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Sample records for bioinformatics programming skills

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

    Science.gov (United States)

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

    2007-01-01

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

  2. Challenge: A Multidisciplinary Degree Program in Bioinformatics

    Directory of Open Access Journals (Sweden)

    Mudasser Fraz Wyne

    2006-06-01

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

  3. '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.

  4. ‘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

  5. 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.

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

    Science.gov (United States)

    Lawlor, Brendan; Walsh, Paul

    2015-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Liu Huai

    2009-01-01

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

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

    Science.gov (United States)

    Fourment, Mathieu; Gillings, Michael R

    2008-02-05

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

  9. 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,…

  10. "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).…

  11. 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…

  12. 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

  13. Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics network.

    Science.gov (United States)

    Jongeneel, C Victor; Achinike-Oduaran, Ovokeraye; Adebiyi, Ezekiel; Adebiyi, Marion; Adeyemi, Seun; Akanle, Bola; Aron, Shaun; Ashano, Efejiro; Bendou, Hocine; Botha, Gerrit; Chimusa, Emile; Choudhury, Ananyo; Donthu, Ravikiran; Drnevich, Jenny; Falola, Oluwadamila; Fields, Christopher J; Hazelhurst, Scott; Hendry, Liesl; Isewon, Itunuoluwa; Khetani, Radhika S; Kumuthini, Judit; Kimuda, Magambo Phillip; Magosi, Lerato; Mainzer, Liudmila Sergeevna; Maslamoney, Suresh; Mbiyavanga, Mamana; Meintjes, Ayton; Mugutso, Danny; Mpangase, Phelelani; Munthali, Richard; Nembaware, Victoria; Ndhlovu, Andrew; Odia, Trust; Okafor, Adaobi; Oladipo, Olaleye; Panji, Sumir; Pillay, Venesa; Rendon, Gloria; Sengupta, Dhriti; Mulder, Nicola

    2017-06-01

    The H3ABioNet pan-African bioinformatics network, which is funded to support the Human Heredity and Health in Africa (H3Africa) program, has developed node-assessment exercises to gauge the ability of its participating research and service groups to analyze typical genome-wide datasets being generated by H3Africa research groups. We describe a framework for the assessment of computational genomics analysis skills, which includes standard operating procedures, training and test datasets, and a process for administering the exercise. We present the experiences of 3 research groups that have taken the exercise and the impact on their ability to manage complex projects. Finally, we discuss the reasons why many H3ABioNet nodes have declined so far to participate and potential strategies to encourage them to do so.

  14. Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics network.

    Directory of Open Access Journals (Sweden)

    C Victor Jongeneel

    2017-06-01

    Full Text Available The H3ABioNet pan-African bioinformatics network, which is funded to support the Human Heredity and Health in Africa (H3Africa program, has developed node-assessment exercises to gauge the ability of its participating research and service groups to analyze typical genome-wide datasets being generated by H3Africa research groups. We describe a framework for the assessment of computational genomics analysis skills, which includes standard operating procedures, training and test datasets, and a process for administering the exercise. We present the experiences of 3 research groups that have taken the exercise and the impact on their ability to manage complex projects. Finally, we discuss the reasons why many H3ABioNet nodes have declined so far to participate and potential strategies to encourage them to do so.

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

    Science.gov (United States)

    Loucif, Samia

    2014-01-01

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

  16. "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,…

  17. 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…

  18. Ostomy Home Skills Program

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  19. 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.

  20. Ostomy Home Skills Program

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  1. "Broadband" Bioinformatics Skills Transfer with the Knowledge Transfer Programme (KTP: Educational Model for Upliftment and Sustainable Development.

    Directory of Open Access Journals (Sweden)

    Emile R Chimusa

    2015-11-01

    Full Text Available A shortage of practical skills and relevant expertise is possibly the primary obstacle to social upliftment and sustainable development in Africa. The "omics" fields, especially genomics, are increasingly dependent on the effective interpretation of large and complex sets of data. Despite abundant natural resources and population sizes comparable with many first-world countries from which talent could be drawn, countries in Africa still lag far behind the rest of the world in terms of specialized skills development. Moreover, there are serious concerns about disparities between countries within the continent. The multidisciplinary nature of the bioinformatics field, coupled with rare and depleting expertise, is a critical problem for the advancement of bioinformatics in Africa. We propose a formalized matchmaking system, which is aimed at reversing this trend, by introducing the Knowledge Transfer Programme (KTP. Instead of individual researchers travelling to other labs to learn, researchers with desirable skills are invited to join African research groups for six weeks to six months. Visiting researchers or trainers will pass on their expertise to multiple people simultaneously in their local environments, thus increasing the efficiency of knowledge transference. In return, visiting researchers have the opportunity to develop professional contacts, gain industry work experience, work with novel datasets, and strengthen and support their ongoing research. The KTP develops a network with a centralized hub through which groups and individuals are put into contact with one another and exchanges are facilitated by connecting both parties with potential funding sources. This is part of the PLOS Computational Biology Education collection.

  2. "Broadband" Bioinformatics Skills Transfer with the Knowledge Transfer Programme (KTP): Educational Model for Upliftment and Sustainable Development.

    Science.gov (United States)

    Chimusa, Emile R; Mbiyavanga, Mamana; Masilela, Velaphi; Kumuthini, Judit

    2015-11-01

    A shortage of practical skills and relevant expertise is possibly the primary obstacle to social upliftment and sustainable development in Africa. The "omics" fields, especially genomics, are increasingly dependent on the effective interpretation of large and complex sets of data. Despite abundant natural resources and population sizes comparable with many first-world countries from which talent could be drawn, countries in Africa still lag far behind the rest of the world in terms of specialized skills development. Moreover, there are serious concerns about disparities between countries within the continent. The multidisciplinary nature of the bioinformatics field, coupled with rare and depleting expertise, is a critical problem for the advancement of bioinformatics in Africa. We propose a formalized matchmaking system, which is aimed at reversing this trend, by introducing the Knowledge Transfer Programme (KTP). Instead of individual researchers travelling to other labs to learn, researchers with desirable skills are invited to join African research groups for six weeks to six months. Visiting researchers or trainers will pass on their expertise to multiple people simultaneously in their local environments, thus increasing the efficiency of knowledge transference. In return, visiting researchers have the opportunity to develop professional contacts, gain industry work experience, work with novel datasets, and strengthen and support their ongoing research. The KTP develops a network with a centralized hub through which groups and individuals are put into contact with one another and exchanges are facilitated by connecting both parties with potential funding sources. This is part of the PLOS Computational Biology Education collection.

  3. Ostomy Home Skills Program

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  4. Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia.

    Science.gov (United States)

    Schneider, Maria Victoria; Griffin, Philippa C; Tyagi, Sonika; Flannery, Madison; Dayalan, Saravanan; Gladman, Simon; Watson-Haigh, Nathan; Bayer, Philipp E; Charleston, Michael; Cooke, Ira; Cook, Rob; Edwards, Richard J; Edwards, David; Gorse, Dominique; McConville, Malcolm; Powell, David; Wilkins, Marc R; Lonie, Andrew

    2017-06-30

    EMBL Australia Bioinformatics Resource (EMBL-ABR) is a developing national research infrastructure, providing bioinformatics resources and support to life science and biomedical researchers in Australia. EMBL-ABR comprises 10 geographically distributed national nodes with one coordinating hub, with current funding provided through Bioplatforms Australia and the University of Melbourne for its initial 2-year development phase. The EMBL-ABR mission is to: (1) increase Australia's capacity in bioinformatics and data sciences; (2) contribute to the development of training in bioinformatics skills; (3) showcase Australian data sets at an international level and (4) enable engagement in international programs. The activities of EMBL-ABR are focussed in six key areas, aligning with comparable international initiatives such as ELIXIR, CyVerse and NIH Commons. These key areas-Tools, Data, Standards, Platforms, Compute and Training-are described in this article. © The Author 2017. Published by Oxford University Press.

  5. 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...

  6. 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…

  7. Bioinformatics programs are 31-fold over-represented among the highest impact scientific papers of the past two decades.

    Science.gov (United States)

    Wren, Jonathan D

    2016-09-01

    To analyze the relative proportion of bioinformatics papers and their non-bioinformatics counterparts in the top 20 most cited papers annually for the past two decades. When defining bioinformatics papers as encompassing both those that provide software for data analysis or methods underlying data analysis software, we find that over the past two decades, more than a third (34%) of the most cited papers in science were bioinformatics papers, which is approximately a 31-fold enrichment relative to the total number of bioinformatics papers published. More than half of the most cited papers during this span were bioinformatics papers. Yet, the average 5-year JIF of top 20 bioinformatics papers was 7.7, whereas the average JIF for top 20 non-bioinformatics papers was 25.8, significantly higher (P papers, bioinformatics journals tended to have higher Gini coefficients, suggesting that development of novel bioinformatics resources may be somewhat 'hit or miss'. That is, relative to other fields, bioinformatics produces some programs that are extremely widely adopted and cited, yet there are fewer of intermediate success. jdwren@gmail.com Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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

    Science.gov (United States)

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

    2010-11-01

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

  9. Ostomy Home Skills Program

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  10. Is there room for ethics within bioinformatics education?

    Science.gov (United States)

    Taneri, Bahar

    2011-07-01

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

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

    Science.gov (United States)

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

    2007-02-01

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

  12. 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.

  13. 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…

  14. 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…

  15. Ostomy Home Skills Program

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

    Science.gov (United States)

    Rein, Diane C

    2006-07-01

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

  17. Ostomy Home Skills Program

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

    Science.gov (United States)

    Goto, Naohisa; Prins, Pjotr; Nakao, Mitsuteru; Bonnal, Raoul; Aerts, Jan; Katayama, Toshiaki

    2010-10-15

    The BioRuby software toolkit contains a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, written in the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO. BioRuby comes with a tutorial, documentation and an interactive environment, which can be used in the shell, and in the web browser. BioRuby is free and open source software, made available under the Ruby license. BioRuby runs on all platforms that support Ruby, including Linux, Mac OS X and Windows. And, with JRuby, BioRuby runs on the Java Virtual Machine. The source code is available from http://www.bioruby.org/. katayama@bioruby.org

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

    Science.gov (United States)

    Brazas, Michelle D; Ouellette, B F Francis

    2016-06-01

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

  1. Ostomy Home Skills Program

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    Full Text Available ... Congress Educational Program Events and Special Activities Resources Housing and Travel Exhibitors Media Information Clinical Congress 2017 ... Surgical Skills for Exposure in Trauma Advanced Trauma Life Support Advanced Trauma Operative Management Basic Endovascular Skills ...

  2. Ostomy Home Skills Program

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    Full Text Available ... Mentoring for Excellence in Trauma Surgery Advanced Trauma Life Support Verification, Review, and Consultation Program for Hospitals ... Surgical Skills for Exposure in Trauma Advanced Trauma Life Support Advanced Trauma Operative Management Basic Endovascular Skills ...

  3. 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

  4. Ostomy Home Skills Program

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    Full Text Available ... Stay Up to Date with ACS Association Management Jobs Events Find a Surgeon Patients and Family Contact My Profile Shop ( 0 ) Cart Donate American College of Surgeons Education Patients and Family Skills Programs Ostomy Home Skills ...

  5. Ostomy Home Skills Program

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    Full Text Available ... Up to Date with ACS Association Management JACS Jobs Events Find a Surgeon Patients and Family Contact My Profile Shop ( 0 ) Cart Donate American College of Surgeons Education Patients and Family Skills Programs Ostomy Home Skills ...

  6. Ostomy Home Skills Program

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    Full Text Available ... Safety Resources About the Patient Education Program The Recovery Room Choosing Wisely Educational Programs Educational Programs Educational ... and practice the skills needed for optimal postoperative recovery. The kit supports the entire surgical team with ...

  7. 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).

  8. The GMOD Drupal bioinformatic server framework.

    Science.gov (United States)

    Papanicolaou, Alexie; Heckel, David G

    2010-12-15

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

  9. 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…

  10. Ostomy Home Skills Program

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    Full Text Available ... The Ostomy Home Skills Kit supports patients with educational and simulation materials to learn and practice the skills needed for optimal postoperative recovery. The kit supports the entire surgical team with quality, comprehensive education. The standardized interactive program has been ...

  11. Ostomy Home Skills Program

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    Full Text Available ... Contact My Profile Shop ( 0 ) Cart Donate American College of Surgeons Education Patients and Family Skills Programs Ostomy Home Skills ... facs.org Copyright © 1996-2018 by the American College of Surgeons, Chicago, IL 60611-3295 | Privacy Policy | Terms of Use

  12. Ostomy Home Skills Program

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    Full Text Available ... de Destrezas para manejo Doméstico de Ostomía Ostomy Home Skills Program Adult Ostomy Pediatric Ostomy Programa de Destrezas para manejo Doméstico de Ostomía The Ostomy Home Skills Kit supports patients with educational and simulation ...

  13. 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.

  14. The GMOD Drupal Bioinformatic Server Framework

    Science.gov (United States)

    Papanicolaou, Alexie; Heckel, David G.

    2010-01-01

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

  15. Making Bioinformatics Projects a Meaningful Experience in an Undergraduate Biotechnology or Biomedical Science Programme

    Science.gov (United States)

    Sutcliffe, Iain C.; Cummings, Stephen P.

    2007-01-01

    Bioinformatics has emerged as an important discipline within the biological sciences that allows scientists to decipher and manage the vast quantities of data (such as genome sequences) that are now available. Consequently, there is an obvious need to provide graduates in biosciences with generic, transferable skills in bioinformatics. We present…

  16. Ostomy Home Skills Program

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    Full Text Available ... Use Patient Opioid Use Position Statements and Task Force Patient Education Initiatives Advocacy and Health Policy Updates Selected Research ... at ACS ACS and Veterans Diversity at ACS Benefits ... Profile Shop ( 0 ) Cart Donate American College of Surgeons Education Patients and Family Skills Programs Ostomy Home Skills ...

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

    Science.gov (United States)

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

    2018-02-01

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

  18. 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

  19. 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

  20. Maine's Employability Skills Program

    Science.gov (United States)

    McMahon, John M.; Wolffe, Karen E.; Wolfe, Judy; Brooker, Carrie

    2013-01-01

    This Practice Report describes the development and implementation of the "Maine Employability Skills Program," a model employment program developed by the Maine Division for the Blind and Visually Impaired (DBVI). The program was designed to support the efforts of the chronically unemployed or underemployed. These consumers were either…

  1. 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.

  2. Adapting bioinformatics curricula for big data.

    Science.gov (United States)

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

    2016-01-01

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

  3. BioSmalltalk: a pure object system and library for bioinformatics.

    Science.gov (United States)

    Morales, Hernán F; Giovambattista, Guillermo

    2013-09-15

    We have developed BioSmalltalk, a new environment system for pure object-oriented bioinformatics programming. Adaptive end-user programming systems tend to become more important for discovering biological knowledge, as is demonstrated by the emergence of open-source programming toolkits for bioinformatics in the past years. Our software is intended to bridge the gap between bioscientists and rapid software prototyping while preserving the possibility of scaling to whole-system biology applications. BioSmalltalk performs better in terms of execution time and memory usage than Biopython and BioPerl for some classical situations. BioSmalltalk is cross-platform and freely available (MIT license) through the Google Project Hosting at http://code.google.com/p/biosmalltalk hernan.morales@gmail.com Supplementary data are available at Bioinformatics online.

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

    Science.gov (United States)

    Fristensky, Brian

    2007-01-01

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

  5. 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.

  6. 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.

  7. Ostomy Home Skills Program

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    Full Text Available ... Workforce Trauma and EMS Cancer and Research Health Information Technology Scope of Practice Pediatric Issues Other Federal Legislative Issues Regulatory Issues Regulatory Issues Regulatory Issues Stop Overregulating My OR ... American Urological Association (AUA), Certified Enterostomal Therapy Nurses (CETN), and the United Ostomy Associations of America (UOAA). Program Overview The skills kit contains: A booklet with information on the operation, home skills such as emptying ...

  8. Bioinformatic tools for PCR Primer design

    African Journals Online (AJOL)

    ES

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

  9. Assessment of a Bioinformatics across Life Science Curricula Initiative

    Science.gov (United States)

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

    2007-01-01

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

  10. Ostomy Home Skills Program

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    Full Text Available ... Online Guide to Choosing a Surgical Residency Practice Management Workshops Patients and Family Patient Education Patient Education Patients Medical Professionals Skills Programs Find ...

  11. Ostomy Home Skills Program

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    Full Text Available ... ACS/ASE Medical Student Core Curriculum ACS/ASE Medical Student Simulation-Based Surgical Skills Curriculum Cancer Education Cancer Education Cancer Education Cancer Programs Conference: Learn. ...

  12. Softball: Special Olympics Sports Skills Instructional Program.

    Science.gov (United States)

    Special Olympics, Inc., Washington, DC.

    One of seven instructional units on Special Olympics Sports Skills Instructional Programs, this guide presents suggestions for coaching softball for mentally retarded persons. An overview section provides information on teaching suggestions, followed by a list of program goals, objectives, and benefits. Sports skill assessments measure athletes'…

  13. Ostomy Home Skills Program

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    Full Text Available ... for Hospitals Ostomy Home Skills Hospital Quality Improvement Package The standardized interactive program has been developed by the American College of Surgeons ... and Associates Medical Students International Surgeons ...

  14. Ostomy Home Skills Program

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    Full Text Available ... Resources Online Guide to Choosing a Surgical Residency Practice Management Workshops Patients and Family Patient Education Patient Education Patients Medical Professionals Skills Programs Find a Treatment Center Patient ...

  15. Ostomy Home Skills Program

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    Full Text Available ... ASE Resident Prep Curriculum ACS/ASE Medical Student Core Curriculum ACS/ASE Medical Student Simulation-Based Surgical Skills Curriculum Cancer Education Cancer Education Cancer Education Cancer Programs Conference: Learn. ...

  16. Ostomy Home Skills Program

    Medline Plus

    Full Text Available ... ASCRS), American Urological Association (AUA), Certified Enterostomal Therapy Nurses (CETN), and the United Ostomy Associations of America (UOAA). Program Overview The skills kit contains: A booklet with information on the ...

  17. Measuring Science Inquiry Skills in Youth Development Programs: The Science Process Skills Inventory

    Directory of Open Access Journals (Sweden)

    Mary E. Arnold

    2013-03-01

    Full Text Available In recent years there has been an increased emphasis on science learning in 4-H and other youth development programs. In an effort to increase science capacity in youth, it is easy to focus only on developing the concrete skills and knowledge that a trained scientist must possess. However, when science learning is presented in a youth-development setting, the context of the program also matters. This paper reports the development and testing of the Science Process Skills Inventory (SPSI and its usefulness for measuring science inquiry skill development in youth development science programs. The results of the psychometric testing of the SPSI indicated the instrument is reliable and measures a cohesive construct called science process skills, as reflected in the 11 items that make up this group of skills. The 11 items themselves are based on the cycle of science inquiry, and represent the important steps of the complete inquiry process.

  18. Ostomy Home Skills Program

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    Full Text Available ... to Be a Surgeon Resident Resources Teaching Resources Online Guide to Choosing a Surgical Residency Practice Management Workshops Patients and Family Patient Education Patient Education Patients Medical Professionals Skills Programs Find ...

  19. Buying in to bioinformatics: an introduction to commercial sequence analysis software.

    Science.gov (United States)

    Smith, David Roy

    2015-07-01

    Advancements in high-throughput nucleotide sequencing techniques have brought with them state-of-the-art bioinformatics programs and software packages. Given the importance of molecular sequence data in contemporary life science research, these software suites are becoming an essential component of many labs and classrooms, and as such are frequently designed for non-computer specialists and marketed as one-stop bioinformatics toolkits. Although beautifully designed and powerful, user-friendly bioinformatics packages can be expensive and, as more arrive on the market each year, it can be difficult for researchers, teachers and students to choose the right software for their needs, especially if they do not have a bioinformatics background. This review highlights some of the currently available and most popular commercial bioinformatics packages, discussing their prices, usability, features and suitability for teaching. Although several commercial bioinformatics programs are arguably overpriced and overhyped, many are well designed, sophisticated and, in my opinion, worth the investment. If you are just beginning your foray into molecular sequence analysis or an experienced genomicist, I encourage you to explore proprietary software bundles. They have the potential to streamline your research, increase your productivity, energize your classroom and, if anything, add a bit of zest to the often dry detached world of bioinformatics. © The Author 2014. Published by Oxford University Press.

  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. 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…

  2. 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…

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

    Science.gov (United States)

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

    2007-03-08

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

  4. Biowep: a workflow enactment portal for bioinformatics applications

    Directory of Open Access Journals (Sweden)

    Romano Paolo

    2007-03-01

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

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

    Science.gov (United States)

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

    2015-06-02

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

  6. Ostomy Home Skills Program

    Medline Plus

    Full Text Available ... You Want to Be a Surgeon Resident Resources Teaching Resources Online Guide to Choosing a Surgical Residency Practice Management Workshops Patients and Family Patient Education Patient Education Patients Medical Professionals Skills Programs Find ...

  7. Ostomy Home Skills Program

    Medline Plus

    Full Text Available ... Education Patients Medical Professionals Skills Programs Find a Treatment Center Patient Safety Resources About the Patient Education ... Surgeons (ASCRS), American Urological Association (AUA), Certified Enterostomal Therapy Nurses (CETN), and the United Ostomy Associations of ...

  8. Ostomy Home Skills Program

    Medline Plus

    Full Text Available ... Systems Consultation Program Trauma Education Achieving Zero Preventable Deaths Conference Publications and Posters National Trauma System Injury ... Education Trauma Education Trauma Education Achieving Zero Preventable Deaths Trauma Systems Conference Advanced Surgical Skills for Exposure ...

  9. Ostomy Home Skills Program

    Medline Plus

    Full Text Available ... Nurses (CETN), and the United Ostomy Associations of America (UOAA). Program Overview The skills kit contains: A ... Nurses (CETN), and the United Ostomy Associations of America (UOAA). Back to Top Find A Surgeon Find ...

  10. PubData: search engine for bioinformatics databases worldwide

    OpenAIRE

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

    2016-01-01

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

  11. Ostomy Home Skills Program

    Medline Plus

    Full Text Available ... CME Accreditation PartnerCME Joint Providership Program Verification of Knowledge and Skills Academy of Master Surgeon Educators Academy ... Online Guide to Choosing a Surgical Residency Practice Management Workshops Patients and Family Patient Education Patient Education ...

  12. Ostomy Home Skills Program

    Medline Plus

    Full Text Available ... and Family Patient Education Patient Education Patients Medical Professionals Skills Programs Find a Treatment Center Patient Safety ... Involved Get Involved SurgeonsVoice American College of Surgeons Professional Association State Legislative Action Center Leadership & Advocacy Summit ...

  13. Ostomy Home Skills Program

    Medline Plus

    Full Text Available ... ASE Medical Student Core Curriculum ACS/ASE Medical Student Simulation-Based Surgical Skills Curriculum Cancer Education Cancer Education Cancer Education Cancer Programs Conference: Learn. Interact. Transform. CoC Events Quality Education Quality Education Quality Education ...

  14. Two Reading Assessments for Youth in Alternative Basic Skills and Livelihood Skills Training Programs

    Science.gov (United States)

    Comings, John P.; Strucker, John; Bell, Brenda

    2017-01-01

    This article describes two assessment tools that have been used to assess the reading skills of youth participating in alternative basic skills and livelihood skills training programs. The Rapid Assessment of Reading Skills (RARS) was developed to identify potential participants who needed to improve their reading skills before beginning training…

  15. 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.

  16. 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

  17. Ostomy Home Skills Program

    Medline Plus

    Full Text Available ... in Residence Clinical Trials Methods Course Health Services Research Methods Course Surgeon Specific Registry Trauma Education Trauma Education Trauma Education Advanced Surgical Skills for Exposure in Trauma Advanced Trauma Life Support ... Quality Program Initiatives Communications to the Profession ...

  18. 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.

  19. 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.

  20. Outdoor Leadership Skills: A Program Perspective

    Science.gov (United States)

    Shooter, Wynn; Sibthorp, Jim; Paisley, Karen

    2009-01-01

    Successful hiring, training, and pairing or grouping of staff requires administrators to consider the relationship between their programs' goals and the specific outdoor leadership skills of individual leaders. Authors have divided outdoor leadership skills into a three-category structure, and models of outdoor leadership have focused on skills…

  1. Now Enhancing Working Skills: The ``NEWS`` Program. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Kuiper, A. [Merex Corp. (United States)

    1995-01-23

    In October of 1992, Los Alamos National Laboratory and Merex Corporation began a pilot basic skills program to enhance workers` skills. The program, known as the NEWS (Now Enhancing Working Skills) Program, was implemented by the Training and Development Group of the Human Resources Division. A group of 106 employees known as Radiological Control Technicians (RCTs) from ESH-1 (Environmental, Safety, and Health) were targeted to take mandated DOE (Department of Energy) training. The main goal of the LANL/Merex partnership was to help RCTs prepare for mandated DOE Rad Con training and job performance by improving their information processing and math skills. A second goal of this project was to use the information from this small group to make some predictions about the Laboratory as a whole. This final report contains the description and an appendix for the ``NEWS`` program. The topics in this report include Merex class descriptions, test score results for the MAT, the WAT, the TABE, and Challenge test, a follow-up survey to Merex IPS and math training, student feedback statistics for skills programs, and lessons learned from the program.

  2. Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets.

    Science.gov (United States)

    Rideout, Jai Ram; Chase, John H; Bolyen, Evan; Ackermann, Gail; González, Antonio; Knight, Rob; Caporaso, J Gregory

    2016-06-13

    Bioinformatics software often requires human-generated tabular text files as input and has specific requirements for how those data are formatted. Users frequently manage these data in spreadsheet programs, which is convenient for researchers who are compiling the requisite information because the spreadsheet programs can easily be used on different platforms including laptops and tablets, and because they provide a familiar interface. It is increasingly common for many different researchers to be involved in compiling these data, including study coordinators, clinicians, lab technicians and bioinformaticians. As a result, many research groups are shifting toward using cloud-based spreadsheet programs, such as Google Sheets, which support the concurrent editing of a single spreadsheet by different users working on different platforms. Most of the researchers who enter data are not familiar with the formatting requirements of the bioinformatics programs that will be used, so validating and correcting file formats is often a bottleneck prior to beginning bioinformatics analysis. We present Keemei, a Google Sheets Add-on, for validating tabular files used in bioinformatics analyses. Keemei is available free of charge from Google's Chrome Web Store. Keemei can be installed and run on any web browser supported by Google Sheets. Keemei currently supports the validation of two widely used tabular bioinformatics formats, the Quantitative Insights into Microbial Ecology (QIIME) sample metadata mapping file format and the Spatially Referenced Genetic Data (SRGD) format, but is designed to easily support the addition of others. Keemei will save researchers time and frustration by providing a convenient interface for tabular bioinformatics file format validation. By allowing everyone involved with data entry for a project to easily validate their data, it will reduce the validation and formatting bottlenecks that are commonly encountered when human-generated data files are

  3. A bioinformatics potpourri.

    Science.gov (United States)

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

    2018-01-19

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

  4. The Effect of the Cherry Hill Study Skills Program on Eighth Grade Students' Reading Comprehension and Study Skills.

    Science.gov (United States)

    La Marca, Marilyn Tierney

    A study was conducted to determine the effects of the "Cherry Hill Study Skills Program" on eighth grade students' reading comprehension and study skills. The "Cherry Hill Study Skills Program" is a process oriented course dealing with the sequential development of nine specific skills deemed essential to the retrieval and retention of information…

  5. Using Bioinformatics to Develop and Test Hypotheses: E. coli-Specific Virulence Determinants

    Directory of Open Access Journals (Sweden)

    Joanna R. Klein

    2012-09-01

    Full Text Available Bioinformatics, the use of computer resources to understand biological information, is an important tool in research, and can be easily integrated into the curriculum of undergraduate courses. Such an example is provided in this series of four activities that introduces students to the field of bioinformatics as they design PCR based tests for pathogenic E. coli strains. A variety of computer tools are used including BLAST searches at NCBI, bacterial genome searches at the Integrated Microbial Genomes (IMG database, protein analysis at Pfam and literature research at PubMed. In the process, students also learn about virulence factors, enzyme function and horizontal gene transfer. Some or all of the four activities can be incorporated into microbiology or general biology courses taken by students at a variety of levels, ranging from high school through college. The activities build on one another as they teach and reinforce knowledge and skills, promote critical thinking, and provide for student collaboration and presentation. The computer-based activities can be done either in class or outside of class, thus are appropriate for inclusion in online or blended learning formats. Assessment data showed that students learned general microbiology concepts related to pathogenesis and enzyme function, gained skills in using tools of bioinformatics and molecular biology, and successfully developed and tested a scientific hypothesis.

  6. Increasing team skills: an evaluation of program effectiveness.

    Science.gov (United States)

    Jacobsen-Webb, M L

    1985-11-01

    The need for health professionals with caring values and good communication skills is well established. To develop these skills requires building self-esteem, as is supported by the work of Carl Rogers, Maslow, and Jourard, and the development of communication skills, as is supported by Carkhuff. A six-hour developmental program was evaluated using alternate forms of the highly validated Personal Skills Map. The differences in participants' scores showed increases in self-esteem, comfort, and management skills (p less than .00), while aggression (p = .05) and deference (p less than .00) decreased. A longitudinal follow-up of participants showed that 65% continued to use the assessment tool six months to one year later. The program appears to be well suited for service settings, continuing education, and academic settings, and meets the need of a high tech, high touch era of change.

  7. 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…

  8. Enhancing clinical skills education: University of Virginia School of Medicine's Clerkship Clinical Skills Workshop Program.

    Science.gov (United States)

    Corbett, Eugene C; Payne, Nancy J; Bradley, Elizabeth B; Maughan, Karen L; Heald, Evan B; Wang, Xin Qun

    2007-07-01

    In 1993, the University of Virginia School of Medicine began a clinical skills workshop program in an effort to improve the preparation of all clerkship students to participate in clinical care. This program involved the teaching of selected basic clinical skills by interested faculty to small groups of third-year medical students. Over the past 14 years, the number of workshops has increased from 11 to 31, and they now involve clerkship faculty from family medicine, internal medicine, and pediatrics. Workshops include a variety of common skills from the communication, physical examination, and clinical test and procedure domains such as pediatric phone triage, shoulder examination, ECG interpretation, and suturing. Workshop sessions allow students to practice skills on each other, with standardized patients, or with models, with the goal of improving competence and confidence in the performance of basic clinical skills. Students receive direct feedback from faculty on their skill performance. The style and content of these workshops are guided by an explicit set of educational criteria.A formal evaluation process ensures that faculty receive regular feedback from student evaluation comments so that adherence to workshop criteria is continuously reinforced. Student evaluations confirm that these workshops meet their skill-learning needs. Preliminary outcome measures suggest that workshop teaching can be linked to student assessment data and may improve students' skill performance. This program represents a work-in-progress toward the goal of providing a more comprehensive and developmental clinical skills curriculum in the school of medicine.

  9. Has the inclusion of a longitudinally integrated communication skills program improved consultation skills in medical students? A pilot study.

    Science.gov (United States)

    Shah, Sameena; Andrades, Marie; Basir, Fasia; Jaleel, Anila; Azam, Iqbal; Islam, Muhammad; Ahmed, Rashida

    2016-01-01

    Evidence highlights a lack of communication skills in doctors leading to dysfunctional consultations. To address this deficit, a private medical college instituted curricular reforms with inclusion of a longitudinal communication skills program. A pilot study was undertaken to evaluate the effectiveness of this program by comparing the consultation skills of medical students of this college with a medical college without a communication skills program. A 4-station Objective Structured Clinical Examination (OSCE) was conducted in the third and final year. Mann-Whitney U-test was used to compare the difference in the distribution between OSCE stations total and construct scores. At the end of the third year, 21 (31.34%), students of the study site (medical college 1 [college with integrated longitudinal communication skills program]) and 31 (46.26%) students from the comparison site (medical college 2 [comparable college without communication skills program]) consented. Medical college 1 achieved a significantly higher overall mean total station score of 68.0% (standard deviation [SD] =13.5) versus 57.2% (SD = 15.4) (P skills in an undergraduate curriculum positively impacted consultation skills. Community-based training and faculty development are required to develop effective patient-centered consultation skills.

  10. Data mining for bioinformatics applications

    CERN Document Server

    Zengyou, He

    2015-01-01

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

  11. Using Contemporary Leadership Skills in Medication Safety Programs.

    Science.gov (United States)

    Hertig, John B; Hultgren, Kyle E; Weber, Robert J

    2016-04-01

    The discipline of studying medication errors and implementing medication safety programs in hospitals dates to the 1970s. These initial programs to prevent errors focused only on pharmacy operation changes - and not the broad medication use system. In the late 1990s, research showed that faulty systems, and not faulty people, are responsible for errors and require a multidisciplinary approach. The 2013 ASHP Statement on the Role of the Medication Safety Leader recommended that medication safety leaders be integrated team members rather than a single point of contact. Successful medication safety programs must employ a new approach - one that embraces the skills of all health care team members and positions many leaders to improve safety. This approach requires a new set of leadership skills based on contemporary management principles, including followership, team-building, tracking and assessing progress, storytelling and communication, and cultivating innovation, all of which promote transformational change. The application of these skills in developing or changing a medication safety program is reviewed in this article.

  12. Application of Higher Diploma Program training skills

    African Journals Online (AJOL)

    RPO

    This article examines the application Higher Diploma training skills in classroom instruction as .... the intention of articulating the extent to which the ... graduates are applying HDP training skills ... HDP) to revisit their procedure, which result ..... not believe in the usefulness of the ... of this study perceived CPD as a program.

  13. Effectiveness and safety of wheelchair skills training program in improving the wheelchair skills capacity: a systematic review.

    Science.gov (United States)

    Tu, Chun-Jing; Liu, Lin; Wang, Wei; Du, He-Ping; Wang, Yu-Ming; Xu, Yan-Bing; Li, Ping

    2017-12-01

    To comprehensively assess the effectiveness and safety of wheelchair skills training program in improving wheelchair skills capacity. PubMed, OVID, EBSCO, ScienceDirect, Web of Science, CINAHL, Cochrane Library, Google Scholar, and China Knowledge Resource Integrated Database were searched up to March 2017. Controlled clinical trials that compared a wheelchair skills training program with a control group that received other interventions and used the wheelchair skills test scores to evaluate wheelchair skills capacity were included. Two authors independently screened articles, extracted data, and assessed the methodological quality using the Cochrane risk-of-bias tool in randomized controlled trial (RCT) and methodological index for non-randomized studies. The data results of wheelchair skills test scores were extracted. Data from 455 individuals in 10 RCTs and from 140 participants in seven non-randomized studies were included for meta-analysis using Stata version 12.0 (Stata Corporation, College Station, TX, USA). In the short term (immediately to one week) post-intervention, relative to a control group, manual wheelchair skills training could increase the total wheelchair skills test scores by 13.26% in RCTs (95% confidence interval (CI), 6.19%-20.34%; P skills training and the long-term (3-12 months) advantage of manual wheelchair skills training ( P = 0.755). The limited evidence suggests that wheelchair skills training program is beneficial in the short term, but its long-term effects remain unclear.

  14. Clinical skills assessment of procedural and advanced communication skills: performance expectations of residency program directors

    Science.gov (United States)

    Langenau, Erik E.; Zhang, Xiuyuan; Roberts, William L.; DeChamplain, Andre F.; Boulet, John R.

