Integration of Bioinformatics into an Undergraduate Biology Curriculum and the Impact on Development of Mathematical Skills

ERIC Educational Resources Information Center

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…

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

ERIC Educational Resources Information Center

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…

Evaluating the effectiveness of a practical inquiry-based learning bioinformatics module on undergraduate student engagement and applied skills.

PubMed

Brown, James A L

2016-05-06

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, qualitative student-based module evaluation and the novelty, scientific validity and quality of written student reports. Bioinformatics is often the starting point for laboratory-based research projects, therefore high importance was placed on allowing students to individually develop and apply processes and methods of scientific research. Students led a bioinformatic inquiry-based project (within a framework of inquiry), discovering, justifying and exploring individually discovered research targets. Detailed assessable reports were produced, displaying data generated and the resources used. Mimicking research settings, undergraduates were divided into small collaborative groups, with distinctive central themes. The module was evaluated by assessing the quality and originality of the students' targets through reports, reflecting students' use and understanding of concepts and tools required to generate their data. Furthermore, evaluation of the bioinformatic module was assessed semi-quantitatively using pre- and post-module quizzes (a non-assessable activity, not contributing to their grade), which incorporated process- and content-specific questions (indicative of their use of the online tools). Qualitative assessment of the teaching intervention was performed using post-module surveys, exploring student satisfaction and other module specific elements. Overall, a positive experience was found, as was a post module increase in correct process-specific answers. In conclusion, an inquiry-based peer-assisted learning module increased students' engagement, practical bioinformatic skills and process-specific knowledge. © 2016 by The International Union of Biochemistry and Molecular Biology, 44:304-313 2016. © 2016 The International Union of Biochemistry and Molecular Biology.

KISS for STRAP: user extensions for a protein alignment editor.

PubMed

Gille, Christoph; Lorenzen, Stephan; Michalsky, Elke; Frömmel, Cornelius

2003-12-12

The Structural Alignment Program STRAP is a comfortable comprehensive editor and analyzing tool for protein alignments. A wide range of functions related to protein sequences and protein structures are accessible with an intuitive graphical interface. Recent features include mapping of mutations and polymorphisms onto structures and production of high quality figures for publication. Here we address the general problem of multi-purpose program packages to keep up with the rapid development of bioinformatical methods and the demand for specific program functions. STRAP was remade implementing a novel design which aims at Keeping Interfaces in STRAP Simple (KISS). KISS renders STRAP extendable to bio-scientists as well as to bio-informaticians. Scientists with basic computer skills are capable of implementing statistical methods or embedding existing bioinformatical tools in STRAP themselves. For bio-informaticians STRAP may serve as an environment for rapid prototyping and testing of complex algorithms such as automatic alignment algorithms or phylogenetic methods. Further, STRAP can be applied as an interactive web applet to present data related to a particular protein family and as a teaching tool. JAVA-1.4 or higher. http://www.charite.de/bioinf/strap/

Navigating the changing learning landscape: perspective from bioinformatics.ca

PubMed Central

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 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. PMID:23515468

The Development of Computational Biology in South Africa: Successes Achieved and Lessons Learnt

PubMed Central

Mulder, Nicola J.; Christoffels, Alan; de Oliveira, Tulio; Gamieldien, Junaid; Hazelhurst, Scott; Joubert, Fourie; Kumuthini, Judit; Pillay, Ché S.; Snoep, Jacky L.; Tastan Bishop, Özlem; Tiffin, Nicki

2016-01-01

Bioinformatics is now a critical skill in many research and commercial environments as biological data are increasing in both size and complexity. South African researchers recognized this need in the mid-1990s and responded by working with the government as well as international bodies to develop initiatives to build bioinformatics capacity in the country. Significant injections of support from these bodies provided a springboard for the establishment of computational biology units at multiple universities throughout the country, which took on teaching, basic research and support roles. Several challenges were encountered, for example with unreliability of funding, lack of skills, and lack of infrastructure. However, the bioinformatics community worked together to overcome these, and South Africa is now arguably the leading country in bioinformatics on the African continent. Here we discuss how the discipline developed in the country, highlighting the challenges, successes, and lessons learnt. PMID:26845152

The Development of Computational Biology in South Africa: Successes Achieved and Lessons Learnt.

PubMed

Mulder, Nicola J; Christoffels, Alan; de Oliveira, Tulio; Gamieldien, Junaid; Hazelhurst, Scott; Joubert, Fourie; Kumuthini, Judit; Pillay, Ché S; Snoep, Jacky L; Tastan Bishop, Özlem; Tiffin, Nicki

2016-02-01

Bioinformatics is now a critical skill in many research and commercial environments as biological data are increasing in both size and complexity. South African researchers recognized this need in the mid-1990s and responded by working with the government as well as international bodies to develop initiatives to build bioinformatics capacity in the country. Significant injections of support from these bodies provided a springboard for the establishment of computational biology units at multiple universities throughout the country, which took on teaching, basic research and support roles. Several challenges were encountered, for example with unreliability of funding, lack of skills, and lack of infrastructure. However, the bioinformatics community worked together to overcome these, and South Africa is now arguably the leading country in bioinformatics on the African continent. Here we discuss how the discipline developed in the country, highlighting the challenges, successes, and lessons learnt.

BioPCD - A Language for GUI Development Requiring a Minimal Skill Set.

PubMed

Alvare, Graham Gm; Roche-Lima, Abiel; Fristensky, Brian

2012-11-01

BioPCD is a new language whose purpose is to simplify the creation of Graphical User Interfaces (GUIs) by biologists with minimal programming skills. The first step in developing BioPCD was to create a minimal superset of the language referred to as PCD (Pythonesque Command Description). PCD defines the core of terminals and high-level nonterminals required to describe data of almost any type. BioPCD adds to PCD the constructs necessary to describe GUI components and the syntax for executing system commands. BioPCD is implemented using JavaCC to convert the grammar into code. BioPCD is designed to be terse and readable and simple enough to be learned by copying and modifying existing BioPCD files. We demonstrate that BioPCD can easily be used to generate GUIs for existing command line programs. Although BioPCD was designed to make it easier to run bioinformatics programs, it could be used in any domain in which many useful command line programs exist that do not have GUI interfaces.

Bioinformatics workflows and web services in systems biology made easy for experimentalists.

PubMed

Jimenez, Rafael C; Corpas, Manuel

2013-01-01

Workflows are useful to perform data analysis and integration in systems biology. Workflow management systems can help users create workflows without any previous knowledge in programming and web services. However the computational skills required to build such workflows are usually above the level most biological experimentalists are comfortable with. In this chapter we introduce workflow management systems that reuse existing workflows instead of creating them, making it easier for experimentalists to perform computational tasks.

OpenHelix: bioinformatics education outside of a different box.

PubMed

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.

OpenHelix: bioinformatics education outside of a different box

PubMed Central

Mangan, Mary E.; Perreault-Micale, Cynthia; Lathe, Scott; Sirohi, Neeraj; Lathe, Warren C.

2010-01-01

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. PMID:20798181

Expanding roles in a library-based bioinformatics service program: a case study

PubMed Central

Li, Meng; Chen, Yi-Bu; Clintworth, William A

2013-01-01

Question: How can a library-based bioinformatics support program be implemented and expanded to continuously support the growing and changing needs of the research community? Setting: A program at a health sciences library serving a large academic medical center with a strong research focus is described. Methods: The bioinformatics service program was established at the Norris Medical Library in 2005. As part of program development, the library assessed users' bioinformatics needs, acquired additional funds, established and expanded service offerings, and explored additional roles in promoting on-campus collaboration. Results: Personnel and software have increased along with the number of registered software users and use of the provided services. Conclusion: With strategic efforts and persistent advocacy within the broader university environment, library-based bioinformatics service programs can become a key part of an institution's comprehensive solution to researchers' ever-increasing bioinformatics needs. PMID:24163602

Bioinformatics and School Biology

ERIC Educational Resources Information Center

Dalpech, Roger

2006-01-01

The rapidly changing field of bioinformatics is fuelling the need for suitably trained personnel with skills in relevant biological "sub-disciplines" such as proteomics, transcriptomics and metabolomics, etc. But because of the complexity--and sheer weight of data--associated with these new areas of biology, many school teachers feel…

An open-source java platform for automated reaction mapping.

PubMed

Crabtree, John D; Mehta, Dinesh P; Kouri, Tina M

2010-09-27

This article presents software applications that have been built upon a modular, open-source, reaction mapping library that can be used in both cheminformatics and bioinformatics research. We first describe the theoretical underpinnings and modular architecture of the core software library. We then describe two applications that have been built upon that core. The first is a generic reaction viewer and mapper, and the second classifies reactions according to rules that can be modified by end users with little or no programming skills.

BioPCD - A Language for GUI Development Requiring a Minimal Skill Set

PubMed Central

Alvare, Graham GM; Roche-Lima, Abiel; Fristensky, Brian

2016-01-01

BioPCD is a new language whose purpose is to simplify the creation of Graphical User Interfaces (GUIs) by biologists with minimal programming skills. The first step in developing BioPCD was to create a minimal superset of the language referred to as PCD (Pythonesque Command Description). PCD defines the core of terminals and high-level nonterminals required to describe data of almost any type. BioPCD adds to PCD the constructs necessary to describe GUI components and the syntax for executing system commands. BioPCD is implemented using JavaCC to convert the grammar into code. BioPCD is designed to be terse and readable and simple enough to be learned by copying and modifying existing BioPCD files. We demonstrate that BioPCD can easily be used to generate GUIs for existing command line programs. Although BioPCD was designed to make it easier to run bioinformatics programs, it could be used in any domain in which many useful command line programs exist that do not have GUI interfaces. PMID:27818582

Next-generation sequencing: a challenge to meet the increasing demand for training workshops in Australia.

PubMed

Watson-Haigh, Nathan S; Shang, Catherine A; Haimel, Matthias; Kostadima, Myrto; Loos, Remco; Deshpande, Nandan; Duesing, Konsta; Li, Xi; McGrath, Annette; McWilliam, Sean; Michnowicz, Simon; Moolhuijzen, Paula; Quenette, Steve; Revote, Jerico Nico De Leon; Tyagi, Sonika; Schneider, Maria V

2013-09-01

The widespread adoption of high-throughput next-generation sequencing (NGS) technology among the Australian life science research community is highlighting an urgent need to up-skill biologists in tools required for handling and analysing their NGS data. There is currently a shortage of cutting-edge bioinformatics training courses in Australia as a consequence of a scarcity of skilled trainers with time and funding to develop and deliver training courses. To address this, a consortium of Australian research organizations, including Bioplatforms Australia, the Commonwealth Scientific and Industrial Research Organisation and the Australian Bioinformatics Network, have been collaborating with EMBL-EBI training team. A group of Australian bioinformaticians attended the train-the-trainer workshop to improve training skills in developing and delivering bioinformatics workshop curriculum. A 2-day NGS workshop was jointly developed to provide hands-on knowledge and understanding of typical NGS data analysis workflows. The road show-style workshop was successfully delivered at five geographically distant venues in Australia using the newly established Australian NeCTAR Research Cloud. We highlight the challenges we had to overcome at different stages from design to delivery, including the establishment of an Australian bioinformatics training network and the computing infrastructure and resource development. A virtual machine image, workshop materials and scripts for configuring a machine with workshop contents have all been made available under a Creative Commons Attribution 3.0 Unported License. This means participants continue to have convenient access to an environment they had become familiar and bioinformatics trainers are able to access and reuse these resources.

Next-generation sequencing: a challenge to meet the increasing demand for training workshops in Australia

PubMed Central

Watson-Haigh, Nathan S.; Shang, Catherine A.; Haimel, Matthias; Kostadima, Myrto; Loos, Remco; Deshpande, Nandan; Duesing, Konsta; Li, Xi; McGrath, Annette; McWilliam, Sean; Michnowicz, Simon; Moolhuijzen, Paula; Quenette, Steve; Revote, Jerico Nico De Leon; Tyagi, Sonika; Schneider, Maria V.

2013-01-01

The widespread adoption of high-throughput next-generation sequencing (NGS) technology among the Australian life science research community is highlighting an urgent need to up-skill biologists in tools required for handling and analysing their NGS data. There is currently a shortage of cutting-edge bioinformatics training courses in Australia as a consequence of a scarcity of skilled trainers with time and funding to develop and deliver training courses. To address this, a consortium of Australian research organizations, including Bioplatforms Australia, the Commonwealth Scientific and Industrial Research Organisation and the Australian Bioinformatics Network, have been collaborating with EMBL-EBI training team. A group of Australian bioinformaticians attended the train-the-trainer workshop to improve training skills in developing and delivering bioinformatics workshop curriculum. A 2-day NGS workshop was jointly developed to provide hands-on knowledge and understanding of typical NGS data analysis workflows. The road show–style workshop was successfully delivered at five geographically distant venues in Australia using the newly established Australian NeCTAR Research Cloud. We highlight the challenges we had to overcome at different stages from design to delivery, including the establishment of an Australian bioinformatics training network and the computing infrastructure and resource development. A virtual machine image, workshop materials and scripts for configuring a machine with workshop contents have all been made available under a Creative Commons Attribution 3.0 Unported License. This means participants continue to have convenient access to an environment they had become familiar and bioinformatics trainers are able to access and reuse these resources. PMID:23543352

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

ERIC Educational Resources Information Center

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…

4273π: Bioinformatics education on low cost ARM hardware

PubMed Central

2013-01-01

Background Teaching bioinformatics at universities is complicated by typical computer classroom settings. As well as running software locally and online, students should gain experience of systems administration. For a future career in biology or bioinformatics, the installation of software is a useful skill. We propose that this may be taught by running the course on GNU/Linux running on inexpensive Raspberry Pi computer hardware, for which students may be granted full administrator access. Results We release 4273π, an operating system image for Raspberry Pi based on Raspbian Linux. This includes minor customisations for classroom use and includes our Open Access bioinformatics course, 4273π Bioinformatics for Biologists. This is based on the final-year undergraduate module BL4273, run on Raspberry Pi computers at the University of St Andrews, Semester 1, academic year 2012–2013. Conclusions 4273π is a means to teach bioinformatics, including systems administration tasks, to undergraduates at low cost. PMID:23937194

4273π: bioinformatics education on low cost ARM hardware.

PubMed

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.

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

ERIC Educational Resources Information Center

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…

Bioinformatics Education—Perspectives and Challenges out of Africa

PubMed Central

Adebiyi, Ezekiel F.; Alzohairy, Ahmed M.; Everett, Dean; Ghedira, Kais; Ghouila, Amel; Kumuthini, Judit; Mulder, Nicola J.; Panji, Sumir; Patterton, Hugh-G.

2015-01-01

The discipline of bioinformatics has developed rapidly since the complete sequencing of the first genomes in the 1990s. The development of many high-throughput techniques during the last decades has ensured that bioinformatics has grown into a discipline that overlaps with, and is required for, the modern practice of virtually every field in the life sciences. This has placed a scientific premium on the availability of skilled bioinformaticians, a qualification that is extremely scarce on the African continent. The reasons for this are numerous, although the absence of a skilled bioinformatician at academic institutions to initiate a training process and build sustained capacity seems to be a common African shortcoming. This dearth of bioinformatics expertise has had a knock-on effect on the establishment of many modern high-throughput projects at African institutes, including the comprehensive and systematic analysis of genomes from African populations, which are among the most genetically diverse anywhere on the planet. Recent funding initiatives from the National Institutes of Health and the Wellcome Trust are aimed at ameliorating this shortcoming. In this paper, we discuss the problems that have limited the establishment of the bioinformatics field in Africa, as well as propose specific actions that will help with the education and training of bioinformaticians on the continent. This is an absolute requirement in anticipation of a boom in high-throughput approaches to human health issues unique to data from African populations. PMID:24990350

Bio-Docklets: virtualization containers for single-step execution of NGS pipelines.

PubMed

Kim, Baekdoo; Ali, Thahmina; Lijeron, Carlos; Afgan, Enis; Krampis, Konstantinos

2017-08-01

Processing of next-generation sequencing (NGS) data requires significant technical skills, involving installation, configuration, and execution of bioinformatics data pipelines, in addition to specialized postanalysis visualization and data mining software. In order to address some of these challenges, developers have leveraged virtualization containers toward seamless deployment of preconfigured bioinformatics software and pipelines on any computational platform. We present an approach for abstracting the complex data operations of multistep, bioinformatics pipelines for NGS data analysis. As examples, we have deployed 2 pipelines for RNA sequencing and chromatin immunoprecipitation sequencing, preconfigured within Docker virtualization containers we call Bio-Docklets. Each Bio-Docklet exposes a single data input and output endpoint and from a user perspective, running the pipelines as simply as running a single bioinformatics tool. This is achieved using a "meta-script" that automatically starts the Bio-Docklets and controls the pipeline execution through the BioBlend software library and the Galaxy Application Programming Interface. The pipeline output is postprocessed by integration with the Visual Omics Explorer framework, providing interactive data visualizations that users can access through a web browser. Our goal is to enable easy access to NGS data analysis pipelines for nonbioinformatics experts on any computing environment, whether a laboratory workstation, university computer cluster, or a cloud service provider. Beyond end users, the Bio-Docklets also enables developers to programmatically deploy and run a large number of pipeline instances for concurrent analysis of multiple datasets. © The Authors 2017. Published by Oxford University Press.

Bio-Docklets: virtualization containers for single-step execution of NGS pipelines

PubMed Central

Kim, Baekdoo; Ali, Thahmina; Lijeron, Carlos; Afgan, Enis

2017-01-01

Abstract Processing of next-generation sequencing (NGS) data requires significant technical skills, involving installation, configuration, and execution of bioinformatics data pipelines, in addition to specialized postanalysis visualization and data mining software. In order to address some of these challenges, developers have leveraged virtualization containers toward seamless deployment of preconfigured bioinformatics software and pipelines on any computational platform. We present an approach for abstracting the complex data operations of multistep, bioinformatics pipelines for NGS data analysis. As examples, we have deployed 2 pipelines for RNA sequencing and chromatin immunoprecipitation sequencing, preconfigured within Docker virtualization containers we call Bio-Docklets. Each Bio-Docklet exposes a single data input and output endpoint and from a user perspective, running the pipelines as simply as running a single bioinformatics tool. This is achieved using a “meta-script” that automatically starts the Bio-Docklets and controls the pipeline execution through the BioBlend software library and the Galaxy Application Programming Interface. The pipeline output is postprocessed by integration with the Visual Omics Explorer framework, providing interactive data visualizations that users can access through a web browser. Our goal is to enable easy access to NGS data analysis pipelines for nonbioinformatics experts on any computing environment, whether a laboratory workstation, university computer cluster, or a cloud service provider. Beyond end users, the Bio-Docklets also enables developers to programmatically deploy and run a large number of pipeline instances for concurrent analysis of multiple datasets. PMID:28854616

Is there room for ethics within bioinformatics education?

PubMed

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.

Scalability and Validation of Big Data Bioinformatics Software.

PubMed

Yang, Andrian; Troup, Michael; Ho, Joshua W K

2017-01-01

This review examines two important aspects that are central to modern big data bioinformatics analysis - software scalability and validity. We argue that not only are the issues of scalability and validation common to all big data bioinformatics analyses, they can be tackled by conceptually related methodological approaches, namely divide-and-conquer (scalability) and multiple executions (validation). Scalability is defined as the ability for a program to scale based on workload. It has always been an important consideration when developing bioinformatics algorithms and programs. Nonetheless the surge of volume and variety of biological and biomedical data has posed new challenges. We discuss how modern cloud computing and big data programming frameworks such as MapReduce and Spark are being used to effectively implement divide-and-conquer in a distributed computing environment. Validation of software is another important issue in big data bioinformatics that is often ignored. Software validation is the process of determining whether the program under test fulfils the task for which it was designed. Determining the correctness of the computational output of big data bioinformatics software is especially difficult due to the large input space and complex algorithms involved. We discuss how state-of-the-art software testing techniques that are based on the idea of multiple executions, such as metamorphic testing, can be used to implement an effective bioinformatics quality assurance strategy. We hope this review will raise awareness of these critical issues in bioinformatics.

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

ERIC Educational Resources Information Center

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…

Improving medical students' knowledge of genetic disease: a review of current and emerging pedagogical practices.

PubMed

Wolyniak, Michael J; Bemis, Lynne T; Prunuske, Amy J

2015-01-01

Genetics is an essential subject to be mastered by health professional students of all types. However, technological advances in genomics and recent pedagogical research have changed the way in which many medical training programs teach genetics to their students. These advances favor a more experience-based education focused primarily on developing student's critical thinking skills. In this review, we examine the current state of genetics education at both the preclinical and clinical levels and the ways in which medical and pedagogical research have guided reforms to current and emerging teaching practices in genetics. We discover exciting trends taking place in which genetics is integrated with other scientific disciplines both horizontally and vertically across medical curricula to emphasize training in scientific critical thinking skills among students via the evaluation of clinical evidence and consultation of online databases. These trends will produce future health professionals with the skills and confidence necessary to embrace the new tools of medical practice that have emerged from scientific advances in genetics, genomics, and bioinformatics.

Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ditty, Jayna L.; Kvaal, Christopher A.; Goodner, Brad

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

Bringing the human genome and the revolution in bioinformatics to the medical school classroom: a case report from Washington University School of Medicine.

PubMed

Magee, J; Gordon, J I; Whelan, A

2001-08-01

The human genome project is revolutionizing medical research and the practice of clinical medicine. To understand and participate in this revolution, physicians must be fluent in human genomics and bioinformatics. At Washington University School of Medicine (WUSM), the authors designed a module for teaching these skills to first-year students. The module uses clinical cases as a platform for accessing information stored in GenBank, Online Mendelian Inheritance in Man (OMIM), and PubMed databases at the National Center for Biotechnology Information (NCBI). This module, which is also designed to reinforce problem-solving skills, has been integrated into WUSM's first-year medical genetics course.

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

PubMed

Mertz, Pamela; Streu, Craig

2015-01-01

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

Continuing Education Workshops in Bioinformatics Positively Impact Research and Careers

PubMed Central

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

2016-01-01

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. PMID:27281025

Continuing Education Workshops in Bioinformatics Positively Impact Research and Careers.

PubMed

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.

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

PubMed Central

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

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

PubMed

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 < 4.5 × 10(-29)). The 20-year trend in the average JIF between the two groups suggests the gap does not appear to be significantly narrowing. For a sampling of the journals producing top 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.

