WorldWideScience

Sample records for bioinformatic resources students

  1. 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.

  2. 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...

  3. 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.

  4. 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…

  5. 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...

  6. 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.

  7. 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…

  8. E-MSD: an integrated data resource for bioinformatics.

    Science.gov (United States)

    Velankar, S; McNeil, P; Mittard-Runte, V; Suarez, A; Barrell, D; Apweiler, R; Henrick, K

    2005-01-01

    The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the worldwide Protein Data Bank (wwPDB) and to work towards the integration of various bioinformatics data resources. One of the major obstacles to the improved integration of structural databases such as MSD and sequence databases like UniProt is the absence of up to date and well-maintained mapping between corresponding entries. We have worked closely with the UniProt group at the EBI to clean up the taxonomy and sequence cross-reference information in the MSD and UniProt databases. This information is vital for the reliable integration of the sequence family databases such as Pfam and Interpro with the structure-oriented databases of SCOP and CATH. This information has been made available to the eFamily group (http://www.efamily.org.uk/) and now forms the basis of the regular interchange of information between the member databases (MSD, UniProt, Pfam, Interpro, SCOP and CATH). This exchange of annotation information has enriched the structural information in the MSD database with annotation from wider sequence-oriented resources. This work was carried out under the 'Structure Integration with Function, Taxonomy and Sequences (SIFTS)' initiative (http://www.ebi.ac.uk/msd-srv/docs/sifts) in the MSD group.

  9. 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.

  10. 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...

  11. 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 …

  12. Bioinformatics resources for cancer research with an emphasis on gene function and structure prediction tools

    Directory of Open Access Journals (Sweden)

    Daisuke Kihara

    2006-01-01

    Full Text Available The immensely popular fields of cancer research and bioinformatics overlap in many different areas, e.g. large data repositories that allow for users to analyze data from many experiments (data handling, databases, pattern mining, microarray data analysis, and interpretation of proteomics data. There are many newly available resources in these areas that may be unfamiliar to most cancer researchers wanting to incorporate bioinformatics tools and analyses into their work, and also to bioinformaticians looking for real data to develop and test algorithms. This review reveals the interdependence of cancer research and bioinformatics, and highlight the most appropriate and useful resources available to cancer researchers. These include not only public databases, but general and specific bioinformatics tools which can be useful to the cancer researcher. The primary foci are function and structure prediction tools of protein genes. The result is a useful reference to cancer researchers and bioinformaticians studying cancer alike.

  13. 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

  14. G2LC: Resources Autoscaling for Real Time Bioinformatics Applications in IaaS

    Directory of Open Access Journals (Sweden)

    Rongdong Hu

    2015-01-01

    Full Text Available Cloud computing has started to change the way how bioinformatics research is being carried out. Researchers who have taken advantage of this technology can process larger amounts of data and speed up scientific discovery. The variability in data volume results in variable computing requirements. Therefore, bioinformatics researchers are pursuing more reliable and efficient methods for conducting sequencing analyses. This paper proposes an automated resource provisioning method, G2LC, for bioinformatics applications in IaaS. It enables application to output the results in a real time manner. Its main purpose is to guarantee applications performance, while improving resource utilization. Real sequence searching data of BLAST is used to evaluate the effectiveness of G2LC. Experimental results show that G2LC guarantees the application performance, while resource is saved up to 20.14%.

  15. G2LC: Resources Autoscaling for Real Time Bioinformatics Applications in IaaS.

    Science.gov (United States)

    Hu, Rongdong; Liu, Guangming; Jiang, Jingfei; Wang, Lixin

    2015-01-01

    Cloud computing has started to change the way how bioinformatics research is being carried out. Researchers who have taken advantage of this technology can process larger amounts of data and speed up scientific discovery. The variability in data volume results in variable computing requirements. Therefore, bioinformatics researchers are pursuing more reliable and efficient methods for conducting sequencing analyses. This paper proposes an automated resource provisioning method, G2LC, for bioinformatics applications in IaaS. It enables application to output the results in a real time manner. Its main purpose is to guarantee applications performance, while improving resource utilization. Real sequence searching data of BLAST is used to evaluate the effectiveness of G2LC. Experimental results show that G2LC guarantees the application performance, while resource is saved up to 20.14%.

  16. Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat

    NARCIS (Netherlands)

    Babbitt, P.C.; Bagos, P.G.; Bairoch, A.; Bateman, A.; Chatonnet, A.; Chen, M.J.; Craik, D.J.; Finn, R.D.; Gloriam, D.; Haft, D.H.; Henrissat, B.; Holliday, G.L.; Isberg, V.; Kaas, Q.; Landsman, D.; Lenfant, N.; Manning, G.; Nagano, N.; Srinivasan, N.; O'Donovan, C.; Pruitt, K.D.; Sowdhamini, R.; Rawlings, N.D.; Saier, M.H., Jr.; Sharman, J.L.; Spedding, M.; Tsirigos, K.D.; Vastermark, A.; Vriend, G.

    2015-01-01

    During 11-12 August 2014, a Protein Bioinformatics and Community Resources Retreat was held at the Wellcome Trust Genome Campus in Hinxton, UK. This meeting brought together the principal investigators of several specialized protein resources (such as CAZy, TCDB and MEROPS) as well as those from

  17. Web-based bioinformatic resources for protein and nucleic acids ...

    African Journals Online (AJOL)

    The advent of the Internet and the World Wide Web (WWW) has substantially increased the availability of information and computational resources available to experimental biologists. This review will describe the current on-line resources available, including protein and nucleic acids sequence alignment. Key words: ...

  18. 'Students-as-partners' scheme enhances postgraduate students' employability skills while addressing gaps in bioinformatics education.

    Science.gov (United States)

    Mello, Luciane V; Tregilgas, Luke; Cowley, Gwen; Gupta, Anshul; Makki, Fatima; Jhutty, Anjeet; Shanmugasundram, Achchuthan

    2017-01-01

    Teaching bioinformatics is a longstanding challenge for educators who need to demonstrate to students how skills developed in the classroom may be applied to real world research. This study employed an action research methodology which utilised student-staff partnership and peer-learning. It was centred on the experiences of peer-facilitators, students who had previously taken a postgraduate bioinformatics module, and had applied knowledge and skills gained from it to their own research. It aimed to demonstrate to peer-receivers, current students, how bioinformatics could be used in their own research while developing peer-facilitators' teaching and mentoring skills. This student-centred approach was well received by the peer-receivers, who claimed to have gained improved understanding of bioinformatics and its relevance to research. Equally, peer-facilitators also developed a better understanding of the subject and appreciated that the activity was a rare and invaluable opportunity to develop their teaching and mentoring skills, enhancing their employability.

  19. Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat.

    Science.gov (United States)

    Babbitt, Patricia C; Bagos, Pantelis G; Bairoch, Amos; Bateman, Alex; Chatonnet, Arnaud; Chen, Mark Jinan; Craik, David J; Finn, Robert D; Gloriam, David; Haft, Daniel H; Henrissat, Bernard; Holliday, Gemma L; Isberg, Vignir; Kaas, Quentin; Landsman, David; Lenfant, Nicolas; Manning, Gerard; Nagano, Nozomi; Srinivasan, Narayanaswamy; O'Donovan, Claire; Pruitt, Kim D; Sowdhamini, Ramanathan; Rawlings, Neil D; Saier, Milton H; Sharman, Joanna L; Spedding, Michael; Tsirigos, Konstantinos D; Vastermark, Ake; Vriend, Gerrit

    2015-01-01

    During 11-12 August 2014, a Protein Bioinformatics and Community Resources Retreat was held at the Wellcome Trust Genome Campus in Hinxton, UK. This meeting brought together the principal investigators of several specialized protein resources (such as CAZy, TCDB and MEROPS) as well as those from protein databases from the large Bioinformatics centres (including UniProt and RefSeq). The retreat was divided into five sessions: (1) key challenges, (2) the databases represented, (3) best practices for maintenance and curation, (4) information flow to and from large data centers and (5) communication and funding. An important outcome of this meeting was the creation of a Specialist Protein Resource Network that we believe will improve coordination of the activities of its member resources. We invite further protein database resources to join the network and continue the dialogue.

  20. 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…

  1. Students developing resources for students.

    Science.gov (United States)

    Pearce, Michael; Evans, Darrell

    2012-06-01

    The development of new technologies has provided medical education with the ability to enhance the student learning experience and meet the needs of changing curricula. Students quickly adapt to using multimedia learning resources, but these need to be well designed, learner-centred and interactive for students to become significantly engaged. One way to ensure that students become committed users and that resources become distinct elements of the learning cycle is to involve students in resource design and production. Such an approach enables resources to accommodate student needs and preferences, but also provides opportunities for them to develop their own teaching and training skills. The aim of the medical student research project was to design and produce an electronic resource that was focused on a particular anatomical region. The views of other medical students were used to decide what features were suitable for inclusion and the resulting package contained basic principles and clinical relevance, and used a variety of approaches such as images of cadaveric material, living anatomy movies and quizzes. The completed package was assessed using a survey matrix and found to compare well with commercially available products. Given the ever-diversifying arena of multimedia instruction and the ability of students to be fully conversant with technology, this project demonstrates that students are ideal participants and creators of multimedia resources. It is hoped that such an approach will help to further develop the skill base of students, but will also provide an avenue of developing packages that are student user friendly, and that are focused towards particular curricula requirements. © Blackwell Publishing Ltd 2012.

  2. Bioinformatics in the plant genomic and phenomic domain: The German contribution to resources, services and perspectives.

    Science.gov (United States)

    Schmutzer, Thomas; Bolger, Marie E; Rudd, Stephen; Chen, Jinbo; Gundlach, Heidrun; Arend, Daniel; Oppermann, Markus; Weise, Stephan; Lange, Matthias; Spannagl, Manuel; Usadel, Björn; Mayer, Klaus F X; Scholz, Uwe

    2017-11-10

    Plant genetic resources are a substantial opportunity for plant breeding, preservation and maintenance of biological diversity. As part of the German Network for Bioinformatics Infrastructure (de.NBI) the German Crop BioGreenformatics Network (GCBN) focuses mainly on crop plants and provides both data and software infrastructure which are tailored to the needs of the plant research community. Our mission and key objectives include: (1) provision of transparent access to germplasm seeds, (2) the delivery of improved workflows for plant gene annotation, and (3) implementation of bioinformatics services that link genotypes and phenotypes. This review introduces the GCBN's spectrum of web-services and integrated data resources that address common research problems in the plant genomics community. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  3. Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat

    DEFF Research Database (Denmark)

    Babbitt, Patricia C.; Bagos, Pantelis G.; Bairoch, Amos

    2015-01-01

    protein databases from the large Bioinformatics centres (including UniProt and RefSeq). The retreat was divided into five sessions: (1) key challenges, (2) the databases represented, (3) best practices for maintenance and curation, (4) information flow to and from large data centers and (5) communication...... and funding. An important outcome of this meeting was the creation of a Specialist Protein Resource Network that we believe will improve coordination of the activities of its member resources. We invite further protein database resources to join the network and continue the dialogue....

  4. 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

  5. Engaging Students in a Bioinformatics Activity to Introduce Gene Structure and Function

    Directory of Open Access Journals (Sweden)

    Barbara J. May

    2013-02-01

    Full Text Available Bioinformatics spans many fields of biological research and plays a vital role in mining and analyzing data. Therefore, there is an ever-increasing need for students to understand not only what can be learned from this data, but also how to use basic bioinformatics tools.  This activity is designed to provide secondary and undergraduate biology students to a hands-on activity meant to explore and understand gene structure with the use of basic bioinformatic tools.  Students are provided an “unknown” sequence from which they are asked to use a free online gene finder program to identify the gene. Students then predict the putative function of this gene with the use of additional online databases.

  6. 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

  7. Bioinformatics and Systems Biology: bridging the gap between heterogeneous student backgrounds.

    NARCIS (Netherlands)

    Abeln, S.; Molenaar, D.; Feenstra, K.A.; Hoefsloot, H.C.J.; Teusink, B.; Heringa, J.

    2013-01-01

    Teaching students with very diverse backgrounds can be extremely challenging. This article uses the Bioinformatics and Systems Biology MSc in Amsterdam as a case study to describe how the knowledge gap for students with heterogeneous backgrounds can be bridged. We show that a mix in backgrounds can

  8. Evaluating the Effectiveness of a Practical Inquiry-Based Learning Bioinformatics Module on Undergraduate Student Engagement and Applied Skills

    Science.gov (United States)

    Brown, James A. L.

    2016-01-01

    A pedagogic intervention, in the form of an inquiry-based peer-assisted learning project (as a practical student-led bioinformatics module), was assessed for its ability to increase students' engagement, practical bioinformatic skills and process-specific knowledge. Elements assessed were process-specific knowledge following module completion,…

  9. "Students-as-Partners" Scheme Enhances Postgraduate Students' Employability Skills While Addressing Gaps in Bioinformatics Education

    Science.gov (United States)

    Mello, Luciane V.; Tregilgas, Luke; Cowley, Gwen; Gupta, Anshul; Makki, Fatima; Jhutty, Anjeet; Shanmugasundram, Achchuthan

    2017-01-01

    Teaching bioinformatics is a longstanding challenge for educators who need to demonstrate to students how skills developed in the classroom may be applied to real world research. This study employed an action research methodology which utilised student-staff partnership and peer-learning. It was centred on the experiences of peer-facilitators,…

  10. Assessing an effective undergraduate module teaching applied bioinformatics to biology students.

    Science.gov (United States)

    Madlung, Andreas

    2018-01-01

    Applied bioinformatics skills are becoming ever more indispensable for biologists, yet incorporation of these skills into the undergraduate biology curriculum is lagging behind, in part due to a lack of instructors willing and able to teach basic bioinformatics in classes that don't specifically focus on quantitative skill development, such as statistics or computer sciences. To help undergraduate course instructors who themselves did not learn bioinformatics as part of their own education and are hesitant to plunge into teaching big data analysis, a module was developed that is written in plain-enough language, using publicly available computing tools and data, to allow novice instructors to teach next-generation sequence analysis to upper-level undergraduate students. To determine if the module allowed students to develop a better understanding of and appreciation for applied bioinformatics, various tools were developed and employed to assess the impact of the module. This article describes both the module and its assessment. Students found the activity valuable for their education and, in focus group discussions, emphasized that they saw a need for more and earlier instruction of big data analysis as part of the undergraduate biology curriculum.

  11. 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.

  12. 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...

  13. Model-driven user interfaces for bioinformatics data resources: regenerating the wheel as an alternative to reinventing it

    Directory of Open Access Journals (Sweden)

    Swainston Neil

    2006-12-01

    Full Text Available Abstract Background The proliferation of data repositories in bioinformatics has resulted in the development of numerous interfaces that allow scientists to browse, search and analyse the data that they contain. Interfaces typically support repository access by means of web pages, but other means are also used, such as desktop applications and command line tools. Interfaces often duplicate functionality amongst each other, and this implies that associated development activities are repeated in different laboratories. Interfaces developed by public laboratories are often created with limited developer resources. In such environments, reducing the time spent on creating user interfaces allows for a better deployment of resources for specialised tasks, such as data integration or analysis. Laboratories maintaining data resources are challenged to reconcile requirements for software that is reliable, functional and flexible with limitations on software development resources. Results This paper proposes a model-driven approach for the partial generation of user interfaces for searching and browsing bioinformatics data repositories. Inspired by the Model Driven Architecture (MDA of the Object Management Group (OMG, we have developed a system that generates interfaces designed for use with bioinformatics resources. This approach helps laboratory domain experts decrease the amount of time they have to spend dealing with the repetitive aspects of user interface development. As a result, the amount of time they can spend on gathering requirements and helping develop specialised features increases. The resulting system is known as Pierre, and has been validated through its application to use cases in the life sciences, including the PEDRoDB proteomics database and the e-Fungi data warehouse. Conclusion MDAs focus on generating software from models that describe aspects of service capabilities, and can be applied to support rapid development of repository

  14. 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…

  15. Students-as-partners’ scheme enhances postgraduate students’ employability skills while addressing gaps in bioinformatics education

    Science.gov (United States)

    Mello, Luciane V.; Tregilgas, Luke; Cowley, Gwen; Gupta, Anshul; Makki, Fatima; Jhutty, Anjeet; Shanmugasundram, Achchuthan

    2017-01-01

    Abstract Teaching bioinformatics is a longstanding challenge for educators who need to demonstrate to students how skills developed in the classroom may be applied to real world research. This study employed an action research methodology which utilised student–staff partnership and peer-learning. It was centred on the experiences of peer-facilitators, students who had previously taken a postgraduate bioinformatics module, and had applied knowledge and skills gained from it to their own research. It aimed to demonstrate to peer-receivers, current students, how bioinformatics could be used in their own research while developing peer-facilitators’ teaching and mentoring skills. This student-centred approach was well received by the peer-receivers, who claimed to have gained improved understanding of bioinformatics and its relevance to research. Equally, peer-facilitators also developed a better understanding of the subject and appreciated that the activity was a rare and invaluable opportunity to develop their teaching and mentoring skills, enhancing their employability. PMID:29098185

  16. EERE Resources for Undergraduate Students

    Energy Technology Data Exchange (ETDEWEB)

    None

    2016-10-01

    Looking to expand your experience outside of the classroom? The Office of Energy Efficiency and Renewable Energy (EERE) at the U.S. Department of Energy (DOE) has a number of resources available for undergraduate students, including competitions, internships, and career planning information to help you navigate the education to employment pathway in energy.

  17. EERE Resources for Undergraduate Students

    Energy Technology Data Exchange (ETDEWEB)

    None

    2015-04-01

    Looking to expand your experience outside of the classroom? The Office of Energy Efficiency and Renewable Energy (EERE) at the U.S. Department of Energy (DOE) has a number of resources available for undergraduate students, including competitions, internships, and career planning information to help you navigate the education to employment pathway in energy.

  18. EERE Resources for Graduate Students

    Energy Technology Data Exchange (ETDEWEB)

    None

    2015-04-01

    The Office of Energy Efficiency and Renewable Energy (EERE) at the U.S. Department of Energy (DOE) has a number of resources available for graduate students, including research positions, internships, and career-planning information to help you navigate the education-to-employment pathway in energy.

  19. Improved genomic resources and new bioinformatic workflow for the carcinogenic parasite Clonorchis sinensis: Biotechnological implications.

    Science.gov (United States)

    Wang, Daxi; Korhonen, Pasi K; Gasser, Robin B; Young, Neil D

    2018-02-15

    Clonorchis sinensis (family Opisthorchiidae) is an important foodborne parasite that has a major socioeconomic impact on ~35 million people predominantly in China, Vietnam, Korea and the Russian Far East. In humans, infection with C. sinensis causes clonorchiasis, a complex hepatobiliary disease that can induce cholangiocarcinoma (CCA), a malignant cancer of the bile ducts. Central to understanding the epidemiology of this disease is knowledge of genetic variation within and among populations of this parasite. Although most published molecular studies seem to suggest that C. sinensis represents a single species, evidence of karyotypic variation within C. sinensis and cryptic species within a related opisthorchiid fluke (Opisthorchis viverrini) emphasise the importance of studying and comparing the genes and genomes of geographically distinct isolates of C. sinensis. Recently, we sequenced, assembled and characterised a draft nuclear genome of a C. sinensis isolate from Korea and compared it with a published draft genome of a Chinese isolate of this species using a bioinformatic workflow established for comparing draft genome assemblies and their gene annotations. We identified that 50.6% and 51.3% of the Korean and Chinese C. sinensis genomic scaffolds were syntenic, respectively. Within aligned syntenic blocks, the genomes had a high level of nucleotide identity (99.1%) and encoded 15 variable proteins likely to be involved in diverse biological processes. Here, we review current technical challenges of using draft genome assemblies to undertake comparative genomic analyses to quantify genetic variation between isolates of the same species. Using a workflow that overcomes these challenges, we report on a high-quality draft genome for C. sinensis from Korea and comparative genomic analyses, as a basis for future investigations of the genetic structures of C. sinensis populations, and discuss the biotechnological implications of these explorations. Copyright © 2018

  20. SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss

    Science.gov (United States)

    Di Génova, Alex; Aravena, Andrés; Zapata, Luis; González, Mauricio; Maass, Alejandro; Iturra, Patricia

    2011-01-01

    SalmonDB is a new multiorganism database containing EST sequences from Salmo salar, Oncorhynchus mykiss and the whole genome sequence of Danio rerio, Gasterosteus aculeatus, Tetraodon nigroviridis, Oryzias latipes and Takifugu rubripes, built with core components from GMOD project, GOPArc system and the BioMart project. The information provided by this resource includes Gene Ontology terms, metabolic pathways, SNP prediction, CDS prediction, orthologs prediction, several precalculated BLAST searches and domains. It also provides a BLAST server for matching user-provided sequences to any of the databases and an advanced query tool (BioMart) that allows easy browsing of EST databases with user-defined criteria. These tools make SalmonDB database a valuable resource for researchers searching for transcripts and genomic information regarding S. salar and other salmonid species. The database is expected to grow in the near feature, particularly with the S. salar genome sequencing project. Database URL: http://genomicasalmones.dim.uchile.cl/ PMID:22120661

  1. The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud.

    Science.gov (United States)

    Karimi, Kamran; Vize, Peter D

    2014-01-01

    As a model organism database, Xenbase has been providing informatics and genomic data on Xenopus (Silurana) tropicalis and Xenopus laevis frogs for more than a decade. The Xenbase database contains curated, as well as community-contributed and automatically harvested literature, gene and genomic data. A GBrowse genome browser, a BLAST+ server and stock center support are available on the site. When this resource was first built, all software services and components in Xenbase ran on a single physical server, with inherent reliability, scalability and inter-dependence issues. Recent advances in networking and virtualization techniques allowed us to move Xenbase to a virtual environment, and more specifically to a private cloud. To do so we decoupled the different software services and components, such that each would run on a different virtual machine. In the process, we also upgraded many of the components. The resulting system is faster and more reliable. System maintenance is easier, as individual virtual machines can now be updated, backed up and changed independently. We are also experiencing more effective resource allocation and utilization. Database URL: www.xenbase.org. © The Author(s) 2014. Published by Oxford University Press.

  2. Tutorial videos of bioinformatics resources: online distribution trial in Japan named TogoTV.

    Science.gov (United States)

    Kawano, Shin; Ono, Hiromasa; Takagi, Toshihisa; Bono, Hidemasa

    2012-03-01

    In recent years, biological web resources such as databases and tools have become more complex because of the enormous amounts of data generated in the field of life sciences. Traditional methods of distributing tutorials include publishing textbooks and posting web documents, but these static contents cannot adequately describe recent dynamic web services. Due to improvements in computer technology, it is now possible to create dynamic content such as video with minimal effort and low cost on most modern computers. The ease of creating and distributing video tutorials instead of static content improves accessibility for researchers, annotators and curators. This article focuses on online video repositories for educational and tutorial videos provided by resource developers and users. It also describes a project in Japan named TogoTV (http://togotv.dbcls.jp/en/) and discusses the production and distribution of high-quality tutorial videos, which would be useful to viewer, with examples. This article intends to stimulate and encourage researchers who develop and use databases and tools to distribute how-to videos as a tool to enhance product usability.

  3. Assembly, Annotation, and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center.

    Science.gov (United States)

    Wattam, Alice R; Brettin, Thomas; Davis, James J; Gerdes, Svetlana; Kenyon, Ronald; Machi, Dustin; Mao, Chunhong; Olson, Robert; Overbeek, Ross; Pusch, Gordon D; Shukla, Maulik P; Stevens, Rick; Vonstein, Veronika; Warren, Andrew; Xia, Fangfang; Yoo, Hyunseung

    2018-01-01

    In the "big data" era, research biologists are faced with analyzing new types that usually require some level of computational expertise. A number of programs and pipelines exist, but acquiring the expertise to run them, and then understanding the output can be a challenge.The Pathosystems Resource Integration Center (PATRIC, www.patricbrc.org ) has created an end-to-end analysis platform that allows researchers to take their raw reads, assemble a genome, annotate it, and then use a suite of user-friendly tools to compare it to any public data that is available in the repository. With close to 113,000 bacterial and more than 1000 archaeal genomes, PATRIC creates a unique research experience with "virtual integration" of private and public data. PATRIC contains many diverse tools and functionalities to explore both genome-scale and gene expression data, but the main focus of this chapter is on assembly, annotation, and the downstream comparative analysis functionality that is freely available in the resource.

  4. An object-oriented programming system for the integration of internet-based bioinformatics resources.

    Science.gov (United States)

    Beveridge, Allan

    2006-01-01

    The Internet consists of a vast inhomogeneous reservoir of data. Developing software that can integrate a wide variety of different data sources is a major challenge that must be addressed for the realisation of the full potential of the Internet as a scientific research tool. This article presents a semi-automated object-oriented programming system for integrating web-based resources. We demonstrate that the current Internet standards (HTML, CGI [common gateway interface], Java, etc.) can be exploited to develop a data retrieval system that scans existing web interfaces and then uses a set of rules to generate new Java code that can automatically retrieve data from the Web. The validity of the software has been demonstrated by testing it on several biological databases. We also examine the current limitations of the Internet and discuss the need for the development of universal standards for web-based data.

  5. Social tagging in the life sciences: characterizing a new metadata resource for bioinformatics.

    Science.gov (United States)

    Good, Benjamin M; Tennis, Joseph T; Wilkinson, Mark D

    2009-09-25

    Academic social tagging systems, such as Connotea and CiteULike, provide researchers with a means to organize personal collections of online references with keywords (tags) and to share these collections with others. One of the side-effects of the operation of these systems is the generation of large, publicly accessible metadata repositories describing the resources in the collections. In light of the well-known expansion of information in the life sciences and the need for metadata to enhance its value, these repositories present a potentially valuable new resource for application developers. Here we characterize the current contents of two scientifically relevant metadata repositories created through social tagging. This investigation helps to establish how such socially constructed metadata might be used as it stands currently and to suggest ways that new social tagging systems might be designed that would yield better aggregate products. We assessed the metadata that users of CiteULike and Connotea associated with citations in PubMed with the following metrics: coverage of the document space, density of metadata (tags) per document, rates of inter-annotator agreement, and rates of agreement with MeSH indexing. CiteULike and Connotea were very similar on all of the measurements. In comparison to PubMed, document coverage and per-document metadata density were much lower for the social tagging systems. Inter-annotator agreement within the social tagging systems and the agreement between the aggregated social tagging metadata and MeSH indexing was low though the latter could be increased through voting. The most promising uses of metadata from current academic social tagging repositories will be those that find ways to utilize the novel relationships between users, tags, and documents exposed through these systems. For more traditional kinds of indexing-based applications (such as keyword-based search) to benefit substantially from socially generated metadata in

  6. Social tagging in the life sciences: characterizing a new metadata resource for bioinformatics

    Directory of Open Access Journals (Sweden)

    Tennis Joseph T

    2009-09-01

    Full Text Available Abstract Background Academic social tagging systems, such as Connotea and CiteULike, provide researchers with a means to organize personal collections of online references with keywords (tags and to share these collections with others. One of the side-effects of the operation of these systems is the generation of large, publicly accessible metadata repositories describing the resources in the collections. In light of the well-known expansion of information in the life sciences and the need for metadata to enhance its value, these repositories present a potentially valuable new resource for application developers. Here we characterize the current contents of two scientifically relevant metadata repositories created through social tagging. This investigation helps to establish how such socially constructed metadata might be used as it stands currently and to suggest ways that new social tagging systems might be designed that would yield better aggregate products. Results We assessed the metadata that users of CiteULike and Connotea associated with citations in PubMed with the following metrics: coverage of the document space, density of metadata (tags per document, rates of inter-annotator agreement, and rates of agreement with MeSH indexing. CiteULike and Connotea were very similar on all of the measurements. In comparison to PubMed, document coverage and per-document metadata density were much lower for the social tagging systems. Inter-annotator agreement within the social tagging systems and the agreement between the aggregated social tagging metadata and MeSH indexing was low though the latter could be increased through voting. Conclusion The most promising uses of metadata from current academic social tagging repositories will be those that find ways to utilize the novel relationships between users, tags, and documents exposed through these systems. For more traditional kinds of indexing-based applications (such as keyword-based search to

  7. miRToolsGallery: a tag-based and rankable microRNA bioinformatics resources database portal

    Science.gov (United States)

    Chen, Liang; Heikkinen, Liisa; Wang, ChangLiang; Yang, Yang; Knott, K Emily

    2018-01-01

    Abstract Hundreds of bioinformatics tools have been developed for MicroRNA (miRNA) investigations including those used for identification, target prediction, structure and expression profile analysis. However, finding the correct tool for a specific application requires the tedious and laborious process of locating, downloading, testing and validating the appropriate tool from a group of nearly a thousand. In order to facilitate this process, we developed a novel database portal named miRToolsGallery. We constructed the portal by manually curating > 950 miRNA analysis tools and resources. In the portal, a query to locate the appropriate tool is expedited by being searchable, filterable and rankable. The ranking feature is vital to quickly identify and prioritize the more useful from the obscure tools. Tools are ranked via different criteria including the PageRank algorithm, date of publication, number of citations, average of votes and number of publications. miRToolsGallery provides links and data for the comprehensive collection of currently available miRNA tools with a ranking function which can be adjusted using different criteria according to specific requirements. Database URL: http://www.mirtoolsgallery.org

  8. Development of bioinformatics resources for display and analysis of copy number and other structural variants in the human genome.

    Science.gov (United States)

    Zhang, J; Feuk, L; Duggan, G E; Khaja, R; Scherer, S W

    2006-01-01

    The discovery of an abundance of copy number variants (CNVs; gains and losses of DNA sequences >1 kb) and other structural variants in the human genome is influencing the way research and diagnostic analyses are being designed and interpreted. As such, comprehensive databases with the most relevant information will be critical to fully understand the results and have impact in a diverse range of disciplines ranging from molecular biology to clinical genetics. Here, we describe the development of bioinformatics resources to facilitate these studies. The Database of Genomic Variants (http://projects.tcag.ca/variation/) is a comprehensive catalogue of structural variation in the human genome. The database currently contains 1,267 regions reported to contain copy number variation or inversions in apparently healthy human cases. We describe the current contents of the database and how it can serve as a resource for interpretation of array comparative genomic hybridization (array CGH) and other DNA copy imbalance data. We also present the structure of the database, which was built using a new data modeling methodology termed Cross-Referenced Tables (XRT). This is a generic and easy-to-use platform, which is strong in handling textual data and complex relationships. Web-based presentation tools have been built allowing publication of XRT data to the web immediately along with rapid sharing of files with other databases and genome browsers. We also describe a novel tool named eFISH (electronic fluorescence in situ hybridization) (http://projects.tcag.ca/efish/), a BLAST-based program that was developed to facilitate the choice of appropriate clones for FISH and CGH experiments, as well as interpretation of results in which genomic DNA probes are used in hybridization-based experiments. Copyright (c) 2006 S. Karger AG, Basel.

  9. Medical student use of digital learning resources.

    Science.gov (United States)

    Scott, Karen; Morris, Anne; Marais, Ben

    2018-02-01

    University students expect to use technology as part of their studies, yet health professional teachers can struggle with the change in student learning habits fuelled by technology. Our research aimed to document the learning habits of contemporary medical students during a clinical rotation by exploring the use of locally and externally developed digital and print self-directed learning resources, and study groups. We investigated the learning habits of final-stage medical students during their clinical paediatric rotation using mixed methods, involving learning analytics and a student questionnaire. Learning analytics tracked aggregate student usage statistics of locally produced e-learning resources on two learning management systems and mobile learning resources. The questionnaire recorded student-reported use of digital and print learning resources and study groups. The students made extensive use of digital self-directed learning resources, especially in the 2 weeks before the examination, which peaked the day before the written examination. All students used locally produced digital formative assessment, and most (74/98; 76%) also used digital resources developed by other institutions. Most reported finding locally produced e-learning resources beneficial for learning. In terms of traditional forms of self-directed learning, one-third (28/94; 30%) indicated that they never read the course textbook, and few students used face-to-face 39/98 (40%) or online 6/98 (6%) study groups. Learning analytics and student questionnaire data confirmed the extensive use of digital resources for self-directed learning. Through clarification of learning habits and experiences, we think teachers can help students to optimise effective learning strategies; however, the impact of contemporary learning habits on learning efficacy requires further evaluation. Health professional teachers can struggle with the change in student learning habits fuelled by technology. © 2017 John

  10. 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.

  11. 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…

  12. Human Resource Subjects Allocation and Students' Academic ...

    African Journals Online (AJOL)

    This study investigated human resource subjects' allocation and students' academic performance in Secondary Schools in Obudu, Nigeria. The relevant variables of teachers subject was used as independent variable while the dependent variables were students' academic performance. Six hundred teachers from 20 ...

  13. 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.