    2012-01-01

    Background High stakes medical licensing programs are planning to augment and adapt current examinations to be relevant for a two-decision point model for licensure: entry into supervised practice and entry into unsupervised practice. Therefore, identifying which skills should be assessed at each decision point is critical for informing examination development, and gathering input from residency program directors is important. Methods Using data from previously developed surveys and expert panels, a web-delivered survey was distributed to 3,443 residency program directors. For each of the 28 procedural and 18 advanced communication skills, program directors were asked which clinical skills should be assessed, by whom, when, and how. Descriptive statistics were collected, and Intraclass Correlations (ICC) were conducted to determine consistency across different specialties. Results Among 347 respondents, program directors reported that all advanced communication and some procedural tasks are important to assess. The following procedures were considered ‘important’ or ‘extremely important’ to assess: sterile technique (93.8%), advanced cardiovascular life support (ACLS) (91.1%), basic life support (BLS) (90.0%), interpretation of electrocardiogram (89.4%) and blood gas (88.7%). Program directors reported that most clinical skills should be assessed at the end of the first year of residency (or later) and not before graduation from medical school. A minority were considered important to assess prior to the start of residency training: demonstration of respectfulness (64%), sterile technique (67.2%), BLS (68.9%), ACLS (65.9%) and phlebotomy (63.5%). Discussion Results from this study support that assessing procedural skills such as cardiac resuscitation, sterile technique, and phlebotomy would be amenable to assessment at the end of medical school, but most procedural and advanced communications skills would be amenable to assessment at the end of the first

  15. Learning clinical communication skills: outcomes of a program for professional practitioners.

    Science.gov (United States)

    Carvalho, Irene P; Pais, Vanessa G; Almeida, Susana S; Ribeiro-Silva, Raquel; Figueiredo-Braga, Margarida; Teles, Ana; Castro-Vale, Ivone; Mota-Cardoso, Rui

    2011-07-01

    To assess the effects of a communication skills program on professional practitioners' performance and self-confidence in clinical interviewing. Twenty-five health professionals took 3 months of basic communication skills followed by 3 months of advanced communication skills. An additional quarter dealt with self-awareness and communication in special situations. Participants' performances were evaluated in clinical interviews with standardized patients before, during and after the program by external observers and standardized patients, using standardized instruments. Participants assessed their own confidence in their communication skills before and after the program. Data were analysed using GLM repeated-measures procedures in SPSS. Basic communication skills and self-confidence improved throughout the 6 months; competencies declined but self-confidence continued to increase 4 months later. Compared with taking no course, differences were statistically significant after the 6 months (external observers only) and 4 months later (external observers and participants). The program effectively improved communication skills, although significantly only when assessed by external observers. Four months later, effects were significant in communication skills (external observers), despite the decline and in self-confidence. While periodical enrollment in programs for the practice of communication skills may help maintain performance, more knowledge on communication and self-awareness may enhance self-confidence. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  16. Residency Programs and Clinical Leadership Skills Among New Saudi Graduate Nurses.

    Science.gov (United States)

    Al-Dossary, Reem Nassar; Kitsantas, Panagiota; Maddox, P J

    2016-01-01

    Nurse residency programs have been adopted by health care organizations to assist new graduate nurses with daily challenges such as intense working environments, increasing patient acuity, and complex technologies. Overall, nurse residency programs are proven beneficial in helping nurses transition from the student role to independent practitioners and bedside leaders. The purpose of this study was to assess the impact of residency programs on leadership skills of new Saudi graduate nurses who completed a residency program compared to new Saudi graduate nurses who did not participate in residency programs. The study design was cross-sectional involving a convenience sample (n = 98) of new graduate nurses from three hospitals in Saudi Arabia. The Clinical Leadership Survey was used to measure the new graduate nurses' clinical leadership skills based on whether they completed a residency program or not. Descriptive statistics, correlation, and multiple linear regression analyses were conducted to examine leadership skills in this sample of new Saudi graduate nurses. A significant difference was found between residents and nonresidents in their leadership skills (t = 10.48, P = .000). Specifically, residents were significantly more likely to show higher levels of leadership skills compared to their counterparts. Attending a residency program was associated with a significant increase in clinical leadership skills. The findings of this study indicate that there is a need to implement more residency programs in hospitals of Saudi Arabia. It is imperative that nurse managers and policy makers in Saudi Arabia consider these findings to improve nurses' leadership skills, which will in turn improve patient care. Further research should examine how residency programs influence new graduate nurses' transition from student to practitioner with regard to clinical leadership skills in Saudi Arabia. Copyright © 2016 Elsevier Inc. All rights reserved.

  17. Teaching-skills training programs for family medicine residents: systematic review of formats, content, and effects of existing programs.

    Science.gov (United States)

    Lacasse, Miriam; Ratnapalan, Savithiri

    2009-09-01

    To review the literature on teaching-skills training programs for family medicine residents and to identify formats and content of these programs and their effects. Ovid MEDLINE (1950 to mid-July 2008) and the Education Resources Information Center database (pre-1966 to mid-July 2008) were searched using and combining the MeSH terms teaching, internship and residency, and family practice; and teaching, graduate medical education, and family practice. The initial MEDLINE and Education Resources Information Center database searches identified 362 and 33 references, respectively. Titles and abstracts were reviewed and studies were included if they described the format or content of a teaching-skills program or if they were primary studies of the effects of a teaching-skills program for family medicine residents or family medicine and other specialty trainees. The bibliographies of those articles were reviewed for unidentified studies. A total of 8 articles were identified for systematic review. Selection was limited to articles published in English. Teaching-skills training programs for family medicine residents vary from half-day curricula to a few months of training. Their content includes leadership skills, effective clinical teaching skills, technical teaching skills, as well as feedback and evaluation skills. Evaluations mainly assessed the programs' effects on teaching behaviour, which was generally found to improve following participation in the programs. Evaluations of learner reactions and learning outcomes also suggested that the programs have positive effects. Family medicine residency training programs differ from all other residency training programs in their shorter duration, usually 2 years, and the broader scope of learning within those 2 years. Few studies on teaching-skills training, however, were designed specifically for family medicine residents. Further studies assessing the effects of teaching-skills training in family medicine residents are

  18. A Quick Guide for Building a Successful Bioinformatics Community

    Science.gov (United States)

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

    2015-01-01

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

  19. 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.

  20. Developing nurse leaders: a program enhancing staff nurse leadership skills and professionalism.

    Science.gov (United States)

    Abraham, Pauline J

    2011-01-01

    This study aims to determine whether participation in the Nursing Leadership Perspectives Program (NLPP) at Mayo Clinic in Rochester, Minnesota, produced a change in leadership skills, increased professional activities, leadership promotion, and retention rates of participants. The NLPP is an educational program designed to enhance leadership skills and promote professionalism of registered nurses. The 6-month program provides participants with theoretical knowledge, core competencies, and opportunities to practice application of leadership skills. Outcome metrics were collected from registered nurses who completed the program (n = 15). Data analysis included descriptive and nonparametric methods. Participants reported statistically significant changes in their leadership skills after participation in the program (P = .007) on the Leadership Practices Inventory. Changes in professional behavior were also statistically significant as rated by the Nursing Activity Scale (P = .001). Participants demonstrated a change in leadership skills and professional behavior following the program.

  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

    downstream interpretation of prioritized variants. To provide support for these and other bioinformatics queries, an online bioinformatics helpdesk backed by broad consortium expertise has been established. Further support is provided by means of various modes of bioinformatics training. For the past 4 years, the development of infrastructure support and human capacity through H3ABioNet, have significantly contributed to the establishment of African scientific networks, data analysis facilities, and training programs. Here, we describe the infrastructure and how it has affected genomics and bioinformatics research in Africa. Copyright © 2017 World Heart Federation (Geneva). Published by Elsevier B.V. All rights reserved.

  2. Procedures and reasoning for skill proficiency testing in physical education teacher education programs

    Directory of Open Access Journals (Sweden)

    Timothy Baghurst

    2015-12-01

    Full Text Available This study sought to determine how the testing of skill proficiency is being conducted in physical education teacher education (PETE programs in the USA and how fitness or skill proficiencies, as attributes of a physical educator, are perceived. Participants were 312 college PETE program coordinators who completed an online survey about skill testing in their program. The eligible respondents yielded a 52.7% total response rate. Most participants believed that skill proficiency for PETE students was important, but only 46% of programs reported testing within their program. Many participants stated it was possible for their students to graduate without demonstrating proficiency in skill technique, yet were confident their students would pass an independent skill test. Only 46.2% of respondents indicated their students needed to demonstrate proper skill technique in order to graduate, and there was no consistent method of assessment. Responses were evenly split regarding the importance of a physical educator being able to demonstrate proper skill technique or be physically fit. The lack of skill testing in programs, combined with the variation in assessment, is concerning, and the development of a standardized skill-based test may provide more rigor to this important area of teacher credibility and effectiveness.

  3. Identification of Essential Food Skills for Skill-Based Healthful Eating Programs in Secondary Schools

    Science.gov (United States)

    Fordyce-Voorham, Sandra

    2011-01-01

    Objective: To identify the food skills deemed essential to include in skill-based healthful eating programs in secondary schools. Methods: Fifty-one food experts including home economics educators, chefs, nutritionists and dietitians, community educators, homemakers, and young people were recruited by invitation, mail, and advertising. Data were…

  4. 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…

  5. jORCA: easily integrating bioinformatics Web Services.

    Science.gov (United States)

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

    2010-02-15

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

  6. The eBioKit, a stand-alone educational platform for bioinformatics.

    Science.gov (United States)

    Hernández-de-Diego, Rafael; de Villiers, Etienne P; Klingström, Tomas; Gourlé, Hadrien; Conesa, Ana; Bongcam-Rudloff, Erik

    2017-09-01

    Bioinformatics skills have become essential for many research areas; however, the availability of qualified researchers is usually lower than the demand and training to increase the number of able bioinformaticians is an important task for the bioinformatics community. When conducting training or hands-on tutorials, the lack of control over the analysis tools and repositories often results in undesirable situations during training, as unavailable online tools or version conflicts may delay, complicate, or even prevent the successful completion of a training event. The eBioKit is a stand-alone educational platform that hosts numerous tools and databases for bioinformatics research and allows training to take place in a controlled environment. A key advantage of the eBioKit over other existing teaching solutions is that all the required software and databases are locally installed on the system, significantly reducing the dependence on the internet. Furthermore, the architecture of the eBioKit has demonstrated itself to be an excellent balance between portability and performance, not only making the eBioKit an exceptional educational tool but also providing small research groups with a platform to incorporate bioinformatics analysis in their research. As a result, the eBioKit has formed an integral part of training and research performed by a wide variety of universities and organizations such as the Pan African Bioinformatics Network (H3ABioNet) as part of the initiative Human Heredity and Health in Africa (H3Africa), the Southern Africa Network for Biosciences (SAnBio) initiative, the Biosciences eastern and central Africa (BecA) hub, and the International Glossina Genome Initiative.

  7. 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.

  8. Bioinformatics and moonlighting proteins

    Directory of Open Access Journals (Sweden)

    Sergio eHernández

    2015-06-01

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

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

    Science.gov (United States)

    Vetrivel, Umashankar; Pilla, Kalabharath

    2008-01-01

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

  10. The Skills Enhancement Training Program. Performance Report.

    Science.gov (United States)

    Food and Beverage Workers Union, Local 32, Washington, DC.

    This report describes a joint labor-management workplace literacy program called SET (Skills Enhancement Training) that targeted the more than 2,000 unionized employees of food service contractors at U.S. government institutions in Washington, D.C. Nineteen classes were offered and a total of 191 people self-selected themselves into the program.…

  11. Evaluation of a class wide teaching program for developing preschool life skills.

    Science.gov (United States)

    Hanley, Gregory P; Heal, Nicole A; Tiger, Jeffrey H; Ingvarsson, Einar T

    2007-01-01

    Recently, nonmaternal center-based child care has been linked to problem behavior in young children (National Institute of Child Health and Human Development, 2003). In response, a comprehensive program to promote prosocial skills was evaluated in a classroom of 16 children between the ages of 3 and 5 years. Classroom observations were conducted during evocative situations to determine the likelihood of problem behavior (noncompliance, vocal or motor disruptions, aggression) and preschool life skills. A classwide teaching program was then implemented in a staggered manner across instruction following, functional communication, delay tolerance, and friendship skills. These four categories of preschool life skills, which included two to four related skills, were selected for classwide teaching because they were either identified by educators as important for early school success, have often been taught following functional assessments of more severe problem behavior, or both. Skills were taught on a classwide basis during typically scheduled activities (circle, free play, transitions, meals) via instructions, modeling, role play, and feedback. A multiple probe design showed that the program resulted in an 74% reduction in problem behavior and a more than four-fold increase in preschool life skills. Similar beneficial effects of the program were evident in questionnaire data gathered prior to and at the close of the evaluation. Finally, the teachers who implemented the program reported overall high levels of satisfaction with the classwide teaching program, the target skills, and the results. Implications for the design of early childhood experiences for preempting the development of serious problem behavior are discussed.

  12. Has the inclusion of a longitudinally integrated communication skills program improved consultation skills in medical students? A pilot study

    Directory of Open Access Journals (Sweden)

    Sameena Shah

    2016-01-01

    Full Text Available Background: Evidence highlights a lack of communication skills in doctors leading to dysfunctional consultations. To address this deficit, a private medical college instituted curricular reforms with inclusion of a longitudinal communication skills program. A pilot study was undertaken to evaluate the effectiveness of this program by comparing the consultation skills of medical students of this college with a medical college without a communication skills program. Methods: A 4-station Objective Structured Clinical Examination (OSCE was conducted in the third and final year. Mann-Whitney U-test was used to compare the difference in the distribution between OSCE stations total and construct scores. Results: At the end of the third year, 21 (31.34%, students of the study site (medical college 1 [college with integrated longitudinal communication skills program] and 31 (46.26% students from the comparison site (medical college 2 [comparable college without communication skills program] consented. Medical college 1 achieved a significantly higher overall mean total station score of 68.0% (standard deviation [SD] =13.5 versus 57.2% (SD = 15.4 (P < 0.001. Significantly higher mean scores were achieved on three stations. At the end of the final year, 19 students (29.3% from medical college 1 and 22 (34% students from medical college 2 consented. The difference in overall mean total station score reduced from 9.2% to 7.1% (70.2 (SD = 13.7 versus 63.1 (SD = 15.2 (P = 0.004. The mean scores of both colleges decreased in "Patient presenting with Hepatitis C Report" station (P values 0.004 and 0.775 and in "Patient Request for Faith Healing Therapy in Diabetes Mellitus" station (P values 0.0046 and 0.036, respectively. Conclusion: Longitudinal communication skills in an undergraduate curriculum positively impacted consultation skills. Community-based training and faculty development are required to develop effective patient-centered consultation skills.

  13. 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.

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

    African Journals Online (AJOL)

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

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

    OpenAIRE

    Whyte, Barry James

    2008-01-01

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

  16. A Meta-Analysis of Skills Training Programs for Rehabilitation Clients.

    Science.gov (United States)

    Bolton, Brian; Akridge, Robert L.

    1995-01-01

    Summarized the results of 15 experimental studies of 10 small-group skills training interventions developed for use with vocational rehabilitation clients. Concluded that the typical participant in skills training interventions received substantial benefit from the activity. Skills training programs should be implemented more widely with clients…

  17. A Mathematical Program to Develop the Skills of Thinking of Children

    Directory of Open Access Journals (Sweden)

    Magda M. Saleh

    2009-10-01

    Full Text Available The importance of this study emerges from the importance of the points it discusses as it attempts to study the effectiveness of the suggested program of mathematics that develop the thinking skill of the children in preschool age. Accordingly, it comes from the attempt to teach the children the skill of thinking as one of the important and required skills for the children to accommodate with the surrounded environment and to help them develop and grow completely and to accommodate with themselves and their society. The purpose of this study is, thus, summarized in the answering of the following questions: 1- How can we create a program that uses mathematical activities and that contribute in the development of thinking skill of the preschool child? 2- To what extent is that program effective to develop the skills of thinking of the preschool child? The research sample is composed of 35 children for the experimental group and the same number for the controller group from the KJ2 children. The results of the research showed the effectiveness of the suggested program and its obvious contribution in the development of the thinking skills for the preschool children in a more effective way than the traditional methods used.

  18. Program Director Participation in a Leadership and Management Skills Fellowship and Characteristics of Program Quality.

    Science.gov (United States)

    Carek, Peter J; Mims, Lisa D; Conry, Colleen M; Maxwell, Lisa; Greenwood, Vicki; Pugno, Perry A

    2015-01-01

    The association between a residency program director completing a leadership and management skills fellowship and characteristics of quality and innovation of his/her residency program has not been studied. Therefore, the aim of this study is to examine the association between a residency program director's completion of a specific fellowship addressing these skills (National Institute for Program Director Development or NIPDD) and characteristics of quality and innovation of the program they direct. Using information from the American Academy of Family Physicians (AAFP), National Resident Matching Program (NRMP) and FREIDA® program characteristics were obtained. Descriptive statistics were used to summarize the data. The relationship between programs with a NIPDD graduate as director and program quality measures and indicators of innovation was analyzed using both chi square and logistic regression. Initial analyses showed significant associations between the NIPDD graduate status of a program director and regional location, mean years of program director tenure, and the program's 5-year aggregate ABFM board pass rate from 2007--2011. After grouping the programs into tertiles, the regression model showed significant positive associations with programs offering international experiences and being a NIPDD graduate. Program director participation in a fellowship addressing leadership and management skills (ie, NIPDD) was found to be associated with higher pass rates of new graduates on a Board certification examination and predictive of programs being in the upper tertile of programs in terms of Board pass rates.

  19. 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.

  20. 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.

  1. Establishing bioinformatics research in the Asia Pacific

    Directory of Open Access Journals (Sweden)

    Tammi Martti

    2006-12-01

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

  2. 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

  3. Interdisciplinary skills in architectural and engineering education programs

    DEFF Research Database (Denmark)

    Andersson, Niclas; Andersson, Pernille Hammar

    2006-01-01

    and requirements for reinforcement of the interdisciplinary skills within the architectural and engineering education programs as to face the challenges from industry. The study claims that the development of interdisciplinary skills should be regarded a pedagogical issue that can be accomplished by integrative...... project. Besides, new and more integrated forms of co-operation between the various actors make the prevalent professional disciplines more ambiguous and it compels into a need for trans-professional skills among the actors. In contrast to the requirements for interdisciplinary skills, the educational...... training programmes of architects and engineers are traditionally characterised by strict disciplinary boundaries. Thus, the prevailing educational system is challenged to meet the demands for trans-professional skills within industry. The purpose of this paper is to outline some pedagogical prerequisites...

  4. COMPARISON OF POPULAR BIOINFORMATICS DATABASES

    OpenAIRE

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

    2016-01-01

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

  5. 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 necessary tools for answering this question, their outputs are dependent on their quality. Our study 1) reviews the central importance of reliability and construct validity evidence in the development and evaluation of science assessments and 2) examines the extent to which published assessments in genomics and bioinformatics education (GBE) have been developed using such evidence. We identified 95 GBE articles (out of 226) that contained claims of knowledge increases, affective changes, or skill acquisition. We found that 1) the purpose of most of these studies was to assess summative learning gains associated with curricular change at the undergraduate level, and 2) a minority (<10%) of studies provided any reliability or validity evidence, and only one study out of the 95 sampled mentioned both validity and reliability. Our findings raise concerns about the quality of evidence derived from these instruments. We end with recommendations for improving assessment quality in GBE. PMID:24006400

  6. Computational biology and bioinformatics in Nigeria.

    Science.gov (United States)

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

    2014-04-01

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

  7. Computational biology and bioinformatics in Nigeria.

    Directory of Open Access Journals (Sweden)

    Segun A Fatumo

    2014-04-01

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

  8. 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.

  9. Establishing bioinformatics research in the Asia Pacific

    OpenAIRE

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

    2006-01-01

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

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

    Science.gov (United States)

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

    2006-01-01

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

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

    Science.gov (United States)

    Counsell, Damian

    2002-01-01

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

  12. Do Workplace Literacy Programs Promote High Skills or Low Wages? Suggestions for Future Evaluations of Workplace Literacy Programs.

    Science.gov (United States)

    Sarmiento, Tony

    Workplace literacy programs can support the path toward either low wages or high skills. Instead of the "high skill" path, most U.S. companies follow the "low wage" path. Depending on who is involved, which program goals are selected, and what planning process is followed, a workplace literacy program can maintain outdated workplaces or foster…

  13. Generalized Centroid Estimators in Bioinformatics

    Science.gov (United States)

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

    2011-01-01

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

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

    Science.gov (United States)

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

    2003-01-01

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

  15. Introduction to bioinformatics.

    Science.gov (United States)

    Can, Tolga

    2014-01-01

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

  16. A multi-media computer program for training in basic professional counseling skills

    NARCIS (Netherlands)

    Adema, J.; Van der Zee, K.I.

    2003-01-01

    This paper concerns the development of a self-instructional program for training in basic counseling skills. The product was a multimedia computer program, named GEVAT. The training under consideration was based on a traditional training in which students enhance these skills under supervision.

  17. The implementation and evaluation of a communication skills training program for oncology nurses.

    Science.gov (United States)

    Banerjee, Smita C; Manna, Ruth; Coyle, Nessa; Penn, Stacey; Gallegos, Tess E; Zaider, Talia; Krueger, Carol A; Bialer, Philip A; Bylund, Carma L; Parker, Patricia A

    2017-09-01

    Many nurses express difficulty in communicating with their patients, especially in oncology settings where there are numerous challenges and high-stake decisions during the course of diagnosis and treatment. Providing specific training in communication skills is one way to enhance the communication between nurses and their patients. We developed and implemented a communication skills training program for nurses, consisting of three teaching modules: responding empathically to patients; discussing death, dying, and end-of-life goals of care; and responding to challenging interactions with families. Training included didactic and experiential small group role plays. This paper presents results on program evaluation, self-efficacy, and behavioral demonstration of learned communication skills. Three hundred forty-two inpatient oncology nurses participated in a 1-day communication skills training program and completed course evaluations, self-reports, and pre- and post-standardized patient assessments. Participants rated the training favorably, and they reported significant gains in self-efficacy in their ability to communicate with patients in various contexts. Participants also demonstrated significant improvement in several empathic skills, as well as in clarifying skill. Our work demonstrates that implementation of a nurse communication skills training program at a major cancer center is feasible and acceptable and has a significant impact on participants' self-efficacy and uptake of communication skills.

  18. 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.

  19. Long-term effect of social skills training program for second graders

    OpenAIRE

    Motiejūnaitė, Miglė; Žardeckaitė-Matulaitienė, Kristina

    2017-01-01

    Middle childhood is an important period for reducing social and behavioural difficulties, though existing social skills training programs in Lithuania are not effective to help solving these problems. The aim of this study was to create and evaluate the short-term and long-term effects of a social skills training program based on an integrated theoretical model for second grade schoolchildren. The purpose of the program was to teach children non-verbal language, empathy, conflict resolution, ...

  20. 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.

  1. 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.

  2. 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...

  3. 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.

  4. Bioinformatics clouds for big data manipulation

    KAUST Repository

    Dai, Lin

    2012-11-28

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

  5. XML schemas for common bioinformatic data types and their application in workflow systems.

    Science.gov (United States)

    Seibel, Philipp N; Krüger, Jan; Hartmeier, Sven; Schwarzer, Knut; Löwenthal, Kai; Mersch, Henning; Dandekar, Thomas; Giegerich, Robert

    2006-11-06

    Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create such workflows, the tools involved have to be able to work with each other's data--therefore, a common set of well-defined data formats is needed. Unfortunately, current bioinformatic tools use a great variety of heterogeneous formats. Acknowledging the need for common formats, the Helmholtz Open BioInformatics Technology network (HOBIT) identified several basic data types used in bioinformatics and developed appropriate format descriptions, formally defined by XML schemas, and incorporated them in a Java library (BioDOM). These schemas currently cover sequence, sequence alignment, RNA secondary structure and RNA secondary structure alignment formats in a form that is independent of any specific program, thus enabling seamless interoperation of different tools. All XML formats are available at http://bioschemas.sourceforge.net, the BioDOM library can be obtained at http://biodom.sourceforge.net. The HOBIT XML schemas and the BioDOM library simplify adding XML support to newly created and existing bioinformatic tools, enabling these tools to interoperate seamlessly in workflow scenarios.

  6. XML schemas for common bioinformatic data types and their application in workflow systems

    Science.gov (United States)

    Seibel, Philipp N; Krüger, Jan; Hartmeier, Sven; Schwarzer, Knut; Löwenthal, Kai; Mersch, Henning; Dandekar, Thomas; Giegerich, Robert

    2006-01-01

    Background Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create such workflows, the tools involved have to be able to work with each other's data – therefore, a common set of well-defined data formats is needed. Unfortunately, current bioinformatic tools use a great variety of heterogeneous formats. Results Acknowledging the need for common formats, the Helmholtz Open BioInformatics Technology network (HOBIT) identified several basic data types used in bioinformatics and developed appropriate format descriptions, formally defined by XML schemas, and incorporated them in a Java library (BioDOM). These schemas currently cover sequence, sequence alignment, RNA secondary structure and RNA secondary structure alignment formats in a form that is independent of any specific program, thus enabling seamless interoperation of different tools. All XML formats are available at , the BioDOM library can be obtained at . Conclusion The HOBIT XML schemas and the BioDOM library simplify adding XML support to newly created and existing bioinformatic tools, enabling these tools to interoperate seamlessly in workflow scenarios. PMID:17087823

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

    DEFF Research Database (Denmark)

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

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

  8. 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…

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

    Science.gov (United States)

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

    2006-01-01

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

  10. 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

  11. The growing need for microservices in bioinformatics.

    Science.gov (United States)

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

    2016-01-01

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

  12. The growing need for microservices in bioinformatics

    Science.gov (United States)

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

    2016-01-01

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

  13. A Systematic Review of Life Skill Development Through Sports Programs Serving Socially Vulnerable Youth

    NARCIS (Netherlands)

    Hermens, Niels; Super, Sabina; Verkooijen, Kirsten T.; Koelen, Maria A.

    2017-01-01

    Despite the strong belief in sports programs as a setting in which socially vulnerable youth can develop life skills, no overview exists of life skill development in sports programs serving this youth group. Therefore, the present systematic review provides an overview of the evidence on life skill

  14. Concrete Steps for Assessing the "Soft Skills" in an MBA Program

    Science.gov (United States)

    Ingols, Cynthia; Shapiro, Mary

    2014-01-01

    In 2006, our School of Management began the serious path of assessing both the "hard skills" (such as accounting, finance, and strategy) and the "soft skills" (such as leadership, team work, and ethics) of our MBA Program. The data generated from examining the "soft skills" that we want students to learn within our…

  15. An Open-Source Sandbox for Increasing the Accessibility of Functional Programming to the Bioinformatics and Scientific Communities.

    Science.gov (United States)

    Fenwick, Matthew; Sesanker, Colbert; Schiller, Martin R; Ellis, Heidi Jc; Hinman, M Lee; Vyas, Jay; Gryk, Michael R

    2012-01-01

    Scientists are continually faced with the need to express complex mathematical notions in code. The renaissance of functional languages such as LISP and Haskell is often credited to their ability to implement complex data operations and mathematical constructs in an expressive and natural idiom. The slow adoption of functional computing in the scientific community does not, however, reflect the congeniality of these fields. Unfortunately, the learning curve for adoption of functional programming techniques is steeper than that for more traditional languages in the scientific community, such as Python and Java, and this is partially due to the relative sparseness of available learning resources. To fill this gap, we demonstrate and provide applied, scientifically substantial examples of functional programming, We present a multi-language source-code repository for software integration and algorithm development, which generally focuses on the fields of machine learning, data processing, bioinformatics. We encourage scientists who are interested in learning the basics of functional programming to adopt, reuse, and learn from these examples. The source code is available at: https://github.com/CONNJUR/CONNJUR-Sandbox (see also http://www.connjur.org).

  16. 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.

  17. 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.

  18. PENGEMBANGAN MODEL PENDIDIKAN SOFT SKILL MELALUI PEMBELAJARAN PADA PROGRAM STUDI PENDIDIKAN TEKNIK MESIN FT UM

    Directory of Open Access Journals (Sweden)

    Dwi Agus Sudjimat

    2012-08-01

    Full Text Available The purpose of this research was to develop the soft skill education model at the Mechanical Engineering Education Study Program, State University of Malang included the curriculum and its implementation on the instructional activities. The research found that: (1 the soft skill curriculum needed by the Mechanical Engi­neering Education Study Program consists of fundamental skill, personal skill, and social skill; and (2 for implementing the soft skill curriculum entire the instructional activities strive for each lecture to take one or more soft skills statement for development, using the various strategies/methods of teaching refer to student-centered, giving tasks, and introducing the HES (Health and Environment Safety particularly in the practicum activities. Tujuan penelitian ini adalah untuk mengembangkan model pendidikan soft skill pada Program Studi Teknik Mesin Universitas Negeri Malang termasuk kuriku­lum dan implementasinya dalam kegiatan pembelajaran. Temuan penelitian ini adalah: (1 kurikulum soft skill yang diperlukan oleh Program Studi Teknik Mesin terdiri dari keterampilan dasar, keterampilan pribadi, dan keterampilan sosial, dan (2 menerap­kan kurikulum soft skill dalam pembelajaran pada masing-masing dasar, mengambil satu atau lebih soft skill untuk dikembangkan, menggunakan berbagai strategi/metode pengajaran berpusat pada mahasiswa, memberikan tugas, dan memperkenalkan K3 (Kesehatan dan Keselamatan Kerja, terutama dalam kegiatan praktikum.

  19. 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.

  20. Testing Algorithmic Skills in Traditional and Non-Traditional Programming Environments

    Science.gov (United States)

    Csernoch, Mária; Biró, Piroska; Máth, János; Abari, Kálmán

    2015-01-01

    The Testing Algorithmic and Application Skills (TAaAS) project was launched in the 2011/2012 academic year to test first year students of Informatics, focusing on their algorithmic skills in traditional and non-traditional programming environments, and on the transference of their knowledge of Informatics from secondary to tertiary education. The…

  1. 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...

  2. Implementation of the thinking skills for work program in a psychosocial clubhouse.

    Science.gov (United States)

    McGurk, Susan R; Schiano, Diane; Mueser, Kim T; Wolfe, Rosemarie

    2010-01-01

    Cognitive remediation programs aimed at improving role functioning have been implemented in a variety of different mental health treatment settings, but not in psychosocial clubhouses. This study sought to determine the feasibility and preliminary outcomes of providing a cognitive remediation program (the Thinking Skills for Work program), developed and previously implemented in supported employment programs at mental health agencies, in a psychosocial club-house. Twenty-three members with a history of difficulties getting or keeping jobs, who were participating in a supported employment program at a psychosocial clubhouse, were enrolled in the Thinking Skills for Work program. A neurocognitive battery was administered at baseline and 3 months later after completion of the computer cognitive training component of the program. Hours of competitive work were tracked for the 2 years before enrollment and 2 years following enrollment. Other work-related activities (school, volunteer) were also tracked for 2 years following enrollment. Twenty-one members (91%) completed 6 or more computer cognitive training sessions. Participants demonstrated significant improvements on neurocognitive measures of processing speed, verbal learning and memory, and executive functions. Sixty percent of the members obtained a competitive job during the 2-year follow-up, and 74% were involved in some type of work-related activity. Participants worked significantly more competitive hours over the 2 years after joining the Thinking Skills for Work program than before. The findings support the feasibility and promise of implementing the Thinking Skills for Work program in the context of supported employment provided at psychosocial clubhouses.

  3. Predicting Treatment Success in Social Skills Training for Adolescents with Autism Spectrum Disorders: The UCLA Program for the Education and Enrichment of Relational Skills

    Science.gov (United States)

    Chang, Ya-Chih; Laugeson, Elizabeth A.; Gantman, Alexander; Ellingsen, Ruth; Frankel, Fred; Dillon, Ashley R.

    2014-01-01

    This study seeks to examine the predictors of positive social skills outcomes from the University of California, Los Angeles Program for the Education and Enrichment of Relational Skills, an evidence-based parent-assisted social skills program for high-functioning middle school and high school adolescents with autism spectrum disorders. The…

  4. 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…

  5. What's Working: Program Factors Influencing California Community College Basic Skills Mathematics Students' Advancement to Transfer Level

    Science.gov (United States)

    Fiero, Diane M.

    2013-01-01

    Purpose: The purpose of this study was to determine which basic skills program factors were exhibited by successful basic skills programs that helped students advance to transfer-level mathematics. This study specifically examined California community college basic skills programs that assist students who place in mathematics courses 2 levels…

  6. 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.

  7. Evaluation of a Soft Skills Training Program

    Science.gov (United States)

    Charoensap-Kelly, Piyawan; Broussard, Lauren; Lindsly, Mallory; Troy, Megan

    2016-01-01

    This study was conducted to determine the effectiveness of a soft skills employee training program. We examined willingness to learn and delivery methods (face-to-face vs. online) and their associations with the training outcomes in terms of learning and behavioral change. Results showed that neither participants' willingness to learn nor delivery…

  8. 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.

  9. An Open-Source Sandbox for Increasing the Accessibility of Functional Programming to the Bioinformatics and Scientific Communities

    Science.gov (United States)

    Fenwick, Matthew; Sesanker, Colbert; Schiller, Martin R.; Ellis, Heidi JC; Hinman, M. Lee; Vyas, Jay; Gryk, Michael R.

    2012-01-01

    Scientists are continually faced with the need to express complex mathematical notions in code. The renaissance of functional languages such as LISP and Haskell is often credited to their ability to implement complex data operations and mathematical constructs in an expressive and natural idiom. The slow adoption of functional computing in the scientific community does not, however, reflect the congeniality of these fields. Unfortunately, the learning curve for adoption of functional programming techniques is steeper than that for more traditional languages in the scientific community, such as Python and Java, and this is partially due to the relative sparseness of available learning resources. To fill this gap, we demonstrate and provide applied, scientifically substantial examples of functional programming, We present a multi-language source-code repository for software integration and algorithm development, which generally focuses on the fields of machine learning, data processing, bioinformatics. We encourage scientists who are interested in learning the basics of functional programming to adopt, reuse, and learn from these examples. The source code is available at: https://github.com/CONNJUR/CONNJUR-Sandbox (see also http://www.connjur.org). PMID:25328913

  10. The essential skills required by librarians to support medical virtual learning programs.

    Science.gov (United States)

    Soleymani, Mohammad Reza; Akbari, Zahra; Mojiri, Shahin

    2016-01-01

    Background: With the recent spread of virtual learning programs in universities, especially in the field of medical sciences, libraries play a crucial role to support these programs. This study aimed at investigating the skills required by librarians to support virtual learning programs in Isfahan University and Isfahan University of Medical Sciences. Methods: This was an applied survey study. The population of the study includes all librarians working in Isfahan University and Isfahan University of Medical Sciences. A sample of 89 librarians was selected by stratified random sampling. Data were collected by a researcher-made questionnaire, the validity of which was confirmed by specialists in the fields of librarianship and information sciences and virtual learning, and its reliability was determined to be 0.92, using Cronbach's Alpha. The questionnaire consisted of 51 items designed to evaluate the librarians' virtual learning skills using Likert scale. Descriptive and inferential statistics were used to analyze the findings. Results: The findings of this study revealed that librarians had low level of skills with respect to the online reference services, and familiarity with virtual learning environment. They also showed low and average level of skills with respect to their general information technology, communication skills, ability to teach electronic information literacy and ability to create access to electronic resources. The results revealed no significant difference between the librarians of the two universities, or between male and female librarians. However, librarians with educational background in librarianship and information sciences were significantly more skillful and competent than their colleagues. Conclusion: Despite the crucial role of libraries in supporting virtual learning programs, the librarians in Isfahan University and Isfahan University of Medical Sciences had low-level skills to play such an important role. Therefore, it is essential

  11. A Qualitative Evaluation of Student Learning and Skills Use in a School-Based Mindfulness and Yoga Program.

    Science.gov (United States)

    Dariotis, Jacinda K; Mirabal-Beltran, Roxanne; Cluxton-Keller, Fallon; Gould, Laura Feagans; Greenberg, Mark T; Mendelson, Tamar

    2016-02-01

    Previous studies on school-based mindfulness and yoga programs have focused primarily on quantitative measurement of program outcomes. This study used qualitative data to investigate program content and skills that students remembered and applied in their daily lives. Data were gathered following a 16-week mindfulness and yoga intervention delivered at three urban schools by a community non-profit organization. We conducted focus groups and interviews with nine classroom teachers who did not participate in the program and held six focus groups with 22 fifth and sixth grade program participants. This study addresses two primary research questions: (1) What skills did students learn, retain, and utilize outside the program? and (2) What changes did classroom teachers expect and observe among program recipients? Four major themes related to skill learning and application emerged as follows: (1) youths retained and utilized program skills involving breath work and poses; (2) knowledge about health benefits of these techniques promoted self-utilization and sharing of skills; (3) youths developed keener emotional appraisal that, coupled with new and improved emotional regulation skills, helped de-escalate negative emotions, promote calm, and reduce stress; and (4) youths and teachers reported realistic and optimistic expectations for future impact of acquired program skills. We discuss implications of these findings for guiding future research and practice.

