 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.

  4. The Aspergillus Mine - publishing bioinformatics

    DEFF Research Database (Denmark)

    Vesth, Tammi Camilla; Rasmussen, Jane Lind Nybo; Theobald, Sebastian

    with the Joint Genome Institute. The Aspergillus Mine is not intended as a genomic data sharing service but instead focuses on creating an environment where the results of bioinformatic analysis is made available for inspection. The data and code is public upon request and figures can be obtained directly from...

  5. 75 FR 14565 - NIST Summer Institute for Middle School Science Teachers; Availability of Funds

    Science.gov (United States)

    2010-03-26

    ... human embryonic stem cells in research. On July 30, 2009, President Obama issued a memorandum directing that agencies that support and conduct stem cell research adopt the ``National Institutes of Health Guidelines for Human Stem Cell Research'' (NIH Guidelines), which became effective on July 7, 2009, ``to the...

  6. 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.

  7. 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…

  8. 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.

  9. 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

  10. 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

  11. 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

    2014-01-01

    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. PMID:24763310

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. Bioinformatics in the information age

    Energy Technology Data Exchange (ETDEWEB)

    Spengler, Sylvia J.

    2000-02-01

    There is a well-known story about the blind man examining the elephant: the part of the elephant examined determines his perception of the whole beast. Perhaps bioinformatics--the shotgun marriage between biology and mathematics, computer science, and engineering--is like an elephant that occupies a large chair in the scientific living room. Given the demand for and shortage of researchers with the computer skills to handle large volumes of biological data, where exactly does the bioinformatics elephant sit? There are probably many biologists who feel that a major product of this bioinformatics elephant is large piles of waste material. If you have tried to plow through Web sites and software packages in search of a specific tool for analyzing and collating large amounts of research data, you may well feel the same way. But there has been progress with major initiatives to develop more computing power, educate biologists about computers, increase funding, and set standards. For our purposes, bioinformatics is not simply a biologically inclined rehash of information theory (1) nor is it a hodgepodge of computer science techniques for building, updating, and accessing biological data. Rather bioinformatics incorporates both of these capabilities into a broad interdisciplinary science that involves both conceptual and practical tools for the understanding, generation, processing, and propagation of biological information. As such, bioinformatics is the sine qua non of 21st-century biology. Analyzing gene expression using cDNA microarrays immobilized on slides or other solid supports (gene chips) is set to revolutionize biology and medicine and, in so doing, generate vast quantities of data that have to be accurately interpreted (Fig. 1). As discussed at a meeting a few months ago (Microarray Algorithms and Statistical Analysis: Methods and Standards; Tahoe City, California; 9-12 November 1999), experiments with cDNA arrays must be subjected to quality control

  19. 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.

  20. 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.

  1. 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.)

  2. Intensive Training Academy During Winter Breaks (Winternships) at a Two-Year Hispanic Serving Institution to Prepare STEM Students for Summer Internships

    Science.gov (United States)

    Farmer, J. C.; Sim, A. M.; Usher, T. D.

    2014-12-01

    College of the Desert, in partnership with California State University San Bernardino, both Hispanic serving institutions, with the support of a 3-year grant through the NASA Curriculum Improvements Partnership Award for the Integration of Research (CIPAIR) has provided training for community college students, especially those from underrepresented groups, to better prepare them for summer internships opportunities at four-year schools and national laboratories. The Winternships provided an enhanced alternative learning environment for students pursuing degrees in the STEM fields through faculty and peer mentoring in guided undergraduate research activities. All activities associated with undergraduate research were covered including literature searches, hands-on laboratory and field research, collection and analysis of data, culminating in oral and written presentations at College of the Desert and regional student conferences. In addition, students received assistance in searching for summer internships in their area of interest, completing applications, and guidance on follow-up communication with the programs to which they applied. During the funding period, 44 students participated in the Winternship activity in which all submitted a minimum of 3 applications for summer internship opportunities. Results presented will include student success at receiving summer internships, examples of projects completed during the summer and winter activities, and impact on student success. Adaption of this program to other community colleges and into a sophomore level research experience course will be described. This activity has now been funded through the NSF Centers of Research Excellence in Science and Technology (CREST) Program for an additional five years in a partnership with California State University at San Bernardino.

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

    Science.gov (United States)

    Schneider, Maria V; Walter, Peter; Blatter, Marie-Claude; Watson, James; Brazas, Michelle D; Rother, Kristian; Budd, Aidan; Via, Allegra; van Gelder, Celia W G; Jacob, Joachim; Fernandes, Pedro; Nyrönen, Tommi H; De Las Rivas, Javier; Blicher, Thomas; Jimenez, Rafael C; Loveland, Jane; McDowall, Jennifer; Jones, Phil; Vaughan, Brendan W; Lopez, Rodrigo; Attwood, Teresa K; Brooksbank, Catherine

    2012-05-01

    Funding bodies are increasingly recognizing the need to provide graduates and researchers with access to short intensive courses in a variety of disciplines, in order both to improve the general skills base and to provide solid foundations on which researchers may build their careers. In response to the development of 'high-throughput biology', the need for training in the field of bioinformatics, in particular, is seeing a resurgence: it has been defined as a key priority by many Institutions and research programmes and is now an important component of many grant proposals. Nevertheless, when it comes to planning and preparing to meet such training needs, tension arises between the reward structures that predominate in the scientific community which compel individuals to publish or perish, and the time that must be devoted to the design, delivery and maintenance of high-quality training materials. Conversely, there is much relevant teaching material and training expertise available worldwide that, were it properly organized, could be exploited by anyone who needs to provide training or needs to set up a new course. To do this, however, the materials would have to be centralized in a database 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 it, respectively, to similar initiatives and collections.

  4. Teaching bioinformatics to engineers.

    Science.gov (United States)

    Mihalas, George I; Tudor, Anca; Paralescu, Sorin; Andor, Minodora; Stoicu-Tivadar, Lacramioara

    2014-01-01

    The paper refers to our methodology and experience in establishing the content of the course in bioinformatics introduced to the school of "Information Systems in Healthcare" (SIIS), master level. The syllabi of both lectures and laboratory works are presented and discussed.

  5. 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

    Funding bodies are increasingly recognizing the need to provide graduates and researchers with access to short intensive courses in a variety of disciplines, in order both to improve the general skills base and to provide solid foundations on which researchers may build their careers. In response...... to the development of ‘high-throughput biology’, the need for training in the field of bioinformatics, in particular, is seeing a resurgence: it has been defined as a key priority by many Institutions and research programmes and is now an important component of many grant proposals. Nevertheless, when it comes...... to planning and preparing to meet such training needs, tension arises between the reward structures that predominate in the scientific community which compel individuals to publish or perish, and the time that must be devoted to the design, delivery and maintenance of high-quality training materials...

  6. 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.)

  7. 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…

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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…

  13. Environmental Studies in the Boreal Forest Zone: Summer IPY Institute at Central Boreal Forest Reserve, Fedorovskoe, Tver area, Russia (14-28 August, 2007)

    Science.gov (United States)

    Sparrow, E. B.; Kurbatova, Y.; Groisman, P.; Alexeev, V.

    2007-12-01

    The Summer Institute was organized by the International Arctic Research Center (IARC) at the University of Alaska Fairbanks, in collaboration with the A.N. Severtsov Institute for Ecology and Evolution of the Russian Academy of Sciences in Moscow, Russia, and the Central Forest State Nature Biosphere Reserve in Fedorovskoe, Russia. The Institute was arranged as a part of the education/outreach activities of the International Polar Year (IPY) at the University of Alaska and the Northern Eurasia Earth Science Partnership Initiative (NEESPI) and was held in Russia. The Institute provided a unique opportunity for participants to learn about the climate and environment of Northern Eurasia from leading scientists and educators, in a wide spectrum of polar and Earth system science disciplines from meteorology, biology, chemistry, and earth system modeling. Additionally, the Institute attendees observed and participated in the biospheric research activities under the guidance of experienced scientists. During a two-week-interval, the School attendees heard 40 lectures, attended several field trips and participated in three brainstorming Round Table Workshop Sessions devoted to perspectives of the boreal forest zone research and major unresolved problems that it faces. Thirty professors and experts in different areas of climate and biosphere research from Russia, the United States, Germany, Finland, and Japan, shared their expertise in lectures and in round table discussions with the Institute participants. Among the Institute participants there were 31 graduate students/early career scientists from six countries (China, Russia, Estonia, Finland, UK, and the United States) and eight K-12 teachers from Russia. The two groups joined together for several workshop sessions and for the field work components of the Institute. The field work was focused on land-atmosphere interactions and wetland studies in the boreal forest zone. Several field trips in and outside the Forest

  14. 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...

  15. Flow cytometry bioinformatics.

    Directory of Open Access Journals (Sweden)

    Kieran O'Neill

    Full Text Available Flow cytometry bioinformatics is the application of bioinformatics to flow cytometry data, which involves storing, retrieving, organizing, and analyzing flow cytometry data using extensive computational resources and tools. Flow cytometry bioinformatics requires extensive use of and contributes to the development of techniques from computational statistics and machine learning. Flow cytometry and related methods allow the quantification of multiple independent biomarkers on large numbers of single cells. The rapid growth in the multidimensionality and throughput of flow cytometry data, particularly in the 2000s, has led to the creation of a variety of computational analysis methods, data standards, and public databases for the sharing of results. Computational methods exist to assist in the preprocessing of flow cytometry data, identifying cell populations within it, matching those cell populations across samples, and performing diagnosis and discovery using the results of previous steps. For preprocessing, this includes compensating for spectral overlap, transforming data onto scales conducive to visualization and analysis, assessing data for quality, and normalizing data across samples and experiments. For population identification, tools are available to aid traditional manual identification of populations in two-dimensional scatter plots (gating, to use dimensionality reduction to aid gating, and to find populations automatically in higher dimensional space in a variety of ways. It is also possible to characterize data in more comprehensive ways, such as the density-guided binary space partitioning technique known as probability binning, or by combinatorial gating. Finally, diagnosis using flow cytometry data can be aided by supervised learning techniques, and discovery of new cell types of biological importance by high-throughput statistical methods, as part of pipelines incorporating all of the aforementioned methods. Open standards, data

  16. 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.)

  17. 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.

  18. 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...

  19. Bioinformatics meets parasitology.

    Science.gov (United States)

    Cantacessi, C; Campbell, B E; Jex, A R; Young, N D; Hall, R S; Ranganathan, S; Gasser, R B

    2012-05-01

    The advent and integration of high-throughput '-omics' technologies (e.g. genomics, transcriptomics, proteomics, metabolomics, glycomics and lipidomics) are revolutionizing the way biology is done, allowing the systems biology of organisms to be explored. These technologies are now providing unique opportunities for global, molecular investigations of parasites. For example, studies of a transcriptome (all transcripts in an organism, tissue or cell) have become instrumental in providing insights into aspects of gene expression, regulation and function in a parasite, which is a major step to understanding its biology. The purpose of this article was to review recent applications of next-generation sequencing technologies and bioinformatic tools to large-scale investigations of the transcriptomes of parasitic nematodes of socio-economic significance (particularly key species of the order Strongylida) and to indicate the prospects and implications of these explorations for developing novel methods of parasite intervention. © 2011 Blackwell Publishing Ltd.

  20. 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…

  1. 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…

  2. 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.

  3. 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.

  4. Vistazos Intimos De Puebla; Una Compilacion De Informes Individuales Preparados Por Los Participantes Del Instituto De Verano (NDEA) (Close-ups on Puebla; A Compilation of Individual Reports Prepared by the Participants of the NDEA Summer Institute).

    Science.gov (United States)

    Wichita State Univ., KS.

    The individual and committee reports on the sociology of Puebla, Mexico, which are collected here, were written by participants in an NDEA Summer Institute program of the University of Wichita, Kansas. The underlying motives of the program, described in the preface, were to provide participants with real language experience and a chance to…

  5. 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...

  6. 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.

  7. 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.

  8. How to test bioinformatics software?

    Science.gov (United States)

    Kamali, Amir Hossein; Giannoulatou, Eleni; Chen, Tsong Yueh; Charleston, Michael A; McEwan, Alistair L; Ho, Joshua W K

    2015-09-01

    Bioinformatics is the application of computational, mathematical and statistical techniques to solve problems in biology and medicine. Bioinformatics programs developed for computational simulation and large-scale data analysis are widely used in almost all areas of biophysics. The appropriate choice of algorithms and correct implementation of these algorithms are critical for obtaining reliable computational results. Nonetheless, it is often very difficult to systematically test these programs as it is often hard to verify the correctness of the output, and to effectively generate failure-revealing test cases. Software testing is an important process of verification and validation of scientific software, but very few studies have directly dealt with the issues of bioinformatics software testing. In this work, we review important concepts and state-of-the-art methods in the field of software testing. We also discuss recent reports on adapting and implementing software testing methodologies in the bioinformatics field, with specific examples drawn from systems biology and genomic medicine.

  9. 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.

  10. Genome Exploitation and Bioinformatics Tools

    Science.gov (United States)

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

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

  11. Emerging strengths in Asia Pacific bioinformatics

    OpenAIRE

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

    2008-01-01

    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,...