  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. Assessing Student Understanding of the "New Biology": Development and Evaluation of a Criterion-Referenced Genomics and Bioinformatics Assessment

    Science.gov (United States)

    Campbell, Chad Edward

    Over the past decade, hundreds of studies have introduced genomics and bioinformatics (GB) curricula and laboratory activities at the undergraduate level. While these publications have facilitated the teaching and learning of cutting-edge content, there has yet to be an evaluation of these assessment tools to determine if they are meeting the quality control benchmarks set forth by the educational research community. An analysis of these assessment tools indicated that valid and reliable inferences about student learning. To remedy this situation the development of a robust GB assessment aligned with the quality control benchmarks was undertaken in order to ensure evidence-based evaluation of student learning outcomes. Content validity is a central piece of construct validity, and it must be used to guide instrument and item development. This study reports on: (1) the correspondence of content validity evidence gathered from independent sources; (2) the process of item development using this evidence; (3) the results from a pilot administration of the assessment; (4) the subsequent modification of the assessment based on the pilot administration results and; (5) the results from the second administration of the assessment. Twenty-nine different subtopics within GB (Appendix B: Genomics and Bioinformatics Expert Survey) were developed based on preliminary GB textbook analyses. These subtopics were analyzed using two methods designed to gather content validity evidence: (1) a survey of GB experts (n=61) and (2) a detailed content analyses of GB textbooks (n=6). By including only the subtopics that were shown to have robust support across these sources, 22 GB subtopics were established for inclusion in the assessment. An expert panel subsequently developed, evaluated, and revised two multiple-choice items to align with each of the 22 subtopics, producing a final item pool of 44 items. These items were piloted with student samples of varying content exposure levels

  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 anatomy (Mouse Brain Library), quantitative trait locus analysis (WebQTL from GeneNetwork), bioinformatics and gene expression analyses (University of California, Santa Cruz Genome Browser, National Center for Biotechnology Information's Entrez Gene, and the Allen Brain Atlas), and information resources (PubMed). Instructors can use these various websites in concert to teach genetics from the phenotypic level to the molecular level, aspects of neuroanatomy and histology, statistics, quantitative trait locus analysis, and molecular biology (including in situ hybridization and microarray analysis), and to introduce bioinformatic resources. Students use these resources to discover 1) the region(s) of chromosome(s) influencing the phenotypic trait, 2) a list of candidate genes-narrowed by expression data, 3) the in situ pattern of a given gene in the region of interest, 4) the nucleotide sequence of the candidate gene, and 5) articles describing the gene. Teaching materials such as a detailed student/instructor's manual, PowerPoints, sample exams, and links to free Web resources can be found at http://mdcune.psych.ucla.edu/modules/bioinformatics.

  17. Comparative Modeling of Proteins: A Method for Engaging Students' Interest in Bioinformatics Tools

    Science.gov (United States)

    Badotti, Fernanda; Barbosa, Alan Sales; Reis, André Luiz Martins; do Valle, Ítalo Faria; Ambrósio, Lara; Bitar, Mainá

    2014-01-01

    The huge increase in data being produced in the genomic era has produced a need to incorporate computers into the research process. Sequence generation, its subsequent storage, interpretation, and analysis are now entirely computer-dependent tasks. Universities from all over the world have been challenged to seek a way of encouraging students to…

  18. 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...

  19. Relationship between learning resources and student's academic ...

    African Journals Online (AJOL)

    The study investigated relationship between learning resources and student's academic achievement in science subjects in Taraba State Secondary Schools. A total of 35 science teachers and 18 science head of departments from 6 schools from three geopolitical zones of Taraba State were involved in the study.

  20. Resource Allocation Patterns and Student Achievement

    Science.gov (United States)

    James, Lori; Pate, James; Leech, Donald; Martin, Ellice; Brockmeier, Lantry; Dees, Elizabeth

    2011-01-01

    This quantitative research study was designed to examine the relationship between system resource allocation patterns and student achievement, as measured by eighth grade Criterion-Referenced Competency Test (CRCT) mathematics, eighth grade CRCT reading, eleventh grade Georgia High School Graduation Test (GHSGT) mathematics, eleventh grade and…

  1. Agrigenomics for Microalgal Biofuel Production: An Overview of Various Bioinformatics Resources and Recent Studies to Link OMICS to Bioenergy and Bioeconomy

    Science.gov (United States)

    Misra, Namrata; Parida, Bikram Kumar

    2013-01-01

    Abstract Microalgal biofuels offer great promise in contributing to the growing global demand for alternative sources of renewable energy. However, to make algae-based fuels cost competitive with petroleum, lipid production capabilities of microalgae need to improve substantially. Recent progress in algal genomics, in conjunction with other “omic” approaches, has accelerated the ability to identify metabolic pathways and genes that are potential targets in the development of genetically engineered microalgal strains with optimum lipid content. In this review, we summarize the current bioeconomic status of global biofuel feedstocks with particular reference to the role of “omics” in optimizing sustainable biofuel production. We also provide an overview of the various databases and bioinformatics resources available to gain a more complete understanding of lipid metabolism across algal species, along with the recent contributions of “omic” approaches in the metabolic pathway studies for microalgal biofuel production. PMID:24044362

  2. Agrigenomics for microalgal biofuel production: an overview of various bioinformatics resources and recent studies to link OMICS to bioenergy and bioeconomy.

    Science.gov (United States)

    Misra, Namrata; Panda, Prasanna Kumar; Parida, Bikram Kumar

    2013-11-01

    Microalgal biofuels offer great promise in contributing to the growing global demand for alternative sources of renewable energy. However, to make algae-based fuels cost competitive with petroleum, lipid production capabilities of microalgae need to improve substantially. Recent progress in algal genomics, in conjunction with other "omic" approaches, has accelerated the ability to identify metabolic pathways and genes that are potential targets in the development of genetically engineered microalgal strains with optimum lipid content. In this review, we summarize the current bioeconomic status of global biofuel feedstocks with particular reference to the role of "omics" in optimizing sustainable biofuel production. We also provide an overview of the various databases and bioinformatics resources available to gain a more complete understanding of lipid metabolism across algal species, along with the recent contributions of "omic" approaches in the metabolic pathway studies for microalgal biofuel production.

  3. 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.

  4. 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.

  5. International and Local Student Satisfaction: Resources and Capabilities Perspective

    Science.gov (United States)

    Mavondo, Felix T.; Tsarenko, Yelena; Gabbott, Mark

    2004-01-01

    In this paper, we develop a conceptual model for assessing student satisfaction with universities and the likelihood of students recommending their institutions to other prospective students. Student satisfaction is conceptualised as a mediator between resources and capabilities and recommendation. The resources and capabilities that contribute to…

  6. GALT protein database, a bioinformatics resource for the management and analysis of structural features of a galactosemia-related protein and its mutants.

    Science.gov (United States)

    d'Acierno, Antonio; Facchiano, Angelo; Marabotti, Anna

    2009-06-01

    We describe the GALT-Prot database and its related web-based application that have been developed to collect information about the structural and functional effects of mutations on the human enzyme galactose-1-phosphate uridyltransferase (GALT) involved in the genetic disease named galactosemia type I. Besides a list of missense mutations at gene and protein sequence levels, GALT-Prot reports the analysis results of mutant GALT structures. In addition to the structural information about the wild-type enzyme, the database also includes structures of over 100 single point mutants simulated by means of a computational procedure, and the analysis to each mutant was made with several bioinformatics programs in order to investigate the effect of the mutations. The web-based interface allows querying of the database, and several links are also provided in order to guarantee a high integration with other resources already present on the web. Moreover, the architecture of the database and the web application is flexible and can be easily adapted to store data related to other proteins with point mutations. GALT-Prot is freely available at http://bioinformatica.isa.cnr.it/GALT/.

  7. Applications and methods utilizing the Simple Semantic Web Architecture and Protocol (SSWAP for bioinformatics resource discovery and disparate data and service integration

    Directory of Open Access Journals (Sweden)

    Nelson Rex T

    2010-06-01

    Full Text Available Abstract Background Scientific data integration and computational service discovery are challenges for the bioinformatic community. This process is made more difficult by the separate and independent construction of biological databases, which makes the exchange of data between information resources difficult and labor intensive. A recently described semantic web protocol, the Simple Semantic Web Architecture and Protocol (SSWAP; pronounced "swap" offers the ability to describe data and services in a semantically meaningful way. We report how three major information resources (Gramene, SoyBase and the Legume Information System [LIS] used SSWAP to semantically describe selected data and web services. Methods We selected high-priority Quantitative Trait Locus (QTL, genomic mapping, trait, phenotypic, and sequence data and associated services such as BLAST for publication, data retrieval, and service invocation via semantic web services. Data and services were mapped to concepts and categories as implemented in legacy and de novo community ontologies. We used SSWAP to express these offerings in OWL Web Ontology Language (OWL, Resource Description Framework (RDF and eXtensible Markup Language (XML documents, which are appropriate for their semantic discovery and retrieval. We implemented SSWAP services to respond to web queries and return data. These services are registered with the SSWAP Discovery Server and are available for semantic discovery at http://sswap.info. Results A total of ten services delivering QTL information from Gramene were created. From SoyBase, we created six services delivering information about soybean QTLs, and seven services delivering genetic locus information. For LIS we constructed three services, two of which allow the retrieval of DNA and RNA FASTA sequences with the third service providing nucleic acid sequence comparison capability (BLAST. Conclusions The need for semantic integration technologies has preceded

  8. Applications and methods utilizing the Simple Semantic Web Architecture and Protocol (SSWAP) for bioinformatics resource discovery and disparate data and service integration.

    Science.gov (United States)

    Nelson, Rex T; Avraham, Shulamit; Shoemaker, Randy C; May, Gregory D; Ware, Doreen; Gessler, Damian Dg

    2010-06-04

    Scientific data integration and computational service discovery are challenges for the bioinformatic community. This process is made more difficult by the separate and independent construction of biological databases, which makes the exchange of data between information resources difficult and labor intensive. A recently described semantic web protocol, the Simple Semantic Web Architecture and Protocol (SSWAP; pronounced "swap") offers the ability to describe data and services in a semantically meaningful way. We report how three major information resources (Gramene, SoyBase and the Legume Information System [LIS]) used SSWAP to semantically describe selected data and web services. We selected high-priority Quantitative Trait Locus (QTL), genomic mapping, trait, phenotypic, and sequence data and associated services such as BLAST for publication, data retrieval, and service invocation via semantic web services. Data and services were mapped to concepts and categories as implemented in legacy and de novo community ontologies. We used SSWAP to express these offerings in OWL Web Ontology Language (OWL), Resource Description Framework (RDF) and eXtensible Markup Language (XML) documents, which are appropriate for their semantic discovery and retrieval. We implemented SSWAP services to respond to web queries and return data. These services are registered with the SSWAP Discovery Server and are available for semantic discovery at http://sswap.info. A total of ten services delivering QTL information from Gramene were created. From SoyBase, we created six services delivering information about soybean QTLs, and seven services delivering genetic locus information. For LIS we constructed three services, two of which allow the retrieval of DNA and RNA FASTA sequences with the third service providing nucleic acid sequence comparison capability (BLAST). The need for semantic integration technologies has preceded available solutions. We report the feasibility of mapping high

  9. 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.

  10. 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.

  11. 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…

  12. 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…

  13. 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....

  14. Bioinformatics education in high school: implications for promoting science, technology, engineering, and mathematics careers.

    Science.gov (United States)

    Kovarik, Dina N; Patterson, Davis G; Cohen, Carolyn; Sanders, Elizabeth A; Peterson, Karen A; Porter, Sandra G; Chowning, Jeanne Ting

    2013-01-01

    We investigated the effects of our Bio-ITEST teacher professional development model and bioinformatics curricula on cognitive traits (awareness, engagement, self-efficacy, and relevance) in high school teachers and students that are known to accompany a developing interest in science, technology, engineering, and mathematics (STEM) careers. The program included best practices in adult education and diverse resources to empower teachers to integrate STEM career information into their classrooms. The introductory unit, Using Bioinformatics: Genetic Testing, uses bioinformatics to teach basic concepts in genetics and molecular biology, and the advanced unit, Using Bioinformatics: Genetic Research, utilizes bioinformatics to study evolution and support student research with DNA barcoding. Pre-post surveys demonstrated significant growth (n = 24) among teachers in their preparation to teach the curricula and infuse career awareness into their classes, and these gains were sustained through the end of the academic year. Introductory unit students (n = 289) showed significant gains in awareness, relevance, and self-efficacy. While these students did not show significant gains in engagement, advanced unit students (n = 41) showed gains in all four cognitive areas. Lessons learned during Bio-ITEST are explored in the context of recommendations for other programs that wish to increase student interest in STEM careers.

  15. Bioinformatics Education in High School: Implications for Promoting Science, Technology, Engineering, and Mathematics Careers

    Science.gov (United States)

    Kovarik, Dina N.; Patterson, Davis G.; Cohen, Carolyn; Sanders, Elizabeth A.; Peterson, Karen A.; Porter, Sandra G.; Chowning, Jeanne Ting

    2013-01-01

    We investigated the effects of our Bio-ITEST teacher professional development model and bioinformatics curricula on cognitive traits (awareness, engagement, self-efficacy, and relevance) in high school teachers and students that are known to accompany a developing interest in science, technology, engineering, and mathematics (STEM) careers. The program included best practices in adult education and diverse resources to empower teachers to integrate STEM career information into their classrooms. The introductory unit, Using Bioinformatics: Genetic Testing, uses bioinformatics to teach basic concepts in genetics and molecular biology, and the advanced unit, Using Bioinformatics: Genetic Research, utilizes bioinformatics to study evolution and support student research with DNA barcoding. Pre–post surveys demonstrated significant growth (n = 24) among teachers in their preparation to teach the curricula and infuse career awareness into their classes, and these gains were sustained through the end of the academic year. Introductory unit students (n = 289) showed significant gains in awareness, relevance, and self-efficacy. While these students did not show significant gains in engagement, advanced unit students (n = 41) showed gains in all four cognitive areas. Lessons learned during Bio-ITEST are explored in the context of recommendations for other programs that wish to increase student interest in STEM careers. PMID:24006393

  16. 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).

  17. 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

  18. 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.

  19. National Library of Medicine Web Resources for Student Health Professionals

    Energy Technology Data Exchange (ETDEWEB)

    Womble, R.

    2010-04-02

    Familiarize students affiliated with the Student National Medical Association with the National Library of Medicine's online resources that address medical conditions, health disparities, and public health preparedness needs.

  20. Bioinformatics as a pedagogical resource for the biology course in the State University of Ceara - UECE - Fortaleza, Ceará State - doi: 10.4025/actascieduc.v34i1.14584

    Directory of Open Access Journals (Sweden)

    Howard Lopes Ribeiro Junior

    2012-05-01

    Full Text Available The objective of this study was to evaluate and apply the Bioinformatics theoretical contents and practical for the course students in Biological Sciences Degree Fully enrolled in the disciplines of General Genetics and Molecular Biology, State University of Ceara in 2010. The theoretical approach previously tested (RIBEIRO JUNIOR, 2011 consisted of a presentation of historical concepts, basic and specific to current advances in research involved the areas of molecular biology. The practice of "Building a Molecular Phylogeny in Silico" is designed to become functional in practice the concepts presented above, using the database of the National Center for Biotechnology Information, NCBI, and their sequence alignment tool, the BLASTp (Basic Local Alignment Search Tool Protein-Protein. positive results obtained with the application of the lecture Introduction to Bioinformatics and practical activities were highlighted with the characterizations of molecular phylogenies of the sequences hypothetical proposals for the implementation of the alignments and the statements of students mentioned above. These activities were seen as essential so that students could experience step by step to a better understanding of the emerging field of life sciences: the Bioinformatics

  1. Using CSL with Special Education and Reading Resource Students.

    Science.gov (United States)

    Ellis, Barbara Carter

    1993-01-01

    Describes the experiences of an elementary school resource room teacher in Staten Island (New York) in using community service learning (CSL) with special education and reading resource students. Students planned and carried out a cupcake sale to benefit UNICEF. Parent participation was an important part of the process. (SLD)

  2. Bioinformatics resource manager v2.3: an integrated software environment for systems biology with microRNA and cross-species analysis tools

    Science.gov (United States)

    2012-01-01

    Background MicroRNAs (miRNAs) are noncoding RNAs that direct post-transcriptional regulation of protein coding genes. Recent studies have shown miRNAs are important for controlling many biological processes, including nervous system development, and are highly conserved across species. Given their importance, computational tools are necessary for analysis, interpretation and integration of high-throughput (HTP) miRNA data in an increasing number of model species. The Bioinformatics Resource Manager (BRM) v2.3 is a software environment for data management, mining, integration and functional annotation of HTP biological data. In this study, we report recent updates to BRM for miRNA data analysis and cross-species comparisons across datasets. Results BRM v2.3 has the capability to query predicted miRNA targets from multiple databases, retrieve potential regulatory miRNAs for known genes, integrate experimentally derived miRNA and mRNA datasets, perform ortholog mapping across species, and retrieve annotation and cross-reference identifiers for an expanded number of species. Here we use BRM to show that developmental exposure of zebrafish to 30 uM nicotine from 6–48 hours post fertilization (hpf) results in behavioral hyperactivity in larval zebrafish and alteration of putative miRNA gene targets in whole embryos at developmental stages that encompass early neurogenesis. We show typical workflows for using BRM to integrate experimental zebrafish miRNA and mRNA microarray datasets with example retrievals for zebrafish, including pathway annotation and mapping to human ortholog. Functional analysis of differentially regulated (p<0.05) gene targets in BRM indicates that nicotine exposure disrupts genes involved in neurogenesis, possibly through misregulation of nicotine-sensitive miRNAs. Conclusions BRM provides the ability to mine complex data for identification of candidate miRNAs or pathways that drive phenotypic outcome and, therefore, is a useful hypothesis

  3. Bioinformatics resource manager v2.3: an integrated software environment for systems biology with microRNA and cross-species analysis tools

    Directory of Open Access Journals (Sweden)

    Tilton Susan C

    2012-11-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are noncoding RNAs that direct post-transcriptional regulation of protein coding genes. Recent studies have shown miRNAs are important for controlling many biological processes, including nervous system development, and are highly conserved across species. Given their importance, computational tools are necessary for analysis, interpretation and integration of high-throughput (HTP miRNA data in an increasing number of model species. The Bioinformatics Resource Manager (BRM v2.3 is a software environment for data management, mining, integration and functional annotation of HTP biological data. In this study, we report recent updates to BRM for miRNA data analysis and cross-species comparisons across datasets. Results BRM v2.3 has the capability to query predicted miRNA targets from multiple databases, retrieve potential regulatory miRNAs for known genes, integrate experimentally derived miRNA and mRNA datasets, perform ortholog mapping across species, and retrieve annotation and cross-reference identifiers for an expanded number of species. Here we use BRM to show that developmental exposure of zebrafish to 30 uM nicotine from 6–48 hours post fertilization (hpf results in behavioral hyperactivity in larval zebrafish and alteration of putative miRNA gene targets in whole embryos at developmental stages that encompass early neurogenesis. We show typical workflows for using BRM to integrate experimental zebrafish miRNA and mRNA microarray datasets with example retrievals for zebrafish, including pathway annotation and mapping to human ortholog. Functional analysis of differentially regulated (p Conclusions BRM provides the ability to mine complex data for identification of candidate miRNAs or pathways that drive phenotypic outcome and, therefore, is a useful hypothesis generation tool for systems biology. The miRNA workflow in BRM allows for efficient processing of multiple miRNA and mRNA datasets in a single

  4. International Students as a Resource for Internationalization of Higher Education

    Science.gov (United States)

    Urban, Ewa L.; Palmer, Louann Bierlein

    2014-01-01

    This study used a cross-sectional survey to examine the perceptions of undergraduate and graduate international students enrolled at a public university in the Midwest, regarding international students' perspectives on how their university engages them as cultural resources, and how such engagement might impact students' perceptions of the value…

  5. Student Satisfaction with Electronic Library Resources at Wayne State University

    Science.gov (United States)

    Holley, Robert P.; Powell, Ronald R.

    2004-01-01

    This paper reports the results of a survey of student satisfaction with electronic library resources other than the online catalog at Wayne State University. Undertaken in Fall Term 2000 as a class project for a marketing course, a student team designed, administered, and analyzed a survey of a random sample of students. Almost 40% of the…

  6. 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.

  7. 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...

  8. Modeling Human Serum Albumin Tertiary Structure to Teach Upper-Division Chemistry Students Bioinformatics and Homology Modeling Basics

    Science.gov (United States)

    Petrovic, Dus?an; Zlatovic´, Mario

    2015-01-01

    A homology modeling laboratory experiment has been developed for an introductory molecular modeling course for upper-division undergraduate chemistry students. With this experiment, students gain practical experience in homology model preparation and assessment as well as in protein visualization using the educational version of PyMOL…

  9. 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.

  10. 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.

  11. Stressors, academic performance, and learned resourcefulness in baccalaureate nursing students.

    Science.gov (United States)

    Goff, Anne-Marie

    2011-01-01

    High stress levels in nursing students may affect memory, concentration, and problem-solving ability, and may lead to decreased learning, coping, academic performance, and retention. College students with higher levels of learned resourcefulness develop greater self-confidence, motivation, and academic persistence, and are less likely to become anxious, depressed, and frustrated, but no studies specifically involve nursing students. This explanatory correlational study used Gadzella's Student-life Stress Inventory (SSI) and Rosenbaum's Self Control Scale (SCS) to explore learned resourcefulness, stressors, and academic performance in 53 baccalaureate nursing students. High levels of personal and academic stressors were evident, but not significant predictors of academic performance (p = .90). Age was a significant predictor of academic performance (p = < .01) and males and African-American/Black participants had higher learned resourcefulness scores than females and Caucasians. Studies in larger, more diverse samples are necessary to validate these findings.

  12. Social Studies for "All" Students. Teacher's Resources.

    Science.gov (United States)

    Porter, Priscilla H., Ed.

    1995-01-01

    Maintains that the inclusive classroom is one in which all students, regardless of differences can flourish. Discusses the role of cooperative learning in establishing and maintaining an inclusive classroom. Maintains that inclusion promotes tolerance. (CFR)

  13. Beyond Host Language Proficiency: Coping Resources Predicting International Students' Satisfaction

    Science.gov (United States)

    Mak, Anita S.; Bodycott, Peter; Ramburuth, Prem

    2015-01-01

    As international students navigate in a foreign educational environment, having higher levels of coping or stress-resistance resources--both internal and external--could be related to increased satisfaction with personal and university life. The internal coping resources examined in this study were host language proficiency, self-esteem,…

  14. Barriers and Perceptions of Natural Resource Careers by Minority Students

    Science.gov (United States)

    Haynes, Nia A.; Jacobson, Susan

    2015-01-01

    Using a framework based on social cognitive career theory, we conducted 38 interviews and four focus groups with college students to identify motivations and barriers faced by underrepresented groups to natural resource careers. Interviews revealed career satisfaction as the most important goal for both natural resource and a comparison of liberal…

  15. International Students' Enhanced Academic Performance: Effects of Campus Resources

    Science.gov (United States)

    Banjong, Delphine N.

    2015-01-01

    This article investigates international students' challenges, such as financial, English proficiency, loneliness/homesickness in the United States. In addition, it assesses how these students coped with such difficulties by making use of resources on campus, such as an international center, writing center, counseling center, and the student…

  16. The use of Academic Library Resources among Students of Ogun ...

    African Journals Online (AJOL)

    This Study is a survey of students use of the academic library resources at the Olabisi Onabanjo University Ago-Iwoye and Federal University of Agriculture Abeokuta Ogun State. It used questionnaire for data collection and simple percentage for data analysis , A total of 200 students were randomly selected from each ...

  17. Secondary School Students: Alcohol, Tobacco, and Other Drugs Resource Guide.

    Science.gov (United States)

    Substance Abuse and Mental Health Services Administration (DHHS/PHS), Rockville, MD. Center for Substance Abuse Prevention.

    This resource guide contains a list of materials on drug and alcohol prevention for secondary school students. The information is divided into three sections: (1) prevention materials, including information on inhalants, AIDS, sports and drugs, and sex and alcohol; (2) studies, articles, and reports on secondary school students, including…

  18. Health sciences students' contribution to human resources for health ...

    African Journals Online (AJOL)

    Health sciences students' contribution to human resources for health strategy: A rural health careers day for grade 12 learners in the North West Province of South ... scholarship programme, which highlighted the challenges faced by students from rural communities who try to gain access to institutions of higher education.

  19. Access to electronic information resources by students of federal ...

    African Journals Online (AJOL)

    The paper discusses access to electronic information resources by students of Federal Colleges of Education in Eha-Amufu and Umunze. Descriptive survey design was used to investigate sample of 526 students. Sampling technique used was a Multi sampling technique. Data for the study were generated using ...

  20. Students Against Tobacco. A School Resource Guide.

    Science.gov (United States)

    Texas State Dept. of Health, Austin. Office of Smoking and Health.

    Most smokers begin smoking as teenagers. The younger teenagers are when they start smoking, the more likely it is they will become heavy smokers, and the less likely that they will ever quit. This resource guide points out the problems of teenage smoking and provides action plans to combat using tobacco. Background information is presented about…

  1. Online learning resources in anatomy: What do students think?

    Science.gov (United States)

    Johnson, I P; Palmer, E; Burton, J; Brockhouse, M

    2013-07-01

    An interventional cohort comparison study with pretesting and post-testing in semesters 1 and 2 was undertaken of 159 medical students in year 3 of the MMBS course at the University of Adelaide in 2010. The intervention comprised the provision of a number of additional online resources in semester 2. Students' views on online anatomy were also sought by a questionnaire delivered at the end of semesters 1 and 2 and via a small focus group at the end of the study. Anatomy assessment results after the introduction of online anatomy were compared with a total of three control semesters in 2009 and 2010. There was >90% broad agreement before the intervention that wet specimens, tutors and discussions with other students helped students learn anatomy. After the intervention, these views remained, but there was additionally >90% broad agreement that text books helped them learn anatomy, that they had good access to anatomical specimens, and there was less agreement that lectures helped. The intervention left students' views on online anatomy largely unchanged and made no significant difference to summative assessment scores. Focus group discussions revealed that students want anatomy tutors to help direct them to reputable and relevant sites. The provision of more online resources in anatomy did not affect student views or learning outcomes. While students may need help from tutors in selecting appropriate online resources, wet specimens, textbooks, and discussions with tutors and other students remain the preferred means of learning anatomy. Copyright © 2013 Wiley Periodicals, Inc.

  2. Teacher Resource Packet for Vietnamese Students.

    Science.gov (United States)

    Washington Office of the State Superintendent of Public Instruction, Olympia.

    This packet provides information for classroom teachers who will be working with Vietnamese students. Among the subject matter discussed in the history and general information section are the Republic of Vietnam, family loyalty, professional man, politeness and restraint, village life, fruits and vegetables, meat dishes, festivals, and religion.…

  3. A learning resources centre: its utilization by medical students.

    Science.gov (United States)

    Premkumar, K; Baumber, J S

    1996-11-01

    Innovations in medical education have led to the increasing use of problem-based learning techniques, a committee system organization, and more time for independent study in many undergraduate programmes. There has been an increase in availability of alternative methods for presentation of information. To encourage self-directed learning, resources such as computers, videos and models, among others, should be readily available to students. The University of Calgary Faculty of Medicine has provided various resources contained in one area, called the Bacs Learning Resource Centre (BLRC). Since the maintenance and further development of such a centre requires significant resources, it is important to determine student utilization of the various components used in their learning. For those who are about to set up such a learning resource centre this information gives guidance on which materials are most useful. The utilization of the centre by 69 first year medical students was studied using questionnaires. The utilization during a specific course was determined by analysing the entries in the individual log books given to the students at the beginning of the Integrative Course. With the exception of one student, all those who responded to the questionnaire used the Centre, with 20% or less of their total study time being spent there. The BLRC was most used for the Musculoskeletal, Cardiovascular and Reticulo-Endothelial courses. All categories of resources were found to be useful, with the tape/slides least utilized. Utilization was most influenced by the quality of resources available and recommendations by peers. The development of a centre such as the BLRC, with a variety of resources concentrated in one area, suitable for individual or group study and accessible 24 hours a day, should be considered by all medical schools to enhance self-directed learning in medical students.

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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'…

  9. 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.

  10. Reading interests and use of library resources by students in ...

    African Journals Online (AJOL)

    This study investigated the reading interest and use of school library resources in selected secondary schools in Ijebu-Remo zone of Ogun- State. Survey research design was adopted, while random sampling technique was used to sample 330 students from the five schools surveyed. A self-designed questionnaire was ...

  11. Exploring Spirituality of University FCS Students: A Resource for Resiliency

    Science.gov (United States)

    Rehm, Marsha L.; Allison, Barbara N.

    2009-01-01

    This interview study explored the role of spirituality in the career preparation experiences of 25 university family and consumer sciences (FCS) students. All participants viewed spirituality as both a steadfast higher power and a flexible resource for providing resiliency. Participants believed their career-related experiences were meaningful…

  12. Veterinary students' usage and perception of video teaching resources

    Directory of Open Access Journals (Sweden)

    Jones Michael A

    2011-01-01

    Full Text Available Abstract Background The purpose of our study was to use a student-centred approach to develop an online video learning resource (called 'Moo Tube' at the School of Veterinary Medicine and Science, University of Nottingham, UK and also to provide guidance for other academics in the School wishing to develop a similar resource in the future. Methods A focus group in the format of the nominal group technique was used to garner the opinions of 12 undergraduate students (3 from year-1, 4 from year-2 and 5 from year-3. Students generated lists of items in response to key questions, these responses were thematically analysed to generate key themes which were compared between the different year groups. The number of visits to 'Moo Tube' before and after an objective structured practical examination (OSPE was also analysed to provide data on video usage. Results Students highlighted a number of strengths of video resources which can be grouped into four overarching themes: (1 teaching enhancement, (2 accessibility, (3 technical quality and (4 video content. Of these themes, students rated teaching enhancement and accessibility most highly. Video usage was seen to significantly increase (P Conclusions The students had a positive perception of video usage in higher education. Video usage increases prior to practical examinations. Image quality was a greater concern with year-3 students than with either year-1 or 2 students but all groups highlighted the following as important issues: i good sound quality, ii accessibility, including location of videos within electronic libraries, and iii video content. Based on the findings from this study, guidelines are suggested for those developing undergraduate veterinary videos. We believe that many aspects of our list will have resonance in other areas of medicine education and higher education.

  13. Veterinary students' usage and perception of video teaching resources.

    Science.gov (United States)

    Roshier, Amanda L; Foster, Neil; Jones, Michael A

    2011-01-10

    The purpose of our study was to use a student-centred approach to develop an online video learning resource (called 'Moo Tube') at the School of Veterinary Medicine and Science, University of Nottingham, UK and also to provide guidance for other academics in the School wishing to develop a similar resource in the future. A focus group in the format of the nominal group technique was used to garner the opinions of 12 undergraduate students (3 from year-1, 4 from year-2 and 5 from year-3). Students generated lists of items in response to key questions, these responses were thematically analysed to generate key themes which were compared between the different year groups. The number of visits to 'Moo Tube' before and after an objective structured practical examination (OSPE) was also analysed to provide data on video usage. Students highlighted a number of strengths of video resources which can be grouped into four overarching themes: (1) teaching enhancement, (2) accessibility, (3) technical quality and (4) video content. Of these themes, students rated teaching enhancement and accessibility most highly. Video usage was seen to significantly increase (P students had a positive perception of video usage in higher education. Video usage increases prior to practical examinations. Image quality was a greater concern with year-3 students than with either year-1 or 2 students but all groups highlighted the following as important issues: i) good sound quality, ii) accessibility, including location of videos within electronic libraries, and iii) video content. Based on the findings from this study, guidelines are suggested for those developing undergraduate veterinary videos. We believe that many aspects of our list will have resonance in other areas of medicine education and higher education.

  14. 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.

  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. 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.…

  18. Improvement of Student Understanding of How Kinetic Data Facilitates the Determination of Amino Acid Catalytic Function through an Alkaline Phosphatase Structure/Mechanism Bioinformatics Exercise

    Science.gov (United States)

    Grunwald, Sandra K.; Krueger, Katherine J.

    2008-01-01

    Laboratory exercises, which utilize alkaline phosphatase as a model enzyme, have been developed and used extensively in undergraduate biochemistry courses to illustrate enzyme steady-state kinetics. A bioinformatics laboratory exercise for the biochemistry laboratory, which complements the traditional alkaline phosphatase kinetics exercise, was…

  19. Resources

    Science.gov (United States)

    ... Colon cancer - resources Cystic fibrosis - resources Depression - resources Diabetes - resources Digestive disease - resources Drug abuse - resources Eating disorders - resources Elder care - resources Epilepsy - resources Family ...

  20. Students Teaching Students ­ A Unique Approach to Learning about the Complexities of Marine Resource Management

    OpenAIRE

    Berkson, Jim

    2010-01-01

    The National Mairne Fisheries Service and Virginia Tech have teamed to develop a unique learning experience for top undergraduate students from across the country. During the six week summer program, students learn about the complexities of an important marine resources issue first‐hand from the experts who know the subject the best. In the summer of 2006, six students learned about marine protected areas (MPAs), and in particular, methods to evaluate the effectiveness of MPAs. The six studen...

  1. 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

  2. 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.

  3. 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

  4. 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.

  5. 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…

  6. 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.

  7. Connecting students to institutions: the relationship between program resources and student retention in respiratory care education programs.

    Science.gov (United States)

    Ari, Arzu

    2009-09-01

    Respiratory care education programs are being held accountable for student retention. Increasing student retention is necessary for the respiratory therapy profession, which suffers from a shortage of qualified therapists needed to meet the increased demand. The present study investigated the relationship between student retention rate and program resources, in order to understand which and to what extent the different components of program resources predict student retention rate. The target population of this study was baccalaureate of science degree respiratory care education programs. After utilizing a survey research method, Pearson correlations and multiple regression analysis were used for data analysis. With a 63% response rate (n = 36), this study found a statistically significant relationship between program resources and student retention rate. Financial and personnel resources had a statistically significant positive relationship with student retention. The mean financial resources per student was responsible for 33% of the variance in student retention, while the mean personnel resources per student accounted for 12% of the variance in student retention. Program financial resources available to students was the single best predictor of program performance on student retention. Respiratory care education programs spending more money per student and utilizing more personnel in the program have higher mean performance in student retention. Therefore, respiratory care education programs must devote sufficient resources to retaining students so that they can produce more respiratory therapists and thereby make the respiratory therapy profession stronger.