  12. Life lessons after classes: investigating the influence of an afterschool sport program on adolescents’ life skills development

    Science.gov (United States)

    Lee, Okseon; Park, Mirim; Jang, Kyunghwan; Park, Yongnam

    2017-01-01

    ABSTRACT The purpose of this study was to investigate the influence of an afterschool sport program on adolescents’ life skills development and to identify which characteristics of the program would have an influence on their life skills acquisition. The participants were six children (4 boys, 2 girls) who participated in a 12-week afterschool program implemented in two elementary schools, as well as the two program instructors who implemented the afterschool sport program. Data were collected from individual interviews with program participants and instructors. The inductive analysis of data revealed four categories of life skills developed through program participation: (1) playing well and being more active, (2) connecting well and having better social skills, (3) coping well and becoming a better problem solver, and (4) dreaming well and having a better sense of purpose. Regarding the characteristics of the program that influenced life skills development, three themes emerged: (1) having a clear goal and building consensus with stakeholders, (2) establishing a firm yet flexible structure, and (3) instructors’ use of effective strategies for teaching life skills. PMID:28367697

  13. Life lessons after classes: investigating the influence of an afterschool sport program on adolescents' life skills development.

    Science.gov (United States)

    Lee, Okseon; Park, Mirim; Jang, Kyunghwan; Park, Yongnam

    2017-12-01

    The purpose of this study was to investigate the influence of an afterschool sport program on adolescents' life skills development and to identify which characteristics of the program would have an influence on their life skills acquisition. The participants were six children (4 boys, 2 girls) who participated in a 12-week afterschool program implemented in two elementary schools, as well as the two program instructors who implemented the afterschool sport program. Data were collected from individual interviews with program participants and instructors. The inductive analysis of data revealed four categories of life skills developed through program participation: (1) playing well and being more active, (2) connecting well and having better social skills, (3) coping well and becoming a better problem solver, and (4) dreaming well and having a better sense of purpose. Regarding the characteristics of the program that influenced life skills development, three themes emerged: (1) having a clear goal and building consensus with stakeholders, (2) establishing a firm yet flexible structure, and (3) instructors' use of effective strategies for teaching life skills.

  14. The Effect of In-Service Training of Computer Science Teachers on Scratch Programming Language Skills Using an Electronic Learning Platform on Programming Skills and the Attitudes towards Teaching Programming

    Science.gov (United States)

    Alkaria, Ahmed; Alhassan, Riyadh

    2017-01-01

    This study was conducted to examine the effect of in-service training of computer science teachers in Scratch language using an electronic learning platform on acquiring programming skills and attitudes towards teaching programming. The sample of this study consisted of 40 middle school computer science teachers. They were assigned into two…

  15. Bioinformatics for cancer immunotherapy target discovery

    DEFF Research Database (Denmark)

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

    2014-01-01

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

  16. Evaluation of a Music Therapy Social Skills Development Program for Youth with Limited Resources.

    Science.gov (United States)

    Pasiali, Varvara; Clark, Cherie

    2018-05-21

    Children living in low-resource communities are at risk for poorer socio-emotional development and academic performance. Emerging evidence supports use of group music therapy experiences to support social development through community afterschool programming. To examine the potential benefit of a music therapy social skills development program to improve social skills and academic performance of school-aged children with limited resources in an afterschool program. We used a single-group pre/post-test design, and recruited 20 students (11 females, 9 males), ages 5 to 11 years, from an afterschool program. The music therapy social skills program consisted of eight 50-minute sessions, and we measured social competence and antisocial behavior using the Home & Community Social Behavioral Scale (HCSBS; Merrell & Caldarella, 2008), and social skills, problem behaviors, and academic competence using the Social Skills Improvement System (SSIS; Gresham & Elliot, 2008a, 2008b). Only students who attended a minimum of six sessions (N = 14) were included in data analysis. Results showed no significant change in individual HBSC subscale scores; however, the total number of low-performance/high-risk skills significantly decreased. SSIS teacher results indicated significant improvement in communication, significant decrease of hyperactivity, autistic behavioral tendencies and overall problem behaviors, and marginal decreases in internalization. Parent ratings mirrored, in part, those of the teacher. Results indicated that music therapy has the potential of being an effective intervention for promoting social competence of school-aged children with limited resources, particularly in the areas of communication and low-performance/high-risk behaviors. Teaching skills through song lyrics and improvisation emerged as salient interventions.

  17. Preparing for the European Championships: A six-step mental skills training program in disability sports

    DEFF Research Database (Denmark)

    Larsen, Carsten Hvid

    2014-01-01

    with the woman's national goalball team in Denmark (high-performance athletes with visual impairment). The author provides a detailed description of six steps from initiation of the program, group sessions, and action plans, to on-court training and evaluation of the program across six months, and finishes......This article presents a case example and six-step mental-skills training program for high-performance athletes in disability sports. Starting out with a basic description about applied sport psychology in disability sports, the author proceeds to describe the mental skills training program...... with reviewing coach and player reflections on the application of the mental-skills training program....

  18. Ice Skating: Special Olympics Sports Skills Instructional Program.

    Science.gov (United States)

    Special Olympics, Inc., Washington, DC.

    One of seven booklets on Special Olympics Sports Skills Instructional Programs, this guide presents teaching suggestions for ice skating coaches working with mentally retarded persons. An overview section introduces the sport and considers ideas for effective teaching. Goals, objectives, and benefits are considered along with information on…

  19. Implementation of a new social skills training program for adults with intellectual disabilities

    Directory of Open Access Journals (Sweden)

    Fernanda Sequera Fernández

    2016-12-01

    Full Text Available The present study has the purpose to develop and apply a new training program in order to promote the use of social skills in a group of adults with intellectual disabilities. It contains a quasi-experimental methodological design to prove the program effectiveness. The sample used consists of 21 adults with intellectual disabilities, users of an occupational therapy day entity (10 persons participated in the program and 11 did not. The social skills were evaluated using an adjusted version of the Social Skills Scale Model of Gismero (2010. The outcomes of this study show a significant improvement in the overall score of the group included in the program in comparison with the rest of the group. Likewise, the group under the program obtained an increase in the scores within 5 out of 6 subscales evaluated. The identified improvements are key elements for the individual development of this group. The implications of the results are discussed.

  20. Implementing a Cardiac Skills Orientation and Simulation Program.

    Science.gov (United States)

    Hemingway, Maureen W; Osgood, Patrice; Mannion, Mildred

    2018-02-01

    Patients with cardiac morbidities admitted for cardiac surgical procedures require perioperative nurses with a high level of complex nursing skills. Orienting new cardiac team members takes commitment and perseverance in light of variable staffing levels, high-acuity patient populations, an active cardiac surgical schedule, and the unpredictability of scheduling patients undergoing cardiac transplantation. At an academic medical center in Boston, these issues presented opportunities to orient new staff members to the scrub person role, but hampered efforts to provide active learning opportunities in a safe environment. As a result, facility personnel created a program to increase new staff members' skills, confidence, and proficiency, while also increasing the number of staff members who were proficient at scrubbing complex cardiac procedures. To address the safe learning requirement, personnel designed a simulation program to provide scrubbing experience, decrease orientees' supervision time, and increase staff members' confidence in performing the scrub person role. © AORN, Inc, 2018.

  1. Why Choose This One? Factors in Scientists' Selection of Bioinformatics Tools

    Science.gov (United States)

    Bartlett, Joan C.; Ishimura, Yusuke; Kloda, Lorie A.

    2011-01-01

    Purpose: The objective was to identify and understand the factors involved in scientists' selection of preferred bioinformatics tools, such as databases of gene or protein sequence information (e.g., GenBank) or programs that manipulate and analyse biological data (e.g., BLAST). Methods: Eight scientists maintained research diaries for a two-week…

  2. A Systematic Review of Life Skill Development Through Sports Programs Serving Socially Vulnerable Youth

    NARCIS (Netherlands)

    Hermens, N.J.; Super, Sabina; verkooijen, kirsten; Koelen, Maria

    2017-01-01

    Purpose: Despite the strong belief in sports programs as a setting in which socially vulnerable youth can develop life skills, no overview exists of life skill development in sports programs serving this youth group. Therefore, the present systematic review provides an overview of the evidence on

  3. Ostomy Home Skills Program

    Medline Plus

    Full Text Available ... Overview The skills kit contains: A booklet with information on the operation, home skills such as emptying and changing a pouch, problem solving, and home management. A DVD with demonstration of each skill Stoma ...

  4. Ostomy Home Skills Program

    Medline Plus

    Full Text Available ... Medical Student Core Curriculum ACS/ASE Medical Student Simulation-Based Surgical Skills Curriculum Cancer Education Cancer Education ... Home Skills Kit supports patients with educational and simulation materials to learn and practice the skills needed ...

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

    Science.gov (United States)

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

    2005-12-01

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

  6. 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.

  7. Reinforcing Productivity in a Job-Skills Training Program for Unemployed Substance-Abusing Adults.

    Science.gov (United States)

    Subramaniam, Shrinidhi; Everly, Jeffrey J; Silverman, Kenneth

    2017-05-01

    Chronically unemployed adults may benefit from intensive job-skills training; however, training programs do not always reliably engage participants in mastering skills. This study examined effects of voucher reinforcement for performance on a job-skills training program in the therapeutic workplace. Participants were four unemployed, substance abusing adults who earned monetary vouchers for working on programs targeting typing skills. Participants were exposed to two payment conditions that differed in whether or not pay was dependent on performance in a within-subject reversal design. In the productivity-pay condition, participants earned $8.00 per hour for attending the workplace plus a bonus for performance. In the base-pay condition, participants were paid an hourly wage that was equivalent to the total hourly earnings from the previous productivity-pay condition. Participants completed less work on the typing programs in the base- than the productivity-pay condition, but the amount of time spent in the workroom and the accuracy and rate of typing were not affected by the pay manipulation. All participants reported preferring base pay over productivity pay. Explicit reinforcement of productivity maintains consistent work in training programs, but more aspects of productivity pay need to be refined for effective, efficient, and socially valid implementation with unemployed, substance-abusing adults.

  8. A Case Study of 21st Century Skills Programs and Practices

    Science.gov (United States)

    McLachlan, Kurt

    2012-01-01

    Skills, such as critical thinking, problem-solving, and innovation are necessary for the 21st Century. The economy and the forums of international business and globalization demand skilled workers. Some schools in the United States are producing such workers, however it is unclear the programs and practices these schools utilize. This study…

  9. Student Perceptions of the Importance of Employability Skill Provision in Business Undergraduate Programs

    Science.gov (United States)

    Jackson, Denise

    2013-01-01

    Studies examining student perceptions of employability skill development in business undergraduate programs are limited. Assurance of student buy-in is important to ensure learners engage with skill provision; to enable them to articulate their capabilities to potential employers; and to facilitate the transfer of acquired skills. The author…

  10. Transfer of communication skills to the workplace: impact of a 38-hour communication skills training program designed for radiotherapy teams.

    Science.gov (United States)

    Merckaert, Isabelle; Delevallez, France; Gibon, Anne-Sophie; Liénard, Aurore; Libert, Yves; Delvaux, Nicole; Marchal, Serge; Etienne, Anne-Marie; Bragard, Isabelle; Reynaert, Christine; Slachmuylder, Jean-Louis; Scalliet, Pierre; Van Houtte, Paul; Coucke, Philippe; Razavi, Darius

    2015-03-10

    This study assessed the efficacy of a 38-hour communication skills training program designed to train a multidisciplinary radiotherapy team. Four radiotherapy teams were randomly assigned to a training program or a waiting list. Assessments were scheduled at baseline and after training for the training group and at baseline and 4 months later for the waiting list group. Assessments included an audio recording of a radiotherapy planning session to assess team members' communication skills and expression of concerns of patients with breast cancer (analyzed with content analysis software) and an adapted European Organisation for Research and Treatment of Cancer satisfaction with care questionnaire completed by patients at the end of radiotherapy. Two hundred thirty-seven radiotherapy planning sessions were recorded. Compared with members of the untrained teams, members of the trained teams acquired, over time, more assessment skills (P = .003) and more supportive skills (P = .050) and provided more setting information (P = .010). Over time, patients interacting with members of the trained teams asked more open questions (P = .022), expressed more emotional words (P = .025), and exhibited a higher satisfaction level regarding nurses' interventions (P = .028). The 38-hour training program facilitated transfer of team member learned communication skills to the clinical practice and improved patients' satisfaction with care. © 2015 by American Society of Clinical Oncology.

  11. 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…

  12. Evaluation of a Life Skills Program for Women Inmates in Michigan.

    Science.gov (United States)

    Schram, Pamela J.; Morash, Merry

    2002-01-01

    Describes and evaluates a life skills program that focuses on addressing the special needs of female inmates. Analyses of pre- and post-test scores of program participants compared emotional empathy, self-esteem, coping resources, problem solving, parenting stress, employability, and well-being. Results suggest tat the program does address some of…

  13. 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.

  14. The Effectiveness of Social Skills Training Program via Peer Tutoring on Aggression Level

    Directory of Open Access Journals (Sweden)

    İsmail YELPAZE

    2015-12-01

    Full Text Available The purpose of this study was to investigate the effectiveness of social skills intervention program via peer tutoring on aggression level of secondary school students. The study was a semi-experimental model using experimental group with pre and post-tests. Eleven (eighth class students were selected to have skills for being peer helper. The population of this research consisted 56 secondary school students at Kahramanmaraş. In order to evaluate aggression level of students, Aggression Scale developed by Tuzgöl (1998 was used. . Additionally, a Personal Information Sheet developed by the researcher was used to record certain demographic variables. Researcher applied social skills invention program to 11 students (peer helpers for eight weeks. Later, peer helpers applied intervention program to selected 56 students as well. After application, last-test was applied to selected 56 students, again. To analyze the data collected, SPSS 15 for computer was used. Results of the research revealed that the social skill program via peer helping (peer guidance considerably decreased the level of aggression of students at secondary school students. Students’ aggression level differentiated according to their sex, but not their class levels. Results were discussed in the light of literature

  15. Initiating a Developmental Motor Skills Program for Identified Primary Students.

    Science.gov (United States)

    Harville, Valerie Terrill

    A physical education specialist at an elementary school in one of the fastest growing sections of the country developed and implemented a developmental motor skills program for primary school students. The program focused on: (1) developing a method of referring students for testing; (2) providing a specialized motor diagnostic test; (3) improving…

  16. An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics

    International Nuclear Information System (INIS)

    Taylor, Ronald C.

    2010-01-01

    Bioinformatics researchers are increasingly confronted with analysis of ultra large-scale data sets, a problem that will only increase at an alarming rate in coming years. Recent developments in open source software, that is, the Hadoop project and associated software, provide a foundation for scaling to petabyte scale data warehouses on Linux clusters, providing fault-tolerant parallelized analysis on such data using a programming style named MapReduce. An overview is given of the current usage within the bioinformatics community of Hadoop, a top-level Apache Software Foundation project, and of associated open source software projects. The concepts behind Hadoop and the associated HBase project are defined, and current bioinformatics software that employ Hadoop is described. The focus is on next-generation sequencing, as the leading application area to date.

  17. Toward an objective assessment of technical skills: a national survey of surgical program directors in Saudi Arabia.

    Science.gov (United States)

    Alkhayal, Abdullah; Aldhukair, Shahla; Alselaim, Nahar; Aldekhayel, Salah; Alhabdan, Sultan; Altaweel, Waleed; Magzoub, Mohi Elden; Zamakhshary, Mohammed

    2012-01-01

    After almost a decade of implementing competency-based programs in postgraduate training programs, the assessment of technical skills remains more subjective than objective. National data on the assessment of technical skills during surgical training are lacking. We conducted this study to document the assessment tools for technical skills currently used in different surgical specialties, their relationship with remediation, the recommended tools from the program directors' perspective, and program directors' attitudes toward the available objective tools to assess technical skills. This study was a cross-sectional survey of surgical program directors (PDs). The survey was initially developed using a focus group and was then sent to 116 PDs. The survey contains demographic information about the program, the objective assessment tools used, and the reason for not using assessment tools. The last section discusses the recommended tools to be used from the PDs' perspective and the PDs' attitude and motivation to apply these tools in each program. The associations between the responses to the assessment questions and remediation were statistically evaluated. Seventy-one (61%) participants responded. Of the respondents, 59% mentioned using only nonstandardized, subjective, direct observation for technical skills assessment. Sixty percent use only summative evaluation, whereas 15% perform only formative evaluations of their residents, and the remaining 22% conduct both summative and formative evaluations of their residents' technical skills. Operative portfolios are kept by 53% of programs. The percentage of programs with mechanisms for remediation is 29% (19 of 65). The survey showed that surgical training programs use different tools to assess surgical skills competency. Having a clear remediation mechanism was highly associated with reporting remediation, which reflects the capability to detect struggling residents. Surgical training leadership should invest more in

  18. French Speaking Skills of Grade 8 English Program Students. Research Report 82-08.

    Science.gov (United States)

    Wightman, Margaret

    The speaking skills of grade 8 students in a core French program in Ottawa were compared with the skills of grade 6 students enrolled in the core program. A total of 337 grade 8 students were given a French speaking test. Two-hundred and nine students had taken the test in grade 6. In general, the grade 8 students seemed prepared to express basic…

  19. Bioinformatics and Cancer

    Science.gov (United States)

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

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

    Science.gov (United States)

    Bloom, Mark

    2001-01-01

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

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

    Science.gov (United States)

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

    2008-01-01

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

  2. Clinical program leadership: skill requirements for contemporary leaders.

    Science.gov (United States)

    Spallina, Joseph M

    2002-01-01

    With knowledge of these leadership requirements and a shrinking base of experienced managers, healthcare organizations and professional societies have little choice in their approach to prepare for the leadership development challenges of the future. Organizations will focus leadership development, training, and continuing management education on integrating business tools and skills into clinical program management. The management requirements for clinical programs will continue to grow in complexity and the number of qualified managers will continue to diminish, New approaches to solving this shortage will evolve. Professional, forprofit companies, healthcare provider organizations, and academic programs will develop clinical program management training tracks. Organizations that create solutions to this management imperative will maintain their competitive edge in the challenging times that will greet the industry in the future.

  3. 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

  4. Fostering computational thinking skills with a tangible blocks programming environment

    OpenAIRE

    Turchi, T; Malizia, A

    2016-01-01

    Computational Thinking has recently returned into the limelight as an essential skill to have for both the general public and disciplines outside Computer Science. It encapsulates those thinking skills integral to solving complex problems using a computer, thus widely applicable in our technological society. Several public initiatives such as the Hour of Code successfully introduced it to millions of people of different ages and backgrounds, mostly using Blocks Programming Environments like S...

  5. Investigating the key factors in designing a communication skills program for medical students: A qualitative study.

    Science.gov (United States)

    Mahdi Hazavehei, Seyyed M; Karimi Moonaghi, Hossein; Moeini, Babak; Moghimbeigi, Abbas; Emadzadeh, Ali

    2015-11-01

    Medical students have a serious need to acquire communication skills with others. In many medical schools, special curriculums are developed to improve such skills. Effective training of communication skills requires expert curriculum design. The aim of this study was to explore the experiences and views of experts and stakeholders in order to design a suitable training program in communication skills for medical students. The content analysis approach was used in this qualitative study. Forty-three participants were selected from the faculty, nurses, physicians, residents, and medical students at Mashhad University of Medical Sciences using purposive sampling. The data were collected through focus group discussions and semi-structured interviews. To ensure the accuracy of the data, the criteria of credibility, transferability, dependability, and conformability were met. The data were analyzed by MAXQDA software using the Graneheim & Lundman model. The findings of this study consisted of two main themes, i.e., "The vast nature of the present communication skills training" and "administrative requirements of the training program regarding communication skills." The first theme included the educational needs of students, the problems associated with training people to have good communication skills, the importance of good communication skills in performing professional duties, communication skills and job requirements, the learning environment of communication skills, and the status of existing training programs for communication skills. Strategies and suitable methods for teaching communication skills and methods of evaluating the students in this regard also were obtained. The findings of this study were the elements required to design a proper and local model to teach communication skills to medical students through analyzing the concepts of effective communication. The results of this study can be useful for medical faculties in designing a proper program for

  6. Investigating the key factors in designing a communication skills program for medical students: A qualitative study

    Science.gov (United States)

    Mahdi Hazavehei, Seyyed M.; Moonaghi, Hossein Karimi; Moeini, Babak; Moghimbeigi, Abbas; Emadzadeh, Ali

    2015-01-01

    Introduction Medical students have a serious need to acquire communication skills with others. In many medical schools, special curriculums are developed to improve such skills. Effective training of communication skills requires expert curriculum design. The aim of this study was to explore the experiences and views of experts and stakeholders in order to design a suitable training program in communication skills for medical students. Methods The content analysis approach was used in this qualitative study. Forty-three participants were selected from the faculty, nurses, physicians, residents, and medical students at Mashhad University of Medical Sciences using purposive sampling. The data were collected through focus group discussions and semi-structured interviews. To ensure the accuracy of the data, the criteria of credibility, transferability, dependability, and conformability were met. The data were analyzed by MAXQDA software using the Graneheim & Lundman model. Results The findings of this study consisted of two main themes, i.e., “The vast nature of the present communication skills training” and “administrative requirements of the training program regarding communication skills.” The first theme included the educational needs of students, the problems associated with training people to have good communication skills, the importance of good communication skills in performing professional duties, communication skills and job requirements, the learning environment of communication skills, and the status of existing training programs for communication skills. Strategies and suitable methods for teaching communication skills and methods of evaluating the students in this regard also were obtained. Conclusion The findings of this study were the elements required to design a proper and local model to teach communication skills to medical students through analyzing the concepts of effective communication. The results of this study can be useful for medical

  7. 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.

  8. Application of machine learning methods in bioinformatics

    Science.gov (United States)

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

    2018-05-01

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

  9. A retrospective study of past graduates of a residential life skills program for youth with physical disabilities.

    Science.gov (United States)

    Kingsnorth, S; King, G; McPherson, A; Jones-Galley, K

    2015-05-01

    Young people with physical disabilities experience issues regarding employment, schooling, independent living and establishing meaningful personal relationships. A lack of life skills has been recognized as an important factor contributing to this lag. The Independence Program (TIP) is a short-term residential life skills program that aims to equip youth with the foundational life skills required to assume adult roles. This study retrospectively examined the achievements, skills acquired and program attributions of youth and young adults who took part in this three-week immersive teen independence program over a 20-year period. A total of 162 past graduates were invited to take part, with 78 doing so (a 48% response rate). These past graduates completed an online survey assessing objective outcomes such as employment and independent living; subjective outcomes such as feeling in control and living meaningful lives; and reflections on skills acquired, opportunities experienced and attributions to TIP. The majority of respondents were female (71%), had a diagnosis of cerebral palsy (55%) and ranged from 20 to 35 years of age (92%). Despite a range of outcomes related to the achievement of adult roles, high levels of life satisfaction and overall quality of life were reported. Nearly every respondent reported using the skills they learned at the program in their lives afterwards and a high percentage attributed the acquisition and consolidation of core life skills to participating in this intensive immersive program. Although causality cannot be assumed, respondents reflected very positively on the opportunities provided by TIP to develop their independent living and life skills, extend their social networks and understand their strengths and weaknesses. Such findings validate the importance of targeted skill development to assist young people with physical disabilities in attaining their life goals and encourage focused investigations of key features in program

  10. Empowering adolescents with life skills education in schools - School mental health program: Does it work?

    Science.gov (United States)

    Srikala, Bharath; Kishore, Kumar K V

    2010-10-01

    Mental Health Promotion among adolescents in schools using life skills education (LSE) and teachers as life skill educators is a novel idea. Implementation and impact of the NIMHANS model of life skills education program studied. The impact of the program is evaluated at the end of 1 year in 605 adolescents from two secondary schools in comparison to 423 age, sex, socioeconomic status-matched adolescents from nearby schools not in the program. The adolescents in the program had significantly better self-esteem (P=0.002), perceived adequate coping (P=0.000), better adjustment generally (P=0.000), specifically with teachers (P=0.000), in school (P=0.001), and prosocial behavior (P=0.001). There was no difference between the two groups in psychopathology (P - and adjustment at home and with peers (P=0.088 and 0.921). Randomly selected 100 life skill educator-teachers also perceived positive changes in the students in the program in class room behavior and interaction. LSE integrated into the school mental health program using available resources of schools and teachers is seen as an effective way of empowering adolescents.

  11. Improving Reading Comprehension Skills through the SCRATCH Program

    Science.gov (United States)

    Papatga, Erdal; Ersoy, Ali

    2016-01-01

    The aim of this study was to reveal how reading comprehension skills of elementary fourth graders who have problems in reading comprehension can be improved by means of the SCRATCH program. The study was designed as a participant action research. It was carried out within a 15- week process at an elementary school with middle socio-economic level…

  12. Teaching citizen science skills online: Implications for invasive species training programs

    Science.gov (United States)

    Newman, G.; Crall, A.; Laituri, M.; Graham, J.; Stohlgren, T.; Moore, J.C.; Kodrich, K.; Holfelder, K.A.

    2010-01-01

    Citizen science programs are emerging as an efficient way to increase data collection and help monitor invasive species. Effective invasive species monitoring requires rigid data quality assurances if expensive control efforts are to be guided by volunteer data. To achieve data quality, effective online training is needed to improve field skills and reach large numbers of remote sentinel volunteers critical to early detection and rapid response. The authors evaluated the effectiveness of online static and multimedia tutorials to teach citizen science volunteers (n = 54) how to identify invasive plants; establish monitoring plots; measure percent cover; and use Global Positioning System (GPS) units. Participants trained using static and multimedia tutorials provided less (p plant cover estimates between static (??10%) and multimedia (??13%) participants did not differ (p =.86 and.08, respectively) from those of professionals (??9%). Trained volunteers struggled with plot setup and GPS skills. Overall, the online approach used did not influence conferred field skills and abilities. Traditional or multimedia online training augmented with more rigorous, repeated, and hands-on, in-person training in specialized skills required for more difficult tasks will likely improve volunteer abilities, data quality, and overall program effectiveness. ?? Taylor & Francis Group, LLC.

  13. 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...

  14. Feasibility of a skills-based substance abuse prevention program following traumatic brain injury.

    Science.gov (United States)

    Vungkhanching, Martha; Heinemann, Allen W; Langley, Mervin J; Ridgely, Mary; Kramer, Karen M

    2007-01-01

    To demonstrate the feasibility of a skills-based substance abuse prevention counseling program in a community setting for adults who sustained traumatic brain injury. Convenience sample of 117 participants (mean age=35 years) with preinjury history of alcohol or other drug use. Intervention group participants (n=36) from 3 vocational rehabilitation programs; a no-intervention comparison group (n=81) from an outpatient rehabilitation service. 12 individual counseling sessions featuring skills-based intervention. Changes in self-reported alcohol and other drug use, coping skillfulness, affect, and employment status from baseline to 9 months postintervention. Significant differences were noted at baseline for the intervention and comparison groups on ethnicity, time postinjury, marital status, and employment (Pcoping skillfulness (Pskills-based intervention provides a promising approach to promoting abstinence from all substances and increasing readiness for employment for adults with traumatic brain injuries in outpatient settings.

  15. Residential immersive life skills programs for youth with disabilities: service providers' perceptions of change processes.

    Science.gov (United States)

    King, Gillian; McPherson, Amy; Kingsnorth, Shauna; Stewart, Debra; Glencross-Eimantas, Tanya; Jones-Galley, Kimberlea; Morrison, Andrea; Isihi, Ana Maria; Gorter, Jan Willem

    2015-05-01

    Residential immersive life skills (RILS) programs are designed to equip youth with physical disabilities with the foundational life skills required to assume adult roles. The objective was to determine RILS service providers' perceptions of the active ingredients of the intervention change process. Thirty-seven service providers from various disciplines completed measures to assess expertise status and participated in qualitative interviews. Qualitative themes were derived, and similarities and differences in themes were identified for blinded groups of novices, intermediates, and experts. The three main themes, reflecting change processes, were: (a) creating a supportive program atmosphere with multiple opportunities for learning, (b) using strategies to support, encourage, and engage youth, and (c) intentionally fostering youth experiences of skill development, social interaction, and pride in accomplishment. In contrast to the novices, experts displayed a more holistic perspective and paid attention to higher-order issues such as providing opportunities and enabling youth. The findings indicate how RILS service providers work to create a program atmosphere and employ strategies to intentionally foster particular youth experiences. The findings explicate service providers' theories of practice, the intentional design of RILS program environments to bring about client change, and the value of service provider expertise. Implications for Rehabilitation Service providers of youth independence-oriented life skills programs can intentionally create a learning-oriented and supportive program atmosphere by using non-directive, coaching/guiding, and engagement strategies Youth experiences of skill development, shared experience with others, and pride in accomplishment can be cultivated by providing a range of learning opportunities, including choice making, problem-solving, and skill mastery Compared to more novice service providers, experts discussed managing the

  16. Empirical Studies of Agile Software Development to Learn Programming Skills

    Directory of Open Access Journals (Sweden)

    Yasuyo Kofune

    2014-06-01

    Full Text Available This paper presents a programming education support method based on Agile Development that encourages and builds on communication between students. Through mutual discussion, students using our approach transform their ideas into software and cooperate to write a program. The students complete the software through repetition and programming. Before completing the software program, the students learn to solve problems by working together. The students are encouraged to think and share ideas, and gain experience writing software. With this approach, students not only learn how to write programs, but also increase their logical thinking, problem-solving, and communication skills.

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

    DEFF Research Database (Denmark)

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

    2012-01-01

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

  18. 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

  19. Ostomy Home Skills Program

    Medline Plus

    Full Text Available ... Surgical Skills for Exposure in Trauma Advanced Trauma Life Support Advanced Trauma Operative Management Basic Endovascular Skills for Trauma Disaster Management and Emergency ...

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

    Science.gov (United States)

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

    2010-11-01

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

  1. 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.

  2. Toward an objective assessment of technical skills: a national survey of surgical program directors in Saudi Arabia

    Directory of Open Access Journals (Sweden)

    Alkhayal A

    2012-10-01

    Full Text Available Abdullah Alkhayal,1 Shahla Aldhukair,2 Nahar Alselaim,1 Salah Aldekhayel,1 Sultan Alhabdan,1 Waleed Altaweel,3 Mohi Elden Magzoub,4 Mohammed Zamakhshary1,21Department of Surgery, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia; 2Public Health Section, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia; 3Urology Department, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia; 4Department of Medical Education, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi ArabiaBackground: After almost a decade of implementing competency-based programs in postgraduate training programs, the assessment of technical skills remains more subjective than objective. National data on the assessment of technical skills during surgical training are lacking. We conducted this study to document the assessment tools for technical skills currently used in different surgical specialties, their relationship with remediation, the recommended tools from the program directors’ perspective, and program directors’ attitudes toward the available objective tools to assess technical skills.Methods: This study was a cross-sectional survey of surgical program directors (PDs. The survey was initially developed using a focus group and was then sent to 116 PDs. The survey contains demographic information about the program, the objective assessment tools used, and the reason for not using assessment tools. The last section discusses the recommended tools to be used from the PDs’ perspective and the PDs’ attitude and motivation to apply these tools in each program. The associations between the responses to the assessment questions and remediation were statistically evaluated.Results: Seventy-one (61% participants responded. Of the respondents, 59% mentioned using only nonstandardized, subjective, direct observation for technical skills assessment. Sixty percent use only summative

  3. Biogem: an effective tool based approach for scaling up open source software development in bioinformatics

    NARCIS (Netherlands)

    Bonnal, R.J.P.; Smant, G.; Prins, J.C.P.

    2012-01-01

    Biogem provides a software development environment for the Ruby programming language, which encourages community-based software development for bioinformatics while lowering the barrier to entry and encouraging best practices. Biogem, with its targeted modular and decentralized approach, software

  4. School Physical Activity Programming and Gross Motor Skills in Children.

    Science.gov (United States)

    Burns, Ryan D; Fu, You; Hannon, James C; Brusseau, Timothy A

    2017-09-01

    We examined the effect of a comprehensive school physical activity program (CSPAP) on gross motor skills in children. Participants were 959 children (1st-6th grade; Mean age = 9.1 ± 1.5 years; 406 girls, 553 boys) recruited from 5 low-income schools receiving a year-long CSPAP intervention. Data were collected at the beginning of the school year and at a 36-week follow-up. Gross motor skills were assessed using the Test for Gross Motor Development (3rd ed.) (TGMD-3) instrument. Multi-level mixed effects models were employed to examine the effect of CSPAP on TGMD-3 scores, testing age and sex as effect modifiers and adjusting for clustering of observations within the data structure. There were statistically significant coefficients for time (β = 8.1, 95% CI [3.9, 12.3], p skills and ball skills sub-test scores. Children showed improved gross motor skill scores at the end of the 36-week CSPAP that were modified by age, as younger children displayed greater improvements in TGMD-3 scores compared to older children.

  5. Ostomy Home Skills Program

    Medline Plus

    Full Text Available ... skills such as emptying and changing a pouch, problem solving, and home management. A DVD with demonstration of each skill Stoma Practice Model Stoma supplies (measurement guide, marking ...

  6. FM POD: an evidence-based blended teaching skills program for rural preceptors.

    Science.gov (United States)

    Delver, Hilary; Jackson, Wesley; Lee, Sonya; Palacios, Mone

    2014-05-01

    The University of Calgary's Rural Integrated Community Clerkship anchors final-year medical student education in 9 months of family medicine. The purpose of this pilot study was to evaluate the Family Medicine Preceptor Online Development (FM POD) program, designed to meet the faculty development needs of rural preceptors facing challenges of geographical distribution and time constraints. The theoretically based program used a blended learning approach, beginning with a face-to-face workshop to strengthen participants' social presence during online interactions to follow. Asynchronous narrated presentations supplied foundational knowledge prior to facilitated synchronous web conferences, where participants shared experiences and co-constructed new knowledge. The program was evaluated using mixed methods, including surveys and focus group discussion. Evaluation tools generated data with high internal consistency reliability; focus group information substantiated and enriched the quantitative survey data. Participants enjoyed collaborating with colleagues and rated their learning experiences highly, reporting meaningful and statistically significant increases in mean comfort with all the precepting skills taught: giving effective feedback, using questions to teach, teaching communications skills, helping learners in difficulty, and making teaching time-efficient. All effect sizes were large. Increased comfort with distance learning technologies was a positive consequence. Results support the applicability of principles of social constructivism, experiential learning, and reflective learning in these participants. The program was highly rated and effectively increased participants' comfort with teaching skills, offering practical off-the-peg modular faculty development in basic teaching skills for distributed faculty. Participants appreciated the flexible delivery format, which course developers found readily adaptable for additional topics.