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

PubMed

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.

Vignettes: diverse library staff offering diverse bioinformatics services*

PubMed Central

Osterbur, David L.; Alpi, Kristine; Canevari, Catharine; Corley, Pamela M.; Devare, Medha; Gaedeke, Nicola; Jacobs, Donna K.; Kirlew, Peter; Ohles, Janet A.; Vaughan, K.T.L.; Wang, Lili; Wu, Yongchun; Geer, Renata C.

2006-01-01

Objectives: The paper gives examples of the bioinformatics services provided in a variety of different libraries by librarians with a broad range of educational background and training. Methods: Two investigators sent an email inquiry to attendees of the “National Center for Biotechnology Information's (NCBI) Introduction to Molecular Biology Information Resources” or “NCBI Advanced Workshop for Bioinformatics Information Specialists (NAWBIS)” courses. The thirty-five-item questionnaire addressed areas such as educational background, library setting, types and numbers of users served, and bioinformatics training and support services provided. Answers were compiled into program vignettes. Discussion: The bioinformatics support services addressed in the paper are based in libraries with academic and clinical settings. Services have been established through different means: in collaboration with biology faculty as part of formal courses, through teaching workshops in the library, through one-on-one consultations, and by other methods. Librarians with backgrounds from art history to doctoral degrees in genetics have worked to establish these programs. Conclusion: Successful bioinformatics support programs can be established in libraries in a variety of different settings and by staff with a variety of different backgrounds and approaches. PMID:16888664

Carving a niche: establishing bioinformatics collaborations

PubMed Central

Lyon, Jennifer A.; Tennant, Michele R.; Messner, Kevin R.; Osterbur, David L.

2006-01-01

Objectives: The paper describes collaborations and partnerships developed between library bioinformatics programs and other bioinformatics-related units at four academic institutions. Methods: A call for information on bioinformatics partnerships was made via email to librarians who have participated in the National Center for Biotechnology Information's Advanced Workshop for Bioinformatics Information Specialists. Librarians from Harvard University, the University of Florida, the University of Minnesota, and Vanderbilt University responded and expressed willingness to contribute information on their institutions, programs, services, and collaborating partners. Similarities and differences in programs and collaborations were identified. Results: The four librarians have developed partnerships with other units on their campuses that can be categorized into the following areas: knowledge management, instruction, and electronic resource support. All primarily support freely accessible electronic resources, while other campus units deal with fee-based ones. These demarcations are apparent in resource provision as well as in subsequent support and instruction. Conclusions and Recommendations: Through environmental scanning and networking with colleagues, librarians who provide bioinformatics support can develop fruitful collaborations. Visibility is key to building collaborations, as is broad-based thinking in terms of potential partners. PMID:16888668

BioSmalltalk: a pure object system and library for bioinformatics.

PubMed

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.

Design and Implementation of an Interdepartmental Bioinformatics Program across Life Science Curricula

ERIC Educational Resources Information Center

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

2007-01-01

Over the past 10 years, there has been a technical revolution in the life sciences leading to the emergence of a new discipline called bioinformatics. In response, bioinformatics-related topics have been incorporated into various undergraduate courses along with the development of new courses solely focused on bioinformatics. This report describes…

Technosciences in Academia: Rethinking a Conceptual Framework for Bioinformatics Undergraduate Curricula

NASA Astrophysics Data System (ADS)

Symeonidis, Iphigenia Sofia

This paper aims to elucidate guiding concepts for the design of powerful undergraduate bioinformatics degrees which will lead to a conceptual framework for the curriculum. "Powerful" here should be understood as having truly bioinformatics objectives rather than enrichment of existing computer science or life science degrees on which bioinformatics degrees are often based. As such, the conceptual framework will be one which aims to demonstrate intellectual honesty in regards to the field of bioinformatics. A synthesis/conceptual analysis approach was followed as elaborated by Hurd (1983). The approach takes into account the following: bioinfonnatics educational needs and goals as expressed by different authorities, five undergraduate bioinformatics degrees case-studies, educational implications of bioinformatics as a technoscience and approaches to curriculum design promoting interdisciplinarity and integration. Given these considerations, guiding concepts emerged and a conceptual framework was elaborated. The practice of bioinformatics was given a closer look, which led to defining tool-integration skills and tool-thinking capacity as crucial areas of the bioinformatics activities spectrum. It was argued, finally, that a process-based curriculum as a variation of a concept-based curriculum (where the concepts are processes) might be more conducive to the teaching of bioinformatics given a foundational first year of integrated science education as envisioned by Bialek and Botstein (2004). Furthermore, the curriculum design needs to define new avenues of communication and learning which bypass the traditional disciplinary barriers of academic settings as undertaken by Tador and Tidmor (2005) for graduate studies.

MEGAnnotator: a user-friendly pipeline for microbial genomes assembly and annotation.

PubMed

Lugli, Gabriele Andrea; Milani, Christian; Mancabelli, Leonardo; van Sinderen, Douwe; Ventura, Marco

2016-04-01

Genome annotation is one of the key actions that must be undertaken in order to decipher the genetic blueprint of organisms. Thus, a correct and reliable annotation is essential in rendering genomic data valuable. Here, we describe a bioinformatics pipeline based on freely available software programs coordinated by a multithreaded script named MEGAnnotator (Multithreaded Enhanced prokaryotic Genome Annotator). This pipeline allows the generation of multiple annotated formats fulfilling the NCBI guidelines for assembled microbial genome submission, based on DNA shotgun sequencing reads, and minimizes manual intervention, while also reducing waiting times between software program executions and improving final quality of both assembly and annotation outputs. MEGAnnotator provides an efficient way to pre-arrange the assembly and annotation work required to process NGS genome sequence data. The script improves the final quality of microbial genome annotation by reducing ambiguous annotations. Moreover, the MEGAnnotator platform allows the user to perform a partial annotation of pre-assembled genomes and includes an option to accomplish metagenomic data set assemblies. MEGAnnotator platform will be useful for microbiologists interested in genome analyses of bacteria as well as those investigating the complexity of microbial communities that do not possess the necessary skills to prepare their own bioinformatics pipeline. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

PubMed Central

Rein, Diane C.

2006-01-01

Setting: 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. Program Components: 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. Evaluation Mechanisms: 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. Next Steps/Future Directions: 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. PMID:16888666

Extending Asia Pacific bioinformatics into new realms in the "-omics" era.

PubMed

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.

Exploring DNA Structure with Cn3D

ERIC Educational Resources Information Center

Porter, Sandra G.; Day, Joseph; McCarty, Richard E.; Shearn, Allen; Shingles, Richard; Fletcher, Linnea; Murphy, Stephanie; Pearlman, Rebecca

2007-01-01

Researchers in the field of bioinformatics have developed a number of analytical programs and databases that are increasingly important for advancing biological research. Because bioinformatics programs are used to analyze, visualize, and/or compare biological data, it is likely that the use of these programs will have a positive impact on biology…

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

PubMed

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.

Improving medical students’ knowledge of genetic disease: a review of current and emerging pedagogical practices

PubMed Central

Wolyniak, Michael J; Bemis, Lynne T; Prunuske, Amy J

2015-01-01

Genetics is an essential subject to be mastered by health professional students of all types. However, technological advances in genomics and recent pedagogical research have changed the way in which many medical training programs teach genetics to their students. These advances favor a more experience-based education focused primarily on developing student’s critical thinking skills. In this review, we examine the current state of genetics education at both the preclinical and clinical levels and the ways in which medical and pedagogical research have guided reforms to current and emerging teaching practices in genetics. We discover exciting trends taking place in which genetics is integrated with other scientific disciplines both horizontally and vertically across medical curricula to emphasize training in scientific critical thinking skills among students via the evaluation of clinical evidence and consultation of online databases. These trends will produce future health professionals with the skills and confidence necessary to embrace the new tools of medical practice that have emerged from scientific advances in genetics, genomics, and bioinformatics. PMID:26604852

Incorporating a collaborative web-based virtual laboratory in an undergraduate bioinformatics course.

PubMed

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 face-to-face lecture course with a web-based virtual laboratory presents new opportunities for collaborative learning of the conceptual material, and for fostering peer support of technical bioinformatics questions. To explore this combination, an in-person lecture-only undergraduate bioinformatics course was augmented with a remote web-based laboratory, and tested with a large class. This study hypothesized that the collaborative virtual lab would foster active learning and peer support, and tested this hypothesis by conducting a student survey near the end of the semester. Respondents broadly reported strong benefits from the online laboratory, and strong benefits from peer-provided technical support. In comparison with traditional in-person teaching labs, students preferred the virtual lab by a factor of two. Key aspects of the course architecture and design are described to encourage further experimentation in teaching collaborative online bioinformatics laboratories. Copyright © 2010 International Union of Biochemistry and Molecular Biology, Inc.

A comparison of common programming languages used in bioinformatics.

PubMed

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.

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

PubMed Central

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. PMID:28781745

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

PubMed

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.

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

PubMed Central

Mura, Cameron

2016-01-01

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. PMID:27271528

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

PubMed

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.

Integer Linear Programming in Computational Biology

NASA Astrophysics Data System (ADS)

Althaus, Ernst; Klau, Gunnar W.; Kohlbacher, Oliver; Lenhof, Hans-Peter; Reinert, Knut

Computational molecular biology (bioinformatics) is a young research field that is rich in NP-hard optimization problems. The problem instances encountered are often huge and comprise thousands of variables. Since their introduction into the field of bioinformatics in 1997, integer linear programming (ILP) techniques have been successfully applied to many optimization problems. These approaches have added much momentum to development and progress in related areas. In particular, ILP-based approaches have become a standard optimization technique in bioinformatics. In this review, we present applications of ILP-based techniques developed by members and former members of Kurt Mehlhorn’s group. These techniques were introduced to bioinformatics in a series of papers and popularized by demonstration of their effectiveness and potential.

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

PubMed Central

2015-01-01

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. PMID:25183247

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

PubMed

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.

"Extreme Programming" in a Bioinformatics Class

ERIC Educational Resources Information Center

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).…

Development of an undergraduate bioinformatics degree program at a liberal arts college.

PubMed

Bagga, Paramjeet S

2012-09-01

The highly interdisciplinary field of bioinformatics has emerged as a powerful modern science. There has been a great demand for undergraduate- and graduate-level trained bioinformaticists in the industry as well in the academia. In order to address the needs for trained bioinformaticists, its curriculum must be offered at the undergraduate level, especially at four-year colleges, where a majority of the United States gets its education. There are many challenges in developing an undergraduate-level bioinformatics program that needs to be carefully designed as a well-integrated and cohesive interdisciplinary curriculum that prepares the students for a wide variety of career options. This article describes the challenges of establishing a highly interdisciplinary undergraduate major, the development of an undergraduate bioinformatics degree program at Ramapo College of New Jersey, and lessons learned in the last 10 years during its management.

A Mathematical Optimization Problem in Bioinformatics

ERIC Educational Resources Information Center

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…

Assessment of a Bioinformatics across Life Science Curricula Initiative

ERIC Educational Resources Information Center

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…

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

PubMed

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 first used with a bioinformatics system. Simplifying the validation of essential tabular data files, such as sample metadata, will reduce common errors and thereby improve the quality and reliability of research outcomes.

[Integration of clinical and biological data in clinical practice using bioinformatics].

PubMed

Coltell, Oscar; Arregui, María; Fabregat, Antonio; Portolés, Olga

2008-05-01

The aim of our work is to describe essential aspects of Medical Informatics, Bioinformatics and Biomedical Informatics, that are used in biomedical research and clinical practice. These disciplines have emerged from the need to find new scientific and technical approaches to manage, store, analyze and report data generated in clinical practice and molecular biology and other medical specialties. It can be also useful to integrate research information generated in different areas of health care. Moreover, these disciplines are interdisciplinary and integrative, two key features not shared by other areas of medical knowledge. Finally, when Bioinformatics and Biomedical Informatics approach to medical investigation and practice are applied, a new discipline, called Clinical Bioinformatics, emerges. The latter requires a specific training program to create a new professional profile. We have not been able to find a specific training program in Clinical Bioinformatics in Spain.

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

PubMed Central

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

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

ERIC Educational Resources Information Center

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…

Implementation and Assessment of a Molecular Biology and Bioinformatics Undergraduate Degree Program

ERIC Educational Resources Information Center

Pham, Daphne Q. -D.; Higgs, David C.; Statham, Anne; Schleiter, Mary Kay

2008-01-01

The Department of Biological Sciences at the University of Wisconsin-Parkside has developed and implemented an innovative, multidisciplinary undergraduate curriculum in Molecular Biology and Bioinformatics (MBB). The objective of the MBB program is to give students a hands-on facility with molecular biology theories and laboratory techniques, an…

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

PubMed

Fristensky, Brian

2007-02-09

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

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

PubMed Central

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

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

PubMed Central

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

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

PubMed Central

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

2008-01-01

Summer undergraduate research programs in science and engineering facilitate research progress for faculty and provide a close-ended research experience for students, which can prepare them for careers in industry, medicine, and academia. However, ensuring these outcomes is a challenge when the students arrive ill-prepared for substantive research or if projects are ill-defined or impractical for a typical 10-wk summer. We describe how the new Bioengineering and Bioinformatics Summer Institutes (BBSI), developed in response to a call for proposals by the National Institutes of Health (NIH) and the National Science Foundation (NSF), provide an impetus for the enhancement of traditional undergraduate research experiences with intense didactic training in particular skills and technologies. Such didactic components provide highly focused and qualified students for summer research with the goal of ensuring increased student satisfaction with research and mentor satisfaction with student productivity. As an example, we focus on our experiences with the Penn State Biomaterials and Bionanotechnology Summer Institute (PSU-BBSI), which trains undergraduates in core technologies in surface characterization, computational modeling, cell biology, and fabrication to prepare them for student-centered research projects in the role of materials in guiding cell biology. PMID:18316807

Biowep: a workflow enactment portal for bioinformatics applications.

PubMed

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 effective workflows can significantly improve automation of in-silico analysis. Biowep is available for interested researchers as a reference portal. They are invited to submit their workflows to the workflow repository. Biowep is further being developed in the sphere of the Laboratory of Interdisciplinary Technologies in Bioinformatics - LITBIO.

Biowep: a workflow enactment portal for bioinformatics applications

PubMed Central

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

2007-01-01

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 databases and analysis software and the creation of effective workflows can significantly improve automation of in-silico analysis. Biowep is available for interested researchers as a reference portal. They are invited to submit their workflows to the workflow repository. Biowep is further being developed in the sphere of the Laboratory of Interdisciplinary Technologies in Bioinformatics – LITBIO. PMID:17430563

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

PubMed

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.)

Training Multidisciplinary Biomedical Informatics Students: Three Years of Experience

PubMed Central

van Mulligen, Erik M.; Cases, Montserrat; Hettne, Kristina; Molero, Eva; Weeber, Marc; Robertson, Kevin A.; Oliva, Baldomero; de la Calle, Guillermo; Maojo, Victor

2008-01-01

Objective The European INFOBIOMED Network of Excellence 1 recognized that a successful education program in biomedical informatics should include not only traditional teaching activities in the basic sciences but also the development of skills for working in multidisciplinary teams. Design A carefully developed 3-year training program for biomedical informatics students addressed these educational aspects through the following four activities: (1) an internet course database containing an overview of all Medical Informatics and BioInformatics courses, (2) a BioMedical Informatics Summer School, (3) a mobility program based on a ‘brokerage service’ which published demands and offers, including funding for research exchange projects, and (4) training challenges aimed at the development of multi-disciplinary skills. Measurements This paper focuses on experiences gained in the development of novel educational activities addressing work in multidisciplinary teams. The training challenges described here were evaluated by asking participants to fill out forms with Likert scale based questions. For the mobility program a needs assessment was carried out. Results The mobility program supported 20 exchanges which fostered new BMI research, resulted in a number of peer-reviewed publications and demonstrated the feasibility of this multidisciplinary BMI approach within the European Union. Students unanimously indicated that the training challenge experience had contributed to their understanding and appreciation of multidisciplinary teamwork. Conclusion The training activities undertaken in INFOBIOMED have contributed to a multi-disciplinary BMI approach. It is our hope that this work might provide an impetus for training efforts in Europe, and yield a new generation of biomedical informaticians. PMID:18096914

Best practices in bioinformatics training for life scientists.

PubMed

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

2013-09-01

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.

Best practices in bioinformatics training for life scientists

PubMed Central

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

2013-01-01

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. PMID:23803301

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

PubMed

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.

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

PubMed Central

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

2013-01-01

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

The GMOD Drupal bioinformatic server framework.

PubMed

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.

Two interactive Bioinformatics courses at the Bielefeld University Bioinformatics Server.

PubMed

Sczyrba, Alexander; Konermann, Susanne; Giegerich, Robert

2008-05-01

Conferences in computational biology continue to provide tutorials on classical and new methods in the field. This can be taken as an indicator that education is still a bottleneck in our field's process of becoming an established scientific discipline. Bielefeld University has been one of the early providers of bioinformatics education, both locally and via the internet. The Bielefeld Bioinformatics Server (BiBiServ) offers a variety of older and new materials. Here, we report on two online courses made available recently, one introductory and one on the advanced level: (i) SADR: Sequence Analysis with Distributed Resources (http://bibiserv.techfak.uni-bielefeld.de/sadr/) and (ii) ADP: Algebraic Dynamic Programming in Bioinformatics (http://bibiserv.techfak.uni-bielefeld.de/dpcourse/).

LXtoo: an integrated live Linux distribution for the bioinformatics community

PubMed Central

2012-01-01

Background 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. Findings 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. Conclusions 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. PMID:22813356

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

PubMed

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.

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

PubMed

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.

A comparison of common programming languages used in bioinformatics

PubMed Central

Fourment, Mathieu; Gillings, Michael R

2008-01-01

Background 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. Results 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 Conclusion 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. PMID:18251993

A Bioinformatics Module for Use in an Introductory Biology Laboratory

ERIC Educational Resources Information Center

Alaie, Adrienne; Teller, Virginia; Qiu, Wei-gang

2012-01-01

Since biomedical science has become increasingly data-intensive, acquisition of computational and quantitative skills by science students has become more important. For non-science students, an introduction to biomedical databases and their applications promotes the development of a scientifically literate population. Because typical college…

RGG: A general GUI Framework for R scripts

PubMed Central

Visne, Ilhami; Dilaveroglu, Erkan; Vierlinger, Klemens; Lauss, Martin; Yildiz, Ahmet; Weinhaeusel, Andreas; Noehammer, Christa; Leisch, Friedrich; Kriegner, Albert

2009-01-01

Background R is the leading open source statistics software with a vast number of biostatistical and bioinformatical analysis packages. To exploit the advantages of R, extensive scripting/programming skills are required. Results We have developed a software tool called R GUI Generator (RGG) which enables the easy generation of Graphical User Interfaces (GUIs) for the programming language R by adding a few Extensible Markup Language (XML) – tags. RGG consists of an XML-based GUI definition language and a Java-based GUI engine. GUIs are generated in runtime from defined GUI tags that are embedded into the R script. User-GUI input is returned to the R code and replaces the XML-tags. RGG files can be developed using any text editor. The current version of RGG is available as a stand-alone software (RGGRunner) and as a plug-in for JGR. Conclusion RGG is a general GUI framework for R that has the potential to introduce R statistics (R packages, built-in functions and scripts) to users with limited programming skills and helps to bridge the gap between R developers and GUI-dependent users. RGG aims to abstract the GUI development from individual GUI toolkits by using an XML-based GUI definition language. Thus RGG can be easily integrated in any software. The RGG project further includes the development of a web-based repository for RGG-GUIs. RGG is an open source project licensed under the Lesser General Public License (LGPL) and can be downloaded freely at PMID:19254356

A toolbox for developing bioinformatics software

PubMed Central

Potrzebowski, Wojciech; Puton, Tomasz; Rother, Magdalena; Wywial, Ewa; Bujnicki, Janusz M.

2012-01-01

Creating useful software is a major activity of many scientists, including bioinformaticians. Nevertheless, software development in an academic setting is often unsystematic, which can lead to problems associated with maintenance and long-term availibility. Unfortunately, well-documented software development methodology is difficult to adopt, and technical measures that directly improve bioinformatic programming have not been described comprehensively. We have examined 22 software projects and have identified a set of practices for software development in an academic environment. We found them useful to plan a project, support the involvement of experts (e.g. experimentalists), and to promote higher quality and maintainability of the resulting programs. This article describes 12 techniques that facilitate a quick start into software engineering. We describe 3 of the 22 projects in detail and give many examples to illustrate the usage of particular techniques. We expect this toolbox to be useful for many bioinformatics programming projects and to the training of scientific programmers. PMID:21803787

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

PubMed

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.

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

PubMed Central

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

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

PubMed

Krieger, Elmar; Vriend, Gert

2002-02-01

Due to the steadily growing computational demands in bioinformatics and related scientific disciplines, one is forced to make optimal use of the available resources. A straightforward solution is to build a network of idle computers and let each of them work on a small piece of a scientific challenge, as done by Seti@Home (http://setiathome.berkeley.edu), the world's largest distributed computing project. We developed a generally applicable distributed computing solution that uses a screensaver system similar to Seti@Home. The software exploits the coarse-grained nature of typical bioinformatics projects. Three major considerations for the design were: (1) often, many different programs are needed, while the time is lacking to parallelize them. Models@Home can run any program in parallel without modifications to the source code; (2) in contrast to the Seti project, bioinformatics applications are normally more sensitive to lost jobs. Models@Home therefore includes stringent control over job scheduling; (3) to allow use in heterogeneous environments, Linux and Windows based workstations can be combined with dedicated PCs to build a homogeneous cluster. We present three practical applications of Models@Home, running the modeling programs WHAT IF and YASARA on 30 PCs: force field parameterization, molecular dynamics docking, and database maintenance.

Bioinformatics in translational drug discovery.

PubMed

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).

GLAD: a system for developing and deploying large-scale bioinformatics grid.