  12. 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.

  13. 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

  14. 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...

  15. 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…

  16. 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…

  17. 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...

  18. 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).

  19. 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......://www.secondarymetabolites.org) is introduced to provide a one-stop catalog and links to these bioinformatics resources. In addition, an outlook is presented how the existing tools and those to be developed will influence synthetic biology approaches in the natural products field....

  20. 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

  1. 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

  2. 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…

  3. 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...

  4. 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

  5. Computational intelligence techniques in bioinformatics.

    Science.gov (United States)

    Hassanien, Aboul Ella; Al-Shammari, Eiman Tamah; Ghali, Neveen I

    2013-12-01

    Computational intelligence (CI) is a well-established paradigm with current systems having many of the characteristics of biological computers and capable of performing a variety of tasks that are difficult to do using conventional techniques. It is a methodology involving adaptive mechanisms and/or an ability to learn that facilitate intelligent behavior in complex and changing environments, such that the system is perceived to possess one or more attributes of reason, such as generalization, discovery, association and abstraction. The objective of this article is to present to the CI and bioinformatics research communities some of the state-of-the-art in CI applications to bioinformatics and motivate research in new trend-setting directions. In this article, we present an overview of the CI techniques in bioinformatics. We will show how CI techniques including neural networks, restricted Boltzmann machine, deep belief network, fuzzy logic, rough sets, evolutionary algorithms (EA), genetic algorithms (GA), swarm intelligence, artificial immune systems and support vector machines, could be successfully employed to tackle various problems such as gene expression clustering and classification, protein sequence classification, gene selection, DNA fragment assembly, multiple sequence alignment, and protein function prediction and its structure. We discuss some representative methods to provide inspiring examples to illustrate how CI can be utilized to address these problems and how bioinformatics data can be characterized by CI. Challenges to be addressed and future directions of research are also presented and an extensive bibliography is included. Copyright © 2013 Elsevier Ltd. All rights reserved.

  6. 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.

  7. 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.

  8. 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...

  9. 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

  10. Utility library for structural bioinformatics.

    Science.gov (United States)

    Gront, Dominik; Kolinski, Andrzej

    2008-02-15

    In this Note we present a new software library for structural bioinformatics. The library contains programs, computing sequence- and profile-based alignments and a variety of structural calculations with user-friendly handling of various data formats. The software organization is very flexible. Algorithms are written in Java language and may be used by Java programs. Moreover the modules can be accessed from Jython (Python scripting language implemented in Java) scripts. Finally, the new version of BioShell delivers several utility programs that can do typical bioinformatics task from a command-line level. Availability The software is available for download free of charge from its website: http://bioshell.chem.uw.edu.pl. This website provides also numerous examples, code snippets and API documentation.

  11. 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.

  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

    2015-02-01

    "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).

  13. 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.

  14. Bioinformatics goes to school--new avenues for teaching contemporary biology.

    Science.gov (United States)

    Wood, Louisa; Gebhardt, Philipp

    2013-01-01

    Since 2010, the European Molecular Biology Laboratory's (EMBL) Heidelberg laboratory and the European Bioinformatics Institute (EMBL-EBI) have jointly run bioinformatics training courses developed specifically for secondary school science teachers within Europe and EMBL member states. These courses focus on introducing bioinformatics, databases, and data-intensive biology, allowing participants to explore resources and providing classroom-ready materials to support them in sharing this new knowledge with their students. In this article, we chart our progress made in creating and running three bioinformatics training courses, including how the course resources are received by participants and how these, and bioinformatics in general, are subsequently used in the classroom. We assess the strengths and challenges of our approach, and share what we have learned through our interactions with European science teachers.

  15. 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).

  16. 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

  17. Bioinformatics in Africa: The Rise of Ghana?

    Directory of Open Access Journals (Sweden)

    Thomas K Karikari

    2015-09-01

    Full Text Available Until recently, bioinformatics, an important discipline in the biological sciences, was largely limited to countries with advanced scientific resources. Nonetheless, several developing countries have lately been making progress in bioinformatics training and applications. In Africa, leading countries in the discipline include South Africa, Nigeria, and Kenya. However, one country that is less known when it comes to bioinformatics is Ghana. Here, I provide a first description of the development of bioinformatics activities in Ghana and how these activities contribute to the overall development of the discipline in Africa. Over the past decade, scientists in Ghana have been involved in publications incorporating bioinformatics analyses, aimed at addressing research questions in biomedical science and agriculture. Scarce research funding and inadequate training opportunities are some of the challenges that need to be addressed for Ghanaian scientists to continue developing their expertise in bioinformatics.

  18. Bioinformatics in Africa: The Rise of Ghana?

    Science.gov (United States)

    Karikari, Thomas K

    2015-09-01

    Until recently, bioinformatics, an important discipline in the biological sciences, was largely limited to countries with advanced scientific resources. Nonetheless, several developing countries have lately been making progress in bioinformatics training and applications. In Africa, leading countries in the discipline include South Africa, Nigeria, and Kenya. However, one country that is less known when it comes to bioinformatics is Ghana. Here, I provide a first description of the development of bioinformatics activities in Ghana and how these activities contribute to the overall development of the discipline in Africa. Over the past decade, scientists in Ghana have been involved in publications incorporating bioinformatics analyses, aimed at addressing research questions in biomedical science and agriculture. Scarce research funding and inadequate training opportunities are some of the challenges that need to be addressed for Ghanaian scientists to continue developing their expertise in bioinformatics.

  19. Search strategies in structural bioinformatics.

    Science.gov (United States)

    Oakley, Mark T; Barthel, Daniel; Bykov, Yuri; Garibaldi, Jonathan M; Burke, Edmund K; Krasnogor, Natalio; Hirst, Jonathan D

    2008-06-01

    Optimisation problems pervade structural bioinformatics. In this review, we describe recent work addressing a selection of bioinformatics challenges. We begin with a discussion of research into protein structure comparison, and highlight the utility of Kolmogorov complexity as a measure of structural similarity. We then turn to research into de novo protein structure prediction, in which structures are generated from first principles. In this endeavour, there is a compromise between the detail of the model and the extent to which the conformational space of the protein can be sampled. We discuss some developments in this area, including off-lattice structure prediction using the great deluge algorithm. One strategy to reduce the size of the search space is to restrict the protein chain to sites on a regular lattice. In this context, we highlight the use of memetic algorithms, which combine genetic algorithms with local optimisation, to the study of simple protein models on the two-dimensional square lattice and the face-centred cubic lattice.

  20. 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.

  1. 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...

  2. Tufts University Summer Guidance Institute on the Utilization of Occupational Education and Placement (Medford, Mass., Jul 20-31, 1970). Final Report.

    Science.gov (United States)

    Curtin, Elizabeth M.; Morine, John P.

    The purposes of this institute were to (1) provide the information needed to offer vocational courses for the non-college bound handicapped and disadvantaged, (2) point out the need for remedial and psychological services, (3) increase participants' understanding of the role of the counselor in our rapidly changing society, (4) increase emphasis…

  3. 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.

  4. 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.

  5. 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…

  6. 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…

  7. Personalized medicine: challenges and opportunities for translational bioinformatics.

    Science.gov (United States)

    Overby, Casey Lynnette; Tarczy-Hornoch, Peter

    2013-07-01

    Personalized medicine can be defined broadly as a model of healthcare that is predictive, personalized, preventive and participatory. Two US President's Council of Advisors on Science and Technology reports illustrate challenges in personalized medicine (in a 2008 report) and in use of health information technology (in a 2010 report). Translational bioinformatics is a field that can help address these challenges and is defined by the American Medical Informatics Association as "the development of storage, analytic and interpretive methods to optimize the transformation of increasing voluminous biomedical data into proactive, predictive, preventative and participatory health." This article discusses barriers to implementing genomics applications and current progress toward overcoming barriers, describes lessons learned from early experiences of institutions engaged in personalized medicine and provides example areas for translational bioinformatics research inquiry.

  8. 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.

  9. 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.

  10. 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.

  11. Bioinformatics clouds for big data manipulation

    Science.gov (United States)

    2012-01-01

    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. PMID:23190475

  12. 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.

  13. 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.

  14. A quick guide for building a successful bioinformatics community.

    Directory of Open Access Journals (Sweden)

    Aidan Budd

    2015-02-01

    Full Text Available "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.

  15. 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

  16. 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 - Gene tics ; Molecular Biology Impact factor: 3.729, year: 2016

  17. 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.

  18. 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...

  19. 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 -...

  20. 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...

  1. 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...

  2. 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.

  3. 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...

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

    Directory of Open Access Journals (Sweden)

    Teresa K Attwood

    2015-04-01

    Full Text Available 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.

  5. 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

  6. Coronavirus Genomics and Bioinformatics Analysis

    Directory of Open Access Journals (Sweden)

    Kwok-Yung Yuen

    2010-08-01

    Full Text Available The drastic increase in the number of coronaviruses discovered and coronavirus genomes being sequenced have given us an unprecedented opportunity to perform genomics and bioinformatics analysis on this family of viruses. Coronaviruses possess the largest genomes (26.4 to 31.7 kb among all known RNA viruses, with G + C contents varying from 32% to 43%. Variable numbers of small ORFs are present between the various conserved genes (ORF1ab, spike, envelope, membrane and nucleocapsid and downstream to nucleocapsid gene in different coronavirus lineages. Phylogenetically, three genera, Alphacoronavirus, Betacoronavirus and Gammacoronavirus, with Betacoronavirus consisting of subgroups A, B, C and D, exist. A fourth genus, Deltacoronavirus, which includes bulbul coronavirus HKU11, thrush coronavirus HKU12 and munia coronavirus HKU13, is emerging. Molecular clock analysis using various gene loci revealed that the time of most recent common ancestor of human/civet SARS related coronavirus to be 1999-2002, with estimated substitution rate of 4´10-4 to 2´10-2 substitutions per site per year. Recombination in coronaviruses was most notable between different strains of murine hepatitis virus (MHV, between different strains of infectious bronchitis virus, between MHV and bovine coronavirus, between feline coronavirus (FCoV type I and canine coronavirus generating FCoV type II, and between the three genotypes of human coronavirus HKU1 (HCoV-HKU1. Codon usage bias in coronaviruses were observed, with HCoV-HKU1 showing the most extreme bias, and cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape such codon usage bias in coronaviruses.

  7. 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.

  8. 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.

  9. 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.

  10. BIRCH: a user-oriented, locally-customizable, bioinformatics system.

    Science.gov (United States)

    Fristensky, Brian

    2007-02-09

    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. 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. 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.

  11. Bioinformatics for cancer immunotherapy target discovery

    DEFF Research Database (Denmark)

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

    2014-01-01

    cancer immunotherapies has yet to be fulfilled. The insufficient efficacy of existing treatments can be attributed to a number of biological and technical issues. In this review, we detail the current limitations of immunotherapy target selection and design, and review computational methods to streamline...... 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...

  12. 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.

  13. 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.

  14. Report on the 2008 ISAGA Summer School

    Science.gov (United States)

    van de Westelaken, Marleen

    2011-01-01

    This article reports on the 2008 ISAGA Summer School held in New Delhi (Gurgaon), India. This Summer School was hosted by the Institute for Integrated Learning in Management. Participants came from all over the world. This year's theme was "The Art and Science of Simulation and Gaming Design and Facilitation for Business and Management."

  15. 1998 Complex Systems Summer School

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-12-15

    For the past eleven years a group of institutes, centers, and universities throughout the country have sponsored a summer school in Santa Fe, New Mexico as part of an interdisciplinary effort to promote the understanding of complex systems. The goal of these summer schools is to provide graduate students, postdoctoral fellows and active research scientists with an introduction to the study of complex behavior in mathematical, physical, and living systems. The Center for Nonlinear Studies supported the eleventh in this series of highly successful schools in Santa Fe in June, 1998.

  16. 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...

  17. 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

  18. Preliminary Report IPI Institute. Summer 1966.

    Science.gov (United States)

    Research for Better Schools, Inc., Philadelphia, PA.

    Individually Prescribed Instruction (IPI), a project based on a carefully sequenced and detailed listing of behaviorally stated objectives, lesson materials geared to instructional objectives, provision for diagnosis of pupil skills and abilities, written prescriptions to guide the pupil's work, and pupil oriented instruction, is outlined first in…

  19. The Griffiss Institute Summer Faculty Program

    Science.gov (United States)

    2013-05-01

    radar target detection can achieve constant false alarm rate ( CFAR ) performance similar to the corresponding test in the raw data domain. By...Command and Control CDN – Content Delivery Networks CETE – Center for Educational Testing and Evaluation CFAR – Constant False Alarm Rate CMOS

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. Planning bioinformatics workflows using an expert system.

    Science.gov (United States)

    Chen, Xiaoling; Chang, Jeffrey T

    2017-04-15

    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. 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. https://github.com/jefftc/changlab. jeffrey.t.chang@uth.tmc.edu. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  6. 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

  7. A bioinformatics approach to marker development

    NARCIS (Netherlands)

    Tang, J.