  7. Assessing Students' Structured Programming Skills with Java: The "Blue, Berry, and Blueberry" Assignment

    Science.gov (United States)

    Zhang, Xihui

    2010-01-01

    Java is an object-oriented programming language. From a software engineering perspective, object-oriented design and programming is used at the architectural design, and structured design and programming is used at the detailed design within methods. As such, structured programming skills are fundamental to more advanced object-oriented…

  8. Developing a strategy for computational lab skills training through Software and Data Carpentry: Experiences from the ELIXIR Pilot action

    NARCIS (Netherlands)

    Pawlik, A.; Gelder, C.W.G. van; Nenadic, A.; Palagi, P.M.; Korpelainen, E.; Lijnzaad, P.; Marek, D.; Sansone, S.A.; Hancock, J.; Goble, C.

    2017-01-01

    Quality training in computational skills for life scientists is essential to allow them to deliver robust, reproducible and cutting-edge research. A pan-European bioinformatics programme, ELIXIR, has adopted a well-established and progressive programme of computational lab and data skills training

  9. 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.

  10. FameLab: A Communication Skills-Building Program Disguised as an International Competition

    Science.gov (United States)

    Scalice, D.

    2015-12-01

    One of the key pieces of training missing from most graduate studies in science is skills-building in communication. Beyond the responsibility to share their work with the public, good communication skills enhance a scientist's career path, facilitating comprehension of their work by stakeholders and funders, as well as increasing the ability to collaborate interdisciplinarily. FameLab, an American Idol-style communication competition for early career scientists, helps fill this void, and provides an opportunity to pratice communication skills, with the coaching of professionals, in a safe space. The focus is on training and networking with like-minded scientists. NASA's Astrobiology Program has been implementing FameLab in the US since 2011, but over 25 countries take part globally. Come learn about this innovative program, what impact it's had on participants, and how you can get involved.

  11. Ostomy Home Skills Program

    Medline Plus

    Full Text Available ... kit contains: A booklet with information on the operation, home skills such as emptying and changing a pouch, problem solving, and home management. A DVD with demonstration of each skill Stoma ...

  12. Clinically speaking: A communication skills program for students from non-English speaking backgrounds.

    Science.gov (United States)

    Miguel, Caroline San; Rogan, Fran; Kilstoff, Kathleen; Brown, Di

    2006-09-01

    This paper reports on the design, delivery and evaluation of an innovative oral communication skills program for first year students in a Bachelor of Nursing degree at an Australian university. This program was introduced in 2004 to meet the needs of first year undergraduate students from non-English speaking backgrounds who had experienced difficulties with spoken English while on clinical placement. The program consisted of early identification of students in need of communication development, a series of classes incorporated into the degree program to address students' needs, followed by a clinical placement block. This paper describes the structure of the program, discusses some of the major problems encountered by students in the clinical setting and presents some of the teaching strategies used to address these problems. Evaluations of the program suggest that students' communication skills and confidence improved, resulting in a more positive clinical experience for the majority of students.

  13. Ostomy Home Skills Program

    Medline Plus

    Full Text Available ... Surgeon Specific Registry Trauma Education Trauma Education Trauma Education Advanced Surgical Skills for Exposure in Trauma Advanced Trauma Life Support Advanced Trauma Operative Management Basic Endovascular Skills for Trauma Disaster Management and Emergency ...

  14. Ostomy Home Skills Program

    Medline Plus

    Full Text Available ... Education Trauma Education Achieving Zero Preventable Deaths Trauma Systems Conference Advanced Surgical Skills for Exposure in Trauma Advanced Trauma Life Support Advanced Trauma Operative Management Basic Endovascular Skills for Trauma Disaster Management and ...

  15. Ostomy Home Skills Program

    Medline Plus

    Full Text Available ... Specific Registry Surgeon Specific Registry News and Updates Account Setup Resources and FAQs Features of the SSR ... Today Ostomy Home Skills Kit (login or create account first) Skills Kits Broadcast Rights for Hospitals Ostomy ...

  16. Implementation of laparoscopic hysterectomy: maintenance of skills after a mentorship program.

    Science.gov (United States)

    Twijnstra, A R H; Blikkendaal, M D; Kolkman, W; Smeets, M J G H; Rhemrev, J P T; Jansen, F W

    2010-01-01

    To evaluate the implementation and maintenance of advanced laparoscopic skills after a structured mentorship program in laparoscopic hysterectomy (LH). Cohort retrospective analysis of 104 successive LHs performed by two gynecologists during and after a mentorship program. LHs were compared for indication, patient characteristics and intraoperative characteristics. As a frame of reference, 94 LHs performed by the mentor were analyzed. With regard to indication, blood loss and adverse outcomes, both trainees performed LHs during their mentorship program comparable with the LHs performed by the mentor. The difference in mean operating time between trainees and mentor was not clinically significant. Both trainees progressed along a learning curve, while operating time remained statistically constant and comparable to that of the mentor. After completing the mentorship program, both gynecologists maintained their acquired skills as blood loss, adverse outcome rates and operating time were comparable with the results during their traineeship. A mentorship program is an effective and durable tool for implementing a new surgical procedure in a teaching hospital with respect to patient safety aspects, as indications, operating time and adverse outcome rates are comparable to those of the mentor in his own hospital during and after completing the mentorship program. Copyright © 2010 S. Karger AG, Basel.

  17. The Cafeteria Workers' Skills Enhancement Training Program. Performance Report.

    Science.gov (United States)

    Burt, Miriam

    A program was conducted by the Food and Beverage Workers Union in Washington, D.C., to provide workplace literacy classes for food service workers in the city's government agencies, universities, and museums. A curriculum for workplace literacy skills was developed, sites were selected, and students were recruited. From a target audience of…

  18. Ostomy Home Skills Program

    Medline Plus

    Full Text Available ... Workforce Trauma and EMS Cancer and Research Health Information Technology Scope of Practice Pediatric Issues Other Federal Legislative ... Overview The skills kit contains: A booklet with information on the ... and home management. A DVD with demonstration of each skill Stoma ...

  19. 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.

  20. Physical Activity into Socialization: A Movement-Based Social Skills Program for Children with Autism Spectrum Disorder

    Science.gov (United States)

    Lee, Jihyun; Vargo, Kristina K.

    2017-01-01

    Children with autism spectrum disorder (ASD) often exhibit deficits in social-communicative behaviors. Given the increased prevalence of children with ASD, programs designed to teach social-communicative behaviors are necessary. This article introduces a movement-based program that embeds social-skill components to improve the motor skills and…

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

    Science.gov (United States)

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

    2017-05-01

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

  2. Evidence-Based Social Skills Training for Adolescents with Autism Spectrum Disorders: The UCLA PEERS Program

    Science.gov (United States)

    Laugeson, Elizabeth A.; Frankel, Fred; Gantman, Alexander; Dillon, Ashley R.; Mogil, Catherine

    2012-01-01

    The present study examines the efficacy and durability of the PEERS Program, a parent-assisted social skills group intervention for high-functioning adolescents with ASD. Results indicate that teens receiving PEERS significantly improved their social skills knowledge, social responsiveness, and overall social skills in the areas of social…

  3. Improving Deficient Listening Skills in the Language Arts Program at the Middle Grades.

    Science.gov (United States)

    Alonso, Laura

    A project developed a program for improving deficient student-to-student listening skills. The targeted population consisted of 18 seventh-grade middle school students in a culturally diverse, lower middle class community in a near-western suburb of Chicago. The problem of deficient listening skills was evident through teacher observation and…

  4. Generalizable Skills in Individualized Vocational Program Planning for Special Needs Students.

    Science.gov (United States)

    Stodden, Robert A.; Boone, Rosalie

    1986-01-01

    The authors address planning issues and suggest methods of interagency cooperation, integration of generalizable skills in individualized educational planning/programming, developing goals and objectives, and using student assessment and evaluation information. (CT)

  5. Pharmacy resident-led student mentoring program: A focus on developing mentoring skills.

    Science.gov (United States)

    Howard, Meredith L; Steuber, Taylor D; Nisly, Sarah A; Wilhoite, Jessica; Saum, Lindsay

    2017-11-01

    Formalized mentoring programs are often credited for influencing professional development of mentees. Unfortunately, little information exists regarding advancement of mentoring skills. We report the development and evaluation of a program to cultivate mentoring skills in pharmacy residents. Advanced pharmacy practice experience students and pharmacy residents were contacted for program participation. Resident mentors were paired with a student mentee for the program. Mentors were provided resources and support throughout the program. Sessions were held to facilitate mentoring relationships and to discuss professional development topics. Pre- and post-perception surveys were administered to mentors to measure changes in mentoring comfort and ability. Only matched pre- and post-surveys were included for analysis. The program was held and evaluated over two separate academic years FINDINGS: Fifty-three residents mentored 54 students over two cycles of the program. Mentors' matched perception surveys (n = 26) reported increased comfort in mentoring (p effectiveness in provision of written and oral feedback (p = 0.004 and p = 0.013 respectively). Mentors also reported heightened belief that serving as a student mentor will be beneficial to their long-term career goals (p = 0.034). Overall, this formal resident-led student mentoring program improved resident comfort serving in a mentoring role. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. Effect of practical application of intimate relationship skills program in marital commitment of couples

    Directory of Open Access Journals (Sweden)

    Bahareh Chitsazzadeh Alaf

    2017-06-01

    Full Text Available Nowadays, due to the increasing rate of divorce and betrayals, the marital commitment has been concerned in marriage and family studies. The research aimed to evaluate the effect of Practical Application of Intimate Relationship Skills (PAIRS program in marital commitment of couples. The method was quasi-experimental and the design was pretest-posttest with a control group. The convenience sampling method was employed to choose 16 couples whose marital commitment score was below the mean in Isfahan, Iran. These couples were randomly assigned to the experimental and control groups (N=8 in each group. Data gathering was carried out using Adams and Jones dimensions of commitment inventory (DCI that was filled out by the members of both groups in the pretest stage. Then, the experimental group received the PAIRS training program in thirteen 90-minute sessions. 35 percent of the total variance belongs to the group membership due to the effectiveness of this educational program. This educational program attempts to make couples aware of themselves and their spouses, enhance, intimacy and empathy and develop effective relationship skills and problem-solving skills. The results demonstrated that the PAIRS program showed a positive effect on marital commitment. Hence, the PAIRS program can be employed to prevent divorce by increasing marital commitment in couples.

  7. bioalcidae, samjs and vcffilterjs: object-oriented formatters and filters for bioinformatics files.

    Science.gov (United States)

    Lindenbaum, Pierre; Redon, Richard

    2018-04-01

    Reformatting and filtering bioinformatics files are common tasks for bioinformaticians. Standard Linux tools and specific programs are usually used to perform such tasks but there is still a gap between using these tools and the programming interface of some existing libraries. In this study, we developed a set of tools namely bioalcidae, samjs and vcffilterjs that reformat or filter files using a JavaScript engine or a pure java expression and taking advantage of the java API for high-throughput sequencing data (htsjdk). https://github.com/lindenb/jvarkit. pierre.lindenbaum@univ-nantes.fr.

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

    Science.gov (United States)

    Diaz Acosta, B.

    2011-01-01

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

  9. The Effectiveness of Parents' Skills Training Program on Reducing Children's Behavior Problems

    Directory of Open Access Journals (Sweden)

    مریم نعمت‌اللهی

    2015-12-01

    Full Text Available Objectives: The aim of this research was to evaluate the effectiveness of parents' skill training program on reducing children's behavioral problems. Method: In an experimental study (pre-post-test, 4 primary schools were randomly selected from schools of Tehran. Two schools were randomly allocated into experimental group and two into control group. Experimental group (mothers of children aged 7-9 years received parents' skill training program for 8 weeks, two hours sessions. Parents' reports participating in the training program (n=30 mothers were compared with parents' reports of non-trained control group (n=31 mothers. Data were gathered using Child Behavior Checklist (CBCL and analyzed using covariance analyses. Results: There was a significant difference between the experimental and control group after the training. The experimental group reported a significant decrease in children's behavioral problems.

  10. Concepts and introduction to RNA bioinformatics

    DEFF Research Database (Denmark)

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

    2014-01-01

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

  11. Efficacy of a perceptual and visual-motor skill intervention program for students with dyslexia.

    Science.gov (United States)

    Fusco, Natália; Germano, Giseli Donadon; Capellini, Simone Aparecida

    2015-01-01

    To verify the efficacy of a perceptual and visual-motor skill intervention program for students with dyslexia. The participants were 20 students from third to fifth grade of a public elementary school in Marília, São Paulo, aged from 8 years to 11 years and 11 months, distributed into the following groups: Group I (GI; 10 students with developmental dyslexia) and Group II (GII; 10 students with good academic performance). A perceptual and visual-motor intervention program was applied, which comprised exercises for visual-motor coordination, visual discrimination, visual memory, visual-spatial relationship, shape constancy, sequential memory, visual figure-ground coordination, and visual closure. In pre- and post-testing situations, both groups were submitted to the Test of Visual-Perceptual Skills (TVPS-3), and the quality of handwriting was analyzed using the Dysgraphia Scale. The analyzed statistical results showed that both groups of students had dysgraphia in pretesting situation. In visual perceptual skills, GI presented a lower performance compared to GII, as well as in the quality of writing. After undergoing the intervention program, GI increased the average of correct answers in TVPS-3 and improved the quality of handwriting. The developed intervention program proved appropriate for being applied to students with dyslexia, and showed positive effects because it provided improved visual perception skills and quality of writing for students with developmental dyslexia.

  12. Enhancing medical students' communication skills: development and evaluation of an undergraduate training program

    Science.gov (United States)

    2012-01-01

    Background There is a relative lack of current research on the effects of specific communication training offered at the beginning of the medical degree program. The newly developed communication training "Basics and Practice in Communication Skills" was pilot tested in 2008 and expanded in the following year at the University Medical Centre Hamburg-Eppendorf in Germany. The goal was to promote and improve the communicative skills of participants and show the usefulness of an early offered intervention on patient-physician communication within the medical curriculum. Methods The students participating in the project and a comparison group of students from the standard degree program were surveyed at the beginning and end of the courses. The survey consisted of a self-assessment of their skills as well as a standardised expert rating and an evaluation of the modules by means of a questionnaire. Results Students who attended the communication skills course exhibited a considerable increase of communication skills in this newly developed training. It was also observed that students in the intervention group had a greater degree of self-assessed competence following training than the medical students in the comparison group. This finding is also reflected in the results from a standardised objective measure. Conclusions The empirical results of the study showed that the training enabled students to acquire specialised competence in communication through the course of a newly developed training program. These findings will be used to establish new communication training at the University Medical Centre Hamburg-Eppendorf. PMID:22443807

  13. Perceptions of Employees and Supervisors of a Skills Training Program

    Science.gov (United States)

    Calcavecchi, Lincoln Todd

    2018-01-01

    Organizational leaders know that training improves worker performance, but training is often initiated without considering employees' work task requirements. This instrumental case study was conducted to understand the perceptions of employees who completed a skills training program and those of supervisors. The conceptual framework was andragogy,…

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

    Science.gov (United States)

    He, Yongqun; Xiang, Zuoshuang

    2010-09-27

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

  15. Improving reading comprehension skills through the SCRATCH program

    Directory of Open Access Journals (Sweden)

    Erdal Papatga

    2016-09-01

    Full Text Available The aim of this study was to reveal how reading comprehension skills of elementary fourth graders who have problems in reading comprehension can be improved by means of the SCRATCH program. The study was designed as a participant action research. It was carried out within a 15-week process at an elementary school with middle socio-economic level in the Eskisehir province in the fall term of the 2015-2016 school year. The participants of the study were eight fourth graders who had problems in reading comprehension and were selected based on the criterion sampling method. Different data gathering tools were employed in different stages of the study. These were the Informal Reading Inventory, readability assessment rubric, participant selection form and identification forms for developmental level in reading comprehension for the quantitative data, and observation notes, a researcher diary, video recordings, teacher and student observation notes, and the projects the students prepared using the SCRATCH program for the qualitative data. In the study, the analysis of the quantitative data was done with correlation analysis, and Kendall W Test that shows inter-rater reliability. In addition, the identification forms for developmental level in reading comprehension were used to reveal the improvement in reading comprehension skills, and the Informal Reading Inventory was employed to score these forms. On the other hand, the qualitative data were analysed through the thematic analysis method, and MAXQDA was used for the analysis. As a result of the analyses, it was found that the reading level of the eight students who had problems in reading comprehension went up from the anxiety level to the instructional level in some forms, and even to the independent reading level in other forms; in other words, there was an improvement in the reading comprehension skills of all eight students.

  16. Comparing Effectiveness of New Training Program of Local Trainers of Community-Based Rehabilitation Program with the Current Program: A Knowledge, Attitude and Skills Study

    Directory of Open Access Journals (Sweden)

    Mohsen Iravani

    2011-10-01

    Full Text Available Objective: This research aimed at comparison effects of a new and current "training program for community rehabilitation workers of Community Based Rehabilitation", in enhancing their knowledge, attitude and skills. Materials & Methods: In this experimental field trial, a total number of 34 newly engaged local trainers in Lorestan province were divided randomly in two (16 and 18 peoplesinterventional groups based on geographical location of their work places Teaching methods were roll playing, problem solving, and learning by doing in new program and the booklets were revised in terms of fluency and a guideline booklet for trainers were added in this program but the teaching method was reading booklets and demonstration of the skills in current program. Knowledge, Attitude and Skills of trainees assessed just before and after the training course based on the material which were used for the training course. K.A.P. changes of two groups were compared by independent t-test, Mann Whitney, Wilcoxon & Chi square. Results: Mean knowledge and skills scores increments were remarkably more significant after attending new course than after passing the current course (P<0.001 and more rehabilitation workers who attending new course use practical guides in addition to verbal instructions to train disabled people and their families (P=0.028. There were no significant differences in attitude changes among the two groups. Conclusion: As trainees learned more by means of the new training course and the two courses were not so different in the resource allocation, substituting the new method to the current one should get consideration.

  17. A Group Motor Skills Program for Children with Coordination Difficulties: Effect on Fundamental Movement Skills and Physical Activity Participation.

    Science.gov (United States)

    Kane, Kyra J; Staples, Kerri L

    2016-01-01

    Children with coordination difficulties are at risk of low levels of physical activity (PA) participation. This intervention examined the effects of a multidisciplinary program that emphasized parent participation on motor skill performance and PA. Ten boys (5-7 years) completed a group program consisting of conditioning exercises and activities designed to address child-selected goals. Motor proficiency and PA participation were assessed before and after the program using the Test of Gross Motor Development (TGMD-2) and triaxial accelerometers, respectively. Rating scales captured child and parent perceptions of performance for each child's goals. TGMD-2 subtest raw scores, age equivalent and percentile scores improved, along with parent ratings of their child's performance. Six children reported skill improvements. On average, moderate to vigorous PA improved by 10 min per day although these gains were not significant. Time spent in sedentary activities was unchanged. None of the children met the Canadian PA and sedentary behaviour guidelines. The results support effectiveness of a group program to improve gross motor performance and levels of PA in children with coordination difficulties. Gains in both of these domains also have the potential to impact quality of life and reduce health risks associated with inactivity.

  18. Development and evaluation of a learner-centered educational summer camp program on soft skills for baccalaureate nursing students.

    Science.gov (United States)

    Lau, Ying; Wang, Wenru

    2014-01-01

    The objectives were to develop a learner-centered educational camp program for nursing students and to evaluate 4 areas of soft skills, communication ability, clinical interaction, interpersonal relationships, and social problem solving, before and after the program. The results showed that the summer camp program was effective in improving nursing students' soft skills.

  19. The Effect of Montessori Method Supported by Social Skills Training Program on Turkish Kindergarten Children's Skills of Understanding Feelings and Social Problem Solving

    Science.gov (United States)

    Kayili, Gökhan; Ari, Ramazan

    2016-01-01

    The current research was conducted with the purpose of analyzing the effect of Montessori method supported by Social Skills Training Program on kindergarten children's skills of understanding feelings and social problem solving. 53 children attending Ihsan Dogramaci Applied Nursery School affiliated to Selcuk University, Faculty of Health Sciences…

  20. 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 ...

  1. Effect of the essentials of critical care orientation (ECCO) program on the development of nurses' critical thinking skills.

    Science.gov (United States)

    Kaddoura, Mahmoud A

    2010-09-01

    It is essential for nurses to develop critical thinking skills to ensure their ability to provide safe and effective care to patients with complex and variable needs in ever-changing clinical environments. To date, very few studies have been conducted to examine how nursing orientation programs develop the critical thinking skills of novice critical care nurses. Strikingly, no research studies could be found about the American Association of Critical Care Nurses Essentials of Critical Care Orientation (ECCO) program and specifically its effect on the development of nurses' critical thinking skills. This study explored the perceptions of new graduate nurses regarding factors that helped to develop their critical thinking skills throughout their 6-month orientation program in the intensive care unit. A convenient non-probability sample of eight new graduates was selected from a hospital that used the ECCO program. Data were collected with demographic questionnaires and semi-structured interviews. An exploratory qualitative research method with content analysis was used to analyze the data. The study findings showed that new graduate nurses perceived that they developed critical thinking skills that improved throughout the orientation period, although there were some challenges in the ECCO program. This study provides data that could influence the development and implementation of future nursing orientation programs. Copyright 2010, SLACK Incorporated.

  2. Teaching communication skills in clinical settings: comparing two applications of a comprehensive program with standardized and real patients.

    Science.gov (United States)

    Carvalho, Irene P; Pais, Vanessa G; Silva, Filipa R; Martins, Raquel; Figueiredo-Braga, Margarida; Pedrosa, Raquel; Almeida, Susana S; Correia, Luís; Ribeiro-Silva, Raquel; Castro-Vale, Ivone; Teles, Ana; Mota-Cardoso, Rui

    2014-05-09

    Communication is important for the quality of clinical practice, and programs have been implemented to improve healthcare providers' communication skills. However, the consistency of programs teaching communication skills has received little attention, and debate exists about the application of acquired skills to real patients. This study inspects whether (1) results from a communication program are replicated with different samples, and (2) results with standardized patients apply to interviews with real patients. A structured, nine-month communication program was applied in two consecutive years to two different samples of healthcare professionals (25 in the first year, 20 in the second year). Results were assessed at four different points in time, each year, regarding participants' confidence levels (self-rated), basic communication skills in interviews with standardized patients, and basic communication skills in interviews with real patients. Data were analyzed using GLM Repeated-Measures procedures. Improvements were statistically significant in both years in all measures except in simulated patients' assessment of the 2008 group. Differences between the two samples were non-significant. Differences between interviews with standardized and with real patients were also non-significant. The program's positive outcomes were replicated in different samples, and acquired skills were successfully applied to real-patient interviews. This reinforces this type of program structure as a valuable training tool, with results translating into real situations. It also adds to the reliability of the assessment instruments employed, though these may need adaptation in the case of real patients.

  3. The Philosopher's Stone: How Basic Skills Programs Fare in Troubled Financial Times

    Science.gov (United States)

    Ray, Thomas P.

    2012-01-01

    This mixed methods study examined the relative position of basic skills programs with transfer and career technical programs in a large suburban community college in California during the three-year period of budget reductions from 2009-2010 through 2011-2012. The budget line dedicated to part-time or non-contract instruction was analyzed along…

  4. What skills should new internal medicine interns have in july? A national survey of internal medicine residency program directors.

    Science.gov (United States)

    Angus, Steven; Vu, T Robert; Halvorsen, Andrew J; Aiyer, Meenakshy; McKown, Kevin; Chmielewski, Amy F; McDonald, Furman S

    2014-03-01

    The transition from medical student to intern may cause stress and burnout in new interns and the delivery of suboptimal patient care. Despite a formal set of subinternship curriculum guidelines, program directors have expressed concern regarding the skill set of new interns and the lack of standardization in that skill set among interns from different medical schools. To address these issues, the Accreditation Council for Graduate Medical Education's Next Accreditation System focuses on the development of a competency-based education continuum spanning undergraduate, graduate, and continuing medical education. In 2010, the Clerkship Directors in Internal Medicine subinternship task force, in collaboration with the Association of Program Directors in Internal Medicine survey committee, surveyed internal medicine residency program directors to determine which competencies or skills they expected from new medical school graduates. The authors summarized the results using categories of interest. In both an item rank list and free-text responses, program directors were nearly uniform in ranking the skills they deemed most important for new interns-organization and time management and prioritization skills; effective communication skills; basic clinical skills; and knowing when to ask for assistance. Stakeholders should use the results of this survey as they develop a milestone-based curriculum for the fourth year of medical school and for the internal medicine subinternship. By doing so, they should develop a standardized set of skills that meet program directors' expectations, reduce the stress of transitions across the educational continuum, and improve the quality of patient care.

  5. Efficacy of the Social Skills Improvement System Classwide Intervention Program (SSIS-CIP) Primary Version

    Science.gov (United States)

    DiPerna, James Clyde; Lei, Puiwa; Bellinger, Jillian; Cheng, Weiyi

    2015-01-01

    A multisite cluster randomized trial was conducted to examine the effects of the Social Skills Improvement System Classwide Intervention Program (SSIS-CIP; Elliott & Gresham, 2007) on students' classroom social behavior. The final sample included 432 students across 38 second grade classrooms. Social skills and problem behaviors were measured…

  6. Communication Skills Training in Ophthalmology: Results of a Needs Assessment and Pilot Training Program.

    Science.gov (United States)

    Mishra, Anuradha; Browning, David; Haviland, Miriam J; Jackson, Mary Lou; Luff, Donna; Meyer, Elaine C; Talcott, Katherine; Kloek, Carolyn E

    To conduct a needs assessment to identify gaps in communication skills training in ophthalmology residency programs and to use these results to pilot a communication workshop that prepares residents for difficult conversations. A mixed-methods design was used to perform the needs assessment. A pre-and postsurvey was administered to workshop participants. Mass Eye and Ear Infirmary, Harvard Medical School (HMS), Department of Ophthalmology. HMS ophthalmology residents from postgraduate years 2-4 participated in the needs assessment and the workshop. Ophthalmology residency program directors in the United States participated in national needs assessment. Ophthalmology program directors across the United States were queried on their perception of resident communication skills training through an online survey. A targeted needs assessment in the form of a narrative exercise captured resident perspectives on communication in ophthalmology from HMS residents. A group of HMS residents participated in the pilot workshop and a pre- and postsurvey was administered to participants to assess its effectiveness. The survey of program directors yielded a response rate of 40%. Ninety percent of respondents agreed that the communication skills training in their programs could be improved. Fifteen of 24 residents (62%) completed the needs assessment. Qualitative analysis of the narrative material revealed four themes; (1) differing expectations, (2) work role and environment, (3) challenges specific to ophthalmology, and (4) successful strategies adopted. Nine residents participated in the workshop. There was a significant improvement post-workshop in resident reported scores on their ability to manage their emotions during difficult conversations (p = 0.03). There is an opportunity to improve communication skills training in ophthalmology residency through formalized curriculum. Copyright © 2017 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights

  7. How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications.

    Science.gov (United States)

    Khomtchouk, Bohdan B; Weitz, Edmund; Karp, Peter D; Wahlestedt, Claes

    2016-12-31

    We present a rationale for expanding the presence of the Lisp family of programming languages in bioinformatics and computational biology research. Put simply, Lisp-family languages enable programmers to more quickly write programs that run faster than in other languages. Languages such as Common Lisp, Scheme and Clojure facilitate the creation of powerful and flexible software that is required for complex and rapidly evolving domains like biology. We will point out several important key features that distinguish languages of the Lisp family from other programming languages, and we will explain how these features can aid researchers in becoming more productive and creating better code. We will also show how these features make these languages ideal tools for artificial intelligence and machine learning applications. We will specifically stress the advantages of domain-specific languages (DSLs): languages that are specialized to a particular area, and thus not only facilitate easier research problem formulation, but also aid in the establishment of standards and best programming practices as applied to the specific research field at hand. DSLs are particularly easy to build in Common Lisp, the most comprehensive Lisp dialect, which is commonly referred to as the 'programmable programming language'. We are convinced that Lisp grants programmers unprecedented power to build increasingly sophisticated artificial intelligence systems that may ultimately transform machine learning and artificial intelligence research in bioinformatics and computational biology. © The Author 2016. Published by Oxford University Press.

  8. BioWarehouse: a bioinformatics database warehouse toolkit.

    Science.gov (United States)

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

    2006-03-23

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

  9. Social skills to homosexuals: Program toward Inlusion

    Directory of Open Access Journals (Sweden)

    Yanais Gutiérrez Jorge

    2015-09-01

    Full Text Available Male homosexuality in Cuba has been se gregated by means of discrimination what , may hinde r the social interation of this people. The research has carried out problems with the self - esteem , the knowledge of the assertive rights, the preparation to confront the conflicts in the interpersonal rel ationships, the correct use of the extraverbal language and the capacity to vary and to sustain approaches depending on the circumstances . This investigation propose to carry out a Sociocultural Animation Program to develop social skills in 25 male homosex uals in our province as a way to get their social insertion .

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

    Directory of Open Access Journals (Sweden)

    Nora Khaldi

    2012-10-01

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

  11. Investigation of the Effect of Story-Based Social Skills Training Program on the Social Skill Development of 5-6 Year-Old Children

    Science.gov (United States)

    Pekdogan, Serpil

    2016-01-01

    The aim of this study is to investigate the effect of Story-Based Social Skills Training Program on the social skill development of 5-6 year-old children. In the study, the pre-test/post-test and retention test experimental design with a control group was used. 5-6 year-old 60 (30 experimental, 30 control) preschool children participated in the…

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

    Science.gov (United States)

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

    2009-01-01

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

  13. Application of Bioinformatics in Chronobiology Research

    Directory of Open Access Journals (Sweden)

    Robson da Silva Lopes

    2013-01-01

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

  14. Technical Skill Attainment and Post-Program Outcomes: An Analysis of Pennsylvania Secondary Career and Technical Education Graduates

    Science.gov (United States)

    Staklis, Sandra; Klein, Steven

    2010-01-01

    Since the mid-1990s, the Pennsylvania Department of Education (PDE) has required all students concentrating in career and technical education (CTE) programs to complete a standardized technical skill assessment at or near the end of their program. Results of technical skill assessments are used for a number of purposes, including recognizing…

  15. Effectiveness of a Self-Instruction Program for Microcounseling Skills Training

    Science.gov (United States)

    Schonrock-Adema, Johanna; Van der Molen, Henk T.; van der Zee, Karen I.

    2009-01-01

    This article describes the effects of self-instruction training (SIT) in microcounseling skills compared to those of a traditional trainer-guided program (TT) in a pretest-posttest comparison group design. A sample of 193 undergraduate psychology students participated in this study: 97 students followed SIT and 96 students followed TT. We used…

  16. Ostomy Home Skills Program

    Medline Plus

    Full Text Available ... Workforce Trauma and EMS Cancer and Research Health Information Technology Scope of Practice Pediatric Issues Other Federal Legislative Issues Regulatory Issues Regulatory Issues Regulatory Issues Stop Overregulating My OR ... Rectal Surgeons (ASCRS), American Urological Association (AUA), Certified Enterostomal Therapy Nurses (CETN), and the United Ostomy Associations of America (UOAA). The skills kit contains: A booklet with information on the operation, home skills such as emptying ...

  17. Interpersonal Skills Training: Evaluation of a Program with Adult Male Offenders.

    Science.gov (United States)

    Bornstein, Philip H.; And Others

    1979-01-01

    To assess the efficacy of an interpersonal skill training program, adult offenders were randomly assigned to either interpersonal effectiveness training or waiting-list control. Results indicated interpersonal effectiveness training group superiority on Interpersonal Behavior Role-Play Test training and generalization assessment items. Findings…

  18. Fundamental Movement Skills Development under the Influence of a Gymnastics Program and Everyday Physical Activity in Seven-Year-Old Children.

    Science.gov (United States)

    Culjak, Zoran; Miletic, Durdica; Kalinski, Suncica Delas; Kezic, Ana; Zuvela, Frane

    2014-04-01

    The objectives of this study were: a) to examine the influence of an 18-week basic artistic gymnastics program on fundamental movement skills (FMS) development in seven-year-old children; b) to determine correlations between children's daily activities and successful performance of FMS and basic artistic gymnastics skills. Seventy five first grade primary school children took part in this study. A physical education teacher specialized in artistic gymnastics conducted a gymnastics program for 18 weeks, three times a week. The level of gymnastics skills and FMS were identified at the beginning and at the end of the program. The level of gymnastics skills was evaluated by performance of eight artistic gymnastics skills, while FMS were evaluated by the use of FMS-polygon. Physical activity and inactivity was evaluated by using a proxy-questionnaire "Netherlands Physical Activity Questionnaire˝ (NPAQ). According to the dependent samples t test, significant differences were found in the FMS-polygon and all gymnastics skills before and after the 18-week gymnastics program. Increasing correlations were established over time between gymnastics skills and the FMS-polygon. Unorganized daily activity of children significantly correlated with their mastering of gymnastics skills and FMS. The presented findings confirm: (1) the thesis that basic artistic gymnastics skills and FMS could be developed simultaneously, (2) the theory of positive transfer of similar skills between FMS and artistic gymnastic skills. Mastering basic artistic gymnastics skills will provoke improvement of FMS and finally become a prerequisite for successful introduction of learning more complex gymnastics skills. The obtained results imply that an increase of children's unorganized daily activities can improve the mastering of basic gymnastics skills and simultaneously the development of FMS.

  19. Effects of an experiential learning program on the clinical reasoning and critical thinking skills of occupational therapy students.

    Science.gov (United States)

    Coker, Patty

    2010-01-01

    This study examined the effects of participation in a 1-week, experiential, hands-on learning program on the critical thinking and clinical reasoning skills of occupational therapy students. A quasi-experimental, nonrandomized pre- and post-test design was used with a sample of 25 students. The students had completed three semesters of didactic lecture coursework in a master's level OT educational program prior to participation in a hands-on therapy program for children with hemiplegic cerebral palsy. Changes in critical thinking and clinical reasoning skills were evaluated using the following dependent measures: Self-Assessment of Clinical Reflection and Reasoning (SACRR) and the California Critical Thinking Skills Test (CCTST). Changes in pretest and posttest scores on the SACRR and the CCTST were statistically significant (p>0.05) following completion of the experiential learning program. This study supports the use of hands-on learning to develop clinical reasoning and critical thinking skills in healthcare students, who face ever more diverse patient populations upon entry-level practice. Further qualitative and quantitative investigations are needed to support the results of this study and determine which components of experiential learning programs are essential for developing clinical reasoning and critical thinking skills in future allied health professionals.

  20. Preliminary Evaluation of a Practice-Based EBVM Skills Development Program

    Directory of Open Access Journals (Sweden)

    Ava Firth

    2016-12-01

    Full Text Available Whilst there is a small body of research that investigates the development of EBVM skills in veterinary undergraduates there is a paucity of research that aims to understand the development of EBVM skills in practice-based post-graduate veterinary surgeons. This paper is a small step in remedying that shortfall. In particular, the paper provides a progress report on an RCVS Knowledge funded study that is evaluating a practice-based EBVM development program. The program is being conducted with a cohort of 20 veterinary surgeons and veterinary nurses employed in a private practice veterinary company across multiple sites. The facilitated instruction approach incorporates multiple supports including; group based and one-to-one, synchronous and asynchronous, and, face-to-face and online strategies. This paper will provide details of both the facilitation and evaluation approaches that have been adopted. The paper will also report on preliminary results of the evaluation which focuses on barriers and facilitators to EBVM development.This is a podcast of Ava and Ian's talk at the Veterinary Evidence Today conference, Edinburgh November 2, 2016.

  1. Skate Genome Project: Cyber-Enabled Bioinformatics Collaboration

    Science.gov (United States)

    Vincent, J.

    2011-01-01

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

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

    International Nuclear Information System (INIS)

    Rezig, Slim; Sakhri, Saber

    2007-01-01

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

  3. BioWarehouse: a bioinformatics database warehouse toolkit

    Directory of Open Access Journals (Sweden)

    Stringer-Calvert David WJ

    2006-03-01

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

  4. 5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK--Setting the analysis frame.