PubMed

Teo, Yong-Meng; Wang, Xianbing; Ng, Yew-Kwong

2005-03-01

Grid computing is used to solve large-scale bioinformatics problems with gigabytes database by distributing the computation across multiple platforms. Until now in developing bioinformatics grid applications, it is extremely tedious to design and implement the component algorithms and parallelization techniques for different classes of problems, and to access remotely located sequence database files of varying formats across the grid. In this study, we propose a grid programming toolkit, GLAD (Grid Life sciences Applications Developer), which facilitates the development and deployment of bioinformatics applications on a grid. GLAD has been developed using ALiCE (Adaptive scaLable Internet-based Computing Engine), a Java-based grid middleware, which exploits the task-based parallelism. Two bioinformatics benchmark applications, such as distributed sequence comparison and distributed progressive multiple sequence alignment, have been developed using GLAD.

Bioinformatics and the Undergraduate Curriculum

ERIC Educational Resources Information Center

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…

Adapting bioinformatics curricula for big data.

PubMed

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.

Adapting bioinformatics curricula for big data

PubMed Central

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

The GMOD Drupal Bioinformatic Server Framework

PubMed Central

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

Using Microbial Genome Annotation as a Foundation for Collaborative Student Research

ERIC Educational Resources Information Center

Reed, Kelynne E.; Richardson, John M.

2013-01-01

We used the Integrated Microbial Genomes Annotation Collaboration Toolkit as a framework to incorporate microbial genomics research into a microbiology and biochemistry course in a way that promoted student learning of bioinformatics and research skills and emphasized teamwork and collaboration as evidenced through multiple assessment mechanisms.…

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

PubMed

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.

The eBioKit, a stand-alone educational platform for bioinformatics

PubMed Central

Conesa, Ana; Bongcam-Rudloff, Erik

2017-01-01

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. PMID:28910280

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

PubMed

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.

Bioinformatics for Undergraduates: Steps toward a Quantitative Bioscience Curriculum

ERIC Educational Resources Information Center

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…

Bioinformatics projects supporting life-sciences learning in high schools.

PubMed

Marques, Isabel; Almeida, Paulo; Alves, Renato; Dias, Maria João; Godinho, Ana; Pereira-Leal, José B

2014-01-01

The interdisciplinary nature of bioinformatics makes it an ideal framework to develop activities enabling enquiry-based learning. We describe here the development and implementation of a pilot project to use bioinformatics-based research activities in high schools, called "Bioinformatics@school." It includes web-based research projects that students can pursue alone or under teacher supervision and a teacher training program. The project is organized so as to enable discussion of key results between students and teachers. After successful trials in two high schools, as measured by questionnaires, interviews, and assessment of knowledge acquisition, the project is expanding by the action of the teachers involved, who are helping us develop more content and are recruiting more teachers and schools.

Evolving Strategies for the Incorporation of Bioinformatics Within the Undergraduate Cell Biology Curriculum

PubMed Central

Honts, Jerry E.

2003-01-01

Recent advances in genomics and structural biology have resulted in an unprecedented increase in biological data available from Internet-accessible databases. In order to help students effectively use this vast repository of information, undergraduate biology students at Drake University were introduced to bioinformatics software and databases in three courses, beginning with an introductory course in cell biology. The exercises and projects that were used to help students develop literacy in bioinformatics are described. In a recently offered course in bioinformatics, students developed their own simple sequence analysis tool using the Perl programming language. These experiences are described from the point of view of the instructor as well as the students. A preliminary assessment has been made of the degree to which students had developed a working knowledge of bioinformatics concepts and methods. Finally, some conclusions have been drawn from these courses that may be helpful to instructors wishing to introduce bioinformatics within the undergraduate biology curriculum. PMID:14673489

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

PubMed

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.

Advantages and disadvantages in usage of bioinformatic programs in promoter region analysis

NASA Astrophysics Data System (ADS)

Pawełkowicz, Magdalena E.; Skarzyńska, Agnieszka; Posyniak, Kacper; ZiÄ bska, Karolina; PlÄ der, Wojciech; Przybecki, Zbigniew

2015-09-01

An important computational challenge is finding the regulatory elements across the promotor region. In this work we present the advantages and disadvantages from the application of different bioinformatics programs for localization of transcription factor binding sites in the upstream region of genes connected with sex determination in cucumber. We use PlantCARE, PlantPAN and SignalScan to find motifs in the promotor regions. The results have been compared and possible function of chosen motifs has been described.

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

PubMed Central

2010-01-01

Background Bioinformatics researchers are now 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. Description 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. Conclusions Hadoop and the MapReduce programming paradigm already have a substantial base in the bioinformatics community, especially in the field of next-generation sequencing analysis, and such use is increasing. This is due to the cost-effectiveness of Hadoop-based analysis on commodity Linux clusters, and in the cloud via data upload to cloud vendors who have implemented Hadoop/HBase; and due to the effectiveness and ease-of-use of the MapReduce method in parallelization of many data analysis algorithms. PMID:21210976

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

PubMed

Taylor, Ronald C

2010-12-21

Bioinformatics researchers are now 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. Hadoop and the MapReduce programming paradigm already have a substantial base in the bioinformatics community, especially in the field of next-generation sequencing analysis, and such use is increasing. This is due to the cost-effectiveness of Hadoop-based analysis on commodity Linux clusters, and in the cloud via data upload to cloud vendors who have implemented Hadoop/HBase; and due to the effectiveness and ease-of-use of the MapReduce method in parallelization of many data analysis algorithms.

Bioinformatic training needs at a health sciences campus.

PubMed

Oliver, Jeffrey C

2017-01-01

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

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

PubMed

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.

Bioinformatics: Current Practice and Future Challenges for Life Science Education

ERIC Educational Resources Information Center

Hack, Catherine; Kendall, Gary

2005-01-01

It is widely predicted that the application of high-throughput technologies to the quantification and identification of biological molecules will cause a paradigm shift in the life sciences. However, if the biosciences are to evolve from a predominantly descriptive discipline to an information science, practitioners will require enhanced skills in…

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

PubMed Central

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. PMID:28781748

From trace evidence to bioinformatics: putting bryophytes into molecular biology education.

PubMed

Fuselier, Linda; Bougary, Azhar; Malott, Michelle

2011-01-01

Students benefit most from their science education when they participate fully in the process of science in the context of real-world problems. We describe a student-directed open-inquiry lab experience that has no predetermined outcomes and requires students to engage in all components of scientific inquiry from posing a question through evaluating and reporting results. Over 5 weeks, students learn how bryophytes are used in forensics and become proficient in important molecular biology lab skills including DNA isolation, polymerase chain reaction, gel electrophoresis, capillary electrophoresis, and genotyping. For this portion of the experience, there is no specialized equipment necessary outside of gel electrophoresis supplies and a thermocycler. In an optional extension of the experience, students sequence a plastid intron and use introductory bioinformatics skills to identify species related to their forensics case. Students who participated in the lab experience performed well on content-based assessment, and student attitudes toward the experience were positive and indicative of engaged learning. The lab experience is easily modified for higher or lower level courses and can be used in secondary education. Copyright © 2011 Wiley Periodicals, Inc.

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

PubMed

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.

ORBIT: an integrated environment for user-customized bioinformatics tools.

PubMed

Bellgard, M I; Hiew, H L; Hunter, A; Wiebrands, M

1999-10-01

There are a large number of computational programs freely available to bioinformaticians via a client/server, web-based environment. However, the client interface to these tools (typically an html form page) cannot be customized from the client side as it is created by the service provider. The form page is usually generic enough to cater for a wide range of users. However, this implies that a user cannot set as 'default' advanced program parameters on the form or even customize the interface to his/her specific requirements or preferences. Currently, there is a lack of end-user interface environments that can be modified by the user when accessing computer programs available on a remote server running on an intranet or over the Internet. We have implemented a client/server system called ORBIT (Online Researcher's Bioinformatics Interface Tools) where individual clients can have interfaces created and customized to command-line-driven, server-side programs. Thus, Internet-based interfaces can be tailored to a user's specific bioinformatic needs. As interfaces are created on the client machine independent of the server, there can be different interfaces to the same server-side program to cater for different parameter settings. The interface customization is relatively quick (between 10 and 60 min) and all client interfaces are integrated into a single modular environment which will run on any computer platform supporting Java. The system has been developed to allow for a number of future enhancements and features. ORBIT represents an important advance in the way researchers gain access to bioinformatics tools on the Internet.

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

ERIC Educational Resources Information Center

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…

A quick guide for building a successful bioinformatics community.

PubMed

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

2015-02-01

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

Bioinformatics Projects Supporting Life-Sciences Learning in High Schools

PubMed Central

Marques, Isabel; Almeida, Paulo; Alves, Renato; Dias, Maria João; Godinho, Ana; Pereira-Leal, José B.

2014-01-01

The interdisciplinary nature of bioinformatics makes it an ideal framework to develop activities enabling enquiry-based learning. We describe here the development and implementation of a pilot project to use bioinformatics-based research activities in high schools, called “Bioinformatics@school.” It includes web-based research projects that students can pursue alone or under teacher supervision and a teacher training program. The project is organized so as to enable discussion of key results between students and teachers. After successful trials in two high schools, as measured by questionnaires, interviews, and assessment of knowledge acquisition, the project is expanding by the action of the teachers involved, who are helping us develop more content and are recruiting more teachers and schools. PMID:24465192

Open discovery: An integrated live Linux platform of Bioinformatics tools

PubMed Central

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. Availability The Open Discovery is distributed free under Academic Free License (AFL) and can be downloaded from http://www.OpenDiscovery.org.in PMID:19238235

Proteogenomics approaches for studying cancer biology and their potential in the identification of acute myeloid leukemia biomarkers.

PubMed

Hernandez-Valladares, Maria; Vaudel, Marc; Selheim, Frode; Berven, Frode; Bruserud, Øystein

2017-08-01

Mass spectrometry (MS)-based proteomics has become an indispensable tool for the characterization of the proteome and its post-translational modifications (PTM). In addition to standard protein sequence databases, proteogenomics strategies search the spectral data against the theoretical spectra obtained from customized protein sequence databases. Up to date, there are no published proteogenomics studies on acute myeloid leukemia (AML) samples. Areas covered: Proteogenomics involves the understanding of genomic and proteomic data. The intersection of both datatypes requires advanced bioinformatics skills. A standard proteogenomics workflow that could be used for the study of AML samples is described. The generation of customized protein sequence databases as well as bioinformatics tools and pipelines commonly used in proteogenomics are discussed in detail. Expert commentary: Drawing on evidence from recent cancer proteogenomics studies and taking into account the public availability of AML genomic data, the interpretation of present and future MS-based AML proteomic data using AML-specific protein sequence databases could discover new biological mechanisms and targets in AML. However, proteogenomics workflows including bioinformatics guidelines can be challenging for the wide AML research community. It is expected that further automation and simplification of the bioinformatics procedures might attract AML investigators to adopt the proteogenomics strategy.

Precision medicine needs pioneering clinical bioinformaticians.

PubMed

Gómez-López, Gonzalo; Dopazo, Joaquín; Cigudosa, Juan C; Valencia, Alfonso; Al-Shahrour, Fátima

2017-10-25

Success in precision medicine depends on accessing high-quality genetic and molecular data from large, well-annotated patient cohorts that couple biological samples to comprehensive clinical data, which in conjunction can lead to effective therapies. From such a scenario emerges the need for a new professional profile, an expert bioinformatician with training in clinical areas who can make sense of multi-omics data to improve therapeutic interventions in patients, and the design of optimized basket trials. In this review, we first describe the main policies and international initiatives that focus on precision medicine. Secondly, we review the currently ongoing clinical trials in precision medicine, introducing the concept of 'precision bioinformatics', and we describe current pioneering bioinformatics efforts aimed at implementing tools and computational infrastructures for precision medicine in health institutions around the world. Thirdly, we discuss the challenges related to the clinical training of bioinformaticians, and the urgent need for computational specialists capable of assimilating medical terminologies and protocols to address real clinical questions. We also propose some skills required to carry out common tasks in clinical bioinformatics and some tips for emergent groups. Finally, we explore the future perspectives and the challenges faced by precision medicine bioinformatics. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

MutSpec: a Galaxy toolbox for streamlined analyses of somatic mutation spectra in human and mouse cancer genomes.

PubMed

Ardin, Maude; Cahais, Vincent; Castells, Xavier; Bouaoun, Liacine; Byrnes, Graham; Herceg, Zdenko; Zavadil, Jiri; Olivier, Magali

2016-04-18

The nature of somatic mutations observed in human tumors at single gene or genome-wide levels can reveal information on past carcinogenic exposures and mutational processes contributing to tumor development. While large amounts of sequencing data are being generated, the associated analysis and interpretation of mutation patterns that may reveal clues about the natural history of cancer present complex and challenging tasks that require advanced bioinformatics skills. To make such analyses accessible to a wider community of researchers with no programming expertise, we have developed within the web-based user-friendly platform Galaxy a first-of-its-kind package called MutSpec. MutSpec includes a set of tools that perform variant annotation and use advanced statistics for the identification of mutation signatures present in cancer genomes and for comparing the obtained signatures with those published in the COSMIC database and other sources. MutSpec offers an accessible framework for building reproducible analysis pipelines, integrating existing methods and scripts developed in-house with publicly available R packages. MutSpec may be used to analyse data from whole-exome, whole-genome or targeted sequencing experiments performed on human or mouse genomes. Results are provided in various formats including rich graphical outputs. An example is presented to illustrate the package functionalities, the straightforward workflow analysis and the richness of the statistics and publication-grade graphics produced by the tool. MutSpec offers an easy-to-use graphical interface embedded in the popular Galaxy platform that can be used by researchers with limited programming or bioinformatics expertise to analyse mutation signatures present in cancer genomes. MutSpec can thus effectively assist in the discovery of complex mutational processes resulting from exogenous and endogenous carcinogenic insults.

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

PubMed Central

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

Vertical and horizontal integration of bioinformatics education: A modular, interdisciplinary approach.

PubMed

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. Furthermore, we believe that a true interdisciplinary science experience would be best served by introduction of bioinformatics modules within existing courses in biology and chemistry and other complementary departments. To that end, with support from the Howard Hughes Medical Institute, we have developed over a dozen independent bioinformatics modules for our students that are incorporated into courses ranging from general chemistry and biology, advanced specialty courses, and classes in complementary disciplines such as computer science, mathematics, and physics. These activities have largely promoted active learning in our classrooms and have enhanced student understanding of course materials. Herein, we describe our program, the activities we have developed, and assessment of our endeavors in this area. Copyright © 2009 International Union of Biochemistry and Molecular Biology, Inc.

The application of genomics and bioinformatics to accelerate crop improvement in a changing climate.

PubMed

Batley, Jacqueline; Edwards, David

2016-04-01

The changing climate and growing global population will increase pressure on our ability to produce sufficient food. The breeding of novel crops and the adaptation of current crops to the new environment are required to ensure continued food production. Advances in genomics offer the potential to accelerate the genomics based breeding of crop plants. However, relating genomic data to climate related agronomic traits for use in breeding remains a huge challenge, and one which will require coordination of diverse skills and expertise. Bioinformatics, when combined with genomics has the potential to help maintain food security in the face of climate change through the accelerated production of climate ready crops. Copyright © 2016 Elsevier Ltd. All rights reserved.

Intrageneric Primer Design: Bringing Bioinformatics Tools to the Class

ERIC Educational Resources Information Center

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…

The 2015 Bioinformatics Open Source Conference (BOSC 2015).

PubMed

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.

Visiting Scholars Program Application | FNLCR Staging

Cancer.gov

Below are scientific areas and programs that the Frederick National Labisactively seeking scholars to participate: Data Science and Information Technology (including Bioinformatics, Visualization, etc) Advanced Preclinical Researc

An information technology emphasis in biomedical informatics education.

PubMed

Kane, Michael D; Brewer, Jeffrey L

2007-02-01

Unprecedented growth in the interdisciplinary domain of biomedical informatics reflects the recent advancements in genomic sequence availability, high-content biotechnology screening systems, as well as the expectations of computational biology to command a leading role in drug discovery and disease characterization. These forces have moved much of life sciences research almost completely into the computational domain. Importantly, educational training in biomedical informatics has been limited to students enrolled in the life sciences curricula, yet much of the skills needed to succeed in biomedical informatics involve or augment training in information technology curricula. This manuscript describes the methods and rationale for training students enrolled in information technology curricula in the field of biomedical informatics, which augments the existing information technology curriculum and provides training on specific subjects in Biomedical Informatics not emphasized in bioinformatics courses offered in life science programs, and does not require prerequisite courses in the life sciences.

Perspectives on an education in computational biology and medicine.

PubMed

Rubinstein, Jill C

2012-09-01

The mainstream application of massively parallel, high-throughput assays in biomedical research has created a demand for scientists educated in Computational Biology and Bioinformatics (CBB). In response, formalized graduate programs have rapidly evolved over the past decade. Concurrently, there is increasing need for clinicians trained to oversee the responsible translation of CBB research into clinical tools. Physician-scientists with dedicated CBB training can facilitate such translation, positioning themselves at the intersection between computational biomedical research and medicine. This perspective explores key elements of the educational path to such a position, specifically addressing: 1) evolving perceptions of the role of the computational biologist and the impact on training and career opportunities; 2) challenges in and strategies for obtaining the core skill set required of a biomedical researcher in a computational world; and 3) how the combination of CBB with medical training provides a logical foundation for a career in academic medicine and/or biomedical research.

jORCA: easily integrating bioinformatics Web Services.

PubMed

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. .

The GOBLET training portal: a global repository of bioinformatics training materials, courses and trainers

PubMed Central

Corpas, Manuel; Jimenez, Rafael C.; Bongcam-Rudloff, Erik; Budd, Aidan; Brazas, Michelle D.; Fernandes, Pedro L.; Gaeta, Bruno; van Gelder, Celia; Korpelainen, Eija; Lewitter, Fran; McGrath, Annette; MacLean, Daniel; Palagi, Patricia M.; Rother, Kristian; Taylor, Jan; Via, Allegra; Watson, Mick; Schneider, Maria Victoria; Attwood, Teresa K.

2015-01-01

Summary: Rapid technological advances have led to an explosion of biomedical data in recent years. The pace of change has inspired new collaborative approaches for sharing materials and resources to help train life scientists both in the use of cutting-edge bioinformatics tools and databases and in how to analyse and interpret large datasets. A prototype platform for sharing such training resources was recently created by the Bioinformatics Training Network (BTN). Building on this work, we have created a centralized portal for sharing training materials and courses, including a catalogue of trainers and course organizers, and an announcement service for training events. For course organizers, the portal provides opportunities to promote their training events; for trainers, the portal offers an environment for sharing materials, for gaining visibility for their work and promoting their skills; for trainees, it offers a convenient one-stop shop for finding suitable training resources and identifying relevant training events and activities locally and worldwide. Availability and implementation: http://mygoblet.org/training-portal Contact: manuel.corpas@tgac.ac.uk PMID:25189782

A Quick Guide for Building a Successful Bioinformatics Community

PubMed Central

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

The National Institute of Environmental Health Sciences Superfund Research Program: a model for multidisciplinary training of the next generation of environmental health scientists.

PubMed

Carlin, Danielle J; Henry, Heather; Heacock, Michelle; Trottier, Brittany; Drew, Christina H; Suk, William A

2018-03-28

The National Institute of Environmental Health Sciences (NIEHS) Superfund Research Program (SRP) funds university-based, multidisciplinary research on human health and environmental science and engineering with the central goals to understand how hazardous substances contribute to disease and how to prevent exposures to these environmental chemicals. This multi-disciplinary approach allows early career scientists (e.g. graduate students and postdoctoral researchers) to gain experience in problem-based, solution-oriented research and to conduct research in a highly collaborative environment. Training the next generation of environmental health scientists has been an important part of the SRP since its inception. In addition to basic research, the SRP has grown to include support of broader training experiences such as those in research translation and community engagement activities that provide opportunities to give new scientists many of the skills they will need to be successful in their field of research. Looking to the future, the SRP will continue to evolve its training component by tracking and analyzing outcomes from its trainees by using tools such as the NIEHS CareerTrac database system, by increasing opportunities for trainees interested in research that goes beyond US boundaries, and in the areas of bioinformatics and data integration. These opportunities will give them the skills needed to be competitive and successful no matter which employment sector they choose to enter after they have completed their training experience.

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

PubMed Central

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

2017-01-01

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

The 2015 Bioinformatics Open Source Conference (BOSC 2015)

PubMed Central

Harris, Nomi L.; Cock, Peter J. A.; Lapp, Hilmar

2016-01-01

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. PMID:26914653

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

PubMed

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

2017-01-01

Despite the central place held by bioinformatics in modern life sciences and related areas, it has only recently been integrated to a limited extent into high-school teaching and learning programs. Here we describe the assessment of a learning environment entitled 'Bioinformatics in the Service of Biotechnology'. Students' learning outcomes and attitudes toward the bioinformatics learning environment were measured by analyzing their answers to questions embedded within the activities, questionnaires, interviews and observations. Students' difficulties and knowledge acquisition were characterized based on four categories: the required domain-specific knowledge (declarative, procedural, strategic or situational), the scientific field that each question stems from (biology, bioinformatics or their combination), the associated cognitive-process dimension (remember, understand, apply, analyze, evaluate, create) and the type of question (open-ended or multiple choice). Analysis of students' cognitive outcomes revealed learning gains in bioinformatics and related scientific fields, as well as appropriation of the bioinformatics approach as part of the students' scientific 'toolbox'. For students, questions stemming from the 'old world' biology field and requiring declarative or strategic knowledge were harder to deal with. This stands in contrast to their teachers' prediction. Analysis of students' affective outcomes revealed positive attitudes toward bioinformatics and the learning environment, as well as their perception of the teacher's role. Insights from this analysis yielded implications and recommendations for curriculum design, classroom enactment, teacher education and research. For example, we recommend teaching bioinformatics in an integrative and comprehensive manner, through an inquiry process, and linking it to the wider science curriculum. © The Author 2016. Published by Oxford University Press.

New Web-Based Tools Make Systems Pharmacology More Accessible Using Data from the NCI-60 | Center for Cancer Research

Cancer.gov

High-throughput biological techniques, like microarrays and drug screens, generate an enormous amount of data that may be critically important for cancer researchers and clinicians. Being able to manipulate the data to extract those pieces of interest, however, can require computational or bioinformatics skills beyond those of the average scientist.

A Molecular Genetics Laboratory Course Applying Bioinformatics and Cell Biology in the Context of Original Research

ERIC Educational Resources Information Center

Brame, Cynthia J.; Pruitt, Wendy M.; Robinson, Lucy C.