    2008-01-01

    The thesis focuses on two bioinformatics research topics: the development of tools for an efficient and reliable identification of single nucleotides polymorphisms (SNPs) and polymorphic simple sequence repeats (SSRs) from expressed sequence tags (ESTs) (Chapter 2, 3 and 4), and the subsequent

  8. 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...

  9. An integrative bioinformatics pipeline for the genomewide ...

    Indian Academy of Sciences (India)

    An integrative bioinformatics pipeline for the genomewide identification of novel porcine microRNA genes. Wei Fang, Na Zhou, Dengyun Li, Zhigang Chen, Pengfei Jiang and Deli Zhang. J. Genet. 92,587 593. Figure 1. Primary sequence of the predicted SSc-mir-2053 precursor and locations of some terms in the secondary ...

  10. Novel bioinformatic developments for exome sequencing

    NARCIS (Netherlands)

    Lelieveld, S.H.; Veltman, J.A.; Gilissen, C.F.

    2016-01-01

    With the widespread adoption of next generation sequencing technologies by the genetics community and the rapid decrease in costs per base, exome sequencing has become a standard within the repertoire of genetic experiments for both research and diagnostics. Although bioinformatics now offers

  11. An integrative bioinformatics pipeline for the genomewide ...

    Indian Academy of Sciences (India)

    2013-12-06

    Dec 6, 2013 ... The majority of miRNAs in pig (Sus scrofa), an impor- tant domestic animal, remain unknown. From this perspec- tive, we attempted the genomewide identification of novel porcine miRNAs. Here, we propose a novel integrative bioinformatics pipeline to identify conservative and non- conservative novel ...

  12. 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 ...

  13. 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.

  14. 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...

  15. "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).…

  16. 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...

  17. 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:…

  18. 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…

  19. 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…

  20. Bioinformatics applications in proteomics data analysis

    NARCIS (Netherlands)

    Peng, M.

    2015-01-01

    In this thesis, I detail my 4-year efforts in developing bioinformatics tools and algorithms to address the growing demands of current proteomics endeavors, covering a range of facets such as large-scale protein expression profiling, charting post-translation modifications as well as

  1. 7 CFR 250.67 - Charitable institutions.

    Science.gov (United States)

    2010-01-01

    ... foods as charitable institutions: (1) Schools, summer camps, service institutions, and child and adult care institutions that participate in child nutrition programs or as commodity schools; and (2) Adult...) Schools, summer camps, service institutions, and child care institutions that do not participate in child...

  2. 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...

  3. Agile parallel bioinformatics workflow management using Pwrake.

    Science.gov (United States)

    Mishima, Hiroyuki; Sasaki, Kensaku; Tanaka, Masahiro; Tatebe, Osamu; Yoshiura, Koh-Ichiro

    2011-09-08

    In bioinformatics projects, scientific workflow systems are widely used to manage computational procedures. Full-featured workflow systems have been proposed to fulfil the demand for workflow management. However, such systems tend to be over-weighted for actual bioinformatics practices. We realize that quick deployment of cutting-edge software implementing advanced algorithms and data formats, and continuous adaptation to changes in computational resources and the environment are often prioritized in scientific workflow management. These features have a greater affinity with the agile software development method through iterative development phases after trial and error.Here, we show the application of a scientific workflow system Pwrake to bioinformatics workflows. Pwrake is a parallel workflow extension of Ruby's standard build tool Rake, the flexibility of which has been demonstrated in the astronomy domain. Therefore, we hypothesize that Pwrake also has advantages in actual bioinformatics workflows. We implemented the Pwrake workflows to process next generation sequencing data using the Genomic Analysis Toolkit (GATK) and Dindel. GATK and Dindel workflows are typical examples of sequential and parallel workflows, respectively. We found that in practice, actual scientific workflow development iterates over two phases, the workflow definition phase and the parameter adjustment phase. We introduced separate workflow definitions to help focus on each of the two developmental phases, as well as helper methods to simplify the descriptions. This approach increased iterative development efficiency. Moreover, we implemented combined workflows to demonstrate modularity of the GATK and Dindel workflows. Pwrake enables agile management of scientific workflows in the bioinformatics domain. The internal domain specific language design built on Ruby gives the flexibility of rakefiles for writing scientific workflows. Furthermore, readability and maintainability of rakefiles

  4. Agile parallel bioinformatics workflow management using Pwrake

    Science.gov (United States)

    2011-01-01

    Background In bioinformatics projects, scientific workflow systems are widely used to manage computational procedures. Full-featured workflow systems have been proposed to fulfil the demand for workflow management. However, such systems tend to be over-weighted for actual bioinformatics practices. We realize that quick deployment of cutting-edge software implementing advanced algorithms and data formats, and continuous adaptation to changes in computational resources and the environment are often prioritized in scientific workflow management. These features have a greater affinity with the agile software development method through iterative development phases after trial and error. Here, we show the application of a scientific workflow system Pwrake to bioinformatics workflows. Pwrake is a parallel workflow extension of Ruby's standard build tool Rake, the flexibility of which has been demonstrated in the astronomy domain. Therefore, we hypothesize that Pwrake also has advantages in actual bioinformatics workflows. Findings We implemented the Pwrake workflows to process next generation sequencing data using the Genomic Analysis Toolkit (GATK) and Dindel. GATK and Dindel workflows are typical examples of sequential and parallel workflows, respectively. We found that in practice, actual scientific workflow development iterates over two phases, the workflow definition phase and the parameter adjustment phase. We introduced separate workflow definitions to help focus on each of the two developmental phases, as well as helper methods to simplify the descriptions. This approach increased iterative development efficiency. Moreover, we implemented combined workflows to demonstrate modularity of the GATK and Dindel workflows. Conclusions Pwrake enables agile management of scientific workflows in the bioinformatics domain. The internal domain specific language design built on Ruby gives the flexibility of rakefiles for writing scientific workflows. Furthermore, readability

  5. 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

  6. Developing a Bioinformatics Program and Supporting Infrastructure in a Biomedical Library

    Directory of Open Access Journals (Sweden)

    Nathan Hosburgh

    2018-03-01

    Full Text Available Background: Over the last couple decades, the field of bioinformatics has helped spur medical discoveries that offer a better understanding of the genetic basis of disease, which in turn improve public health and save lives. Concomitantly, support requirements for molecular biology researchers have grown in scope and complexity, incorporating specialized resources, technologies, and techniques. Case Presentation: To address this specific need among National Institutes of Health (NIH intramural researchers, the NIH Library hired an expert bioinformatics trainer and consultant with a PhD in biochemistry to implement a bioinformatics support program. This study traces the program from its inception in 2009 to its present form. Discussion involves the particular skills of program staff, development of content, collection of resources, associated technology, assessment, and the impact of the program on the NIH community. Conclusion: Based on quantitative and qualitative data, the bioinformatics support program has been heavily used and appreciated by researchers. Continued success will depend on filling key staff positions, building on the existing program infrastructure, and keeping abreast of developments within the field to remain relevant and in touch with the medical research community utilizing bioinformatics services.

  7. 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 Gagne's Conditions of Learning instructional design theory. This theory, although first published in the early 1970s, is still fundamental in instructional design and instructional technology. First, top-level as well as prerequisite learning objectives for a microarray analysis workshop and a primer design workshop were defined. Then a hierarchy of objectives for each workshop was created. Hands-on tutorials were designed to meet these objectives. Finally, events of learning proposed by Gagne's theory were incorporated into the hands-on tutorials. The resultant manuals were tested on a small number of trainees, revised, and applied in 1-day bioinformatics workshops. Based on this experience and on observations made during the workshops, we conclude that Gagne's Conditions of Learning instructional design theory provides a useful framework for developing bioinformatics training, but may not be optimal as a method for teaching it.

  8. 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.

  9. 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

  10. A Bioinformatics Reference Model: Towards a Framework for Developing and Organising Bioinformatic Resources

    Science.gov (United States)

    Hiew, Hong Liang; Bellgard, Matthew

    2007-11-01

    Life Science research faces the constant challenge of how to effectively handle an ever-growing body of bioinformatics software and online resources. The users and developers of bioinformatics resources have a diverse set of competing demands on how these resources need to be developed and organised. Unfortunately, there does not exist an adequate community-wide framework to integrate such competing demands. The problems that arise from this include unstructured standards development, the emergence of tools that do not meet specific needs of researchers, and often times a communications gap between those who use the tools and those who supply them. This paper presents an overview of the different functions and needs of bioinformatics stakeholders to determine what may be required in a community-wide framework. A Bioinformatics Reference Model is proposed as a basis for such a framework. The reference model outlines the functional relationship between research usage and technical aspects of bioinformatics resources. It separates important functions into multiple structured layers, clarifies how they relate to each other, and highlights the gaps that need to be addressed for progress towards a diverse, manageable, and sustainable body of resources. The relevance of this reference model to the bioscience research community, and its implications in progress for organising our bioinformatics resources, are discussed.

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

    African Journals Online (AJOL)

    The aim of this review is to discuss the importance of bioinformatics and emphasize the need to acquire bioinformatics training and skills so as to maximize its potentials for improved delivery of animal health. In this review, bioinformatics is introduced, challenges to effective animal disease diagnosis, prevention and control, ...

  12. 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…

  13. 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.

  14. 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.

  15. 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.

  16. Bioinformatics Approaches for Human Gut Microbiome Research

    Directory of Open Access Journals (Sweden)

    Zhijun Zheng

    2016-07-01

    Full Text Available The human microbiome has received much attention because many studies have reported that the human gut microbiome is associated with several diseases. The very large datasets that are produced by these kinds of studies means that bioinformatics approaches are crucial for their analysis. Here, we systematically reviewed bioinformatics tools that are commonly used in microbiome research, including a typical pipeline and software for sequence alignment, abundance profiling, enterotype determination, taxonomic diversity, identifying differentially abundant species/genes, gene cataloging, and functional analyses. We also summarized the algorithms and methods used to define metagenomic species and co-abundance gene groups to expand our understanding of unclassified and poorly understood gut microbes that are undocumented in the current genome databases. Additionally, we examined the methods used to identify metagenomic biomarkers based on the gut microbiome, which might help to expand the knowledge and approaches for disease detection and monitoring.

  17. 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...... changes. These methods have been developed further and applied for computational screens of genomic sequence. Furthermore, a number of additional directions have emerged. These include methods to search for RNA 3D structure, RNA-RNA interactions, and design of interfering RNAs (RNAi) as well as methods...... 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....

  18. VLSI Microsystem for Rapid Bioinformatic Pattern Recognition

    Science.gov (United States)

    Fang, Wai-Chi; Lue, Jaw-Chyng

    2009-01-01

    A system comprising very-large-scale integrated (VLSI) circuits is being developed as a means of bioinformatics-oriented analysis and recognition of patterns of fluorescence generated in a microarray in an advanced, highly miniaturized, portable genetic-expression-assay instrument. Such an instrument implements an on-chip combination of polymerase chain reactions and electrochemical transduction for amplification and detection of deoxyribonucleic acid (DNA).

  19. 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

  20. 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

  1. 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

  2. ballaxy: web services for structural bioinformatics.

    Science.gov (United States)

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

    2015-01-01

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

  3. 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.

  4. 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

  5. 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.

  6. Bioinformatics on the cloud computing platform Azure.

    Directory of Open Access Journals (Sweden)

    Hugh P Shanahan

    Full Text Available 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.

  7. 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.

  8. 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.

  9. Bioinformatics training: a review of challenges, actions and support requirements.

    Science.gov (United States)

    Schneider, Maria Victoria; Watson, James; Attwood, Teresa; Rother, Kristian; Budd, Aidan; McDowall, Jennifer; Via, Allegra; Fernandes, Pedro; Nyronen, Tommy; Blicher, Thomas; Jones, Phil; Blatter, Marie-Claude; De Las Rivas, Javier; Judge, David Phillip; van der Gool, Wouter; Brooksbank, Cath

    2010-11-01

    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 Trainer Networking Session held under the auspices of the EU-funded SLING Integrating Activity, which took place in November 2009.

  10. 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...

  11. 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...

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

    Directory of Open Access Journals (Sweden)

    Kim T Gurwitz

    2017-10-01

    Full Text Available 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.

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

    Science.gov (United States)

    Gurwitz, Kim T; Aron, Shaun; Panji, Sumir; Maslamoney, Suresh; Fernandes, Pedro L; Judge, David P; Ghouila, Amel; Domelevo Entfellner, Jean-Baka; Guerfali, Fatma Z; Saunders, Colleen; Mansour Alzohairy, Ahmed; Salifu, Samson P; Ahmed, Rehab; Cloete, Ruben; Kayondo, Jonathan; Ssemwanga, Deogratius; Mulder, Nicola

    2017-10-01

    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.

  14. 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.

  15. 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.

  16. 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.

  17. Bioinformatic analysis of whole genome sequencing data

    OpenAIRE

    Maqbool, Khurram

    2014-01-01

    Evolution has shaped the life forms for billion of years. Domestication is an accelerated process that can be used as a model for evolutionary changes. The aim of this thesis project has been to carry out extensive bioinformatic analyses of whole genome sequencing data to reveal SNPs, InDels and selective sweeps in the chicken, pig and dog genome. Pig genome sequencing revealed loci under selection for elongation of back and increased number of vertebrae, associated with the NR6A1, PLAG1,...