    Science.gov (United States)

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

    2005-09-01

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

  5. Measures of Student Non-Cognitive Skills and Political Tolerance after Two Years of the Louisiana Scholarship Program. Louisiana Scholarship Program Evaluation Report #2. Technical Report

    Science.gov (United States)

    Mills, Jonathan N.; Cheng, Albert; Hitt, Collin E.; Wolf, Patrick J.; Greene, Jay P.

    2016-01-01

    This report examines the short-term effects of the Louisiana Scholarship Program (LSP) on students' non-cognitive skills and civic values. While a growing number of studies have evaluated K-12 school voucher programs along academic dimensions, few have focused on the development of non-cognitive skills and civic values. This study aims to address…

  6. Exploring the Impact of a Library Summer Reading Literacy Coach Program on Teen Personal Skills Development

    Directory of Open Access Journals (Sweden)

    Lina Zhao

    2012-09-01

    Full Text Available In the Summer of 2011 The Free Library of Philadelphia (FLP hired 90 teenagers into its six-week Summer Reading Literacy Coach Program (SRLCP as Teen Literacy Coaches (TLCs. Data was collected at Time 1, Time 2 and Time 3. The two study hypotheses were: (1 there will be a significant improvement in TLCs personal development skills from Time 1 to Time 3 and (2 demographic data and program specific skills measured at Time 2 will account for significant variance in each Time 3 personal development skill beyond the Time 1 personal development skills. We did not find support for H1 but did find support for H2. Specific to H2 we found that team-related and higher education interest each had a significant positive impact (p

  7. Skill improvement among coalition members in the California Healthy Cities and Communities Program.

    Science.gov (United States)

    Kegler, Michelle C; Norton, Barbara L; Aronson, Robert

    2007-06-01

    Community-driven, collaborative approaches to health promotion have the potential to enhance skills among community members and, in turn, increase community capacity. This study uses data from an evaluation of the California Healthy Cities and Communities (CHCC) Program to examine whether, and how, community problem-solving and collaboration skills are improved among coalition members and local coordinators in 20 participating communities. Methods include semi-structured interviews with coordinators and mailed surveys with coalition members (n=330 in planning phase and n=243 in implementation phase). The largest number of coordinators reported skill improvement in defining health broadly and assessing needs and assets. Similarly, coalition members reported greatest skill improvement for defining health broadly, assessing needs and assets and setting priorities and developing action plans. Modest correlations were observed between number of roles played in the local healthy cities and communities project and each skill area assessed. Time committed to the local CHCC coalition and its activities was not meaningfully correlated with any of the skills. Types of skill-building opportunities may be more important than number of hours devoted to meetings and activities in strengthening community problem-solving and collaboration skills among coalition members.

  8. ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR.

    Science.gov (United States)

    Larcombe, L; Hendricusdottir, R; Attwood, T K; Bacall, F; Beard, N; Bellis, L J; Dunn, W B; Hancock, J M; Nenadic, A; Orengo, C; Overduin, B; Sansone, S-A; Thurston, M; Viant, M R; Winder, C L; Goble, C A; Ponting, C P; Rustici, G

    2017-01-01

    ELIXIR-UK is the UK node of ELIXIR, the European infrastructure for life science data. Since its foundation in 2014, ELIXIR-UK has played a leading role in training both within the UK and in the ELIXIR Training Platform, which coordinates and delivers training across all ELIXIR members. ELIXIR-UK contributes to the Training Platform's coordination and supports the development of training to address key skill gaps amongst UK scientists. As part of this work it acts as a conduit for nationally-important bioinformatics training resources to promote their activities to the ELIXIR community. ELIXIR-UK also leads ELIXIR's flagship Training Portal, TeSS, which collects information about a diverse range of training and makes it easily accessible to the community. ELIXIR-UK also works with others to provide key digital skills training, partnering with the Software Sustainability Institute to provide Software Carpentry training to the ELIXIR community and to establish the Data Carpentry initiative, and taking a lead role amongst national stakeholders to deliver the StaTS project - a coordinated effort to drive engagement with training in statistics.

  9. Investigating the key factors in designing a communication skills program for medical students: A qualitative study

    OpenAIRE

    Mahdi Hazavehei, Seyyed M.; Moonaghi, Hossein Karimi; Moeini, Babak; Moghimbeigi, Abbas; Emadzadeh, Ali

    2015-01-01

    Introduction Medical students have a serious need to acquire communication skills with others. In many medical schools, special curriculums are developed to improve such skills. Effective training of communication skills requires expert curriculum design. The aim of this study was to explore the experiences and views of experts and stakeholders in order to design a suitable training program in communication skills for medical students. Methods The content analysis approach was used in this qu...

  10. 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…

  11. Formulating Employability Skills for Graduates of Public Health Study Program

    Science.gov (United States)

    Qomariyah, Nurul; Savitri, Titi; Hadianto, Tridjoko; Claramita, Mora

    2016-01-01

    Employability skills (ES) are important for effective and successful individual participation in the workplace. The main aims of the research were to identify important ES needed by graduates of Public Health Study Program Universitas Ahmad Dahlan (PHSP UAD) and to assess the achievement of the ES development that has been carried out by PHSP UAD.…

  12. Preparing Teens for Success: Building 21st Century Skills through a 4-H Work-Based Learning Program

    Directory of Open Access Journals (Sweden)

    Theresa M. Ferrari

    2008-06-01

    Full Text Available There is widespread concern that youth lack the skills essential for job success and are entering the workplace unprepared. To address issues of workforce preparation, Extension educators at an urban 4-H education center created the Job Experience and Training (JET program, a work-based learning program for teens. JET is conducted over a six-month period, culminating in an eight-week summer work experience in collaboration with a local park district. Supervisors and teens completed a performance appraisal measure based on SCANS workforce skills at two points during the program. Both teens and supervisors provided written comments addressing teens’ strengths and areas for growth, as well as comments on their satisfaction with the program itself. Overall, the experience appears to have produced improvements in teens’ workforce skills, as evidenced by their own self-assessment and that of their supervisors. We conclude with implications for conducting work-based learning programs.

  13. 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.

  14. Integrating critical Web skills and content knowledge: Development and evaluation of a 5th grade educational program

    NARCIS (Netherlands)

    Kuiper, E.; Volman, M.L.L.; Terwel, J.

    2008-01-01

    Although the Web is almost omnipresent in many children's lives, most children lack adequate Web searching skills as well as skills to process and critically evaluate Web information. In this article, we describe and evaluate an educational program that aimed at acquiring Web skills in the context

  15. 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 ...

  16. 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 ...

  17. Facilitating the implementation of the American College of Surgeons/Association of Program Directors in Surgery phase III skills curriculum: training faculty in the assessment of team skills.

    Science.gov (United States)

    Hull, Louise; Arora, Sonal; Stefanidis, Dimitrios; Sevdalis, Nick

    2015-11-01

    Effective teamwork is critical to safety in the operating room; however, implementation of phase III of the American College of Surgeons (ACS) and Association of Program Directors in Surgery (APDS) Curriculum that focuses on team-based skills remains worryingly low. Training and assessing the complexities of teamwork is challenging. The objective of this study was to establish guidelines and recommendations for training faculty in assessing/debriefing team skills. A multistage survey-based consensus study was completed by 108 experts responsible for training and assessing surgical residents from the ACS Accredited Educational Institutes. Experts agreed that a program to teach faculty to assess team-based skills should include training in the recognition of teamwork skills, practice rating these skills, and training in the provision of feedback/debriefing. Agreement was reached that faculty responsible for conducting team-based skills assessment should be revalidated every 2 years and stringent proficiency criteria should be met. Faculty development is critical to ensure high-quality, standardized training and assessment. Training faculty to assess team-based skills has the potential to facilitate the effective implementation of phase III of the ACS and APDS Curriculum. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. Adolescents' Development of Skills for Agency in Youth Programs: Learning to Think Strategically

    Science.gov (United States)

    Larson, Reed W.; Angus, Rachel M.

    2011-01-01

    This research examines how youth in arts and leadership programs develop skills for organizing actions over time to achieve goals. Ethnically diverse youth (ages 13-21) in 11 high-quality urban and rural programs were interviewed as they carried out projects. Qualitative analyses of 712 interviews with 108 youth yielded preliminary grounded theory…

  19. Mathematics and evolutionary biology make bioinformatics education comprehensible

    Science.gov (United States)

    Weisstein, Anton E.

    2013-01-01

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

  20. Mathematics and evolutionary biology make bioinformatics education comprehensible.

    Science.gov (United States)

    Jungck, John R; Weisstein, Anton E

    2013-09-01

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

  1. Bioinformatics of cardiovascular miRNA biology.

    Science.gov (United States)

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

    2015-12-01

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

  2. Feasibility and preliminary efficacy of a web-based parenting skills program for young children with traumatic brain injury.

    Science.gov (United States)

    Wade, Shari L; Oberjohn, Karen; Burkhardt, Abby; Greenberg, Ira

    2009-01-01

    To report the feasibility and preliminary efficacy of a Web-based parenting skills program to reduce behavior problems following traumatic brain injury (TBI) in young children. Families of 9 children between the ages of 3 and 8 years with TBI, injured less than 24 months earlier, participated in a pilot study of a Web-based parenting skills program designed to increase positive parenting skills and to improve caregiver stress management and coping. The program consisted of 10 core sessions and up to 4 supplemental sessions. Each session consisted of self-guided didactic information, video modeling skills, and exercises. Online sessions were followed by synchronous sessions providing in vivo coaching of target skills. Caregivers completed an average of 12 sessions (range 5-24). Ratings of ease of use and satisfaction were high. Paired t tests revealed significant improvements in target parenting behaviors between baseline and session 2 and between sessions 2 and 4. These improvements were maintained at follow-up. Among the 5 families who completed the follow-up assessment, there were trends for reductions in the overall number of behavior problems. This study provides preliminary evidence of the potential feasibility and efficacy of an online parenting skills intervention for improving positive parenting skills and for reducing child behavior problems following early TBI.

  3. 76 FR 59265 - Medicare Program; Prospective Payment System and Consolidated Billing for Skilled Nursing...

    Science.gov (United States)

    2011-09-26

    ... [CMS-1351-CN] RIN 0938-AQ29 Medicare Program; Prospective Payment System and Consolidated Billing for... rule entitled ``Medicare Program; Prospective Payment System and Consolidated Billing for Skilled... Payment System (PPS) final rule (76 FR 48486, 48540) inadvertently included several technical errors in...

  4. Atlas – a data warehouse for integrative bioinformatics

    Directory of Open Access Journals (Sweden)

    Yuen Macaire MS

    2005-02-01

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

  5. A Cluster Randomized Trial of the Social Skills Improvement System-Classwide Intervention Program (SSIS-CIP) in First Grade

    Science.gov (United States)

    DiPerna, James Clyde; Lei, Puiwa; Cheng, Weiyi; Hart, Susan Crandall; Bellinger, Jillian

    2018-01-01

    The purpose of this study was to evaluate the efficacy of a universal social skills program, the Social Skills Improvement System Classwide Intervention Program (SSIS-CIP; Elliott & Gresham, 2007), for students in first grade. Classrooms from 6 elementary schools were randomly assigned to treatment or business-as-usual control conditions.…

  6. The effect of a multi-component camp-based weight-loss program on children's motor skills and physical fitness

    DEFF Research Database (Denmark)

    Larsen, Kristian Traberg; Huang, Tao; Larsen, Lisbeth Runge

    2016-01-01

    BACKGROUND: Many weight-loss programs in children are performed without specific foci on training both physical fitness and motor skills. The aim of this study was to describe the effect of a one-year weight-loss program on children's motor skills and physical fitness. METHODS: Participants......-respiratory fitness test. Motor skills were assessed by the Movement Assessment Battery for Children - second edition (M-ABC-2), age band 3. RESULTS: Loss to follow-up after 52 weeks was 19 % and 32 % in the DCIA and SIA, respectively. Balance skills were improved post-camp, but not after 52 weeks in children from....... CONCLUSION: In conclusion, the day-camp intervention led to improvements in physical fitness but not in motor skills compared to the standard intervention. Including both motor skills and physical fitness could advantageously be considered in future immersive intervention programmes. TRIAL REGISTRATION...

  7. Is adolescence a critical period for learning formal thinking skills? A case study investigating the development of formal thinking skills in a short-term inquiry-based intervention program

    Science.gov (United States)

    Towne, Forrest S.

    Current domestic and international comparative studies of student achievement in science are demonstrating that the U.S. needs to improve science education if it wants to remain competitive in the global economy. One of the causes of the poor performance of U.S. science education is the lack of students who have developed the formal thinking skills that are necessary to obtain scientific literacy. Previous studies have demonstrated that formal thinking skills can be taught to adolescents, however only 25% of incoming college freshman have these necessary skills. There is some evidence that adolescence (girls aged 11-13, boys aged 12-14) is a critical period where students must learn formal thinking skills, similar to the critical period that exists for young children learning languages. It is not known whether it is more difficult for students to learn formal thinking skills either prior to or following adolescence. The purpose of this quantitative case study is to determine whether adolescence is a critical period for students to learn formal thinking skills. The study also investigates whether a formal thinking skills focused program can improve students' intelligence. In this study 32 students who had not developed any formal thinking skills, ranging in age from 10-16, underwent an intensive four-week, inquiry-based, formal thinking skill intervention program that focused on two formal thinking skills: (1) the ability to control and exclude variables; and (2) the ability to manipulate ratios and proportionalities. The students undergoing the training were matched with control students by age, gender, formal thinking skill ability, and intelligence. The control group attended their traditional science course during the intervention periods. The results of the study showed that the intervention program was successful in developing students' formal thinking skills. The pre-adolescents (males, age 10-11, females, age 10) were unable to learn formal thinking skills

  8. Improving Empathy and Communication Skills of Visually Impaired Early Adolescents through a Psycho-Education Program

    Science.gov (United States)

    Yildiz, Mehmet Ali; Duy, Baki

    2013-01-01

    The purpose of this study was to investigate the effectiveness of an interpersonal communication skills psycho-education program to improve empathy and communication skills of visually impaired adolescents. Participants of the study were sixteen early adolescents schooling in an elementary school for visually impaired youth in Diyarbakir. The…

  9. Teaching communication skills in clinical settings: comparing two applications of a comprehensive program with standardized and real patients

    Science.gov (United States)

    2014-01-01

    Background Communication is important for the quality of clinical practice, and programs have been implemented to improve healthcare providers’ communication skills. However, the consistency of programs teaching communication skills has received little attention, and debate exists about the application of acquired skills to real patients. This study inspects whether (1) results from a communication program are replicated with different samples, and (2) results with standardized patients apply to interviews with real patients. Methods A structured, nine-month communication program was applied in two consecutive years to two different samples of healthcare professionals (25 in the first year, 20 in the second year). Results were assessed at four different points in time, each year, regarding participants’ confidence levels (self-rated), basic communication skills in interviews with standardized patients, and basic communication skills in interviews with real patients. Data were analyzed using GLM Repeated-Measures procedures. Results Improvements were statistically significant in both years in all measures except in simulated patients’ assessment of the 2008 group. Differences between the two samples were non-significant. Differences between interviews with standardized and with real patients were also non-significant. Conclusions The program’s positive outcomes were replicated in different samples, and acquired skills were successfully applied to real-patient interviews. This reinforces this type of program structure as a valuable training tool, with results translating into real situations. It also adds to the reliability of the assessment instruments employed, though these may need adaptation in the case of real patients. PMID:24886341

  10. Improve Problem Solving Skills through Adapting Programming Tools

    Science.gov (United States)

    Shaykhian, Linda H.; Shaykhian, Gholam Ali

    2007-01-01

    There are numerous ways for engineers and students to become better problem-solvers. The use of command line and visual programming tools can help to model a problem and formulate a solution through visualization. The analysis of problem attributes and constraints provide insight into the scope and complexity of the problem. The visualization aspect of the problem-solving approach tends to make students and engineers more systematic in their thought process and help them catch errors before proceeding too far in the wrong direction. The problem-solver identifies and defines important terms, variables, rules, and procedures required for solving a problem. Every step required to construct the problem solution can be defined in program commands that produce intermediate output. This paper advocates improved problem solving skills through using a programming tool. MatLab created by MathWorks, is an interactive numerical computing environment and programming language. It is a matrix-based system that easily lends itself to matrix manipulation, and plotting of functions and data. MatLab can be used as an interactive command line or a sequence of commands that can be saved in a file as a script or named functions. Prior programming experience is not required to use MatLab commands. The GNU Octave, part of the GNU project, a free computer program for performing numerical computations, is comparable to MatLab. MatLab visual and command programming are presented here.

  11. The Development of Productivity Practical Management Model at Automotive Mechanical Technology Skill Program in Semarang Vocational Schools, Indonesia

    Science.gov (United States)

    Hadromi; Rachman, Maman; Soesanto; Kartana, Tri Jaka

    2015-01-01

    The purpose of this research is to develop automotive Mechanical Technology Skill Program (TMO) in Vocational School. The Research and Development (R&D) object was done in SMK 1, 4 and 7 Semarang, Indonesia. The result was achieved productivity Practical Management Final Model at TMO skill Program in Vocational school named momanticproter.…

  12. The impact of residency programs on new nurse graduates' clinical decision-making and leadership skills: a systematic review.

    Science.gov (United States)

    AL-Dossary, Reem; Kitsantas, Panagiota; Maddox, P J

    2014-06-01

    Health care institutions have adapted residency programs to help new graduate nurses to become fully competent and transition from a student nurse to an independent practicing nurse and a bedside leader. The study's aim is to review the literature on the impact of residency programs on new graduate nurses' clinical decision-making and leadership skills. An electronic search was conducted between 1980 and 2013 using databases of the scientific literature in Medline, PubMed, Cochrane EPOC, Cumulative Index to Nursing & Allied Health Literature database guide (CINAHL), and PsychInfo using a range of keywords. Information gathered was evaluated for relevance. Thirteen studies that met the inclusion criteria were used in this systematic review. In several studies considered in this review, residency programs were developed to improve new graduates skills and promote their transition into the nursing workforce. In fact, the transition programs reduced turnover in that first year of practice and promoted professional growth of the new graduate such as hand-on nursing skills, clinical decision-making and leadership skills, satisfaction, and retention. There is a need for effective residency programs that are designed to prepare new graduate nurses in providing safe, competent and effective patient care. © 2013.

  13. Assessing Interpersonal and Communication Skills in Radiation Oncology Residents: A Pilot Standardized Patient Program

    International Nuclear Information System (INIS)

    Ju, Melody; Berman, Abigail T.; Hwang, Wei-Ting; LaMarra, Denise; Baffic, Cordelia; Suneja, Gita; Vapiwala, Neha

    2014-01-01

    Purpose: There is a lack of data for the structured development and evaluation of communication skills in radiation oncology residency training programs. Effective communication skills are increasingly emphasized by the Accreditation Council for Graduate Medical Education and are critical for a successful clinical practice. We present the design of a novel, pilot standardized patient (SP) program and the evaluation of communication skills among radiation oncology residents. Methods and Materials: Two case scenarios were developed to challenge residents in the delivery of “bad news” to patients: one scenario regarding treatment failure and the other regarding change in treatment plan. Eleven radiation oncology residents paired with 6 faculty participated in this pilot program. Each encounter was scored by the SPs, observing faculty, and residents themselves based on the Kalamazoo guidelines. Results: Overall resident performance ratings were “good” to “excellent,” with faculty assigning statistically significant higher scores and residents assigning lower scores. We found inconsistent inter rater agreement among faculty, residents, and SPs. SP feedback was also valuable in identifying areas of improvement, including more collaborative decision making and less use of medical jargon. Conclusions: The program was well received by residents and faculty and regarded as a valuable educational experience that could be used as an annual feedback tool. Poor inter rater agreement suggests a need for residents and faculty physicians to better calibrate their evaluations to true patient perceptions. High scores from faculty members substantiate the concern that resident evaluations are generally positive and nondiscriminating. Faculty should be encouraged to provide honest and critical feedback to hone residents' interpersonal skills

  14. Bioinformatics-Aided Venomics

    Directory of Open Access Journals (Sweden)

    Quentin Kaas

    2015-06-01

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

  15. Measuring the Impacts of a Volunteer-Based Community Development Program in Developing Volunteers' Leadership Skills

    Science.gov (United States)

    Meier, Amy; Singletary, Loretta; Hill, George

    2012-01-01

    This article summarizes the results of an evaluation of the impacts of a community development program to develop leadership skills in its adult volunteers. The evaluation featured 20 questions about leadership skills learned as a result of volunteer experiences. Data analysis strategies beyond a simple means ranking resulted in evidence…

  16. An Examination of Job Skills Posted on Internet Databases: Implications for Information Systems Degree Programs.

    Science.gov (United States)

    Liu, Xia; Liu, Lai C.; Koong, Kai S.; Lu, June

    2003-01-01

    Analysis of 300 information technology job postings in two Internet databases identified the following skill categories: programming languages (Java, C/C++, and Visual Basic were most frequent); website development (57% sought SQL and HTML skills); databases (nearly 50% required Oracle); networks (only Windows NT or wide-area/local-area networks);…

  17. BioXSD: the common data-exchange format for everyday bioinformatics web services.

    Science.gov (United States)

    Kalas, Matús; Puntervoll, Pål; Joseph, Alexandre; Bartaseviciūte, Edita; Töpfer, Armin; Venkataraman, Prabakar; Pettifer, Steve; Bryne, Jan Christian; Ison, Jon; Blanchet, Christophe; Rapacki, Kristoffer; Jonassen, Inge

    2010-09-15

    The world-wide community of life scientists has access to a large number of public bioinformatics databases and tools, which are developed and deployed using diverse technologies and designs. More and more of the resources offer programmatic web-service interface. However, efficient use of the resources is hampered by the lack of widely used, standard data-exchange formats for the basic, everyday bioinformatics data types. BioXSD has been developed as a candidate for standard, canonical exchange format for basic bioinformatics data. BioXSD is represented by a dedicated XML Schema and defines syntax for biological sequences, sequence annotations, alignments and references to resources. We have adapted a set of web services to use BioXSD as the input and output format, and implemented a test-case workflow. This demonstrates that the approach is feasible and provides smooth interoperability. Semantics for BioXSD is provided by annotation with the EDAM ontology. We discuss in a separate section how BioXSD relates to other initiatives and approaches, including existing standards and the Semantic Web. The BioXSD 1.0 XML Schema is freely available at http://www.bioxsd.org/BioXSD-1.0.xsd under the Creative Commons BY-ND 3.0 license. The http://bioxsd.org web page offers documentation, examples of data in BioXSD format, example workflows with source codes in common programming languages, an updated list of compatible web services and tools and a repository of feature requests from the community.

  18. 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.

  19. 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

  20. 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

  1. The MetSkill Program — Rapidly Developing Effective Young Engineers in the Workplace

    Science.gov (United States)

    Drinkwater, Diana; Bianco, Nina

    MetSkill is a professional development program for metallurgical engineers that integrates with normal duties in their first one or two years of service. Graduates work together on a structured technical project, facilitated by specialists and supported by formal learning, and ultimately reported to their technical managers. The program enables graduates to "fill the gaps" in their undergraduate education, which is increasingly pertinent as engineering degrees become more general. Participants report that they enjoy the focus on more challenging (rewarding) aspects of their jobs and feel more confident about problem solving. Sponsor companies add that the relationships developed with external technical specialists enhances opportunities for innovation and development. MetSkill was delivered to two major resource companies in Australia in 2012. This paper provides an outline of the program and the reasons for its success, and demonstrates how the learning model could be applied to groups of graduates in other engineering disciplines.

  2. Kodak Skills Enhancement Program. U.S. Department of Education National Workplace Literacy Project. Final Report.

    Science.gov (United States)

    Beaudin, Bart P.

    The Kodak Skills Enhancement program was a workplace literacy project funded through the U.S. Department of Education's National Workplace Literacy Program. The project goals were as follows: (1) establish a positive climate within the Kodak corporate environment to ensure program effectiveness by garnering support at all levels; (2) determine the…

  3. Game-based programming towards developing algorithmic thinking skills in primary education

    Directory of Open Access Journals (Sweden)

    Hariklia Tsalapatas

    2012-06-01

    Full Text Available This paper presents cMinds, a learning intervention that deploys game-based visual programming towards building analytical, computational, and critical thinking skills in primary education. The proposed learning method exploits the structured nature of programming, which is inherently logical and transcends cultural barriers, towards inclusive learning that exposes learners to algorithmic thinking. A visual programming environment, entitled ‘cMinds Learning Suite’, has been developed aimed for classroom use. Feedback from the deployment of the learning methods and tools in classrooms in several European countries demonstrates elevated learner motivation for engaging in logical learning activities, fostering of creativity and an entrepreneurial spirit, and promotion of problem-solving capacity

  4. When process mining meets bioinformatics

    NARCIS (Netherlands)

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

    2011-01-01

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

  5. Exploiting graphics processing units for computational biology and bioinformatics.

    Science.gov (United States)

    Payne, Joshua L; Sinnott-Armstrong, Nicholas A; Moore, Jason H

    2010-09-01

    Advances in the video gaming industry have led to the production of low-cost, high-performance graphics processing units (GPUs) that possess more memory bandwidth and computational capability than central processing units (CPUs), the standard workhorses of scientific computing. With the recent release of generalpurpose GPUs and NVIDIA's GPU programming language, CUDA, graphics engines are being adopted widely in scientific computing applications, particularly in the fields of computational biology and bioinformatics. The goal of this article is to concisely present an introduction to GPU hardware and programming, aimed at the computational biologist or bioinformaticist. To this end, we discuss the primary differences between GPU and CPU architecture, introduce the basics of the CUDA programming language, and discuss important CUDA programming practices, such as the proper use of coalesced reads, data types, and memory hierarchies. We highlight each of these topics in the context of computing the all-pairs distance between instances in a dataset, a common procedure in numerous disciplines of scientific computing. We conclude with a runtime analysis of the GPU and CPU implementations of the all-pairs distance calculation. We show our final GPU implementation to outperform the CPU implementation by a factor of 1700.

  6. 9th International Conference on Practical Applications of Computational Biology and Bioinformatics

    CERN Document Server

    Rocha, Miguel; Fdez-Riverola, Florentino; Paz, Juan

    2015-01-01

    This proceedings presents recent practical applications of Computational Biology and  Bioinformatics. It contains the proceedings of the 9th International Conference on Practical Applications of Computational Biology & Bioinformatics held at University of Salamanca, Spain, at June 3rd-5th, 2015. The International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB) is an annual international meeting dedicated to emerging and challenging applied research in Bioinformatics and Computational Biology. Biological and biomedical research are increasingly driven by experimental techniques that challenge our ability to analyse, process and extract meaningful knowledge from the underlying data. The impressive capabilities of next generation sequencing technologies, together with novel and ever evolving distinct types of omics data technologies, have put an increasingly complex set of challenges for the growing fields of Bioinformatics and Computational Biology. The analysis o...

  7. Programming Not Required: Skills and Knowledge for the Digital Library Environment

    Science.gov (United States)

    Howard, Katherine

    2010-01-01

    Education for Library and Information professionals in managing the digital environment has been a key topic for discussion within the LIS environment for some time. However, before designing and implementing a program for digital library education, it is prudent to ensure that the skills and knowledge required to work in this environment are…

  8. Evaluation of a Classwide Teaching Program for Developing Preschool Life Skills

    Science.gov (United States)

    Hanley, Gregory P.; Heal, Nicole A.; Tiger, Jeffrey H.; Ingvarsson, Einar T.

    2007-01-01

    Recently, nonmaternal center-based child care has been linked to problem behavior in young children (National Institute of Child Health and Human Development, 2003). In response, a comprehensive program to promote prosocial skills was evaluated in a classroom of 16 children between the ages of 3 years and 5 years. Classroom observations were…

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

    DEFF Research Database (Denmark)

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

    2004-01-01

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

  10. Development of a Positive Youth Development Program: Helping Parents to Improve Their Parenting Skills

    Directory of Open Access Journals (Sweden)

    Daniel T.L. Shek

    2006-01-01

    Full Text Available The Project P.A.T.H.S. (Positive Adolescent Training through Holistic Social Programs is a positive youth development program that attempts to promote holistic development in adolescents in Hong Kong. In the Tier 2 Program of this project, social workers are expected to develop positive youth development programs for adolescents having greater psychosocial needs. They are required to submit proposals that will be evaluated in terms of whether the proposals are evidence based, and appropriate evaluation mechanisms are included. With reference to the literature on parental control processes that Chinese parents may be loose in their behavioral control and they tend to overemphasize academic excellence, it is argued that improvement of the parenting skills of parents of Chinese adolescents is an important area to be addressed. To facilitate social workers to prepare the related proposals, a sample proposal on how to improve the parenting skills of Chinese parents is described, including its conceptual framework, proposed program, and evaluation plan. It is argued that this supportive approach (i.e., preparation of a sample proposal can help social workers to develop quality proposals on positive youth development programs in Hong Kong.

  11. Peer Mentoring for Bioinformatics presentation

    OpenAIRE

    Budd, Aidan

    2014-01-01

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

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

    African Journals Online (AJOL)

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

  13. Pilot Evaluation of a Communication Skills Training Program for Psychiatry Residents Using Standardized Patient Assessment.

    Science.gov (United States)

    Ditton-Phare, Philippa; Sandhu, Harsimrat; Kelly, Brian; Kissane, David; Loughland, Carmel

    2016-10-01

    Mental health clinicians can experience difficulties communicating diagnostic information to patients and their families/carers, especially about distressing psychiatric disorders such as schizophrenia. There is evidence for the effectiveness of communication skills training (CST) for improving diagnostic discussions, particularly in specialties such as oncology, but only limited evidence exists about CST for psychiatry. This study evaluated a CST program specifically developed for psychiatry residents called ComPsych that focuses on conveying diagnostic and prognostic information about schizophrenia. The ComPsych program consists of an introductory lecture, module booklets for trainees, and exemplary skills videos, followed by small group role-plays with simulated patients (SPs) led by a trained facilitator. A standardized patient assessment (SPA) was digitally recorded pre- and post-training with a SP using a standardized scenario in a time-limited (15 min) period. Recorded SPAs were independently rated using a validated coding system (ComSkil) to identify frequency of skills used in five skills categories (agenda setting, checking, questioning, information organization, and empathic communication). Thirty trainees (15 males and 15 females; median age = 32) undertaking their vocational specialty training in psychiatry participated in ComPsych training and pre- and post-ComPsych SPAs. Skills increased post-training for agenda setting (d = -0.82), while questioning skills (d = 0.56) decreased. There were no significant differences in any other skills grouping, although checking, information organization, and empathic communication skills tended to increase post-training. A dose effect was observed for agenda setting, with trainees who attended more CST sessions outperforming those attending fewer. Findings support the generalization and translation of ComPsych CST to psychiatry.

  14. The Mental Health Nurse Incentive Program: desirable knowledge, skills and attitudes from the perspective of nurses.

    Science.gov (United States)

    Happell, Brenda; Palmer, Christine; Tennent, Rebeka

    2011-03-01

    To enhance the understanding of the skills and attitudes of mental health nurses working in the Australian Mental Health Nurse Incentive Program. The Mental Health Nurse Incentive Program places qualified mental health nurses alongside community-based general practitioners, private psychiatric practices and other appropriate organisations to provide clients with mental health conditions with a more integrated treatment plan. An exploratory, qualitative approach was undertaken, given the paucity of relevant research in this area. Exploratory individual interviews were conducted with ten mental health nurses working in this scheme. Data analysis was organised and managed using QSR NVivo qualitative analysis software. Respondents identified specific skills and attitudes required for practice under the Mental Health Nurse Incentive Program. Eight areas of skill and attitude were identified as essential for mental health nurses working in this field. This study highlights that many of these skills and attitudes are specific to the setting where mental health nurses are working. Mental health nurses working under this programme have a role to play in the dissemination of knowledge about their practice. More needs to be done by governments and other institutions to ensure that general practitioners and other health professionals understand the role played by mental health nurses in the provision of care. The extent to which the Mental Health Nurse Incentive Program becomes a sustainable strategy to promote quality and accessible mental health care will depend to some degree on the capacity to identify the skills and attitudes necessary for practice. The findings presented in this paper provide a significant contribution to articulating the essential characteristics required for this area of practice. © 2011 Blackwell Publishing Ltd.

  15. Developing a strategy for computational lab skills training through Software and Data Carpentry: Experiences from the ELIXIR Pilot action.

    Science.gov (United States)

    Pawlik, Aleksandra; van Gelder, Celia W G; Nenadic, Aleksandra; Palagi, Patricia M; Korpelainen, Eija; Lijnzaad, Philip; Marek, Diana; Sansone, Susanna-Assunta; Hancock, John; Goble, Carole

    2017-01-01

    Quality training in computational skills for life scientists is essential to allow them to deliver robust, reproducible and cutting-edge research. A pan-European bioinformatics programme, ELIXIR, has adopted a well-established and progressive programme of computational lab and data skills training from Software and Data Carpentry, aimed at increasing the number of skilled life scientists and building a sustainable training community in this field. This article describes the Pilot action, which introduced the Carpentry training model to the ELIXIR community.

  16. A Multisite Randomized Trial of a Cognitive Skills Program for Male Mentally Disordered Offenders: Violence and Antisocial Behavior Outcomes

    Science.gov (United States)

    Cullen, Alexis E.; Clarke, Amory Y.; Kuipers, Elizabeth; Hodgins, Sheilagh; Dean, Kimberlie; Fahy, Tom

    2012-01-01

    Objective: Despite a large evidence base indicating that cognitive skills programs can reduce reoffending in individuals without mental illness, there have been no randomized controlled trials (RCTs) to determine their effectiveness in mentally disordered offenders (MDOs). In the first RCT of a cognitive skills program for MDOs, we aimed to…

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

    Directory of Open Access Journals (Sweden)

    Ting Dong

    2017-09-01

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

  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. 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

  20. The profile of students’ problem-solving skill in physics across interest program in the secondary school

    Science.gov (United States)

    Jua, S. K.; Sarwanto; Sukarmin

    2018-05-01

    Problem-solving skills are important skills in physics. However, according to some researchers, the problem-solving skill of Indonesian students’ problem in physics learning is categorized still low. The purpose of this study was to identify the profile of problem-solving skills of students who follow the across the interests program of physics. The subjects of the study were high school students of Social Sciences, grade X. The type of this research was descriptive research. The data which used to analyze the problem-solving skills were obtained through student questionnaires and the test results with impulse materials and collision. From the descriptive analysis results, the percentage of students’ problem-solving skill based on the test was 52.93% and indicators respectively. These results indicated that students’ problem-solving skill is categorized low.

  1. Development of emergency response training program for on-site commanders (2). Extraction of non-technical skills

    International Nuclear Information System (INIS)

    Matsui, Yuko; Hikono, Masaru; Iwasaki, Mari; Morita, Miduho

    2017-01-01

    This study aimed at characterizing a non-technical skill exercise for on-site managers in charge of initial response at an emergency response center by extracting and clarifying the behavior examples of non-technical skills shown in the exercise scenario. From video observations, the non-technical skill examples were identified from seven of the eight non-technical skill categories which had been defined when the training program was developed. At the same time, the limitation when extracting the cases by observations was identified. The extracted non-technical skill cases are expected to be used for characterizing exercise scenarios, as well as provide knowledge to raise the awareness of exercise participants. (author)

  2. Basic Business and Economics: Stress Managerial Skills in High School Business Program

    Science.gov (United States)

    Clayton, Dean; Ruby, Ralph, Jr.