2008-01-01

Research based laboratory courses have been shown to stimulate student interest in science and to improve scientific skills. We describe here a project developed for a semester-long research-based laboratory course that accompanies a genetics lecture course. The project was designed to allow students to become familiar with the use of…

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

PubMed

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.

Visiting Scholars Program Application | Frederick National Laboratory for Cancer Research

Cancer.gov

Below are scientific areas and programs that the Frederick National Labisactively seeking scholars to participate: Data Science and Information Technology (including Bioinformatics, Visualization, etc) Advanced Preclinical Researc

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

PubMed

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.

Design and implementation of a library-based information service in molecular biology and genetics at the University of Pittsburgh

PubMed Central

Chattopadhyay, Ansuman; Tannery, Nancy Hrinya; Silverman, Deborah A. L.; Bergen, Phillip; Epstein, Barbara A.

2006-01-01

Setting: In summer 2002, the Health Sciences Library System (HSLS) at the University of Pittsburgh initiated an information service in molecular biology and genetics to assist researchers with identifying and utilizing bioinformatics tools. Program Components: This novel information service comprises hands-on training workshops and consultation on the use of bioinformatics tools. The HSLS also provides an electronic portal and networked access to public and commercial molecular biology databases and software packages. Evaluation Mechanisms: Researcher feedback gathered during the first three years of workshops and individual consultation indicate that the information service is meeting user needs. Next Steps/Future Directions: The service's workshop offerings will expand to include emerging bioinformatics topics. A frequently asked questions database is also being developed to reuse advice on complex bioinformatics questions. PMID:16888665

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Taylor, Ronald C.

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 HBasemore » 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.« less

Bioinformatics for Exploration

NASA Technical Reports Server (NTRS)

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.

Scalable computing for evolutionary genomics.

PubMed

Prins, Pjotr; Belhachemi, Dominique; Möller, Steffen; Smant, Geert

2012-01-01

Genomic data analysis in evolutionary biology is becoming so computationally intensive that analysis of multiple hypotheses and scenarios takes too long on a single desktop computer. In this chapter, we discuss techniques for scaling computations through parallelization of calculations, after giving a quick overview of advanced programming techniques. Unfortunately, parallel programming is difficult and requires special software design. The alternative, especially attractive for legacy software, is to introduce poor man's parallelization by running whole programs in parallel as separate processes, using job schedulers. Such pipelines are often deployed on bioinformatics computer clusters. Recent advances in PC virtualization have made it possible to run a full computer operating system, with all of its installed software, on top of another operating system, inside a "box," or virtual machine (VM). Such a VM can flexibly be deployed on multiple computers, in a local network, e.g., on existing desktop PCs, and even in the Cloud, to create a "virtual" computer cluster. Many bioinformatics applications in evolutionary biology can be run in parallel, running processes in one or more VMs. Here, we show how a ready-made bioinformatics VM image, named BioNode, effectively creates a computing cluster, and pipeline, in a few steps. This allows researchers to scale-up computations from their desktop, using available hardware, anytime it is required. BioNode is based on Debian Linux and can run on networked PCs and in the Cloud. Over 200 bioinformatics and statistical software packages, of interest to evolutionary biology, are included, such as PAML, Muscle, MAFFT, MrBayes, and BLAST. Most of these software packages are maintained through the Debian Med project. In addition, BioNode contains convenient configuration scripts for parallelizing bioinformatics software. Where Debian Med encourages packaging free and open source bioinformatics software through one central project, BioNode encourages creating free and open source VM images, for multiple targets, through one central project. BioNode can be deployed on Windows, OSX, Linux, and in the Cloud. Next to the downloadable BioNode images, we provide tutorials online, which empower bioinformaticians to install and run BioNode in different environments, as well as information for future initiatives, on creating and building such images.

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

PubMed Central

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

2018-01-01

Abstract 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. PMID:28040748

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

PubMed

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

2018-05-01

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 Instituto Gulbenkian de Ciência and its Outreach

PubMed Central

Leão, Maria João; Godinho, Ana; Fernandes, Pedro

2012-01-01

The Instituto Gulbenkian de Ciência (IGC) is biomedical research institute that acts as a host institution for small research groups, in Portugal. Most of its activities reach out to the scientific community in several ways. The IGC organizes regular series of seminars with invited international speakers, workshops, courses and conferences, and an in-house PhD programme. Specific outreach needs had to be met in the two instances that are described here. GTPB The Gulbenkian Training Programme in Bioinformatics (GTPB) started as a regular activity in 1999 in response to the demand of users seeking opportunities to acquire hands-on practical skills in Bioinformatics in an effective way. Training provision in Bioinformatics requires the conciliation of a variety of interests into a series of highly effective training events, in which scientists can acquire skills and a high degree of independence in their usage. The GTPB programme currently offers more than 30 themes, of which 15 to 20 are chosen for single events in each year. The GTPB has provided training to more than 2000 researchers and students, so far. IGC Outreach A dedicated outreach programme targets science education and public engagement in science, for different audience groups. The aim of the outreach programme is to promote scientific literacy, foster careers in science and empower citizens to engage in cutting-edge biomedical research. Activities include Open Days, seminars and laboratory workshops for teachers, development of online, multimedia and hard-copy resources and experimental protocols to be used in schools, visits to schools with hands-on experiments and career talks by researchers and facility staff. Less conventional outreach activities include direct participation in venues for the general public (such a a music festival, for example) have created unexpected opportunities for fundraising and direct financial support for students engaged in research projects.

Building a bioinformatics community of practice through library education programs.

PubMed

Moore, Margaret E; Vaughan, K T L; Hayes, Barrie E

2004-01-01

This paper addresses the following questions:What makes the community of practice concept an intriguing framework for developing library services for bioinformatics? What is the campus context and setting? What has been the Health Sciences Library's role in bioinformatics at the University of North Carolina (UNC) Chapel Hill? What are the Health Sciences Library's goals? What services are currently offered? How will these services be evaluated and developed? How can libraries demonstrate their value? Providing library services for an emerging community such as bioinformatics and computational biology presents special challenges for libraries including understanding needs, defining and communicating the library's role, building relationships within the community, preparing staff, and securing funding. Like many academic health sciences libraries, the University of North Carolina (UNC) at Chapel Hill Health Sciences Library is addressing these challenges in the context of its overall mission and goals.

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

PubMed

Bonnal, Raoul J P; Aerts, Jan; Githinji, George; Goto, Naohisa; MacLean, Dan; Miller, Chase A; Mishima, Hiroyuki; Pagani, Massimiliano; Ramirez-Gonzalez, Ricardo; Smant, Geert; Strozzi, Francesco; Syme, Rob; Vos, Rutger; Wennblom, Trevor J; Woodcroft, Ben J; Katayama, Toshiaki; Prins, Pjotr

2012-04-01

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 generator, tools and tight web integration, is an improved general model for scaling up collaborative open source software development in bioinformatics. Biogem and modules are free and are OSS. Biogem runs on all systems that support recent versions of Ruby, including Linux, Mac OS X and Windows. Further information at http://www.biogems.info. A tutorial is available at http://www.biogems.info/howto.html bonnal@ingm.org.

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics.

PubMed

Egea, Jose A; Henriques, David; Cokelaer, Thomas; Villaverde, Alejandro F; MacNamara, Aidan; Danciu, Diana-Patricia; Banga, Julio R; Saez-Rodriguez, Julio

2014-05-10

Optimization is the key to solving many problems in computational biology. Global optimization methods, which provide a robust methodology, and metaheuristics in particular have proven to be the most efficient methods for many applications. Despite their utility, there is a limited availability of metaheuristic tools. We present MEIGO, an R and Matlab optimization toolbox (also available in Python via a wrapper of the R version), that implements metaheuristics capable of solving diverse problems arising in systems biology and bioinformatics. The toolbox includes the enhanced scatter search method (eSS) for continuous nonlinear programming (cNLP) and mixed-integer programming (MINLP) problems, and variable neighborhood search (VNS) for Integer Programming (IP) problems. Additionally, the R version includes BayesFit for parameter estimation by Bayesian inference. The eSS and VNS methods can be run on a single-thread or in parallel using a cooperative strategy. The code is supplied under GPLv3 and is available at http://www.iim.csic.es/~gingproc/meigo.html. Documentation and examples are included. The R package has been submitted to BioConductor. We evaluate MEIGO against optimization benchmarks, and illustrate its applicability to a series of case studies in bioinformatics and systems biology where it outperforms other state-of-the-art methods. MEIGO provides a free, open-source platform for optimization that can be applied to multiple domains of systems biology and bioinformatics. It includes efficient state of the art metaheuristics, and its open and modular structure allows the addition of further methods.

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics

PubMed Central

2014-01-01

Background Optimization is the key to solving many problems in computational biology. Global optimization methods, which provide a robust methodology, and metaheuristics in particular have proven to be the most efficient methods for many applications. Despite their utility, there is a limited availability of metaheuristic tools. Results We present MEIGO, an R and Matlab optimization toolbox (also available in Python via a wrapper of the R version), that implements metaheuristics capable of solving diverse problems arising in systems biology and bioinformatics. The toolbox includes the enhanced scatter search method (eSS) for continuous nonlinear programming (cNLP) and mixed-integer programming (MINLP) problems, and variable neighborhood search (VNS) for Integer Programming (IP) problems. Additionally, the R version includes BayesFit for parameter estimation by Bayesian inference. The eSS and VNS methods can be run on a single-thread or in parallel using a cooperative strategy. The code is supplied under GPLv3 and is available at http://www.iim.csic.es/~gingproc/meigo.html. Documentation and examples are included. The R package has been submitted to BioConductor. We evaluate MEIGO against optimization benchmarks, and illustrate its applicability to a series of case studies in bioinformatics and systems biology where it outperforms other state-of-the-art methods. Conclusions MEIGO provides a free, open-source platform for optimization that can be applied to multiple domains of systems biology and bioinformatics. It includes efficient state of the art metaheuristics, and its open and modular structure allows the addition of further methods. PMID:24885957

A Molecular Genetics Laboratory Course Applying Bioinformatics and Cell Biology in the Context of Original Research

PubMed Central

Pruitt, Wendy M.; Robinson, Lucy C.

2008-01-01

Research based laboratory courses have been shown to stimulate student interest in science and to improve scientific skills. We describe here a project developed for a semester-long research-based laboratory course that accompanies a genetics lecture course. The project was designed to allow students to become familiar with the use of bioinformatics tools and molecular biology and genetic approaches while carrying out original research. Students were required to present their hypotheses, experiments, and results in a comprehensive lab report. The lab project concerned the yeast casein kinase 1 (CK1) protein kinase Yck2. CK1 protein kinases are present in all organisms and are well conserved in primary structure. These enzymes display sequence features that differ from other protein kinase subfamilies. Students identified such sequences within the CK1 subfamily, chose a sequence to analyze, used available structural data to determine possible functions for their sequences, and designed mutations within the sequences. After generating the mutant alleles, these were expressed in yeast and tested for function by using two growth assays. The student response to the project was positive, both in terms of knowledge and skills increases and interest in research, and several students are continuing the analysis of mutant alleles as summer projects. PMID:19047427

JASPAR RESTful API: accessing JASPAR data from any programming language.

PubMed

Khan, Aziz; Mathelier, Anthony

2018-05-01

JASPAR is a widely used open-access database of curated, non-redundant transcription factor binding profiles. Currently, data from JASPAR can be retrieved as flat files or by using programming language-specific interfaces. Here, we present a programming language-independent application programming interface (API) to access JASPAR data using the Representational State Transfer (REST) architecture. The REST API enables programmatic access to JASPAR by most programming languages and returns data in eight widely used formats. Several endpoints are available to access the data and an endpoint is available to infer the TF binding profile(s) likely bound by a given DNA binding domain protein sequence. Additionally, it provides an interactive browsable interface for bioinformatics tool developers. This REST API is implemented in Python using the Django REST Framework. It is accessible at http://jaspar.genereg.net/api/ and the source code is freely available at https://bitbucket.org/CBGR/jaspar under GPL v3 license. aziz.khan@ncmm.uio.no or anthony.mathelier@ncmm.uio.no. Supplementary data are available at Bioinformatics online.

GénoPlante-Info (GPI): a collection of databases and bioinformatics resources for plant genomics

PubMed Central

Samson, Delphine; Legeai, Fabrice; Karsenty, Emmanuelle; Reboux, Sébastien; Veyrieras, Jean-Baptiste; Just, Jeremy; Barillot, Emmanuel

2003-01-01

Génoplante is a partnership program between public French institutes (INRA, CIRAD, IRD and CNRS) and private companies (Biogemma, Bayer CropScience and Bioplante) that aims at developing genome analysis programs for crop species (corn, wheat, rapeseed, sunflower and pea) and model plants (Arabidopsis and rice). The outputs of these programs form a wealth of information (genomic sequence, transcriptome, proteome, allelic variability, mapping and synteny, and mutation data) and tools (databases, interfaces, analysis software), that are being integrated and made public at the public bioinformatics resource centre of Génoplante: GénoPlante-Info (GPI). This continuous flood of data and tools is regularly updated and will grow continuously during the coming two years. Access to the GPI databases and tools is available at http://genoplante-info.infobiogen.fr/. PMID:12519976

Combining medical informatics and bioinformatics toward tools for personalized medicine.

PubMed

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.

Transcriptome Analysis of Human Immune Responses Following Live Vaccine Strain (LVS) Francisella Tularensis Vaccination

DTIC Science & Technology

2007-03-08

with CD3D 50848 PAR1/UBE3A Prader–Willi syndrome chromosome region 1, GMCSFRalpha precursor, IL3Ralpha precursor (CD123) Brain development...intervention programs justifiable? Emerg. Infect. Dis. 3, 83–94. iebel, U., Kindler , B., Pepperkok, R., 2004. ‘Harvester’: a fast meta search engine of human...protein resources. Bioinformatics 20, 1962–1963. iebel, U., Kindler , B., Pepperkok, R., 2005. Bioinformatic “Harvester”: a search engine for genome

Special Focus

PubMed Central

Nawrocki, Eric P.; Burge, Sarah W.

2013-01-01

The development of RNA bioinformatic tools began more than 30 y ago with the description of the Nussinov and Zuker dynamic programming algorithms for single sequence RNA secondary structure prediction. Since then, many tools have been developed for various RNA sequence analysis problems such as homology search, multiple sequence alignment, de novo RNA discovery, read-mapping, and many more. In this issue, we have collected a sampling of reviews and original research that demonstrate some of the many ways bioinformatics is integrated with current RNA biology research. PMID:23948768

Meeting review: 2002 O'Reilly Bioinformatics Technology Conference.

PubMed

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.

WIWS: a protein structure bioinformatics Web service collection.

PubMed

Hekkelman, M L; Te Beek, T A H; Pettifer, S R; Thorne, D; Attwood, T K; Vriend, G

2010-07-01

The WHAT IF molecular-modelling and drug design program is widely distributed in the world of protein structure bioinformatics. Although originally designed as an interactive application, its highly modular design and inbuilt control language have recently enabled its deployment as a collection of programmatically accessible web services. We report here a collection of WHAT IF-based protein structure bioinformatics web services: these relate to structure quality, the use of symmetry in crystal structures, structure correction and optimization, adding hydrogens and optimizing hydrogen bonds and a series of geometric calculations. The freely accessible web services are based on the industry standard WS-I profile and the EMBRACE technical guidelines, and are available via both REST and SOAP paradigms. The web services run on a dedicated computational cluster; their function and availability is monitored daily.

Meeting Review: 2002 O'Reilly Bioinformatics Technology Conference

PubMed Central

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 [14]. 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. PMID:18628852

BioRuby: bioinformatics software for the Ruby programming language.

PubMed

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

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shi, Lizhen; Wang, Zhong; Yu, Weikuan

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

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

PubMed Central

Beck, Tim N.; Chikwem, Adaeze J.; Solanki, Nehal R.

2014-01-01

Bioinformatic approaches are intended to provide systems level insight into the complex biological processes that underlie serious diseases such as cancer. In this review we describe current bioinformatic resources, and illustrate how they have been used to study a clinically important example: epithelial-to-mesenchymal transition (EMT) in lung cancer. Lung cancer is the leading cause of cancer-related deaths and is often diagnosed at advanced stages, leading to limited therapeutic success. While EMT is essential during development and wound healing, pathological reactivation of this program by cancer cells contributes to metastasis and drug resistance, both major causes of death from lung cancer. Challenges of studying EMT include its transient nature, its molecular and phenotypic heterogeneity, and the complicated networks of rewired signaling cascades. Given the biology of lung cancer and the role of EMT, it is critical to better align the two in order to advance the impact of precision oncology. This task relies heavily on the application of bioinformatic resources. Besides summarizing recent work in this area, we use four EMT-associated genes, TGF-β (TGFB1), NEDD9/HEF1, β-catenin (CTNNB1) and E-cadherin (CDH1), as exemplars to demonstrate the current capacities and limitations of probing bioinformatic resources to inform hypothesis-driven studies with therapeutic goals. PMID:25096367

Cloudgene: A graphical execution platform for MapReduce programs on private and public clouds

PubMed Central

2012-01-01

Background The MapReduce framework enables a scalable processing and analyzing of large datasets by distributing the computational load on connected computer nodes, referred to as a cluster. In Bioinformatics, MapReduce has already been adopted to various case scenarios such as mapping next generation sequencing data to a reference genome, finding SNPs from short read data or matching strings in genotype files. Nevertheless, tasks like installing and maintaining MapReduce on a cluster system, importing data into its distributed file system or executing MapReduce programs require advanced knowledge in computer science and could thus prevent scientists from usage of currently available and useful software solutions. Results Here we present Cloudgene, a freely available platform to improve the usability of MapReduce programs in Bioinformatics by providing a graphical user interface for the execution, the import and export of data and the reproducibility of workflows on in-house (private clouds) and rented clusters (public clouds). The aim of Cloudgene is to build a standardized graphical execution environment for currently available and future MapReduce programs, which can all be integrated by using its plug-in interface. Since Cloudgene can be executed on private clusters, sensitive datasets can be kept in house at all time and data transfer times are therefore minimized. Conclusions Our results show that MapReduce programs can be integrated into Cloudgene with little effort and without adding any computational overhead to existing programs. This platform gives developers the opportunity to focus on the actual implementation task and provides scientists a platform with the aim to hide the complexity of MapReduce. In addition to MapReduce programs, Cloudgene can also be used to launch predefined systems (e.g. Cloud BioLinux, RStudio) in public clouds. Currently, five different bioinformatic programs using MapReduce and two systems are integrated and have been successfully deployed. Cloudgene is freely available at http://cloudgene.uibk.ac.at. PMID:22888776

cl-dash: rapid configuration and deployment of Hadoop clusters for bioinformatics research in the cloud.

PubMed

Hodor, Paul; Chawla, Amandeep; Clark, Andrew; Neal, Lauren

2016-01-15

: One of the solutions proposed for addressing the challenge of the overwhelming abundance of genomic sequence and other biological data is the use of the Hadoop computing framework. Appropriate tools are needed to set up computational environments that facilitate research of novel bioinformatics methodology using Hadoop. Here, we present cl-dash, a complete starter kit for setting up such an environment. Configuring and deploying new Hadoop clusters can be done in minutes. Use of Amazon Web Services ensures no initial investment and minimal operation costs. Two sample bioinformatics applications help the researcher understand and learn the principles of implementing an algorithm using the MapReduce programming pattern. Source code is available at https://bitbucket.org/booz-allen-sci-comp-team/cl-dash.git. hodor_paul@bah.com. © The Author 2015. Published by Oxford University Press.

An integrated bioinformatics infrastructure essential for advancing pharmacogenomics and personalized medicine in the context of the FDA's Critical Path Initiative.

PubMed

Tong, Weida; Harris, Stephen C; Fang, Hong; Shi, Leming; Perkins, Roger; Goodsaid, Federico; Frueh, Felix W

2007-01-01

Pharmacogenomics (PGx) is identified in the FDA Critical Path document as a major opportunity for advancing medical product development and personalized medicine. An integrated bioinformatics infrastructure for use in FDA data review is crucial to realize the benefits of PGx for public health. We have developed an integrated bioinformatics tool, called ArrayTrack, for managing, analyzing and interpreting genomic and other biomarker data (e.g. proteomic and metabolomic data). ArrayTrack is a highly flexible and robust software platform, which allows evolving with technological advances and changing user needs. ArrayTrack is used in the routine review of genomic data submitted to the FDA; here, three hypothetical examples of its use in the Voluntary eXploratory Data Submission (VXDS) program are illustrated.: © Published by Elsevier Ltd.

In silico methods for evaluating human allergenicity to novel proteins: International Bioinformatics Workshop Meeting Report, 23-24 February 2005.

PubMed

Thomas, Karluss; Bannon, Gary; Hefle, Susan; Herouet, Corinne; Holsapple, Michael; Ladics, Gregory; MacIntosh, Sue; Privalle, Laura

2005-12-01

The ILSI Health and Environmental Sciences Institute (HESI) hosted an expert workshop 22-24 February 2005 in Mallorca, Spain, to review the state-of-the-science for conducting a sequence homology/bioinformatics evaluation in the context of a comprehensive allergenicity assessment for novel proteins, to obtain consensus on the value and role of bioinformatics in evaluating novel proteins, and to discuss the utility and methods of allergen-specific IgE testing in the diagnosis of food allergy. The workshop participants included over forty international experts from academia, industry, and government. The workshop was hosted by the HESI Protein Allergenicity Technical committee, which has established a long-term program whose mission is to advance the scientific understanding of the relevant parameters for characterizing the allergenic potential of novel proteins.

cl-dash: rapid configuration and deployment of Hadoop clusters for bioinformatics research in the cloud

PubMed Central

Hodor, Paul; Chawla, Amandeep; Clark, Andrew; Neal, Lauren

2016-01-01

Summary: One of the solutions proposed for addressing the challenge of the overwhelming abundance of genomic sequence and other biological data is the use of the Hadoop computing framework. Appropriate tools are needed to set up computational environments that facilitate research of novel bioinformatics methodology using Hadoop. Here, we present cl-dash, a complete starter kit for setting up such an environment. Configuring and deploying new Hadoop clusters can be done in minutes. Use of Amazon Web Services ensures no initial investment and minimal operation costs. Two sample bioinformatics applications help the researcher understand and learn the principles of implementing an algorithm using the MapReduce programming pattern. Availability and implementation: Source code is available at https://bitbucket.org/booz-allen-sci-comp-team/cl-dash.git. Contact: hodor_paul@bah.com PMID:26428290

Using EMBL-EBI services via Web interface and programmatically via Web Services

PubMed Central

Lopez, Rodrigo; Cowley, Andrew; Li, Weizhong; McWilliam, Hamish

2015-01-01

The European Bioinformatics Institute (EMBL-EBI) provides access to a wide range of databases and analysis tools that are of key importance in bioinformatics. As well as providing Web interfaces to these resources, Web Services are available using SOAP and REST protocols that enable programmatic access to our resources and allow their integration into other applications and analytical workflows. This unit describes the various options available to a typical researcher or bioinformatician who wishes to use our resources via Web interface or programmatically via a range of programming languages. PMID:25501941

KMC 3: counting and manipulating k-mer statistics.