  8. School resources and student achievment: worldwide findings and methodological issues

    Directory of Open Access Journals (Sweden)

    Paulo A. Meyer. M. Nascimento

    2008-03-01

    Full Text Available The issues raised in the Education Production Function literature since the US 1966 Coleman Report have fuelled high controversy on the role of school resources in relation to student performance. In several literature reviews and some self estimates, Erik Hanushek (1986, 1997, 2006 systematically affirms that these two factors are not associated one to another – neither in the US nor abroad. In recent cross-country analyses, Ludger Woessmann (2003; 2005a; 2005b links international differences in attainment to institutional differences across educational systems – not to resourcing levels. In the opposite direction, Stephen Heyneman and William Loxley (1982, 1983 tried to demonstrate in the 1980’s that, at least for low income countries, school factors seemed to outweigh family characteristics on the determination of students’ outcomes – although other authors show evidence that such a phenomenon may have existed only during a limited period of the 20th Century. In the 1990s, meta-analyses raised the argument that school resources were sufficiently significant to be regarded as pedagogically important. The turn of the Century witnessed a new movement: the recognition that endogenous determination of resource allocation is a substantial methodological issue. Therefore, efforts have been made to incorporate the decision-making processes that involve families, schools and policy-makers in economic models. This implies changes in research designs that may affect the direction of future policy advices patronised by international development and educational organisations.

  9. 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.

  10. 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

  11. 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

  12. 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...

  13. 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.

  14. 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…

  15. Teaching bioinformatics in concert.

    Directory of Open Access Journals (Sweden)

    Anya L Goodman

    2014-11-01

    Full Text Available Can biology students without programming skills solve problems that require computational solutions? They can if they learn to cooperate effectively with computer science students. The goal of the in-concert teaching approach is to introduce biology students to computational thinking by engaging them in collaborative projects structured around the software development process. Our approach emphasizes development of interdisciplinary communication and collaboration skills for both life science and computer science students.

  16. The Integrate Student Portal: Online Resources to Prepare Students for the Workforce of a Sustainable Future

    Science.gov (United States)

    Bruckner, M. Z.; Manduca, C. A.; Egger, A. E.; Macdonald, H.

    2014-12-01

    The InTeGrate Student Portal is a suite of web pages that utilize InTeGrate resources to support student success by providing undergraduates with tools and information necessary to be proactive in their career choices and development. Drawn from various InTeGrate workshops and programming, the Portal organizes these resources to illuminate a variety of career opportunities and pathways to both traditional and non-traditional jobs that support a sustainable future. Informed from a variety of sources including employers, practitioners, faculty, students, reports, and articles, the pages explore five facets: (1) sustainability across the disciplines, (2) workforce preparation, (3) professional communication, (4) teaching and teaching careers, and (5) the future of green research and technology. The first three facets explore how sustainability is integrated across disciplines and how sustainability and 'green' jobs are available in a wide range of traditional and non-traditional workplaces within and beyond science. They provide students guidance in preparing for this sustainability workforce, including where to learn about jobs and how to pursue them, advice for strengthening their job applications, and how to build a set of skills that employers seek. This advice encompasses classroom skills as well as those acquired and strengthened as part of extracurricular or workplace experiences. The fourth facet, aimed at teaching assistants with little or no experience as well as at students who are interested in pursuing teaching as a career, provides information and resources about teaching. The fifth facet explores future directions of technology and the need for innovations in the workforce of the future to address sustainability issues. We seek your input and invite you to explore the Portal at: serc.carleton.edu/integrate/students/

  17. 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.

  18. Development of a cloud-based Bioinformatics Training Platform

    Science.gov (United States)

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

    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

  19. Microbial bioinformatics 2020.

    Science.gov (United States)

    Pallen, Mark J

    2016-09-01

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

  20. 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…

  1. Computer Programming and Biomolecular Structure Studies: A Step beyond Internet Bioinformatics

    Science.gov (United States)

    Likic, Vladimir A.

    2006-01-01

    This article describes the experience of teaching structural bioinformatics to third year undergraduate students in a subject titled "Biomolecular Structure and Bioinformatics." Students were introduced to computer programming and used this knowledge in a practical application as an alternative to the well established Internet bioinformatics…

  2. 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…

  3. Students as ‘resourceful peers’: collaboration with and between students

    OpenAIRE

    Moehrke, Diana; Rajaratnam, Nimalan; Perselli, Victoria

    2014-01-01

    The presentation reports on a research project which explored the term ‘resourceful peers’ in the context of the MA Education (ELT) and was funded by the KU Learning and Teaching Development Fund. It concerned aspects of the taught Research Project module and students’ views towards various activities which sought to engage students with intercultural learning. The findings demonstrated that students’ varied cultural backgrounds clearly impacted their learning; the interactive nature of the v...

  4. 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.

  5. 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.

  6. 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.

  7. Relations between Faculty Use of Online Academic Resources and Student Class Attendance

    Science.gov (United States)

    Kinlaw, C. Ryan; Dunlap, Linda L.; D'Angelo, Jeffrey A.

    2012-01-01

    We investigated connections between faculty use of online resources and student class attendance. Of particular interest was whether online submission of course assignments is detrimental to attendance. Students and faculty at a small, liberal arts college completed surveys about student attendance patterns, student reasons for non-attendance,…

  8. Writing throughout the biochemistry curriculum: Synergistic inquiry-based writing projects for biochemistry students.

    Science.gov (United States)

    Mertz, Pamela; Streu, Craig

    2015-01-01

    This article describes a synergistic two-semester writing sequence for biochemistry courses. In the first semester, students select a putative protein and are tasked with researching their protein largely through bioinformatics resources. In the second semester, students develop original ideas and present them in the form of a research grant proposal. Both projects involve multiple drafts and peer review. The complementarity of the projects increases student exposure to bioinformatics and literature resources, fosters higher-order thinking skills, and develops teamwork and communication skills. Student feedback and responses on perception surveys demonstrated that the students viewed both projects as favorable learning experiences. © 2015 The International Union of Biochemistry and Molecular Biology.

  9. 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.

  10. 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.

  11. 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

  12. 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.

  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 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.

  14. Perceptions of agriculture and natural resource careers among minority students in a national organization

    Science.gov (United States)

    Corliss Wilson Outley

    2008-01-01

    The purpose of the study was to identify factors that influence the career choice behaviors among students who were members of Minorities in Agriculture, Natural Resources and Related Sciences (MANRRS) National Society. A secondary purpose was to identify perceptions and attitudes among students that chose careers in agriculture and natural resources. The MANRRS...

  15. Video Killed the Radio Star: Language Students' Use of Electronic Resources-Reading or Viewing?

    Science.gov (United States)

    Kiliçkaya, Ferit

    2016-01-01

    The current study aimed to investigate language students' use of print and electronic resources for their research papers required in research techniques class, focusing on which reading strategies they used while reading these resources. The participants of the study were 90 sophomore students enrolled in the research techniques class offered at…

  16. Impact of e-resources on learning in biochemistry: first-year medical students' perceptions.

    Science.gov (United States)

    Varghese, Joe; Faith, Minnie; Jacob, Molly

    2012-05-16

    E-learning resources (e-resources) have been widely used to facilitate self-directed learning among medical students. The Department of Biochemistry at Christian Medical College (CMC), Vellore, India, has made available e-resources to first-year medical students to supplement conventional lecture-based teaching in the subject. This study was designed to assess students' perceptions of the impact of these e-resources on various aspects of their learning in biochemistry. Sixty first-year medical students were the subjects of this study. At the end of the one-year course in biochemistry, the students were administered a questionnaire that asked them to assess the impact of the e-resources on various aspects of their learning in biochemistry. Ninety-eight percent of students had used the e-resources provided to varying extents. Most of them found the e-resources provided useful and of a high quality. The majority of them used these resources to prepare for periodic formative and final summative assessments in the course. The use of these resources increased steadily as the academic year progressed. Students said that the extent to which they understood the subject (83%) and their ability to answer questions in assessments (86%) had improved as a result of using these resources. They also said that they found biochemistry interesting (73%) and felt motivated to study the subject (59%). We found that first-year medical students extensively used the e-resources in biochemistry that were provided. They perceived that these resources had made a positive impact on various aspects of their learning in biochemistry. We conclude that e-resources are a useful supplement to conventional lecture-based teaching in the medical curriculum.

  17. An International Survey of Veterinary Students to Assess Their Use of Online Learning Resources.

    Science.gov (United States)

    Gledhill, Laura; Dale, Vicki H M; Powney, Sonya; Gaitskell-Phillips, Gemma H L; Short, Nick R M

    Today's veterinary students have access to a wide range of online resources that support self-directed learning. To develop a benchmark of current global student practice in e-learning, this study measured self-reported access to, and use of, these resources by students internationally. An online survey was designed and promoted via veterinary student mailing lists and international organizations, resulting in 1,070 responses. Analysis of survey data indicated that students now use online resources in a wide range of ways to support their learning. Students reported that access to online veterinary learning resources was now integral to their studies. Almost all students reported using open educational resources (OERs). Ownership of smartphones was widespread, and the majority of respondents agreed that the use of mobile devices, or m-learning, was essential. Social media were highlighted as important for collaborating with peers and sharing knowledge. Constraints to e-learning principally related to poor or absent Internet access and limited institutional provision of computer facilities. There was significant geographical variation, with students from less developed countries disadvantaged by limited access to technology and networks. In conclusion, the survey provides an international benchmark on the range and diversity in terms of access to, and use of, online learning resources by veterinary students globally. It also highlights the inequalities of access among students in different parts of the world.

  18. 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,...

  19. Correlation between Students Academic Performance and Entrepreneurial Ability When Taught Saponification Reaction Using Kitchen Resources

    OpenAIRE

    NJA Cecilia OBI; NEJI Hope Amba

    2014-01-01

    This paper examined the correlation between chemistry student?s academic performance and entrepreneurial ability when told saponification reaction using kitchen resources. Saponification reaction was taught using kitchen resources such as, ashes from unripe plantain, ashes from cocoa pods peels, ashes from oil palm husks, vegetable oil, coconut oil and kernel oil. The sample comprised of 50 students from Community Secondary School, Akparabong in Ikom Local Government Area of Cross River State...

  20. 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.

  1. 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

  2. Understanding the information and resource needs of UK health and social care placement students.

    Science.gov (United States)

    Callaghan, Lynne; Doherty, Alan; Lea, Susan J; Webster, Daniel

    2008-12-01

    Students on health and social care degree programmes spend 50% of their time on practice placements. Because of the diversity of settings and the need to evidence their work, it is vital to understand the information and resource needs of placement students. The aim of this investigation was to understand the needs of placement students in terms of accessing resources whilst they are in the field in order to inform a guide to meet these needs. Focus groups were conducted with students on midwifery, social work and post-registration health professions degree programmes on three different sites across the region. Data were analysed using Thematic Content Analysis. Three themes emerged from the data: inequality, user education needs and students' solutions and strategies. It is essential to speak to placement students in order to understand their needs in terms of accessing and using library resources. The timing and content of information skills training is key to meeting student needs while on placement.

  3. Choice of Study Resources in General Chemistry by Students Who Have Little Time to Study

    Science.gov (United States)

    Bunce, Diane M.; Komperda, Regis; Dillner, Debra K.; Lin, Shirley; Schroeder, Maria J.; Hartman, JudithAnn R.

    2017-01-01

    Students with an insufficient amount of time to study are becoming more prevalent in the general college population as many who enroll in college have competing responsibilities (full-time jobs, childcare, etc.). Such students are likely to choose study resources that they consider to be both effective and efficient. Students at the U.S. Naval…

  4. The Effect of Modeling and Visualization Resources on Student Understanding of Physical Hydrology

    Science.gov (United States)

    Marshall, Jilll A.; Castillo, Adam J.; Cardenas, M. Bayani

    2015-01-01

    We investigated the effect of modeling and visualization resources on upper-division, undergraduate and graduate students' performance on an open-ended assessment of their understanding of physical hydrology. The students were enrolled in one of five sections of a physical hydrology course. In two of the sections, students completed homework…

  5. Disparities in Debt: Parents' Socioeconomic Resources and Young Adult Student Loan Debt

    Science.gov (United States)

    Houle, Jason N.

    2014-01-01

    In an era of rising college costs and stagnant grant-based student aid, many young adults rely on their parents' resources and student loans to pay for their postsecondary education. In this study I ask how parents' income and education are linked to young adults' student loan debt. I develop and test two perspectives regarding the…

  6. Use of internet and E-Resources by Agricultural students in a ...

    African Journals Online (AJOL)

    The study examined the use of internet and e- resources by Agricultural students in a Nigerian university. The total population of students was 1, 200. The population sample for this study was 200 sets of questionnaire were administered to students between 200 and 500 leves in the departments of Agricultural Economics ...

  7. Analysis of Social Sciences High School Students' Remarks on Underground Resources--Kütahya Sample

    Science.gov (United States)

    Hilmi, Sahin Suleyman

    2016-01-01

    The purpose of this study is to explain secondary school students' perceptions of underground resources through metaphors. 154 students studying at Social Sciences High School of Kütahya during 2014-2015 educational year are included in this study. Questions asked in this study are (1) Which metaphors did the secondary school students use in order…

  8. What educational resources are medical students using for personal study during primary care attachments?

    Science.gov (United States)

    Baudains, Catherine; Metters, Emma; Easton, Graham; Booton, Paul

    2013-09-01

    Today's medical students have grown up in a technological world, with access to a wide variety of educational resources for their personal study. Although there is some evidence from the USA that students prefer the internet to textbooks, there is little evidence of UK students' preferences, particularly during their primary care attachments. To identify what educational resources medical students are using for their personal study during primary care attachments and why they make these choices. We held two focus groups, one with five, and one with seven fifth-year UK medical students after their primary care attachment. We analysed the transcripts using thematic analysis to identify the educational resources used, and identified themes to describe why the students made these choices. Textbooks remain students' resource of choice for personal study. The most popular textbook was The Oxford Handbook of Clinical Medicine and internet sites were Google and GP Notebook. The choice of resource was influenced by convenience, purpose, recommendation, exam focus, reliability and learning styles. Two further overarching themes influencing their choices were the broad nature of general practice and the use of GP tutors as an important learning resource. In contrast to the USA, textbooks remain the most popular resource for these UK students. Students felt that the style of learning within general practice was fundamentally different to other specialities due to the breadth of the subject matter and this influenced the resources used. This research could help inform the development of educational resources tailored to the learners, and provides further evidence for the need to develop a more structured curriculum for students in primary care. Further research could explore the ideal role of GP tutors.

  9. Counseling Centers Lack Resources to Help Troubled Students

    Science.gov (United States)

    Farrell, Elizabeth F.

    2008-01-01

    The fatal shootings at Northern Illinois University this month were shocking yet familiar. For the second time in 10 months, a student with a record of mental-health problems went on a killing spree at a large public university. Ever since a disturbed student fatally shot 32 students and professors at Virginia Tech last April, college…

  10. Aplicación de un trabajo práctico autoguiado para la formación en el uso de herramientas bioinformáticas de alumnos de pregrado en Bioquímica Clínica Self-guided training program in the use of bioinformatic tools for undergraduate students of clinical biochemistry

    Directory of Open Access Journals (Sweden)

    Ariel Ernesto Cariaga Martínez

    2006-12-01

    introduce students of clinical biochemistry to the use of bioinformatic resources. The activities comprised genomic, transcriptomic and proteomic analysis of a gene with biomedical implications. The design of specific primers for the amplification of a fragment of the gene was proposed as a technological application. The RasMol program, version 2.7.2 (" by Herbert Bernstein 1998-2000 was used to analyses biological functions. In groups of three or four, students studying cellular and molecular biology as part of their degree in biochemistry at the National University of Misiones were asked to provide concrete answers to questions using bioinformatic analysis. The results showed that 100% of the students were able to answer all the questions. However, a wider-ranging treatment of molecular visualization programs is needed for future applications.

  11. 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

    Undergraduate life sciences education needs an overhaul, as clearly described in the National Research Council of the National Academies publication BIO 2010: Transforming Undergraduate Education for Future Research Biologists. Among BIO 2010's top recommendations is the need to involve students in working with real data and tools that reflect the nature of life sciences research in the 21st century. Education research studies support the importance of utilizing primary literature, designing and implementing experiments, and analyzing results in the context of a bona fide scientific question in cultivating the analytical skills necessary to become a scientist. Incorporating these basic scientific methodologies in undergraduate education leads to increased undergraduate and post-graduate retention in the sciences. Toward this end, many undergraduate teaching organizations offer training and suggestions for faculty to update and improve their teaching approaches to help students learn as scientists, through design and discovery (e.g., Council of Undergraduate Research [www.cur.org] and Project Kaleidoscope [www.pkal.org]). With the advent of genome sequencing and bioinformatics, many scientists now formulate biological questions and interpret research results in the context of genomic information. Just as the use of bioinformatic tools and databases changed the way scientists investigate problems, it must change how scientists teach to create new opportunities for students to gain experiences reflecting the influence of genomics, proteomics, and bioinformatics on modern life sciences research. Educators have responded by incorporating bioinformatics into diverse life science curricula. While these published exercises in, and guidelines for, bioinformatics curricula are helpful and inspirational, faculty new to the area of bioinformatics inevitably need training in the theoretical underpinnings of the algorithms. Moreover, effectively integrating bioinformatics

  12. School Infrastructure and Resources Do Matter: Analysis of the Incidence of School Resources on the Performance of Latin American Students

    Science.gov (United States)

    Murillo, F. Javier; Roman, Marcela

    2011-01-01

    The purpose of this investigation is to determine the incidence of school infrastructure and resources and its impact on the academic performance of primary education students in Latin America. A 4-level multilevel model was applied to the data of the Second Regional Comparative and Explanatory Study (SERCE) conducted by UNESCO, which researched…

  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. 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…

  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. 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…

  17. 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

  18. 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...

  19. 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...

  20. Bioinformatics of genomic association mapping

    NARCIS (Netherlands)

    Vaez Barzani, Ahmad

    2015-01-01

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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. Achieving Inclusion? Effective Resourcing of Students with Special Educational Needs

    Science.gov (United States)

    Banks, Joanne; Frawley, Denise; McCoy, Selina

    2015-01-01

    In line with the increasing policy emphasis on inclusive education, there is now a greater focus on how best to provide for students special educational needs (SEN) in mainstream schools. However, there is little consensus internationally as to the most equitable way in which to support these students. Despite ongoing evaluations of the existing…

  7. Student feedback on an adapted appraisal model in resource ...

    African Journals Online (AJOL)

    Conclusion. Despite failing to build a rapport with their appraisers, students indicated that the chance to discuss academic and personal problems, and their appraisers' advice on study and career matters, had been beneficial. To improve the rapport between students and appraisers a number of suggestions that require ...

  8. Supporting International Students through Strengthening Their Social Resources

    Science.gov (United States)

    Arthur, Nancy

    2017-01-01

    Efforts to recruit international students to higher education must be matched with preparation of the campus community for engaging with this diverse population. The motives of international students for pursuing international studies, including academic and career goals, are facilitated through building strong relationships with members of the…

  9. Teaching Medical Students Basic Neurotransmitter Pharmacology Using Primary Research Resources

    Science.gov (United States)

    Halliday, Amy C.; Devonshire, Ian M.; Greenfield, Susan A.; Dommett, Eleanor J.

    2010-01-01

    Teaching pharmacology to medical students has long been seen as a challenge, and one to which a number of innovative approaches have been taken. In this article, we describe and evaluate the use of primary research articles in teaching second-year medical students both in terms of the information learned and the use of the papers themselves. We…

  10. Students' interim literacies as a dynamic resource for teaching and ...

    African Journals Online (AJOL)

    This article explores the notion of 'interim literacies'by drawing on data from a research project which used linguistic and intertextual analysis of first year student writing in economics to investigate the intersection of academic discourse and student voice. This research has provided a rich set of data to illustrate the ways in ...

  11. 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...

  12. Regular education teacher’s perception about resources and strategies for teaching disabled students

    Directory of Open Access Journals (Sweden)

    Walquíria Gonçalves Reganhan

    2009-09-01

    Full Text Available The resources and strategies adapted for disabled students are an important activity so that the special education needs in the inclusion environment are reached. Thus, the goal of this study was to identify how regular education teacher that have disabled student in theirs classrooms acknowledge the resources and strategies for these students. Five teachers were interviewed. The results indicated that the interviewees: 1 defined the resources the same way the literature of the area does; 2 performed adaptations in the pedagogic resources to reach the needs of the students but they all claimed the need for external aid from other professionals; and 3 expressed difficulty to acknowledge and to describe the strategies of the teaching used. The conclusion indicated that a more solid theoretical ground in the education of these teachers is necessary so that they explain their pedagogic actions.

  13. 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

  14. Teaching medical students about fair distribution of healthcare resources.

    NARCIS (Netherlands)

    Leget, C.J.W.; Hoedemaekers, R.H.M.V.

    2007-01-01

    Healthcare package decisions are complex. Different judgements about effectiveness, cost-effectiveness and disease burden influence the decision-making process. Moreover, different concepts of justice generate different ideas about fair distribution of healthcare resources. This paper presents a

  15. Fostering postgraduate student engagement: online resources supporting self-directed learning in a diverse cohort

    Directory of Open Access Journals (Sweden)

    Luciane V. Mello

    2016-03-01

    Full Text Available The research question for this study was: ‘Can the provision of online resources help to engage and motivate students to become self-directed learners?’ This study presents the results of an action research project to answer this question for a postgraduate module at a research-intensive university in the United Kingdom. The analysis of results from the study was conducted dividing the students according to their programme degree – Masters or PhD – and according to their language skills. The study indicated that the online resources embedded in the module were consistently used, and that the measures put in place to support self-directed learning (SDL were both perceived and valued by the students, irrespective of their programme or native language. Nevertheless, a difference was observed in how students viewed SDL: doctoral students seemed to prefer the approach and were more receptive to it than students pursuing their Masters degree. Some students reported that the SDL activity helped them to achieve more independence than did traditional approaches to teaching. Students who engaged with the online resources were rewarded with higher marks and claimed that they were all the more motivated within the module. Despite the different learning experiences of the diverse cohort, the study found that the blended nature of the course and its resources in support of SDL created a learning environment which positively affected student learning.

  16. 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.

  17. Student perceptions on learning with online resources in a flipped mathematics classroom

    OpenAIRE

    Triantafyllou, Evangelia; Timcenko, Olga

    2015-01-01

    This article discusses student perceptions of if and how online resources contribute to mathematics learning and motivation. It includes results from an online survey we conducted at the Media Technology department of Aalborg University, Copenhagen, Denmark. For this study, students were given links to various online resources (screencasts, online readings and quizzes, and lecture notes) for out-of-class preparation in a flipped classroom in mathematics. The survey results show support for st...

  18. 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

  19. 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

  20. Evaluation of CalMHSA Student Mental Health Online Resources

    OpenAIRE

    Sontag-Padilla, Lisa; Kase, Courtney Ann; Woodbridge, Michelle W.; Stein, Bradley D.

    2016-01-01

    Analysis of visitors to CalMHSA-funded student mental health websites shows that visitors at educational institutions comprised the largest audience segment and promotional campaigns likely increased traffic.

  1. College Students and Alcohol Abuse: New Resources Can Help

    Science.gov (United States)

    ... of Contents From curbing binge drinking to reducing drunk driving, NIH research is developing new intervention tools and ... college students, as well as heavy drinking and drunk driving, all rose. Drinking-related deaths increased, particularly among ...

  2. Student perceptions on learning with online resources in a flipped mathematics classroom

    DEFF Research Database (Denmark)

    Triantafyllou, Eva; Timcenko, Olga

    2015-01-01

    links to various online resources (screencasts, online readings and quizzes, and lecture notes) for out-of-class preparation in a flipped classroom in mathematics. The survey results show support for student perceptions that online resources enhance learning, by providing visual and in depth...

  3. Medical Student Preferences for Self-Directed Study Resources in Gross Anatomy

    Science.gov (United States)

    Choi-Lundberg, Derek L.; Low, Tze Feng; Patman, Phillip; Turner, Paul; Sinha, Sankar N.

    2016-01-01

    Gross anatomy instruction in medical curricula involve a range of resources and activities including dissection, prosected specimens, anatomical models, radiological images, surface anatomy, textbooks, atlases, and computer-assisted learning (CAL). These resources and activities are underpinned by the expectation that students will actively engage…

  4. South Asian and East Asian International Students' Perceived Prejudice, Acculturation, and Frequency of Help Resource Utilization

    Science.gov (United States)

    Frey, Lisa L.; Roysircar, Gargi

    2006-01-01

    Relationships of perceived prejudice and acculturation with frequency of help resource utilization were examined for South Asian and East Asian international students (N = 110). All predictors, including interactions, were significant but showed different relationships for the 2 groups. The mean frequency of help resource utilization was…

  5. Listening to Students: Customer Journey Mapping at Birmingham City University Library and Learning Resources

    Science.gov (United States)

    Andrews, Judith; Eade, Eleanor

    2013-01-01

    Birmingham City University's Library and Learning Resources' strategic aim is to improve student satisfaction. A key element is the achievement of the Customer Excellence Standard. An important component of the standard is the mapping of services to improve quality. Library and Learning Resources has developed a methodology to map these…

  6. Access and Use of E-Resources by the Lecturers and Students of ...

    African Journals Online (AJOL)

    This study examines the use and access of various e-resource databases in Modibbo Adama University of Technology, Yola. The study specifically highlights the preferences and importance of online resources among the lecturers and students of the School of Management and Information Technology of the university.

  7. How 7th Grade Students Are Using Resources for Learning in an Online Science Course

    Science.gov (United States)

    Schafer-Mayse, Diane L.

    2015-01-01

    In this study, 7th grade students were observed completing a series of lessons in an online science course to explore their thinking and strategies for: (1) using curriculum resources for learning, (2) developing thinking and strategies for self-assessing "assessment readiness," and (3) exploring the relationship between resource use and…

  8. Target, Act, Graph (TAG): Teachers Empowering Classroom Resource Personnel in Monitoring Student Progress

    Science.gov (United States)

    Rizzi, Gleides A. L.

    2016-01-01

    This article provides teachers in rural settings with suggestions on how to engage classroom resource personnel (i.e., volunteers, instructional assistants) in monitoring students' achievement. The target, act, and graph (TAG) strategy offers rural special educators ways to empower classroom resource persons through training and use of the TAG…

  9. 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.

  10. Theoretical and methodological support of educational process of students-powerlifters using Internet resources

    OpenAIRE

    Stetsenko Anatolij Ivanovich

    2011-01-01

    It is reviewed scientific journals that have free public access. Investigated the information resources of powerlifting on the internet. Accentuated the importance of using professionally-oriented information resources in the learning process. It is established that Ukrainian language environment of the internet in the sphere of powerlifting has been relatively much attention in comparison with other power sports. Formed the base of internet resources for students of physical culture and spor...

  11. Microcomputers versus Resource Rooms for LD Students: A Preliminary Investigation of the Effects on Math Skills.

    Science.gov (United States)

    Trifiletti, John J.; And Others

    1984-01-01

    Mid-year assessment produced significantly greater results in mastered skills and problem solving by 12 learning disabled (LD) students with 40 minutes daily instruction in the SPARK-80 Computerized Mathematics System on Radio Shack terminals as opposed to nine LD students with traditional resource room mathematics instruction by experienced…

  12. Teaching and Learning Strategies for Serving Underrepresented Students: A Collection of Resource Documents.

    Science.gov (United States)

    Grosz, Karen S., Comp.

    Designed as a resource on teaching and learning strategies geared specifically toward underrepresented community college students, this collection of articles and reports includes the following: (1) "Successful Teaching Strategies: Instruction for Black and Hispanic Students in the California Community Colleges," by Olivia Mercado, Cheryl Fong,…

  13. College students' preferences for health care providers when accessing sexual health resources.

    Science.gov (United States)

    Garcia, Carolyn M; Lechner, Kate E; Frerich, Ellen A; Lust, Katherine A; Eisenberg, Marla E

    2014-01-01

    Many emerging adults (18-25 year olds) report unmet health needs and disproportionately experience problems such as sexually transmitted infections. This study was conducted to examine college students' perceptions of health care providers, specifically in the context of accessing sexual health resources. Students (N = 52) were recruited from five diverse colleges in one state to participate in a one-to-one interview that involved walking and virtually exploring resources on and near campus. Interviews were conducted from May to November 2010. Open-ended one-to-one interview questions. Inductive qualitative analysis yielded six themes summarizing students' perceptions of provider characteristics, health care resources, the role of their peers, and students' suggestions for strengthening health care services. Importantly, students consider a variety of staff-and their student peers-to be resources for sexual health information and services. Findings emphasize the importance of collaboration between health service staff and broader campus staff because students often turn to campus staff initially. Postsecondary students welcome opportunities to know a provider through interactive websites that include details about providers on campus; their decisions to seek sexual health care services are influenced by their perceptions of providers' characteristics and interpersonal skills. © 2014 Wiley Periodicals, Inc.

  14. Aligning Demographics and Resources: A Call to Support Spiritual-but-Not-Religious College Students

    Science.gov (United States)

    Mendizabal, Juan Cruz

    2018-01-01

    This article discusses the rapidly growing population of spiritual-but-not-religious (SBNR) college students and describes the disparity in SBNR-dedicated resources for student support. This disparity is embedded in various tensions that cause low SBNR visibility in universities, including a lack of SBNR programming models in broader higher…

  15. Technology in College Unions and Student Activities: A Collection of Technology Resources from the ACUI Community

    Science.gov (United States)

    Association of College Unions International (NJ1), 2012

    2012-01-01

    This publication presents a collection of technology resources from the Association of College Unions International (ACUI) community. Contents include: (1) Podcasting (Jeff Lail); (2) Video Podcasting (Ed Cabellon); (3) Building a Multimedia Production Center (Nathan Byrer); (4) Cloud Computing in the Student Union and Student Activities (TJ…

  16. Innovative Resources Based on ICTs and Authentic Materials to Improve EFL Students' Communicative Needs

    Science.gov (United States)

    González Otero, Rebeca

    2016-01-01

    Our global society and our current communication needs have put a strain on English as a Foreign Language (EFL) teaching, since common resources such as textbooks may fail to adapt to the needs and interests of our students. The present action research study aims at identifying EFL students' communicative needs and developing their oral skills…

  17. Assessing Student Attitudes toward Animal Welfare, Resource Use, and Food Safety.

    Science.gov (United States)

    Nordstrom, Patricia A.; Richards, Martha J.; Wilson, Lowell L.; Coe, Brenda L.; Fivek, Marianne L.; Brown, Michele B.

    2000-01-01

    Students participating in the Pennsylvania Governor's School for Agricultural Sciences (n=192) studied animal welfare, resource use, and food safety. They ranked food safety as a primary concern. Students with and without agricultural backgrounds showed positive changes in knowledge and perception of issues after the course. (SK)

  18. Investigating Deaf Students' Use of Visual Multimedia Resources in Reading Comprehension

    Science.gov (United States)

    Nikolaraizi, Magda; Vekiri, Ioanna; Easterbrooks, Susan R.

    2013-01-01

    A mixed research design was used to examine how deaf students used the visual resources of a multimedia software package that was designed to support reading comprehension. The viewing behavior of 8 deaf students, ages 8-12 years, was recorded during their interaction with multimedia software that included narrative texts enriched with Greek Sign…

  19. Resources for Deaf and Hard-of-Hearing Students in Mainstream Schools in Sweden. A Survey

    Science.gov (United States)

    Holmström, Ingela; Schönström, Krister

    2017-01-01

    Although once placed solely in deaf schools, a growing number of deaf students in Sweden are now enrolling in mainstream schools. In order to maintain a functional educational environment for these students, municipalities are required to provide a variety of supporting resources, e.g. technological equipment and specialized personnel. However,…

  20. What Is the Impact of Online Resource Materials on Student Self-Learning Strategies?

    Science.gov (United States)

    Dowell, David John; Small, Felicity A.

    2011-01-01

    The purpose of this article is to examine how students are incorporating online resources into their self-regulated learning strategies. The process of developing these learning strategies and the importance of these strategies has been widely researched, but there has been little empirical research into how the students are affected by online…

  1. Empowering Teachers to Author Multimedia Learning Resources That Support Students' Critical Thinking

    Science.gov (United States)

    Holley, Debbie; Boyle, Tom

    2012-01-01

    Students studying Marketing, Fashion, Public Relations, Advertising and similar subjects need to develop a "critical eye" in relation to images, media and digital technologies. This project aims to empower teachers to develop multimedia learning resources that would support students engaging in this essential activity. Developing such…

  2. Students' Multilingual Resources and Policy-in-Action: An Australian Case Study

    Science.gov (United States)

    French, Mei

    2016-01-01

    In the context of increasing linguistic and cultural diversity in Australian schools, it is important to consider the value of students' multilingual resources for learning. This paper reports on an ethnographic case study conducted in an Australian metropolitan secondary school where the student body represented more than 40 cultures and…

  3. Optional Anatomy and Physiology e-Learning Resources: Student Access, Learning Approaches, and Academic Outcomes

    Science.gov (United States)

    Guy, Richard,; Byrne, Bruce; Dobos, Marian

    2018-01-01

    Anatomy and physiology interactive video clips were introduced into a blended learning environment, as an optional resource, and were accessed by ~50% of the cohort. Student feedback indicated that clips were engaging, assisted understanding of course content, and provided lecture support. Students could also access two other optional online…

  4. 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.

  5. 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.

  6. Students' Use of Their Plurilingual Resources in Australian Schools

    Science.gov (United States)

    Fielding, Ruth

    2016-01-01

    Research involving the plurilingualism of young people has begun to focus upon how we must re-conceptualise language learning to acknowledge the language resources of children with plurilingual experiences. This is particularly important in countries like Australia with a traditionally monolingual mindset embedded in policy, education, and the…

  7. Development of a digital storytelling resource to support children's nursing students in neonatal care.

    Science.gov (United States)

    Petty, Julia; Treves, Richard

    2017-03-06

    A digital storytelling resource focusing on the experience of nursing in neonatal care was developed using the narratives of six undergraduate children's nursing students who had undergone a practice placement on a neonatal unit. An evaluation of the resource in relation to its contribution to learning for students in a new, specialised area of practice revealed that storytelling based on peers' experiences is a valuable and insightful approach to learning. This is particularly important in a specialty such as neonatal care where the unfamiliarity of the environment and patient group can cause anxiety and uncertainty among students. Overall, the resource was seen to be useful to children's nursing students who are preparing for a practice placement in an unfamiliar clinical area.