    1978-01-01

    Discusses the development of a curriculum in business ownership and management for secondary business education programs in Arkansas. Content was determined from community small businesses, the Small Business Administration, and an advisory committee. The curriculum concentrated on generic skills varying instructional strategies to localize…

  3. Communication Skills assessed at OSCE are not affected by Participation in the Adolescent Healthy Sexuality Program

    Directory of Open Access Journals (Sweden)

    Deborah Penava

    2002-12-01

    Full Text Available We proposed that first year medical students who voluntarily participated in the Healthy Sexuality adolescent program would perform better than their peers on an adolescent counseling station at the year-end OSCE (Objective Structured Clinical Examination. In addition we compared medical students’ communication skills at the time of the program as assessed by self, peers and participating adolescents. Methods: Nineteen first year medical students voluntarily participated in the ongoing Healthy Sexuality program. Adolescent participants, medical student peer participants and medical students assessed communication components on a 7-point Likert scale at the end of the program. At the year-end OSCE, all first year medical students at the University of Western Ontario were assessed at an adolescent counseling station by a standardized patient (SP and a physician examiner. Statistical analysis examined differences between the two groups. Results: Students who participated in the Healthy Sexuality program did not perform better than their colleagues on the year-end OSCE. A statistically significant correlation between physician examiner and SP evaluations was found (r = 0.62. Adolescent participants communication skills assessments in the Healthy Sexuality Program demonstrated no significant correlation with medical student assessments (self or peer. Conclusions:Voluntary intervention with adolescents did not result in improved communication skills at the structured year-end examination. Further investigation will be directed towards delineating differences between SP and physician examiner assessments.

  4. PayDIBI: Pay-as-you-go data integration for bioinformatics

    NARCIS (Netherlands)

    Wanders, B.

    2012-01-01

    Background: Scientific research in bio-informatics is often data-driven and supported by biolog- ical databases. In a growing number of research projects, researchers like to ask questions that require the combination of information from more than one database. Most bio-informatics papers do not

  5. Evaluating the short-term effects of a communication skills program for preclinical medical students.

    Science.gov (United States)

    Lee, Young-Mee; Lee, Young Hee

    2014-09-01

    Regardless of the growing importance of communication skills as a core clinical competence, few studies have determined the effects of communication skills courses in undergraduate medical curricula in Asian medical schools. The purpose of this study was to examine the effectiveness of a communication skills program for preclinical medical students. A communication skills course was provided to 111 second-year medical students in a medical college in Korea. Students' self-assessed competency of communication skills was evaluated by a questionnaire survey. To examine the improvement in observed communication skills, the students' encounters with standardized patients (SPs) were assessed at the first session and at the final course assessment. A structured checklist, consisting of 25 communication skills items, was used for the assessment. Students' self-assessed competency of communication skills increased significantly after completion of the course (pcommunication skills scores also improved significantly at the end of the course; the mean scores of the first SPs encounters was 49.6 (standard deviation [SD], 11.1), and those of cases A and B at the final assessment were 61.5 (SD, 8.4) and 69.6 (SD, 7.8), respectively (F61=269.54, pcommunication skills course was beneficial in developing and improving communication skills competency in preclinical medical students. Further studies should be followed to examine whether the acquisition of communication skills during preclinical studies can be sustained into clerkship and actual practice.

  6. Bellman's GAP--a language and compiler for dynamic programming in sequence analysis.

    Science.gov (United States)

    Sauthoff, Georg; Möhl, Mathias; Janssen, Stefan; Giegerich, Robert

    2013-03-01

    Dynamic programming is ubiquitous in bioinformatics. Developing and implementing non-trivial dynamic programming algorithms is often error prone and tedious. Bellman's GAP is a new programming system, designed to ease the development of bioinformatics tools based on the dynamic programming technique. In Bellman's GAP, dynamic programming algorithms are described in a declarative style by tree grammars, evaluation algebras and products formed thereof. This bypasses the design of explicit dynamic programming recurrences and yields programs that are free of subscript errors, modular and easy to modify. The declarative modules are compiled into C++ code that is competitive to carefully hand-crafted implementations. This article introduces the Bellman's GAP system and its language, GAP-L. It then demonstrates the ease of development and the degree of re-use by creating variants of two common bioinformatics algorithms. Finally, it evaluates Bellman's GAP as an implementation platform of 'real-world' bioinformatics tools. Bellman's GAP is available under GPL license from http://bibiserv.cebitec.uni-bielefeld.de/bellmansgap. This Web site includes a repository of re-usable modules for RNA folding based on thermodynamics.

  7. Bilingual Skills Training Program. Barbering/Cosmetology. Module 7.0: Endocrine System.

    Science.gov (United States)

    Northern New Mexico Community Coll., El Rito.

    This module on the endocrine system is the seventh of ten (CE 028 308-318) in the barbering/cosmetology course of a bilingual skills training program. (A Vocabulary Development Workbook for modules 6-10 is available as CE 028 313.) The course is designed to furnish theoretical and laboratory epxerience. Module objectives are for students to…

  8. Bilingual Skills Training Program. Barbering/Cosmetology. Module 4.0: Skeletal System.

    Science.gov (United States)

    Northern New Mexico Community Coll., El Rito.

    This module on the skeletal system is the fourth of ten (CE 028 308-318) in the barbering/cosmetology course of a bilingual skill training program. (A Vocabulary Development Workbook for modules 6-10 is available as CE 028 313.) The course is designed to furnish theoretical and laboratory experience. Module objectives are for students to develop…

  9. Bilingual Skills Training Program. Barbering/Cosmetology. Module 6.0: Muscular System.

    Science.gov (United States)

    Northern New Mexico Community Coll., El Rito.

    This module on the muscular system is the sixth of ten (CE 028 308-318) in the barbering/cosmetology course of a bilingual skills training program. (A Vocabulary Development Workbook for modules 6-10 is available as CE 028 313.) The course is designed to furnish theoretical and laboratory experience. Module objectives are for students to develop…

  10. Bellman’s GAP—a language and compiler for dynamic programming in sequence analysis

    Science.gov (United States)

    Sauthoff, Georg; Möhl, Mathias; Janssen, Stefan; Giegerich, Robert

    2013-01-01

    Motivation: Dynamic programming is ubiquitous in bioinformatics. Developing and implementing non-trivial dynamic programming algorithms is often error prone and tedious. Bellman’s GAP is a new programming system, designed to ease the development of bioinformatics tools based on the dynamic programming technique. Results: In Bellman’s GAP, dynamic programming algorithms are described in a declarative style by tree grammars, evaluation algebras and products formed thereof. This bypasses the design of explicit dynamic programming recurrences and yields programs that are free of subscript errors, modular and easy to modify. The declarative modules are compiled into C++ code that is competitive to carefully hand-crafted implementations. This article introduces the Bellman’s GAP system and its language, GAP-L. It then demonstrates the ease of development and the degree of re-use by creating variants of two common bioinformatics algorithms. Finally, it evaluates Bellman’s GAP as an implementation platform of ‘real-world’ bioinformatics tools. Availability: Bellman’s GAP is available under GPL license from http://bibiserv.cebitec.uni-bielefeld.de/bellmansgap. This Web site includes a repository of re-usable modules for RNA folding based on thermodynamics. Contact: robert@techfak.uni-bielefeld.de Supplementary information: Supplementary data are available at Bioinformatics online PMID:23355290

  11. 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…

  12. 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

  13. Effects of the Skills4Genius sports-based training program in creative behavior.

    Directory of Open Access Journals (Sweden)

    Sara Santos

    Full Text Available Team Sports has been suggested as a suitable environment to investigate creative behavior. This study's purpose was two-fold: first, it intended to identify the effects of the Skills4Genius sports-bases training program in thinking, motor, and in-game creative behavior in team sports. Second, it aimed to investigate the relationship between creative thinking and in-game creativity. Forty children from primary school were allocated into control (n = 18, age: 9.2±0.4 and experimental (n = 22, age: 9.5±0.7 groups. The experimental group participated in a five-month training program involving either creative thinking, diversification, physical literacy, and nonlinear pedagogy approaches (Skills4Genius. Variables in the study included: a creative thinking; b motor performance (vertical jump, speed, and agility; c in-game individual creative behavior (attempts, fluency, and versatility; and d in-game collective behavior (positional regularity. The results suggested that the Skills4Genius program fostered creative thinking, agility, and speed performance. Moreover, it stretched the in-game individual creative behavior mainly through the improvement of the attempts and versatility of the player's actions. Lastly, it nurtured a better learning of the tactical principles, whereas the children were more coordinated with their teammates' and opponents' positioning. Additionally, this study presents a positive correlation linking creative thinking and in-game creative performance. These findings highlighted that creativity is facilitated while players become more thinking and game-skilled. Coaches and educators may apply this functional environment to inspire children's disposition to move outside the box and trigger a creative spark in team sports players. Notwithstanding, the sports environment is ideally suited for fostering creative behavior, a higher-order disposition that will go on to differentiate the everyday life of a child.

  14. Effects of the Skills4Genius sports-based training program in creative behavior.

    Science.gov (United States)

    Santos, Sara; Jiménez, Sergio; Sampaio, Jaime; Leite, Nuno

    2017-01-01

    Team Sports has been suggested as a suitable environment to investigate creative behavior. This study's purpose was two-fold: first, it intended to identify the effects of the Skills4Genius sports-bases training program in thinking, motor, and in-game creative behavior in team sports. Second, it aimed to investigate the relationship between creative thinking and in-game creativity. Forty children from primary school were allocated into control (n = 18, age: 9.2±0.4) and experimental (n = 22, age: 9.5±0.7) groups. The experimental group participated in a five-month training program involving either creative thinking, diversification, physical literacy, and nonlinear pedagogy approaches (Skills4Genius). Variables in the study included: a) creative thinking; b) motor performance (vertical jump, speed, and agility); c) in-game individual creative behavior (attempts, fluency, and versatility); and d) in-game collective behavior (positional regularity). The results suggested that the Skills4Genius program fostered creative thinking, agility, and speed performance. Moreover, it stretched the in-game individual creative behavior mainly through the improvement of the attempts and versatility of the player's actions. Lastly, it nurtured a better learning of the tactical principles, whereas the children were more coordinated with their teammates' and opponents' positioning. Additionally, this study presents a positive correlation linking creative thinking and in-game creative performance. These findings highlighted that creativity is facilitated while players become more thinking and game-skilled. Coaches and educators may apply this functional environment to inspire children's disposition to move outside the box and trigger a creative spark in team sports players. Notwithstanding, the sports environment is ideally suited for fostering creative behavior, a higher-order disposition that will go on to differentiate the everyday life of a child.

  15. Using the community-based health planning and services program to promote skilled delivery in rural Ghana: socio-demographic factors that influence women utilization of skilled attendants at birth in northern Ghana.

    Science.gov (United States)

    Sakeah, Evelyn; Doctor, Henry V; McCloskey, Lois; Bernstein, Judith; Yeboah-Antwi, Kojo; Mills, Samuel

    2014-04-10

    The burden of maternal mortality in sub-Saharan Africa is enormous. In Ghana the maternal mortality ratio was 350 per 100,000 live births in 2010. Skilled birth attendance has been shown to reduce maternal deaths and disabilities, yet in 2010 only 68% of mothers in Ghana gave birth with skilled birth attendants. In 2005, the Ghana Health Service piloted an enhancement of its Community-Based Health Planning and Services (CHPS) program, training Community Health Officers (CHOs) as midwives, to address the gap in skilled attendance in rural Upper East Region (UER). The study determined the extent to which CHO-midwives skilled delivery program achieved its desired outcomes in UER among birthing women. We conducted a cross-sectional household survey with women who had ever given birth in the three years prior to the survey. We employed a two stage sampling techniques: In the first stage we proportionally selected enumeration areas, and the second stage involved random selection of households. In each household, where there is more than one woman with a child within the age limit, we interviewed the woman with the youngest child. We collected data on awareness of the program, use of the services and factors that are associated with skilled attendants at birth. A total of 407 households/women were interviewed. Eighty three percent of respondents knew that CHO-midwives provided delivery services in CHPS zones. Seventy nine percent of the deliveries were with skilled attendants; and over half of these skilled births (42% of total) were by CHO-midwives. Multivariate analyses showed that women of the Nankana ethnic group and those with uneducated husbands were less likely to access skilled attendants at birth in rural settings. The implementation of the CHO-midwife program in UER appeared to have contributed to expanded skilled delivery care access and utilization for rural women. However, women of the Nankana ethnic group and uneducated men must be targeted with health

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

    Science.gov (United States)

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

    2016-09-29

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

  17. 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.

  18. Critical thinking dispositions and skills of senior nursing students in associate, baccalaureate, and RN-to-BSN programs.

    Science.gov (United States)

    Shin, Kyungrim; Jung, Duk Yoo; Shin, Sujin; Kim, Myoung Soo

    2006-06-01

    This study investigated the critical thinking dispositions and skills of senior nursing students. Study participants were students enrolled in associate (n = 137), baccalaureate (n = 102), and RN-to-BSN (n = 66) programs accredited by the Korean Ministry of Education. The California Critical Thinking Disposition Inventory (CCTDI) and California Critical Thinking Skills Test (CCTST) were used. A comparison of the CCTDI scores revealed a statistically significant difference between the students enrolled in different programs (F = 4.159, p = 0.017), as did a comparison of the CCTST scores (F = 24.205, p critical thinking skills to make the decisions required of them in their nursing practice. In line with this, when conducting a survey of the effectiveness of nursing education, the necessity of critical thinking skills cannot be overlooked. In fact, the National League for Nursing Accrediting Commission (NLNAC) (1999) and American Association of Colleges of Nursing (AACN) (1998) require the concept of critical thinking be included as one of the core elements of curricula and that it be measured as an outcome when evaluating nursing education. In 1998, during the evaluation of colleges of nursing conducted by the South Korean Council for University Education, several universities presented the fostering of critical thinking as one of the terminal learning goals of nursing education based on the idea that critical thinking is important not only in the nursing workplace, but also in nursing education. To evaluate the effectiveness of Korea's current nursing education curriculum, focus was placed on current students in South Korea's three systems of nursing education. Each curriculum's effectiveness can be evaluated by indexing critical thinking dispositions and skills. This article intends to offer insight into the first steps necessary in reorganizing nursing education by comparing these evaluations of each of the three systems. To this end, we conducted a comparative

  19. Improving Nurses' Peripheral Intravenous Catheter Insertion Knowledge, Confidence, and Skills Using a Simulation-Based Blended Learning Program

    Science.gov (United States)

    Keleekai, Nowai L.; Schuster, Catherine A.; Murray, Connie L.; King, Mary Anne; Stahl, Brian R.; Labrozzi, Laura J.; Gallucci, Susan; LeClair, Matthew W.; Glover, Kevin R.

    2016-01-01

    Introduction Peripheral intravenous catheter (PIVC) insertion is one of the most common invasive procedures performed in a hospital, but most nurses receive little formal training in this area. Blended PIVC insertion training programs that incorporate deliberate simulated practice have the potential to improve clinical practice and patient care. Methods The study was a randomized, wait-list control group with crossover using nurses on three medical/surgical units. Baseline PIVC knowledge, confidence, and skills assessments were completed for both groups. The intervention group then received a 2-hour PIVC online course, followed by an 8-hour live training course using a synergistic mix of three simulation tools. Both groups were then reassessed. After crossover, the wait-list group received the same intervention and both groups were reassessed. Results At baseline, both groups were similar for knowledge, confidence, and skills. Compared with the wait-list group, the intervention group had significantly higher scores for knowledge, confidence, and skills upon completing the training program. After crossover, the wait-list group had similarly higher scores for knowledge, confidence, and skills than the intervention group. Between the immediate preintervention and postintervention periods, the intervention group improved scores for knowledge by 31%, skills by 24%, and decreased confidence by 0.5%, whereas the wait-list group improved scores for knowledge by 28%, confidence by 16%, and skills by 15%. Conclusions Results demonstrate significant improvements in nurses' knowledge, confidence, and skills with the use of a simulation-based blended learning program for PIVC insertion. Transferability of these findings from a simulated environment into clinical practice should be further explored. PMID:27504890

  20. Best practices in bioinformatics training for life scientists

    DEFF Research Database (Denmark)

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

    2013-01-01

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

  1. 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…

  2. A Mobile Phone-Based Life Skills Training Program for Substance Use Prevention Among Adolescents: Pre-Post Study on the Acceptance and Potential Effectiveness of the Program, Ready4life.

    Science.gov (United States)

    Haug, Severin; Paz Castro, Raquel; Meyer, Christian; Filler, Andreas; Kowatsch, Tobias; Schaub, Michael P

    2017-10-04

    Substance use and misuse often first emerge during adolescence. Generic life skills training that is typically conducted within the school curriculum is effective at preventing the onset and escalation of substance use among adolescents. However, the dissemination of such programs is impeded by their large resource requirements in terms of personnel, money, and time. Life skills training provided via mobile phones might be a more economic and scalable approach, which additionally matches the lifestyle and communication habits of adolescents. The aim of this study was to test the acceptance and initial effectiveness of an individually tailored mobile phone-based life skills training program in vocational school students. The fully automated program, named ready4life, is based on social cognitive theory and addresses self-management skills, social skills, and substance use resistance skills. Program participants received up to 3 weekly text messages (short message service, SMS) over 6 months. Active program engagement was stimulated by interactive features such as quiz questions, message- and picture-contests, and integration of a friendly competition with prizes in which program users collected credits with each interaction. Generalized estimating equation (GEE) analyses were used to investigate for changes between baseline and 6-month follow-up in the following outcomes: perceived stress, self-management skills, social skills, at-risk alcohol use, tobacco smoking, and cannabis use. The program was tested in 118 school classes at 13 vocational schools in Switzerland. A total of 1067 students who owned a mobile phone and were not regular cigarette smokers were invited to participate in the life skills program. Of these, 877 (82.19%, 877/1067; mean age=17.4 years, standard deviation [SD]=2.7; 58.3% females) participated in the program and the associated study. A total of 43 students (4.9%, 43/877) withdrew their program participation during the intervention period

  3. Ostomy Home Skills Program

    Medline Plus

    Full Text Available ... in Residence Clinical Trials Methods Course Health Services Research Methods Course Surgeon Specific Registry Trauma Education Trauma Education Trauma Education Advanced Surgical Skills for ...

  4. 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.

  5. BioXSD: the common data-exchange format for everyday bioinformatics web services

    Science.gov (United States)

    Kalaš, Matúš; Puntervoll, Pæl; Joseph, Alexandre; Bartaševičiūtė, Edita; Töpfer, Armin; Venkataraman, Prabakar; Pettifer, Steve; Bryne, Jan Christian; Ison, Jon; Blanchet, Christophe; Rapacki, Kristoffer; Jonassen, Inge

    2010-01-01

    Motivation: The world-wide community of life scientists has access to a large number of public bioinformatics databases and tools, which are developed and deployed using diverse technologies and designs. More and more of the resources offer programmatic web-service interface. However, efficient use of the resources is hampered by the lack of widely used, standard data-exchange formats for the basic, everyday bioinformatics data types. Results: BioXSD has been developed as a candidate for standard, canonical exchange format for basic bioinformatics data. BioXSD is represented by a dedicated XML Schema and defines syntax for biological sequences, sequence annotations, alignments and references to resources. We have adapted a set of web services to use BioXSD as the input and output format, and implemented a test-case workflow. This demonstrates that the approach is feasible and provides smooth interoperability. Semantics for BioXSD is provided by annotation with the EDAM ontology. We discuss in a separate section how BioXSD relates to other initiatives and approaches, including existing standards and the Semantic Web. Availability: The BioXSD 1.0 XML Schema is freely available at http://www.bioxsd.org/BioXSD-1.0.xsd under the Creative Commons BY-ND 3.0 license. The http://bioxsd.org web page offers documentation, examples of data in BioXSD format, example workflows with source codes in common programming languages, an updated list of compatible web services and tools and a repository of feature requests from the community. Contact: matus.kalas@bccs.uib.no; developers@bioxsd.org; support@bioxsd.org PMID:20823319

  6. The PEWTER Study: Breaking Bad News Communication Skills Training for Counseling Programs

    Science.gov (United States)

    Keefe-Cooperman, Kathleen; Savitsky, Devyn; Koshel, Walter; Bhat, Varsha; Cooperman, Jessica

    2018-01-01

    The efficacy of teaching communication skills for breaking bad news in graduate-level counseling programs was examined. A structured model, PEWTER (Prepare, Evaluate, Warning, Telling, Emotional Response, Regrouping; Keefe-Cooperman and Nardi 2004), provides a method for this difficult task. Prior to training in using the model, students reported…

  7. Perceptions of Skill Development in a Living-Learning First-Year Experience Program

    Science.gov (United States)

    Smith, Kerri Anna

    2012-01-01

    The purpose of this study was to explore the perceptions of students and faculty involved in a living-learning first-year experience program at a small, liberal arts institution about developing skills for life-long learning including critical thinking, written communication, and reflection and engagement across disciplines. The researcher…

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

    Directory of Open Access Journals (Sweden)

    Katrina Pavelin

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

  9. Bioinformatics on the Cloud Computing Platform Azure

    Science.gov (United States)

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

    2014-01-01

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

  10. BioShaDock: a community driven bioinformatics shared Docker-based tools registry.

    Science.gov (United States)

    Moreews, François; Sallou, Olivier; Ménager, Hervé; Le Bras, Yvan; Monjeaud, Cyril; Blanchet, Christophe; Collin, Olivier

    2015-01-01

    Linux container technologies, as represented by Docker, provide an alternative to complex and time-consuming installation processes needed for scientific software. The ease of deployment and the process isolation they enable, as well as the reproducibility they permit across environments and versions, are among the qualities that make them interesting candidates for the construction of bioinformatic infrastructures, at any scale from single workstations to high throughput computing architectures. The Docker Hub is a public registry which can be used to distribute bioinformatic software as Docker images. However, its lack of curation and its genericity make it difficult for a bioinformatics user to find the most appropriate images needed. BioShaDock is a bioinformatics-focused Docker registry, which provides a local and fully controlled environment to build and publish bioinformatic software as portable Docker images. It provides a number of improvements over the base Docker registry on authentication and permissions management, that enable its integration in existing bioinformatic infrastructures such as computing platforms. The metadata associated with the registered images are domain-centric, including for instance concepts defined in the EDAM ontology, a shared and structured vocabulary of commonly used terms in bioinformatics. The registry also includes user defined tags to facilitate its discovery, as well as a link to the tool description in the ELIXIR registry if it already exists. If it does not, the BioShaDock registry will synchronize with the registry to create a new description in the Elixir registry, based on the BioShaDock entry metadata. This link will help users get more information on the tool such as its EDAM operations, input and output types. This allows integration with the ELIXIR Tools and Data Services Registry, thus providing the appropriate visibility of such images to the bioinformatics community.

  11. Contributions of On-the-Job Training Program to the Skills, Personal Qualities and Competencies of Tourism Graduates

    Directory of Open Access Journals (Sweden)

    Elroy Joseph C. Valdez

    2015-11-01

    Full Text Available This study ascertains the contributions of on-the-job training (OJT program of a university to the development of skills, personal qualities and competencies of tourism students. The study is descriptive and uses survey questionnaire for data gathering. Respondents consist of 74 tourism graduates from 2009 to 2013, which is 75.5% of the total number of graduates. Results show that the OJT program of the university has significant contributions to the development of students’ basic skills, thinking skills, personal qualities and competencies on resources, interpersonal, information, systems and technology. Further, the similarities of OJT contributions for males and females imply that there is no gender bias in the training places while the differences on OJT contributions for self-employed, casual, contractual and permanent employees indicate that those with more skills and competencies are more inclined to entrepreneurial activities than to employment. The OJT program is also consistent throughout the years in providing skills and personal qualities as indicated by the non-difference on OJT contributions when grouped according to graduation year. Of immediate concern, however, is the decline of OJT contributions to the competencies of 2013 graduates. The study recommends that the university should tie-up with more tourism industry partners that can give excellent trainings for students and offer more international OJT for them to be more globally competitive. The training of students should also be regularly monitored by university training coordinators. Finally, the university may also consider and study ways on how to develop the entrepreneurial skills of tourism students.

  12. 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...

  13. BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS.

    Science.gov (United States)

    Fosso, Bruno; Santamaria, Monica; Marzano, Marinella; Alonso-Alemany, Daniel; Valiente, Gabriel; Donvito, Giacinto; Monaco, Alfonso; Notarangelo, Pasquale; Pesole, Graziano

    2015-07-01

    Substantial advances in microbiology, molecular evolution and biodiversity have been carried out in recent years thanks to Metagenomics, which allows to unveil the composition and functions of mixed microbial communities in any environmental niche. If the investigation is aimed only at the microbiome taxonomic structure, a target-based metagenomic approach, here also referred as Meta-barcoding, is generally applied. This approach commonly involves the selective amplification of a species-specific genetic marker (DNA meta-barcode) in the whole taxonomic range of interest and the exploration of its taxon-related variants through High-Throughput Sequencing (HTS) technologies. The accessibility to proper computational systems for the large-scale bioinformatic analysis of HTS data represents, currently, one of the major challenges in advanced Meta-barcoding projects. BioMaS (Bioinformatic analysis of Metagenomic AmpliconS) is a new bioinformatic pipeline designed to support biomolecular researchers involved in taxonomic studies of environmental microbial communities by a completely automated workflow, comprehensive of all the fundamental steps, from raw sequence data upload and cleaning to final taxonomic identification, that are absolutely required in an appropriately designed Meta-barcoding HTS-based experiment. In its current version, BioMaS allows the analysis of both bacterial and fungal environments starting directly from the raw sequencing data from either Roche 454 or Illumina HTS platforms, following two alternative paths, respectively. BioMaS is implemented into a public web service available at https://recasgateway.ba.infn.it/ and is also available in Galaxy at http://galaxy.cloud.ba.infn.it:8080 (only for Illumina data). BioMaS is a friendly pipeline for Meta-barcoding HTS data analysis specifically designed for users without particular computing skills. A comparative benchmark, carried out by using a simulated dataset suitably designed to broadly represent

  14. Suicide Intervention Training for College Staff: Program Evaluation and Intervention Skill Measurement

    Science.gov (United States)

    Shannonhouse, Laura; Lin, Yung-Wei Dennis; Shaw, Kelly; Wanna, Reema; Porter, Michael

    2017-01-01

    Objective: Suicide remains a pressing issue for college communities. Consequently, gatekeeper trainings are often provided for staff. This study examines the effect of one such program, Applied Suicide Intervention Skills Training (ASIST). Participants: 51 college employees received ASIST in August of 2014 and were compared to 30 wait-list control…

  15. Ostomy Home Skills Program

    Medline Plus

    Full Text Available ... with demonstration of each skill Stoma Practice Model Stoma supplies (measurement guide, marking pen, scissors, sample pouch) Ostomy self-care checklist Evaluation (Complete the Ostomy Patient Survey . We ...

  16. Learning Under the Tree : Evaluating Skillful Parenting Program in West Kenya ICS Full Evaluation Report

    NARCIS (Netherlands)

    van Esch, R.P.|info:eu-repo/dai/nl/371571502; de Haan, M.J.|info:eu-repo/dai/nl/074405624

    2016-01-01

    Summary The central purpose of this evaluation is to determine if and how the Skillful Parenting Program (SPP) effects the parenting of its participants. In addition, it aims to determine how the parenting program was adapted to the West Kenyan setting, and how the specific content and processes of

  17. Rel8: demonstrating the feasibility of delivering an 8-week social skills program in a public mental health setting.

    Science.gov (United States)

    Wauchope, Bronwyn; Terlich, Alissa; Lee, Stuart

    2016-06-01

    As community mental health services integrate recovery-oriented practices, treatments that focus on skills development and social integration are desirable. This study aimed to examine the feasibility of implementing "Rel8", an 8-week social skills training group adapted to suit a public community mental health setting. A retrospective audit was conducted of quantitative and qualitative data from four groups run between 2011 and 2013. Pre- and post-group measures were collected, assessing self-rated friendships and confidence with social skills and clinician-rated social skill performance. Qualitative feedback about group participation was also collected through use of a developed questionnaire. Analysis revealed significant improvements in participants' confidence with their social skills following group participation, with a trend also found for improved social skill performance. "Rel8", an adapted 8-week social skills training group, is a feasible program in the context of community mental health services. The program added to the recovery-centred practice of the community mental health service while also adding to the diversity of clinician skills for psychosocial-oriented practice. © The Royal Australian and New Zealand College of Psychiatrists 2015.

  18. The positive impact of a facilitated peer mentoring program on academic skills of women faculty.

    Science.gov (United States)

    Varkey, Prathibha; Jatoi, Aminah; Williams, Amy; Mayer, Anita; Ko, Marcia; Files, Julia; Blair, Janis; Hayes, Sharonne

    2012-03-23

    In academic medicine, women physicians lag behind their male counterparts in advancement and promotion to leadership positions. Lack of mentoring, among other factors, has been reported to contribute to this disparity. Peer mentoring has been reported as a successful alternative to the dyadic mentoring model for women interested in improving their academic productivity. We describe a facilitated peer mentoring program in our institution's department of medicine. Nineteen women enrolled in the program were divided into 5 groups. Each group had an assigned facilitator. Members of the respective groups met together with their facilitators at regular intervals during the 12 months of the project. A pre- and post-program evaluation consisting of a 25-item self-assessment of academic skills, self-efficacy, and academic career satisfaction was administered to each participant. At the end of 12 months, a total of 9 manuscripts were submitted to peer-reviewed journals, 6 of which are in press or have been published, and another 2 of which have been invited to be revised and resubmitted. At the end of the program, participants reported an increase in their satisfaction with academic achievement (mean score increase, 2.32 to 3.63; P = 0.0001), improvement in skills necessary to effectively search the medical literature (mean score increase, 3.32 to 4.05; P = 0.0009), an improvement in their ability to write a comprehensive review article (mean score increase, 2.89 to 3.63; P = 0.0017), and an improvement in their ability to critically evaluate the medical literature (mean score increased from 3.11 to 3.89; P = 0.0008). This facilitated peer mentoring program demonstrated a positive impact on the academic skills and manuscript writing for junior women faculty. This 1-year program required minimal institutional resources, and suggests a need for further study of this and other mentoring programs for women faculty.

  19. Bioinformatics Methods for Interpreting Toxicogenomics Data: The Role of Text-Mining

    NARCIS (Netherlands)

    Hettne, K.M.; Kleinjans, J.; Stierum, R.H.; Boorsma, A.; Kors, J.A.

    2014-01-01

    This chapter concerns the application of bioinformatics methods to the analysis of toxicogenomics data. The chapter starts with an introduction covering how bioinformatics has been applied in toxicogenomics data analysis, and continues with a description of the foundations of a specific

  20. 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...

  1. 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...

  2. Transfer of communication skills to the workplace during clinical rounds: impact of a program for residents.

    Directory of Open Access Journals (Sweden)

    Aurore Liénard

    2010-08-01

    Full Text Available Communication with patients is a core clinical skill in medicine that can be acquired through communication skills training. Meanwhile, the importance of transfer of communication skills to the workplace has not been sufficiently studied. This study aims to assess the efficacy of a 40-hour training program designed to improve patients' satisfaction and residents' communication skills during their daily clinical rounds.Residents were randomly assigned to the training program or to a waiting list. Patients' satisfaction was assessed with a visual analog scale after each visit. Transfer of residents' communication skills was assessed in audiotaped actual inpatient visits during a half-day clinical round. Transcripted audiotapes were analyzed using content analysis software (LaComm. Training effects were tested with Mann-Whitney tests and generalized linear Poisson regression models.Eighty-eight residents were included. First, patients interacting with trained residents reported a higher satisfaction with residents' communication (Median=92 compared to patients interacting with untrained residents (Median=88 (p=.046. Second, trained residents used more assessment utterances (Relative Risk (RR=1.17; 95% Confidence intervals (95%CI=1.02-1.34; p=.023. Third, transfer was also observed when residents' training attendance was considered: residents' use of assessment utterances (RR=1.01; 95%CI=1.01-1.02; p=.018 and supportive utterances (RR=0.99; 95%CI=0.98-1.00; p=.042 (respectively 1.15 (RR, 1.08-1.23 (95%CI, p<.001 for empathy and 0.95 (RR, 0.92-0.99 (95%CI, p=.012 for reassurance was proportional to the number of hours of training attendance.The training program improved patients' satisfaction and allowed the transfer of residents' communication skills learning to the workplace. Transfer was directly related to training attendance but remained limited. Future studies should therefore focus on the improvement of the efficacy of communication skills

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

    Science.gov (United States)

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

    2014-01-01

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

  4. Systems Bioinformatics: increasing precision of computational diagnostics and therapeutics through network-based approaches.

    Science.gov (United States)

    Oulas, Anastasis; Minadakis, George; Zachariou, Margarita; Sokratous, Kleitos; Bourdakou, Marilena M; Spyrou, George M

    2017-11-27

    Systems Bioinformatics is a relatively new approach, which lies in the intersection of systems biology and classical bioinformatics. It focuses on integrating information across different levels using a bottom-up approach as in systems biology with a data-driven top-down approach as in bioinformatics. The advent of omics technologies has provided the stepping-stone for the emergence of Systems Bioinformatics. These technologies provide a spectrum of information ranging from genomics, transcriptomics and proteomics to epigenomics, pharmacogenomics, metagenomics and metabolomics. Systems Bioinformatics is the framework in which systems approaches are applied to such data, setting the level of resolution as well as the boundary of the system of interest and studying the emerging properties of the system as a whole rather than the sum of the properties derived from the system's individual components. A key approach in Systems Bioinformatics is the construction of multiple networks representing each level of the omics spectrum and their integration in a layered network that exchanges information within and between layers. Here, we provide evidence on how Systems Bioinformatics enhances computational therapeutics and diagnostics, hence paving the way to precision medicine. The aim of this review is to familiarize the reader with the emerging field of Systems Bioinformatics and to provide a comprehensive overview of its current state-of-the-art methods and technologies. Moreover, we provide examples of success stories and case studies that utilize such methods and tools to significantly advance research in the fields of systems biology and systems medicine. © The Author 2017. Published by Oxford University Press.

  5. Is it possible to improve radiotherapy team members’ communication skills? A randomized study assessing the efficacy of a 38-h communication skills training program

    International Nuclear Information System (INIS)

    Gibon, Anne-Sophie; Merckaert, Isabelle; Liénard, Aurore; Libert, Yves; Delvaux, Nicole; Marchal, Serge; Etienne, Anne-Marie; Reynaert, Christine; Slachmuylder, Jean-Louis; Scalliet, Pierre; Van Houtte, Paul; Coucke, Philippe; Salamon, Emile

    2013-01-01

    Background and purpose: Optimizing communication between radiotherapy team members and patients and between colleagues requires training. This study applies a randomized controlled design to assess the efficacy of a 38-h communication skills training program. Material and methods: Four radiotherapy teams were randomly assigned either to a training program or to a waiting list. Team members’ communication skills and their self-efficacy to communicate in the context of an encounter with a simulated patient were the primary endpoints. These encounters were scheduled at the baseline and after training for the training group, and at the baseline and four months later for the waiting list group. Encounters were audiotaped and transcribed. Transcripts were analyzed with content analysis software (LaComm) and by an independent rater. Results: Eighty team members were included in the study. Compared to untrained team members, trained team members used more turns of speech with content oriented toward available resources in the team (relative rate [RR] = 1.38; p = 0.023), more assessment utterances (RR = 1.69; p < 0.001), more empathy (RR = 4.05; p = 0.037), more negotiation (RR = 2.34; p = 0.021) and more emotional words (RR = 1.32; p = 0.030), and their self-efficacy to communicate increased (p = 0.024 and p = 0.008, respectively). Conclusions: The training program was effective in improving team members’ communication skills and their self-efficacy to communicate in the context of an encounter with a simulated patient. Future study should assess the effect of this training program on communication with actual patients and their satisfaction. Moreover a cost-benefit analysis is needed, before implementing such an intensive training program on a broader scale

  6. A Peer-Assisted Learning Program and Its Effect on Student Skill Demonstration

    Science.gov (United States)

    Carr, W. David; Volberding, Jennifer; Vardiman, Phillip

    2011-01-01

    Objective: To explore the effect of an intentional Peer-Assisted Learning (PAL) program on peer-tutors and peer-tutees for performance on specific psychomotor skills. Design and Setting: Randomized, pretest-posttest experimental design. Participants: Undergraduate students (N = 69, 42 females and 27 males, all participants were 18 to 22 years old,…

  7. A Randomized Controlled Trial to Improve Social Skills in Young Adults with Autism Spectrum Disorder: The UCLA PEERS® Program

    Science.gov (United States)

    Laugeson, Elizabeth A.; Gantman, Alexander; Kapp, Steven K.; Orenski, Kaely; Ellingsen, Ruth

    2015-01-01

    Research suggests that impaired social skills are often the most significant challenge for those with autism spectrum disorder (ASD), yet few evidence-based social skills interventions exist for adults on the spectrum. This replication trial tested the effectiveness of PEERS, a caregiver-assisted social skills program for high-functioning young…

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

    Science.gov (United States)

    Römer, Michael; Eichner, Johannes; Dräger, Andreas; Wrzodek, Clemens; Wrzodek, Finja; Zell, Andreas

    2016-01-01

    Bioinformatics analysis has become an integral part of research in biology. However, installation and use of scientific software can be difficult and often requires technical expert knowledge. Reasons are dependencies on certain operating systems or required third-party libraries, missing graphical user interfaces and documentation, or nonstandard input and output formats. In order to make bioinformatics software easily accessible to researchers, we here present a web-based platform. The Center for Bioinformatics Tuebingen (ZBIT) Bioinformatics Toolbox provides web-based access to a collection of bioinformatics tools developed for systems biology, protein sequence annotation, and expression data analysis. Currently, the collection encompasses software for conversion and processing of community standards SBML and BioPAX, transcription factor analysis, and analysis of microarray data from transcriptomics and proteomics studies. All tools are hosted on a customized Galaxy instance and run on a dedicated computation cluster. Users only need a web browser and an active internet connection in order to benefit from this service. The web platform is designed to facilitate the usage of the bioinformatics tools for researchers without advanced technical background. Users can combine tools for complex analyses or use predefined, customizable workflows. All results are stored persistently and reproducible. For each tool, we provide documentation, tutorials, and example data to maximize usability. The ZBIT Bioinformatics Toolbox is freely available at https://webservices.cs.uni-tuebingen.de/.