PubMed

Kokot, Marek; Dlugosz, Maciej; Deorowicz, Sebastian

2017-09-01

Counting all k -mers in a given dataset is a standard procedure in many bioinformatics applications. We introduce KMC3, a significant improvement of the former KMC2 algorithm together with KMC tools for manipulating k -mer databases. Usefulness of the tools is shown on a few real problems. Program is freely available at http://sun.aei.polsl.pl/REFRESH/kmc . sebastian.deorowicz@polsl.pl. 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

H3Africa: current perspectives

PubMed Central

Mulder, Nicola; Abimiku, Alash’le; Adebamowo, Sally N; de Vries, Jantina; Matimba, Alice; Olowoyo, Paul; Ramsay, Michele; Skelton, Michelle; Stein, Dan J

2018-01-01

Precision medicine is being enabled in high-income countries by the growing availability of health data, increasing knowledge of the genetic determinants of disease and variation in response to treatment (pharmacogenomics), and the decreasing costs of data generation, which promote routine application of genomic technologies in the health sector. However, there is uncertainty about the feasibility of applying precision medicine approaches in low- and middle-income countries, due to the lack of population-specific knowledge, skills, and resources. The Human Heredity and Health in Africa (H3Africa) initiative was established to drive new research into the genetic and environmental basis for human diseases of relevance to Africans as well as to build capacity for genomic research on the continent. Precision medicine requires this capacity, in addition to reference data on local populations, and skills to analyze and interpret genomic data from the bedside. The H3Africa consortium is collectively processing samples and data for over 70,000 participants across the continent, accompanied in most cases by rich clinical information on a variety of non-communicable and infectious diseases. These projects are increasingly providing novel insights into the genetic basis of diseases in indigenous populations, insights that have the potential to drive the development of new diagnostics and treatments. The consortium has also invested significant resources into establishing high-quality biorepositories in Africa, a bioinformatic network, and a strong training program that has developed skills in genomic data analysis and interpretation among bioinformaticians, wet-lab researchers, and health-care professionals. Here, we describe the current perspectives of the H3Africa consortium and how it can contribute to making precision medicine in Africa a reality. PMID:29692621

Developing an occupational skills profile for the emerging profession of "big-data-enabled professional"

NASA Astrophysics Data System (ADS)

Kastens, K. A.; Malyn-Smith, J.; Ippolito, J.; Krumhansl, R.

2014-12-01

In August of 2014, the Oceans of Data Institute at Education Development Center, Inc. (EDC) is convening an expert panel to begin the process of developing an occupational skills profile for the "big-data-enabled professional." We define such a professional as an "individual who works with large complex data sets on a regular basis, asking and answering questions, analyzing trends, and finding meaningful patterns, in order to increase the efficiency of processes, make decisions and predictions, solve problems, generate hypotheses, and/or develop new understandings." The expert panel includes several geophysicists, as well as data professionals from engineering, higher education, analytical journalism, forensics, bioinformatics, and telecommunications. Working with experienced facilitators, the expert panel will create a detailed synopsis of the tasks and responsibilities characteristic of their profession, as well as the skills, knowledge and behaviors that enable them to succeed in the workplace. After the panel finishes their work, the task matrix and associated narrative will be vetted and validated by a larger group of additional professionals, and then disseminated for use by educators and employers. The process we are using is called DACUM (Developing a Curriculum), adapted by EDC and optimized for emergent professions, such as the "big-data-enabled professional." DACUM is a well-established method for analyzing jobs and occupations, commonly used in technical fields to develop curriculum and training programs that reflect authentic work tasks found in scientific and technical workplaces. The premises behind the DACUM approach are that: expert workers are better able to describe their own occupation than anyone else; any job can be described in terms of the tasks that successful workers in the occupation perform; all tasks have direct implications for the knowledge, skills, understandings and attitudes that must be taught and learned in preparation for the targeted career. At AGU, we will describe the process and present the finalized occupational profile.

Metavisitor, a Suite of Galaxy Tools for Simple and Rapid Detection and Discovery of Viruses in Deep Sequence Data

PubMed Central

Vernick, Kenneth D.

2017-01-01

Metavisitor is a software package that allows biologists and clinicians without specialized bioinformatics expertise to detect and assemble viral genomes from deep sequence datasets. The package is composed of a set of modular bioinformatic tools and workflows that are implemented in the Galaxy framework. Using the graphical Galaxy workflow editor, users with minimal computational skills can use existing Metavisitor workflows or adapt them to suit specific needs by adding or modifying analysis modules. Metavisitor works with DNA, RNA or small RNA sequencing data over a range of read lengths and can use a combination of de novo and guided approaches to assemble genomes from sequencing reads. We show that the software has the potential for quick diagnosis as well as discovery of viruses from a vast array of organisms. Importantly, we provide here executable Metavisitor use cases, which increase the accessibility and transparency of the software, ultimately enabling biologists or clinicians to focus on biological or medical questions. PMID:28045932

KDE Bioscience: platform for bioinformatics analysis workflows.

PubMed

Lu, Qiang; Hao, Pei; Curcin, Vasa; He, Weizhong; Li, Yuan-Yuan; Luo, Qing-Ming; Guo, Yi-Ke; Li, Yi-Xue

2006-08-01

Bioinformatics is a dynamic research area in which a large number of algorithms and programs have been developed rapidly and independently without much consideration so far of the need for standardization. The lack of such common standards combined with unfriendly interfaces make it difficult for biologists to learn how to use these tools and to translate the data formats from one to another. Consequently, the construction of an integrative bioinformatics platform to facilitate biologists' research is an urgent and challenging task. KDE Bioscience is a java-based software platform that collects a variety of bioinformatics tools and provides a workflow mechanism to integrate them. Nucleotide and protein sequences from local flat files, web sites, and relational databases can be entered, annotated, and aligned. Several home-made or 3rd-party viewers are built-in to provide visualization of annotations or alignments. KDE Bioscience can also be deployed in client-server mode where simultaneous execution of the same workflow is supported for multiple users. Moreover, workflows can be published as web pages that can be executed from a web browser. The power of KDE Bioscience comes from the integrated algorithms and data sources. With its generic workflow mechanism other novel calculations and simulations can be integrated to augment the current sequence analysis functions. Because of this flexible and extensible architecture, KDE Bioscience makes an ideal integrated informatics environment for future bioinformatics or systems biology research.

The Eukaryotic Pathogen Databases: a functional genomic resource integrating data from human and veterinary parasites.

PubMed

Harb, Omar S; Roos, David S

2015-01-01

Over the past 20 years, advances in high-throughput biological techniques and the availability of computational resources including fast Internet access have resulted in an explosion of large genome-scale data sets "big data." While such data are readily available for download and personal use and analysis from a variety of repositories, often such analysis requires access to seldom-available computational skills. As a result a number of databases have emerged to provide scientists with online tools enabling the interrogation of data without the need for sophisticated computational skills beyond basic knowledge of Internet browser utility. This chapter focuses on the Eukaryotic Pathogen Databases (EuPathDB: http://eupathdb.org) Bioinformatic Resource Center (BRC) and illustrates some of the available tools and methods.

Composable languages for bioinformatics: the NYoSh experiment

PubMed Central

Simi, Manuele

2014-01-01

Language WorkBenches (LWBs) are software engineering tools that help domain experts develop solutions to various classes of problems. Some of these tools focus on non-technical users and provide languages to help organize knowledge while other workbenches provide means to create new programming languages. A key advantage of language workbenches is that they support the seamless composition of independently developed languages. This capability is useful when developing programs that can benefit from different levels of abstraction. We reasoned that language workbenches could be useful to develop bioinformatics software solutions. In order to evaluate the potential of language workbenches in bioinformatics, we tested a prominent workbench by developing an alternative to shell scripting. To illustrate what LWBs and Language Composition can bring to bioinformatics, we report on our design and development of NYoSh (Not Your ordinary Shell). NYoSh was implemented as a collection of languages that can be composed to write programs as expressive and concise as shell scripts. This manuscript offers a concrete illustration of the advantages and current minor drawbacks of using the MPS LWB. For instance, we found that we could implement an environment-aware editor for NYoSh that can assist the programmers when developing scripts for specific execution environments. This editor further provides semantic error detection and can be compiled interactively with an automatic build and deployment system. In contrast to shell scripts, NYoSh scripts can be written in a modern development environment, supporting context dependent intentions and can be extended seamlessly by end-users with new abstractions and language constructs. We further illustrate language extension and composition with LWBs by presenting a tight integration of NYoSh scripts with the GobyWeb system. The NYoSh Workbench prototype, which implements a fully featured integrated development environment for NYoSh is distributed at http://nyosh.campagnelab.org. PMID:24482760

Composable languages for bioinformatics: the NYoSh experiment.

PubMed

Simi, Manuele; Campagne, Fabien

2014-01-01

Language WorkBenches (LWBs) are software engineering tools that help domain experts develop solutions to various classes of problems. Some of these tools focus on non-technical users and provide languages to help organize knowledge while other workbenches provide means to create new programming languages. A key advantage of language workbenches is that they support the seamless composition of independently developed languages. This capability is useful when developing programs that can benefit from different levels of abstraction. We reasoned that language workbenches could be useful to develop bioinformatics software solutions. In order to evaluate the potential of language workbenches in bioinformatics, we tested a prominent workbench by developing an alternative to shell scripting. To illustrate what LWBs and Language Composition can bring to bioinformatics, we report on our design and development of NYoSh (Not Your ordinary Shell). NYoSh was implemented as a collection of languages that can be composed to write programs as expressive and concise as shell scripts. This manuscript offers a concrete illustration of the advantages and current minor drawbacks of using the MPS LWB. For instance, we found that we could implement an environment-aware editor for NYoSh that can assist the programmers when developing scripts for specific execution environments. This editor further provides semantic error detection and can be compiled interactively with an automatic build and deployment system. In contrast to shell scripts, NYoSh scripts can be written in a modern development environment, supporting context dependent intentions and can be extended seamlessly by end-users with new abstractions and language constructs. We further illustrate language extension and composition with LWBs by presenting a tight integration of NYoSh scripts with the GobyWeb system. The NYoSh Workbench prototype, which implements a fully featured integrated development environment for NYoSh is distributed at http://nyosh.campagnelab.org.

Evaluating bacterial gene-finding HMM structures as probabilistic logic programs.

PubMed

Mørk, Søren; Holmes, Ian

2012-03-01

Probabilistic logic programming offers a powerful way to describe and evaluate structured statistical models. To investigate the practicality of probabilistic logic programming for structure learning in bioinformatics, we undertook a simplified bacterial gene-finding benchmark in PRISM, a probabilistic dialect of Prolog. We evaluate Hidden Markov Model structures for bacterial protein-coding gene potential, including a simple null model structure, three structures based on existing bacterial gene finders and two novel model structures. We test standard versions as well as ADPH length modeling and three-state versions of the five model structures. The models are all represented as probabilistic logic programs and evaluated using the PRISM machine learning system in terms of statistical information criteria and gene-finding prediction accuracy, in two bacterial genomes. Neither of our implementations of the two currently most used model structures are best performing in terms of statistical information criteria or prediction performances, suggesting that better-fitting models might be achievable. The source code of all PRISM models, data and additional scripts are freely available for download at: http://github.com/somork/codonhmm. Supplementary data are available at Bioinformatics online.

SOBA: sequence ontology bioinformatics analysis.

PubMed

Moore, Barry; Fan, Guozhen; Eilbeck, Karen

2010-07-01

The advent of cheaper, faster sequencing technologies has pushed the task of sequence annotation from the exclusive domain of large-scale multi-national sequencing projects to that of research laboratories and small consortia. The bioinformatics burden placed on these laboratories, some with very little programming experience can be daunting. Fortunately, there exist software libraries and pipelines designed with these groups in mind, to ease the transition from an assembled genome to an annotated and accessible genome resource. We have developed the Sequence Ontology Bioinformatics Analysis (SOBA) tool to provide a simple statistical and graphical summary of an annotated genome. We envisage its use during annotation jamborees, genome comparison and for use by developers for rapid feedback during annotation software development and testing. SOBA also provides annotation consistency feedback to ensure correct use of terminology within annotations, and guides users to add new terms to the Sequence Ontology when required. SOBA is available at http://www.sequenceontology.org/cgi-bin/soba.cgi.

Computer Science Research Funding: How Much Is Too Little?

DTIC Science & Technology

2009-06-01

Bioinformatics Parallel computing Computational biology Principles of programming Computational neuroscience Real-time and embedded systems Scientific...National Security Agency ( NSA ) • Missile Defense Agency (MDA) and others The various research programs have been coordinated through the DDR&E...DOD funding included only DARPA and OSD programs. FY07 and FY08 PBR funding included DARPA, NSA , some of the Services’ basic and applied research

Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists.

PubMed

Zhu, Xun; Wolfgruber, Thomas K; Tasato, Austin; Arisdakessian, Cédric; Garmire, David G; Garmire, Lana X

2017-12-05

Single-cell RNA sequencing (scRNA-Seq) is an increasingly popular platform to study heterogeneity at the single-cell level. Computational methods to process scRNA-Seq data are not very accessible to bench scientists as they require a significant amount of bioinformatic skills. We have developed Granatum, a web-based scRNA-Seq analysis pipeline to make analysis more broadly accessible to researchers. Without a single line of programming code, users can click through the pipeline, setting parameters and visualizing results via the interactive graphical interface. Granatum conveniently walks users through various steps of scRNA-Seq analysis. It has a comprehensive list of modules, including plate merging and batch-effect removal, outlier-sample removal, gene-expression normalization, imputation, gene filtering, cell clustering, differential gene expression analysis, pathway/ontology enrichment analysis, protein network interaction visualization, and pseudo-time cell series construction. Granatum enables broad adoption of scRNA-Seq technology by empowering bench scientists with an easy-to-use graphical interface for scRNA-Seq data analysis. The package is freely available for research use at http://garmiregroup.org/granatum/app.

Using EMBL-EBI Services via Web Interface and Programmatically via Web Services.

PubMed

Lopez, Rodrigo; Cowley, Andrew; Li, Weizhong; McWilliam, Hamish

2014-12-12

The European Bioinformatics Institute (EMBL-EBI) provides access to a wide range of databases and analysis tools that are of key importance in bioinformatics. As well as providing Web interfaces to these resources, Web Services are available using SOAP and REST protocols that enable programmatic access to our resources and allow their integration into other applications and analytical workflows. This unit describes the various options available to a typical researcher or bioinformatician who wishes to use our resources via Web interface or programmatically via a range of programming languages. Copyright © 2014 John Wiley & Sons, Inc.

ISMB 2016 offers outstanding science, networking, and celebration

PubMed Central

Fogg, Christiana

2016-01-01

The annual international conference on Intelligent Systems for Molecular Biology (ISMB) is the major meeting of the International Society for Computational Biology (ISCB). Over the past 23 years the ISMB conference has grown to become the world's largest bioinformatics/computational biology conference. ISMB 2016 will be the year's most important computational biology event globally. The conferences provide a multidisciplinary forum for disseminating the latest developments in bioinformatics/computational biology. ISMB brings together scientists from computer science, molecular biology, mathematics, statistics and related fields. Its principal focus is on the development and application of advanced computational methods for biological problems. ISMB 2016 offers the strongest scientific program and the broadest scope of any international bioinformatics/computational biology conference. Building on past successes, the conference is designed to cater to variety of disciplines within the bioinformatics/computational biology community.  ISMB 2016 takes place July 8 - 12 at the Swan and Dolphin Hotel in Orlando, Florida, United States. For two days preceding the conference, additional opportunities including Satellite Meetings, Student Council Symposium, and a selection of Special Interest Group Meetings and Applied Knowledge Exchange Sessions (AKES) are all offered to enable registered participants to learn more on the latest methods and tools within specialty research areas. PMID:27347392

ISMB 2016 offers outstanding science, networking, and celebration.

PubMed

Fogg, Christiana

2016-01-01

The annual international conference on Intelligent Systems for Molecular Biology (ISMB) is the major meeting of the International Society for Computational Biology (ISCB). Over the past 23 years the ISMB conference has grown to become the world's largest bioinformatics/computational biology conference. ISMB 2016 will be the year's most important computational biology event globally. The conferences provide a multidisciplinary forum for disseminating the latest developments in bioinformatics/computational biology. ISMB brings together scientists from computer science, molecular biology, mathematics, statistics and related fields. Its principal focus is on the development and application of advanced computational methods for biological problems. ISMB 2016 offers the strongest scientific program and the broadest scope of any international bioinformatics/computational biology conference. Building on past successes, the conference is designed to cater to variety of disciplines within the bioinformatics/computational biology community.  ISMB 2016 takes place July 8 - 12 at the Swan and Dolphin Hotel in Orlando, Florida, United States. For two days preceding the conference, additional opportunities including Satellite Meetings, Student Council Symposium, and a selection of Special Interest Group Meetings and Applied Knowledge Exchange Sessions (AKES) are all offered to enable registered participants to learn more on the latest methods and tools within specialty research areas.

Development of Bioinformatics Infrastructure for Genomics Research.

PubMed

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

2017-06-01

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

BioWord: A sequence manipulation suite for Microsoft Word

PubMed Central

2012-01-01

Background The ability to manipulate, edit and process DNA and protein sequences has rapidly become a necessary skill for practicing biologists across a wide swath of disciplines. In spite of this, most everyday sequence manipulation tools are distributed across several programs and web servers, sometimes requiring installation and typically involving frequent switching between applications. To address this problem, here we have developed BioWord, a macro-enabled self-installing template for Microsoft Word documents that integrates an extensive suite of DNA and protein sequence manipulation tools. Results BioWord is distributed as a single macro-enabled template that self-installs with a single click. After installation, BioWord will open as a tab in the Office ribbon. Biologists can then easily manipulate DNA and protein sequences using a familiar interface and minimize the need to switch between applications. Beyond simple sequence manipulation, BioWord integrates functionality ranging from dyad search and consensus logos to motif discovery and pair-wise alignment. Written in Visual Basic for Applications (VBA) as an open source, object-oriented project, BioWord allows users with varying programming experience to expand and customize the program to better meet their own needs. Conclusions BioWord integrates a powerful set of tools for biological sequence manipulation within a handy, user-friendly tab in a widely used word processing software package. The use of a simple scripting language and an object-oriented scheme facilitates customization by users and provides a very accessible educational platform for introducing students to basic bioinformatics algorithms. PMID:22676326

BioWord: a sequence manipulation suite for Microsoft Word.

PubMed

Anzaldi, Laura J; Muñoz-Fernández, Daniel; Erill, Ivan

2012-06-07

The ability to manipulate, edit and process DNA and protein sequences has rapidly become a necessary skill for practicing biologists across a wide swath of disciplines. In spite of this, most everyday sequence manipulation tools are distributed across several programs and web servers, sometimes requiring installation and typically involving frequent switching between applications. To address this problem, here we have developed BioWord, a macro-enabled self-installing template for Microsoft Word documents that integrates an extensive suite of DNA and protein sequence manipulation tools. BioWord is distributed as a single macro-enabled template that self-installs with a single click. After installation, BioWord will open as a tab in the Office ribbon. Biologists can then easily manipulate DNA and protein sequences using a familiar interface and minimize the need to switch between applications. Beyond simple sequence manipulation, BioWord integrates functionality ranging from dyad search and consensus logos to motif discovery and pair-wise alignment. Written in Visual Basic for Applications (VBA) as an open source, object-oriented project, BioWord allows users with varying programming experience to expand and customize the program to better meet their own needs. BioWord integrates a powerful set of tools for biological sequence manipulation within a handy, user-friendly tab in a widely used word processing software package. The use of a simple scripting language and an object-oriented scheme facilitates customization by users and provides a very accessible educational platform for introducing students to basic bioinformatics algorithms.

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

PubMed Central

2011-01-01

Background Bioinformatic analyses typically proceed as chains of data-processing tasks. A pipeline, or 'workflow', is a well-defined protocol, with a specific structure defined by the topology of data-flow interdependencies, and a particular functionality arising from the data transformations applied at each step. In computer science, the dataflow programming (DFP) paradigm defines software systems constructed in this manner, as networks of message-passing components. Thus, bioinformatic workflows can be naturally mapped onto DFP concepts. Results To enable the flexible creation and execution of bioinformatics dataflows, we have written a modular framework for parallel pipelines in Python ('PaPy'). A PaPy workflow is created from re-usable components connected by data-pipes into a directed acyclic graph, which together define nested higher-order map functions. The successive functional transformations of input data are evaluated on flexibly pooled compute resources, either local or remote. Input items are processed in batches of adjustable size, all flowing one to tune the trade-off between parallelism and lazy-evaluation (memory consumption). An add-on module ('NuBio') facilitates the creation of bioinformatics workflows by providing domain specific data-containers (e.g., for biomolecular sequences, alignments, structures) and functionality (e.g., to parse/write standard file formats). Conclusions PaPy offers a modular framework for the creation and deployment of parallel and distributed data-processing workflows. Pipelines derive their functionality from user-written, data-coupled components, so PaPy also can be viewed as a lightweight toolkit for extensible, flow-based bioinformatics data-processing. The simplicity and flexibility of distributed PaPy pipelines may help users bridge the gap between traditional desktop/workstation and grid computing. PaPy is freely distributed as open-source Python code at http://muralab.org/PaPy, and includes extensive documentation and annotated usage examples. PMID:21352538

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

PubMed

Cieślik, Marcin; Mura, Cameron

2011-02-25

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

Lifeskills Program Evaluation at Mammoth Heights Elementary School

ERIC Educational Resources Information Center

Tanner, Emma Moss

2016-01-01

This study is a program evaluation of the Life Skills Program at Mammoth Heights Elementary in the Douglas County School District. The overall goal of the Life Skills Program is to increase students' independent and daily living skills through the teaching of communication, social-emotional skills and academic skills. Students in the Life Skills…

Johns Hopkins University Announces Frederick CREST Classes for Fall 2016 | Poster

Cancer.gov

Johns Hopkins University’s (JHU) Advanced Academic Programs (AAP) division recently announced two classes that will be hosted at the Frederick Center for Research and Education in Science and Technology (CREST) this fall. According to a JHU press release, the classes are Biochemistry, which is part of the M.S. in Biotechnology program at JHU AAP, and Molecular Biology, a part of the M.S. in Bioinformatics program at JHU AAP.