  18. Top considerations for creating bioinformatics software documentation.

    Science.gov (United States)

    Karimzadeh, Mehran; Hoffman, Michael M

    2017-01-14

    Investing in documenting your bioinformatics software well can increase its impact and save your time. To maximize the effectiveness of your documentation, we suggest following a few guidelines we propose here. We recommend providing multiple avenues for users to use your research software, including a navigable HTML interface with a quick start, useful help messages with detailed explanation and thorough examples for each feature of your software. By following these guidelines, you can assure that your hard work maximally benefits yourself and others. © The Author 2017. Published by Oxford University Press.

  19. 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.

  20. 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.

  1. 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.

  2. Teaching the ABCs of bioinformatics: a brief introduction to the Applied Bioinformatics Course.

    Science.gov (United States)

    Luo, Jingchu

    2014-11-01

    With the development of the Internet and the growth of online resources, bioinformatics training for wet-lab biologists became necessary as a part of their education. This article describes a one-semester course 'Applied Bioinformatics Course' (ABC, http://abc.cbi.pku.edu.cn/) that the author has been teaching to biological graduate students at the Peking University and the Chinese Academy of Agricultural Sciences for the past 13 years. ABC is a hands-on practical course to teach students to use online bioinformatics resources to solve biological problems related to their ongoing research projects in molecular biology. With a brief introduction to the background of the course, detailed information about the teaching strategies of the course are outlined in the 'How to teach' section. The contents of the course are briefly described in the 'What to teach' section with some real examples. The author wishes to share his teaching experiences and the online teaching materials with colleagues working in bioinformatics education both in local and international universities. © The Author 2013. Published by Oxford University Press.

  3. 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…

  4. Bioinformatics tools for predicting GPCR gene functions.

    Science.gov (United States)

    Suwa, Makiko

    2014-01-01

    The automatic classification of GPCRs by bioinformatics methodology can provide functional information for new GPCRs in the whole 'GPCR proteome' and this information is important for the development of novel drugs. Since GPCR proteome is classified hierarchically, general ways for GPCR function prediction are based on hierarchical classification. Various computational tools have been developed to predict GPCR functions; those tools use not simple sequence searches but more powerful methods, such as alignment-free methods, statistical model methods, and machine learning methods used in protein sequence analysis, based on learning datasets. The first stage of hierarchical function prediction involves the discrimination of GPCRs from non-GPCRs and the second stage involves the classification of the predicted GPCR candidates into family, subfamily, and sub-subfamily levels. Then, further classification is performed according to their protein-protein interaction type: binding G-protein type, oligomerized partner type, etc. Those methods have achieved predictive accuracies of around 90 %. Finally, I described the future subject of research of the bioinformatics technique about functional prediction of GPCR.

  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. Summer camp nurtures student

    OpenAIRE

    Earl Anderson

    2017-01-01

    Summer camp is a coordinated program for youths or teenagers driven in the midst of the late spring months in a couple of countries. Adolescents and young people who go to summer camp are known as campers. It is each parent's stress: What is the perfect way for your adolescent to contribute his or her free vitality in the midst of summer and school breaks? Research Paper Help. To a couple, it is a period for youths to play and have an incredible time. By joining the late spring camp, yout...

  8. The Changing Demographics of Summer Session Administrators.

    Science.gov (United States)

    Cullivan, Kathryn Gould

    1997-01-01

    A survey of 39 colleges/universities sought information on characteristics of 1973-93 summer school administrators. Results indicate large changes in some characteristics (e.g., gender), very small changes in others (highest degree held). Some variations emerged by institution type or location. Some theories for the changes are proposed for…

  9. 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…

  10. A Innovative Engineering Summer School V2.0

    DEFF Research Database (Denmark)

    Bennedsen, Jens; Larsen, Peter Gorm

    2010-01-01

    This article describes a summer school which focuses on a conceive-design project. The summer school has been run three times; each of the implementations is described. The last implementation (v2.0) is discussed and four challenges are identified and discussed in detail: assignments, the role...... of the teacher, secondary students as trainees and cultural differences. We discuss challenges to the summer school, if it should held be in a traditional institutional setting....

  11. 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...

  12. Summer Steelhead Distribution [ds341

    Data.gov (United States)

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

  13. 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...

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

    Science.gov (United States)

    Karikari, Thomas K.; Quansah, Emmanuel; Mohamed, Wael M.Y.

    2015-01-01

    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. PMID:26767163

  15. 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.

  16. Applied bioinformatics: Genome annotation and transcriptome analysis

    DEFF Research Database (Denmark)

    Gupta, Vikas

    and dhurrin, which have not previously been characterized in blueberries. There are more than 44,500 spider species with distinct habitats and unique characteristics. Spiders are masters of producing silk webs to catch prey and using venom to neutralize. The exploration of the genetics behind these properties...... japonicus (Lotus), Vaccinium corymbosum (blueberry), Stegodyphus mimosarum (spider) and Trifolium occidentale (clover). From a bioinformatics data analysis perspective, my work can be divided into three parts; genome annotation, small RNA, and gene expression analysis. Lotus is a legume of significant...... has just started. We have assembled and annotated the first two spider genomes to facilitate our understanding of spiders at the molecular level. The need for analyzing the large and increasing amount of sequencing data has increased the demand for efficient, user friendly, and broadly applicable...

  17. 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.

  18. Applied bioinformatics: Genome annotation and transcriptome analysis

    DEFF Research Database (Denmark)

    Gupta, Vikas

    japonicus (Lotus), Vaccinium corymbosum (blueberry), Stegodyphus mimosarum (spider) and Trifolium occidentale (clover). From a bioinformatics data analysis perspective, my work can be divided into three parts; genome annotation, small RNA, and gene expression analysis. Lotus is a legume of significant...... biology and genetics studies. We present an improved Lotus genome assembly and annotation, a catalog of natural variation based on re-sequencing of 29 accessions, and describe the involvement of small RNAs in the plant-bacteria symbiosis. Blueberries contain anthocyanins, other pigments and various...... polyphenolic compounds, which have been linked to protection against diabetes, cardiovascular disease and age-related cognitive decline. We present the first genome- guided approach in blueberry to identify genes involved in the synthesis of health-protective compounds. Using RNA-Seq data from five stages...

  19. 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...

  20. 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

  1. 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.

  2. Rust-Bio: a fast and safe bioinformatics library

    NARCIS (Netherlands)

    J. Köster (Johannes)

    2015-01-01

    textabstractWe present Rust-Bio, the first general purpose bioinformatics library for the innovative Rust programming language. Rust-Bio leverages the unique combination of speed, memory safety and high-level syntax offered by Rust to provide a fast and safe set of bioinformatics algorithms and data

  3. 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 ...

  4. The 2015 Bioinformatics Open Source Conference (BOSC 2015.

    Directory of Open Access Journals (Sweden)

    Nomi L Harris

    2016-02-01

    Full Text Available 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.

  5. 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 ...

  6. 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.

  7. Perspectives on presentation and pedagogy in aid of bioinformatics education.

    Science.gov (United States)

    Buttigieg, Pier Luigi

    2010-11-01

    Using live presentation to communicate the interdisciplinary and abstract content of bioinformatics to its educationally diverse studentship is a sizeable challenge. This review collects a number of perspectives on multimedia presentation, visual communication and pedagogy. The aim is to encourage educators to reflect on the great potential of live presentation in facilitating bioinformatics education.

  8. 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 ...

  9. 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…

  10. 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…

  11. 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…

  12. 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.

  13. 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

  14. 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.

  15. 4273π: Bioinformatics education on low cost ARM hardware

    Science.gov (United States)

    2013-01-01

    Background 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. Results 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. Conclusions 4273π is a means to teach bioinformatics, including systems administration tasks, to undergraduates at low cost. PMID:23937194

  16. 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.

  17. Summer syncope syndrome redux.

    Science.gov (United States)

    Huang, Jennifer Juxiang; Desai, Chirag; Singh, Nirmal; Sharda, Natasha; Fernandes, Aaron; Riaz, Irbaz Bin; Alpert, Joseph S

    2015-10-01

    While antihypertensive therapy is known to reduce the risk for heart failure, myocardial infarction, and stroke, it can often cause orthostatic hypotension and syncope, especially in the setting of polypharmacy and possibly, a hot and dry climate. The objective of the present study was to investigate whether the results of our prior study involving continued use of antihypertensive drugs at the same dosage in the summer as in the winter months for patients living in the Sonoran desert resulted in an increase in syncopal episodes during the hot summer months. All hypertensive patients who were treated with medications and admitted with International Classification of Diseases, 9th Revision code diagnosis of syncope were included. This is a 3-year retrospective chart review study. They were defined as "cases" if they presented during the summer months (May to September) and "controls" if they presented during the winter months (November to March). The primary outcome measure was the presence of clinical dehydration. The statistical significance was determined using the 2-sided Fisher's exact test. A total of 834 patients with an International Classification of Diseases, 9th Revision code diagnosis of syncope were screened: 477 in the summer months and 357 in the winter months. In patients taking antihypertensive medications, there was a significantly higher number of cases of syncope secondary to dehydration during the summer months (40.5%) compared with the winter months (29%) (P = .04). No difference was observed in the type of antihypertensive medication used and syncope rate. The number of antihypertensives used did not increase the cases of syncope in either summer or winter. An increased number of syncope events was observed in the summer months among people who reside in a dry desert climate and who are taking antihypertensive medications. The data confirm our earlier observations that demonstrated a greater number of cases of syncope among people who reside

  18. 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

  19. 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.

  20. MEMOSys: Bioinformatics platform for genome-scale metabolic models.

    Science.gov (United States)

    Pabinger, Stephan; Rader, Robert; Agren, Rasmus; Nielsen, Jens; Trajanoski, Zlatko

    2011-01-31

    Recent advances in genomic sequencing have enabled the use of genome sequencing in standard biological and biotechnological research projects. The challenge is how to integrate the large amount of data in order to gain novel biological insights. One way to leverage sequence data is to use genome-scale metabolic models. We have therefore designed and implemented a bioinformatics platform which supports the development of such metabolic models. MEMOSys (MEtabolic MOdel research and development System) is a versatile platform for the management, storage, and development of genome-scale metabolic models. It supports the development of new models by providing a built-in version control system which offers access to the complete developmental history. Moreover, the integrated web board, the authorization system, and the definition of user roles allow collaborations across departments and institutions. Research on existing models is facilitated by a search system, references to external databases, and a feature-rich comparison mechanism. MEMOSys provides customizable data exchange mechanisms using the SBML format to enable analysis in external tools. The web application is based on the Java EE framework and offers an intuitive user interface. It currently contains six annotated microbial metabolic models. We have developed a web-based system designed to provide researchers a novel application facilitating the management and development of metabolic models. The system is freely available at http://www.icbi.at/MEMOSys.

  1. MEMOSys: Bioinformatics platform for genome-scale metabolic models

    Directory of Open Access Journals (Sweden)

    Agren Rasmus

    2011-01-01

    Full Text Available Abstract Background Recent advances in genomic sequencing have enabled the use of genome sequencing in standard biological and biotechnological research projects. The challenge is how to integrate the large amount of data in order to gain novel biological insights. One way to leverage sequence data is to use genome-scale metabolic models. We have therefore designed and implemented a bioinformatics platform which supports the development of such metabolic models. Results MEMOSys (MEtabolic MOdel research and development System is a versatile platform for the management, storage, and development of genome-scale metabolic models. It supports the development of new models by providing a built-in version control system which offers access to the complete developmental history. Moreover, the integrated web board, the authorization system, and the definition of user roles allow collaborations across departments and institutions. Research on existing models is facilitated by a search system, references to external databases, and a feature-rich comparison mechanism. MEMOSys provides customizable data exchange mechanisms using the SBML format to enable analysis in external tools. The web application is based on the Java EE framework and offers an intuitive user interface. It currently contains six annotated microbial metabolic models. Conclusions We have developed a web-based system designed to provide researchers a novel application facilitating the management and development of metabolic models. The system is freely available at http://www.icbi.at/MEMOSys.

  2. 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.

  3. 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.

  4. Bioinformatic landscapes for plant transcription factor system research.

    Science.gov (United States)

    Wang, Yijun; Lu, Wenjie; Deng, Dexiang

    2016-02-01

    Diverse bioinformatic resources have been developed for plant transcription factor (TF) research. This review presents the bioinformatic resources and methodologies for the elucidation of plant TF-mediated biological events. Such information is helpful to dissect the transcriptional regulatory systems in the three reference plants Arabidopsis , rice, and maize and translation to other plants. Transcription factors (TFs) orchestrate diverse biological programs by the modulation of spatiotemporal patterns of gene expression via binding cis-regulatory elements. Advanced sequencing platforms accompanied by emerging bioinformatic tools revolutionize the scope and extent of TF research. The system-level integration of bioinformatic resources is beneficial to the decoding of TF-involved networks. Herein, we first briefly introduce general and specialized databases for TF research in three reference plants Arabidopsis, rice, and maize. Then, as proof of concept, we identified and characterized heat shock transcription factor (HSF) members through the TF databases. Finally, we present how the integration of bioinformatic resources at -omics layers can aid the dissection of TF-mediated pathways. We also suggest ways forward to improve the bioinformatic resources of plant TFs. Leveraging these bioinformatic resources and methodologies opens new avenues for the elucidation of transcriptional regulatory systems in the three model systems and translation to other plants.