  9. Component analysis of a school-based substance use prevention program in Spain: contributions of problem solving and social skills training content.

    Science.gov (United States)

    Espada, José P; Griffin, Kenneth W; Pereira, Juan R; Orgilés, Mireia; García-Fernández, José M

    2012-02-01

    The objective of the present research was to examine the contribution of two intervention components, social skills training and problem solving training, to alcohol- and drug-related outcomes in a school-based substance use prevention program. Participants included 341 Spanish students from age 12 to 15 who received the prevention program Saluda in one of four experimental conditions: full program, social skills condition, problem solving condition, and a wait-list control group. Students completed self-report surveys at the pretest, posttest and 12-month follow-up assessments. Compared to the wait-list control group, the three intervention conditions produced reductions in alcohol use and intentions to use other substances. The intervention effect size for alcohol use was greatest in magnitude for the full program with all components. Problem-solving skills measured at the follow-up were strongest in the condition that received the full program with all components. We discuss the implications of these findings, including the advantages and disadvantages of implementing tailored interventions to students by selecting intervention components after a skills-based needs assessment.

  10. Transfer of Life Skills in Sport-Based Youth Development Programs: A Conceptual Framework Bridging Learning to Application

    Science.gov (United States)

    Jacobs, Jennifer M.; Wright, Paul M.

    2018-01-01

    Research has demonstrated that many quality sport-based youth development programs promote life skill acquisition (e.g., leadership, self-control) with the ultimate goal of facilitating positive outcomes in youth participants' social and academic environments. Researchers call this "transfer of life skills" (i.e., the idea that physical,…

  11. 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…

  12. Hospital Job Skills Enhancement Program: A Workplace Literacy Project. Final Evaluation Report.

    Science.gov (United States)

    Nurss, Joanne R.

    A workplace literacy program was designed to improve the literacy skills of entry-level workers in the housekeeping, food service, and laundry departments of Grady Memorial Hospital in Atlanta. Classes were held twice per week for 36 weeks at the hospital on job time. Literacy was defined as reading, writing, oral communication, and problem…

  13. Ostomy Home Skills Program

    Medline Plus

    Full Text Available ... to Choosing a Surgical Residency Education Modules Practice Management Workshops Patients and Family Patient Education Patient Education ... Trauma Advanced Trauma Life Support Advanced Trauma Operative Management Basic Endovascular Skills for Trauma Disaster Management and ...

  14. Ostomy Home Skills Program

    Medline Plus

    Full Text Available JACS Jobs Events Find a Surgeon Patients and Family Contact My Profile Shop ( 0 ) Cart Donate Become ... a Surgical Residency Practice Management Workshops Patients and Family Patient Education Patient Education Patients Medical Professionals Skills ...

  15. Ostomy Home Skills Program

    Medline Plus

    Full Text Available ... AUA), Certified Enterostomal Therapy Nurses (CETN), and the United Ostomy Associations of America (UOAA). The skills kit ... AUA), Certified Enterostomal Therapy Nurses (CETN), and the United Ostomy Associations of America (UOAA). Back to Top ...

  16. Ostomy Home Skills Program

    Medline Plus

    Full Text Available ... Trauma and EMS Cancer and Research Health Information Technology Scope of Practice Pediatric Issues Other Federal Legislative ... The Ostomy Home Skills Kit supports patients with educational and simulation materials to learn and practice the ...

  17. Ostomy Home Skills Program

    Medline Plus

    Full Text Available ... Online Guide to Choosing a Surgical Residency Practice Management Workshops Patients and Family Patient Education Patient Education ... Trauma Advanced Trauma Life Support Advanced Trauma Operative Management Basic Endovascular Skills for Trauma Disaster Management and ...

  18. 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.

  19. A decade of Web Server updates at the Bioinformatics Links Directory: 2003-2012.

    Science.gov (United States)

    Brazas, Michelle D; Yim, David; Yeung, Winston; Ouellette, B F Francis

    2012-07-01

    The 2012 Bioinformatics Links Directory update marks the 10th special Web Server issue from Nucleic Acids Research. Beginning with content from their 2003 publication, the Bioinformatics Links Directory in collaboration with Nucleic Acids Research has compiled and published a comprehensive list of freely accessible, online tools, databases and resource materials for the bioinformatics and life science research communities. The past decade has exhibited significant growth and change in the types of tools, databases and resources being put forth, reflecting both technology changes and the nature of research over that time. With the addition of 90 web server tools and 12 updates from the July 2012 Web Server issue of Nucleic Acids Research, the Bioinformatics Links Directory at http://bioinformatics.ca/links_directory/ now contains an impressive 134 resources, 455 databases and 1205 web server tools, mirroring the continued activity and efforts of our field.

  20. BioQueue: a novel pipeline framework to accelerate bioinformatics analysis.

    Science.gov (United States)

    Yao, Li; Wang, Heming; Song, Yuanyuan; Sui, Guangchao

    2017-10-15

    With the rapid development of Next-Generation Sequencing, a large amount of data is now available for bioinformatics research. Meanwhile, the presence of many pipeline frameworks makes it possible to analyse these data. However, these tools concentrate mainly on their syntax and design paradigms, and dispatch jobs based on users' experience about the resources needed by the execution of a certain step in a protocol. As a result, it is difficult for these tools to maximize the potential of computing resources, and avoid errors caused by overload, such as memory overflow. Here, we have developed BioQueue, a web-based framework that contains a checkpoint before each step to automatically estimate the system resources (CPU, memory and disk) needed by the step and then dispatch jobs accordingly. BioQueue possesses a shell command-like syntax instead of implementing a new script language, which means most biologists without computer programming background can access the efficient queue system with ease. BioQueue is freely available at https://github.com/liyao001/BioQueue. The extensive documentation can be found at http://bioqueue.readthedocs.io. li_yao@outlook.com or gcsui@nefu.edu.cn. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  1. Employers' Perception of Graduates with Entry-Level Technical Skills from Construction Industry Programs in Ghana and Nigeria

    Science.gov (United States)

    Acheampong, Philip

    2013-01-01

    The purpose of this comparative study was to identify the technical skills and abilities needed by prospective employees of construction industries in Ghana and Nigeria. Potential employees were defined here as recent graduates of construction industry programs with entry-level technical skills. The continuous growth in and expansion of these two…

  2. 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…

  3. An Introduction to Programming for Bioscientists: A Python-Based Primer.

    Directory of Open Access Journals (Sweden)

    Berk Ekmekci

    2016-06-01

    Full Text Available Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in molecular biology, biochemistry, and other biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware, software, and algorithms. These advances have influenced, and even engendered, a phenomenal array of bioscience fields, including molecular evolution and bioinformatics; genome-, proteome-, transcriptome- and metabolome-wide experimental studies; structural genomics; and atomistic simulations of cellular-scale molecular assemblies as large as ribosomes and intact viruses. In short, much of post-genomic biology is increasingly becoming a form of computational biology. The ability to design and write computer programs is among the most indispensable skills that a modern researcher can cultivate. Python has become a popular programming language in the biosciences, largely because (i its straightforward semantics and clean syntax make it a readily accessible first language; (ii it is expressive and well-suited to object-oriented programming, as well as other modern paradigms; and (iii the many available libraries and third-party toolkits extend the functionality of the core language into virtually every biological domain (sequence and structure analyses, phylogenomics, workflow management systems, etc.. This primer offers a basic introduction to coding, via Python, and it includes concrete examples and exercises to illustrate the language's usage and capabilities; the main text culminates with a final project in structural bioinformatics. A suite of Supplemental Chapters is also provided. Starting with basic concepts, such as that of a "variable," the Chapters methodically advance the reader to the point of writing a graphical user interface to compute the Hamming distance between two DNA sequences.

  4. An Introduction to Programming for Bioscientists: A Python-Based Primer.

    Science.gov (United States)

    Ekmekci, Berk; McAnany, Charles E; Mura, Cameron

    2016-06-01

    Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in molecular biology, biochemistry, and other biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware, software, and algorithms. These advances have influenced, and even engendered, a phenomenal array of bioscience fields, including molecular evolution and bioinformatics; genome-, proteome-, transcriptome- and metabolome-wide experimental studies; structural genomics; and atomistic simulations of cellular-scale molecular assemblies as large as ribosomes and intact viruses. In short, much of post-genomic biology is increasingly becoming a form of computational biology. The ability to design and write computer programs is among the most indispensable skills that a modern researcher can cultivate. Python has become a popular programming language in the biosciences, largely because (i) its straightforward semantics and clean syntax make it a readily accessible first language; (ii) it is expressive and well-suited to object-oriented programming, as well as other modern paradigms; and (iii) the many available libraries and third-party toolkits extend the functionality of the core language into virtually every biological domain (sequence and structure analyses, phylogenomics, workflow management systems, etc.). This primer offers a basic introduction to coding, via Python, and it includes concrete examples and exercises to illustrate the language's usage and capabilities; the main text culminates with a final project in structural bioinformatics. A suite of Supplemental Chapters is also provided. Starting with basic concepts, such as that of a "variable," the Chapters methodically advance the reader to the point of writing a graphical user interface to compute the Hamming distance between two DNA sequences.

  5. The effect of a music therapy social skills training program on improving social competence in children and adolescents with social skills deficits.

    Science.gov (United States)

    Gooding, Lori F

    2011-01-01

    Three separate studies were conducted in school, residential and after-school care settings to test the effectiveness of a music therapy-based social skills intervention program on improving social competence in children and adolescents. A total of 45 children (n = 12; n = 13; n = 20) aged 6-17 years with social skills deficits participated in a group-based five session intervention program. The same curriculum, adapted to be age appropriate, was used at all 3 sites. Specific deficits within the social skills areas of peer relations and self-management skills were targeted. Active interventions like music performance, movement to music and improvisation were used. Cognitive-behavioral techniques like modeling, feedback, transfer training and problem solving were also incorporated. Data on social functioning were collected before, during, and after the music therapy intervention from participants, appropriate adult personnel and via behavioral observations. Results indicated that significant improvements in social functioning were found in (a) school participant pre and post self-ratings, (b) researcher pre and post ratings of school participants, (c) case manager's pre and post treatment ratings for the residential participants, (d) after-school care participants' pre and post self-ratings, and (e) behavioral observations at all three settings. Additional changes, although not significant, were noted in teacher ratings, residential participant self- and peer ratings, and after-school case manager ratings. Results from these studies suggest that the music therapy intervention was effective in improving social competence in children and adolescents with social deficits. More research is warranted to provide additional guidance about the use of music therapy interventions to improve social functioning.

  6. 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...

  7. A Program Implementation for the Development of Life Skills of Primary School 4th Grade Students

    Science.gov (United States)

    Akfirat, Osman Nejat; Kezer, Fatih

    2016-01-01

    Life skills are the competencies that an individual must have in order to be able to carry on his/her existence effectively in the process of change. By means of life skills, the individual is aimed to facilitate his/her life by using all his/her achievements in the education process. In this study, a program covering the dimensions of…

  8. 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.

  9. Parallel evolutionary computation in bioinformatics applications.

    Science.gov (United States)

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

    2013-05-01

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

  10. Public service electric and gas company technical supervisory skills programs for nuclear power plant personnel

    International Nuclear Information System (INIS)

    Meredith, J.B.

    1985-01-01

    A series of training programs entitled Technical Supervisory Skills Programs for management personnel are described. The first level of this program, TSSP-1, is a seven week program designed for first-line supervisors and other selected management personnel responsible for directing the work forces in the stations. TSSP-1 includes training in PWR/BWR Technology, Supervision, Aberrant Behavior Identification, Labor Relations and Ethics, Technical Administration, Quality Assurance Program, On-the-job Training, and Specific Departmental Training. TSSP-2, TSSP-3, and TSSP-4 courses are described in this paper

  11. The Effects of the Wildlife Habitat Evaluation Program on Targeted Life Skills

    Science.gov (United States)

    Allen, Kevin; Elmore, R. Dwayne

    2012-01-01

    Does participation in the Wildlife Habitat Evaluation Program (WHEP) help develop life skills? 4-H members and coaches who participated in the National WHEP Contest between the years 2003-2005 and 2007-2009 were asked to complete an evaluation at the end of each contest. A portion of the evaluation asked participants and coaches to determine if…

  12. The Effect of Scratch- and Lego Mindstorms Ev3-Based Programming Activities on Academic Achievement, Problem-Solving Skills and Logical-Mathematical Thinking Skills of Students

    Science.gov (United States)

    Korkmaz, Özgen

    2016-01-01

    The aim of this study was to investigate the effect of the Scratch and Lego Mindstorms Ev3 programming activities on academic achievement with respect to computer programming, and on the problem-solving and logical-mathematical thinking skills of students. This study was a semi-experimental, pretest-posttest study with two experimental groups and…

  13. Moderating Effect of Residential History on the Effects of a Fatherhood Program on Parenting Skills Satisfaction among Nonresident African American Fathers.

    Science.gov (United States)

    Qian, Yiqing; De Loney, E Hill; Caldwell, Cleopatra Howard

    2018-02-09

    Nonresident African American (AA) fathers sometimes face challenges to achieving satisfaction with their parenting skills, which may inhibit their motivations for parenting. Studies have found that residential history of fathers is associated with parental involvement; however, current fatherhood programs rarely consider the influence of different residential history on fathering. In the current study, we examined whether nonresident AA fathers' residential history with their sons moderated their parenting skills satisfaction after participating in the Fathers and Sons Program. Our results indicated that after controlling for fathers' pretest parenting skills satisfaction, age, education, marital status, employment, and ever lived with their son's mother; there was a moderating effect of residential history on the intervention's effects on posttest parenting skills satisfaction. The regression analyses showed that fathers in the intervention group who had lived with their son increased their parenting skills satisfaction more at posttest compared with fathers who had never lived with their sons. However, fathers in the comparison group who had lived with their sons had lower posttest parenting skills satisfaction. Future fatherhood programs for nonresident AA fathers should develop more nuanced group-specific interventions that consider residential history as a critical factor to enhance their parenting skills satisfaction as a strategy for improving father involvement.

  14. Moderating Effect of Residential History on the Effects of a Fatherhood Program on Parenting Skills Satisfaction among Nonresident African American Fathers

    Directory of Open Access Journals (Sweden)

    Yiqing Qian

    2018-02-01

    Full Text Available Nonresident African American (AA fathers sometimes face challenges to achieving satisfaction with their parenting skills, which may inhibit their motivations for parenting. Studies have found that residential history of fathers is associated with parental involvement; however, current fatherhood programs rarely consider the influence of different residential history on fathering. In the current study, we examined whether nonresident AA fathers’ residential history with their sons moderated their parenting skills satisfaction after participating in the Fathers and Sons Program. Our results indicated that after controlling for fathers’ pretest parenting skills satisfaction, age, education, marital status, employment, and ever lived with their son’s mother; there was a moderating effect of residential history on the intervention’s effects on posttest parenting skills satisfaction. The regression analyses showed that fathers in the intervention group who had lived with their son increased their parenting skills satisfaction more at posttest compared with fathers who had never lived with their sons. However, fathers in the comparison group who had lived with their sons had lower posttest parenting skills satisfaction. Future fatherhood programs for nonresident AA fathers should develop more nuanced group-specific interventions that consider residential history as a critical factor to enhance their parenting skills satisfaction as a strategy for improving father involvement.

  15. Transfer of communication skills to the workplace during clinical rounds: impact of a program for residents.

    Science.gov (United States)

    Liénard, Aurore; Merckaert, Isabelle; Libert, Yves; Bragard, Isabelle; Delvaux, Nicole; Etienne, Anne-Marie; Marchal, Serge; Meunier, Julie; Reynaert, Christine; Slachmuylder, Jean-Louis; Razavi, Darius

    2010-08-26

    Communication with patients is a core clinical skill in medicine that can be acquired through communication skills training. Meanwhile, the importance of transfer of communication skills to the workplace has not been sufficiently studied. This study aims to assess the efficacy of a 40-hour training program designed to improve patients' satisfaction and residents' communication skills during their daily clinical rounds. Residents were randomly assigned to the training program or to a waiting list. Patients' satisfaction was assessed with a visual analog scale after each visit. Transfer of residents' communication skills was assessed in audiotaped actual inpatient visits during a half-day clinical round. Transcripted audiotapes were analyzed using content analysis software (LaComm). Training effects were tested with Mann-Whitney tests and generalized linear Poisson regression models. Eighty-eight residents were included. First, patients interacting with trained residents reported a higher satisfaction with residents' communication (Median=92) compared to patients interacting with untrained residents (Median=88) (p=.046). Second, trained residents used more assessment utterances (Relative Risk (RR)=1.17; 95% Confidence intervals (95%CI)=1.02-1.34; p=.023). Third, transfer was also observed when residents' training attendance was considered: residents' use of assessment utterances (RR=1.01; 95%CI=1.01-1.02; p=.018) and supportive utterances (RR=0.99; 95%CI=0.98-1.00; p=.042) (respectively 1.15 (RR), 1.08-1.23 (95%CI), ptransfer of residents' communication skills learning to the workplace. Transfer was directly related to training attendance but remained limited. Future studies should therefore focus on the improvement of the efficacy of communication skills training in order to ensure a more important training effect size on transfer.

  16. A virtual reality-integrated program for improving social skills in patients with schizophrenia: a pilot study.

    Science.gov (United States)

    Rus-Calafell, Mar; Gutiérrez-Maldonado, José; Ribas-Sabaté, Joan

    2014-03-01

    Social skills training (SST) intervention has shown its efficacy to improve social dysfunction in patients with psychosis; however the implementation of new skills into patients' everyday functioning is difficult to achieve. In this study, we report results from the application of a virtual reality (VR) integrated program as an adjunct technique to a brief social skills intervention for patients with schizophrenia. It was predicted that the intervention would improve social cognition and performance of patients as well as generalisation of the learned responses into patient's daily life. Twelve patients with schizophrenia or schizoaffective disorder completed the study. They attended sixteen individual one-hour sessions, and outcome assessments were conducted at pre-treatment, post-treatment and four-month follow-up. The results of a series of repeated measures ANOVA revealed significant improvement in negative symptoms, psychopathology, social anxiety and discomfort, avoidance and social functioning. Objective scores obtained through the use of the VR program showed a pattern of learning in emotion perception, assertive behaviours and time spent in a conversation. Most of these gains were maintained at four-month follow-up. The reported results are based on a small, uncontrolled pilot study. Although there was an independent rater for the self-reported and informant questionnaires, assessments were not blinded. The results showed that the intervention may be effective for improving social dysfunction. The use of the VR program contributed to the generalisation of new skills into the patient's everyday functioning. Copyright © 2013 Elsevier Ltd. All rights reserved.

  17. Lecturing skills as predictors of tutoring skills in a problem-based medical curriculum.

    Science.gov (United States)

    Kassab, Salah Eldin; Hassan, Nahla; Abu-Hijleh, Marwan F; Sequeira, Reginald P

    2016-01-01

    Recruitment of tutors to work in problem-based learning (PBL) programs is challenging, especially in that most of them are graduated from discipline-based programs. Therefore, this study aims at examining whether lecturing skills of faculty could predict their PBL tutoring skills. This study included evaluation of faculty (n=69) who participated in both tutoring and lecturing within particular PBL units at the College of Medicine and Medical Sciences (CMMS), Arabian Gulf University, Bahrain. Each faculty was evaluated by medical students (n=45±8 for lecturing and 8±2 for PBL tutoring) using structured evaluation forms based on a Likert-type scale (poor to excellent). The prediction of tutoring skills using lecturing skills was statistically analyzed using stepwise linear regression. Among the parameters used to judge lecturing skills, the most important predictor for tutoring skills was subject matter mastery in the lecture by explaining difficult concepts and responding effectively to students' questions. Subject matter mastery in the lecture positively predicted five tutoring skills and accounted for 25% of the variance in overall effectiveness of the PBL tutors (F=22.39, P=0.000). Other important predictors for tutoring skills were providing a relaxed class atmosphere and effective use of audiovisual aids in the lecture. Predicting the tutoring skills based on lecturing skills could have implications for recruiting tutors in PBL medical programs and for tutor training initiatives.

  18. Bioinformatics in New Generation Flavivirus Vaccines

    Directory of Open Access Journals (Sweden)

    Penelope Koraka

    2010-01-01

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

  19. Ostomy Home Skills Program

    Medline Plus

    Full Text Available ... emptying and changing a pouch, problem solving, and home management. A DVD with demonstration of each skill Stoma Practice Model Stoma supplies (measurement guide, marking pen, scissors, sample pouch) Ostomy self-care checklist Evaluation (Complete the Ostomy Patient Survey . We ...

  20. Ostomy Home Skills Program

    Medline Plus

    Full Text Available ... Workforce Trauma and EMS Cancer and Research Health Information Technology Scope of Practice Pediatric Issues Other Federal Legislative ... supports the entire surgical team with quality, comprehensive education. The ... A booklet with information on the operation, home skills such as emptying ...

  1. Communication skills training in orthopaedics.

    Science.gov (United States)

    Lundine, Kristopher; Buckley, Richard; Hutchison, Carol; Lockyer, Jocelyn

    2008-06-01

    Communication skills play a key role in many aspects of both medical education and clinical patient care. The objectives of this study were to identify the key components of communication skills from the perspectives of both orthopaedic residents and their program directors and to understand how these skills are currently taught. This study utilized a mixed methods design. Quantitative data were collected with use of a thirty-item questionnaire distributed to all Canadian orthopaedic residents. Qualitative data were collected through focus groups with orthopaedic residents and semistructured interviews with orthopaedic program directors. One hundred and nineteen (37%) of 325 questionnaires were completed, twelve residents participated in two focus groups, and nine of sixteen program directors from across the country were interviewed. Both program directors and residents identified communication skills as being the accurate and appropriate use of language (i.e., content skills), not how the communication was presented (i.e., process skills). Perceived barriers to effective communication included time constraints and the need to adapt to the many personalities and types of people encountered daily in the hospital. Residents rarely have explicit training in communication skills. They rely on communication training implicitly taught through observation of their preceptors and clinical experience interacting with patients, peers, and other health-care professionals. Orthopaedic residents and program directors focus on content and flexibility within communication skills as well as on the importance of being concise. They value the development of communication skills in the clinical environment through experiential learning and role modeling. Education should focus on developing residents' process skills in communication. Care should be taken to avoid large-group didactic teaching sessions, which are perceived as ineffective.

  2. Good Talking Words: A Social Communications Skills Program for Preschool and Kindergarten Classes.

    Science.gov (United States)

    Paulson, Lucy Hart; van den Pol, Rick

    The "Good Talking Words" program aims to help children develop and demonstrate the social communication skills that are vital to school and life success. It uses an active, direct instructional approach for preschool and kindergarten students that uses language experiences to teach specific, prosocial behaviors that will help children…

  3. Contributions of After School Programs to the Development of Fundamental Movement Skills in Children.

    Science.gov (United States)

    Burrows, E Jean; Keats, Melanie R; Kolen, Angela M

    Fundamental movement skill (FMS) proficiency or the ability to perform basic skills (e.g., throwing, catching and jumping) has been linked to participation in lifelong physical activity. FMS proficiency amongst children has declined in the previous 15 years, with more children performing FMS at a low-mastery level. These declines may help explain the insufficient levels of participation in health promoting physical activity seen in today's youth. The after school time period (e.g., 3 to 6 p.m.), is increasingly considered an opportune time for physical activity interventions. To date, little research has examined the potential for after school programming to improve FMS proficiency. Participants (n=40, 6-10 years) of two existent physical activity based after school programs, a low-organized games and a sports-based program, were pre- and post-tested for FMS proficiency using the Test of Gross Motor Development-2 (TGMD-2) over an 11-week period. The sports-based program participants showed no improvement in FMS over the 11-week study ( p =0.91, eta 2 =0.00) and the games-based program participants significantly improved their proficiency ( p =0.00, eta 2 =0.30). No significant ( p =0.13, eta 2 = 0.06), differences were found in change in FMS scores between the low-organized games program participants and the sport-based program participants. These results suggest that after school programs with a low-organized games-based focus may support a moderate improvement in FMS proficiency in young children. Better training of after school program leaders on how to teach FMS may be necessary to assist children in acquiring sufficient proficiency in FMS.

  4. Improvements in primary care skills and knowledge with a vocational training program – a pre–post survey

    Directory of Open Access Journals (Sweden)

    Djalali S

    2017-07-01

    Full Text Available Sima Djalali, Ryan Tandjung, Thomas Rosemann, Stefan Markun Institute of Primary Care, University of Zurich, University Hospital Zurich, Zurich, Switzerland Background: Facing the upcoming shortage of primary care physicians (PCPs, medical and governmental organizations have recently made major investments to foster vocational training programs in Switzerland, designed to provide context-specific training for trainees in primary care practices. Less is known about the impact of these programs on the skills and specific knowledge of trainees. We aimed to evaluate the Cantonal program for vocational primary care training in the Canton of Zurich, Switzerland’s largest Canton.Methods: We undertook a pretest–posttest study and surveyed physicians before and after participating in the Cantonal program for vocational primary care training in the Swiss Canton of Zurich. All trainees who participated in the program from 2013 until the end of 2015 were eligible. Primary outcome was the proportion of trainees being confident about their professional, organizational, examination and management skills before and after completing vocational training. Secondary outcomes were the proportion of trainees stating knowledge gain in entrepreneurship and the proportion of trainees being motivated to pursue a career as PCP.Results: Data of 47 trainees participating in the vocational training between 2013 and 2015 were eligible. In total, 35 (74.5% participated in the T1 survey and 34 (72.3% in the T2 survey. At T2, significantly more trainees (T1: 11%−89%, T2: 79%−100% stated to be at least “slightly confident” about their skills (p<0.05 for each individual skill. Knowledge gain in entrepreneurship was highly expected and experienced by the trainees (55%−77% of respondents in case of medicine-specific contents, but hardly expected in case of general business contents (≤47% of respondents. Concerning trainees’ motivation to pursue a career as PCP

  5. Teaching MBA Students Teamwork and Team Leadership Skills: An Empirical Evaluation of a Classroom Educational Program

    Science.gov (United States)

    Hobson, Charles J.; Strupeck, David; Griffin, Andrea; Szostek, Jana; Rominger, Anna S.

    2014-01-01

    A comprehensive educational program for teaching behavioral teamwork and team leadership skills was rigorously evaluated with 148 MBA students enrolled at an urban regional campus of a Midwestern public university. Major program components included (1) videotaped student teams in leaderless group discussion (LGD) exercises at the course beginning…

  6. Developing the leadership skills of new graduates to influence practice environments: a novice nurse leadership program.

    Science.gov (United States)

    Dyess, Susan; Sherman, Rose

    2011-01-01

    The authors of the recently published Institute of Medicine on the Future of Nursing report emphasized the importance of preparing nurses to lead change to advance health care in the United States. Other scholars linked practice environments to safe quality care. In order for nurses to fully actualize this role in practice environments, they need to possess leadership skills sets that identify and respond to challenges faced. New nurses are no exception. This article presents a program with a 5-year track record that is designed to support transition and enhance the skill sets of leadership for new nurses in their first year of practice. Qualitative and quantitative evaluation measurements at baseline and postprogram provided data for evaluation of the first 4 cohorts in the program. Evaluative outcomes presented indicate that new nurses gained leadership and translational research skills that contributed to their ability to influence practice environments. Nonetheless, practice environments continue to need improvement and ongoing leadership from all levels of nursing must be upheld.

  7. The Effectiveness of an Interactive Training Program in Developing a Set of Non-Cognitive Skills in Students at University of Petra

    Science.gov (United States)

    Gheith, Eman; Aljaberi, Nahil M.

    2017-01-01

    This study aimed to investigate the effectiveness of interactive training programs in developing a set of non-cognitive skills in students at the University of Petra. Furthermore, it sought to examine the impact of the sex, academic year, and university major variables on developing these skills in students who underwent the training program, as…

  8. The positive impact of a facilitated peer mentoring program on academic skills of women faculty

    Directory of Open Access Journals (Sweden)

    Varkey Prathibha

    2012-03-01

    Full Text Available Abstract Background In academic medicine, women physicians lag behind their male counterparts in advancement and promotion to leadership positions. Lack of mentoring, among other factors, has been reported to contribute to this disparity. Peer mentoring has been reported as a successful alternative to the dyadic mentoring model for women interested in improving their academic productivity. We describe a facilitated peer mentoring program in our institution's department of medicine. Methods Nineteen women enrolled in the program were divided into 5 groups. Each group had an assigned facilitator. Members of the respective groups met together with their facilitators at regular intervals during the 12 months of the project. A pre- and post-program evaluation consisting of a 25-item self-assessment of academic skills, self-efficacy, and academic career satisfaction was administered to each participant. Results At the end of 12 months, a total of 9 manuscripts were submitted to peer-reviewed journals, 6 of which are in press or have been published, and another 2 of which have been invited to be revised and resubmitted. At the end of the program, participants reported an increase in their satisfaction with academic achievement (mean score increase, 2.32 to 3.63; P = 0.0001, improvement in skills necessary to effectively search the medical literature (mean score increase, 3.32 to 4.05; P = 0.0009, an improvement in their ability to write a comprehensive review article (mean score increase, 2.89 to 3.63; P = 0.0017, and an improvement in their ability to critically evaluate the medical literature (mean score increased from 3.11 to 3.89; P = 0.0008. Conclusions This facilitated peer mentoring program demonstrated a positive impact on the academic skills and manuscript writing for junior women faculty. This 1-year program required minimal institutional resources, and suggests a need for further study of this and other mentoring programs for women faculty.

  9. mORCA: sailing bioinformatics world with mobile devices.

    Science.gov (United States)

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

    2018-03-01

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

  10. p3d--Python module for structural bioinformatics.

    Science.gov (United States)

    Fufezan, Christian; Specht, Michael

    2009-08-21

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

  11. Developing communication skills training in 5 educational programs

    DEFF Research Database (Denmark)

    Nielsen, Annegrethe; Ringby, Betina

    Understanding the ability to communicate with patients as a central clinical skill, the importance of developing communication teaching in healthcare educations is obvious. Following the establishment of a room specially equipped for training communication skills in 2010, implementation of commun......Understanding the ability to communicate with patients as a central clinical skill, the importance of developing communication teaching in healthcare educations is obvious. Following the establishment of a room specially equipped for training communication skills in 2010, implementation....... As a result of the combination of easy access to technical resources in the dedicated room and the opportunity to continuously develop the facilitation skills needed to train students, communication skills training has been integrated in the curriculum of all five healthcare educational programmes....

  12. Dogs in the Hall: A Case Study of Affective Skill Development in an Urban Veterinary Program

    Science.gov (United States)

    Martin, Michael; Tummons, John; Ball, Anna; Bird, William

    2014-01-01

    The purpose of this bounded single case study was to explore how an urban high school veterinary program impacted students' affective skill development. The program was unique because students were required to participate in internships with local animal care businesses and care for animals within the school veterinary laboratory. The…

  13. Effect of the Creative Drama-Based Assertiveness Program on the Assertiveness Skill of Psychological Counsellor Candidates

    Science.gov (United States)

    Gundogdu, Rezzan

    2012-01-01

    The purpose of this quasi-experimental research is to study the effects of the creative drama-based assertiveness program (CDBAP) on the assertiveness skill of Psychological Counselling and Guidance (PCG) department students. The opinions of experimental group students on the program were obtained through the CDBAP evaluation form. The sample of…

  14. A global perspective on evolving bioinformatics and data science training needs.

    Science.gov (United States)

    Attwood, Teresa K; Blackford, Sarah; Brazas, Michelle D; Davies, Angela; Schneider, Maria Victoria

    2017-08-29

    Bioinformatics is now intrinsic to life science research, but the past decade has witnessed a continuing deficiency in this essential expertise. Basic data stewardship is still taught relatively rarely in life science education programmes, creating a chasm between theory and practice, and fuelling demand for bioinformatics training across all educational levels and career roles. Concerned by this, surveys have been conducted in recent years to monitor bioinformatics and computational training needs worldwide. This article briefly reviews the principal findings of a number of these studies. We see that there is still a strong appetite for short courses to improve expertise and confidence in data analysis and interpretation; strikingly, however, the most urgent appeal is for bioinformatics to be woven into the fabric of life science degree programmes. Satisfying the relentless training needs of current and future generations of life scientists will require a concerted response from stakeholders across the globe, who need to deliver sustainable solutions capable of both transforming education curricula and cultivating a new cadre of trainer scientists. © The Author 2017. Published by Oxford University Press.

  15. A Bioinformatic Pipeline for Monitoring of the Mutational Stability of Viral Drug Targets with Deep-Sequencing Technology.

    Science.gov (United States)

    Kravatsky, Yuri; Chechetkin, Vladimir; Fedoseeva, Daria; Gorbacheva, Maria; Kravatskaya, Galina; Kretova, Olga; Tchurikov, Nickolai

    2017-11-23

    The efficient development of antiviral drugs, including efficient antiviral small interfering RNAs (siRNAs), requires continuous monitoring of the strict correspondence between a drug and the related highly variable viral DNA/RNA target(s). Deep sequencing is able to provide an assessment of both the general target conservation and the frequency of particular mutations in the different target sites. The aim of this study was to develop a reliable bioinformatic pipeline for the analysis of millions of short, deep sequencing reads corresponding to selected highly variable viral sequences that are drug target(s). The suggested bioinformatic pipeline combines the available programs and the ad hoc scripts based on an original algorithm of the search for the conserved targets in the deep sequencing data. We also present the statistical criteria for the threshold of reliable mutation detection and for the assessment of variations between corresponding data sets. These criteria are robust against the possible sequencing errors in the reads. As an example, the bioinformatic pipeline is applied to the study of the conservation of RNA interference (RNAi) targets in human immunodeficiency virus 1 (HIV-1) subtype A. The developed pipeline is freely available to download at the website http://virmut.eimb.ru/. Brief comments and comparisons between VirMut and other pipelines are also presented.