GProX, a user-friendly platform for bioinformatics analysis and visualization of quantitative proteomics data.

PubMed

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.

GProX, a User-Friendly Platform for Bioinformatics Analysis and Visualization of Quantitative Proteomics Data*

PubMed Central

Rigbolt, Kristoffer T. G.; Vanselow, Jens T.; Blagoev, Blagoy

2011-01-01

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. PMID:21602510

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

PubMed

Stocker, Gernot; Rieder, Dietmar; Trajanoski, Zlatko

2004-03-22

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

Open source tools and toolkits for bioinformatics: significance, and where are we?

PubMed

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.

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

PubMed Central

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

Exploiting graphics processing units for computational biology and bioinformatics.

PubMed

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.

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

PubMed

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).

TANGO: a generic tool for high-throughput 3D image analysis for studying nuclear organization.

PubMed

Ollion, Jean; Cochennec, Julien; Loll, François; Escudé, Christophe; Boudier, Thomas

2013-07-15

The cell nucleus is a highly organized cellular organelle that contains the genetic material. The study of nuclear architecture has become an important field of cellular biology. Extracting quantitative data from 3D fluorescence imaging helps understand the functions of different nuclear compartments. However, such approaches are limited by the requirement for processing and analyzing large sets of images. Here, we describe Tools for Analysis of Nuclear Genome Organization (TANGO), an image analysis tool dedicated to the study of nuclear architecture. TANGO is a coherent framework allowing biologists to perform the complete analysis process of 3D fluorescence images by combining two environments: ImageJ (http://imagej.nih.gov/ij/) for image processing and quantitative analysis and R (http://cran.r-project.org) for statistical processing of measurement results. It includes an intuitive user interface providing the means to precisely build a segmentation procedure and set-up analyses, without possessing programming skills. TANGO is a versatile tool able to process large sets of images, allowing quantitative study of nuclear organization. TANGO is composed of two programs: (i) an ImageJ plug-in and (ii) a package (rtango) for R. They are both free and open source, available (http://biophysique.mnhn.fr/tango) for Linux, Microsoft Windows and Macintosh OSX. Distribution is under the GPL v.2 licence. thomas.boudier@snv.jussieu.fr Supplementary data are available at Bioinformatics online.

Building international genomics collaboration for global health security

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cui, Helen H.; Erkkila, Tracy; Chain, Patrick S. G.

Genome science and technologies are transforming life sciences globally in many ways and becoming a highly desirable area for international collaboration to strengthen global health. The Genome Science Program at the Los Alamos National Laboratory is leveraging a long history of expertise in genomics research to assist multiple partner nations in advancing their genomics and bioinformatics capabilities. The capability development objectives focus on providing a molecular genomics-based scientific approach for pathogen detection, characterization, and biosurveillance applications. The general approaches include introduction of basic principles in genomics technologies, training on laboratory methodologies and bioinformatic analysis of resulting data, procurement, and installationmore » of next-generation sequencing instruments, establishing bioinformatics software capabilities, and exploring collaborative applications of the genomics capabilities in public health. Genome centers have been established with public health and research institutions in the Republic of Georgia, Kingdom of Jordan, Uganda, and Gabon; broader collaborations in genomics applications have also been developed with research institutions in many other countries.« less

Building international genomics collaboration for global health security

DOE PAGES

Cui, Helen H.; Erkkila, Tracy; Chain, Patrick S. G.; ...

2015-12-07

Genome science and technologies are transforming life sciences globally in many ways and becoming a highly desirable area for international collaboration to strengthen global health. The Genome Science Program at the Los Alamos National Laboratory is leveraging a long history of expertise in genomics research to assist multiple partner nations in advancing their genomics and bioinformatics capabilities. The capability development objectives focus on providing a molecular genomics-based scientific approach for pathogen detection, characterization, and biosurveillance applications. The general approaches include introduction of basic principles in genomics technologies, training on laboratory methodologies and bioinformatic analysis of resulting data, procurement, and installationmore » of next-generation sequencing instruments, establishing bioinformatics software capabilities, and exploring collaborative applications of the genomics capabilities in public health. Genome centers have been established with public health and research institutions in the Republic of Georgia, Kingdom of Jordan, Uganda, and Gabon; broader collaborations in genomics applications have also been developed with research institutions in many other countries.« less

BioPig: a Hadoop-based analytic toolkit for large-scale sequence data.

PubMed

Nordberg, Henrik; Bhatia, Karan; Wang, Kai; Wang, Zhong

2013-12-01

The recent revolution in sequencing technologies has led to an exponential growth of sequence data. As a result, most of the current bioinformatics tools become obsolete as they fail to scale with data. To tackle this 'data deluge', here we introduce the BioPig sequence analysis toolkit as one of the solutions that scale to data and computation. We built BioPig on the Apache's Hadoop MapReduce system and the Pig data flow language. Compared with traditional serial and MPI-based algorithms, BioPig has three major advantages: first, BioPig's programmability greatly reduces development time for parallel bioinformatics applications; second, testing BioPig with up to 500 Gb sequences demonstrates that it scales automatically with size of data; and finally, BioPig can be ported without modification on many Hadoop infrastructures, as tested with Magellan system at National Energy Research Scientific Computing Center and the Amazon Elastic Compute Cloud. In summary, BioPig represents a novel program framework with the potential to greatly accelerate data-intensive bioinformatics analysis.

TeachEnG: a Teaching Engine for Genomics.

PubMed

Kim, Minji; Kim, Yeonsung; Qian, Lei; Song, Jun S

2017-10-15

Bioinformatics is a rapidly growing field that has emerged from the synergy of computer science, statistics and biology. Given the interdisciplinary nature of bioinformatics, many students from diverse fields struggle with grasping bioinformatic concepts only from classroom lectures. Interactive tools for helping students reinforce their learning would be thus desirable. Here, we present an interactive online educational tool called TeachEnG (acronym for Teaching Engine for Genomics) for reinforcing key concepts in sequence alignment and phylogenetic tree reconstruction. Our instructional games allow students to align sequences by hand, fill out the dynamic programming matrix in the Needleman-Wunsch global sequence alignment algorithm, and reconstruct phylogenetic trees via the maximum parsimony, Unweighted Pair Group Method with Arithmetic mean (UPGMA) and Neighbor-Joining algorithms. With an easily accessible interface and instant visual feedback, TeachEnG will help promote active learning in bioinformatics. TeachEnG is freely available at http://teacheng.illinois.edu. The source code is available from https://github.com/KnowEnG/TeachEnG under the Artistic License 2.0. It is written in JavaScript and compatible with Firefox, Safari, Chrome and Microsoft Edge. songj@illinois.edu. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

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

PubMed

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.

BioMake: a GNU make-compatible utility for declarative workflow management.

PubMed

Holmes, Ian H; Mungall, Christopher J

2017-11-01

The Unix 'make' program is widely used in bioinformatics pipelines, but suffers from problems that limit its application to large analysis datasets. These include reliance on file modification times to determine whether a target is stale, lack of support for parallel execution on clusters, and restricted flexibility to extend the underlying logic program. We present BioMake, a make-like utility that is compatible with most features of GNU Make and adds support for popular cluster-based job-queue engines, MD5 signatures as an alternative to timestamps, and logic programming extensions in Prolog. BioMake is available for MacOSX and Linux systems from https://github.com/evoldoers/biomake under the BSD3 license. The only dependency is SWI-Prolog (version 7), available from http://www.swi-prolog.org/. ihholmes + biomake@gmail.com or cmungall + biomake@gmail.com. Feature table comparing BioMake to similar tools. 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

A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications.

PubMed

Haque, Ashraful; Engel, Jessica; Teichmann, Sarah A; Lönnberg, Tapio

2017-08-18

RNA sequencing (RNA-seq) is a genomic approach for the detection and quantitative analysis of messenger RNA molecules in a biological sample and is useful for studying cellular responses. RNA-seq has fueled much discovery and innovation in medicine over recent years. For practical reasons, the technique is usually conducted on samples comprising thousands to millions of cells. However, this has hindered direct assessment of the fundamental unit of biology-the cell. Since the first single-cell RNA-sequencing (scRNA-seq) study was published in 2009, many more have been conducted, mostly by specialist laboratories with unique skills in wet-lab single-cell genomics, bioinformatics, and computation. However, with the increasing commercial availability of scRNA-seq platforms, and the rapid ongoing maturation of bioinformatics approaches, a point has been reached where any biomedical researcher or clinician can use scRNA-seq to make exciting discoveries. In this review, we present a practical guide to help researchers design their first scRNA-seq studies, including introductory information on experimental hardware, protocol choice, quality control, data analysis and biological interpretation.

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

ERIC Educational Resources Information Center

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…

MAAMD: a workflow to standardize meta-analyses and comparison of affymetrix microarray data

PubMed Central

2014-01-01

Background Mandatory deposit of raw microarray data files for public access, prior to study publication, provides significant opportunities to conduct new bioinformatics analyses within and across multiple datasets. Analysis of raw microarray data files (e.g. Affymetrix CEL files) can be time consuming, complex, and requires fundamental computational and bioinformatics skills. The development of analytical workflows to automate these tasks simplifies the processing of, improves the efficiency of, and serves to standardize multiple and sequential analyses. Once installed, workflows facilitate the tedious steps required to run rapid intra- and inter-dataset comparisons. Results We developed a workflow to facilitate and standardize Meta-Analysis of Affymetrix Microarray Data analysis (MAAMD) in Kepler. Two freely available stand-alone software tools, R and AltAnalyze were embedded in MAAMD. The inputs of MAAMD are user-editable csv files, which contain sample information and parameters describing the locations of input files and required tools. MAAMD was tested by analyzing 4 different GEO datasets from mice and drosophila. MAAMD automates data downloading, data organization, data quality control assesment, differential gene expression analysis, clustering analysis, pathway visualization, gene-set enrichment analysis, and cross-species orthologous-gene comparisons. MAAMD was utilized to identify gene orthologues responding to hypoxia or hyperoxia in both mice and drosophila. The entire set of analyses for 4 datasets (34 total microarrays) finished in ~ one hour. Conclusions MAAMD saves time, minimizes the required computer skills, and offers a standardized procedure for users to analyze microarray datasets and make new intra- and inter-dataset comparisons. PMID:24621103

Foodomics and Food Safety: Where We Are.

PubMed

Andjelković, Uroš; Šrajer Gajdošik, Martina; Gašo-Sokač, Dajana; Martinović, Tamara; Josić, Djuro

2017-09-01

The power of foodomics as a discipline that is now broadly used for quality assurance of food products and adulteration identification, as well as for determining the safety of food, is presented. Concerning sample preparation and application, maintenance of highly sophisticated instruments for both high-performance and high-throughput techniques, and analysis and data interpretation, special attention has to be paid to the development of skilled analysts. The obtained data shall be integrated under a strong bioinformatics environment. Modern mass spectrometry is an extremely powerful analytical tool since it can provide direct qualitative and quantitative information about a molecule of interest from only a minute amount of sample. Quality of this information is influenced by the sample preparation procedure, the type of mass spectrometer used and the analyst's skills. Technical advances are bringing new instruments of increased sensitivity, resolution and speed to the market. Other methods presented here give additional information and can be used as complementary tools to mass spectrometry or for validation of obtained results. Genomics and transcriptomics, as well as affinity-based methods, still have a broad use in food analysis. Serious drawbacks of some of them, especially the affinity-based methods, are the cross-reactivity between similar molecules and the influence of complex food matrices. However, these techniques can be used for pre-screening in order to reduce the large number of samples. Great progress has been made in the application of bioinformatics in foodomics. These developments enabled processing of large amounts of generated data for both identification and quantification, and for corresponding modeling.

Foodomics and Food Safety: Where We Are

PubMed Central

Andjelković, Uroš

2017-01-01

Summary The power of foodomics as a discipline that is now broadly used for quality assurance of food products and adulteration identification, as well as for determining the safety of food, is presented. Concerning sample preparation and application, maintenance of highly sophisticated instruments for both high-performance and high-throughput techniques, and analysis and data interpretation, special attention has to be paid to the development of skilled analysts. The obtained data shall be integrated under a strong bioinformatics environment. Modern mass spectrometry is an extremely powerful analytical tool since it can provide direct qualitative and quantitative information about a molecule of interest from only a minute amount of sample. Quality of this information is influenced by the sample preparation procedure, the type of mass spectrometer used and the analyst’s skills. Technical advances are bringing new instruments of increased sensitivity, resolution and speed to the market. Other methods presented here give additional information and can be used as complementary tools to mass spectrometry or for validation of obtained results. Genomics and transcriptomics, as well as affinity-based methods, still have a broad use in food analysis. Serious drawbacks of some of them, especially the affinity-based methods, are the cross-reactivity between similar molecules and the influence of complex food matrices. However, these techniques can be used for pre-screening in order to reduce the large number of samples. Great progress has been made in the application of bioinformatics in foodomics. These developments enabled processing of large amounts of generated data for both identification and quantification, and for corresponding modeling. PMID:29089845

Workflows for microarray data processing in the Kepler environment.

PubMed

Stropp, Thomas; McPhillips, Timothy; Ludäscher, Bertram; Bieda, Mark

2012-05-17

Microarray data analysis has been the subject of extensive and ongoing pipeline development due to its complexity, the availability of several options at each analysis step, and the development of new analysis demands, including integration with new data sources. Bioinformatics pipelines are usually custom built for different applications, making them typically difficult to modify, extend and repurpose. Scientific workflow systems are intended to address these issues by providing general-purpose frameworks in which to develop and execute such pipelines. The Kepler workflow environment is a well-established system under continual development that is employed in several areas of scientific research. Kepler provides a flexible graphical interface, featuring clear display of parameter values, for design and modification of workflows. It has capabilities for developing novel computational components in the R, Python, and Java programming languages, all of which are widely used for bioinformatics algorithm development, along with capabilities for invoking external applications and using web services. We developed a series of fully functional bioinformatics pipelines addressing common tasks in microarray processing in the Kepler workflow environment. These pipelines consist of a set of tools for GFF file processing of NimbleGen chromatin immunoprecipitation on microarray (ChIP-chip) datasets and more comprehensive workflows for Affymetrix gene expression microarray bioinformatics and basic primer design for PCR experiments, which are often used to validate microarray results. Although functional in themselves, these workflows can be easily customized, extended, or repurposed to match the needs of specific projects and are designed to be a toolkit and starting point for specific applications. These workflows illustrate a workflow programming paradigm focusing on local resources (programs and data) and therefore are close to traditional shell scripting or R/BioConductor scripting approaches to pipeline design. Finally, we suggest that microarray data processing task workflows may provide a basis for future example-based comparison of different workflow systems. We provide a set of tools and complete workflows for microarray data analysis in the Kepler environment, which has the advantages of offering graphical, clear display of conceptual steps and parameters and the ability to easily integrate other resources such as remote data and web services.

A curricula-based comparison of biomedical and health informatics programs in the USA

PubMed Central

Hemminger, Bradley M

2011-01-01

Objective The field of Biomedical and Health Informatics (BMHI) continues to define itself, and there are many educational programs offering ‘informatics’ degrees with varied foci. The goal of this study was to develop a scheme for systematic comparison of programs across the entire BMHI spectrum and to identify commonalities among informatics curricula. Design Guided by several published competency sets, a grounded theory approach was used to develop a program/curricula categorization scheme based on the descriptions of 636 courses offered by 73 public health, nursing, health, medical, and bioinformatics programs in the USA. The scheme was then used to compare the programs in the aforementioned five informatics disciplines. Results The authors developed a Course-Based Informatics Program Categorization (CBIPC) scheme that can be used both to classify coursework for any BMHI educational program and to compare programs from the same or related disciplines. The application of CBIPC scheme to the analysis of public health, nursing, health, medical, and bioinformatics programs reveals distinct intradisciplinary curricular patterns and a common core of courses across the entire BMHI education domain. Limitations The study is based on descriptions of courses from the university's webpages. Thus, it is limited to sampling courses at one moment in time, and classification for the coding scheme is based primarily on course titles and course descriptions. Conclusion The CBIPC scheme combines empirical data about educational curricula from diverse informatics programs and several published competency sets. It also provides a foundation for discussion of BMHI education as a whole and can help define subdisciplinary competencies. PMID:21292707

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

PubMed

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 needed to stimulate development of adapted programs for the discipline. Future research should also assess how residents' teaching-skills training can affect their learners' clinical training and eventually patient care.

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

PubMed

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

2017-12-01

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 development in sports programs serving socially vulnerable youth and, insofar as it was investigated in the included studies, of the conditions conducive to life skill development in these sports programs. Potentially relevant studies published during 1990 to 2014 were identified by a search in 7 electronic databases. The search combined terms relating to (a) sport, (b) youth AND socially vulnerable, and (c) life skills. Eighteen of the 2,076 unique studies met the inclusion criteria. Each included study reported that at least 1 life skill improved in youth who participated in the studied sports program. Improvements in cognitive and social life skills were more frequently reported than were improvements in emotional life skills. Only a few of the included studies investigated the conditions in the studied sports programs that made these programs conducive to life skill development. Sports programs have the potential to make a difference in the life skill development of socially vulnerable youth. This conclusion needs to be treated with some caution, because the studies experienced many challenges in reducing the risk for bias. Several alternative research strategies are suggested for future studies in this field.

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

PubMed

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 the currently known bacterial and fungal world, showed that BioMaS outperforms QIIME and MOTHUR in terms of extent and accuracy of deep taxonomic sequence assignments.

Analysis of the study skills of undergraduate pharmacy students of the University of Zambia School of Medicine.

PubMed

Ezeala, Christian Chinyere; Siyanga, Nalucha

2015-01-01

It aimed to compare the study skills of two groups of undergraduate pharmacy students in the School of Medicine, University of Zambia using the Study Skills Assessment Questionnaire (SSAQ), with the goal of analysing students' study skills and identifying factors that affect study skills. A questionnaire was distributed to 67 participants from both programs using stratified random sampling. Completed questionnaires were rated according to participants study skill. The total scores and scores within subscales were analysed and compared quantitatively. Questionnaires were distributed to 37 students in the regular program, and to 30 students in the parallel program. The response rate was 100%. Students had moderate to good study skills: 22 respondents (32.8%) showed good study skills, while 45 respondents (67.2%) were found to have moderate study skills. Students in the parallel program demonstrated significantly better study skills (mean SSAQ score, 185.4±14.5), particularly in time management and writing, than the students in the regular program (mean SSAQ score 175±25.4; P<0.05). No significant differences were found according to age, gender, residential or marital status, or level of study. The students in the parallel program had better time management and writing skills, probably due to their prior work experience. The more intensive training to students in regular program is needed in improving time management and writing skills.

Program Bytes - Satellite Meetings, SIGs, and AKEs at ISMB 2016

PubMed Central

Fogg, Christiana

2016-01-01

The International Society for Computational Biology (ISCB) is gearing up for its flagship meeting, ISMB.  The conference is the world’s largest gathering of computational biology and bioinformatics researchers. The ISMB 2016 pre-conference program will feature 17 special interest group and satellite meetings over the course of two days. This article previews those special meetings at ISCB’s flagship meeting, ISMB. PMID:27347388

A Systematic Review of Life Skill Development through Sports Programs Serving Socially Vulnerable Youth

ERIC Educational Resources Information Center

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

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 life skill development in sports programs serving…

The Impact of a Sport-Based Life Skill Program on Adolescent Prosocial Values

ERIC Educational Resources Information Center

Brunelle, John; Danish, Steven J.; Forneris, Tanya

2007-01-01

This article describes the implementation and evaluation of a sport-based life skills and community service program. The purpose of this investigation was to determine the impact of a combined life skills and community service program on adolescents' prosocial values. The program was part of a national golf and life skills enrichment academy for…

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

ERIC Educational Resources Information Center

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…

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

PubMed

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.

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

PubMed Central

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

Teaching-skills training programs for family medicine residents

PubMed Central

Lacasse, Miriam; Ratnapalan, Savithiri

2009-01-01

ABSTRACT OBJECTIVE 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. DATA SOURCES 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. STUDY SELECTION 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. SYNTHESIS 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. CONCLUSION 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 needed to stimulate development of adapted programs for the discipline. Future research should also assess how residents’ teaching-skills training can affect their learners’ clinical training and eventually patient care. PMID:19752261

m6aViewer: software for the detection, analysis, and visualization of N6-methyladenosine peaks from m6A-seq/ME-RIP sequencing data.

PubMed

Antanaviciute, Agne; Baquero-Perez, Belinda; Watson, Christopher M; Harrison, Sally M; Lascelles, Carolina; Crinnion, Laura; Markham, Alexander F; Bonthron, David T; Whitehouse, Adrian; Carr, Ian M

2017-10-01

Recent methods for transcriptome-wide N 6 -methyladenosine (m 6 A) profiling have facilitated investigations into the RNA methylome and established m 6 A as a dynamic modification that has critical regulatory roles in gene expression and may play a role in human disease. However, bioinformatics resources available for the analysis of m 6 A sequencing data are still limited. Here, we describe m6aViewer-a cross-platform application for analysis and visualization of m 6 A peaks from sequencing data. m6aViewer implements a novel m 6 A peak-calling algorithm that identifies high-confidence methylated residues with more precision than previously described approaches. The application enables data analysis through a graphical user interface, and thus, in contrast to other currently available tools, does not require the user to be skilled in computer programming. m6aViewer and test data can be downloaded here: http://dna2.leeds.ac.uk/m6a. © 2017 Antanaviciute et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

A De Novo-Assembly Based Data Analysis Pipeline for Plant Obligate Parasite Metatranscriptomic Studies.