  5. 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.

  6. Bioinformatics Tools for Extracellular Vesicles Research.

    Science.gov (United States)

    Keerthikumar, Shivakumar; Gangoda, Lahiru; Gho, Yong Song; Mathivanan, Suresh

    2017-01-01

    Extracellular vesicles (EVs) are a class of membranous vesicles that are released by multiple cell types into the extracellular environment. This unique class of extracellular organelles which play pivotal role in intercellular communication are conserved across prokaryotes and eukaryotes. Depending upon the cell origin and the functional state, the molecular cargo including proteins, lipids, and RNA within the EVs are modulated. Owing to this, EVs are considered as a subrepertoire of the host cell and are rich reservoirs of disease biomarkers. In addition, the availability of EVs in multiple bodily fluids including blood has created significant interest in biomarker and signaling research. With the advancement in high-throughput techniques, multiple EV studies have embarked on profiling the molecular cargo. To benefit the scientific community, existing free Web-based resources including ExoCarta, EVpedia, and Vesiclepedia catalog multiple datasets. These resources aid in elucidating molecular mechanism and pathophysiology underlying different disease conditions from which EVs are isolated. Here, the existing bioinformatics tools to perform integrated analysis to identify key functional components in the EV datasets are discussed.

  7. 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.

  8. 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)

  9. Evolution of web services in bioinformatics.

    Science.gov (United States)

    Neerincx, Pieter B T; Leunissen, Jack A M

    2005-06-01

    Bioinformaticians have developed large collections of tools to make sense of the rapidly growing pool of molecular biological data. Biological systems tend to be complex and in order to understand them, it is often necessary to link many data sets and use more than one tool. Therefore, bioinformaticians have experimented with several strategies to try to integrate data sets and tools. Owing to the lack of standards for data sets and the interfaces of the tools this is not a trivial task. Over the past few years building services with web-based interfaces has become a popular way of sharing the data and tools that have resulted from many bioinformatics projects. This paper discusses the interoperability problem and how web services are being used to try to solve it, resulting in the evolution of tools with web interfaces from HTML/web form-based tools not suited for automatic workflow generation to a dynamic network of XML-based web services that can easily be used to create pipelines.

  10. Books for Summer Reading.

    Science.gov (United States)

    Phi Delta Kappan, 1991

    1991-01-01

    To help replenish educators' supply of ideas, "Kappan" editors suggest several books for summer reading, including many noncurrent titles not specifically on education such as Peter Novick's "That Noble Dream," Joy Kogawa's "Obasan," Zora Neale Hurston's "Their Eyes Were Watching God," Kate Chopin's "The Awakening," Willa Cather's "My Antonia,"…

  11. 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

  12. Superheroes and Summer Reading.

    Science.gov (United States)

    Meyer, Ron; Buckner, Joyce

    1980-01-01

    To combat summer learning loss among remedial readers, teachers and consultants in the Omaha, Nebraska, Title I program designed a series of comic-book reading units and mailed them to students' homes. Parents were pleased with the project and it appeared that less reading skill had been lost by September. (SJL)

  13. Books for Summer Reading.

    Science.gov (United States)

    Phi Delta Kappan, 1995

    1995-01-01

    Recommends many books for summer reading enjoyment, concentrating on historical and contemporary fiction. Different cultures clash in William T. Vollman's "Fathers and Crows" and John Demos's adventuresome "Unredeemed Captive." Other suggestions: "Snow Falling on Cedar Mountain" (David Gutterman) and "Foxfire" (Joyce Carol Oates). For professional…

  14. Books for Summer Reading.

    Science.gov (United States)

    [Editors

    2001-01-01

    Teachers and education professors suggest various nonfiction and fiction books for summer reading enjoyment, from Robert Putnam's "Bowling Alone," C.A. Bowers's "Let Them Eat Data," and Larry McMurtry's "Roads: Driving America's Great Highways" to Kent Hauf's "Plainsong, J.M. Coetzee's "Disgrace," and Michael Cunningham's "The Hours." (MLH)

  15. My Summer Vacation

    Science.gov (United States)

    Galus, Pamela

    2010-01-01

    In this article, a science teacher from the Midwest reflects on her summer vacation to the Gulf of Mexico. She felt that this vacation would help improve her teaching about the environmental problems in the gulf and elsewhere. After all, anyone can show photos of oil-laden birds and dead sea turtles and read news clips of a distant place, but to…

  16. Use Your Summer Wisely

    Science.gov (United States)

    Vick, Julie Miller; Furlong, Jennifer S.

    2007-01-01

    Academics welcome summer with a collective sigh of relief. Finally they can get to those tasks that are nearly impossible to accomplish during a busy academic year: working on that manuscript, completing the revisions on an article, learning the new laboratory technique from the colleague across the hall. However, those going on the job market in…

  17. Summer student report

    CERN Document Server

    Peedo, Kreete

    2017-01-01

    This report is an overview of the work done in the course of the summer student program. Analysing different OPC-UA stacks. Implemented and evaluated using the OPC-UA Local Discovery Server. Tested the OPC-UA software for calibration curve fitting and analog signal quality measurements.

  18. 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…

  19. 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

  20. 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.

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

    Science.gov (United States)

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

    2017-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Eduardo N. Taboada

    2017-05-01

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

  3. The potential of translational bioinformatics approaches for pharmacology research.

    Science.gov (United States)

    Li, Lang

    2015-10-01

    The field of bioinformatics has allowed the interpretation of massive amounts of biological data, ushering in the era of 'omics' to biomedical research. Its potential impact on pharmacology research is enormous and it has shown some emerging successes. A full realization of this potential, however, requires standardized data annotation for large health record databases and molecular data resources. Improved standardization will further stimulate the development of system pharmacology models, using translational bioinformatics methods. This new translational bioinformatics paradigm is highly complementary to current pharmacological research fields, such as personalized medicine, pharmacoepidemiology and drug discovery. In this review, I illustrate the application of transformational bioinformatics to research in numerous pharmacology subdisciplines. © 2015 The British Pharmacological Society.

  4. Development of a cloud-based Bioinformatics Training Platform

    Science.gov (United States)

    Revote, Jerico; Watson-Haigh, Nathan S.; Quenette, Steve; Bethwaite, Blair; McGrath, Annette

    2017-01-01

    Abstract 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. PMID:27084333

  5. 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 ...

  6. 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.

  7. Bioinformatics Analyst | Center for Cancer Research

    Science.gov (United States)

    BASIC QUALIFICATIONS To be considered for this position, you must minimally meet the knowledge, skills, and abilities listed below: Bachelor’s degree in life science/bioinformatics/math/physics/computer related field from an accredited college or university according to the Council for Higher Education Accreditation (CHEA). (Additional qualifying experience may be substituted for the required education). Foreign degrees must be evaluated for U.S. equivalency. In addition to the educational requirements, a minimum of five (5) years of progressively responsible relevant experience. Must be able to obtain and maintain a security clearance. PREFERRED QUALIFICATIONS Candidates with these desired skills will be given preferential consideration: A Masters’ or PhD degree in any quantitative science is preferred. Commitment to solving biological problems and communicating these solutions. Ability to multi-task across projects. Experience in submitting data sets to public repositories. Management of large genomic data sets including integration with data available from public sources. Prior customer-facing role. Record of scientific achievements including journal publications and conference presentations. Expected Competencies: Deep understanding of and experience in processing high throughput biomedical data: data cleaning, normalization, analysis, interpretation and visualization. Ability to understand and analyze data from complex experimental designs. Proficiency in at least two of the following programming languages: Perl, Python, R, Java and C/C++. Experience in at least two of the following areas: metagenomics, ChIPSeq, RNASeq, ExomeSeq, DHS-Seq, microarray analysis. Familiarity with public databases: NCBI, Ensembl, TCGA, cBioPortal, Broad FireHose. Knowledge of working in a cluster environment.

  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. 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

    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.......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...

  10. Use of BEXA Family Algorithms in Bioinformatics Data Classification

    OpenAIRE

    Gasparoviča-Asīte, M; Aleksejeva, L; Gersons, V

    2012-01-01

    This article studies the possibilities of BEXA family classification algorithms – BEXA, FuzzyBexa and FuzzyBexa II in data, especially bioinformatics data, classification. Three different types of data sets were used in the study – data sets often used in the literature (like Iris data set), UCI data repository real life data sets (like breast cancer data set) and real bioinformatics data sets that have the specific character – a large number of attributes (several thousands) and a small numb...

  11. 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

  12. Making Summer Count: How Summer Programs Can Boost Children's Learning

    Science.gov (United States)

    McCombs, Jennifer Sloan; Augustine, Catherine; Schwartz, Heather; Bodilly, Susan; McInnis, Brian; Lichter, Dahlia; Cross, Amanda Brown

    2012-01-01

    During summer vacation, many students lose knowledge and skills. By the end of summer, students perform, on average, one month behind where they left off in the spring. Participation in summer learning programs should mitigate learning loss and could even produce achievement gains. Indeed, educators and policymakers increasingly promote summer…

  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. 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.

  15. Indian summer monsoon experiments

    OpenAIRE

    Bhat, GS; Narasimha, R

    2007-01-01

    Eight major field experiments have been carried out so far addressing the Indian summer monsoon. While these experiments were international and the impetus was external till 1980, India’s own monsoon programmes evolved since then. In this article, objectives and outcomes from some of these experiments are described. It is shown that monsoon experiments have contributed in several ways. Each experiment enhanced the infrastructure facilities in the country, brought together scientists from diff...

  16. 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.

  17. 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

  18. 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.)

  19. 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 ...

  20. 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...

  1. Promethean Summer: Professional Development Boldly Focuses on the Classics

    Science.gov (United States)

    Dubin, Jennifer

    2014-01-01

    This article describes the Sue Rose Summer Institute for Teachers at the Dallas Institute of Humanities and Culture, which, for 30 years, has treated teachers as intellectuals. To that end, the nonprofit educational organization offers teachers from all grade levels and all disciplines an experience that either reacquaints them with or introduces…

  2. 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

  3. Bioinformatics analysis of circulating cell-free DNA sequencing data.

    Science.gov (United States)

    Chan, Landon L; Jiang, Peiyong

    2015-10-01

    The discovery of cell-free DNA molecules in plasma has opened up numerous opportunities in noninvasive diagnosis. Cell-free DNA molecules have become increasingly recognized as promising biomarkers for detection and management of many diseases. The advent of next generation sequencing has provided unprecedented opportunities to scrutinize the characteristics of cell-free DNA molecules in plasma in a genome-wide fashion and at single-base resolution. Consequently, clinical applications of circulating cell-free DNA analysis have not only revolutionized noninvasive prenatal diagnosis but also facilitated cancer detection and monitoring toward an era of blood-based personalized medicine. With the remarkably increasing throughput and lowering cost of next generation sequencing, bioinformatics analysis becomes increasingly demanding to understand the large amount of data generated by these sequencing platforms. In this Review, we highlight the major bioinformatics algorithms involved in the analysis of cell-free DNA sequencing data. Firstly, we briefly describe the biological properties of these molecules and provide an overview of the general bioinformatics approach for the analysis of cell-free DNA. Then, we discuss the specific upstream bioinformatics considerations concerning the analysis of sequencing data of circulating cell-free DNA, followed by further detailed elaboration on each key clinical situation in noninvasive prenatal diagnosis and cancer management where downstream bioinformatics analysis is heavily involved. We also discuss bioinformatics analysis as well as clinical applications of the newly developed massively parallel bisulfite sequencing of cell-free DNA. Finally, we offer our perspectives on the future development of bioinformatics in noninvasive diagnosis. Copyright © 2015 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

  4. 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

  5. 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...

  6. 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.

  7. Survey of MapReduce frame operation in bioinformatics.

    Science.gov (United States)

    Zou, Quan; Li, Xu-Bin; Jiang, Wen-Rui; Lin, Zi-Yu; Li, Gui-Lin; Chen, Ke

    2014-07-01

    Bioinformatics is challenged by the fact that traditional analysis tools have difficulty in processing large-scale data from high-throughput sequencing. The open source Apache Hadoop project, which adopts the MapReduce framework and a distributed file system, has recently given bioinformatics researchers an opportunity to achieve scalable, efficient and reliable computing performance on Linux clusters and on cloud computing services. In this article, we present MapReduce frame-based applications that can be employed in the next-generation sequencing and other biological domains. In addition, we discuss the challenges faced by this field as well as the future works on parallel computing in bioinformatics. © The Author 2013. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

  8. Developing expertise in bioinformatics for biomedical research in Africa.

    Science.gov (United States)

    Karikari, Thomas K; Quansah, Emmanuel; Mohamed, Wael M Y

    2015-09-01

    Research in bioinformatics has a central role in helping to advance biomedical research. However, its introduction to Africa has been met with some challenges (such as inadequate infrastructure, training opportunities, research funding, human resources, biorepositories and databases) that have contributed to the slow pace of development in this field across the continent. Fortunately, recent improvements in areas such as research funding, infrastructural support and capacity building are helping to develop bioinformatics into an important discipline in Africa. These contributions are leading to the establishment of world-class research facilities, biorepositories, training programmes, scientific networks and funding schemes to improve studies into disease and health in Africa. With increased contribution from all stakeholders, these developments could be further enhanced. Here, we discuss how the recent developments are contributing to the advancement of bioinformatics in Africa.