  8. Mass Media: A Student's Guide to Reference Resources.

    Science.gov (United States)

    Waiser, Joni

    Intended to assist students in locating information and literature for the sociological study of the media, this guide concentrates largely on radio, television, newspaper, and magazine reference sources. The first section of the guide lists reference works, including handbooks; English, French, and bilingual dictionaries and encyclopedias;…

  9. Professionalising the use of the student resource for innovation

    DEFF Research Database (Denmark)

    Vetner, Mikael; Lund, Marie Fallgaard; Dahlgaard, Morten

    2015-01-01

    of the fact that the full potential of student driven innovation has not yet been realized. Therefore two different approaches to collaboration between HEI’s and industry have been developed; Solution Hub and U-CrAc. For both approaches it has been essential to provide a framework that will help solve “wicked...

  10. Students with Cancer: A Resource for the Educator. Revised.

    Science.gov (United States)

    National Cancer Inst. (NIH), Bethesda, MD.

    Intended for teachers, the booklet provides information on managing a child with cancer in the classroom. Sections deal with the following topics: cancer in the young and its treatment, effects of the disease and treatment, school reentry, the teacher's role, what to find out, dealing with parents, what to do, the student in the classroom,…

  11. Probability of Corporal Punishment: Lack of Resources and Vulnerable Students

    Science.gov (United States)

    Han, Seunghee

    2011-01-01

    The author examined corporal punishment practices in the United States based on data from 362 public school principals where corporal punishment is available. Results from multiple regression analyses show that schools with multiple student violence prevention programs and teacher training programs had fewer possibilities of use corporal…

  12. Knowledge of Indonesian University Students on the Sustainable Management of Natural Resources

    Directory of Open Access Journals (Sweden)

    Susanne Bögeholz

    2013-03-01

    Full Text Available Graduates of university programs addressing sustainable resource management are likely to shape strategies for natural resource use in the future. Their academic training needs to foster student knowledge of the multiple dimensions of natural resource management. This paper investigates university student understanding of such challenges. We differentiated situational, conceptual, and procedural types of knowledge, and three domains of knowledge (ecological, socio-economic and institutional knowledge, and sampled beginners (third semester and seniors (seventh semester of seven natural resource related programs at the leading Indonesian institution of higher education in the field of natural resource management (IPB Bogor; n = 882. The questionnaire consisted of multiple choice and rating scale items covering ‘locally’ relevant open-access resource use issues. With a confirmatory tau-equivalent LISREL model, construct validity was assessed. The ability to extract relevant information from problem descriptions provided (situational knowledge did not differ between third and seventh semester students. While it was high for ecological and socio-economic items, it was markedly lower for institutional knowledge. Knowledge of relevant scientific concepts (conceptual knowledge increased in the ecological and socio-economic domains but the effect was small. Conceptual knowledge in the socio-economical and institutional domains tended to be lower than ecological knowledge. Although there was certain improvement, student judgments on the efficacy of resource management options (procedural knowledge differed strongly from expert judgments for beginners as well as for senior students. We conclude that many of the university students in the sampled programs displayed substantial gaps in their capacity to solve complex, real-world natural resource management problems. Specifically, the socio-economic and institutional knowledge domains—and their

  13. 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.

  14. Choosing Wisely Canada Students and Trainees Advocating for Resource Stewardship (STARS) campaign: a descriptive evaluation.

    Science.gov (United States)

    Cardone, Franco; Cheung, Daphne; Han, Angela; Born, Karen B; Alexander, Lisa; Levinson, Wendy; Wong, Brian M

    2017-12-19

    Resource stewardship is being increasingly recognized as an essential competency for physicians, but medical schools are just beginning to integrate this into education. We describe the evaluation of Choosing Wisely Canada's Students and Trainees Advocating for Resource Stewardship (STARS) campaign, a student-led campaign to advance resource stewardship education in medical schools across Canada. We evaluated the campaign 6 months after its launch, in November 2015. STARS students were administered a telephone survey eliciting a description of the initiatives that they had implemented or planned to implement at their schools to promote resource stewardship, and exploring their perceptions of facilitators of and barriers to successful implementation of their initiatives. We used a mixed-methods approach to analyze and summarize the data. Twenty-seven (82%) of the 33 eligible students representing all 17 medical schools responded. In 14 schools (82%), students led various local activities (e.g., interest groups, campaign weeks) to raise awareness about resource stewardship among medical students and faculty. Students contributed to curriculum change (both planned and implemented) at 10 schools (59%). Thematic analysis revealed key program characteristics that facilitated success (e.g., pan-Canadian student network, local faculty champion) as well as barriers to implementing change (e.g., complex processes to change curriculum, hierarchical nature of medical school). This student-led campaign, with support from local faculty and Choosing Wisely Canada staff, led to awareness-building activities and early curricula change at medical schools across Canada. Future plans will build on the initial momentum created by the STARS campaign to sustain and spread local initiatives. Copyright 2017, Joule Inc. or its licensors.

  15. Factors Influencing Students' Use of Electronic Resources and their Opinions About this Use: The Case of Students at An-Najah National University

    Directory of Open Access Journals (Sweden)

    Wajeeh M. Daher

    2010-12-01

    Full Text Available Electronic resources are becoming an integral part of the modern life and of the educational scene, especially the high education scene. In this research we wanted to verify what influences first degree university students' use of electronic resources and their opinions regarding this use. Collecting data from 202 students and analyzing it using SPSS, we found that more than one half of the participants had high level of electronic media use and more than one third had moderate level of electronic media use. These levels of use indicate the students' awareness of the role and benefits of electronic media use. Regarding the factors that influence the students' se of electronic resources we found that the student's use of electronic resources had significant strong positive relationships with the provision of electronic resources by the academic institution. It had significant moderate positive relationships with the resources characteristics and the course requirement, and had significant weak relationships with the instructor's support and the student's characteristics. We explained these relationships as resulting from the influence of the surrounding community. Regarding the students' opinions about the use of electronic resources, we found that the student's opinion of electronic resources has significant strong positive relationships with student's use of electronic resources, level of this use, the academic institution available facilities, student's characteristics and resources characteristics. It does not have significant relationships with the instructor's support or the course requirement. We explained these relationships depending on activity theory and its integration with ecological psychology.

  16. Investigating deaf students' use of visual multimedia resources in reading comprehension.

    Science.gov (United States)

    Nikolaraizi, Magda; Vekiri, Ioanna; Easterbrooks, Susan R

    2013-01-01

    A mixed research design was used to examine how deaf students used the visual resources of a multimedia software package that was designed to support reading comprehension. The viewing behavior of 8 deaf students, ages 8-12 years, was recorded during their interaction with multimedia software that included narrative texts enriched with Greek Sign Language videos, pictures, and concept maps. Also, students' reading comprehension was assessed through reading comprehension questions and retelling. Analysis of the students' viewing behavior data, their answers to reading comprehension questions, their "think alouds," and their story retells indicated that they used visual resources, but they did not exploit them in a strategic manner to aid their reading comprehension. The study underscores the important role of mediated instruction in "visual literacy" skills that enable students to learn how to process visual aids in a way that supports their reading comprehension.

  17. Measuring the Value of Library Resources and Student Academic Performance through Relational Datasets

    Directory of Open Access Journals (Sweden)

    Margie Jantti

    2013-06-01

    Full Text Available Objective – This article describes a project undertaken by the University of Wollongong Library (UWL to identify whether a correlation exists between usage of library resources and academic performance.Methods – A multidimensional approach to systems design was implemented, requiring collaboration between among the library, university administration, Performance Indicator Project team (PIP, and information technology services. The project centers on the integration and interrogation of a series of discrete datasets containing student performance, attrition, demographic, borrowing, and electronic resources usage data. PIP built a cube for the library that links usage of library resources to student demographic data and academic performance (the “Library Cube”. Other cubes will be linked later.Results – While initial reports are rudimentary and do not yet incorporate data on e-resource usage, results are favourable in demonstrating the value of using the library information resources in coursework. Based on the data generated to date, students who borrow library resources do outperform students who do not. Early trend data shows up to a 12-point difference in grades.Conclusion – The Library Cube signals a new milestone in the UWL’s quality assessment journey. Well-established measures of effectiveness and efficiency will be further complemented by measures of impact and value, allowing the library to step even closer to the goal of having effective and valued partnerships with the university community to realize teaching, learning, research, and internalization goals.

  18. A Survey of Bioinformatics Database and Software Usage through Mining the Literature.

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    Geraint Duck

    Full Text Available Computer-based resources are central to much, if not most, biological and medical research. However, while there is an ever expanding choice of bioinformatics resources to use, described within the biomedical literature, little work to date has provided an evaluation of the full range of availability or levels of usage of database and software resources. Here we use text mining to process the PubMed Central full-text corpus, identifying mentions of databases or software within the scientific literature. We provide an audit of the resources contained within the biomedical literature, and a comparison of their relative usage, both over time and between the sub-disciplines of bioinformatics, biology and medicine. We find that trends in resource usage differs between these domains. The bioinformatics literature emphasises novel resource development, while database and software usage within biology and medicine is more stable and conservative. Many resources are only mentioned in the bioinformatics literature, with a relatively small number making it out into general biology, and fewer still into the medical literature. In addition, many resources are seeing a steady decline in their usage (e.g., BLAST, SWISS-PROT, though some are instead seeing rapid growth (e.g., the GO, R. We find a striking imbalance in resource usage with the top 5% of resource names (133 names accounting for 47% of total usage, and over 70% of resources extracted being only mentioned once each. While these results highlight the dynamic and creative nature of bioinformatics research they raise questions about software reuse, choice and the sharing of bioinformatics practice. Is it acceptable that so many resources are apparently never reused? Finally, our work is a step towards automated extraction of scientific method from text. We make the dataset generated by our study available under the CC0 license here: http://dx.doi.org/10.6084/m9.figshare.1281371.

  19. Writing throughout the Biochemistry Curriculum: Synergistic Inquiry-Based Writing Projects for Biochemistry Students

    Science.gov (United States)

    Mertz, Pamela; Streu, Craig

    2015-01-01

    This article describes a synergistic two-semester writing sequence for biochemistry courses. In the first semester, students select a putative protein and are tasked with researching their protein largely through bioinformatics resources. In the second semester, students develop original ideas and present them in the form of a research grant…

  20. First Year Medical Students Use Library Resources Emphasized During Instruction Sessions

    Directory of Open Access Journals (Sweden)

    Laura Newton Miller

    2014-03-01

    Full Text Available Objective – To determine if library instruction has an effect on resources cited in student reports. Design – Citation analysis. Setting – The study took place in the medical school of a large American university. Subjects - One hundred eighteen of 120 first-year medical student reports were analyzed. Two reports did not include any works cited and were excluded from the study. Methods - Over the course of 3 years, 15 20-minute library instruction sessions were conducted. The sessions, based on five clinical cases presented each year were conducted approximately two weeks before each report due date. Eighty-five case-specific resources were demonstrated, with teaching plans being modified from year to year based on the frequency of citation of a particular resource cited the prior year. A LibGuide online course guide also directed students to specific resources shown in the class, with content updated every year based on citation trends from the previous year. Every citation referenced in a report was then categorized into a those that were discussed during an instruction session, b those found on a course guide, c those accessible through the library, d those available from course material (i.e., PowerPoint presentation, lecture notes, or e those which did not fall under any of the other categories. A citation could be included in multiple categories. Main Results – The 118 reports included 2983 citations. Over the 3 year period, an average of 77.51% of all citations were from library resources, 49.55% of the citations from a resource demonstrated in the class, and 21.68% from resources found in the course guide. Although citations from sources discussed in class did not increase significantly from year to year, the percent of citations from resources on the course guide significantly increased from 19.40% to 25.63%. Conclusion – Medical students cite library resources emphasized during instruction sessions.

  1. The Lifestyle Project: Challenging Students to Redefine their Approach to Resource Use (Invited)

    Science.gov (United States)

    Kirk, K.

    2009-12-01

    The Lifestyle Project is a way for students to learn about environmental impacts by changing their own lifestyles. It is a three-week exercise during which students reduce their energy use, waste output and water use by changing the way they live from day to day. The project has fairly rigid parameters, allowing students to achieve a gradual but definitive change in their everyday habits. Students begin by taking baseline measurements of their resource use, and then they select three different areas in which they are interested in reducing their environmental impact. Within each area there are clearly defined rules that provide a structured means for achieving significant changes. Each week the project becomes more rigorous, because students will have to meet the requirements more frequently. They write about their experiences in journals, which are incredibly insightful and illustrate just how profoundly the project affects them. The Lifestyle Project has been used across several campuses and in many educational settings such as traditional courses, online courses and in informal settings. Its strength lies in allowing students to quantify and modify their own use of resources, then compare their personal reductions to what could be applied in a larger population. This helps them apply and personalize many of the concepts addressed in courses about environmental geology, climate change, or energy resources. The incremental nature of the project allows students several opportunities to practice new behaviors, so that they become adept at using far fewer resources than they thought would be possible. Results from the Lifestyle Project indicate that students save significant amounts of energy, on the order of 1 to 2 million BTUs per day. Journal reflections illustrate a corresponding shift in students’ personal awareness of their use of resources and the repercussions of their daily decisions. Although many students find the project frustrating at first, after

  2. Understanding the Greenhouse Effect by Embodiment - Analysing and Using Students' and Scientists' Conceptual Resources

    Science.gov (United States)

    Niebert, Kai; Gropengießer, Harald

    2014-01-01

    Over the last 20 years, science education studies have reported that there are very different understandings among students of science regarding the key aspects of climate change. We used the cognitive linguistic framework of experientialism to shed new light on this valuable pool of studies to identify the conceptual resources of understanding climate change. In our study, we interviewed 35 secondary school students on their understanding of the greenhouse effect and analysed the conceptions of climate scientists as drawn from textbooks and research reports. We analysed all data by metaphor analysis and qualitative content analysis to gain insight into students' and scientists' resources for understanding. In our analysis, we found that students and scientists refer to the same schemata to understand the greenhouse effect. We categorised their conceptions into three different principles the conceptions are based on: warming by more input, warming by less output, and warming by a new equilibrium. By interrelating students' and scientists' conceptions, we identified the students' learning demand: First, our students were afforded with experiences regarding the interactions of electromagnetic radiation and CO2. Second, our students reflected about the experience-based schemata they use as source domains for metaphorical understanding of the greenhouse effect. By uncovering the-mostly unconscious-deployed schemata, we gave students access to their source domains. We implemented these teaching guidelines in interventions and evaluated them in teaching experiments to develop evidence-based and theory-guided learning activities on the greenhouse effect.

  3. Google, Mathletics and Khan Academy: students' self-initiated use of online mathematical resources

    Science.gov (United States)

    Muir, Tracey

    2014-12-01

    Today's students increasingly engage in online environments, with ready access to digital resources and mobile technologies. While much of this activity is socially motivated, the internet is also a source of knowledge for students and frequently accessed for school assignments, projects and assessment purposes. As mathematics continues to be an area in which many students experience difficulties, it is not surprising that a recent Google search produced 57,600,000 results for `help with mathematics'. Current research, however, is limited in terms of documenting students' use of such resources, particularly when they are self-initiated and often accessed in an out of classroom environment. This paper reports on a study that investigated the use of mathematical online resources accessed by students in Grades 5-9, with a particular focus on evaluating the effectiveness of Khan Academy, an online tutorial site. Data collected through surveys and interviews showed that while students did access online sites, particularly in the later years of schooling, they varied in both their reasons for doing so and their perceptions of how useful these sites were. The findings add to the limited research in this area and have practical implications for students and teachers, including the potential to challenge the traditional role of the teacher.

  4. 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.

  5. Professionalising the use of the student resource for innovation

    DEFF Research Database (Denmark)

    Vetner, Mikael; Lund, Marie Fallgaard; Dahlgaard, Morten

    2015-01-01

    is placed on both project based learning and problem based learning, involving industry, commercial partners, NGOs and public organisations. Working with such partners is an integrated part of both organizations DNA, to the great satisfaction of both academia and industry. But also with knowledge...... problems” for industry. Solution Hub does this by facilitating interdisciplinary work between student groups with very different skill sets, but working with the same industrial collaborator, and U-CrAc does this by creating true interdisciplinary groups, who each has their own industrial collaborator.......University College Northern Denmark and Aalborg University are the only higher education institutions located in the North Denmark region and both are playing a major role in regional development. A major reason is the particular learning models applied by both institutions, where strong emphasis...

  6. 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.

  7. The World-Wide Web: An Interface between Research and Teaching in Bioinformatics

    Directory of Open Access Journals (Sweden)

    James F. Aiton

    1994-01-01

    Full Text Available The rapid expansion occurring in World-Wide Web activity is beginning to make the concepts of ‘global hypermedia’ and ‘universal document readership’ realistic objectives of the new revolution in information technology. One consequence of this increase in usage is that educators and students are becoming more aware of the diversity of the knowledge base which can be accessed via the Internet. Although computerised databases and information services have long played a key role in bioinformatics these same resources can also be used to provide core materials for teaching and learning. The large datasets and arch ives th at have been compiled for biomedical research can be enhanced with the addition of a variety of multimedia elements (images. digital videos. animation etc.. The use of this digitally stored information in structured and self-directed learning environments is likely to increase as activity across World-Wide Web increases.

  8. 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.

  9. 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

  10. Dental and Medical Students' Use and Perceptions of Learning Resources in a Human Physiology Course.

    Science.gov (United States)

    Tain, Monica; Schwartzstein, Richard; Friedland, Bernard; Park, Sang E

    2017-09-01

    The aim of this study was to determine the use and perceived utility of various learning resources available during the first-year Integrated Human Physiology course at the dental and medical schools at Harvard University. Dental and medical students of the Class of 2018 were surveyed anonymously online in 2015 regarding their use of 29 learning resources in this combined course. The learning resources had been grouped into four categories to discern frequency of use and perceived usefulness among the categories. The survey was distributed to 169 students, and 73 responded for a response rate of 43.2%. There was no significant difference among the learning resource categories in frequency of use; however, there was a statistically significant difference among categories in students' perceptions of usefulness. No correlation was found between frequency of use and perceived usefulness of each category. Students seemingly were not choosing the most useful resources for them. These results suggest that, in the current educational environment, where new technologies and self-directed learning are highly sought after, there remains a need for instructor-guided learning.

  11. The Developing on Awareness of Water Resources Management of Grade 6 Students in Namphong Sub-Basin

    Science.gov (United States)

    Seehamat, Lumyai; Sanrattana, Unchalee; Tungkasamit, Angkana

    2016-01-01

    Awareness of water resources management is expression behavior as receive, response, valuing, and organization. Water resources is an important for everyone in the world and the recently water resources are be risky as lack of water, waste water, and blooding. The development on awareness of water resources management for grade 6 students is very…

  12. Physics Instructional Resource Usage by High-, Medium-, and Low-Skilled MOOC Students

    Science.gov (United States)

    Balint, Trevor A.; Teodorescu, Raluca; Colvin, Kimberly; Choi, Youn-Jeng; Pritchard, David

    2017-04-01

    In this paper we examine how different types of participants in a physics Massive Open Online Course (MOOC) tend to use the existing course resources. We use data from the 2013 offering of the Massive Open Online Course 8.MReVx designed by the RELATE (REsearch in Learning Assessing and Tutoring Effectively) Group at the Massachusetts Institute of Technology and offered on the edX platform. We propose six measures of student performance in a course, and, based on these measures, we divide the student population into clusters and analyze the resource usage of the students from each cluster. This course contains a wide variety of physics problems targeting various levels of thinking. Our analysis focuses on 1080 participants (out of 16,787 enrolled in the course) who attempted more than 50% of available problems, as this is an indicator of students who participated actively in the entire course.

  13. Theme--Achieving 2020. Goal 3: All Students Are Conversationally Literate in Agriculture, Food, Fiber, and Natural Resource Systems.

    Science.gov (United States)

    Trexler, Cary, Ed.

    2000-01-01

    Nine theme articles focus on the need for students to be conversationally literate about agriculture, food, fiber, and natural resources systems. Discusses the definition of conversational literacy, the human and institutional resources needed, and exemplary models for promoting literacy. (JOW)

  14. Nursing students' perceptions of their resources toward the development of competencies in nursing informatics.

    Science.gov (United States)

    Jetté, Sylvie; Tribble, Denise St-Cyr; Gagnon, Johanne; Mathieu, Luc

    2010-11-01

    This article presents the findings of a doctoral study about the internal and external resources required to develop nursing informatics competencies in student nurses. Colleges and universities are responsible for training nursing students, including in the area of nursing informatics. Even though nursing informatics is a specialty recognized by the American Nursing Association (2001), it has received limited attention in Quebec, Canada. A total of 131 college-level nursing students were randomly surveyed with a mail questionnaire designed to describe their perceptions about their internal and external resources in nursing informatics. Nursing students perceive that their internal and external resources necessary to ensure "knowledge to act" in nursing informatics is moderately high. They said they lacked knowledge about using spreadsheet programs, presentation software, and courseware, about data security, and about how to analyze the quality of a health-related Web site and search electronic scientific databases. These results show that, even if nursing students have access to a computer and the Internet at home and even if they feel competent using informatics in nursing, they still lack important resources for developing competencies in nursing informatics. We recommend that faculties and colleges focus on these elements. Copyright © 2010 Elsevier Ltd. All rights reserved.

  15. 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.

  16. 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.

  17. Institutional Resource Allocation, Student Engagement, and Student Satisfaction at Ontario Universities

    Science.gov (United States)

    Malik, Alana Jayne

    2010-01-01

    This study examined the relationship between institutional expenditures in student services, levels of student engagement, and measures of student satisfaction across 18 (out of 19) universities in the Province of Ontario, Canada. Information regarding these variables for each institution was assembled from four extant datasets: (a) the "2006…

  18. Explain bioinformatics to your grandmother!

    Directory of Open Access Journals (Sweden)

    Virginie Bernard

    2013-10-01

    Full Text Available What are you working on? You have certainly been asked that question many times, whether it be at a Saturday night party, during a discussion with your neighbors, or at a family gathering. Communicating with a lay audience about scientific subjects and making them attractive is a difficult task. But difficult or not, you will have to do it for many years, not only with your family and friends, but also with your colleagues and collaborators. So, better learn now! Although not usually taught, the ability to explain your work to others is an essential skill in science, where communication plays a key role. Using some examples of the French Regional Student Group activities, we discuss here (i why it is important to have such communication skills, (ii how you can get involved in these activities by using existing resources or working with people who have previous experience, and (iii what you get out of this amazing experience. We aim to motivate you and provide you with tips and ideas to get involved in promoting scientific activities while getting all the benefits.

  19. Theoretical and methodological support of educational process of students-powerlifters using Internet resources

    Directory of Open Access Journals (Sweden)

    Stetsenko Anatolij Ivanovich

    2011-11-01

    Full Text Available It is reviewed scientific journals that have free public access. Investigated the information resources of powerlifting on the internet. Accentuated the importance of using professionally-oriented information resources in the learning process. It is established that Ukrainian language environment of the internet in the sphere of powerlifting has been relatively much attention in comparison with other power sports. Formed the base of internet resources for students of physical culture and sports institutions that specialize in powerlifting. The need to continue and complete the work to create an electronic library on physical education and sport.

  20. Use of Mobile Devices to Access Resources Among Health Professions Students: A Systematic Review.

    Science.gov (United States)

    Mi, Misa; Wu, Wendy; Qiu, Maylene; Zhang, Yingting; Wu, Lin; Li, Jie

    2016-01-01

    This systematic review examines types of mobile devices used by health professions students, kinds of resources and tools accessed via mobile devices, and reasons for using the devices to access the resources and tools. The review included 20 studies selected from articles published in English between January 2010 and April 2015, retrieved from PubMed and other sources. Data extracted included participants, study designs, mobile devices used, mobile resources/apps accessed, outcome measures, and advantages of and barriers to using mobile devices. The review indicates significant variability across the studies in terms of research methods, types of mobile programs implemented, resources accessed, and outcomes. There were beneficial effects of using mobile devices to access resources as well as conspicuous challenges or barriers in using mobile devices.

  1. Freedom in Our Lifetime: South Africa's Struggle. [Student Text and] Teacher Resource Book. Choices for the 21st Century.

    Science.gov (United States)

    Fox, Sarah Cleveland

    This document includes a student text and a teacher resource book. The student text booklet introduces students to precolonial and colonial South Africa and the development of apartheid. Students have the opportunity to evaluate decisions made by anti-apartheid activists and to reflect on South Africa's transition to a post-apartheid society. The…

  2. Correlating students' educational background, study habits, and resource usage with learning success in medical histology.

    Science.gov (United States)

    Selvig, Daniel; Holaday, Louisa W; Purkiss, Joel; Hortsch, Michael

    2015-01-01

    Histology is a traditional core basic science component of most medical and dental education programs and presents a didactic challenge for many students. Identifying students that are likely to struggle with histology would allow for early intervention to support and encourage their learning success. To identify student characteristics that are associated with learning success in histology, three first-year medical school classes at the University of Michigan (>440 students) were surveyed about their educational background, attitudes toward learning histology, and their use of histology learning strategies and resources. These characteristics were linked with the students' quiz and examination results in histology. Students who reported previous experience in histology or pathology and hold science or biomedical science college degrees usually did well in histology. Learning success in histology was also positively associated with students' perception that histology is important for their professional career. Other positive indicators were in-person participation in teacher-guided learning experiences, specifically lecture and laboratory sessions. In contrast, students who relied on watching histology lectures by video rather than going to lectures in-person performed significantly worse. These characteristics and learning strategies of students who did well in this very visual and challenging study subject should be of help for identifying and advising students early, who might be at risk of failing a histology course or component. © 2014 American Association of Anatomists.

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

    Directory of Open Access Journals (Sweden)

    Wagener Johannes

    2007-02-01

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

  4. Fundamentals of bioinformatics and computational biology methods and exercises in matlab

    CERN Document Server

    Singh, Gautam B

    2015-01-01

    This book offers comprehensive coverage of all the core topics of bioinformatics, and includes practical examples completed using the MATLAB bioinformatics toolbox™. It is primarily intended as a textbook for engineering and computer science students attending advanced undergraduate and graduate courses in bioinformatics and computational biology. The book develops bioinformatics concepts from the ground up, starting with an introductory chapter on molecular biology and genetics. This chapter will enable physical science students to fully understand and appreciate the ultimate goals of applying the principles of information technology to challenges in biological data management, sequence analysis, and systems biology. The first part of the book also includes a survey of existing biological databases, tools that have become essential in today’s biotechnology research. The second part of the book covers methodologies for retrieving biological information, including fundamental algorithms for sequence compar...

  5. Learning About Energy Resources Through Student Created Video Documentaries in the University Science Classroom

    Science.gov (United States)

    Wade, P.; Courtney, A.

    2010-12-01

    Students enrolled in an undergraduate non-science majors’ Energy Perspectives course created 10-15 minute video documentaries on topics related to Energy Resources and the Environment. Video project topics included wave, biodiesel, clean coal, hydro, solar and “off-the-grid” energy technologies. No student had any prior experience with creating video projects. Students had Liberal Arts academic backgrounds that included Anthropology, Theater Arts, International Studies, English and Early Childhood Education. Students were required to: 1) select a topic, 2) conduct research, 3) write a narrative, 4) construct a project storyboard, 5) shoot or acquire video and photos (from legal sources), 6) record the narrative, and 7) construct the video documentary. This study describes the instructional approach of using student created video documentaries as projects in an undergraduate non-science majors’ science course. Two knowledge survey instruments were used for assessment purposes. Each instrument was administered Pre-, Mid- and Post course. One survey focused on the skills necessary to research and produce video documentaries. Results showed students acquired enhanced technology skills especially with regard to research techniques, writing skills and video editing. The second survey assessed students’ content knowledge acquired from each documentary. Results indicated students’ increased their content knowledge of energy resource topics. Students reported very favorable evaluations concerning their experience with creating “Ken Burns” video project documentaries.

  6. Psychological Resources as Stress Buffers: Their Relationship to University Students' Anxiety and Depression

    Science.gov (United States)

    McCarthy, Christopher J.; Fouladi, Rachel T.; Juncker, Brian D.; Matheny, Kenneth B.

    2006-01-01

    The association of protective resources, personality variables, life events, and gender with anxiety and depression was examined with university students. Building on regression analyses, a structural equation model was generated with good fit, indicating that with respect to both anxiety and depression, negative life events and coping resources…

  7. Students' perception of E-Resources in an Academic Library: The ...

    African Journals Online (AJOL)

    This paper examines students' perception of e-resources in academic libraries: case study of the serial's section of 'Nimbe Adedipe Library, Federal University of Agriculture, Abeokuta, Ogun State, Nigeria. The survey research method was adopted for this study. A structured questionnaire was designed and used to collect ...

  8. Fostering Postgraduate Student Engagement: Online Resources Supporting Self-Directed Learning in a Diverse Cohort

    Science.gov (United States)

    Mello, Luciane V.

    2016-01-01

    The research question for this study was: "Can the provision of online resources help to engage and motivate students to become self-directed learners?" This study presents the results of an action research project to answer this question for a postgraduate module at a research-intensive university in the United Kingdom. The analysis of…

  9. Indians and Eskimos of Canada: A Student's Guide to Reference Resources.

    Science.gov (United States)

    Slavin, Suzy M.

    Emphasizing reference resources for ethnological research on Canadian American Indians and Eskimos, this guide constitutes a revised and expanded edition of an earlier student's guide entitled "Canadian Ethnology" and includes both reference sources and annotated bibliographic references for the following: (1) Handbooks (8 references);…

  10. Lost in Transition: Secondary School Students' Understanding of Landscapes and Natural Resource Management

    Science.gov (United States)

    Kruger, Tarnya; Beilin, Ruth

    2012-01-01

    In 2007, a study titled "Living in the landscapes of the 21st century" was conducted in 11 high schools in metropolitan and rural Victoria. The research team investigated Year 10 students' conceptions of landscapes in order to explore their understandings of natural resource management (NRM), including agriculture, food, land and water…

  11. Exploring the Learning Problems and Resource Usage of Undergraduate Industrial Design Students in Design Studio Courses

    Science.gov (United States)

    Chen, Wenzhi

    2016-01-01

    Design is a powerful weapon for modern companies so it is important to have excellent designers in the industry. The purpose of this study is to explore the learning problems and the resources that students use to overcome problems in undergraduate industrial design studio courses. A survey with open-type questions was conducted to collect data.…

  12. Is Wikipedia a Reliable Learning Resource for Medical Students? Evaluating Respiratory Topics

    Science.gov (United States)

    Azer, Samy A.

    2015-01-01

    The aim of the present study was to critically evaluate the accuracy and readability of English Wikipedia articles on the respiratory system and its disorders and whether they can be a suitable resource for medical students. On April 27, 2014, English Wikipedia was searched for articles on respiratory topics. Using a modified DISCERN instrument,…

  13. Understanding the Greenhouse Effect by Embodiment--Analysing and Using Students' and Scientists' Conceptual Resources

    Science.gov (United States)

    Niebert, Kai; Gropengießer, Harald

    2014-01-01

    Over the last 20 years, science education studies have reported that there are very different understandings among students of science regarding the key aspects of climate change. We used the cognitive linguistic framework of experientialism to shed new light on this valuable pool of studies to identify the conceptual resources of understanding…

  14. Visiting students work with professors to research water resources management issues

    OpenAIRE

    Davis, Lynn

    2009-01-01

    Undergraduate students visiting from universities across the continent, as well as one from Virginia Tech, are working with professors at Virginia Tech on individual research projects in a 10-week summer program that addresses issues related to sustainable management of water resources.

  15. Do Resource Bases Enable Social Inclusion of Students with Asperger Syndrome in a Mainstream Secondary School?

    Science.gov (United States)

    Landor, Floriane; Perepa, Prithvi

    2017-01-01

    This research identifies the way in which one secondary school with a resourced provision for students with Asperger syndrome promotes social inclusion for them, and the perceptions of staff members and parents on the social experience of schooling for these children. Interviews were conducted with five teachers, two learning support assistants,…

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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…

  1. Perceived stress in first year medical students - associations with personal resources and emotional distress.

    Science.gov (United States)

    Heinen, Ines; Bullinger, Monika; Kocalevent, Rüya-Daniela

    2017-01-06

    Medical students have been found to report high levels of perceived stress, yet there is a lack of theoretical frameworks examining possible reasons. This cross-sectional study examines correlates of perceived stress in medical students on the basis of a conceptual stress model originally developed for and applied to the general population. The aim was to identify via structural equation modeling the associations between perceived stress and emotional distress (anxiety and depression), taking into account the activation of personal resources (optimism, self-efficacy and resilient coping). Within this cross-sectional study, 321 first year medical students (age 22 ± 4 years, 39.3% men) completed the Perceived Stress Questionnaire (PSQ-20), the Self-Efficacy Optimism Scale (SWOP) and the Brief Resilient Coping Scale (BRCS) as well as the Patient Health Questionnaire (PHQ-4). The statistical analyses used t-tests, ANOVA, Spearman Rho correlation and multiple regression analysis as well as structural equation modeling. Medical students reported higher levels of perceived stress and higher levels of anxiety and depression than reference samples. No statistically significant differences in stress levels were found within the sample according to gender, migration background or employment status. Students reported more self-efficacy, optimism, and resilient coping and higher emotional distress compared to validation samples and results in other studies. Structural equation analysis revealed a satisfactory fit between empirical data and the proposed stress model indicating that personal resources modulated perceived stress, which in turn had an impact on emotional distress. Medical students' perceived stress and emotional distress levels are generally high, with personal resources acting as a buffer, thus supporting the population-based general stress model. Results suggest providing individual interventions for those students, who need support in dealing with the

  2. Developing Emotional Intelligence as a key psychological resource reservoir for sustained student success

    Directory of Open Access Journals (Sweden)

    Gina Görgens-Ekermans

    2015-07-01

    Motivation for the study: Non-cognitive personal resources (such as EI may indirectly contribute to student success. Research design, approach and method: A controlled experimental research design was conducted to test the effect of an EI developmental intervention on affect balance, academic self-efficacy, cognitive thought-pattern strategies, and perceived stress, using a sample of first-year students (n = 114. Main findings: Limited support of the utility of the intervention to increase EI emerged; whilst stronger support emerged that academic self-efficacy was affected by the intervention. No direct empirical support for the impact of increased EI on the other measured psychological resources was obtained, although some trends in the data could be observed. Practical/managerial implications: Investments in EI developmental interventions, as part of student-support initiatives, should be further investigated to sufficiently justify its potential to influence sustained student success. Contribution/value-add: The results of this study lay a foundation that suggest EI could be malleable and influence academic self-efficacy. More research is necessary regarding supplementary teaching and learning initiatives focused on non-cognitive personal resources, which are complementary to the academic offering at tertiary institutions, with the expectation of increasing the student success rates.