PubMed

Guo, Li; Allen, Kelly S; Deiulio, Greg; Zhang, Yong; Madeiras, Angela M; Wick, Robert L; Ma, Li-Jun

2016-01-01

Current and emerging plant diseases caused by obligate parasitic microbes such as rusts, downy mildews, and powdery mildews threaten worldwide crop production and food safety. These obligate parasites are typically unculturable in the laboratory, posing technical challenges to characterize them at the genetic and genomic level. Here we have developed a data analysis pipeline integrating several bioinformatic software programs. This pipeline facilitates rapid gene discovery and expression analysis of a plant host and its obligate parasite simultaneously by next generation sequencing of mixed host and pathogen RNA (i.e., metatranscriptomics). We applied this pipeline to metatranscriptomic sequencing data of sweet basil (Ocimum basilicum) and its obligate downy mildew parasite Peronospora belbahrii, both lacking a sequenced genome. Even with a single data point, we were able to identify both candidate host defense genes and pathogen virulence genes that are highly expressed during infection. This demonstrates the power of this pipeline for identifying genes important in host-pathogen interactions without prior genomic information for either the plant host or the obligate biotrophic pathogen. The simplicity of this pipeline makes it accessible to researchers with limited computational skills and applicable to metatranscriptomic data analysis in a wide range of plant-obligate-parasite systems.

Bioinformatics: indispensable, yet hidden in plain sight?

PubMed

Bartlett, Andrew; Penders, Bart; Lewis, Jamie

2017-06-21

Bioinformatics has multitudinous identities, organisational alignments and disciplinary links. This variety allows bioinformaticians and bioinformatic work to contribute to much (if not most) of life science research in profound ways. The multitude of bioinformatic work also translates into a multitude of credit-distribution arrangements, apparently dismissing that work. We report on the epistemic and social arrangements that characterise the relationship between bioinformatics and life science. We describe, in sociological terms, the character, power and future of bioinformatic work. The character of bioinformatic work is such that its cultural, institutional and technical structures allow for it to be black-boxed easily. The result is that bioinformatic expertise and contributions travel easily and quickly, yet remain largely uncredited. The power of bioinformatic work is shaped by its dependency on life science work, which combined with the black-boxed character of bioinformatic expertise further contributes to situating bioinformatics on the periphery of the life sciences. Finally, the imagined futures of bioinformatic work suggest that bioinformatics will become ever more indispensable without necessarily becoming more visible, forcing bioinformaticians into difficult professional and career choices. Bioinformatic expertise and labour is epistemically central but often institutionally peripheral. In part, this is a result of the ways in which the character, power distribution and potential futures of bioinformatics are constituted. However, alternative paths can be imagined.

Skills for Adolescence. What Works Clearinghouse Intervention Report

ERIC Educational Resources Information Center

What Works Clearinghouse, 2006

2006-01-01

Lions Quest "Skills for Adolescence" is a schoolwide program designed for middle school students (grades 6-8). The program was designed to promote good citizenship skills, core character values, and social-emotional skills and discourage the use of drugs, alcohol, and violence. The program includes a classroom curriculum, schoolwide…

GeneLab for High Schools: Data Mining for the Next Generation

NASA Technical Reports Server (NTRS)

Blaber, Elizabeth A.; Ly, Diana; Sato, Kevin Y.; Taylor, Elizabeth

2016-01-01

Modern biological sciences have become increasingly based on molecular biology and high-throughput molecular techniques, such as genomics, transcriptomics, and proteomics. NASA Scientists and the NASA Space Biology Program have aimed to examine the fundamental building blocks of life (RNA, DNA and protein) in order to understand the response of living organisms to space and aid in fundamental research discoveries on Earth. In an effort to enable NASA funded science to be available to everyone, NASA has collected the data from omics studies and curated them in a data system called GeneLab. Whilst most college-level interns, academics and other scientists have had some interaction with omics data sets and analysis tools, high school students often have not. Therefore, the Space Biology Program is implementing a new Summer Program for high-school students that aims to inspire the next generation of scientists to learn about and get involved in space research using GeneLabs Data System. The program consists of three main components core learning modules, focused on developing students knowledge on the Space Biology Program and Space Biology research, Genelab and the data system, and previous research conducted on model organisms in space; networking and team work, enabling students to interact with guest lecturers from local universities and their fellow peers, and also enabling them to visit local universities and genomics centers around the Bay area; and finally an independent learning project, whereby students will be required to form small groups, analyze a dataset on the Genelab platform, generate a hypothesis and develop a research plan to test their hypothesis. This program will not only help inspire high-school students to become involved in space-based research but will also help them develop key critical thinking and bioinformatics skills required for most college degrees and furthermore, will enable them to establish networks with their peers and connections with university Professors that may help them achieve their educational goals.

G2S: a web-service for annotating genomic variants on 3D protein structures.

PubMed

Wang, Juexin; Sheridan, Robert; Sumer, S Onur; Schultz, Nikolaus; Xu, Dong; Gao, Jianjiong

2018-06-01

Accurately mapping and annotating genomic locations on 3D protein structures is a key step in structure-based analysis of genomic variants detected by recent large-scale sequencing efforts. There are several mapping resources currently available, but none of them provides a web API (Application Programming Interface) that supports programmatic access. We present G2S, a real-time web API that provides automated mapping of genomic variants on 3D protein structures. G2S can align genomic locations of variants, protein locations, or protein sequences to protein structures and retrieve the mapped residues from structures. G2S API uses REST-inspired design and it can be used by various clients such as web browsers, command terminals, programming languages and other bioinformatics tools for bringing 3D structures into genomic variant analysis. The webserver and source codes are freely available at https://g2s.genomenexus.org. g2s@genomenexus.org. Supplementary data are available at Bioinformatics online.

Predicting treatment success in social skills training for adolescents with autism spectrum disorders: the UCLA Program for the Education and Enrichment of Relational Skills.

PubMed

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

2014-05-01

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 results revealed that adolescents with higher parent-reported baseline social skills and lower self-reported perceived social functioning demonstrated greater improvement in social skills following the intervention.

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

PubMed

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.

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

ERIC Educational Resources Information Center

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…

Effects of the Higher Order Thinking Skills Program on At-Risk Young Adolescents' Self-Concept, Reading Achievement, and Thinking Skills.

ERIC Educational Resources Information Center

Eisenman, Gordon; Payne, Beverly D.

1997-01-01

Contrasted effects of Higher Order Thinking Skills (HOTS) program to those of Chapter 1 programs on fourth and fifth graders' reading achievement, self-concept, and higher-order thinking skills. Found that HOTS is more effective in raising self-concept and some higher-order thinking skills in fifth grade and after two years of treatment, with…

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

PubMed Central

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

2016-01-01

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. PMID:26918064

Canary: an atomic pipeline for clinical amplicon assays.

PubMed

Doig, Kenneth D; Ellul, Jason; Fellowes, Andrew; Thompson, Ella R; Ryland, Georgina; Blombery, Piers; Papenfuss, Anthony T; Fox, Stephen B

2017-12-15

High throughput sequencing requires bioinformatics pipelines to process large volumes of data into meaningful variants that can be translated into a clinical report. These pipelines often suffer from a number of shortcomings: they lack robustness and have many components written in multiple languages, each with a variety of resource requirements. Pipeline components must be linked together with a workflow system to achieve the processing of FASTQ files through to a VCF file of variants. Crafting these pipelines requires considerable bioinformatics and IT skills beyond the reach of many clinical laboratories. Here we present Canary, a single program that can be run on a laptop, which takes FASTQ files from amplicon assays through to an annotated VCF file ready for clinical analysis. Canary can be installed and run with a single command using Docker containerization or run as a single JAR file on a wide range of platforms. Although it is a single utility, Canary performs all the functions present in more complex and unwieldy pipelines. All variants identified by Canary are 3' shifted and represented in their most parsimonious form to provide a consistent nomenclature, irrespective of sequencing variation. Further, proximate in-phase variants are represented as a single HGVS 'delins' variant. This allows for correct nomenclature and consequences to be ascribed to complex multi-nucleotide polymorphisms (MNPs), which are otherwise difficult to represent and interpret. Variants can also be annotated with hundreds of attributes sourced from MyVariant.info to give up to date details on pathogenicity, population statistics and in-silico predictors. Canary has been used at the Peter MacCallum Cancer Centre in Melbourne for the last 2 years for the processing of clinical sequencing data. By encapsulating clinical features in a single, easily installed executable, Canary makes sequencing more accessible to all pathology laboratories. Canary is available for download as source or a Docker image at https://github.com/PapenfussLab/Canary under a GPL-3.0 License.

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

ERIC Educational Resources Information Center

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…

The growing need for microservices in bioinformatics.

PubMed

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 implementation of reliable and innovative software, made possible in a highly collaborative setting.

The growing need for microservices in bioinformatics

PubMed Central

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 methodology for the fabrication and implementation of reliable and innovative software, made possible in a highly collaborative setting. PMID:27994937

New graduate nurses, new graduate nurse transition programs, and clinical leadership skill: a systematic review.

PubMed

Chappell, Kathy B; Richards, Kathy C

2015-01-01

This systematic review evaluated the relationship between new graduate nurses and clinical leadership skill, and between new graduate nurse transition programs and clinical leadership skill. New graduate nurse transition programs have been cited as one strategy to improve clinical leadership skill, but to our knowledge, no one has synthesized the evidence on new graduate nurse transition programs and clinical leadership skill. Results of this review showed that new graduate nurse transition programs that were at least 24 weeks in length had a positive impact on clinical leadership skill. New graduate nurse transition programs using the University HealthSystem Consortium/American Association of Colleges of Nursing Nurse Residency curriculum had the greatest impact, followed by curriculum developed by the Versant New Graduate RN Residency, an important finding for nursing professional development specialists.

Translation of etiology into evidence-based prevention: the life skills program IPSY.

PubMed

Weichold, Karina

2014-01-01

IPSY (Information + Psychosocial Competence = Protection) is a universal life skills program aiming at the promotion of generic intra- and interpersonal life skills, substance specific skills (for example, resistance skills), school bonding, knowledge, and the prevention of substance misuse with a focus on alcohol and tobacco in youth. This program is based on the WHO's life skills approach as well as on theories and empirical findings concerning the development of substance misuse during early adolescence. IPSY is implemented by teachers over three years of schooling (grades 5-7 in Germany). Guided by models of translational research dealing with conditions of a successful translation of etiological findings into evidence-based prevention programs, the chapter highlights the results of a more than ten-year research program focusing on the development and evaluation of the IPSY program. Findings on long-term general effects, mediators and moderators of program effectiveness, and cross-cultural transferability of the program to other European countries are summarized and discussed in light of dissemination issues. © WILEY PERIODICALS, INC.

Progress Report for Student Research: Fire Safety Skills for Mentally Retarded Children.

ERIC Educational Resources Information Center

Hayden, Mary F.; Lefcowitz, M. Jack

A comprehensive fire safety skills program was evaluated with 32 moderately to mildly retarded adolescents. The program used a fire safety program manual and lessons in basic preventive fire skills, fire safety procedures, and fire escape skills. Across-group comparisons indicated differences in performance between males and females. Fire safety…

Feasibility and effectiveness of a brief, intensive phylogenetics workshop in a middle-income country.

PubMed

Pollett, S; Leguia, M; Nelson, M I; Maljkovic Berry, I; Rutherford, G; Bausch, D G; Kasper, M; Jarman, R; Melendrez, M

2016-01-01

There is an increasing role for bioinformatic and phylogenetic analysis in tropical medicine research. However, scientists working in low- and middle-income regions may lack access to training opportunities in these methods. To help address this gap, a 5-day intensive bioinformatics workshop was offered in Lima, Peru. The syllabus is presented here for others who want to develop similar programs. To assess knowledge gained, a 20-point knowledge questionnaire was administered to participants (21 participants) before and after the workshop, covering topics on sequence quality control, alignment/formatting, database retrieval, models of evolution, sequence statistics, tree building, and results interpretation. Evolution/tree-building methods represented the lowest scoring domain at baseline and after the workshop. There was a considerable median gain in total knowledge scores (increase of 30%, p<0.001) with gains as high as 55%. A 5-day workshop model was effective in improving the pathogen-applied bioinformatics knowledge of scientists working in a middle-income country setting. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Using the QCM Biosensor-Based T7 Phage Display Combined with Bioinformatics Analysis for Target Identification of Bioactive Small Molecule.

PubMed

Takakusagi, Yoichi; Takakusagi, Kaori; Sugawara, Fumio; Sakaguchi, Kengo

2018-01-01

Identification of target proteins that directly bind to bioactive small molecule is of great interest in terms of clarifying the mode of action of the small molecule as well as elucidating the biological phenomena at the molecular level. Of the experimental technologies available, T7 phage display allows comprehensive screening of small molecule-recognizing amino acid sequence from the peptide libraries displayed on the T7 phage capsid. Here, we describe the T7 phage display strategy that is combined with quartz-crystal microbalance (QCM) biosensor for affinity selection platform and bioinformatics analysis for small molecule-recognizing short peptides. This method dramatically enhances efficacy and throughput of the screening for small molecule-recognizing amino acid sequences without repeated rounds of selection. Subsequent execution of bioinformatics programs allows combinatorial and comprehensive target protein discovery of small molecules with its binding site, regardless of protein sample insolubility, instability, or inaccessibility of the fixed small molecules to internally located binding site on larger target proteins when conventional proteomics approaches are used.

Illinois Occupational Skill Standards: Machining Skills Cluster.

ERIC Educational Resources Information Center

Illinois Occupational Skill Standards and Credentialing Council, Carbondale.

This document of skill standards for the machining skills cluster serves as a guide to workforce preparation program providers in defining content for their programs and to employers to establish the skills and standards necessary for job acquisition. These 67 occupational skill standards describe what people should know and be able to do in an…

Program Evaluation Interest and Skills of School Counselors

ERIC Educational Resources Information Center

Astramovich, Randall L.

2017-01-01

School counselors participated in a study examining their program evaluation interest and skills. Findings suggest that school counselors understand the importance of program evaluation, yet they may lack the skills and confidence to successfully engage in program evaluation activities. Professional development training may be an important method…

"On the job" learning: A bioinformatics course incorporating undergraduates in actual research projects and manuscript submissions.

PubMed

Smith, Jason T; Harris, Justine C; Lopez, Oscar J; Valverde, Laura; Borchert, Glen M

2015-01-01

The sequencing of whole genomes and the analysis of genetic information continues to fundamentally change biological and medical research. Unfortunately, the people best suited to interpret this data (biologically trained researchers) are commonly discouraged by their own perceived computational limitations. To address this, we developed a course to help alleviate this constraint. Remarkably, in addition to equipping our undergraduates with an informatic toolset, we found our course design helped prepare our students for collaborative research careers in unexpected ways. Instead of simply offering a traditional lecture- or laboratory-based course, we chose a guided inquiry method, where an instructor-selected research question is examined by students in a collaborative analysis with students contributing to experimental design, data collection, and manuscript reporting. While students learn the skills needed to conduct bioinformatic research throughout all sections of the course, importantly, students also gain experience in working as a team and develop important communication skills through working with their partner and the class as a whole, and by contributing to an original research article. Remarkably, in its first three semesters, this novel computational genetics course has generated 45 undergraduate authorships across three peer-reviewed articles. More importantly, the students that took this course acquired a positive research experience, newfound informatics technical proficiency, unprecedented familiarity with manuscript preparation, and an earned sense of achievement. Although this course deals with analyses of genetic systems, we suggest the basic concept of integrating actual research projects into a 16-week undergraduate course could be applied to numerous other research-active academic fields. © 2015 The International Union of Biochemistry and Molecular Biology.

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

PubMed

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 standardizing the assessment of surgical skills.

Appreciative Inquiry and Video Self Modeling Leadership Program: Achieving Skill or Behavior Change

ERIC Educational Resources Information Center

Bilodeau, Bethany Jewell

2013-01-01

A leadership program was created for students to gain skills and/or change their behavior using Appreciative Inquiry and Video Self Modeling, VSM. In 2011a youth that experiences a disability had been unable to achieve a skill utilizing traditional methods of skill acquisition. He employed the Appreciative Inquiry and VSM leadership program and…

Trained, Generalized, and Collateral Behavior Changes of Preschool Children Receiving Gross-Motor Skills Training.

ERIC Educational Resources Information Center

Kirby, Kimberly C.; Holborn, Stephen W.

1986-01-01

Three preschool children participated in a behavioral training program to improve their gross-motor skills. Results indicated that the program improved the 10 targeted gross-motor skills and that improvements sometimes generalized to other settings. The program did not produce changes in fine-motor skills or social behaviors. Implications are…

Generalization of Social Skills: Strategies and Results of a Training Program in Problem Solving Skills.

ERIC Educational Resources Information Center

Paraschiv, Irina; Olley, J. Gregory

This paper describes the "Problem Solving for Life" training program which trains adolescents and adults with mental retardation in skills for solving social problems. The program requires group participants to solve social problems by practicing two prerequisite skills (relaxation and positive self-statements) and four problem solving steps: (1)…

Profiles of Learning. The Basic Skills Testing Program in New South Wales: 1989.

ERIC Educational Resources Information Center

Masters, Geofferey; And Others

This publication on the New South Wales' Basic Skills Testing Program (BSTP) describes the development of the program's tests, the analysis of students' results, and the communication of results to parents, teachers, and schools. In BSTP tests, basic skills are defined not as low-level, rudimentary survival skills, but as major areas of learning…

22 CFR 63.3 - Grants to foreign participants to observe, consult, demonstrate special skills, or engage in...

Code of Federal Regulations, 2011 CFR

2011-04-01

..., consult, demonstrate special skills, or engage in specialized programs. 63.3 Section 63.3 Foreign... observe, consult, demonstrate special skills, or engage in specialized programs. A citizen or national of... special skills, or engage in specialized programs, may be entitled to any or all of the following benefits...

22 CFR 63.3 - Grants to foreign participants to observe, consult, demonstrate special skills, or engage in...

Code of Federal Regulations, 2010 CFR

2010-04-01

..., consult, demonstrate special skills, or engage in specialized programs. 63.3 Section 63.3 Foreign... observe, consult, demonstrate special skills, or engage in specialized programs. A citizen or national of... special skills, or engage in specialized programs, may be entitled to any or all of the following benefits...

Towards a career in bioinformatics

PubMed Central

2009-01-01

The 2009 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation from 1998, was organized as the 8th International Conference on Bioinformatics (InCoB), Sept. 9-11, 2009 at Biopolis, Singapore. InCoB has actively engaged researchers from the area of life sciences, systems biology and clinicians, to facilitate greater synergy between these groups. To encourage bioinformatics students and new researchers, tutorials and student symposium, the Singapore Symposium on Computational Biology (SYMBIO) were organized, along with the Workshop on Education in Bioinformatics and Computational Biology (WEBCB) and the Clinical Bioinformatics (CBAS) Symposium. However, to many students and young researchers, pursuing a career in a multi-disciplinary area such as bioinformatics poses a Himalayan challenge. A collection to tips is presented here to provide signposts on the road to a career in bioinformatics. An overview of the application of bioinformatics to traditional and emerging areas, published in this supplement, is also presented to provide possible future avenues of bioinformatics investigation. A case study on the application of e-learning tools in undergraduate bioinformatics curriculum provides information on how to go impart targeted education, to sustain bioinformatics in the Asia-Pacific region. The next InCoB is scheduled to be held in Tokyo, Japan, Sept. 26-28, 2010. PMID:19958508

Towards a career in bioinformatics.

PubMed

Ranganathan, Shoba

2009-12-03

The 2009 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation from 1998, was organized as the 8th International Conference on Bioinformatics (InCoB), Sept. 9-11, 2009 at Biopolis, Singapore. InCoB has actively engaged researchers from the area of life sciences, systems biology and clinicians, to facilitate greater synergy between these groups. To encourage bioinformatics students and new researchers, tutorials and student symposium, the Singapore Symposium on Computational Biology (SYMBIO) were organized, along with the Workshop on Education in Bioinformatics and Computational Biology (WEBCB) and the Clinical Bioinformatics (CBAS) Symposium. However, to many students and young researchers, pursuing a career in a multi-disciplinary area such as bioinformatics poses a Himalayan challenge. A collection to tips is presented here to provide signposts on the road to a career in bioinformatics. An overview of the application of bioinformatics to traditional and emerging areas, published in this supplement, is also presented to provide possible future avenues of bioinformatics investigation. A case study on the application of e-learning tools in undergraduate bioinformatics curriculum provides information on how to go impart targeted education, to sustain bioinformatics in the Asia-Pacific region. The next InCoB is scheduled to be held in Tokyo, Japan, Sept. 26-28, 2010.

Importance of databases of nucleic acids for bioinformatic analysis focused to genomics

NASA Astrophysics Data System (ADS)

Jimenez-Gutierrez, L. R.; Barrios-Hernández, C. J.; Pedraza-Ferreira, G. R.; Vera-Cala, L.; Martinez-Perez, F.

2016-08-01

Recently, bioinformatics has become a new field of science, indispensable in the analysis of millions of nucleic acids sequences, which are currently deposited in international databases (public or private); these databases contain information of genes, RNA, ORF, proteins, intergenic regions, including entire genomes from some species. The analysis of this information requires computer programs; which were renewed in the use of new mathematical methods, and the introduction of the use of artificial intelligence. In addition to the constant creation of supercomputing units trained to withstand the heavy workload of sequence analysis. However, it is still necessary the innovation on platforms that allow genomic analyses, faster and more effectively, with a technological understanding of all biological processes.

Analogy Mapping Development for Learning Programming

NASA Astrophysics Data System (ADS)

Sukamto, R. A.; Prabawa, H. W.; Kurniawati, S.

2017-02-01

Programming skill is an important skill for computer science students, whereas nowadays, there many computer science students are lack of skills and information technology knowledges in Indonesia. This is contrary with the implementation of the ASEAN Economic Community (AEC) since the end of 2015 which is the qualified worker needed. This study provided an effort for nailing programming skills by mapping program code to visual analogies as learning media. The developed media was based on state machine and compiler principle and was implemented in C programming language. The state of every basic condition in programming were successful determined as analogy visualization.

A structural equation model on the attributes of a skills enhancement program affecting clinical competence of pre-graduate nursing students.