  9. Developing expertise in bioinformatics for biomedical research in Africa

    Directory of Open Access Journals (Sweden)

    Thomas K. Karikari

    2015-09-01

    Full Text Available Research in bioinformatics has a central role in helping to advance biomedical research. However, its introduction to Africa has been met with some challenges (such as inadequate infrastructure, training opportunities, research funding, human resources, biorepositories and databases that have contributed to the slow pace of development in this field across the continent. Fortunately, recent improvements in areas such as research funding, infrastructural support and capacity building are helping to develop bioinformatics into an important discipline in Africa. These contributions are leading to the establishment of world-class research facilities, biorepositories, training programmes, scientific networks and funding schemes to improve studies into disease and health in Africa. With increased contribution from all stakeholders, these developments could be further enhanced. Here, we discuss how the recent developments are contributing to the advancement of bioinformatics in Africa.

  10. 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.

  11. Bioinformatic training needs at a health sciences campus.

    Science.gov (United States)

    Oliver, Jeffrey C

    2017-01-01

    Health sciences research is increasingly focusing on big data applications, such as genomic technologies and precision medicine, to address key issues in human health. These approaches rely on biological data repositories and bioinformatic analyses, both of which are growing rapidly in size and scope. Libraries play a key role in supporting researchers in navigating these and other information resources. With the goal of supporting bioinformatics research in the health sciences, the University of Arizona Health Sciences Library established a Bioinformation program. To shape the support provided by the library, I developed and administered a needs assessment survey to the University of Arizona Health Sciences campus in Tucson, Arizona. The survey was designed to identify the training topics of interest to health sciences researchers and the preferred modes of training. Survey respondents expressed an interest in a broad array of potential training topics, including "traditional" information seeking as well as interest in analytical training. Of particular interest were training in transcriptomic tools and the use of databases linking genotypes and phenotypes. Staff were most interested in bioinformatics training topics, while faculty were the least interested. Hands-on workshops were significantly preferred over any other mode of training. The University of Arizona Health Sciences Library is meeting those needs through internal programming and external partnerships. The results of the survey demonstrate a keen interest in a variety of bioinformatic resources; the challenge to the library is how to address those training needs. The mode of support depends largely on library staff expertise in the numerous subject-specific databases and tools. Librarian-led bioinformatic training sessions provide opportunities for engagement with researchers at multiple points of the research life cycle. When training needs exceed library capacity, partnering with intramural and

  12. Eastern summer school in nuclear chemistry

    International Nuclear Information System (INIS)

    Katcoff, S.

    1990-01-01

    Start of the ACS school at Brookhaven National Laboratory in 1989 was preceded by almost two years of preparation. Although the ACS Summer School at San Jose, California, served as a model there were problems at BNL related to the differences between a national laboratory and a university. Laboratory space is normally dedicated to specific research projects and suitable unused space for student experiments is difficult to locate. Also, most research equipment is not available or adaptable for instruction, and the scientific staff is normally fully engaged in ongoing research. Generous assistance came from the ACS, the BNL Chemistry Department, the BNL Office of Educational Programs, State University of NY at Stony Brook, Rensselaer Polytechnic Institute, Canberra Industries, and others. Experience of the first two summers will be reviewed

  13. Information Visualization Techniques in Bioinformatics during the Postgenomic Era

    Science.gov (United States)

    Tao, Ying; Liu, Yang; Friedman, Carol

    2010-01-01

    Information visualization techniques, which take advantage of the bandwidth of human vision, are powerful tools for organizing and analyzing a large amount of data. In the postgenomic era, information visualization tools are indispensable for biomedical research. This paper aims to present an overview of current applications of information visualization techniques in bioinformatics for visualizing different types of biological data, such as from genomics, proteomics, expression profiling and structural studies. Finally, we discuss the challenges of information visualization in bioinformatics related to dealing with more complex biological information in the emerging fields of systems biology and systems medicine. PMID:20976032

  14. Bioinformatic scaling of allosteric interactions in biomedical isozymes

    Science.gov (United States)

    Phillips, J. C.

    2016-09-01

    Allosteric (long-range) interactions can be surprisingly strong in proteins of biomedical interest. Here we use bioinformatic scaling to connect prior results on nonsteroidal anti-inflammatory drugs to promising new drugs that inhibit cancer cell metabolism. Many parallel features are apparent, which explain how even one amino acid mutation, remote from active sites, can alter medical results. The enzyme twins involved are cyclooxygenase (aspirin) and isocitrate dehydrogenase (IDH). The IDH results are accurate to 1% and are overdetermined by adjusting a single bioinformatic scaling parameter. It appears that the final stage in optimizing protein functionality may involve leveling of the hydrophobic limits of the arms of conformational hydrophilic hinges.

  15. Bioinformatics Tools for the Discovery of New Nonribosomal Peptides

    DEFF Research Database (Denmark)

    Leclère, Valérie; Weber, Tilmann; Jacques, Philippe

    2016-01-01

    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 decip......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...

  16. Tsunami Summer! 2003 Young Adult Summer Library Program.

    Science.gov (United States)

    Alabama Public Library Service, Montgomery.

    This manual is designed to assist public libraries in Alabama with setting up "Tsunami Summer!," a summer program for young adults, i.e., students in grades 6 through 12. The manual contains the following sections: (1) Publicity and Promotion; (2) Working with Schools; (3) Involving the Students, including teen volunteers, teen advisory…

  17. 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

  18. 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.

  19. Probabilistic models and machine learning in structural bioinformatics.

    Science.gov (United States)

    Hamelryck, Thomas

    2009-10-01

    Structural bioinformatics is concerned with the molecular structure of biomacromolecules on a genomic scale, using computational methods. Classic problems in structural bioinformatics include the prediction of protein and RNA structure from sequence, the design of artificial proteins or enzymes, and the automated analysis and comparison of biomacromolecules in atomic detail. The determination of macromolecular structure from experimental data (for example coming from nuclear magnetic resonance, X-ray crystallography or small angle X-ray scattering) has close ties with the field of structural bioinformatics. Recently, probabilistic models and machine learning methods based on Bayesian principles are providing efficient and rigorous solutions to challenging problems that were long regarded as intractable. In this review, I will highlight some important recent developments in the prediction, analysis and experimental determination of macromolecular structure that are based on such methods. These developments include generative models of protein structure, the estimation of the parameters of energy functions that are used in structure prediction, the superposition of macromolecules and structure determination methods that are based on inference. Although this review is not exhaustive, I believe the selected topics give a good impression of the exciting new, probabilistic road the field of structural bioinformatics is taking.

  20. 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.

  1. Science Academies' Refresher Course on Bioinformatics in Modern ...

    Indian Academy of Sciences (India)

    IAS Admin

    A Refresher Course on 'Bioinformatics in Modern Biology' for graduate and postgraduate college/university teachers will be held at School of Life Sciences, Manipal University, Manipal for two weeks from 5 to 17 May 2014. The objective of this Course is to improvise on teaching methodologies incorporating online teaching ...

  2. 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

  3. 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

  4. 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 ...

  5. Robust enzyme design: bioinformatic tools for improved protein stability.

    Science.gov (United States)

    Suplatov, Dmitry; Voevodin, Vladimir; Švedas, Vytas

    2015-03-01

    The ability of proteins and enzymes to maintain a functionally active conformation under adverse environmental conditions is an important feature of biocatalysts, vaccines, and biopharmaceutical proteins. From an evolutionary perspective, robust stability of proteins improves their biological fitness and allows for further optimization. Viewed from an industrial perspective, enzyme stability is crucial for the practical application of enzymes under the required reaction conditions. In this review, we analyze bioinformatic-driven strategies that are used to predict structural changes that can be applied to wild type proteins in order to produce more stable variants. The most commonly employed techniques can be classified into stochastic approaches, empirical or systematic rational design strategies, and design of chimeric proteins. We conclude that bioinformatic analysis can be efficiently used to study large protein superfamilies systematically as well as to predict particular structural changes which increase enzyme stability. Evolution has created a diversity of protein properties that are encoded in genomic sequences and structural data. Bioinformatics has the power to uncover this evolutionary code and provide a reproducible selection of hotspots - key residues to be mutated in order to produce more stable and functionally diverse proteins and enzymes. Further development of systematic bioinformatic procedures is needed to organize and analyze sequences and structures of proteins within large superfamilies and to link them to function, as well as to provide knowledge-based predictions for experimental evaluation. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Science Academies' Refresher Course on Bioinformatics in Modern ...

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 19; Issue 2. Science Academies' Refresher Course on Bioinformatics in Modern Biology. Information and Announcements Volume 19 Issue 2 February 2014 pp 192-192. Fulltext. Click here to view fulltext PDF. Permanent link:

  7. 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

  8. Bioinformatics Analysis of Envelope Glycoprotein E epitopes of ...

    African Journals Online (AJOL)

    User

    2011-05-02

    May 2, 2011 ... A virus-neutralizing antibody by a virus-specific synthetic peptide. J. Virol. 55(3): 836-839. Geourjon C, Deléage G (1995). SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Bioinformatics, 11(6): 681-684. Guex N, Peitsch MC ...

  9. 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...

  10. 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…

  11. 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…

  12. Bioinformatic analyses of kappa casein gene in mammalian ...

    African Journals Online (AJOL)

    Kappa casein (CSN3) gene is a variant of the milk protein highly conserved in mammalian species. Genetic variations in CSN3 gene of six mammalian livestock species were investigated using bioinformatics approach. A total of twenty-seven CSN3 gene sequences with corresponding amino acids belonging to the six ...

  13. 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…

  14. BIOINFORMATICS SOFTWARE FROM INDIA: CURRENT STATUS AND CHALLENGES

    Directory of Open Access Journals (Sweden)

    Deepti D. Deobagkar

    2017-09-01

    Full Text Available Bioinformatics software and visualisation tools have been a key factor in the rapid and phenomenal advances in genomics, proteomics, medicine, drug discovery, systems approaches and in fact in every area of new development. Indian scientists have also made a mark in a few specific areas. India has an advantage of an early start and extensive and organised network in the Bioinformatics education and research with substantial inputs from the Indian government. India has a strong hold in computation and IT and has a pool of bright and young talent with demographic dividend along with experienced and excellent mentors and researchers. Although small in number and scale, Bioinformatics Industry also has a presence and is making its mark in India. There are a number of high throughput and extremely useful resources available which are critical in biological data analysis and interpretation. This has made a paradigm shift in the way research can be carried out and discoveries can be made in any area of biological, biochemical and chemical research. This article summarises the current status and contributions from India in the development of software and web servers for Bioinformatics applications.

  15. Bioinformatics and phylogenetic analysis of human Tp73 gene

    African Journals Online (AJOL)

    Imtiaz

    2013-06-26

    Jun 26, 2013 ... 2Bioinformatics and Biotechnology, DES, FBAS International Islamic University, Islamabad, Pakistan. Accepted 26 April, 2013. The Tp73 ... New discoveries about the control and function of p73 are still in progress and it is ..... modern research for diagnostics and evolutionary history of p73. REFERENCES.

  16. 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…

  17. 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...

  18. Summer music festivals

    CERN Multimedia

    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...

  19. 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, ...

  20. 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...

  1. 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

  2. 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.

  3. 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

  4. 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 …

  5. 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

  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. 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...

  8. 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...

  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. 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

  11. 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'…

  12. 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.…

  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. 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.].

  15. 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.

  16. 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...

  17. Data Mining for Grammatical Inference with Bioinformatics Criteria

    Science.gov (United States)

    López, Vivian F.; Aguilar, Ramiro; Alonso, Luis; Moreno, María N.; Corchado, Juan M.

    In this paper we describe both theoretical and practical results of a novel data mining process that combines hybrid techniques of association analysis and classical sequentiation algorithms of genomics to generate grammatical structures of a specific language. We used an application of a compilers generator system that allows the development of a practical application within the area of grammarware, where the concepts of the language analysis are applied to other disciplines, such as Bioinformatic. The tool allows the complexity of the obtained grammar to be measured automatically from textual data. A technique of incremental discovery of sequential patterns is presented to obtain simplified production rules, and compacted with bioinformatics criteria to make up a grammar.

  18. 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.  .

  19. Bioinformatics data distribution and integration via Web Services and XML.

    Science.gov (United States)

    Li, Xiao; Zhang, Yizheng

    2003-11-01

    It is widely recognized that exchange, distribution, and integration of biological data are the keys to improve bioinformatics and genome biology in post-genomic era. However, the problem of exchanging and integrating biology data is not solved satisfactorily. The eXtensible Markup Language (XML) is rapidly spreading as an emerging standard for structuring documents to exchange and integrate data on the World Wide Web (WWW). Web service is the next generation of WWW and is founded upon the open standards of W3C (World Wide Web Consortium) and IETF (Internet Engineering Task Force). This paper presents XML and Web Services technologies and their use for an appropriate solution to the problem of bioinformatics data exchange and integration.