  3. Student burnout and engagement: a test of the conservation of resources theory.

    Science.gov (United States)

    Alarcon, Gene M; Edwards, Jean M; Menke, Lauren E

    2011-01-01

    The current study explored predictors of burnout and engagement in 1st-year college students. The theory of conservation of resources was used to create a path model for burnout and engagement. Specifically, the theory suggests that perceptions of demands mediate the relationship between resources and coping strategies. In turn, coping mediates the relationship of demands on the outcomes of burnout and engagement. Results indicate demands partially mediated the relationship between resources and coping strategies. Similarly, coping partially mediated the relationship between demands and burnout and engagement. Results suggest that teaching students adaptive ways of coping and extinguishing maladaptive ways of coping with the academic environment can increase engagement and decrease burnout. Implications for research, theory, and practice are discussed.

  4. Dental Students' Knowledge of Resources for LGBT Persons: Findings from Three Dental Schools.

    Science.gov (United States)

    Feng, Xiaoying; Mugayar, Leda; Perez, Edna; Nagasawa, Pamela R; Brown, David G; Behar-Horenstein, Linda S

    2017-01-01

    Recently, there has been increased attention to including cultural diversity in the education of health professionals, including concern for lesbian, gay, bisexual, and transgender (LGBT) inclusion and visibility. Studies regarding cultural exposure and acceptance of LGBT populations have been concentrated in medicine, with findings showing that medical providers often graduate having missed the preparation required to care for LGBT persons. A visible, comprehensive, culturally competent environment in dental schools would help ensure that all oral health professionals and students are aware of services available to address the particular needs of LGBT students. The aims of this survey-based study conducted in 2015-16 were to determine dental students' perceptions regarding LGBT students' needs and to assess dental students' knowledge of resources for LGBT persons at three U.S. dental schools, one each in the Midwest, West, and South. Of the 849 students invited to participate, 364 completed the survey (338 dental, 26 dental hygiene), for an overall response rate of 43%. The response rate at individual schools ranged from 30% to 55%. The results showed perceptions of insufficient LGBT information, resources, and support at these institutions, especially at the Western school. There were significant differences among the three schools, with students at the Western school more than the other two schools perceiving that their institution was less aware of whether it met the academic, social support, and spiritual needs of LGBT students. There were no significant differences between LGBT and non-LGBT students' perceptions. The authors urge dental school administrators to explore the degree to which their programs teach respectful and caring behavior towards LGBT students and, by extension, LGBT patient populations.

  5. Development and evaluation of online video teaching resources to enhance student knowledge of livestock handling.

    Science.gov (United States)

    Klupiec, C; Pope, S; Taylor, R; Carroll, D; Ward, M H; Celi, P

    2014-07-01

    To evaluate the effectiveness of online audiovisual materials to support the acquisition of animal handling skills by students of veterinary and animal science. A series of video clips (Livestock Handling modules) demonstrating livestock handling procedures was created and delivered online to students enrolled in the Faculty of Veterinary Science, University of Sydney. The effectiveness of these modules for supporting student learning was evaluated via an online survey. The survey also sought feedback on how students could be better prepared for handling livestock. The survey indicated that students found the videos a useful part of their learning experience, particularly by familiarising them with correct handling procedures and emphasising the importance of safety when handling livestock. Students also highlighted that online delivery supported flexible learning. Suggested improvements of the Livestock Handling modules centred around broadening the content of the videos and improving the user-friendliness of online access. Student feedback regarding how the Faculty could better prepare them for livestock handling was dominated by requests for more opportunities to practise animal handling using live animals. The Livestock Handling audiovisual tool is a valuable supplementary resource for developing students' proficiency in safe and effective handling of livestock. However, the results also clearly reveal a perception by students that more hands-on experience is required for acquisition of animal handling skills. These findings will inform future development of the Faculty's animal handling program. © 2014 Australian Veterinary Association.

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. Resources

    Science.gov (United States)

    English in Australia, 1973

    1973-01-01

    Contains seven short resources''--units, lessons, and activities on the power of observation, man and his earth, snakes, group discussion, colloquial and slang, the continuous story, and retelling a story. (DD)

  13. 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.

  14. 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.

  15. Teachers’ Relationship Closeness with Students as a Resource for Teacher Wellbeing: A Response Surface Analytical Approach

    Science.gov (United States)

    Milatz, Anne; Lüftenegger, Marko; Schober, Barbara

    2015-01-01

    Teachers’ relationship quality with students has been argued to be an important source of teacher wellbeing. Thus, the current study aimed to investigate to what extent teachers’ relationship closeness toward students, combined with attachment security is a resource protecting against teacher burnout. Eighty-three elementary school teachers reported on their most and least attached student’s relationship closeness, their attachment security and levels of burnout, as measured by emotional exhaustion, depersonalization and personal accomplishment. Response surface analysis (RSA), enabling researchers to investigate the effect of congruence/incongruence of two predictors on an outcome, revealed that teachers’ depersonalization and emotional exhaustion were lowest when they developed homogenous close relationships toward the students within their classroom and when teachers in general made congruent relationship experiences. No RSA model could be specified for personal accomplishment, even though a correlational analysis revealed that increasing closeness with students fostered teachers’ personal accomplishment. Teachers’ secure attachment experiences were not directly related to burnout, but enhanced their capability to establish close relationships toward their students. Findings suggest that teachers’ relationships toward students are a resource for the teacher’s wellbeing, which highlights once again the importance of student–teacher relationships in education. PMID:26779045

  16. Tracing Discursive Resources: How Students Use Prior Genre Knowledge to Negotiate New Writing Contexts in First-Year Composition

    Science.gov (United States)

    Reiff, Mary Jo; Bawarshi, Anis

    2011-01-01

    While longitudinal research within the field of writing studies has contributed to our understanding of postsecondary students' writing development, there has been less attention given to the discursive resources students bring with them into writing classrooms and how they make use of these resources in first-year composition courses. This…

  17. Secondary Students' Attitudes to Animal Research: Examining the Potential of a Resource to Communicate the Scientist's Perspective

    Science.gov (United States)

    France, Bev; Birdsall, Sally

    2015-01-01

    A DVD resource that provided a scientist's perspective on the use of animals in research and teaching was evaluated with a questionnaire that asked students' views pre and post their access to the resource. Thirty-nine secondary students (Y10-Y13) took part in three different teaching programmes that provided information about animal research and…

  18. Investigating Student Use and Value of E-Learning Resources to Develop Academic Writing within the Discipline of Environmental Science

    Science.gov (United States)

    Taffs, Kathryn H.; Holt, Julienne I.

    2013-01-01

    The use of information and communication technologies (ICTs) in higher education to support student learning is expanding. However, student usage has been low and the value of e-learning resources has been under investigation. We reflect on best practices for pedagogical design of e-learning resources to support academic writing in environmental…

  19. Use of Online Information Resources by RMIT University Economics, Finance, and Marketing Students Participating in a Cooperative Education Program

    Science.gov (United States)

    Costa, Cathy

    2009-01-01

    This paper examines the use of online information resources by Economics, Finance, and Marketing 3rd year students in a cooperative education program and explores some possible factors and issues that influence how students use these resources. The nature of Work Integrated Learning (WIL) programs, the business information environment, and the…

  20. Protecting the health of medical students on international electives in low-resource settings.

    Science.gov (United States)

    Johnston, Niall; Sandys, Nichola; Geoghegan, Rosemary; O'Donovan, Diarmuid; Flaherty, Gerard

    2018-01-01

    Increasingly, medical students from developed countries are undertaking international medical electives in developing countries. Medical students understand the many benefits of these electives, such as the opportunity to develop clinical skills, to gain insight into global health issues and to travel to interesting regions of the world. However, they may be much less aware of the risk to their health and wellbeing while abroad. Compounding this problem, medical students may not seek advice from travel medicine practitioners and often receive inadequate or no information from their medical school prior to departure. The PubMed database was searched for relevant literature relating to the health of medical elective students. Combinations of the following key words were used as search terms: 'international health elective', 'medical student' and 'health risks'. Articles were restricted to those published in English from 1997 through June 2017. A secondary review of the reference lists of these articles was performed. The grey literature was also searched for relevant material. This narrative literature review outlines the risks of clinical electives in resource-poor settings which include exposure to infectious illness, trauma, sexual health problems, excessive sun exposure, mental health issues and crime. Medical students may mitigate these health risks by being informed and well prepared for high-risk situations. The authors provide evidence-based travel advice which aims to improve pre-travel preparation and maximize student traveller safety. A safer and more enjoyable elective may be achieved if students follow road safety advice, take personal safety measures, demonstrate cultural awareness, attend to their psychological wellbeing and avoid risk-taking behaviours. This article may benefit global health educators, international elective coordinators and travel medicine practitioners. For students, a comprehensive elective checklist, an inventory of health kit

  1. 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.

  2. Assessing attitudes toward computers and the use of Internet resources among undergraduate microbiology students

    Science.gov (United States)

    Anderson, Delia Marie Castro

    Computer literacy and use have become commonplace in our colleges and universities. In an environment that demands the use of technology, educators should be knowledgeable of the components that make up the overall computer attitude of students and be willing to investigate the processes and techniques of effective teaching and learning that can take place with computer technology. The purpose of this study is two fold. First, it investigates the relationship between computer attitudes and gender, ethnicity, and computer experience. Second, it addresses the question of whether, and to what extent, students' attitudes toward computers change over a 16 week period in an undergraduate microbiology course that supplements the traditional lecture with computer-driven assignments. Multiple regression analyses, using data from the Computer Attitudes Scale (Loyd & Loyd, 1985), showed that, in the experimental group, no significant relationships were found between computer anxiety and gender or ethnicity or between computer confidence and gender or ethnicity. However, students who used computers the longest (p = .001) and who were self-taught (p = .046) had the lowest computer anxiety levels. Likewise students who used computers the longest (p = .001) and who were self-taught (p = .041) had the highest confidence levels. No significant relationships between computer liking, usefulness, or the use of Internet resources and gender, ethnicity, or computer experience were found. Dependent T-tests were performed to determine whether computer attitude scores (pretest and posttest) increased over a 16-week period for students who had been exposed to computer-driven assignments and other Internet resources. Results showed that students in the experimental group were less anxious about working with computers and considered computers to be more useful. In the control group, no significant changes in computer anxiety, confidence, liking, or usefulness were noted. Overall, students in

  3. Trained Cohorts of University Students are a Useful Resource for Conducting Dietary Surveys in Mongolia.

    Science.gov (United States)

    Bromage, Sabri; Chung, Holly Ya-Fan; Bonville, Hannah; Sprenger, Jeannie Choi; Lander, Rebecca; Ganmaa, Davaasambuu

    2017-06-01

    Population-based dietary assessment is important for informing national nutrition policy. The developing country setting presents challenges for robust implementation of dietary surveys, yet effective nutrition interventions are often urgently required. To develop and evaluate a low-cost approach to epidemiologic dietary assessment in Mongolia, involving the use of large cohorts of local public health and medical students as research assistants for collecting diet records. From 2011 to 2016, over 200 Mongolian medical and public health university students were trained to collect paired summer and winter 3-day weighed diet records from urban and rural study populations across the geographic expanse of Mongolia. Students were supervised during data collection, and their performance and experience during training and data collection were qualitatively evaluated from their own perspectives as well as those of the investigators. Students collected detailed and thorough diet records and generally reported positive feedback regarding training and data collection. Frequent supervision of students during data collection proved to be extremely worthwhile. While rural participants were amenable to having students follow them, students faced several challenges in assessing the diets of urban participants. These challenges may best be addressed by separately training these participants beforehand. With adequate training and supervision, university students may be a useful and cost-effective resource for large-scale dietary surveys in regions where their use would be practical and culturally appropriate. Further research is warranted to study how well this approach may be adapted outside Mongolia and to other dietary assessment methods and technologies.

  4. Student attitudes towards clinical teaching resources in complementary medicine: a focus group examination of Australian naturopathic medicine students.

    Science.gov (United States)

    Wardle, Jonathan Lee; Sarris, Jerome

    2014-06-01

    Complementary medicine is forming an increasingly large part of health care in developed countries and is increasingly being formally taught in tertiary academic settings. An exploratory study of naturopathic student perceptions of, use of and attitudes towards teaching resources in naturopathic clinical training and education. Focus groups were conducted with current and recent students of 4-year naturopathic degree programmes in Brisbane and Sydney to ascertain how they interact with clinical teaching materials, and their perceptions and attitudes towards teaching materials in naturopathic education. Naturopathic students have a complex and critical relationship with their learning materials. Although naturopathic practice is often defined by traditional evidence, students want information that both supports and is critical of traditional naturopathic practices, and focuses heavily on evidence-based medicine. Students remain largely ambivalent about new teaching technologies and would prefer that these develop organically as an evolution from printed materials, rather than depart from dramatically and radically from these previously established materials. Findings from this study will assist publishers, librarians and academics develop clinical information sources that appropriately meet student expectations and support their learning requirements. © 2014 The authors. Health Information and Libraries Journal © 2014 Health Libraries Group.

  5. Using mobile technologies to give health students access to learning resources in the UK community setting.

    Science.gov (United States)

    Walton, Graham; Childs, Susan; Blenkinsopp, Elizabeth

    2005-12-01

    This article describes a project which explored the potential for mobile technologies to give health students in the community access to learning resources. The purpose included the need to identify possible barriers students could face in using mobile technologies. Another focus was to assess the students perceptions of the importance of being able to access learning resources in the community. This 1-year project used two main approaches for data collection. A review of the literature on mobile technologies in the health context was conducted. This was used in a systematic way to identify key issues and trends. The literature review was used to inform the design and production of a questionnaire. This was distributed to and completed by a group of community health students at Northumbria University, UK. The questionnaire was piloted and there was a 100% completion rate with 49 returned forms. The literature review indicated that most mobile technology applications were occurring in the US. At the time of the review the most prevalent mobile technologies were PDAs, laptops, WAP phones and portable radios with use being concentrated around doctors in the acute sector. A range of advantages and disadvantages to the technology were discovered. Mobile technologies were mainly being used for clinical rather than learning applications. The students showed a low level of awareness of the technology but placed great importance to accessing learning resources from the community. Significant development and changes are taking place in mobile technologies. Since the data collection for this work was completed in 2004 podcasting and videocasting have become significant in mobile learning for health professionals. Librarians will need to address the relevance and implications of m-learning for their practice. Care and consideration needs to be given on the time and resources librarians allocate for the necessary development work around mobile technologies. Collaboration and

  6. Computational Biology and Bioinformatics in Nigeria

    Science.gov (United States)

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

    2014-01-01

    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

  7. Computational biology and bioinformatics in Nigeria.

    Directory of Open Access Journals (Sweden)

    Segun A Fatumo

    2014-04-01

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

  8. 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.

  9. Investigation of blended learning video resources to teach health students clinical skills: An integrative review.

    Science.gov (United States)

    Coyne, Elisabeth; Rands, Hazel; Frommolt, Valda; Kain, Victoria; Plugge, Melanie; Mitchell, Marion

    2018-04-01

    The aim of this review is to inform future educational strategies by synthesising research related to blended learning resources using simulation videos to teach clinical skills for health students. An integrative review methodology was used to allow for the combination of diverse research methods to better understand the research topic. This review was guided by the framework described by Whittemore and Knafl (2005), DATA SOURCES: Systematic search of the following databases was conducted in consultation with a librarian using the following databases: SCOPUS, MEDLINE, COCHRANE, PsycINFO databases. Keywords and MeSH terms: clinical skills, nursing, health, student, blended learning, video, simulation and teaching. Data extracted from the studies included author, year, aims, design, sample, skill taught, outcome measures and findings. After screening the articles, extracting project data and completing summary tables, critical appraisal of the projects was completed using the Mixed Methods Appraisal Tool (MMAT). Ten articles met all the inclusion criteria and were included in this review. The MMAT scores varied from 50% to 100%. Thematic analysis was undertaken and we identified the following three themes: linking theory to practice, autonomy of learning and challenges of developing a blended learning model. Blended learning allowed for different student learning styles, repeated viewing, and enabled links between theory and practice. The video presentation needed to be realistic and culturally appropriate and this required both time and resources to create. A blended learning model, which incorporates video-assisted online resources, may be a useful tool to teach clinical skills to students of health including nursing. Blended learning not only increases students' knowledge and skills, but is often preferred by students due to its flexibility. Copyright © 2018 Elsevier Ltd. All rights reserved.

  10. [Teaching non-technical skills for critical incidents: Crisis resource management training for medical students].

    Science.gov (United States)

    Krüger, A; Gillmann, B; Hardt, C; Döring, R; Beckers, S K; Rossaint, R

    2009-06-01

    Physicians have to demonstrate non-technical skills, such as communication and team leading skills, while coping with critical incidents. These skills are not taught during medical education. A crisis resource management (CRM) training was established for 4th to 6th year medical students using a full-scale simulator mannikin (Emergency Care Simulator, ECS, METI). The learning objectives of the course were defined according to the key points of Gaba's CRM concept. The training consisted of theoretical and practical parts (3 simulation scenarios with debriefing). Students' self-assessment before and after the training provided the data for evaluation of the training outcome. A total of 65 students took part in the training. The course was well received in terms of overall course quality, debriefings and didactic presentation, the mean overall mark being 1.4 (1: best, 6: worst). After the course students felt significantly more confident when facing incidents in clinical practice. The main learning objectives were achieved. The effectiveness of applying the widely used ECS full-scale simulator in interdisciplinary teaching has been demonstrated. The training exposes students to crisis resource management issues and motivates them to develop non-technical skills.

  11. 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.

  12. Gymnasium network educational resource as a form of interactive communication of a teacher and a student

    Directory of Open Access Journals (Sweden)

    Sidorova N.N.

    2017-08-01

    Full Text Available this article presents the experience of the Surgut gymnasium «Laboratory Salahova» teachers in creating a network educational resource on various subjects. Developed course gives students and teachers an opportunity to increase the level of self-employment high-school students and to expand the distance learning in high school. The individual characteristics of every class are considered in the tasks, and this is an advantage of the course developed by the teachers of the gymnasium. The article gives examples of history lesson technological map with assignments and texts proposed for study and already-learned topic check.

  13. A new educational resource to improve veterinary students' animal welfare learning experience.

    Science.gov (United States)

    Kerr, Annie J; Mullan, Siobhan M; Main, David C J

    2013-01-01

    A computer-aided learning (CAL) educational resource based on experiential learning principles has been developed. Its aim is to improve veterinary students' ability to critically review the effect on welfare of husbandry systems observed during their work placement on sheep farms. The CAL consisted of lectures, multiple-choice questions, video recordings of animals in various husbandry conditions, open questions, and concept maps. An intervention group of first-year veterinary students (N=31) was selected randomly to access the CAL before their sheep farm placement, and a control group (N=50) received CAL training after placement. Assessment criteria for the categories remember, understand, apply, analyze, evaluate, and create, based on Bloom's revised taxonomy, were used to evaluate farm reports submitted by all students after their 2-week placement. Students in the intervention group were more likely than their untrained colleagues (pbased measurements relating to the freedom from hunger and thirst; the freedom from discomfort; and the freedom from pain, injury, or disease. Intervention group students were also more likely to analyze the freedom from pain, injury, or disease and the freedom to exhibit normal behavior and to evaluate the freedom from fear and distress. Relatively few students in each group exhibited creativity in their reports. These findings indicate that use of CAL before farm placement improved students' ability to assess and report animal welfare as part of their extramural work experience.

  14. Selection and Use of Online Learning Resources by First-Year Medical Students: Cross-Sectional Study.

    Science.gov (United States)

    Judd, Terry; Elliott, Kristine

    2017-10-02

    Medical students have access to a wide range of learning resources, many of which have been specifically developed for or identified and recommended to them by curriculum developers or teaching staff. There is an expectation that students will access and use these resources to support their self-directed learning. However, medical educators lack detailed and reliable data about which of these resources students use to support their learning and how this use relates to key learning events or activities. The purpose of this study was to comprehensively document first-year medical student selection and use of online learning resources to support their bioscience learning within a case-based curriculum and assess these data in relation to our expectations of student learning resource requirements and use. Study data were drawn from 2 sources: a survey of student learning resource selection and use (2013 cohort; n=326) and access logs from the medical school learning platform (2012 cohort; n=337). The paper-based survey, which was distributed to all first-year students, was designed to assess the frequency and types of online learning resources accessed by students and included items about their perceptions of the usefulness, quality, and reliability of various resource types and sources. Of 237 surveys returned, 118 complete responses were analyzed (36.2% response rate). Usage logs from the learning platform for an entire semester were processed to provide estimates of first-year student resource use on an individual and cohort-wide basis according to method of access, resource type, and learning event. According to the survey data, students accessed learning resources via the learning platform several times per week on average, slightly more often than they did for resources from other online sources. Google and Wikipedia were the most frequently used nonuniversity sites, while scholarly information sites (eg, online journals and scholarly databases) were accessed

  15. 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.

  16. 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.

  17. Application Design of Human Resource Information System on Binus Student Learning Community of Bina Nusantara University

    Directory of Open Access Journals (Sweden)

    Eileen Heriyanni

    2015-09-01

    Full Text Available Information exchange between human resources within an organization is a valuable asset that must be managed properly. Information technology now supports information management between human resources through Human Resource Information System (HRIS. Binus Student Learning Community (BSLC implementsdifferent technologies for each work they performed so that affect the quality of information exchange and performance of their members. This study aims to streamline the used technology in BSLC by combining it all into the same system through the implementation of HRIS constructed by Extreme Programming (XP method. Results of this research is the web-based HRIS BSLC application and expected to improve the quality of information exchange and optimize the performance of BSLC’s members.

  18. 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...

  19. Online dissection audio-visual resources for human anatomy: Undergraduate medical students' usage and learning outcomes.

    Science.gov (United States)

    Choi-Lundberg, Derek L; Cuellar, William A; Williams, Anne-Marie M

    2016-11-01

    In an attempt to improve undergraduate medical student preparation for and learning from dissection sessions, dissection audio-visual resources (DAVR) were developed. Data from e-learning management systems indicated DAVR were accessed by 28% ± 10 (mean ± SD for nine DAVR across three years) of students prior to the corresponding dissection sessions, representing at most 58% ± 20 of assigned dissectors. Approximately 50% of students accessed all available DAVR by the end of semester, while 10% accessed none. Ninety percent of survey respondents (response rate 58%) generally agreed that DAVR improved their preparation for and learning from dissection when used. Of several learning resources, only DAVR usage had a significant positive correlation (P = 0.002) with feeling prepared for dissection. Results on cadaveric anatomy practical examination questions in year 2 (Y2) and year 3 (Y3) cohorts were 3.9% (P learning outcomes of more students. Anat Sci Educ 9: 545-554. © 2016 American Association of Anatomists. © 2016 American Association of Anatomists.

  20. Psycho-corrective humanity actualization resources for students: sport and arts

    Directory of Open Access Journals (Sweden)

    Olha Kostikova

    2017-06-01

    Full Text Available Purpose: to substantiate the perspective effectiveness of the interdisciplinary system "sport – psychoanalysis – art" for effective psychological and pedagogical influence in the development of humanity in students in the teaching and educational process. Material & Methods: observation in higher educational institutions of the pedagogical and sports orientation, theoretical analysis and synthesis of philosophical-psychological and valeo-pedagogical publications on the research problem. Results: considered humanistic significance of sports activities and the arts at the planetary level of human development. The psychoanalytical and philosophical aspects of surrealism are presented in the context of the actualization of humanity in student: future teachers and trainers. Conclusion: theoretically designated psycho-correctional resources in the spectrum of physical, aesthetic and moral education for the progressive dynamics of humanity in the personal development of students.

  1. Quarries as educational resources - a research with students of a secondary school of Portugal

    Science.gov (United States)

    Filipe, Fernanda; Henriques, Maria Helena

    2015-04-01

    This work describes the results obtained in a research on science education involving 18 students of Biology and Geology of the 10th grade (15 years old) of the Secondary School of Figueiró dos Vinhos (Central Portugal). Framed on the curricular topic "Earth, a very special planet", the research included the conception, implementation and evaluation of an educational intervention aiming to answer the question: "How to stimulate meaningful and relevant learning about sustainable exploitation of geological resources, namely limestone?" The intervention occurred along 8 classes of 90 minutes each, which included practical work developed in small groups (3 students/each), and several activities both in the field and in the classroom (prior and after the fieldtrip). From the methodological point of view, this research is qualitative in nature, a study-case type, with data resulting from direct observation and content analysis of the answers presented by students to questionnaires (diagnostic and intervention assessment) and to worksheets, expressly created for the research. The main goal of the intervention was that the students, by developing practical activities centered upon a field trip to an abandoned limestone quarry located close to their homes, could learn to recognize the geological impacts arising from the exploitation of geological resources and acquire skills for collecting and processing relevant information about existing rules that control the operations in quarries, in order to develop critical thinking about the nature of exploitation of these types of resources, which may hinder the promotion of sustainable development. Concerning the intervention assessment, results reinforced the idea that quarries can provide an educational resource of great value for promoting substantive knowledge on geosciences, urgently needed and consistent with the development of critical and intervenient citizens, able to decide, at the right moment, how to behave

  2. Green Infrastructure Research Promotes Students' Deeper Interest in Core Courses of a Water Resources Program

    Science.gov (United States)

    Yerk, W.; Montalto, F. A.; Foti, R.

    2015-12-01

    As one of most innovative among low impact development technologies, Green Infrastructure (GI) is a new technology that presents a range of potential research opportunities. Inherently linked to sustainability, urban quality of life, resilience, and other such topics, GI also represents a unique opportunity to highlight the social relevance of practical STEM research to undergraduate students. The nature of research on urban GI, in fact, as well as the accessibility of the GI sites, allows students to combine hands-on experience with theoretical work. Furthermore, the range of scales of the projects is such that they can be managed within a single term, but does not preclude longer engagement. The Sustainable Water Resource Engineering lab at Drexel University is engaged in two types of GI research outside the classroom. One type is a research co-op research internship. The second is a selective university-wide faculty-mentored summer scholarship STAR (Students Tackling Advanced Research) specifically designed for freshmen. The research projects we developed for those curricula can be accomplished by undergraduate students, but also address a larger research need in this emerging field. The research tasks have included identifying and calibrating affordable instruments, designing and building experimental setups, and monitoring and evaluating performance of GI sites. The work also promoted deeper understanding of the hydrological processes and initiated learning beyond the students' current curricula. The practice of the Lab's research being embedded into the educational process receives positive feedback from the students and achieves meaningful and long-lasting learning objectives. The experience helps students to students acquire hands-on experience, improves their metacognition and evidence-based inquiring into real-world problems, and further advances decision-making and communication skills.

  3. Using registries to integrate bioinformatics tools and services into workbench environments

    DEFF Research Database (Denmark)

    Ménager, Hervé; Kalaš, Matúš; Rapacki, Kristoffer

    2016-01-01

    within convenient, integrated “workbench” environments. Resource descriptions are the core element of registry and workbench systems, which are used to both help the user find and comprehend available software tools, data resources, and Web Services, and to localise, execute and combine them......, a software component that will ease the integration of bioinformatics resources in a workbench environment, using their description provided by the existing ELIXIR Tools and Data Services Registry....

  4. Undergraduate Research in Geoscience with Students from Two-year Colleges: SAGE 2YC Resources

    Science.gov (United States)

    McDaris, J. R.; Hodder, J.; Macdonald, H.; Baer, E. M.; Blodgett, R. H.

    2014-12-01

    provides resources on effective strategies for developing REU programs for community college students, examples of successful multi-year programs, links to other projects working on undergraduate research in the first two years, and references for further reading. serc.carleton.edu/sage2yc/studentsuccess/ug-research/

  5. Digital Cadavers: Online 2D Learning Resources Enhance Student Learning in Practical Head and Neck Anatomy within Dental Programs

    Directory of Open Access Journals (Sweden)

    Mahmoud M. Bakr

    2016-01-01

    Full Text Available Head and neck anatomy provides core concepts within preclinical dental curricula. Increased student numbers, reduced curricula time, and restricted access to laboratory-based human resources have increased technology enhanced learning approaches to support student learning. Potential advantages include cost-effectiveness, off-campus access, and self-directed review or mastery opportunities for students. This study investigated successful student learning within a first-year head and neck anatomy course at the School of Dentistry and Oral Health, Griffith University, Australia, taught by the same teaching team, between 2010 and 2015. Student learning success was compared, for cohorts before and after implementation of a supplementary, purpose-designed online digital library and quiz bank. Success of these online resources was confirmed using overall students’ performance within the course assessment tasks and Student Evaluation of Course surveys and online access data. Engagement with these supplementary 2D online resources, targeted at improving laboratory study, was positively evaluated by students (mean 85% and significantly increased their laboratory grades (mean difference 6%, P<0.027, despite being assessed using cadaveric resources. Written assessments in final exams were not significantly improved. Expanded use of supplementary online resources is planned to support student learning and success in head and neck anatomy, given the success of this intervention.

  6. Relationship Among Dental Students' Class Lecture Attendance, Use of Online Resources, and Performance.

    Science.gov (United States)

    Azab, Ehab; Saksena, Yun; Alghanem, Tofool; Midle, Jennifer Bassett; Molgaard, Kathleen; Albright, Susan; Karimbux, Nadeem

    2016-04-01

    This study aimed to evaluate the relationship among dental students' attendance at class lectures, use of online lecture materials, and performance in didactic courses. The study was conducted with second-year predoctoral students at Tufts University School of Dental Medicine during the fall semester of 2014. Three basic science and three preclinical dental courses were selected for evaluation. Online usage for each participant was collected, and a survey with questions about attendance and online behavior was conducted. The final grade for each participant in each selected course was obtained and matched with his or her online usage and attendance. Out of a total 190 students, 146 (77%) participated. The results showed no significant relationship between students' grades and their class attendance or online usage except for a weak negative relationship between class attendance and online usage for the Epidemiology course (prelationships among class attendance, online usage, and course grades, most of the students reported that having the online resources in addition to the lectures was helpful.

  7. Topics in Current Science Research: Closing the Achievement Gap for Under Resourced Students of Color

    Science.gov (United States)

    Loya Villalpando, Alvaro; Daal, Miguel; Phipps, Arran; Speller, Danielle; Sadoulet, Bernard; Winheld, Rachel; Cryogenic Dark Matter Search Collaboration

    2015-04-01

    Topics in Current Science Research (TCSR) is a five-week summer course offered at the University of California, Berkeley through a collaboration between the Level Playing Field Institute's Summer Math and Science Honors Academy (SMASH) Program and the Cryogenic Dark Matter Search (CDMS) group at UC Berkeley. SMASH is an academic enrichment program geared towards under-resourced, high school students of color. The goals of the course are to expand the students' conception of STEM, to teach the students that science is a method of inquiry and not just a collection of facts that are taught in school, and to expose the scholars to critical thinking within a scientific setting. The course's curriculum engages the scholars in hands-on scientific research, project proposal writing, and presentation of their scientific work to their peers as well as to a panel of UC Berkeley scientists. In this talk, we describe the course and the impact it has had on previous scholars, we discuss how the course's pedagogy has evolved over the past 10 years to enhance students' perception and understanding of science, and we present previous participants' reflections and feedback about the course and its success in providing high school students a genuine research experience at the university level.

  8. Doing science by waving hands: Talk, symbiotic gesture, and interaction with digital content as resources in student inquiry

    Science.gov (United States)

    Gregorcic, Bor; Planinsic, Gorazd; Etkina, Eugenia

    2017-12-01

    In this paper, we investigate some of the ways in which students, when given the opportunity and an appropriate learning environment, spontaneously engage in collaborative inquiry. We studied small groups of high school students interacting around and with an interactive whiteboard equipped with Algodoo software, as they investigated orbital motion. Using multimodal discourse analysis, we found that in their discussions the students relied heavily on nonverbal meaning-making resources, most notably hand gestures and resources in the surrounding environment (items displayed on the interactive whiteboard). They juxtaposed talk with gestures and resources in the environment to communicate ideas that they initially were not able to express using words alone. By spontaneously recruiting and combining a diverse set of meaning-making resources, the students were able to express relatively fluently complex ideas on a novel physics topic, and to engage in practices that resemble a scientific approach to exploration of new phenomena.

  9. Doing science by waving hands: Talk, symbiotic gesture, and interaction with digital content as resources in student inquiry

    Directory of Open Access Journals (Sweden)

    Bor Gregorcic

    2017-08-01

    Full Text Available In this paper, we investigate some of the ways in which students, when given the opportunity and an appropriate learning environment, spontaneously engage in collaborative inquiry. We studied small groups of high school students interacting around and with an interactive whiteboard equipped with Algodoo software, as they investigated orbital motion. Using multimodal discourse analysis, we found that in their discussions the students relied heavily on nonverbal meaning-making resources, most notably hand gestures and resources in the surrounding environment (items displayed on the interactive whiteboard. They juxtaposed talk with gestures and resources in the environment to communicate ideas that they initially were not able to express using words alone. By spontaneously recruiting and combining a diverse set of meaning-making resources, the students were able to express relatively fluently complex ideas on a novel physics topic, and to engage in practices that resemble a scientific approach to exploration of new phenomena.

  10. Using online interventions to deliver college student mental health resources: Evidence from randomized clinical trials.