  16. 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'…

  17. Monetary incentives to reinforce engagement and achievement in a job-skills training program for homeless, unemployed adults.

    Science.gov (United States)

    Koffarnus, Mikhail N; Wong, Conrad J; Fingerhood, Michael; Svikis, Dace S; Bigelow, George E; Silverman, Kenneth

    2013-01-01

    The current study examined whether monetary incentives could increase engagement and achievement in a job-skills training program for unemployed, homeless, alcohol-dependent adults. Participants (n=124) were randomized to a no-reinforcement group (n=39), during which access to the training program was provided but no incentives were given; a training reinforcement group (n=42), during which incentives were contingent on attendance and performance; or an abstinence and training reinforcement group (n=43), during which incentives were contingent on attendance and performance, but access was granted only if participants demonstrated abstinence from alcohol. abstinence and training reinforcement and training reinforcement participants advanced further in training and attended more hours than no-reinforcement participants. Monetary incentives were effective in promoting engagement and achievement in a job-skills training program for individuals who often do not take advantage of training programs. © Society for the Experimental Analysis of Behavior.

  18. 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.

  19. A Pilot Study Examining the Effectiveness of the PEERS Program on Social Skills and Anxiety in Adolescents with Autism Spectrum Disorder.

    Science.gov (United States)

    Hill, Trenesha L; Gray, Sarah A O; Baker, Courtney N; Boggs, Koren; Carey, Elizabeth; Johnson, Corinn; Kamps, Jodi L; Varela, R Enrique

    2017-10-01

    The Program for the Evaluation of the Enrichment of Relational Skills (PEERS), a social skills intervention for high functioning adolescents with autism spectrum disorder (ASD), has been proven efficacious in randomized control trials. However, the effectiveness of the PEERS program in community settings has not been studied. The present small-scale pilot study examined the effectiveness of the PEERS program in a community setting. Five adolescents and their caregivers participated in the PEERS intervention. Results indicated that the adolescents showed significant improvement in their social engagement, social cognition, social communication, social motivation, and knowledge of PEERS skills and concepts from pre- to post-intervention. Furthermore, adolescents showed significant reductions in their internalizing and autistic symptoms from pre- to post-intervention. The findings from this small-scale pilot study support the effectiveness of the PEERS program in community-based settings.

  20. A mentor-based portfolio program to evaluate pharmacy students' self-assessment skills.

    Science.gov (United States)

    Kalata, Lindsay R; Abate, Marie A

    2013-05-13

    Objective. To evaluate pharmacy students' self-assessment skills with an electronic portfolio program using mentor evaluators. Design. First-year (P1) and second-year (P2) pharmacy students used online portfolios that required self-assessments of specific graded class assignments. Using a rubric, faculty and alumni mentors evaluated students' self-assessments and provided feedback. Assessment. Eighty-four P1 students, 74 P2 students, and 59 mentors participated in the portfolio program during 2010-2011. Both student groups performed well overall, with only a small number of resubmissions required. P1 students showed significant improvements across semesters for 2 of the self-assessment questions; P2 students' scores did not differ significantly. The P1 scores were significantly higher than P2 scores for 3 questions during spring 2011. Mentors and students had similar levels of agreement with the extent to which students put forth their best effort on the self-assessments. Conclusion. An electronic portfolio using mentors based inside and outside the school provided students with many opportunities to practice their self-assessment skills. This system represents a useful method of incorporating self-assessments into the curriculum that allows for feedback to be provided to the students.

  1. Using a Multimedia-Based Program for Developing Student Teachers' EFL Speaking Fluency Skills

    Science.gov (United States)

    Diyyab, Eman Aly; Abdel-Haq, Eman Muhamad; Aly, Mahsoub Abdel-Sadeq

    2013-01-01

    The objective of the present study was to investigate the effectiveness of using a multimedia-based program for developing EFL speaking fluency skills among second year, English section student teachers. The sample of the present study consisted of thirty students at Sadat Faculty of Education, Minufiya University, Egypt. The study sample was…

  2. Communication skills in pediatric training program: National-based survey of residents' perspectives in Saudi Arabia.

    Science.gov (United States)

    Alofisan, Tariq; Al-Alaiyan, Saleh; Al-Abdulsalam, Moath; Siddiqui, Khawar; Hussain, Ibrahim Bin; Al-Qahtani, Mohammad H

    2016-01-01

    Good communication skills and rapport building are considered the cardinal tools for developing a patient-doctor relationship. A positive, healthy competition among different health care organizations in Saudi Arabia underlines an ever increasing emphasis on effective patient-doctor relationship. Despite the numerous guidelines provided and programs available, there is a significant variation in the acceptance and approach to the use of this important tool among pediatric residents in this part of the world. To determine pediatric residents' attitude toward communication skills, their perception of important communication skills, and their confidence in the use of their communication skills in the performance of their primary duties. A cross-sectional study was conducted among all pediatrics trainee residents working in 13 different hospitals in Saudi Arabia. A standardized self-administered questionnaire developed by the Harvard Medical School was used. A total of 297 residents out of all trainees in these centers participated in the data collection. The 283 (95%) residents considered learning communication skills a priority in establishing a good patient-doctor relationship. Thirty four percent reported being very confident with regard to their communication skills. Few residents had the skills, and the confidence to communicate with children with serious diseases, discuss end-of-life issues, and deal with difficult patients and parents. Pediatric residents perceive the importance of communication skills and competencies as crucial components in their training. A proper comprehensive communication skills training should be incorporated into the pediatric resident training curriculum.

  3. What is bioinformatics? A proposed definition and overview of the field.

    Science.gov (United States)

    Luscombe, N M; Greenbaum, D; Gerstein, M

    2001-01-01

    The recent flood of data from genome sequences and functional genomics has given rise to new field, bioinformatics, which combines elements of biology and computer science. Here we propose a definition for this new field and review some of the research that is being pursued, particularly in relation to transcriptional regulatory systems. Our definition is as follows: Bioinformatics is conceptualizing biology in terms of macromolecules (in the sense of physical-chemistry) and then applying "informatics" techniques (derived from disciplines such as applied maths, computer science, and statistics) to understand and organize the information associated with these molecules, on a large-scale. Analyses in bioinformatics predominantly focus on three types of large datasets available in molecular biology: macromolecular structures, genome sequences, and the results of functional genomics experiments (e.g. expression data). Additional information includes the text of scientific papers and "relationship data" from metabolic pathways, taxonomy trees, and protein-protein interaction networks. Bioinformatics employs a wide range of computational techniques including sequence and structural alignment, database design and data mining, macromolecular geometry, phylogenetic tree construction, prediction of protein structure and function, gene finding, and expression data clustering. The emphasis is on approaches integrating a variety of computational methods and heterogeneous data sources. Finally, bioinformatics is a practical discipline. We survey some representative applications, such as finding homologues, designing drugs, and performing large-scale censuses. Additional information pertinent to the review is available over the web at http://bioinfo.mbb.yale.edu/what-is-it.

  4. An overview of topic modeling and its current applications in bioinformatics.

    Science.gov (United States)

    Liu, Lin; Tang, Lin; Dong, Wen; Yao, Shaowen; Zhou, Wei

    2016-01-01

    With the rapid accumulation of biological datasets, machine learning methods designed to automate data analysis are urgently needed. In recent years, so-called topic models that originated from the field of natural language processing have been receiving much attention in bioinformatics because of their interpretability. Our aim was to review the application and development of topic models for bioinformatics. This paper starts with the description of a topic model, with a focus on the understanding of topic modeling. A general outline is provided on how to build an application in a topic model and how to develop a topic model. Meanwhile, the literature on application of topic models to biological data was searched and analyzed in depth. According to the types of models and the analogy between the concept of document-topic-word and a biological object (as well as the tasks of a topic model), we categorized the related studies and provided an outlook on the use of topic models for the development of bioinformatics applications. Topic modeling is a useful method (in contrast to the traditional means of data reduction in bioinformatics) and enhances researchers' ability to interpret biological information. Nevertheless, due to the lack of topic models optimized for specific biological data, the studies on topic modeling in biological data still have a long and challenging road ahead. We believe that topic models are a promising method for various applications in bioinformatics research.

  5. Galaxy Workflows for Web-based Bioinformatics Analysis of Aptamer High-throughput Sequencing Data

    Directory of Open Access Journals (Sweden)

    William H Thiel

    2016-01-01

    Full Text Available Development of RNA and DNA aptamers for diagnostic and therapeutic applications is a rapidly growing field. Aptamers are identified through iterative rounds of selection in a process termed SELEX (Systematic Evolution of Ligands by EXponential enrichment. High-throughput sequencing (HTS revolutionized the modern SELEX process by identifying millions of aptamer sequences across multiple rounds of aptamer selection. However, these vast aptamer HTS datasets necessitated bioinformatics techniques. Herein, we describe a semiautomated approach to analyze aptamer HTS datasets using the Galaxy Project, a web-based open source collection of bioinformatics tools that were originally developed to analyze genome, exome, and transcriptome HTS data. Using a series of Workflows created in the Galaxy webserver, we demonstrate efficient processing of aptamer HTS data and compilation of a database of unique aptamer sequences. Additional Workflows were created to characterize the abundance and persistence of aptamer sequences within a selection and to filter sequences based on these parameters. A key advantage of this approach is that the online nature of the Galaxy webserver and its graphical interface allow for the analysis of HTS data without the need to compile code or install multiple programs.

  6. 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…

  7. Implementing the LifeSkills Training drug prevention program: factors related to implementation fidelity.

    Science.gov (United States)

    Mihalic, Sharon F; Fagan, Abigail A; Argamaso, Susanne

    2008-01-18

    Widespread replication of effective prevention programs is unlikely to affect the incidence of adolescent delinquency, violent crime, and substance use until the quality of implementation of these programs by community-based organizations can be assured. This paper presents the results of a process evaluation employing qualitative and quantitative methods to assess the extent to which 432 schools in 105 sites implemented the LifeSkills Training (LST) drug prevention program with fidelity. Regression analysis was used to examine factors influencing four dimensions of fidelity: adherence, dosage, quality of delivery, and student responsiveness. Although most sites faced common barriers, such as finding room in the school schedule for the program, gaining full support from key participants (i.e., site coordinators, principals, and LST teachers), ensuring teacher participation in training workshops, and classroom management difficulties, most schools involved in the project implemented LST with very high levels of fidelity. Across sites, 86% of program objectives and activities required in the three-year curriculum were delivered to students. Moreover, teachers were observed using all four recommended teaching practices, and 71% of instructors taught all the required LST lessons. Multivariate analyses found that highly rated LST program characteristics and better student behavior were significantly related to a greater proportion of material taught by teachers (adherence). Instructors who rated the LST program characteristics as ideal were more likely to teach all lessons (dosage). Student behavior and use of interactive teaching techniques (quality of delivery) were positively related. No variables were related to student participation (student responsiveness). Although difficult, high implementation fidelity by community-based organizations can be achieved. This study suggests some important factors that organizations should consider to ensure fidelity, such as

  8. Implementing the LifeSkills Training drug prevention program: factors related to implementation fidelity

    Directory of Open Access Journals (Sweden)

    Fagan Abigail A

    2008-01-01

    Full Text Available Abstract Background Widespread replication of effective prevention programs is unlikely to affect the incidence of adolescent delinquency, violent crime, and substance use until the quality of implementation of these programs by community-based organizations can be assured. Methods This paper presents the results of a process evaluation employing qualitative and quantitative methods to assess the extent to which 432 schools in 105 sites implemented the LifeSkills Training (LST drug prevention program with fidelity. Regression analysis was used to examine factors influencing four dimensions of fidelity: adherence, dosage, quality of delivery, and student responsiveness. Results Although most sites faced common barriers, such as finding room in the school schedule for the program, gaining full support from key participants (i.e., site coordinators, principals, and LST teachers, ensuring teacher participation in training workshops, and classroom management difficulties, most schools involved in the project implemented LST with very high levels of fidelity. Across sites, 86% of program objectives and activities required in the three-year curriculum were delivered to students. Moreover, teachers were observed using all four recommended teaching practices, and 71% of instructors taught all the required LST lessons. Multivariate analyses found that highly rated LST program characteristics and better student behavior were significantly related to a greater proportion of material taught by teachers (adherence. Instructors who rated the LST program characteristics as ideal were more likely to teach all lessons (dosage. Student behavior and use of interactive teaching techniques (quality of delivery were positively related. No variables were related to student participation (student responsiveness. Conclusion Although difficult, high implementation fidelity by community-based organizations can be achieved. This study suggests some important factors that

  9. GProX, a user-friendly platform for bioinformatics analysis and visualization of quantitative proteomics data.

    Science.gov (United States)

    Rigbolt, Kristoffer T G; Vanselow, Jens T; Blagoev, Blagoy

    2011-08-01

    Recent technological advances have made it possible to identify and quantify thousands of proteins in a single proteomics experiment. As a result of these developments, the analysis of data has become the bottleneck of proteomics experiment. To provide the proteomics community with a user-friendly platform for comprehensive analysis, inspection and visualization of quantitative proteomics data we developed the Graphical Proteomics Data Explorer (GProX)(1). The program requires no special bioinformatics training, as all functions of GProX are accessible within its graphical user-friendly interface which will be intuitive to most users. Basic features facilitate the uncomplicated management and organization of large data sets and complex experimental setups as well as the inspection and graphical plotting of quantitative data. These are complemented by readily available high-level analysis options such as database querying, clustering based on abundance ratios, feature enrichment tests for e.g. GO terms and pathway analysis tools. A number of plotting options for visualization of quantitative proteomics data is available and most analysis functions in GProX create customizable high quality graphical displays in both vector and bitmap formats. The generic import requirements allow data originating from essentially all mass spectrometry platforms, quantitation strategies and software to be analyzed in the program. GProX represents a powerful approach to proteomics data analysis providing proteomics experimenters with a toolbox for bioinformatics analysis of quantitative proteomics data. The program is released as open-source and can be freely downloaded from the project webpage at http://gprox.sourceforge.net.

  10. Modern bioinformatics meets traditional Chinese medicine.

    Science.gov (United States)

    Gu, Peiqin; Chen, Huajun

    2014-11-01

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

  11. Coping modeling problem solving versus mastery modeling: effects on adherence, in-session process, and skill acquisition in a residential parent-training program.

    Science.gov (United States)

    Cunningham, C E; Davis, J R; Bremner, R; Dunn, K W; Rzasa, T

    1993-10-01

    This trial compared two approaches used to introduce parenting skills in a residential staff training program. Fifty staff were randomly assigned to: mastery modelling in which videotaped models demonstrated new skills, coping modelling problem solving (CMPS) in which participants formulated their own solutions to the errors depicted by videotaped models, or a waiting-list control group. In both, leaders used modelling, role playing, and homework projects to promote mastery and transfer of new skills. The skills of all groups improved, but CMPS participants attended more sessions, were late to fewer sessions, completed more homework, engaged in more cooperative in-session interaction, rated the program more positively, and reported higher job accomplishment scores. These data suggest that CMPS allowing participants to formulate their own solutions may enhance adherence and reduce the resistance observed in more didactic programs.

  12. A Training Program to Enhance Postgraduate Students' Research Skills in Preparing a Research Proposal in the Field of Curriculum and Instruction Methods of Arabic Language

    Science.gov (United States)

    Alfakih, Ahmed Hassan

    2017-01-01

    The study examined the impact of a training program on enhancing postgraduate students' research skills in preparing a research proposal. The nature of the skills required to prepare a research proposal were first determined using a questionnaire. A training program for improving such skills was then constructed and seven postgraduate students in…

  13. Improving Nurses' Peripheral Intravenous Catheter Insertion Knowledge, Confidence, and Skills Using a Simulation-Based Blended Learning Program: A Randomized Trial.

    Science.gov (United States)

    Keleekai, Nowai L; Schuster, Catherine A; Murray, Connie L; King, Mary Anne; Stahl, Brian R; Labrozzi, Laura J; Gallucci, Susan; LeClair, Matthew W; Glover, Kevin R

    2016-12-01

    Peripheral intravenous catheter (PIVC) insertion is one of the most common invasive procedures performed in a hospital, but most nurses receive little formal training in this area. Blended PIVC insertion training programs that incorporate deliberate simulated practice have the potential to improve clinical practice and patient care. The study was a randomized, wait-list control group with crossover using nurses on three medical/surgical units. Baseline PIVC knowledge, confidence, and skills assessments were completed for both groups. The intervention group then received a 2-hour PIVC online course, followed by an 8-hour live training course using a synergistic mix of three simulation tools. Both groups were then reassessed. After crossover, the wait-list group received the same intervention and both groups were reassessed. At baseline, both groups were similar for knowledge, confidence, and skills. Compared with the wait-list group, the intervention group had significantly higher scores for knowledge, confidence, and skills upon completing the training program. After crossover, the wait-list group had similarly higher scores for knowledge, confidence, and skills than the intervention group. Between the immediate preintervention and postintervention periods, the intervention group improved scores for knowledge by 31%, skills by 24%, and decreased confidence by 0.5%, whereas the wait-list group improved scores for knowledge by 28%, confidence by 16%, and skills by 15%. Results demonstrate significant improvements in nurses' knowledge, confidence, and skills with the use of a simulation-based blended learning program for PIVC insertion. Transferability of these findings from a simulated environment into clinical practice should be further explored.

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

    Directory of Open Access Journals (Sweden)

    Ernest Rossi

    2006-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Ernest Rossi

    2006-01-01

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

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

    Science.gov (United States)

    Dalpé, Gratien; Joly, Yann

    2014-09-01

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

  17. A Longitudinal Study of Handwriting Skills in Pre-Schoolers: The Acquisition of Syllable Oriented Programming Strategies

    Science.gov (United States)

    Soler Vilageliu, Olga; Kandel, Sonia

    2012-01-01

    Previous studies have shown the relevance of the syllable as a programming unit in handwriting production, both in adults and elementary school children. This longitudinal study focuses on the acquisition of writing skills in a group of preschoolers. It examines how and when the syllable structure of the word starts regulating motor programming in…

  18. A Program Based on the Pragmatic Theory to Develop Grammatical Structure Comprehension Skills for Foreign Learners of Arabic

    Science.gov (United States)

    Elsamman, Marwan

    2014-01-01

    This study aimed at designing a program based on the Pragmatic theory to develop grammatical structure comprehension skills for foreign learners of Arabic and examining its effectiveness. Hence, the problem of the study has been summarized in the weakness of grammatical structure comprehension skills for foreign learners of Arabic and in the need…

  19. 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

  20. Improving the Teaching Skills of Residents in a Surgical Training Program: Results of the Pilot Year of a Curricular Initiative in an Ophthalmology Residency Program.

    Science.gov (United States)

    Chee, Yewlin E; Newman, Lori R; Loewenstein, John I; Kloek, Carolyn E

    2015-01-01

    To design and implement a teaching skills curriculum that addressed the needs of an ophthalmology residency training program, to assess the effect of the curriculum, and to present important lessons learned. A teaching skills curriculum was designed for the Harvard Medical School (HMS) Residency Training Program in Ophthalmology. Results of a needs assessment survey were used to guide curriculum objectives. Overall, 3 teaching workshops were conducted between October 2012 and March 2013 that addressed areas of need, including procedural teaching. A postcurriculum survey was used to assess the effect of the curriculum. Massachusetts Eye and Ear Infirmary, a tertiary care institution in Boston, MA. Overall, 24 residents in the HMS Residency Training Program in Ophthalmology were included. The needs assessment survey demonstrated that although most residents anticipated that teaching would be important in their future career, only one-third had prior formal training in teaching. All residents reported they found the teaching workshops to be either very or extremely useful. All residents reported they would like further training in teaching, with most residents requesting additional training in best procedural teaching practices for future sessions. The pilot year of the resident-as-teacher curriculum for the HMS Residency Training Program in Ophthalmology demonstrated a need for this curriculum and was perceived as beneficial by the residents, who reported increased comfort in their teaching skills after attending the workshops. Copyright © 2015 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

  1. Developing a strategy for computational lab skills training through Software and Data Carpentry: Experiences from the ELIXIR Pilot action [version 1; referees: 3 approved

    Directory of Open Access Journals (Sweden)

    Aleksandra Pawlik

    2017-07-01

    Full Text Available Quality training in computational skills for life scientists is essential to allow them to deliver robust, reproducible and cutting-edge research. A pan-European bioinformatics programme, ELIXIR, has adopted a well-established and progressive programme of computational lab and data skills training from Software and Data Carpentry, aimed at increasing the number of skilled life scientists and building a sustainable training community in this field. This article describes the Pilot action, which introduced the Carpentry training model to the ELIXIR community.

  2. Teaching citizen science skills online: Implications for invasive species training programs

    Science.gov (United States)

    Newman, G.; Crall, A.; Laituri, M.; Graham, J.; Stohlgren, T.; Moore, J.C.; Kodrich, K.; Holfelder, K.A.

    2010-01-01

    Citizen science programs are emerging as an efficient way to increase data collection and help monitor invasive species. Effective invasive species monitoring requires rigid data quality assurances if expensive control efforts are to be guided by volunteer data. To achieve data quality, effective online training is needed to improve field skills and reach large numbers of remote sentinel volunteers critical to early detection and rapid response. The authors evaluated the effectiveness of online static and multimedia tutorials to teach citizen science volunteers (n = 54) how to identify invasive plants; establish monitoring plots; measure percent cover; and use Global Positioning System (GPS) units. Participants trained using static and multimedia tutorials provided less (p quality, and overall program effectiveness. ?? Taylor & Francis Group, LLC.

  3. Horses and At-Risk Youth: An Equine Facilitated Learning Program Focusing on Authentic Leadership Skill Development

    Directory of Open Access Journals (Sweden)

    Brittany L. Adams-Pope

    2014-12-01

    Full Text Available Interesting and innovative youth development programs are important to further youth education. Programs focused on developing leadership skills in youth, specifically at-risk youth, are important when thinking of the future of our communities. The primary purpose of the study was to determine the impact of an equine facilitated, authentic leadership program on at-risk youth. Youth participated in a three-day equine facilitated learning program based on authentic leadership with focus groups conducted three days before and three days after the program. In this article, we describe the development and methodology of the program and specific implications for practice.

  4. Routine programs of health care systems as an opportunity toward communication skills training for family physicians: A randomized field trial.

    Science.gov (United States)

    Zamani, Ahmad Reza; Motamedi, Narges; Farajzadegan, Ziba

    2015-01-01

    To have high-quality primary health care services, an adequate doctor-patient communication is necessary. Because of time restrictions and limited budget in health system, an effective, feasible, and continuous training approach is important. The aim of this study is to assess the appropriateness of a communication skills training program simultaneously with routine programs of health care system. It was a randomized field trial in two health network settings during 2013. Twenty-eight family physicians through simple random sampling and 140 patients through convenience sampling participated as intervention and control group. The physicians in the intervention group (n = 14) attended six educational sessions, simultaneous organization meeting, with case discussion and peer education method. In both the groups, physicians completed communication skills knowledge and attitude questionnaires, and patients completed patient satisfaction of medical interview questionnaire at baseline, immediately after intervention, and four months postintervention. Physicians and health network administrators (stakeholders), completed a set of program evaluation forms. Descriptive statistics and Chi-square test, t-test, and repeated measure analysis of variance were used to analyze the data. Use of routine program as a strategy of training was rated by stakeholders highly on "feasibility" (80.5%), "acceptability" (93.5%), "educational content and method appropriateness" (80.75%), and "ability to integrating in the health system programs" (approximate 60%). Significant improvements were found in physicians' knowledge (P Communication skills training program, simultaneous organization meeting was successfully implemented and well received by stakeholders, without considering extra time and manpower. Therefore it can be a valuable opportunity toward communication skills training.

  5. IT Workforce: Key Practices Help Ensure Strong Integrated Program Teams; Selected Departments Need to Assess Skill Gaps

    Science.gov (United States)

    2016-11-01

    principles and steps associated with workforce planning that agencies can utilize in their efforts to assess and address IT skill gaps. See GAO-04-39...As another example, our prior review of the United States Department of Agriculture’s Farm Service Agency’s Modernize and Innovate the Delivery of...IT WORKFORCE Key Practices Help Ensure Strong Integrated Program Teams; Selected Departments Need to Assess Skill Gaps

  6. New Link in Bioinformatics Services Value Chain: Position, Organization and Business Model

    Directory of Open Access Journals (Sweden)

    Mladen Čudanov

    2012-11-01

    Full Text Available This paper presents development in the bioinformatics services industry value chain, based on cloud computing paradigm. As genome sequencing costs per Megabase exponentially drop, industry needs to adopt. Paper has two parts: theoretical analysis and practical example of Seven Bridges Genomics Company. We are focused on explaining organizational, business and financial aspects of new business model in bioinformatics services, rather than technical side of the problem. In the light of that we present twofold business model fit for core bioinformatics research and Information and Communication Technologie (ICT support in the new environment, with higher level of capital utilization and better resistance to business risks.

  7. Communication skills in pediatric training program: National-based survey of residents′ perspectives in Saudi Arabia

    Directory of Open Access Journals (Sweden)

    Tariq Alofisan

    2016-01-01

    Full Text Available Background: Good communication skills and rapport building are considered the cardinal tools for developing a patient-doctor relationship. A positive, healthy competition among different health care organizations in Saudi Arabia underlines an ever increasing emphasis on effective patient-doctor relationship. Despite the numerous guidelines provided and programs available, there is a significant variation in the acceptance and approach to the use of this important tool among pediatric residents in this part of the world. Objective: To determine pediatric residents′ attitude toward communication skills, their perception of important communication skills, and their confidence in the use of their communication skills in the performance of their primary duties. Materials and Methods: A cross-sectional study was conducted among all pediatrics trainee residents working in 13 different hospitals in Saudi Arabia. A standardized self-administered questionnaire developed by the Harvard Medical School was used. Results: A total of 297 residents out of all trainees in these centers participated in the data collection. The 283 (95% residents considered learning communication skills a priority in establishing a good patient-doctor relationship. Thirty four percent reported being very confident with regard to their communication skills. Few residents had the skills, and the confidence to communicate with children with serious diseases, discuss end-of-life issues, and deal with difficult patients and parents. Conclusion: Pediatric residents perceive the importance of communication skills and competencies as crucial components in their training. A proper comprehensive communication skills training should be incorporated into the pediatric resident training curriculum.

  8. Bioinformatics in High School Biology Curricula: A Study of State Science Standards

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    Wefer, Stephen H.; Sheppard, Keith

    2008-01-01

    The proliferation of bioinformatics in modern biology marks a modern revolution in science that promises to influence science education at all levels. This study analyzed secondary school science standards of 49 U.S. states (Iowa has no science framework) and the District of Columbia for content related to bioinformatics. The bioinformatics…

  9. Lecturing skills as predictors of tutoring skills in a problem-based medical curriculum

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    Kassab SE

    2016-01-01

    Full Text Available Salah Eldin Kassab,1 Nahla Hassan,1 Marwan F Abu-Hijleh,2 Reginald P Sequeira3 1Department of Medical Education, Faculty of Medicine, Suez Canal University, Ismailia, Egypt; 2College of Medicine, Qatar University, Doha, Qatar; 3College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Kingdom of Bahrain Purpose: Recruitment of tutors to work in problem-based learning (PBL programs is challenging, especially in that most of them are graduated from discipline-based programs. Therefore, this study aims at examining whether lecturing skills of faculty could predict their PBL tutoring skills. Methods: This study included evaluation of faculty (n=69 who participated in both tutoring and lecturing within particular PBL units at the College of Medicine and Medical Sciences (CMMS, Arabian Gulf University, Bahrain. Each faculty was evaluated by medical students (n=45±8 for lecturing and 8±2 for PBL tutoring using structured evaluation forms based on a Likert-type scale (poor to excellent. The prediction of tutoring skills using lecturing skills was statistically analyzed using stepwise linear regression. Results: Among the parameters used to judge lecturing skills, the most important predictor for tutoring skills was subject matter mastery in the lecture by explaining difficult concepts and responding effectively to students' questions. Subject matter mastery in the lecture positively predicted five tutoring skills and accounted for 25% of the variance in overall effectiveness of the PBL tutors (F=22.39, P=0.000. Other important predictors for tutoring skills were providing a relaxed class atmosphere and effective use of audiovisual aids in the lecture. Conclusion: Predicting the tutoring skills based on lecturing skills could have implications for recruiting tutors in PBL medical programs and for tutor training initiatives. Keywords: PBL, tutor, tutoring skills, lecturing skills

  10. The Secret Agent Society Social Skills Program for Children with High-Functioning Autism Spectrum Disorders: A Comparison of Two School Variants

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    Beaumont, Renae; Rotolone, Cassie; Sofronoff, Kate

    2015-01-01

    School is often considered an ideal setting for child social skills training due to the opportunities it provides for skills teaching, modeling, and practice. The current study evaluated the effectiveness of two variants of the Secret Agent Society social skills program for children with high-functioning autism spectrum disorders (HFASD) in a…

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

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    Jung, Sook; Main, Dorrie

    2014-01-01

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

  12. Open source tools and toolkits for bioinformatics: significance, and where are we?

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    Stajich, Jason E; Lapp, Hilmar

    2006-09-01

    This review summarizes important work in open-source bioinformatics software that has occurred over the past couple of years. The survey is intended to illustrate how programs and toolkits whose source code has been developed or released under an Open Source license have changed informatics-heavy areas of life science research. Rather than creating a comprehensive list of all tools developed over the last 2-3 years, we use a few selected projects encompassing toolkit libraries, analysis tools, data analysis environments and interoperability standards to show how freely available and modifiable open-source software can serve as the foundation for building important applications, analysis workflows and resources.

  13. The Effectiveness of the "Lions Quest Program: Skills for Growing" on School Climate, Students' Behaviors, Perceptions of School, and Conflict Resolution Skills

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    Gol-Guven, Mine

    2017-01-01

    This study examines the effectiveness of the Lions Quest Program: Skills for Growing by employing a quasi-experimental design with a control group. The experimental and control group each comprises two primary schools--one public, one private. One classroom at each grade level, 1 through 4, in each school was selected by random sampling for a…

  14. Implementing bioinformatic workflows within the bioextract server

    Science.gov (United States)

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

  15. Examining the Effect of Social Values Education Program Being Applied to Nursery School Students upon Acquiring Social Skills

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    Sapsaglam, Özkan; Ömeroglu, Esra

    2016-01-01

    This study was conducted in an attempt to develop Social Values Education Program aimed at nursery school students and examine the effect of Social Values Education Program upon the social skill acquisition of nursery school students. The effect of the education program that was developed within the scope of the study upon the social skill…

  16. Short-term effects of the "Together at School" intervention program on children's socio-emotional skills: a cluster randomized controlled trial.

    Science.gov (United States)

    Kiviruusu, Olli; Björklund, Katja; Koskinen, Hanna-Leena; Liski, Antti; Lindblom, Jallu; Kuoppamäki, Heini; Alasuvanto, Paula; Ojala, Tiina; Samposalo, Hanna; Harmes, Nina; Hemminki, Elina; Punamäki, Raija-Leena; Sund, Reijo; Santalahti, Päivi

    2016-05-26

    Together at School is a universal intervention program designed to promote socio-emotional skills among primary-school children. It is based on a whole school approach, and implemented in school classes by teachers. The aim of the present study is to examine the short-term effects of the intervention program in improving socio-emotional skills and reducing psychological problems among boys and girls. We also examine whether these effects depend on grade level (Grades 1 to 3) and intervention dosage. This cluster randomized controlled trial design included 79 Finnish primary schools (40 intervention and 39 control) with 3 704 children. The outcome measures were the Strengths and Difficulties Questionnaire (SDQ) and the Multisource Assessment of Social Competence Scale (MASCS) with teachers as raters. The intervention dosage was indicated by the frequencies six central tools were used by the teachers. The data was collected at baseline and 6 months later. Intervention effects were analyzed using multilevel modeling. When analyzed across all grades no intervention effect was observed in improving children's socio-emotional skills or in reducing their psychological problems at 6-month follow-up. Among third (compared to first) graders the intervention decreased psychological problems. Stratified analyses by gender showed that this effect was significant only among boys and that among them the intervention also improved third graders' cooperation skills. Among girls the intervention effects were not moderated by grade. Implementing the intervention with intended intensity (i.e. a high enough dosage) had a significant positive effect on cooperation skills. When analyzed separately among genders, this effect was significant only in girls. These first, short-term results of the Together at School intervention program did not show any main effects on children's socio-emotional skills or psychological problems. This lack of effects may be due to the relatively short follow

  17. Effects of a Multimedia Social Skills Program in Increasing Social Responses and Initiations of Children with Autism Spectrum Disorder

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    Block, Heidi M.; Radley, Keith C.; Jenson, William R.; Clark, Elaine; O'Neill, Robert E.

    2015-01-01

    The current study evaluated the effectiveness of Superheroes Social Skills, a multimedia social skills package, in improving social responsiveness and social initiation behaviors of four elementary school children with an autism spectrum disorder (ASD). The program was implemented in a public school setting in the southwestern United States for…

  18. Building Professional and Technical Skills in the Use of Earth Observations through the NASA DEVELOP National Program: Best Practices & Lessons Learned

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    Crepps, G.; Ross, K. W.; Childs-Gleason, L. M.; Allsbrook, K. N.; Rogers, L.; Ruiz, M. L.; Clayton, A.

    2017-12-01

    The NASA DEVELOP National Program offers 10-week research opportunities to participants to work on rapid feasibility projects utilizing NASA Earth observations in a variety of applications, including ecological forecasting, water resources, disasters, and health and air quality. DEVELOP offers a unique collaborative environment in which students, recent graduates, and transitioning career professionals are placed on interdisciplinary teams to conduct projects. DEVELOP offers a variety of opportunities and resources to build participants technical skills in remote sensing and GIS, as well as interpersonal and leadership skills. As a capacity building program, DEVELOP assesses participants' growth by using entrance and exit personal growth assessments, as well as gathering general program feedback through an exit survey. All of this information is fed back into the program for continual improvement. DEVELOP also offers a progression of opportunities through which participants can advance through the program, allowing participants to build a diverse set of technical and leadership skills. This presentation will explore best practices including the use of pre- and post-growth assessments, offering advanced leadership opportunities, and overall capacity building impacts on participants.

  19. Monetary Incentives to Reinforce Engagement and Achievement in a Job-Skills Training Program for Homeless, Unemployed Adults

    Science.gov (United States)

    Koffarnus, Mikhail N.; Wong, Conrad J.; Fingerhood, Michael; Svikis, Dace S.; Bigelow, George E.; Silverman, Kenneth

    2013-01-01

    The current study examined whether monetary incentives could increase engagement and achievement in a job-skills training program for unemployed, homeless, alcohol-dependent adults. Participants (n?=?124) were randomized to a no-reinforcement group (n?=?39), during which access to the training program was provided but no incentives were given; a…

  20. A Mentor-Based Portfolio Program to Evaluate Pharmacy Students’ Self-Assessment Skills

    Science.gov (United States)

    Kalata, Lindsay R.

    2013-01-01

    Objective. To evaluate pharmacy students' self-assessment skills with an electronic portfolio program using mentor evaluators. Design. First-year (P1) and second-year (P2) pharmacy students used online portfolios that required self-assessments of specific graded class assignments. Using a rubric, faculty and alumni mentors evaluated students' self-assessments and provided feedback. Assessment. Eighty-four P1 students, 74 P2 students, and 59 mentors participated in the portfolio program during 2010-2011. Both student groups performed well overall, with only a small number of resubmissions required. P1 students showed significant improvements across semesters for 2 of the self-assessment questions; P2 students' scores did not differ significantly. The P1 scores were significantly higher than P2 scores for 3 questions during spring 2011. Mentors and students had similar levels of agreement with the extent to which students put forth their best effort on the self-assessments. Conclusion. An electronic portfolio using mentors based inside and outside the school provided students with many opportunities to practice their self-assessment skills. This system represents a useful method of incorporating self-assessments into the curriculum that allows for feedback to be provided to the students. PMID:23716749