  20. 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.

  1. 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.

  2. 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.

  3. 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++)

  4. 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...

  5. 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:

  6. 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.

  7. 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.

  8. Update in research and methods in proteomics and bioinformatics.

    Science.gov (United States)

    Bencharit, Sompop; Border, Michael B; Edelmann, Alex; Byrd, Warren C

    2013-10-01

    The 3rd International Conference on Proteomics & Bioinformatics (Proteomics 2013) Philadelphia, PA, USA, 15-17 July 2013 The Third International Conference on Proteomics & Bioinformatics (Proteomics 2013) was sponsored by the OMICS group and was organized in order to strengthen the future of proteomics science by bringing together professionals, researchers and scholars from leading universities across the globe. The main topics of this conference included the integration of novel platforms in data analysis, the use of a systems biology approach, different novel mass spectrometry platforms and biomarker discovery methods. The conference was divided into proteomic methods and research interests. Among these two categories, interactions between methods in proteomics and bioinformatics, as well as other research methodologies, were discussed. Exceptional topics from the keynote forum, oral presentations and the poster session have been highlighted. The topics range from new techniques for analyzing proteomics data, to new models designed to help better understand genetic variations to the differences in the salivary proteomes of HIV-infected patients.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. Indian Summer Monsoon influence on the Arabian Peninsula Summer Climate

    Science.gov (United States)

    Attada, Raju; Prasad Dasari, Hari; Omar, Knio; Hoteit, Ibrahim

    2017-04-01

    The Indian Summer Monsoon (ISM) is as an integral component of the atmospheric global circulation. During summer, the mid-latitude zone of baroclinic waves in the Middle East region are pushed northward under the influence of ISM. We investigate the impact of ISM on the atmospheric circulation over the Arabian Peninsula on interannual time scale. We analyze various atmospheric variables derived from ECMWF reanalysis. We apply a composite analysis to study the circulation variability over the Middle East during extreme monsoon years. The extreme (strong and weak) monsoon years are identified based on All India Precipitation Index during 1979-2015. Our analysis reveals that ISM is a fundamental driver of the summer circulation over the Middle East. More specifically, during extreme monsoons: (i) the lower tropospheric winds are enhanced and dominated by persistent northerlies along with intensified subsidence due to adiabatic warming, (ii) A prominent baroclinic structure in circulation anomalies are observed, (iii) a meridional shift of the upper tropospheric jet stream (subtropical jet) is noticeable during weak monsoon years; this shift favors a strong Rossby wave response and has a consequent impact on summer circulations over the Middle East, (iv) the upper tropospheric wind anomalies show a well organized train of Rossby waves during strong monsoon years, and (v) Intensification of thermal signal during strong monsoon over West Asia has been noticed. We will present these findings and further discuss the monsoon dynamics controlling the summer Arabian Peninsula circulation.

  16. Bioinformatic analysis and molecular modelling of human ameloblastin suggest a two-domain intrinsically unstructured calcium-binding protein

    Czech Academy of Sciences Publication Activity Database

    Vymětal, Jiří; Slabý, I.; Spahr, A.; Vondrášek, Jiří; Lyngstadaas, S. P.

    2008-01-01

    Roč. 116, č. 2 (2008), s. 124-134 ISSN 0909-8836 R&D Projects: GA ČR GA203/05/0009; GA ČR GA203/06/1727; GA MŠk LC512 Grant - others:EU(XE) QLK3-CT-2001-00090 Institutional research plan: CEZ:AV0Z40550506 Keywords : ameloblastin * bioinformatic modelling * calcium * intrinsically unstructured protein Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.957, year: 2008

  17. 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...

  18. 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...

  19. 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.)

  20. Summer Fun in the Sun

    Science.gov (United States)

    Alexander, D.; Noldon, D.

    2002-05-01

    We report here on the development of a program to incorporate a math/science component, emphasizing space science and solar physics, into an existing set of summer activities sponsored by the National Youth Sports Program (NYSP). NYSP provides summer sports and classroom training components to youth whose families fall within federal poverty guidelines. Recently, a partnership between Lockheed Martin Solar and Astrophysics Lab. and Chabot Community College received NASA IDEAS funding to develop a summer curriculum in math and science to augment the already successful program. This provides an opportunity to significantly enhance the experience of the participating students by giving them access to the latest in space data and direct interaction with space scientists. This paper discusses our goals, our approach and the current status of our curricular materials. We would like to acknowledge funding by the National Youth Sports Program and NASA IDEAS.

  1. Bioinformatics in microbial biotechnology – a mini review

    Directory of Open Access Journals (Sweden)

    Bansal Arvind K

    2005-06-01

    Full Text Available Abstract The revolutionary growth in the computation speed and memory storage capability has fueled a new era in the analysis of biological data. Hundreds of microbial genomes and many eukaryotic genomes including a cleaner draft of human genome have been sequenced raising the expectation of better control of microorganisms. The goals are as lofty as the development of rational drugs and antimicrobial agents, development of new enhanced bacterial strains for bioremediation and pollution control, development of better and easy to administer vaccines, the development of protein biomarkers for various bacterial diseases, and better understanding of host-bacteria interaction to prevent bacterial infections. In the last decade the development of many new bioinformatics techniques and integrated databases has facilitated the realization of these goals. Current research in bioinformatics can be classified into: (i genomics – sequencing and comparative study of genomes to identify gene and genome functionality, (ii proteomics – identification and characterization of protein related properties and reconstruction of metabolic and regulatory pathways, (iii cell visualization and simulation to study and model cell behavior, and (iv application to the development of drugs and anti-microbial agents. In this article, we will focus on the techniques and their limitations in genomics and proteomics. Bioinformatics research can be classified under three major approaches: (1 analysis based upon the available experimental wet-lab data, (2 the use of mathematical modeling to derive new information, and (3 an integrated approach that integrates search techniques with mathematical modeling. The major impact of bioinformatics research has been to automate the genome sequencing, automated development of integrated genomics and proteomics databases, automated genome comparisons to identify the genome function, automated derivation of metabolic pathways, gene

  2. 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

  3. 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

  4. 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...

  5. Multilevel Cellular Automata as a Tool for Studying Bioinformatic Processes

    Science.gov (United States)

    Hogeweg, Paulien

    The signature feature of Cellular Automata is the realization that "simple rules can give rise to complex behavior". In particular how fixed "rock-bottom" simple rules can give rise to multiple levels of organization. Here we describe Multilevel Cellular Automata, in which the microscopic entities (states) and their transition rules themselves are adjusted by the mesoscale patterns that they themselves generate. Thus we study the feedback of higher levels of organization on the lower levels. Such an approach is preeminently important for studying bioinformatic systems. We will here focus on an evolutionary approach to formalize such Multilevel Cellular Automata, and review examples of studies that use them.

  6. [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.

  7. 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)

  8. 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

  9. 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.

  10. Description of a new summer cabbage cultivar

    Directory of Open Access Journals (Sweden)

    Červenski Janko

    2009-01-01

    Full Text Available Cabbage breeding at the Institute of Field and Vegetable Crops is aimed at the development of cultivars and hybrids whose properties meet the demands of the food processing industry and green market, intensive food production and human population, and which are adapted to the local agroclimatic conditions. This paper presents the main characteristics of a cabbage cultivar released by the Ministry of Agriculture, Forestry and Water Management of the Republic of Serbia in 2007. The cabbage cultivar Orion is primarily intended for fresh consumption in summer and pickling. The head is slightly flattened to oval-shaped, reddish white at cross section, with tender inner leaves, good taste and quality. The length of the growing season is 85-95 days (from transplanting to technological maturity. .

  11. Bioinformatics Methods and Tools to Advance Clinical Care. Findings from the Yearbook 2015 Section on Bioinformatics and Translational Informatics.

    Science.gov (United States)

    Soualmia, L F; Lecroq, T

    2015-08-13

    To summarize excellent current research in the field of Bioinformatics and Translational Informatics with application in the health domain and clinical care. We provide a synopsis of the articles selected for the IMIA Yearbook 2015, from which we attempt to derive a synthetic overview of current and future activities in the field. As last year, a first step of selection was performed by querying MEDLINE with a list of MeSH descriptors completed by a list of terms adapted to the section. Each section editor has evaluated separately the set of 1,594 articles and the evaluation results were merged for retaining 15 articles for peer-review. The selection and evaluation process of this Yearbook's section on Bioinformatics and Translational Informatics yielded four excellent articles regarding data management and genome medicine that are mainly tool-based papers. In the first article, the authors present PPISURV a tool for uncovering the role of specific genes in cancer survival outcome. The second article describes the classifier PredictSNP which combines six performing tools for predicting disease-related mutations. In the third article, by presenting a high-coverage map of the human proteome using high resolution mass spectrometry, the authors highlight the need for using mass spectrometry to complement genome annotation. The fourth article is also related to patient survival and decision support. The authors present datamining methods of large-scale datasets of past transplants. The objective is to identify chances of survival. The current research activities still attest the continuous convergence of Bioinformatics and Medical Informatics, with a focus this year on dedicated tools and methods to advance clinical care. Indeed, there is a need for powerful tools for managing and interpreting complex, large-scale genomic and biological datasets, but also a need for user-friendly tools developed for the clinicians in their daily practice. All the recent research and

  12. 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.

  13. Summer Reading Goes High Tech

    Science.gov (United States)

    Fink, Jennifer L. W.

    2012-01-01

    Not long ago, "summer reading" meant settling under a shady tree with a hefty book. Shady trees are still around, but books with pages can seem as out-of-date as vinyl records to many kids, especially older ones. Today, they scroll through content online, swipe pages on tablets, and manage a near-constant stream of media. Teachers can take…

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. Targeting folate metabolism for therapeutic option: A bioinformatics approach.

    Science.gov (United States)

    Hande, Sneha; Goswami, Kalyan; Sharma, Richa; Bhoj, Priyanka; Jena, Lingaraj; Reddy, Maryada Venkata Rami

    2015-11-01

    Lymphatic filariasis, commonly called elephantiasis, poses a burden of estimated level of 5.09 million disability adjusted life year. Limitations of its sole drug, diethylcarbamazine (DEC) drive exploration of effective filarial target. A few plant extracts having polyphenolic ingredients and some synthetic compounds possess potential dihydrofolate reductase (DHFR) inhibitory effect. Here, we postulated a plausible link between folates and polyphenolics based on their common precursor in shikimate metabolism. Considering its implication in structural resemblance based antagonism, we have attempted to validate parasitic DHFR protein as a target. The bioinformatics approach, in the absence of crystal structure of the proposed target, used to authenticate and for virtual docking with suitable tested compounds, showed remarkably lower thermodynamic parameters as opposed to the positive control. A comparative docking analysis between human and Brugia malayi DHFR also showed effective binding parameters with lower inhibition constants of these ligands with parasitic target, but not with human counterpart highlighting safety and efficacy. This study suggests that DHFR could be a valid drug target for lymphatic filariasis, and further reveal that bioinformatics may be an effective tool in reverse pharmacological approach for drug design.

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

    Directory of Open Access Journals (Sweden)

    Karlsson Johan

    2011-10-01

    Full Text Available Abstract Background 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. Results 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. Conclusions 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. 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.

  1. 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.

  2. 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.

  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. 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

  5. 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

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

    Science.gov (United States)

    2010-01-01

    Background 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. Results 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. Conclusions Bioinformatics curation and ontological

  7. 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

  8. 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.

  9. 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 study, we deliberately integrated bioinformatics instruction at multiple course levels into an existing biology curriculum. Students in an introductory biology course, intermediate lab courses, and advanced project-oriented courses all participated in new course components designed to sequentially introduce bioinformatics skills and knowledge, as well as computational approaches that are common to many bioinformatics applications. In each course, bioinformatics learning was embedded in an existing disciplinary instructional sequence, as opposed to having a single course where all bioinformatics learning occurs. We designed direct and indirect assessment tools to follow student progress through the course sequence. Our data show significant gains in both student confidence and ability in bioinformatics during individual courses and as course level increases. Despite evidence of substantial student learning in both bioinformatics and mathematics, students were skeptical about the link between learning bioinformatics and learning mathematics. While our approach resulted in substantial learning gains, student "buy-in" and engagement might be better in longer project-based activities that demand application of skills to research problems. Nevertheless, in situations where a concentrated focus on project-oriented bioinformatics is not possible or desirable, our approach of integrating multiple smaller components into an existing curriculum provides an alternative. Copyright © 2012 Wiley Periodicals, Inc.

  10. 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.

  11. 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.

  12. 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…

  13. 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.

  14. Bioinformatics in the secondary science classroom: A study of state content standards and students' perceptions of, and performance in, bioinformatics lessons

    Science.gov (United States)

    Wefer, Stephen H.