    Science.gov (United States)

    Nguyen-Feng, Viann N; Greer, Christiaan S; Frazier, Patricia

    2017-11-01

    This study evaluated the efficacy of Internet-based stress management programs for college students. This approach is particularly fitting for students owing to a lack of mental health resources on campus and to high levels of Internet use among students. Because a history of interpersonal trauma (IPT) is associated with more distress and poorer academic performance, IPT history was assessed as a moderator of intervention efficacy. Students (N = 365) were randomly assigned to a mindfulness plus present control intervention, a mindfulness only intervention, or a stress management information condition that served as an active comparison. Prior research has supported the efficacy of the mindfulness plus present control intervention (Nguyen-Feng et al., 2015). Outcome measures were self-report measures of stress, anxiety, depression, and perceived stress completed online at preintervention, postintervention, and 2 follow-ups (2-3 weeks and 4-5 weeks postintervention). Linear mixed modeling was used to assess change over time. Participants in all 3 groups reported significant decreases on all primary outcomes. All time-by-intervention group interaction effects were nonsignificant, suggesting that the 3 conditions were equally effective. When examining IPT history as a moderator, the mindfulness plus present control and stress management conditions were both more effective for IPT survivors than the mindfulness only intervention. Results suggested that Internet-based interventions are effective for lowering distress among college students and that specific approaches may be differentially effective for certain subgroups of students. They also suggested that providing students with stress management information without providing training in 1 specific skill may also be helpful. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  11. Work-school conflict and health outcomes: beneficial resources for working college students.

    Science.gov (United States)

    Park, Youngah; Sprung, Justin M

    2013-10-01

    This study extends prior college student employment research by examining health as an outcome variable. Using 2-wave data from a sample of 216 student workers, this study examined work-school conflict as a predictor of psychological and physical health among working college students. Additionally, 3 resource-providing variables--work-school facilitation, supervisor work-school support, and personal fulfillment at work--were tested for buffering effects in the relation between work-school conflict and health. Results demonstrated that work-school conflict was a significant predictor of psychological health but not physical health. All 3 resource-providing variables ameliorated the negative relation between work-school conflict and psychological health, whereas only personal fulfillment weakened the positive relation between work-school conflict and physical symptoms. These findings suggest the benefits of work-school facilitation, supervisor work-school support, and personal fulfillment in minimizing the detrimental effects of work-school conflict on health outcomes. Theoretical and practical implications for researchers, educational institutions, and organizations are discussed.

  12. Do college students use online self-help? A survey of intentions and use of mental health resources

    OpenAIRE

    Levin, Michael E.; Stocke, Krista; Pierce, Benjamin; Levin, Crissa

    2017-01-01

    Online self-help may help increase the reach of mental health services for college students, but little research has examined students’ actual interest/use of these resources. An online survey of 389 college students examined intentions and use of online mental health resources as compared with other support options. Findings indicated the highest intentions/use of informal supports (e.g., parents, friends) for mental health problems and lowest intentions/use for online self-help. However, a ...

  13. An Invaluable Resource for Supporting Transgender, Transsexual, and Gender-Nonconforming Students in School Communities: A Review of "Supporting Transgender and Transsexual Students in K-12 Schools"

    Science.gov (United States)

    Martino, Wayne

    2013-01-01

    This essay provides a review of a resource guide written by Kristopher Wells, Gayle Roberts, and Carol Allan (2012) titled "Supporting Transgender and Transsexual Students in K-12 Schools: A Guide for Educators". The guide is an invaluable resource for educators in schools and teacher education programs.

  14. 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.

  15. Video Productions as Learning Resources in Students' Knowledge Building in the Ubiquitous Society

    DEFF Research Database (Denmark)

    Buhl, Mie; Andreasen, Lars Birch; Ørngreen, Rikke

    2012-01-01

    in mind. The chapter presents an overview of the state-of-the art of research on using video productions as learning resources, followed by discussions of our own research results and practices. From the overview and the discussions concepts are defined and research questions formed, based on a multimodal...... productions developed by the students themselves. This is investigated from a theoretical as well as an empirical perspective, building on the authors’ experiences from researching and teaching dealing with production of video in learning situations, with different learning objectives and didactic designs...... perspective on teaching and educational design. We conclude by arguing where and why there is a need for more knowledge about video productions' potential as learning resources....

  16. Directions of use of electronic resources at training to computer science of students of a teacher training college

    OpenAIRE

    Светлана Анатольева Баженова

    2009-01-01

    Article is devoted questions of use of electronic resources at training to computer science in a teacher training college, principles of pedagogical expediency of use of electronic resources at training are specified computer science and positive aspects of such use for different forms of work of the student and the teacher are allocated.

  17. The Impact of Lack of Resources on Declining Students' Enrolments in Design and Technology in Botswana Junior Secondary Schools

    Science.gov (United States)

    Gaotlhobogwe, Michael

    2012-01-01

    Lack of resources has resulted in declining students' enrolment in design and technology in Botswana junior secondary schools by up to 6% per year over 10 years, despite positive encouragement by the government. Based on the PATT (pupils' attitude towards technology) theoretical framework this study indicated how a lack of resources in Botswana…

  18. An Investigation into Saudi Students' Knowledge of and Attitudes towards E-Resources on BBC Learning English

    Science.gov (United States)

    Alzahrani, Khalid Saleh

    2017-01-01

    The BBC Learning English website has become an important method of learning and studying English as a second language, a resource that enhances the importance of e-learning. The aim of the current research is to find Saudi students' knowledge of and attitude towards e-resources on BBC Learning English. The sample size was 28 participants (17 male…

  19. "Superheroes in the Resource Room": A Study Examining Implementation of the Superhero Social Skills Program by a Resource Teacher with Students with Externalizing Behavior Problems

    Science.gov (United States)

    Springer, Benjamin James

    2012-01-01

    The current study evaluated the effectiveness of the Superhero Social Skills program in increasing the social engagement skills and decreasing the aggressive behavior of students with externalizing behavior problems as implemented by a resource teacher. There have been no empirical evaluations of the Superhero Social Skills program as implemented…

  20. Effects of Student Characteristics, Principal Qualifications, and Organizational Constraints for Assessing Student Achievement: A School Public Relations and Human Resources Concern

    Science.gov (United States)

    Young, I. Phillip; Vang, Maiyoua; Young, Karen Holsey

    2008-01-01

    Standards-based student achievement scores are used to assess the effectiveness of public education and to have important implications regarding school public relations and human resource practices. Often overlooked is that these scores may be moderated by the characteristics of students, the qualifications of principals, and the restraints…

  1. How important are student-selected versus instructor-selected literature resources for students' learning and motivation in problem-based learning?

    NARCIS (Netherlands)

    Wijnia, Lisette; Loyens, Sofie M. M.; Derous, Eva; Schmidt, Henk G.

    2015-01-01

    In problem-based learning students are responsible for their own learning process, which becomes evident when they must act independently, for example, when selecting literature resources for individual study. It is a matter of debate whether it is better to have students select their own literature

  2. Literature review: Use of commercial films as a teaching resource for health sciences students.

    Science.gov (United States)

    Díaz Membrives, Montserrat; Icart Isern, M Teresa; López Matheu, M Carmen

    2016-01-01

    Analyze some of the characteristics of the publications focused on commercial cinema as a learning tool for university students engaged in health sciences degrees. The review was based on the search of information in three electronic databases: MEDLINE, CINAHL and ERIC. 54 papers were selected and analyzed. Cinema is a commonly used resource; however there is still a lack of studies demonstrating its usefulness and validity. This review is limited on its analysis by the fact that a large number of experiences are described as having a loose design. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Evaluation of a webquest on the theme "management of material resources in nursing" by undergraduate students.

    Science.gov (United States)

    Pereira, Marta Cristiane Alves; Melo, Márcia Regina Antonietto da Costa; Silva, Adriana Serafim Bispo E; Evora, Yolanda Dora Martinez

    2010-01-01

    The learning process mediated by information and communication technology has considerable importance in the current context. This study describes the evaluation of a WebQuest on the theme "Management of Material Resources in Nursing". It was developed in three stages: Stage 1 consisted of its pedagogical aspect, that is, elaboration and definition of content; Stage 2 involved the organization of content, inclusion of images and completion; Stage 3 corresponded to its availability to students. Results confirm the importance of information technology and information as instruments for a mediating teaching practice in the integration between valid knowledge and the complex and dynamic reality of health services. As a result of the students' favorable evaluation of the approximation with the reality of nursing work and satisfaction for performing the activity successfully, the WebQuest method was considered valid and innovating for the teaching-learning process.

  4. CHEMISTRY TEACHING BY MEANS OF ICT-BASED RESOURCES WITH THE REGARD FOR PREFERRED LEARNING STYLES OF UNIVERSITY STUDENTS

    Directory of Open Access Journals (Sweden)

    T.M. Derkach

    2013-03-01

    Full Text Available Expediency and effectiveness of the use of various ICT-based learning resources in teaching of basic chemistry disciplines was studied. Preferred learning styles of 46 graduate students were assessed by the Felder-Soloman Index of Learning Styles. More than a half of 45 considered resources were found to be dependent on students’ preferred learning style. Certain corrections in the use of style-dependent resources are necessary to improve conformity with students’ learning preferences.

  5. Three-Dimensional Visualizations in Teaching Genomics and Bioinformatics: Mutations in HIV Envelope Proteins and Their Consequences for Vaccine Design

    Directory of Open Access Journals (Sweden)

    Kathy Takayama

    2009-11-01

    Full Text Available This project addresses the need to provide a visual context to teach the practical applications of genome sequencing and bioinformatics. Present-day research relies on indirect visualization techniques (e.g., fluorescence-labeling of DNA in sequencing reactions and sophisticated computer analysis. Such methods are impractical and prohibitively expensive for laboratory classes. More importantly, there is a need for curriculum resources that visually demonstrate the application of genome sequence information rather than the DNA sequencing methodology itself. This project is a computer-based lesson plan that engages students in collaborative, problem-based learning. The specific example focuses on approaches to Human Immunodeficiency Virus-1 (HIV-1 vaccine design based on HIV-1 genome sequences using a case study. Students performed comparative alignments of variant HIV-1 sequences available from a public database. Students then examined the consequences of HIV-1 mutations by applying the alignments to three-dimensional images of the HIV-1 envelope protein structure, thus visualizing the implications for applications such as vaccine design. The lesson enhances problem solving through the application of one type of information (genomic or protein sequence into concrete visual conceptualizations. Assessment of student comprehension and problem-solving ability revealed marked improvement after the computer tutorial. Furthermore, contextual presentation of these concepts within a case study resulted in student responses that demonstrated higher levels of cognitive ability than was expected by the instructor.

  6. 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.

  7. A Technology Based Program That Matches Enrichment Resources With Student Strengths

    Directory of Open Access Journals (Sweden)

    J.S. Renzulli

    2007-09-01

    Full Text Available Remarkable advances in instructionalcommunication technology (ICT have now made ispossible to provide high levels of enrichment and thekinds of curricular differentiation that facilitateadvanced learning services to students who have accessto a computer and the Internet. But in order tomaximize the potential if ICT it is necessary to constructprograms that are based on learning theory that goesbeyond the didactic and prescriptive models that haveresulted in too much worksheets-on-line and electronicencyclopedias. The Renzulli Learning System (RLSuses a strength-based learning theory called theEnrichment Triad Model that is purposefully designedto promote advanced level learning, creativeproductivity, and high levels of student engagement byfocusing on the application of knowledge rather than themere acquisition and storage of information.The Renzulli Learning System is acomprehensive program that begins by providing acomputer-generated profile of each student’s academicstrengths, interests, learning styles, and preferred modesof expression. A search engine then matches Internetresources to the student’s profile from fourteen carefullyscreened data bases that are categorized by subject area,grade level, state curricular standards, and degree ofcomplexity. There are also hundreds of enrichmentactivities that can be down loaded and reproduced forindividual or group learning activities. A managementsystem called the Wizard Project Maker guides studentsin the application of knowledge to teacher or studentselected assignments, independent research studies, orcreative projects that individuals or small groups wouldlike to pursue. Students and teachers can evaluate thequality of students’ products using a rubric called TheStudent Product Assessment Form. Students can rateeach site visited, conduct a self-assessment of what theyhave gained from the site, and place resources in theirown Total talent Portfolio for future use. RLS alsoincludes a

  8. Linguistic Resources Used in Grade 8 Students' Submicro Level Explanations—Science Items from TIMSS 2007

    Science.gov (United States)

    Frändberg, Birgitta; Lincoln, Per; Wallin, Anita

    2013-12-01

    Explanations involving submicro levels of representation are central to science education, but known to be difficult for students in secondary school. This study examines students' written explanations of physical and chemical phenomena regarding matter and changes in matter, in a large-scale test. This is done in order to understand linguistic challenges in constructing submicro level explanations involving the particle model of matter. Drawing from systemic functional linguistics, the lexicogrammatics used in explanations for realising experiential meaning in student explanations were analysed. We used answers to two partly constructed response items from the Swedish part of Trends in International Mathematics and Science Studies 2007, grade 8, to sort out explanations referring to the particle model of matter. These answers (86 from 954) were analysed regarding choices of vocabulary and grammar to distinguish between macro and submicro level of representation. The results show that students use a wide variety of lexicogrammatical resources to realise what happens on both macro and submicro level of representation, with greater diversity of verbs on the submicro level of explanation. The results suggest an uncertainty about the distinction between macro and submicro level of explanation.

  9. The Inspiring Science Education project and the resources for HEP analysis by university students

    International Nuclear Information System (INIS)

    Fassouliotis, Dimitris; Kourkoumelis, Christine; Vourakis, Stylianos

    2016-01-01

    The Inspiring Science Education outreach project has been running for more than two years, creating a large number of inquiry based educational resources for high-school teachers and students. Its goal is the promotion of science education in schools though new methods built on the inquiry based education techniques, involving large consortia of European partners and implementation of large-scale pilots in schools. Recent hands-on activities, developing and testing the above mentioned innovative applications are reviewed. In general, there is a lack for educational scenaria and laboratory courses earmarked for more advanced, namely university, students. At the University of Athens for the last four years, the HYPATIA on-line event analysis tool has been used as a lab course for fourth year undergraduate physics students, majoring in HEP. Up to now, the course was limited to visual inspection of a few tens of ATLAS events. Recently the course was enriched with additional analysis exercises, which involve large samples of events. The students through a user friendly interface can analyse the samples and optimize the cut selection in order to search for new physics. The implementation of this analysis is described

  10. Effectiveness of a Science Agricultural Summer Experience (SASE) in Recruiting Students to Natural Resources Management

    Science.gov (United States)

    Martinez, Edward; Lindline, Jennifer; Petronis, Michael S.; Pilotti, Maura

    2012-12-01

    The Bureau of Labor Statistics projects an increase in Natural Resource Management (NRM) jobs within the next 10 years due to baby-boomer retirements and a 12% increase in demand for these occupations. Despite this trend, college enrollment in NRM disciplines has declined. Even more critical is the fact that the soon-to-be-majority Hispanic population is underrepresented in NRM disciplines. The goal of the present study was to determine if an in-residence, two-week, summer science program for underrepresented minorities would not only increase interest in science, actual science knowledge, and perceived science knowledge, but also have an overall impact on underrepresented minority students' decisions to attend college, major in a scientific discipline and pursue a career in science. During a four-year period, 76 high school students participated in a Science Agricultural Summer Experience (SASE) in Northern New Mexico. A pre/post science-knowledge exam and satisfaction survey were administered to participants. We demonstrate that participants improved significantly ( p Students not only found science exciting and approachable after participation, but also exhibited increased interest in pursuing a degree and career in science. Of the 76 SASE participants within graduation age ( n = 44), all graduated from high school; and 86% enrolled in college. These findings suggest that the implemented SASE initiative was effective in recruiting and increasing the confidence and abilities of underrepresented minority students in science.

  11. Reallocating Human Resources to Maximize Student Achievement: A Critical Case Study of a Southern California School District

    Science.gov (United States)

    Glazener, Adrianna Kathleen

    2013-01-01

    This study applied the Evidence-Based Model (Odden & Picus, 2008) as a framework for determining how district leadership could potentially reallocate human resources to maximize the opportunity for student achievement, relying heavily on the ten strategies for doubling student performance (Odden, 2009; Odden & Archibald, 2009) and the…

  12. Accommodations and Support Services for Students with Autism Spectrum Disorder (ASD): A National Survey of Disability Resource Providers

    Science.gov (United States)

    Brown, Kirsten R.

    2017-01-01

    Students with Autism Spectrum Disorder (ASD) are participating in postsecondary education at an increasing rate. Yet, we know little about what types of accommodations or services disability resource providers employ to support students with ASD. The purpose of this study was to examine how postsecondary institutions are fostering the academic…

  13. Indian Independence and the Question of Pakistan. [Student Text and] Teacher Resource Book. Choices for the 21st Century.

    Science.gov (United States)

    Fox, Sarah Cleveland

    This document includes a student text and a teacher resource book. The student booklet provides an overview of the history of the Indian subcontinent, focuses on key events leading up to partition, and explores the origins of the conflict in Kashmir. It notes that to understand the conflict in Kashmir, people must examine the period of British…

  14. Challenges and Resources of Mexican American Students within the Family, Peer Group, and University: Age and Gender Patterns.

    Science.gov (United States)

    Lopez, Edward M.

    1995-01-01

    A survey of 100 Mexican American undergraduate students assessed their perceptions of five challenges (and associated resources) to completing college: financial problems, domestic responsibilities, academic discouragement, and racial and gender discrimination. There were no differences between upper- and lower-division students. Males were more…

  15. Demographic Variables and Students Use of E-Learning Resources in Public Secondary Schools Libraries in Rivers State of Nigeria

    Science.gov (United States)

    Owate, C. N.; Afolabi, M.; Akanwa, P. C.

    2017-01-01

    The applications of e-learning resources to studies, teaching and learning by both staff and students have been investigated. However, the provision of e-learning tools for stake-holders is a modern goal to improving as well as achieving the quality of educational system in the twenty first century is imperative. Students' demographic variables…

  16. Helping Students to Learn the English Second Conditional by Blending Internet Resources with Virtual Worlds: The Results of a Study

    Science.gov (United States)

    Kruk, Mariusz

    2013-01-01

    The paper presents the results of a study whose main aim was to investigate the effectiveness of using Internet resources and a browser-based virtual world in helping a group of students to learn the English second conditional. The sample consisted of thirteen third year students studying English at a Polish senior high school. The data were…

  17. Negotiating Power and Access to Second Language Resources: A Study on Short-Term Chinese MBA Students in America

    Science.gov (United States)

    Shi, Xingsong

    2011-01-01

    By looking into a group of 13 Chinese master's in business administration students' study abroad experience in the United States, this study contends that being situated in the second language (L2) communicative context does not guarantee international students complete access to language and cultural resources in the host society. Due to limited…

  18. Analysis of Perceived Stress, Coping Resources and Life Satisfaction among Students at a Newly Established Institution of Higher Learning

    Science.gov (United States)

    Mudhovozi, P.

    2011-01-01

    A survey was conducted to analyse perceived stress, coping resources and life satisfaction among university students at an institution of higher learning. Seventy-three students randomly selected from third year Social Sciences class participated in the study. A self-report questionnaire was administered to the participants. The results showed…

  19. Models@Home: distributed computing in bioinformatics using a screensaver based approach.

    NARCIS (Netherlands)

    Krieger, E.; Vriend, G.

    2002-01-01

    MOTIVATION: Due to the steadily growing computational demands in bioinformatics and related scientific disciplines, one is forced to make optimal use of the available resources. A straightforward solution is to build a network of idle computers and let each of them work on a small piece of a

  20. 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

  1. 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

  2. Storms in Space: Bringing NASA Earth-Sun Science Educational Resources to Hearing- Impaired Students.

    Science.gov (United States)

    Lowry, K.; Sindt, M.; Jahn, J.

    2007-12-01

    Using assistive technology, children with hearing loss can actively participate in the hearing world. However, to develop the necessary skills, hearing-impaired students need to be immersed in a language-rich environment which compensates for the lack of "incidental" learning that typifies the language acquisition of their peers with typical hearing. For any subject matter taught in class, this means that the conceptual and language framework of the topic has to be provided in addition to regular class materials. In a collaboration between the Sunshine Cottage School for Deaf Children and the Southwest Research Institute, we are exploring how NASA-developed educational resources covering Space Science topics can be incorporated successfully in blended classrooms containing children with hearing loss and those with typical hearing in grades 3-5. Utilizing the extensive routine language monitoring performed at Sunshine Cottage, student progress is directly monitored during the year as well as from year to year. This allow us to evaluate the effectiveness of the resources used. Since all instruction at Sunshine Cottage is auditory-oral, our experiences in using those materials can be fed back directly into mainstream classrooms of the same grade levels.

  3. Unlocking Resources: Self-Guided Student Explorations of Science Museum and Aquarium Exhibits

    Science.gov (United States)

    Kirkby, K. C.; Phipps, M.; Hamilton, P.

    2010-12-01

    Remarkably few undergraduate programs take full advantage of the rich resources provided by science museums, aquariums and other informal science education institutions. This is not surprising considering the logistical hurdles of class trips, but an even more fundamental barrier is that these institutions’ exhibit text seldom explicitly convey their information at a level suitable for undergraduate curriculum. Traditionally, this left the burden of interpretation on individual instructors, who rarely have the time to undertake it. To overcome these hurdles, the University of Minnesota has partnered with the Science Museum of Minnesota and Underwater Adventures Aquarium to test the efficacy of self-guided student explorations in revealing the rich data encoded in museum and aquarium exhibits. An initial module at the Science Museum of Minnesota focused on interpreting animal designs, specifically exploring how differences in dinosaur skeletal features reflected variations in the animals’ lifestyles. Students learn to interpret diet and lifestyle not only from characteristics of the skull and teeth, but also from variations in vertebrae and rib design or the relative proportion of limb elements. A follow-up module, based on exhibits at Underwater Adventures Aquarium focuses on interpreting energy flow through ecosystems from the behavior of living organisms. Students explore the information on lifestyle and diet that is encoded in a sturgeon’s ceaseless glide or a muskellunge’s poised stillness. These modules proved to be immensely popular with students. In classes with up to 500 students, half to two-thirds of the students volunteered to complete the modules, despite the additional expense and distances of up to 13 miles between the University and partner institutions. More importantly, quantitative assessment with pre-instruction and post-instruction surveys demonstrate that these ungraded, self-guided explorations match or exceed the efficacy of

  4. Infusing Bioinformatics and Research-Like Experience into a Molecular Biology Laboratory Course

    Science.gov (United States)

    Nogaj, Luiza A.

    2014-01-01

    A nine-week laboratory project designed for a sophomore level molecular biology course is described. Small groups of students (3-4 per group) choose a tumor suppressor gene (TSG) or an oncogene for this project. Each group researches the role of their TSG/oncogene from primary literature articles and uses bioinformatics engines to find the gene…

  5. Bioinformatics Education in High School: Implications for Promoting Science, Technology, Engineering, and Mathematics Careers

    Science.gov (United States)

    Kovarik, Dina N.; Patterson, Davis G.; Cohen, Carolyn; Sanders, Elizabeth A.; Peterson, Karen A.; Porter, Sandra G.; Chowning, Jeanne Ting

    2013-01-01

    We investigated the effects of our Bio-ITEST teacher professional development model and bioinformatics curricula on cognitive traits (awareness, engagement, self-efficacy, and relevance) in high school teachers and students that are known to accompany a developing interest in science, technology, engineering, and mathematics (STEM) careers. The…

  6. A Critical Analysis of Assessment Quality in Genomics and Bioinformatics Education Research

    Science.gov (United States)

    Campbell, Chad E.; Nehm, Ross H.

    2013-01-01

    The growing importance of genomics and bioinformatics methods and paradigms in biology has been accompanied by an explosion of new curricula and pedagogies. An important question to ask about these educational innovations is whether they are having a meaningful impact on students' knowledge, attitudes, or skills. Although assessments are…

  7. Alu Insertions and Genetic Diversity: A Preliminary Investigation by an Undergraduate Bioinformatics Class

    Science.gov (United States)

    Elwess, Nancy L.; Duprey, Stephen L.; Harney, Lindesay A.; Langman, Jessie E.; Marino, Tara C.; Martinez, Carolina; McKeon, Lauren L.; Moss, Chantel I. E.; Myrie, Sasha S.; Taylor, Luke Ryan

    2008-01-01

    "Alu"-insertion polymorphisms were used by an undergraduate Bioinformatics class to study how these insertion sites could be the basis for an investigation in human population genetics. Based on the students' investigation, both allele and genotype "Alu" frequencies were determined for African-American and Japanese populations as well as a…

  8. Learning clinical procedures through Internet visual resources: a qualitative study amongst undergraduate students.

    Science.gov (United States)

    Gao, X; Wong, L M; Chow, D Y S; Law, X J; Ching, L Y L

    2015-02-01

    Acquiring competency in performing clinical procedures is central to professional education of healthcare providers. Internet visual resources (IVR), defined as visual materials openly accessible on public websites, provides a new channel to learn clinical procedures. This qualitative study aimed to profile the experience and opinions of undergraduate students (in dentistry, medicine and nursing) in learning clinical procedures through IVR. From clinical degree programmes (Bachelor of Dental Surgery, Bachelor of Medicine, Bachelor of Surgery, and Bachelor of Nursing) of University of Hong Kong, 31 students were recruited to join six focus group discussions, which were transcribed and subjected to thematic analysis using inductive method, in which themes emerge from data. Students actively looked for IVRs through various means and used them for pre-clinical preparation, post-clinical revision, learning simple and advanced procedures, exploring alternative and updated techniques, and benchmarking against international peers. IVRs were valued for their visual stimulation, inclusion of a wide variety of real-life cases, convenience in access, user-friendliness and time-saving features. Students tended to share and discuss IVRs with their peers rather than with tutors, even when contents deviated from school teaching or faculty's e-learning materials. When doubts persisted, they chose to follow faculty guidelines for examination purpose. Students were frustrated sometimes by difficulties in judging the scientific quality, lack of immediate interactive discussions and loosely structured presentations in some IVRs. Teachers' attitudes towards IVR appeared to vary greatly. Despite the wide spectrum of experience and opinions, IVR was generally viewed by undergraduates from across clinical faculties as enhancing their clinical confidence and self-perceived competency, enriching their learning experience and serving as an important supplement to formal learning in the

  9. Resourcing the clinical complementary medicine information needs of Australian medical students: Results of a grounded theory study.

    Science.gov (United States)

    Templeman, Kate; Robinson, Anske; McKenna, Lisa

    2016-09-01

    The aim of this study was to identify Australian medical students' complementary medicine information needs. Thirty medical students from 10 medical education faculties across Australian universities were recruited. Data were generated using in-depth semi-structured interviews and constructivist grounded theory method was used to analyze and construct data. Students sought complementary medicine information from a range of inadequate sources, such as pharmacological texts, Internet searches, peer-reviewed medical journals, and drug databases. The students identified that many complementary medicine resources may not be regarded as objective, reliable, differentiated, or comprehensive, leaving much that medical education needs to address. Most students sought succinct, easily accessible, evidence-based information to inform safe and appropriate clinical decisions about complementary medicines. A number of preferred resources were identified that can be recommended and actively promoted to medical students. Therefore, specific, evidence-based complementary medicine databases and secondary resources should be subscribed and recommended to medical schools and students, to assist meeting professional responsibilities regarding complementary medicines. These findings may help inform the development of appropriate medical information resources regarding complementary medicines. © 2016 John Wiley & Sons Australia, Ltd.

  10. Quality of faculty, students, curriculum and resources for nursing doctoral education in Korea: a focus group study.

    Science.gov (United States)

    Kim, Mi Ja; Lee, Hyeonkyeong; Kim, Hyun Kyung; Ahn, Yang-Heui; Kim, Euisook; Yun, Soon-Nyoung; Lee, Kwang-Ja

    2010-03-01

    The rapidly increasing number of nursing doctoral programs has caused concern about the quality of nursing doctoral education, including in Korea. To describe the perceived quality of Korean nursing doctoral education in faculty, student, curriculum and resources. Focus group. Fourteen Korean nursing doctoral programs that are research focused and include coursework. Four groups of deans, faculty, students and graduates; students completed three semesters of doctoral program; and graduates completed doctoral programs within the most recent 3 years. Focus groups examined the strengths and weaknesses of faculty, students, curriculum, and resources. Faculty strengths were universities' recognition of faculty research/scholarship and the ability of faculty to attract extramural funding. Faculty weaknesses were aging faculty; high faculty workload; insufficient number of faculty; and teaching without expertise in nursing theories. Student strengths were diverse student backgrounds; multidisciplinary dissertation committee members, and opportunities to socialize with peers and graduates/faculty. Students' weaknesses were overproduction of PhDs with low academic quality; a lower number and quality of doctoral applicants; and lack of full-time students. Curriculum strengths were focusing on specific research areas; emphasis on research ethics; and multidisciplinary courses. Curriculum weaknesses were insufficient time for curriculum development; inadequate courses for core research competencies; and a lack of linkage between theory and practice. Resources strengths were inter-institutional courses with credit transfer. Weaknesses were diminished university financial support for graduate students and limited access to school facilities. Variations in participant groups (providers [deans and faculty] vs. receivers [students and graduates]) and geographical location (capital city vs. regional) were noted on all the four components. The quality characteristics of faculty

  11. Uso da bioinformática na diferenciação molecular da Entamoeba histolytica e Entamoeba díspar - DOI: 10.4025/actascihealthsci.v30i2.2375 Molecular discrimination of Entamoeba histolytica and Entamoeba dispar by bioinformatics resources - DOI: 10.4025/actascihealthsci.v30i2.2375

    Directory of Open Access Journals (Sweden)

    Débora Sommer

    2008-12-01

    Full Text Available Amebíase invasiva, causada por Entamoeba histolytica, é microscopicamente indistinguível da espécie não-patogênica Entamoeba dispar. Com auxílio de ferramentas de bioinformática, objetivou-se diferenciar Entamoeba histolytica e Entamoeba dispar por técnicas moleculares. A análise foi realizada a partir do banco de dados da National Center for Biotechnology Information; pela pesquisa de similaridade de sequências, elegeu-se o gene da cisteína sintase. Um par de primer foi desenhado (programa Web Primer e foi selecionada a enzima de restrição TaqI (programa Web Cutter. Após a atuação da enzima, o fragmento foi dividido em dois, um com 255 pb e outro com 554 pb, padrão característico da E. histolytica. Na ausência de corte, o fragmento apresentou o tamanho de 809 pb, referente à E. dispar.Under microscopic conditions, the invasive Entamoeba histolytica is indistinguishable from the non-pathogenic species Entamoeba dispar. In this way, the present study was carried out to determine a molecular strategy for discriminating both species by the mechanisms of bioinformatics. The gene cysteine synthetase was considered for such a purpose by using the resources of the National Center for Biotechnology Information data bank in the search for similarities in the gene sequence. In this way, a primer pair was designed by the Web Primer program and the restriction enzyme TaqI was selected by the Web Cutter software program. The DNA fragment had a size of 809 bp before cutting, which is consistent with E. dispar. The gene fragment was partitioned in a first fragment with 255 bp and a second one with 554 bp, which is similar to the genetic characteristics of E. histolytica.

  12. Ecosystem-learning blended training for enterprises and assist in the university. Assessment of student resource

    Directory of Open Access Journals (Sweden)

    Emilio ÁLVAREZ ARREGUI

    2011-12-01

    Full Text Available 0 0 1 134 740 Instituto Universitario de Ciencias de la Educación 6 1 873 14.0 Normal 0 21 false false false ES JA X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Tabla normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin-top:0cm; mso-para-margin-right:0cm; mso-para-margin-bottom:10.0pt; mso-para-margin-left:0cm; line-height:115%; mso-pagination:widow-orphan; font-size:11.0pt; font-family:Calibri; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-ansi-language:ES; mso-fareast-language:EN-US;} In this work we present the results obtained in an innovation project that is part of a longitudinal study on ecosystems Training we are developing in collaboration with the University of Algarve and other centers of innovation (Innobridge, Switzerland and Valnalón, Spain. This time we present the assessment of the resources employed students perform in various degrees and courses at the Faculty of Teacher Training and Education at the University of Oviedo. The sample consisted of 120 students and the methodology is quantitative. Results indicate a positive assessment of the context blended learning teaching and technological resources and human resources used because they facilitate knowledge management in a collaborative manner between the educational agents involved and the participation of outside professionals that ecosystem project training the workplace.

  13. Utilisation of Library Information Resources among Generation Z Students: Facts and Fiction

    Directory of Open Access Journals (Sweden)

    Oghenere Gabriel Salubi

    2018-04-01

    Full Text Available Generation Z was the foremost generation to have prevalent access to the Internet from an early age. Technology has strongly influenced this generation in terms of communication, education and consequently their academic information behaviour. With the next generation of scholars already being trained, in a decade, most of the researchers will be mainly digital natives. This study sought to establish the library information resources use pattern in relation to users’ preferred information media in order to render better academic information services to library users. A total of 390 respondents were surveyed at the Nelson Mandela University and the University of Fort Hare using quantitative and qualitative methods. Most of the respondents, 82.3%, were aged between 18 and 23 years; while the average library use time was two hours daily. The most utilised library resource is the Wi-Fi with e-books and e-journals found to be lowly utilised. Records from the E-librarians revealed that undergraduate students account for no more than 6% of total users of electronic databases with 62.3% of the respondents preferring print information resources. Better understanding of library users’ demographics and information media preference is essential in proving the right kind of information services to Generation Z library users.