    The proliferation of bioinformatics in modern Biology marks a new revolution in science, which promises to influence science education at all levels. This thesis examined state standards for content that articulated bioinformatics, and explored secondary students' affective and cognitive perceptions of, and performance in, a bioinformatics mini-unit. The results are presented as three studies. The first study analyzed secondary science standards of 49 U.S States (Iowa has no science framework) and the District of Columbia for content related to bioinformatics at the introductory high school biology level. The bionformatics content of each state's Biology standards were categorized into nine areas and the prevalence of each area documented. The nine areas were: The Human Genome Project, Forensics, Evolution, Classification, Nucleotide Variations, Medicine, Computer Use, Agriculture/Food Technology, and Science Technology and Society/Socioscientific Issues (STS/SSI). Findings indicated a generally low representation of bioinformatics related content, which varied substantially across the different areas. Recommendations are made for reworking existing standards to incorporate bioinformatics and to facilitate the goal of promoting science literacy in this emerging new field among secondary school students. The second study examined thirty-two students' affective responses to, and content mastery of, a two-week bioinformatics mini-unit. The findings indicate that the students generally were positive relative to their interest level, the usefulness of the lessons, the difficulty level of the lessons, likeliness to engage in additional bioinformatics, and were overall successful on the assessments. A discussion of the results and significance is followed by suggestions for future research and implementation for transferability. The third study presents a case study of individual differences among ten secondary school students, whose cognitive and affective percepts were

  15. 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/.

  16. Getting started with microbiome analysis: sample acquisition to bioinformatics.

    Science.gov (United States)

    Kumar, Ranjit; Eipers, Peter; Little, Rebecca B; Crowley, Michael; Crossman, David K; Lefkowitz, Elliot J; Morrow, Casey D

    2014-07-14

    Historically, in order to study microbes, it was necessary to grow them in the laboratory. It was clear though that many microbe communities were refractory to study because none of the members could be grown outside of their native habitat. The development of culture-independent methods to study microbiota using high-throughput sequencing of the 16S ribosomal RNA gene variable regions present in all prokaryotic organisms has provided new opportunities to investigate complex microbial communities. In this unit, the process for a microbiome analysis is described. Many of the components required for this process may already exist. A pipeline is described for acquisition of samples from different sites on the human body, isolation of microbial DNA, and DNA sequencing using the Illumina MiSeq sequencing platform. Finally, a new analytical workflow for basic bioinformatics data analysis, QWRAP, is described, which can be used by clinical and basic science investigators. Copyright © 2014 John Wiley & Sons, Inc.

  17. 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

  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. 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.

  20. 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.

  1. Logical comparison over RDF resources in bio-informatics.

    Science.gov (United States)

    Colucci, S; Donini, F M; Di Sciascio, E

    2017-12-01

    Comparison of resources is a frequent task in different bio-informatics applications, including drug-target interaction, drug repositioning and mechanism of action understanding, among others. This paper proposes a general method for the logical comparison of resources modeled in Resource Description Framework and shows its distinguishing features with reference to the comparison of drugs. In particular, the method returns a description of the commonalities between resources, rather than a numerical value estimating their similarity and/or relatedness. The approach is domain-independent and may be flexibly adapted to heterogeneous use cases, according to a process for setting parameters which is completely explicit. The paper also presents an experiment using the dataset Bioportal as knowledge source; the experiment is fully reproducible, thanks to the elicitation of criteria and values for parameter customization. Copyright © 2017 Elsevier Inc. All rights reserved.

  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. 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.

  4. Bioinformatics tools in predictive ecology: applications to fisheries

    Science.gov (United States)

    Tucker, Allan; Duplisea, Daniel

    2012-01-01

    There has been a huge effort in the advancement of analytical techniques for molecular biological data over the past decade. This has led to many novel algorithms that are specialized to deal with data associated with biological phenomena, such as gene expression and protein interactions. In contrast, ecological data analysis has remained focused to some degree on off-the-shelf statistical techniques though this is starting to change with the adoption of state-of-the-art methods, where few assumptions can be made about the data and a more explorative approach is required, for example, through the use of Bayesian networks. In this paper, some novel bioinformatics tools for microarray data are discussed along with their ‘crossover potential’ with an application to fisheries data. In particular, a focus is made on the development of models that identify functionally equivalent species in different fish communities with the aim of predicting functional collapse. PMID:22144390

  5. A Winter Dream of Summer Wonders!

    Science.gov (United States)

    Herman, Herbert

    1975-01-01

    The Extended School Program consists of 3 phases: 1) a remedial reading and mathematics program in school; 2) an excursion program in the metropolitan area; and 3) a summer camp program to overcome the "summer lag". (Author)

  6. Institutional entrepreneurship:

    DEFF Research Database (Denmark)

    Gretzinger, Susanne

    2018-01-01

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

  7. 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

  8. 77 FR 68134 - Submission for OMB Review; Comment Request (30-day): National Institute of Nursing Research (NINR...

    Science.gov (United States)

    2012-11-15

    ...; Comment Request (30-day): National Institute of Nursing Research (NINR) Summer Genetics Institute Alumni... within 30-days of the date of this publication. Proposed Collection: National Institute of Nursing Research (NINR) Summer Genetics Institute Alumni Survey, -0925-New Need and Use of Information Collection...

  9. Southern California Earthquake Center (SCEC) Summer Internship Programs

    Science.gov (United States)

    Benthien, M. L.; Perry, S.; Jordan, T. H.

    2004-12-01

    For the eleventh consecutive year, the Southern California Earthquake Center (SCEC) coordinated undergraduate research experiences in summer 2004, allowing 35 students with a broad array of backgrounds and interests to work with the world's preeminent earthquake scientists and specialists. Students participate in interdisciplinary, system-level earthquake science and information technology research, and several group activities throughout the summer. Funding for student stipends and activities is made possible by the NSF Research Experiences for Undergraduates (REU) program. SCEC coordinates two intern programs: The SCEC Summer Undergraduate Research Experience (SCEC/SURE) and the SCEC Undergraduate Summer in Earthquake Information Technology (SCEC/USEIT). SCEC/SURE interns work one-on-one with SCEC scientists at their institutions on a variety of earthquake science research projects. The goals of the program are to expand student participation in the earth sciences and related disciplines, encourage students to consider careers in research and education, and to increase diversity of students and researchers in the earth sciences. 13 students participated in this program in 2004. SCEC/USEIT is an NSF REU site that brings undergraduate students from across the country to the University of Southern California each summer. SCEC/USEIT interns interact in a team-oriented research environment and are mentored by some of the nation's most distinguished geoscience and computer science researchers. The goals of the program are to allow undergraduates to use advanced tools of information technology to solve problems in earthquake research; close the gap between computer science and geoscience; and engage non-geoscience majors in the application of earth science to the practical problems of reducing earthquake risk. SCEC/USEIT summer research goals are structured around a grand challenge problem in earthquake information technology. For the past three years the students have

  10. 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…

  11. 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...

  12. 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

  13. 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…

  14. 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…

  15. 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…

  16. 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…

  17. 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…

  18. 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…

  19. 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…

  20. 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...

  1. 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…

  2. Visualizing and Sharing Results in Bioinformatics Projects: GBrowse and GenBank Exports

    Science.gov (United States)

    Effective tools for presenting and sharing data are necessary for collaborative projects, typical for bioinformatics. In order to facilitate sharing our data with other genomics, molecular biology, and bioinformatics researchers, we have developed software to export our data to GenBank and combined ...

  3. 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,…

  4. Summer field work in Utrecht and Wageningen

    NARCIS (Netherlands)

    Klemm, W.

    2013-01-01

    Fieldwork completed in summer 2013 for PhD research project "Green Infrastructure for climate-proof "Cities" Summer field work in Utrecht and Wageningen By Wiebke Klemm In summer 2013 I completed the fieldwork for my research 'Green infrastructure for climate-proof cities'. After I had investigated

  5. 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...

  6. 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.

  7. Summer Research Fellowship Programme 2018

    Indian Academy of Sciences (India)

    Upcoming Refresher Courses. Topology 02 to 14 May, 2018. Ramanujan Institute for Advanced Study in Mathematics, University of Madras Register Mathematics 11 to 25 June, 2018. Dayanand Science College, Latur (M.S.) Register Experimental Physics 14 to 29 June, 2018. Birla Institute of Technology, Mesra, Ranchi

  8. A Marketing Strategy for International Summer School

    OpenAIRE

    Helsky-Lehtola, Ursula

    2015-01-01

    This subject for the study was requested by Director of Higher Education Services and Head of International Office at TAMK. A summer school could be a great way to do marketing on the expertise of TAMK in the world. That is why the suggested summer courses in summer school are chosen from the fields of strong expertise at TAMK. The summer school could offer “appetizers” to the future students who might be paying for their studies in the future. The actual target groups for summer school are n...

  9. 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

  10. Summer Oral Expression English course

    CERN Multimedia

    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

  11. Summer Oral Expression English course

    CERN Multimedia

    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.

  12. 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

  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. Institutional Economics.

    Science.gov (United States)

    Samuels, Warren J.

    1984-01-01

    Institutional economics remains a viable alternative approach to economics. It stresses power, technology, and a holistic and evolutionary approach while critiquing the neoclassical approach. General features of institutional economics are examined, and the work of institutionalists in specific areas is discussed. (RM)

  15. A web services choreography scenario for interoperating bioinformatics applications.

    Science.gov (United States)

    de Knikker, Remko; Guo, Youjun; Li, Jin-Long; Kwan, Albert K H; Yip, Kevin Y; Cheung, David W; Cheung, Kei-Hoi

    2004-03-10

    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. 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 with these web services using a web

  16. 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

  17. A web services choreography scenario for interoperating bioinformatics applications

    Science.gov (United States)

    de Knikker, Remko; Guo, Youjun; Li, Jin-long; Kwan, Albert KH; Yip, Kevin Y; Cheung, David W; Cheung, Kei-Hoi

    2004-01-01

    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 with these web

  18. Colonial Institutions

    DEFF Research Database (Denmark)

    McAtackney, Laura; Palmer, Russell

    2016-01-01

    Archaeologically based explorations of colonialism or institutions are common case-studies in global historical archaeology, but the “colonial institution”—the role of institutions as operatives of colonialism—has often been neglected. In this thematic edition we argue that in order to fully...... understand the interconnected, global world one must explicitly dissect the colonial institution as an entwined, dual manifestation that is central to understanding both power and power relations in the modern world. Following Ann Laura Stoler, we have selected case studies from the Australia, Europe, UK...... 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....

  19. 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 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.

  20. 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

  1. 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/.

  2. ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis.

    Directory of Open Access Journals (Sweden)

    Michael Römer

    Full Text Available 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/.

  3. 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

  4. Summer Research Fellowship Programme 2018

    Indian Academy of Sciences (India)

    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. Residence: (080) 2366 2757

  5. 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:

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Phylogenetic diversity (PD and biodiversity conservation: some bioinformatics challenges

    Directory of Open Access Journals (Sweden)

    Daniel P. Faith

    2006-01-01

    Full Text Available Biodiversity conservation addresses information challenges through estimations encapsulated in measures of diversity. A quantitative measure of phylogenetic diversity, “PD”, has been defined as the minimum total length of all the phylogenetic branches required to span a given set of taxa on the phylogenetic tree (Faith 1992a. While a recent paper incorrectly characterizes PD as not including information about deeper phylogenetic branches, PD applications over the past decade document the proper incorporation of shared deep branches when assessing the total PD of a set of taxa. Current PD applications to macroinvertebrate taxa in streams of New South Wales, Australia illustrate the practical importance of this definition. Phylogenetic lineages, often corresponding to new, “cryptic”, taxa, are restricted to a small number of stream localities. A recent case of human impact causing loss of taxa in one locality implies a higher PD value for another locality, because it now uniquely represents a deeper branch. This molecular-based phylogenetic pattern supports the use of DNA barcoding programs for biodiversity conservation planning. Here, PD assessments side-step the contentious use of barcoding-based “species” designations. Bio-informatics challenges include combining different phylogenetic evidence, optimization problems for conservation planning, and effective integration of phylogenetic information with environmental and socio-economic data.

  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. 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.

  15. 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.

  16. Immunogenicity of novel Dengue virus epitopes identified by bioinformatic analysis.

    Science.gov (United States)

    Sánchez-Burgos, Gilma; Ramos-Castañeda, José; Cedillo-Rivera, Roberto; Dumonteil, Eric

    2010-10-01

    We used T cell epitope prediction tools to identify epitopes from Dengue virus polyprotein sequences, and evaluated in vivo and in vitro the immunogenicity and antigenicity of the corresponding synthetic vaccine candidates. Twenty-two epitopes were predicted to have a high affinity for MHC class I (H-2Kd, H-2Dd, H-2Ld alleles) or class II (IAd alleles). These epitopes were conserved between the four virus serotypes, but with no similarity to human and mouse sequences. Thirteen synthetic peptides induced specific antibodies production with or without T cells activation in mice. Three synthetic peptides induced mostly IgG antibodies, and one of these from the E gene induced a neutralizing response. Ten peptides induced a combination of humoral and cellular responses by CD4+ and CD8+ T cells. Twelve peptides were novel B and T cell epitopes. These results indicate that our bioinformatics strategy is a powerful tool for the identification of novel antigens and its application to human HLA may lead to a potent epitope-based vaccine against Dengue virus and many other pathogens. (c) 2010 Elsevier B.V. All rights reserved.

  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. 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 c...... 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....

  20. 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...