  14. REDIdb: an upgraded bioinformatics resource for organellar RNA editing sites.

    Science.gov (United States)

    Picardi, Ernesto; Regina, Teresa M R; Verbitskiy, Daniil; Brennicke, Axel; Quagliariello, Carla

    2011-03-01

    RNA editing is a post-transcriptional molecular process whereby the information in a genetic message is modified from that in the corresponding DNA template by means of nucleotide substitutions, insertions and/or deletions. It occurs mostly in organelles by clade-specific diverse and unrelated biochemical mechanisms. RNA editing events have been annotated in primary databases as GenBank and at more sophisticated level in the specialized databases REDIdb, dbRES and EdRNA. At present, REDIdb is the only freely available database that focuses on the organellar RNA editing process and annotates each editing modification in its biological context. Here we present an updated and upgraded release of REDIdb with a web-interface refurbished with graphical and computational facilities that improve RNA editing investigations. Details of the REDIdb features and novelties are illustrated and compared to other RNA editing databases. REDIdb is freely queried at http://biologia.unical.it/py_script/REDIdb/. Copyright © 2010 Elsevier B.V. and Mitochondria Research Society. All rights reserved.

  15. Web-based bioinformatic resources for protein and nucleic acids ...

    African Journals Online (AJOL)

    Admin

    DNA sequencing is the deciphering of hereditary information. It is an indispensable prerequisite for many biotechnical applications and technologies and the continual acquisition of genomic information is very important. This opens the door not only for further research and better understanding of the architectural plan of life ...

  16. PeanutBase and other bioinformatic resources for peanut

    Science.gov (United States)

    Large-scale genomic data for peanut have only become available in the last few years, with the advent of low-cost sequencing technologies. To make the data accessible to researchers and to integrate across diverse types of data, the International Peanut Genomics Consortium funded the development of ...

  17. 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

  18. 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...

  19. 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 ...

  20. 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

  1. 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 ...

  2. 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 ...

  3. 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.

  4. 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...

  5. "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).…

  6. 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...

  7. 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:…

  8. 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…

  9. 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…

  10. 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

  11. Developing nursing and midwifery students' capacity for coping with bullying and aggression in clinical settings: Students' evaluation of a learning resource.

    Science.gov (United States)

    Hogan, Rosemarie; Orr, Fiona; Fox, Deborah; Cummins, Allison; Foureur, Maralyn

    2018-03-01

    An innovative blended learning resource for undergraduate nursing and midwifery students was developed in a large urban Australian university, following a number of concerning reports by students on their experiences of bullying and aggression in clinical settings. The blended learning resource included interactive online learning modules, comprising film clips of realistic clinical scenarios, related readings, and reflective questions, followed by in-class role-play practice of effective responses to bullying and aggression. On completion of the blended learning resource 210 participants completed an anonymous survey (65.2% response rate). Qualitative data was collected and a thematic analysis of the participants' responses revealed the following themes: 'Engaging with the blended learning resource'; 'Responding to bullying' and 'Responding to aggression'. We assert that developing nursing and midwifery students' capacity to effectively respond to aggression and bullying, using a self-paced blended learning resource, provides a solution to managing some of the demands of the clinical setting. The blended learning resource, whereby nursing and midwifery students were introduced to realistic portrayals of bullying and aggression in clinical settings, developed their repertoire of effective responding and coping skills for use in their professional practice. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Relax with CouchDB - Into the non-relational DBMS era of Bioinformatics

    Science.gov (United States)

    Manyam, Ganiraju; Payton, Michelle A.; Roth, Jack A.; Abruzzo, Lynne V.; Coombes, Kevin R.

    2012-01-01

    With the proliferation of high-throughput technologies, genome-level data analysis has become common in molecular biology. Bioinformaticians are developing extensive resources to annotate and mine biological features from high-throughput data. The underlying database management systems for most bioinformatics software are based on a relational model. Modern non-relational databases offer an alternative that has flexibility, scalability, and a non-rigid design schema. Moreover, with an accelerated development pace, non-relational databases like CouchDB can be ideal tools to construct bioinformatics utilities. We describe CouchDB by presenting three new bioinformatics resources: (a) geneSmash, which collates data from bioinformatics resources and provides automated gene-centric annotations, (b) drugBase, a database of drug-target interactions with a web interface powered by geneSmash, and (c) HapMap-CN, which provides a web interface to query copy number variations from three SNP-chip HapMap datasets. In addition to the web sites, all three systems can be accessed programmatically via web services. PMID:22609849

  13. Bioinformatic approaches to augment study of epithelial-to-mesenchymal transition in lung cancer.

    Science.gov (United States)

    Beck, Tim N; Chikwem, Adaeze J; Solanki, Nehal R; Golemis, Erica A

    2014-10-01

    Bioinformatic approaches are intended to provide systems level insight into the complex biological processes that underlie serious diseases such as cancer. In this review we describe current bioinformatic resources, and illustrate how they have been used to study a clinically important example: epithelial-to-mesenchymal transition (EMT) in lung cancer. Lung cancer is the leading cause of cancer-related deaths and is often diagnosed at advanced stages, leading to limited therapeutic success. While EMT is essential during development and wound healing, pathological reactivation of this program by cancer cells contributes to metastasis and drug resistance, both major causes of death from lung cancer. Challenges of studying EMT include its transient nature, its molecular and phenotypic heterogeneity, and the complicated networks of rewired signaling cascades. Given the biology of lung cancer and the role of EMT, it is critical to better align the two in order to advance the impact of precision oncology. This task relies heavily on the application of bioinformatic resources. Besides summarizing recent work in this area, we use four EMT-associated genes, TGF-β (TGFB1), NEDD9/HEF1, β-catenin (CTNNB1) and E-cadherin (CDH1), as exemplars to demonstrate the current capacities and limitations of probing bioinformatic resources to inform hypothesis-driven studies with therapeutic goals. Copyright © 2014 the American Physiological Society.

  14. The effects of positive cognitions on the relationship between alienation and resourcefulness in nursing students in Egypt.

    Science.gov (United States)

    Bekhet, Abir K; ElGuenidi, Mervat; Zauszniewski, Jaclene A

    2011-01-01

    Alienation is a subjective state, a feeling of being a stranger, as if one were not one's normal self. It is also a sense of homelessness; a feeling of uneasiness or discomfort, which signifies the person's exclusion from social or cultural participation. Alienation can adversely affect healthy functioning of nursing students. Nursing students are the adolescents of today and the nurses of tomorrow who will deal with human behavior, and their psychological well-being will be important in managing their clients' conditions. Healthy nursing students are likely to become healthy nurses who can then model and promote healthy lifestyles for their patients. This study looked at whether the effects of alienation on adolescents' resourcefulness are influenced by positive cognitions. Zauszniewski's theory of resourcefulness, which is based on the conceptualization of two forms of resourcefulness: personal (self-help) and social (help-seeking) resourcefulness, served as the theoretical framework for the study. A descriptive, correlational, cross-sectional design was used to examine hypothesized relationships among the study variables in a convenience sample of 170 first-year nursing students aged 17 to 20 years. Results showed that positive cognitions had a moderating and a partial mediating effect on the relationship between alienation and resourcefulness. It is imperative for nurse educators to generate interventions to enhance positive cognitions among nursing students.

  15. 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.

  16. 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

  17. Summative assessments are more powerful drivers of student learning than resource intensive teaching formats.

    Science.gov (United States)

    Raupach, Tobias; Brown, Jamie; Anders, Sven; Hasenfuss, Gerd; Harendza, Sigrid

    2013-03-05

    Electrocardiogram (ECG) interpretation is a core clinical skill that needs to be acquired during undergraduate medical education. Intensive teaching is generally assumed to produce more favorable learning outcomes, but recent research suggests that examinations are more powerful drivers of student learning than instructional format. This study assessed the differential contribution of teaching format and examination consequences to learning outcome regarding ECG interpretation skills in undergraduate medical students. A total of 534 fourth-year medical students participated in a six-group (two sets of three), partially randomized trial. Students received three levels of teaching intensity: self-directed learning (two groups), lectures (two groups) or small-group peer teaching facilitated by more advanced students (two groups). One of the two groups on each level of teaching intensity was assessed in a formative, the other in a summative written ECG examination, which provided a maximum of 1% credit points of the total curriculum. The formative examination provided individual feedback without credit points. Main outcome was the correct identification of ≥3 out of 5 diagnoses in original ECG tracings. Secondary outcome measures were time spent on independent study and use of additional study material. Compared with formative assessments, summative assessments increased the odds of correctly identifying at least three out of five ECG diagnoses (OR 5.14; 95% CI 3.26 to 8.09), of spending at least 2 h/week extra on ECG self-study (OR 4.02; 95% CI 2.65 to 6.12) and of using additional learning material (OR 2.86; 95% CI 1.92 to 4.24). Lectures and peer teaching were associated with increased learning effort only, but did not augment examination performance. Medical educators need to be aware of the paramount role of summative assessments in promoting student learning. Consequently, examinations within medical schools need to be closely matched to the desired learning

  18. Analysis of requirements for teaching materials based on the course bioinformatics for plant metabolism

    Science.gov (United States)

    Balqis, Widodo, Lukiati, Betty; Amin, Mohamad

    2017-05-01

    A way to improve the quality of learning in the course of Plant Metabolism in the Department of Biology, State University of Malang, is to develop teaching materials. This research evaluates the needs of bioinformatics-based teaching material in the course Plant Metabolism by the Analyze, Design, Develop, Implement, and Evaluate (ADDIE) development model. Data were collected through questionnaires distributed to the students in the Plant Metabolism course of the Department of Biology, University of Malang, and analysis of the plan of lectures semester (RPS). Learning gains of this course show that it is not yet integrated into the field of bioinformatics. All respondents stated that plant metabolism books do not include bioinformatics and fail to explain the metabolism of a chemical compound of a local plant in Indonesia. Respondents thought that bioinformatics can explain examples and metabolism of a secondary metabolite analysis techniques and discuss potential medicinal compounds from local plants. As many as 65% of the respondents said that the existing metabolism book could not be used to understand secondary metabolism in lectures of plant metabolism. Therefore, the development of teaching materials including plant metabolism-based bioinformatics is important to improve the understanding of the lecture material in plant metabolism.

  19. 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.

  20. 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, ...

  1. Facilitating the use of large-scale biological data and tools in the era of translational bioinformatics

    DEFF Research Database (Denmark)

    Kouskoumvekaki, Irene; Shublaq, Nour; Brunak, Søren

    2014-01-01

    As both the amount of generated biological data and the processing compute power increase, computational experimentation is no longer the exclusivity of bioinformaticians, but it is moving across all biomedical domains. For bioinformatics to realize its translational potential, domain experts need...... access to user-friendly solutions to navigate, integrate and extract information out of biological databases, as well as to combine tools and data resources in bioinformatics workflows. In this review, we present services that assist biomedical scientists in incorporating bioinformatics tools...... into their research.We review recent applications of Cytoscape, BioGPS and DAVID for data visualization, integration and functional enrichment. Moreover, we illustrate the use of Taverna, Kepler, GenePattern, and Galaxy as open-access workbenches for bioinformatics workflows. Finally, we mention services...

  2. Work-life Balance Decision-making of Norwegian Students: Implications for Human Resources Management

    Directory of Open Access Journals (Sweden)

    Remigiusz Gawlik

    2016-12-01

    Full Text Available Objective: The paper aims at identifying and assessing the significance of work-life balance determinants between the Youth of highly developed societies and its implications for human resources management on the example of Norway. Research Design & Methods: The research target group consists of 236 respondents recruited among Norwegian tertiary education students. It employed literature analysis, two-stage exploratory research: direct individual in-depth interviews, survey based on a self-administered, web-based questionnaire with single-answer, limited choice qualitative & quantitative, as well as explanatory research (informal moderated group discussions. Findings: The research on perceptions of determinants of quality of life and attractiveness of life strategies shows that in a country with relatively high socio-economic development level, such as Norway, differences in rankings do exist. They can be observed in relevance to both material and non-material QoL determinants. Implications & Recommendations: The study revealed a need for deeper research on individually driven early decision-making of future employees and entrepreneurs. This will result in closer modelling of socio-economic phenomena, including more accurate adaptation to trends on the labour market and creation of new business models. Contribution & Value Added: Research value added comes from the comparison of perceptions of quality of life determinants between countries at various stages of socio-economic development and its implications for human resource management.

  3. 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.

  4. 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.

  5. 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....

  6. Accuracy and readability of cardiovascular entries on Wikipedia: are they reliable learning resources for medical students?

    Science.gov (United States)

    Azer, Samy A; AlSwaidan, Nourah M; Alshwairikh, Lama A; AlShammari, Jumana M

    2015-01-01

    Objective To evaluate accuracy of content and readability level of English Wikipedia articles on cardiovascular diseases, using quality and readability tools. Methods Wikipedia was searched on the 6 October 2013 for articles on cardiovascular diseases. Using a modified DISCERN (DISCERN is an instrument widely used in assessing online resources), articles were independently scored by three assessors. The readability was calculated using Flesch-Kincaid Grade Level. The inter-rater agreement between evaluators was calculated using the Fleiss κ scale. Results This study was based on 47 English Wikipedia entries on cardiovascular diseases. The DISCERN scores had a median=33 (IQR=6). Four articles (8.5%) were of good quality (DISCERN score 40–50), 39 (83%) moderate (DISCERN 30–39) and 4 (8.5%) were poor (DISCERN 10–29). Although the entries covered the aetiology and the clinical picture, there were deficiencies in the pathophysiology of diseases, signs and symptoms, diagnostic approaches and treatment. The number of references varied from 1 to 127 references; 25.9±29.4 (mean±SD). Several problems were identified in the list of references and citations made in the articles. The readability of articles was 14.3±1.7 (mean±SD); consistent with the readability level for college students. In comparison, Harrison’s Principles of Internal Medicine 18th edition had more tables, less references and no significant difference in number of graphs, images, illustrations or readability level. The overall agreement between the evaluators was good (Fleiss κ 0.718 (95% CI 0.57 to 0.83). Conclusions The Wikipedia entries are not aimed at a medical audience and should not be used as a substitute to recommended medical resources. Course designers and students should be aware that Wikipedia entries on cardiovascular diseases lack accuracy, predominantly due to errors of omission. Further improvement of the Wikipedia content of cardiovascular entries would be needed before they

  7. Medical student disaster medicine education: the development of an educational resource.

    Science.gov (United States)

    Pfenninger, Ernst G; Domres, Bernd D; Stahl, Wolfgang; Bauer, Andreas; Houser, Christine M; Himmelseher, Sabine

    2010-02-16

    Disaster medicine education is an enormous challenge, but indispensable for disaster preparedness. We aimed to develop and implement a disaster medicine curriculum for medical student education that can serve as a peer-reviewed, structured educational guide and resource. Additionally, the process of designing, approving and implementing such a curriculum is presented. The six-step approach to curriculum development for medical education was used as a formal process instrument. Recognized experts from professional and governmental bodies involved in disaster health care provided input using disaster-related physician training programs, scientific evidence if available, proposals for education by international disaster medicine organizations and their expertise as the basis for content development. The final course consisted of 14 modules composed of 2-h units. The concepts of disaster medicine, including response, medical assistance, law, command, coordination, communication, and mass casualty management, are introduced. Hospital preparedness plans and experiences from worldwide disaster assistance are reviewed. Life-saving emergency and limited individual treatment under disaster conditions are discussed. Specifics of initial management of explosive, war-related, radiological/nuclear, chemical, and biological incidents emphasizing infectious diseases and terrorist attacks are presented. An evacuation exercise is completed, and a mass casualty triage is simulated in collaboration with local disaster response agencies. Decontamination procedures are demonstrated at a nuclear power plant or the local fire department, and personal decontamination practices are exercised. Mannequin resuscitation is practiced while personal protective equipment is utilized. An interactive review of professional ethics, stress disorders, psychosocial interventions, and quality improvement efforts complete the training. The curriculum offers medical disaster education in a reasonable time

  8. Student Perceptions of Nutrition Education at Marshall University Joan C. Edwards School of Medicine: A Resource Challenged Institution

    Directory of Open Access Journals (Sweden)

    W. Elaine Hardman

    2015-01-01

    Full Text Available Nutrition education is an essential component of medical education if new physicians are to be equipped to address common chronic diseases, including obesity and the associated diabetes, cardiovascular disease, and cancer. Most medical students recognize this need and desire nutrition education; however, finding time in a medical school curriculum and funding are challenging. Available, free online resources and small group exercises can be utilized to provide basic, up-to-date nutrition information to medical students.

  9. Sexual Health Education Resources, Based on Ideas and Experiences of Students of Two Major Universities in Zahedan, Iran

    OpenAIRE

    Shahrokh Izadi

    2017-01-01

    Background: To determine the most usual resources that adolescents and teenagers are using to learn about sexual issues. A cross-sectional exploratory study implemented in June 2015 in Zahedan, the capital city of Sistan-va-Baluchestan Province, located in the southeast of Iran. Methods: Using convenient sampling method, from among student of two large universities in Zahedan, 134 students 18 to 22 years old, accepted invitation for filling a self-administered anonymized questionnaire con...

  10. 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.

  11. 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.

  12. 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).

  13. 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

  14. 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

  15. 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

  16. 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

  17. Datasets2Tools, repository and search engine for bioinformatics datasets, tools and canned analyses

    Science.gov (United States)

    Torre, Denis; Krawczuk, Patrycja; Jagodnik, Kathleen M.; Lachmann, Alexander; Wang, Zichen; Wang, Lily; Kuleshov, Maxim V.; Ma'Ayan, Avi

    2018-02-01

    Biomedical data repositories such as the Gene Expression Omnibus (GEO) enable the search and discovery of relevant biomedical digital data objects. Similarly, resources such as OMICtools, index bioinformatics tools that can extract knowledge from these digital data objects. However, systematic access to pre-generated 'canned' analyses applied by bioinformatics tools to biomedical digital data objects is currently not available. Datasets2Tools is a repository indexing 31,473 canned bioinformatics analyses applied to 6,431 datasets. The Datasets2Tools repository also contains the indexing of 4,901 published bioinformatics software tools, and all the analyzed datasets. Datasets2Tools enables users to rapidly find datasets, tools, and canned analyses through an intuitive web interface, a Google Chrome extension, and an API. Furthermore, Datasets2Tools provides a platform for contributing canned analyses, datasets, and tools, as well as evaluating these digital objects according to their compliance with the findable, accessible, interoperable, and reusable (FAIR) principles. By incorporating community engagement, Datasets2Tools promotes sharing of digital resources to stimulate the extraction of knowledge from biomedical research data. Datasets2Tools is freely available from: http://amp.pharm.mssm.edu/datasets2tools.

  18. Usability Testing for e-Resource Discovery: How Students Find and Choose e-Resources Using Library Web Sites

    Science.gov (United States)

    Fry, Amy; Rich, Linda

    2011-01-01

    In early 2010, library staff at Bowling Green State University (BGSU) in Ohio designed and conducted a usability study of key parts of the library web site, focusing on the web pages generated by the library's electronic resources management system (ERM) that list and describe the library's databases. The goal was to discover how users find and…

  19. 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.

  20. 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.

  1. Lost in Translation: Understanding Students' Use of Social Networking and Online Resources to Support Early Clinical Practices. A National Survey of Graduate Speech-Language Pathology Students

    Science.gov (United States)

    Boster, Jamie B.; McCarthy, John W.

    2018-01-01

    The Internet is a source of many resources for graduate speech-language pathology (SLP) students. It is important to understand the resources students are aware of, which they use, and why they are being chosen as sources of information for therapy activities. A national online survey of graduate SLP students was conducted to assess their…

  2. How fifth grade Latino/a bilingual students use their linguistic resources in the classroom and laboratory during science instruction

    Science.gov (United States)

    Stevenson, Alma R.

    2013-12-01

    This qualitative, sociolinguistic research study examines how bilingual Latino/a students use their linguistic resources in the classroom and laboratory during science instruction. This study was conducted in a school in the southwestern United States serving an economically depressed, predominantly Latino population. The object of study was a fifth grade science class entirely comprised of language minority students transitioning out of bilingual education. Therefore, English was the means of instruction in science, supported by informal peer-to-peer Spanish-language communication. This study is grounded in a social constructivist paradigm. From this standpoint, learning science is a social process where social, cultural, and linguistic factors are all considered crucial to the process of acquiring scientific knowledge. The study was descriptive in nature, examining specific linguistic behaviors with the purpose of identifying and analyzing the linguistic functions of students' utterances while participating in science learning. The results suggest that students purposefully adapt their use of linguistic resources in order to facilitate their participation in science leaning. What is underscored in this study is the importance of explicitly acknowledging, supporting, and incorporating bilingual students' linguistic resources both in Spanish and English into the science classroom in order to optimize students' participation and facilitate their understanding.

  3. The Effects of Summer Student Teaching on Traditional and Nontraditional Elementary Preservice Teachers: Matching Resources with Student Needs.

    Science.gov (United States)

    Birrell, James R.; And Others

    This study sought to determine if summer student teaching in year-round elementary schools could provide preservice teachers with a viable alternative to traditional spring and fall programs. Data were collected on student demographics, students' attitudes toward year-round schooling, autobiographical surveys, and students' overall attitudes and…

  4. 25 CFR 36.102 - What student resources must be provided by a homeliving program?

    Science.gov (United States)

    2010-04-01

    ... homeliving program? The following minimum resources must be available at all homeliving programs: (a) Library resources such as access to books and resource materials, including school libraries and public libraries...

  5. Social Capital of Non-Traditional Students at a German University. Do Traditional and Non-Traditional Students Access Different Social Resources?

    Science.gov (United States)

    Brändle, Tobias; Häuberer, Julia

    2015-01-01

    Social capital is of particular value for the acquisition of education. Not only does it prevent scholars from dropping out but it improves the educational achievement. The paper focuses on access to social resources by traditional and non-traditional students at a German university and asks if there are group differences considering this…

  6. The changing roles of natural resource professionals: providing tools to students to teach the public about fire

    Science.gov (United States)

    Pat Stephens Williams; Brian P. Oswald; Karen Stafford; Justice Jones; David. Kulhavy

    2011-01-01

    The Arthur Temple College of Forestry and Agriculture (ATCOFA) at Stephen F. Austin State University is taking a proactive stance toward preparing forestry students to work closely with the public on fire planning in wildland-urban interface areas. ATCOFA's incorporation of the "Changing Roles" curriculum provides lessons on how natural resource managers...

  7. Evaluating Online Resources in Terms of Learning Environment and Student Attitudes in Middle-Grade Mathematics Classes

    Science.gov (United States)

    Earle, James E.; Fraser, Barry J.

    2017-01-01

    The main objective of this research was to use learning environment and attitude scales in evaluating online resource materials for supporting a traditional mathematics curriculum. The sample consisted of 914 middle-school students in 49 classes. A second research focus was the validation of the chosen learning environment questionnaire, the…

  8. Advanced Placement (AP) Social Studies Teachers' Use of Academic Course Blogs as a Supplemental Resource for Student Learning

    Science.gov (United States)

    Alper, Seth M.

    2013-01-01

    This mixed-methods study investigated the relationship between Advanced Placement (AP) social studies teachers' utilization of academic course blogs and student achievement. Simultaneously, the study examined the participating teachers' perceptions on the use of course blogs and other social media as supplemental learning resources. The…

  9. The Impact of Perceived Barriers, Academic Anxiety, and Resource Management Strategies on Achievement in First-Year Community College Students

    Science.gov (United States)

    Heller, Monica L.; Cassady, Jerrell C.

    2017-01-01

    The current study explored the impact of internal and external barriers (e.g., academic anxiety, employment) that place subgroups of college students at risk for academic failure in the first year. The mitigating potential of academic resource management strategies (e.g., time-study environment) was also examined. In a sample of 885 first-semester…

  10. Developing Local Curriculum Framework on Water Resource and Disaster Course for Enhancing Students' Learning Achievements in the Basic Educational System

    Science.gov (United States)

    Chunrasaksakun, Chunwadee; Sanrattana, Unchalee; Tungkasamit, Angkana; Srisawat, Niwat

    2015-01-01

    The aim of the paper was to administer and prepare teachers for management to their students' learning achievements within the curriculum framework of water resource and disaster management. This course was compared to manage learning into different school sizes with the sample size in the lower secondary education schools with two groups of 28…

  11. Understanding the Use of Mobile Resources to Enhance Paralympic Boccia Teaching and Learning for Students with Cerebral Palsy

    Science.gov (United States)

    Zioti, Fabiana; Clemente, Giordano; de Paiva Gonçalves, Raphael; Souza, Matheus; Fassbinder, Aracele; Kawashita, Ieda Mayumi

    2016-01-01

    This paper aims to discuss about how mobile technologies and resources can be used to support teaching and improving the performance of students with cerebral palsy during out-door classes in the paralympic boccia court. The Educational Design Research has been used to help us to identify the context and to build two interventions: (i) using an…

  12. Piecing Together the Puzzle of Graduate Employment: Factors that Shape the Graduate Work Expectations of Human Resource Management Students

    Science.gov (United States)

    Parris, Melissa A.; Saville, Kerrie

    2011-01-01

    Providing graduates with a set of skills and attributes relevant to their future employment remains a key topic in both higher education policy and research. This paper reports findings from a pilot study of human resource management (HRM) students' perceptions of the graduate work experience. Specifically, it focuses on how these perceptions are…

  13. Fewer Resources, More Debt: Loan Debt Burdens Students at Historically Black Colleges and Universities

    Science.gov (United States)

    Saunders, Katherine M.; Williams, Krystal L.; Smith, Cheryl L.

    2016-01-01

    Student loans have become an increasingly important way for students and their families to pay for college, but for students at historically black colleges and universities (HBCUs), student loan debt is a substantial burden. Students who attend these institutions--many of whom are low-income and first-generation--must borrow at higher rates and,…

  14. Student use of computer tools designed to scaffold scientific problem-solving with hypermedia resources: A case study

    Science.gov (United States)

    Oliver, Kevin Matthew

    National science standards call for increasing student exposure to inquiry and real-world problem solving. Students can benefit from open-ended learning environments that stress the engagement of real problems and the development of thinking skills and processes. The Internet is an ideal resource for context-bound problems with its seemingly endless supply of resources. Problems may arise, however, since young students are cognitively ill-prepared to manage open-ended learning and may have difficulty processing hypermedia. Computer tools were used in a qualitative case study with 12 eighth graders to determine how such implements might support the process of solving open-ended problems. A preliminary study proposition suggested students would solve open-ended problems more appropriately if they used tools in a manner consistent with higher-order critical and creative thinking. Three research questions sought to identify: how students used tools, the nature of science learning in open-ended environments, and any personal or environmental barriers effecting problem solving. The findings were mixed. The participants did not typically use the tools and resources effectively. They successfully collected basic information, but infrequently organized, evaluated, generated, and justified their ideas. While the students understood how to use most tools procedurally, they lacked strategic understanding for why tool use was necessary. Students scored average to high on assessments of general content understanding, but developed artifacts suggesting their understanding of specific micro problems was naive and rife with misconceptions. Process understanding was also inconsistent, with some students describing basic problem solving processes, but most students unable to describe how tools could support open-ended inquiry. Barriers to effective problem solving were identified in the study. Personal barriers included naive epistemologies, while environmental barriers included a

  15. Resources, social networks, and collective action frames of college students who join the gay and lesbian rights movement.

    Science.gov (United States)

    Swank, Eric; Fahs, Breanne

    2012-01-01

    This article explores the reasons why some college students join the gay and lesbian rights movements. After addressing the frequency of students joining this social movement, the article then considers the contexts and motivations behind such actions. To explore the catalysts to gay and lesbian rights activism, this study utilizes variables from resource, mobilizing, and framing theories of political participation. Using data from 820 heterosexual, lesbian, gay, and bisexual students, we found that economic and educational resources failed to explain participation in gay and lesbian politics. Instead, predictors of gay and lesbian activism were more closely aligned to four key variables: the political orientations of trusted peers, knowing full-fledged activists, an ability to recognize heterosexism, and participants' maintenance of activist identities.

  16. A Web Site that Provides Resources for Assessing Students' Statistical Literacy, Reasoning and Thinking

    Science.gov (United States)

    Garfield, Joan; delMas, Robert

    2010-01-01

    The Assessment Resource Tools for Improving Statistical Thinking (ARTIST) Web site was developed to provide high-quality assessment resources for faculty who teach statistics at the tertiary level but resources are also useful to statistics teachers at the secondary level. This article describes some of the numerous ARTIST resources and suggests…

  17. 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.

  18. 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.

  19. Student Misconceptions about Plants - A First Step in Building a Teaching Resource.

    Science.gov (United States)

    Wynn, April N; Pan, Irvin L; Rueschhoff, Elizabeth E; Herman, Maryann A B; Archer, E Kathleen

    2017-01-01

    Plants are ubiquitous and found in virtually every ecosystem on Earth, but their biology is often poorly understood, and inaccurate ideas about how plants grow and function abound. Many articles have been published documenting student misconceptions about photosynthesis and respiration, but there are substantially fewer on such topics as plant cell structure and growth; plant genetics, evolution, and classification; plant physiology (beyond energy relations); and plant ecology. The available studies of misconceptions held on those topics show that many are formed at a very young age and persist throughout all educational levels. Our goal is to begin building a central resource of plant biology misconceptions that addresses these underrepresented topics, and here we provide a table of published misconceptions organized by topic. For greater utility, we report the age group(s) in which the misconceptions were found and then map them to the ASPB - BSA Core Concepts and Learning Objectives in Plant Biology for Undergraduates, developed jointly by the American Society of Plant Biologists and the Botanical Society of America.

  20. Student Misconceptions about Plants – A First Step in Building a Teaching Resource

    Directory of Open Access Journals (Sweden)

    April N. Wynn

    2017-05-01

    Full Text Available Plants are ubiquitous and found in virtually every ecosystem on Earth, but their biology is often poorly understood, and inaccurate ideas about how plants grow and function abound. Many articles have been published documenting student misconceptions about photosynthesis and respiration, but there are substantially fewer on such topics as plant cell structure and growth; plant genetics, evolution, and classification; plant physiology (beyond energy relations; and plant ecology. The available studies of misconceptions held on those topics show that many are formed at a very young age and persist throughout all educational levels. Our goal is to begin building a central resource of plant biology misconceptions that addresses these underrepresented topics, and here we provide a table of published misconceptions organized by topic. For greater utility, we report the age group(s in which the misconceptions were found and then map them to the ASPB – BSA Core Concepts and Learning Objectives in Plant Biology for Undergraduates, developed jointly by the American Society of Plant Biologists and the Botanical Society of America.

  1. An Information Literacy Course for Doctoral Students: Information Resources and Tools for Research

    Directory of Open Access Journals (Sweden)

    Ann-Louise Paasio

    2015-12-01

    Full Text Available The purpose of this paper is to showcase the information literacy course for doctoral students called Information Resources and Tools for Research. Turku University Library organises this course in collaboration with the University of Turku Graduate School. The course, which was started in 2012, has been organised four times so far, twice in English and twice in Finnish. The course offers training to all doctoral Programs in all of the seven disciplines present at the University of Turku and doctoral candidates of the University. In our presentation we will describe the structure and contents of the course and share our experiences of the collaboration with the University of Turku Graduate School. In addition, we will describe how the information specialists of the Turku University Library have collaborated during the course. We will also discuss the challenges of the course. Based on the course feedback, it can be stated that in general, participants have found this course very useful for their research in the University of Turku.

  2. 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,...

  3. 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.

  4. Introducing bioinformatics, the biosciences' genomic revolution

    CERN Document Server

    Zanella, Paolo

    1999-01-01

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

  5. 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.

  6. 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.

  7. Making authentic science accessible—the benefits and challenges of integrating bioinformatics into a high-school science curriculum

    Science.gov (United States)

    Gelbart, Hadas; Ben-Dor, Shifra; Yarden, Anat

    2017-01-01

    Despite the central place held by bioinformatics in modern life sciences and related areas, it has only recently been integrated to a limited extent into high-school teaching and learning programs. Here we describe the assessment of a learning environment entitled ‘Bioinformatics in the Service of Biotechnology’. Students’ learning outcomes and attitudes toward the bioinformatics learning environment were measured by analyzing their answers to questions embedded within the activities, questionnaires, interviews and observations. Students’ difficulties and knowledge acquisition were characterized based on four categories: the required domain-specific knowledge (declarative, procedural, strategic or situational), the scientific field that each question stems from (biology, bioinformatics or their combination), the associated cognitive-process dimension (remember, understand, apply, analyze, evaluate, create) and the type of question (open-ended or multiple choice). Analysis of students’ cognitive outcomes revealed learning gains in bioinformatics and related scientific fields, as well as appropriation of the bioinformatics approach as part of the students’ scientific ‘toolbox’. For students, questions stemming from the ‘old world’ biology field and requiring declarative or strategic knowledge were harder to deal with. This stands in contrast to their teachers’ prediction. Analysis of students’ affective outcomes revealed positive attitudes toward bioinformatics and the learning environment, as well as their perception of the teacher’s role. Insights from this analysis yielded implications and recommendations for curriculum design, classroom enactment, teacher education and research. For example, we recommend teaching bioinformatics in an integrative and comprehensive manner, through an inquiry process, and linking it to the wider science curriculum. PMID:26801769

  8. A case study of tuning MapReduce for efficient Bioinformatics in the cloud

    Energy Technology Data Exchange (ETDEWEB)

    Shi, Lizhen [Florida State Univ., Tallahassee, FL (United States); Wang, Zhong [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Yu, Weikuan [Florida State Univ., Tallahassee, FL (United States); Meng, Xiandong [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2016-10-06

    The combination of the Hadoop MapReduce programming model and cloud computing allows biological scientists to analyze next-generation sequencing (NGS) data in a timely and cost-effective manner. Cloud computing platforms remove the burden of IT facility procurement and management from end users and provide ease of access to Hadoop clusters. However, biological scientists are still expected to choose appropriate Hadoop parameters for running their jobs. More importantly, the available Hadoop tuning guidelines are either obsolete or too general to capture the particular characteristics of bioinformatics applications. In this paper, we aim to minimize the cloud computing cost spent on bioinformatics data analysis by optimizing the extracted significant Hadoop parameters. When using MapReduce-based bioinformatics tools in the cloud, the default settings often lead to resource underutilization and wasteful expenses. We choose k-mer counting, a representative application used in a large number of NGS data analysis tools, as our study case. Experimental results show that, with the fine-tuned parameters, we achieve a total of 4× speedup compared with the original performance (using the default settings). Finally, this paper presents an exemplary case for tuning MapReduce-based bioinformatics applications in the cloud, and documents the key parameters that could lead to significant performance benefits.

  9. 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…

  10. 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.

  11. Availability, Use and Constraints to Use of Electronic Information Resources by Postgraduates Students at the University of Ibadan

    Directory of Open Access Journals (Sweden)

    Dare Samuel Adeleke

    2017-12-01

    Full Text Available Availability, awareness and use of electronic resources provide access to authoritative, reliable, accurate and timely access to information. The use of electronic information resources (EIRs can enable innovation in teaching and increase timeliness in research of postgraduate students which will eventual result into encouragement of the expected research-led enquiry in this digital age. The study adopted a descriptive survey design. Samples of 300 of postgraduate students within seven out 13 Faculties were randomly selected. Data were collected using questionnaire designed to elicit response from respondents and data were analyzed using descriptive statistics methods percentages, mean, and standard deviation. Results indicated that internet was ranked most available and used in the university. Low level of usage of electronic resources, in particular, full texts data bases is linked to a number of constraints: Interrupted power supply was ranked highest among other factors as speed and capacity of computers, retrieval of records with high recall and low precision, retrieving records relevant to information need, lack of knowledge of search techniques to retrieve information effectively, non possession of requisite IT skills and problems accessing the internet. The study recommended that usage of electronic resources be made compulsory, intensifying awareness campaigns concerning the availability, training on use of electronic resources and the problem of power outage be addressed.

  12. Adaptive Tutorials Versus Web-Based Resources in Radiology: A Mixed Methods Comparison of Efficacy and Student Engagement.

    Science.gov (United States)

    Wong, Vincent; Smith, Ariella J; Hawkins, Nicholas J; Kumar, Rakesh K; Young, Noel; Kyaw, Merribel; Velan, Gary M

    2015-10-01

    Diagnostic imaging is under-represented in medical curricula globally. Adaptive tutorials, online intelligent tutoring systems that provide a personalized learning experience, have the potential to bridge this gap. However, there is limited evidence of their effectiveness for learning about diagnostic imaging. We performed a randomized mixed methods crossover trial to determine the impact of adaptive tutorials on perceived engagement and understanding of the appropriate use and interpretation of common diagnostic imaging investigations. Although concurrently engaged in disparate blocks of study, 99 volunteer medical students (from years 1-4 of the 6-year program) were randomly allocated to one of two groups. In the first arm of the trial on chest X-rays, one group received access to an adaptive tutorial, whereas the other received links to an existing peer-reviewed Web resource. These two groups crossed over in the second arm of the trial, which focused on computed tomography scans of the head, chest, and abdomen. At the conclusion of each arm of the trial, both groups completed an examination-style assessment, comprising questions both related and unrelated to the topics covered by the relevant adaptive tutorial. Online questionnaires were used to evaluate student perceptions of both learning resources. In both arms of the trial, the group using adaptive tutorials obtained significantly higher assessment scores than controls. This was because of higher assessment scores by senior students in the adaptive tutorial group when answering questions related to topics covered in those tutorials. Furthermore, students indicated significantly better engagement with adaptive tutorials than the Web resource and rated the tutorials as a significantly more valuable tool for learning. Medical students overwhelmingly accept adaptive tutorials for diagnostic imaging. The tutorials significantly improve the understanding of diagnostic imaging by senior students. Crown Copyright

  13. ESP Students' Views on Online Language Resources for L2 Text Production Purposes

    Science.gov (United States)

    Kozlova, Inna; Presas, Marisa

    2013-01-01

    The use of online language resources for L2 text production purposes is a recent phenomenon and has not yet been studied in depth. Increasing availability of new online resources seems to be changing the very nature of L2 text production. The traditional dictionary, hitherto a default resource to help with language doubts, is being left behind…

  14. Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud.

    Science.gov (United States)

    Afgan, Enis; Sloggett, Clare; Goonasekera, Nuwan; Makunin, Igor; Benson, Derek; Crowe, Mark; Gladman, Simon; Kowsar, Yousef; Pheasant, Michael; Horst, Ron; Lonie, Andrew

    2015-01-01

    Analyzing high throughput genomics data is a complex and compute intensive task, generally requiring numerous software tools and large reference data sets, tied together in successive stages of data transformation and visualisation. A computational platform enabling best practice genomics analysis ideally meets a number of requirements, including: a wide range of analysis and visualisation tools, closely linked to large user and reference data sets; workflow platform(s) enabling accessible, reproducible, portable analyses, through a flexible set of interfaces; highly available, scalable computational resources; and flexibility and versatility in the use of these resources to meet demands and expertise of a variety of users. Access to an appropriate computational platform can be a significant barrier to researchers, as establishing such a platform requires a large upfront investment in hardware, experience, and expertise. We designed and implemented the Genomics Virtual Laboratory (GVL) as a middleware layer of machine images, cloud management tools, and online services that enable researchers to build arbitrarily sized compute clusters on demand, pre-populated with fully configured bioinformatics tools, reference datasets and workflow and visualisation options. The platform is flexible in that users can conduct analyses through web-based (Galaxy, RStudio, IPython Notebook) or command-line interfaces, and add/remove compute nodes and data resources as required. Best-practice tutorials and protocols provide a path from introductory training to practice. The GVL is available on the OpenStack-based Australian Research Cloud (http://nectar.org.au) and the Amazon Web Services cloud. The principles, implementation and build process are designed to be cloud-agnostic. This paper provides a blueprint for the design and implementation of a cloud-based Genomics Virtual Laboratory. We discuss scope, design considerations and technical and logistical constraints, and explore the

  15. Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud.

    Directory of Open Access Journals (Sweden)

    Enis Afgan

    Full Text Available Analyzing high throughput genomics data is a complex and compute intensive task, generally requiring numerous software tools and large reference data sets, tied together in successive stages of data transformation and visualisation. A computational platform enabling best practice genomics analysis ideally meets a number of requirements, including: a wide range of analysis and visualisation tools, closely linked to large user and reference data sets; workflow platform(s enabling accessible, reproducible, portable analyses, through a flexible set of interfaces; highly available, scalable computational resources; and flexibility and versatility in the use of these resources to meet demands and expertise of a variety of users. Access to an appropriate computational platform can be a significant barrier to researchers, as establishing such a platform requires a large upfront investment in hardware, experience, and expertise.We designed and implemented the Genomics Virtual Laboratory (GVL as a middleware layer of machine images, cloud management tools, and online services that enable researchers to build arbitrarily sized compute clusters on demand, pre-populated with fully configured bioinformatics tools, reference datasets and workflow and visualisation options. The platform is flexible in that users can conduct analyses through web-based (Galaxy, RStudio, IPython Notebook or command-line interfaces, and add/remove compute nodes and data resources as required. Best-practice tutorials and protocols provide a path from introductory training to practice. The GVL is available on the OpenStack-based Australian Research Cloud (http://nectar.org.au and the Amazon Web Services cloud. The principles, implementation and build process are designed to be cloud-agnostic.This paper provides a blueprint for the design and implementation of a cloud-based Genomics Virtual Laboratory. We discuss scope, design considerations and technical and logistical constraints

  16. Integrating technology, curriculum, and online resources: A multilevel model study of impacts on science teachers and students

    Science.gov (United States)

    Ye, Lei

    This scale-up study investigated the impact of a teacher technology tool (Curriculum Customization Service, CCS), curriculum, and online resources on earth science teachers' attitudes, beliefs, and practices and on students' achievement and engagement with science learning. Participants included 73 teachers and over 2,000 ninth-grade students within five public school districts in the western U.S. To assess the impact on teachers, changes between pre- and postsurveys were examined. Results suggest that the CCS tool appeared to significantly increase both teachers' awareness of other earth science teachers' practices and teachers' frequency of using interactive resources in their lesson planning and classroom teaching. A standard multiple regression model was developed. In addition to "District," "Training condition" (whether or not teachers received CCS training) appeared to predict teachers' attitudes, beliefs, and practices. Teachers who received CCS training tended to have lower postsurvey scores than their peers who had no CCS training. Overall, usage of the CCS tool tended to be low, and there were differences among school districts. To assess the impact on students, changes were examined between pre- and postsurveys of (1) knowledge assessment and (2) students' engagement with science learning. Students showed pre- to postsurvey improvements in knowledge assessment, with small to medium effect sizes. A nesting effect (students clustered within teachers) in the Earth's Dynamic Geosphere (EDG) knowledge assessment was identified and addressed by fitting a two-level hierarchical linear model (HLM). In addition, significant school district differences existed for student post-knowledge assessment scores. On the student engagement questionnaire, students tended to be neutral or to slightly disagree that science learning was important in terms of using science in daily life, stimulating their thinking, discovering science concepts, and satisfying their own

  17. Examining Prediction Models of Giving up within a Resource-Based Framework of Coping in Primary School Students with and without Learning Disabilities

    Science.gov (United States)

    Skues, Jason L.; Cunningham, Everarda G.; Theiler, Stephen S.

    2016-01-01

    This study tests a proposed model of coping outcomes for 290 primary school students in Years 5 and 6 (mean age = 11.50 years) with and without learning disabilities (LDs) within a resource-based framework of coping. Group-administered educational and intelligence tests were used to screen students for LDs. Students also completed a questionnaire…

  18. Students Lost in a Flattened World: How Resources from the Catholic Tradition Can Help Business Students Find Their Way

    Science.gov (United States)

    Koehn, Daryl

    2013-01-01

    "Academically Adrift," the recent study of undergraduate performance, has revealed that college students are learning little, if anything, over the course of their four years at university. This article suggests that students are academically adrift, in part, because Americans are culturally marooned between two ways to pursue happiness,…

  19. A discussion on the development of educational resources for college students as family tutors

    Directory of Open Access Journals (Sweden)

    Zhao Da Wei

    2006-02-01

    Full Text Available This article explores the current situation of university students taking part time jobs as tutors in families. This is very popular in China, especially in cities and towns. After systematic investigations, the author suggests that the office of student affairs in Chinese universities should play a substantial role by providing opportunities for these students to become better tutors.

  20. Academic Performance and Burnout: An Efficient Frontier Analysis of Resource Use Efficiency among Employed University Students

    Science.gov (United States)

    Galbraith, Craig S.; Merrill, Gregory B.

    2015-01-01

    We examine the impact of university student burnout on academic achievement. With a longitudinal sample of working undergraduate university business and economics students, we use a two-step analytical process to estimate the efficient frontiers of student productivity given inputs of labour and capital and then analyse the potential determinants…

  1. Challenges for international students in using electronic resources in the Learning Centre : a case study of Oslo University College

    OpenAIRE

    Rahman, Md. Anisur

    2011-01-01

    Joint Master Degree in Digital Library Learning (DILL) The purpose of this study is to find out the challenges facing by international students in using electronic resources in the OUC learning center. This research has used a qualitative approach and purposive, a non-probability techniques used for sampling of this study. A semi-structured face-to-face interviews method is used for the collection of data. The interview questions were open ended and the discourse analysis metho...

  2. A lightweight, flow-based toolkit for parallel and distributed bioinformatics pipelines

    Directory of Open Access Journals (Sweden)

    Cieślik Marcin

    2011-02-01

    Full Text Available Abstract Background Bioinformatic analyses typically proceed as chains of data-processing tasks. A pipeline, or 'workflow', is a well-defined protocol, with a specific structure defined by the topology of data-flow interdependencies, and a particular functionality arising from the data transformations applied at each step. In computer science, the dataflow programming (DFP paradigm defines software systems constructed in this manner, as networks of message-passing components. Thus, bioinformatic workflows can be naturally mapped onto DFP concepts. Results To enable the flexible creation and execution of bioinformatics dataflows, we have written a modular framework for parallel pipelines in Python ('PaPy'. A PaPy workflow is created from re-usable components connected by data-pipes into a directed acyclic graph, which together define nested higher-order map functions. The successive functional transformations of input data are evaluated on flexibly pooled compute resources, either local or remote. Input items are processed in batches of adjustable size, all flowing one to tune the trade-off between parallelism and lazy-evaluation (memory consumption. An add-on module ('NuBio' facilitates the creation of bioinformatics workflows by providing domain specific data-containers (e.g., for biomolecular sequences, alignments, structures and functionality (e.g., to parse/write standard file formats. Conclusions PaPy offers a modular framework for the creation and deployment of parallel and distributed data-processing workflows. Pipelines derive their functionality from user-written, data-coupled components, so PaPy also can be viewed as a lightweight toolkit for extensible, flow-based bioinformatics data-processing. The simplicity and flexibility of distributed PaPy pipelines may help users bridge the gap between traditional desktop/workstation and grid computing. PaPy is freely distributed as open-source Python code at http://muralab.org/PaPy, and

  3. Improving data workflow systems with cloud services and use of open data for bioinformatics research.

    Science.gov (United States)

    Karim, Md Rezaul; Michel, Audrey; Zappa, Achille; Baranov, Pavel; Sahay, Ratnesh; Rebholz-Schuhmann, Dietrich

    2017-04-16

    Data workflow systems (DWFSs) enable bioinformatics researchers to combine components for data access and data analytics, and to share the final data analytics approach with their collaborators. Increasingly, such systems have to cope with large-scale data, such as full genomes (about 200 GB each), public fact repositories (about 100 TB of data) and 3D imaging data at even larger scales. As moving the data becomes cumbersome, the DWFS needs to embed its processes into a cloud infrastructure, where the data are already hosted. As the standardized public data play an increasingly important role, the DWFS needs to comply with Semantic Web technologies. This advancement to DWFS would reduce overhead costs and accelerate the progress in bioinformatics research based on large-scale data and public resources, as researchers would require less specialized IT knowledge for the implementation. Furthermore, the high data growth rates in bioinformatics research drive the demand for parallel and distributed computing, which then imposes a need for scalability and high-throughput capabilities onto the DWFS. As a result, requirements for data sharing and access to public knowledge bases suggest that compliance of the DWFS with Semantic Web standards is necessary. In this article, we will analyze the existing DWFS with regard to their capabilities toward public open data use as well as large-scale computational and human interface requirements. We untangle the parameters for selecting a preferable solution for bioinformatics research with particular consideration to using cloud services and Semantic Web technologies. Our analysis leads to research guidelines and recommendations toward the development of future DWFS for the bioinformatics research community. © The Author 2017. Published by Oxford University Press.

  4. The Revolution in Viral Genomics as Exemplified by the Bioinformatic Analysis of Human Adenoviruses

    Directory of Open Access Journals (Sweden)

    Sarah Torres

    2010-06-01

    Full Text Available Over the past 30 years, genomic and bioinformatic analysis of human adenoviruses has been achieved using a variety of DNA sequencing methods; initially with the use of restriction enzymes and more currently with the use of the GS FLX pyrosequencing technology. Following the conception of DNA sequencing in the 1970s, analysis of adenoviruses has evolved from 100 base pair mRNA fragments to entire genomes. Comparative genomics of adenoviruses made its debut in 1984 when nucleotides and amino acids of coding sequences within the hexon genes of two human adenoviruses (HAdV, HAdV–C2 and HAdV–C5, were compared and analyzed. It was determined that there were three different zones (1-393, 394-1410, 1411-2910 within the hexon gene, of which HAdV–C2 and HAdV–C5 shared zones 1 and 3 with 95% and 89.5% nucleotide identity, respectively. In 1992, HAdV-C5 became the first adenovirus genome to be fully sequenced using the Sanger method. Over the next seven years, whole genome analysis and characterization was completed using bioinformatic tools such as blastn, tblastx, ClustalV and FASTA, in order to determine key proteins in species HAdV-A through HAdV-F. The bioinformatic revolution was initiated with the introduction of a novel species, HAdV-G, that was typed and named by the use of whole genome sequencing and phylogenetics as opposed to traditional serology. HAdV bioinformatics will continue to advance as the latest sequencing technology enables scientists to add to and expand the resource databases. As a result of these advancements, how novel HAdVs are typed has changed. Bioinformatic analysis has become the revolutionary tool that has significantly accelerated the in-depth study of HAdV microevolution through comparative genomics.

  5. A lightweight, flow-based toolkit for parallel and distributed bioinformatics pipelines.

    Science.gov (United States)

    Cieślik, Marcin; Mura, Cameron

    2011-02-25

    Bioinformatic analyses typically proceed as chains of data-processing tasks. A pipeline, or 'workflow', is a well-defined protocol, with a specific structure defined by the topology of data-flow interdependencies, and a particular functionality arising from the data transformations applied at each step. In computer science, the dataflow programming (DFP) paradigm defines software systems constructed in this manner, as networks of message-passing components. Thus, bioinformatic workflows can be naturally mapped onto DFP concepts. To enable the flexible creation and execution of bioinformatics dataflows, we have written a modular framework for parallel pipelines in Python ('PaPy'). A PaPy workflow is created from re-usable components connected by data-pipes into a directed acyclic graph, which together define nested higher-order map functions. The successive functional transformations of input data are evaluated on flexibly pooled compute resources, either local or remote. Input items are processed in batches of adjustable size, all flowing one to tune the trade-off between parallelism and lazy-evaluation (memory consumption). An add-on module ('NuBio') facilitates the creation of bioinformatics workflows by providing domain specific data-containers (e.g., for biomolecular sequences, alignments, structures) and functionality (e.g., to parse/write standard file formats). PaPy offers a modular framework for the creation and deployment of parallel and distributed data-processing workflows. Pipelines derive their functionality from user-written, data-coupled components, so PaPy also can be viewed as a lightweight toolkit for extensible, flow-based bioinformatics data-processing. The simplicity and flexibility of distributed PaPy pipelines may help users bridge the gap between traditional desktop/workstation and grid computing. PaPy is freely distributed as open-source Python code at http://muralab.org/PaPy, and includes extensive documentation and annotated usage

  6. A lightweight, flow-based toolkit for parallel and distributed bioinformatics pipelines

    Science.gov (United States)

    2011-01-01

    Background Bioinformatic analyses typically proceed as chains of data-processing tasks. A pipeline, or 'workflow', is a well-defined protocol, with a specific structure defined by the topology of data-flow interdependencies, and a particular functionality arising from the data transformations applied at each step. In computer science, the dataflow programming (DFP) paradigm defines software systems constructed in this manner, as networks of message-passing components. Thus, bioinformatic workflows can be naturally mapped onto DFP concepts. Results To enable the flexible creation and execution of bioinformatics dataflows, we have written a modular framework for parallel pipelines in Python ('PaPy'). A PaPy workflow is created from re-usable components connected by data-pipes into a directed acyclic graph, which together define nested higher-order map functions. The successive functional transformations of input data are evaluated on flexibly pooled compute resources, either local or remote. Input items are processed in batches of adjustable size, all flowing one to tune the trade-off between parallelism and lazy-evaluation (memory consumption). An add-on module ('NuBio') facilitates the creation of bioinformatics workflows by providing domain specific data-containers (e.g., for biomolecular sequences, alignments, structures) and functionality (e.g., to parse/write standard file formats). Conclusions PaPy offers a modular framework for the creation and deployment of parallel and distributed data-processing workflows. Pipelines derive their functionality from user-written, data-coupled components, so PaPy also can be viewed as a lightweight toolkit for extensible, flow-based bioinformatics data-processing. The simplicity and flexibility of distributed PaPy pipelines may help users bridge the gap between traditional desktop/workstation and grid computing. PaPy is freely distributed as open-source Python code at http://muralab.org/PaPy, and includes extensive

  7. 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...

  8. 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.

  9. 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...

  10. 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...

  11. 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

  12. 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.

  13. THE FACTOR-CRITERIA MODEL OF ASSESSMENT OF ELECTRONIC EDUCATIONAL GAME RESOURCES IN MATHEMATICS FOR PRIMARY SCHOOL STUDENTS

    Directory of Open Access Journals (Sweden)

    Oksana M. Melnyk

    2016-05-01

    Full Text Available This article proves the need for a comprehensive assessment of electronic educational game resources in mathematics for the primary school students; gives the definition of “the factor-criteria model of the electronic educational game resources (EEGR”. It also describes the created model, which consists of requirements for the content, methodological and program parts of the electronic resources for primary school; identifies the factors and the criteria to each of them. It was proposed to assess the ratios within the group of factors and each group of criteria according to the arithmetic progression. The presented model can be a convenient tool both for primary school teachers and EEGR developers. It can also be a basis for a unified state comprehensive system of assessment of the EEGR.

  14. The Development of Resources of Students in Adolescence as a Key Issue in Contemporary Education

    Directory of Open Access Journals (Sweden)

    Gosk Urszula

    2015-08-01

    Full Text Available In the presented paper, the issue of recognition and building of resources in adolescent pupils was discussed, referring to salutogenic concept of A. Antonovsky and Conservation of Resources Theory of S. E. Hobfoll. Coming out from developmental pedagogy and positive orientation in social sciences, benefits of scientific and educational actions concentrated on identifying pupils’ resources and supporting them in generating them, were shown. On the basis of Polish and foreign literature, empirical research treating about pupils’ resource, was analyzed, with special attention put to the sense of coherence and its components, stress management and behavior fostering health.

  15. A Review of Recent Advances in Translational Bioinformatics: Bridges from Biology to Medicine.

    Science.gov (United States)

    Vamathevan, J; Birney, E

    2017-08-01

    Objectives: To highlight and provide insights into key developments in translational bioinformatics between 2014 and 2016. Methods: This review describes some of the most influential bioinformatics papers and resources that have been published between 2014 and 2016 as well as the national genome sequencing initiatives that utilize these resources to routinely embed genomic medicine into healthcare. Also discussed are some applications of the secondary use of patient data followed by a comprehensive view of the open challenges and emergent technologies. Results: Although data generation can be performed routinely, analyses and data integration methods still require active research and standardization to improve streamlining of clinical interpretation. The secondary use of patient data has resulted in the development of novel algorithms and has enabled a refined understanding of cellular and phenotypic mechanisms. New data storage and data sharing approaches are required to enable diverse biomedical communities to contribute to genomic discovery. Conclusion: The translation of genomics data into actionable knowledge for use in healthcare is transforming the clinical landscape in an unprecedented way. Exciting and innovative models that bridge the gap between clinical and academic research are set to open up the field of translational bioinformatics for rapid growth in a digital era. Georg Thieme Verlag KG Stuttgart.

  16. 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

  17. 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 ...

  18. 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.

  19. 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 ...

  20. 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.

  1. 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.

  2. 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 ...

  3. 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…

  4. 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…

  5. 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…

  6. Resource-oriented coaching for reduction of examination-related stress in medical students: an exploratory randomized controlled trial.

    Science.gov (United States)

    Kötter, Thomas; Niebuhr, Frank

    2016-01-01

    The years spent in acquiring medical education is considered a stressful period in the life of many students. Students whose mental health deteriorates during this long period of study are less likely to become empathic and productive physicians. In addition to other specific stressors, academic examinations seem to further induce medical school-related stress and anxiety. Combined group and individual resource-oriented coaching early in medical education might reduce examination-related stress and anxiety and, consequently, enhance academic performance. Good quality evidence, however, remains scarce. In this study, therefore, we explored the question of whether coaching affects examination-related stress and health in medical students. We conducted a randomized controlled trial. Students who registered for the first medical academic examination in August 2014 at the University of Lübeck were recruited and randomized into three groups. The intervention groups 1 and 2 received a 1-hour psychoeducative seminar. Group 1 additionally received two 1-hour sessions of individual coaching during examination preparation. Group 3 served as a control group. We compared changes in self-rated general health (measured by a single item), anxiety and depression (measured by the hospital anxiety and depression scale), as well as medical school stress (measured by the perceived medical school stress instrument). In order to further investigate the influence of group allocation on perceived medical school stress, we conducted a linear regression analysis. We saw a significant deterioration of general health and an increase in anxiety and depression scores in medical students while preparing for an examination. We found a small, but statistically significant, effect of group allocation on the development of perceived medical school stress. However, we could not differentiate between the effects of group coaching only and group coaching in combination with two sessions of individual

  7. 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

  8. 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.

  9. Role of remote sensing, geographical information system (GIS) and bioinformatics in kala-azar epidemiology.

    Science.gov (United States)

    Bhunia, Gouri Sankar; Dikhit, Manas Ranjan; Kesari, Shreekant; Sahoo, Ganesh Chandra; Das, Pradeep

    2011-11-01

    Visceral leishmaniasis or kala-azar is a potent parasitic infection causing death of thousands of people each year. Medicinal compounds currently available for the treatment of kala-azar have serious side effects and decreased efficacy owing to the emergence of resistant strains. The type of immune reaction is also to be considered in patients infected with Leishmania donovani (L. donovani). For complete eradication of this disease, a high level modern research is currently being applied both at the molecular level as well as at the field level. The computational approaches like remote sensing, geographical information system (GIS) and bioinformatics are the key resources for the detection and distribution of vectors, patterns, ecological and environmental factors and genomic and proteomic analysis. Novel approaches like GIS and bioinformatics have been more appropriately utilized in determining the cause of visearal leishmaniasis and in designing strategies for preventing the disease from spreading from one region to another.

  10. A middleware-based platform for the integration of bioinformatic services

    Directory of Open Access Journals (Sweden)

    Guzmán Llambías

    2015-08-01

    Full Text Available Performing Bioinformatic´s experiments involve an intensive access to distributed services and information resources through Internet. Although existing tools facilitate the implementation of workflow-oriented applications, they lack of capabilities to integrate services beyond low-scale applications, particularly integrating services with heterogeneous interaction patterns and in a larger scale. This is particularly required to enable a large-scale distributed processing of biological data generated by massive sequencing technologies. On the other hand, such integration mechanisms are provided by middleware products like Enterprise Service Buses (ESB, which enable to integrate distributed systems following a Service Oriented Architecture. This paper proposes an integration platform, based on enterprise middleware, to integrate Bioinformatics services. It presents a multi-level reference architecture and focuses on ESB-based mechanisms to provide asynchronous communications, event-based interactions and data transformation capabilities. The paper presents a formal specification of the platform using the Event-B model.

  11. Marine microbial biodiversity, bioinformatics and biotechnology (M2B3) data reporting and service standards.

    Science.gov (United States)

    Ten Hoopen, Petra; Pesant, Stéphane; Kottmann, Renzo; Kopf, Anna; Bicak, Mesude; Claus, Simon; Deneudt, Klaas; Borremans, Catherine; Thijsse, Peter; Dekeyzer, Stefanie; Schaap, Dick Ma; Bowler, Chris; Glöckner, Frank Oliver; Cochrane, Guy

    2015-01-01

    Contextual data collected concurrently with molecular samples are critical to the use of metagenomics in the fields of marine biodiversity, bioinformatics and biotechnology. We present here Marine Microbial Biodiversity, Bioinformatics and Biotechnology (M2B3) standards for "Reporting" and "Serving" data. The M2B3 Reporting Standard (1) describes minimal mandatory and recommended contextual information for a marine microbial sample obtained in the epipelagic zone, (2) includes meaningful information for researchers in the oceanographic, biodiversity and molecular disciplines, and (3) can easily be adopted by any marine laboratory with minimum sampling resources. The M2B3 Service Standard defines a software interface through which these data can be discovered and explored in data repositories. The M2B3 Standards were developed by the European project Micro B3, funded under 7(th) Framework Programme "Ocean of Tomorrow", and were first used with the Ocean Sampling Day initiative. We believe that these standards have value in broader marine science.

  12. GeneDig: a web application for accessing genomic and bioinformatics knowledge.

    Science.gov (United States)

    Suciu, Radu M; Aydin, Emir; Chen, Brian E

    2015-02-28

    With the exponential increase and widespread availability of genomic, transcriptomic, and proteomic data, accessing these '-omics' data is becoming increasingly difficult. The current resources for accessing and analyzing these data have been created to perform highly specific functions intended for specialists, and thus typically emphasize functionality over user experience. We have developed a web-based application, GeneDig.org, that allows any general user access to genomic information with ease and efficiency. GeneDig allows for searching and browsing genes and genomes, while a dynamic navigator displays genomic, RNA, and protein information simultaneously for co-navigation. We demonstrate that our application allows more than five times faster and efficient access to genomic information than any currently available methods. We have developed GeneDig as a platform for bioinformatics integration focused on usability as its central design. This platform will introduce genomic navigation to broader audiences while aiding the bioinformatics analyses performed in everyday biology research.

  13. The Development of Resources of Students in Adolescence as a Key Issue in Contemporary Education

    Science.gov (United States)

    Gosk, Urszula; Kuracki, Kamil

    2015-01-01

    In the presented paper, the issue of recognition and building of resources in adolescent pupils was discussed, referring to salutogenic concept of A. Antonovsky and Conservation of Resources Theory of S. E. Hobfoll. Coming out from developmental pedagogy and positive orientation in social sciences, benefits of scientific and educational actions…

  14. Post-Implementation Success Factors for Enterprise Resource Planning Student Administration Systems in Higher Education Institutions

    Science.gov (United States)

    Sullivan, Linda; Bozeman, William

    2010-01-01

    Enterprise Resource Planning (ERP) systems can represent one of the largest investments of human and financial resources by a higher education institution. They also bring a significant process reengineering aspect to the institution and the associated implementation project through the integration of compiled industry best practices into the…

  15. Native American  student perspectives of challenges in natural resource higher education

    Science.gov (United States)

    Breanna Gervais; Chase R. Voirin; Chris Beatty; Grace Bulltail; Stephanie Cowherd; Shawn Defrance; Breana Dorame; Raymond Gutteriez; Jessica Lackey; Candy Lupe; April B. Negrette; Natalya C. Robbins Sherman; Ruth Swaney; Kevin Tso; Marvin Victor; Royale Wilson; Kimberly Yazzie; Jonathan W. Long; Serra J. Hoagland

    2017-01-01

    Native Americans have vital interests in promoting forest management decisions based on sound science and consistent with cultural values to sustain and conserve tribal natural resources. Advancing the next generation of natural resource professionals into key positions is essential to advance the self-determination of tribes; yet, there are unique challenges Native...

  16. Awareness and Misconceptions of High School Students about Renewable Energy Resources and Applications: Turkey Case

    Science.gov (United States)

    Tortop, Hasan Said

    2012-01-01

    Turkey is the one of the countries in the world which has potential of renewable energy resource because of its geographical position. However, being usage of renewable energy resources and applications (RERAs) is low, it shows that awareness and consciousness of RERAs is very low too. Education must play a key role in growing out of an energy…

  17. Liberating literacies: L1-students resources for stance-taking in the literature classroom

    DEFF Research Database (Denmark)

    Kabel, Kristine; Brok, Lene Storgaard

    2015-01-01

    Keywords: Reflection literacy, students’ meaning-making resources, literature education, lower secondary school, qualitative case studies Making aspects of privileged ways of participating visible is central to supporting students’ literacy development within different disciplines. However......, educational linguistics and literacy studies on students’ meaning-making resources in lower secondary school indicate that some significant resources within L1 at this stage of schooling are often part of an invisible curriculum (Christie, 2012; Folkeryd, 2007; Macken-Horarik,1996,2006; Penne, 2006......) and their resources for negotiation and collaboration (Year 5). The purpose of both studies is to develop a metalanguage adequate to characterize interpersonal aspects of students’ actual meaning-making resources, a metalanguage that can support discussions of privileged ways of participating and of co-constructing L...

  18. The Web as an educational tool for/in learning/teaching bioinformatics statistics.

    Science.gov (United States)

    Oliver, J; Pisano, M E; Alonso, T; Roca, P

    2005-12-01

    Statistics provides essential tool in Bioinformatics to interpret the results of a database search or for the management of enormous amounts of information provided from genomics, proteomics and metabolomics. The goal of this project was the development of a software tool that would be as simple as possible to demonstrate the use of the Bioinformatics statistics. Computer Simulation Methods (CSMs) developed using Microsoft Excel were chosen for their broad range of applications, immediate and easy formula calculation, immediate testing and easy graphics representation, and of general use and acceptance by the scientific community. The result of these endeavours is a set of utilities which can be accessed from the following URL: http://gmein.uib.es/bioinformatica/statistics. When tested on students with previous coursework with traditional statistical teaching methods, the general opinion/overall consensus was that Web-based instruction had numerous advantages, but traditional methods with manual calculations were also needed for their theory and practice. Once having mastered the basic statistical formulas, Excel spreadsheets and graphics were shown to be very useful for trying many parameters in a rapid fashion without having to perform tedious calculations. CSMs will be of great importance for the formation of the students and professionals in the field of bioinformatics, and for upcoming applications of self-learning and continuous formation.

  19. 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

  20. A study of the relationship between the study process, motivation resources, and motivation problems of nursing students in different educational systems.

    Science.gov (United States)

    Yardimci, Figen; Bektaş, Murat; Özkütük, Nilay; Muslu, Gonca Karayağız; Gerçeker, Gülçin Özalp; Başbakkal, Zümrüt

    2017-01-01

    The study process is related to students' learning approaches and styles. Motivation resources and problems determine students' internal, external, and negative motivation. Analyzing the study process and motivation of students yields important indications about the nature of educational systems in higher education. This study aims to analyze the relationship between the study process, and motivation resources and problems with regard to nursing students in different educational systems in Turkey and to reveal their effects according to a set of variables. This is a descriptive, cross-sectional and correlational study. Traditional, integrated and problem-based learning (PBL) educational programs for nurses involving students from three nursing schools in Turkey. Nursing students (n=330). The data were collected using the Study Process Questionnaire (R-SPQ-2F) and the Motivation Resources and Problems (MRP) Scale. A statistically significant difference was found between the scores on the study process scale, and motivation resources and problems scale among the educational systems. This study determined that the mean scores of students in the PBL system on learning approaches, intrinsic motivation and negative motivation were higher. A positive significant correlation was found between the scales. The study process, and motivation resources and problems were found to be affected by the educational system. This study determined that the PBL educational system more effectively increases students' intrinsic motivation and helps them to acquire learning skills. Copyright © 2016 Elsevier Ltd. All rights reserved.