PubMed

Rebueno, Ma Carina D R; Tiongco, Dyan Dee D; Macindo, John Rey B

2017-02-01

Clinical competence remains an issue in nursing and has received greater emphasis than academic competence. Although skill enhancement programs are recommended and beneficial, there is limited evidence on its influence on the clinical competence of pre-graduate nursing students. This study explored the attributes of a skills enhancement program that affect the perceived clinical competence of pre-graduate nursing students. A cross-sectional study was conducted in a private higher education institution in the Philippines from April to May 2016. A total of 245 pre-graduate nursing students participated and completed a three-part survey composed of the respondent's robotfoto, the Skills Enhancement Program Questionnaire, and the Clinical Competence Questionnaire. Factor analysis explicated the attributes of the skills enhancement program while structural equation modeling and path analysis analyzed the variables' relationship. Findings showed that a skills enhancement program has 4 attributes: supportive clinical instructor, comprehensive orientation, formative goals and objectives, and conducive learning environment. Although all attributes of the program positively affected clinical competence, a supportive clinical instructor had the strongest influence on all clinical competency dimensions. A skills enhancement program that has a supportive clinical instructor, comprehensive orientation, formative goals and objectives, and conducive learning environment facilitates clinical competency development among pre-graduate nursing students. This knowledge provides momentum for nursing educators to review and refine their skills and the existing design of their skills enhancement program to further develop clinical competency among pre-graduate nursing students. Copyright © 2016 Elsevier Ltd. All rights reserved.

[Development and Testing of a Mastery Learning Program of Nursing Skills for Undergraduate Nursing Students].

PubMed

Park, SoMi; Hur, Hea Kung; Kim, Ki Kyong; Song, Hee Young

2017-08-01

This study was undertaken to develop and test a mastery learning program of nursing skills for undergraduate nursing students. In this methodological study, first, the preliminary draft of a mastery learning program to provide training for nursing skills was developed based on Bloom's framework for mastery learning. Second, to test the developed program, a single-blinded, nonequivalent control group nonsynchronized study was conducted on 50 senior nursing students in a University selected by convenient sampling. Thirteen students were assigned to a control group; 13, 12, and 13 of them were assigned to intravenous therapy, transfusion, and patient transfer groups, respectively. The achievement levels and performance scores of the selected nursing skills were measured before and after the completion of the program in all the groups. Lastly, the final program was confirmed based on the results of the program testing. Intravenous therapy, transfusion, and patient transfer were selected as essential nursing skills for the program based on the priorities rated by clinical instructors and staff nurses. The achievement levels of selected nursing skills were determined by Angoff scores. After participating in the program, the proportion of passers and performance scores of the nursing skills in the experimental groups were significantly higher than those in the control group. The final program was confirmed which included a diagnostic test, enrichment activities for the passers and three repetitions of corrective activities and formative assessments for non-passers. The results suggest that a mastery learning program for undergraduate students can lead to better improvement and performance of essential nursing skills. © 2017 Korean Society of Nursing Science

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

PubMed

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.

The Delaware Department of Correction Life Skills Program. Program Focus.

ERIC Educational Resources Information Center

Finn, Peter

Since 1993, the Delaware Department of Correction has offered a Life Skills Program in its four state prisons. Each year, as many as 300 inmates (of the 5,000 housed inmates) enroll in the program, and nearly 85 percent of them graduate. The 4-month program has three major components: academics, violence reduction, and applied life skills. The…

Sequence analysis reveals genomic factors affecting EST-SSR primer performance and polymorphism

USDA-ARS?s Scientific Manuscript database

Search for simple sequence repeat (SSR) motifs and design of flanking primers in expressed sequence tag (EST) sequences can be easily done at a large scale using bioinformatics programs. However, failed amplification and/or detection, along with lack of polymorphism, is often seen among randomly sel...

Job Skills Education Program. Final Technical Report.

ERIC Educational Resources Information Center

Florida State Univ., Tallahassee. Center for Educational Technology.

This publication provides materials developed by a project designed to transfer a U.S. Army computer-based basic skills curriculum to applications in the vocational skills development of civilian adults. An executive summary of the final report describes the Job Skills Education Program (JSEP), which teaches academic skills that support vocational…

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

PubMed

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.

B-WEST Regional Workforce Training Center. Building Workers Entering Skilled Trades. Program Development Guide.

ERIC Educational Resources Information Center

Portland Community Coll., OR.

This program development guide outlines the procedures for replicating the B-WEST (Building Workers Entering Skilled Trades) program, a two-term professional certificate program designed to prepare women for skilled jobs in the traditionally male-dominated electrical, mechanical, and construction trades. The components and major activities of the…

34 CFR 490.1 - What is the Life Skills for State and Local Prisoners Program?

Code of Federal Regulations, 2011 CFR

2011-07-01

... 34 Education 3 2011-07-01 2011-07-01 false What is the Life Skills for State and Local Prisoners... (Continued) OFFICE OF VOCATIONAL AND ADULT EDUCATION, DEPARTMENT OF EDUCATION LIFE SKILLS FOR STATE AND LOCAL PRISONERS PROGRAM General § 490.1 What is the Life Skills for State and Local Prisoners Program? The...

34 CFR 490.1 - What is the Life Skills for State and Local Prisoners Program?

Code of Federal Regulations, 2010 CFR

2010-07-01

... 34 Education 3 2010-07-01 2010-07-01 false What is the Life Skills for State and Local Prisoners... (Continued) OFFICE OF VOCATIONAL AND ADULT EDUCATION, DEPARTMENT OF EDUCATION LIFE SKILLS FOR STATE AND LOCAL PRISONERS PROGRAM General § 490.1 What is the Life Skills for State and Local Prisoners Program? The...

Duplication, Gaps and Coordination of Publicly Funded Skill Training Programs in 20 Cities. Volume II.

ERIC Educational Resources Information Center

National Planning Association, Washington, DC. Center for Priority Analysis.

A study of duplications in public skill training programs in twenty American cities resulted in a two-volume report. Volume One (ED 068 706) summarized and drew conclusions from the individual city reports contained in Volume Two. "Skill training" is used to mean all programs whose major purpose is the imparting of marketable skills to…

Examining the Effectiveness of Naturalistic Social Skills Training in Developing Social Skills and Theory of Mind in Preschoolers with ASD.

PubMed

Szumski, Grzegorz; Smogorzewska, Joanna; Grygiel, Paweł; Orlando, Ann-Marie

2017-11-20

We compared the effectiveness of two programs for developing social skills, 'Play Time/Social Time' (PT/ST) and 'I Can Problem Solve' (ICPS), in improving the social skills and theory of mind (ToM) of preschoolers with ASD. The experiment took place in a classroom setting. Fifty-two children attended and data were analyzed with latent growth curve models. Comparison with a control group indicated that both programs were effective in developing social skills. The PT/ST program was more effective than ICPS in developing interaction skills; both programs improved children's ability to cope with difficult social situations. The ICPS program was marginally effective in developing ToM when compared with PT/ST and control condition. These results are relevant to children with ASD and their teachers.

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

ERIC Educational Resources Information Center

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…

An Evaluation of the Higher Order Thinking Skills Program with Fourth and Fifth Grade Students.

ERIC Educational Resources Information Center

Eisenman, J. Gordon, Jr.

The Higher Order Thinking Skills Program (HOTS) is a computer-based program for teaching thinking skills developed by Stanley Pogrow at the University of Arizona. It is now used in over 800 U.S. schools. This study investigated the effects of the HOTS program versus the traditional Chapter 1 program on fourth and fifth grade students'…

MICRA: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data.

PubMed

Caboche, Ségolène; Even, Gaël; Loywick, Alexandre; Audebert, Christophe; Hot, David

2017-12-19

The increase in available sequence data has advanced the field of microbiology; however, making sense of these data without bioinformatics skills is still problematic. We describe MICRA, an automatic pipeline, available as a web interface, for microbial identification and characterization through reads analysis. MICRA uses iterative mapping against reference genomes to identify genes and variations. Additional modules allow prediction of antibiotic susceptibility and resistance and comparing the results of several samples. MICRA is fast, producing few false-positive annotations and variant calls compared to current methods, making it a tool of great interest for fully exploiting sequencing data.

Teaching interpersonal skills in family practice: results of a national survey.

PubMed

Kahn, G; Cohen, B; Jason, H

1979-02-01

The increasing recognition of the importance of a well-developed set of interpersonal skills to the competent family physician has resulted in a rapid growth in the formal teaching of interpersonal skills within family practice residencies. Of the 168 programs responding to a national survey of family practice residencies, 88 percent indicated that they have formal programs in interpersonal skills. It is estimated that there are well over 500 family practice faculty members who have special responsibilities in teaching interpersonal skills. While most programs address the component skills of the interpersonal process (eg, demonstrating empathy, information gathering, information giving, and psychological intervention), it is of concern that only about half offer explicit training in patient education (53 percent), specific types of counseling (eg, family counseling, 55 percent), or some of the specific interpersonal skills important in team practice and practice management (eg, supervisory skills). One of the most striking findings was that 88 percent of the reporting programs use videotechnology, with 77 percent of these planning to increase their use. Although most programs evaluate their interpersonal skills training using both indirect and direct assessment methods, only 25 percent attempt to use patient outcome as a measure of teaching effectiveness.

New Directions in the Army's Basic Skills Education Program (BSEP).

ERIC Educational Resources Information Center

Pilgrim, Mark T.

The Army has given to the Training and Doctrine Command the task of developing four Basic Skills Education Program (BSEP) curricula to provide functional, job-related basic skills training. These would be Military Occupational Specialty (MOS) Baseline Skills, English-as-a-Second Language (ESL), Military Life Coping Skills, and Learning Strategies.…

Perceptions of skill development of participants in three national career development programs for women faculty in academic medicine.

PubMed

Helitzer, Deborah L; Newbill, Sharon L; Morahan, Page S; Magrane, Diane; Cardinali, Gina; Wu, Chih-Chieh; Chang, Shine

2014-06-01

The Association of American Medical Colleges (AAMC) and Drexel University College of Medicine have designed and implemented national career development programs (CDPs) to help women faculty acquire and strengthen skills needed for success in academic medicine. The authors hypothesized that skills women acquired in CDPs would vary by career stage and program attended. In 2011, the authors surveyed a national cohort of 2,779 women listed in the AAMC Faculty Roster who also attended one of three CDPs (Early- and Mid-Career Women in Medicine Seminars, and/or Executive Leadership in Academic Medicine) between 1988 and 2010 to examine their characteristics and CDP experiences. Participants indicated from a list of 16 skills whether each skill was newly acquired, improved, or not improved as a result of their program participation. Of 2,537 eligible CDP women, 942 clicked on the link in an invitation e-mail, and 879 (93%) completed the survey. Respondents were representative of women faculty in academic medicine. Participants rated the CDPs highly. Almost all reported gaining and/or improving skills from the CDP. Four skills predominated across all three programs: interpersonal skills, leadership, negotiation, and networking. The skills that attendees endorsed differed by respondents' career stages, more so than by program attended. Women participants perceived varying skills gained or improved from their attendance at the CDPs. Determining ways in which CDPs can support women's advancement in academic medicine requires a deeper understanding of what participants seek from CDPs and how they use program content to advance their careers.

Perceptions of Skill Development of Participants in Three National Career Development Programs For Women Faculty in Academic Medicine

PubMed Central

Helitzer, Deborah L.; Newbill, Sharon L.; Morahan, Page S.; Magrane, Diane; Cardinali, Gina; Wu, Chih-Chieh; Chang, Shine

2014-01-01

Purpose The Association of American Medical Colleges (AAMC) and Drexel University College of Medicine have designed and implemented national career development programs (CDPs) to help women faculty acquire and strengthen skills needed for success in academic medicine. The authors hypothesized that skills women acquired in CDPs would vary by career stage and program attended. Method In 2011, the authors surveyed a national cohort of 2,779 women listed in the AAMC Faculty Roster who also attended one of three CDPs (Early- and Mid-Career Women in Medicine Seminars, and/or Executive Leadership in Academic Medicine) between 1988 and 2010 to examine their characteristics and CDP experiences. Participants indicated from a list of 16 skills whether each skill was newly acquired, improved, or not improved as a result of their program participation. Results Of 2537 eligible CDP women, 942 clicked on the link in an invitation e-mail and 879 (35%) completed the survey. Respondents were representative of women faculty in academic medicine. Participants rated the CDPs highly. Almost all reported gaining and/or improving skills from the CDP. Four skills predominated across all three programs: interpersonal skills, leadership, negotiation, and networking. The skills that attendees endorsed differed by respondents’ career stages, more so than by program attended. Conclusions Women participants perceived varying skills gained or improved from their attendance at the CDPs. Determining ways in which CDPs can support women’s advancement in academic medicine requires a deeper understanding of what participants seek from CDPs and how they use program content to advance their careers. PMID:24871241

Effects of two distinct group motor skill interventions in psychological and motor skills of children with Developmental Coordination Disorder: A pilot study.

PubMed

Caçola, Priscila; Romero, Michael; Ibana, Melvin; Chuang, Jennifer

2016-01-01

Children with Developmental Coordination Disorder (DCD) have an increased risk for mental health difficulties. The present pilot study aimed to determine whether distinct group intervention programs improved several psychological variables (anxiety; adequacy and predilection for physical activity; participation, preferences, and enjoyment for activities) and motor skills from the perspective of a child with DCD as well as parental perceptions of motor skills, rate of function, and strengths and difficulties. Eleven children participated in Program A and thirteen in Program B. Both involved 10 sessions of 1 h each. Program A focused on task-oriented activities in a large group involving motor skill training and collaboration and cooperation among children, while Program B was composed of three groups with a direct goal-oriented approach for training of skills chosen by the children. Results indicated that children improved motor skills after both programs, but showed distinct results in regards to other variables - after Program A, children showed higher anxiety and lower levels of enjoyment, even though parents detected an improvement in rate of function and a decrease in peer problems. With Program B, children decreased anxiety levels, and parents noted a higher control of movement of their children. Regardless of the group approach, children were able to improve motor skills. However, it is possible that the differences between groups may have influenced parents' perception of their children's motor and psychological skills, as well as children's perception of anxiety. Copyright © 2016 Elsevier Inc. All rights reserved.

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

PubMed

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.

A Two-Tier Test-Based Approach to Improving Students' Computer-Programming Skills in a Web-Based Learning Environment

ERIC Educational Resources Information Center

Yang, Tzu-Chi; Hwang, Gwo-Jen; Yang, Stephen J. H.; Hwang, Gwo-Haur

2015-01-01

Computer programming is an important skill for engineering and computer science students. However, teaching and learning programming concepts and skills has been recognized as a great challenge to both teachers and students. Therefore, the development of effective learning strategies and environments for programming courses has become an important…

The use of physical assessment skills by registered nurses in Australia: issues for nursing education.

PubMed

Birks, Melanie; Cant, Robyn; James, Ainsley; Chung, Catherine; Davis, Jenny

2013-01-01

The purpose of pre-service nursing education programs is to prepare competent graduates who are able to function as safe, professional registered nurses. An extensive element of these programs is the teaching of physical assessment skills, with most programs educating students to perform over 120 such skills. Previous research from North America suggests that the majority of skills taught to nurses in their pre-service programs are not used in practice. As part of a larger study, an online survey was used to explore use of 121 physical assessment skills by Australian nurses. Recruitment occurred via mailed invitation to members of the Australian Nursing Federation. Data were extracted from 1220 completed questionnaires returned by nurses who were mostly employed in New South Wales, were female and experienced nurses. Respondents indicated that they used only 34% of skills routinely. Results reinforce evidence found in the literature that many of the skills taught to nurses are either not used at all (35.5%) or are used rarely (31%). These findings have implications for the teaching of physical assessment skills in pre-service nursing programs, and raise questions about the value of extensive skills teaching in the context of contemporary health care. Further research into barriers to the use of physical assessment skills in nursing and the need for comprehensive skills preparation for the generalist nurse is likely to offer some solutions to these questions.

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

PubMed

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.

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

PubMed Central

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

2014-01-01

Abstract Objective 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. Methods 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). Findings 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. Conclusion 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. PMID:25535529

Informal Training in Staff Networks to Support Dissemination of Health Promotion Programs

PubMed Central

Ramanadhan, Shoba; Wiecha, Jean L.; Gortmaker, Steven L.; Emmons, Karen M.; Viswanath, Kasisomayajula

2011-01-01

Purpose To study informal skill transfer via staff networks as a complement to formal training among afterschool childcare providers implementing a health promotion program. Design Cross-sectional, sociometric network analysis. Setting Boston Young Men’s Christian Association (YMCA) afterschool programs implementing the iPLAY program. Participants All 91 staff members at 20 sites were eligible; 80 completed the survey (88% response rate). Measures At the network level, network density measured system-level connectedness. At the staff level, the independent variable was out degree, the number of individuals to whom respondents noted a program-related connection. The dependent variable was skill gains, the number of key implementation skills gained from the network. Analysis We mapped the staff program-related social network. We utilized multiple linear regression to estimate the relationship between out degree and skill gains, and we adjusted for clustering of staff in sites. Results Most staff (77%) reported gaining at least one skill from the network, but only 2% of potential network connections were established. The regression model showed that out degree (i.e., number of program-related contacts) was significantly associated with skill gains (β = .48, p < .01) independent of other variables. Conclusion Informal skill transfer in staff networks may be a useful complement to formal training for implementation of health promotion programs, but informal skill transfer was likely underutilized in this network. Future research employing longitudinal and/or multisite data should examine these findings in greater detail. PMID:20809826

The feasibility of implementing a communication skills training course in pediatric hematology/oncology fellowship.

PubMed

Weintraub, Lauren; Figueiredo, Lisa; Roth, Michael; Levy, Adam

Communication skills are a competency highlighted by the Accreditation Council on Graduate Medical Education; yet, little is known about the frequency with which trainees receive formal training or what programs are willing to invest. We sought to answer this question and designed a program to address identified barriers. We surveyed pediatric fellowship program directors from all disciplines and, separately, pediatric hematology/oncology fellowship program directors to determine current use of formal communication skills training. At our institution, we piloted a standardized patient (SP)-based communication skills training program for pediatric hematology/oncology fellows. Twenty-seven pediatric hematology/oncology program directors and 44 pediatric program directors participated in the survey, of which 56% and 48%, respectively, reported having an established, formal communication skills training course. Multiple barriers to implementation of a communication skills course were identified, most notably time and cost. In the pilot program, 13 pediatric hematology/oncology fellows have participated, and 9 have completed all 3 years of training. Precourse assessment demonstrated fellows had limited comfort in various areas of communication. Following course completion, there was a significant increase in self-reported comfort and/or skill level in such areas of communication, including discussing a new diagnosis (p =.0004), telling a patient they are going to die (p =.005), discussing recurrent disease (p <.001), communicating a poor prognosis (p =.002), or responding to anger (p ≤.001). We have designed a concise communication skills training program, which addresses identified barriers and can feasibly be implemented in pediatric hematology/oncology fellowship.

RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application.

PubMed

D'Antonio, Mattia; D'Onorio De Meo, Paolo; Pallocca, Matteo; Picardi, Ernesto; D'Erchia, Anna Maria; Calogero, Raffaele A; Castrignanò, Tiziana; Pesole, Graziano

2015-01-01

The study of RNA has been dramatically improved by the introduction of Next Generation Sequencing platforms allowing massive and cheap sequencing of selected RNA fractions, also providing information on strand orientation (RNA-Seq). The complexity of transcriptomes and of their regulative pathways make RNA-Seq one of most complex field of NGS applications, addressing several aspects of the expression process (e.g. identification and quantification of expressed genes and transcripts, alternative splicing and polyadenylation, fusion genes and trans-splicing, post-transcriptional events, etc.). In order to provide researchers with an effective and friendly resource for analyzing RNA-Seq data, we present here RAP (RNA-Seq Analysis Pipeline), a cloud computing web application implementing a complete but modular analysis workflow. This pipeline integrates both state-of-the-art bioinformatics tools for RNA-Seq analysis and in-house developed scripts to offer to the user a comprehensive strategy for data analysis. RAP is able to perform quality checks (adopting FastQC and NGS QC Toolkit), identify and quantify expressed genes and transcripts (with Tophat, Cufflinks and HTSeq), detect alternative splicing events (using SpliceTrap) and chimeric transcripts (with ChimeraScan). This pipeline is also able to identify splicing junctions and constitutive or alternative polyadenylation sites (implementing custom analysis modules) and call for statistically significant differences in genes and transcripts expression, splicing pattern and polyadenylation site usage (using Cuffdiff2 and DESeq). Through a user friendly web interface, the RAP workflow can be suitably customized by the user and it is automatically executed on our cloud computing environment. This strategy allows to access to bioinformatics tools and computational resources without specific bioinformatics and IT skills. RAP provides a set of tabular and graphical results that can be helpful to browse, filter and export analyzed data, according to the user needs.

Softball: Special Olympics Sports Skills Instructional Program.

ERIC Educational Resources Information Center

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'…

Competency-Based Employability Skills Program.

ERIC Educational Resources Information Center

North Carolina State Dept. of Public Instruction, Raleigh. Div. of Vocational Education.

This guide is intended for use in incorporating competency-based employability skills curricula into vocational and technical education programs. The guide is divided into five sections. The first is a competency listing that includes the competencies identified as necessary for students participating in an employability skills program and a…

Designing and implementing a skills program Using a clinically integrated, multi-professional approach: Using evaluation to drive curriculum change

PubMed Central

Carr, Sandra E.; Celenza, Antonio; Lake, Fiona

2009-01-01

The essential procedural skills that newly graduated doctors require are rarely defined, do not take into account pre-vocational employer expectations, and differ between Universities. This paper describes how one Faculty used local evaluation data to drive curriculum change and implement a clinically integrated, multi-professional skills program. A curriculum restructure included a review of all undergraduate procedural skills training by academic staff and clinical departments, resulting in a curriculum skills map. Undergraduate training was then linked with postgraduate expectations using the Delphi process to identify the skills requiring structured standardised training. The skills program was designed and implemented without a dedicated simulation center. This paper shows the benefits of an alternate model in which clinical integration of training and multi-professional collaboration encouraged broad ownership of a program and, in turn, impacted the clinical experience obtained. PMID:20165528

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

ERIC Educational Resources Information Center

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…

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

PubMed

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.

Simulation of Two Dimensional Electrophoresis and Tandem Mass Spectrometry for Teaching Proteomics

ERIC Educational Resources Information Center

Fisher, Amanda; Sekera, Emily; Payne, Jill; Craig, Paul

2012-01-01

In proteomics, complex mixtures of proteins are separated (usually by chromatography or electrophoresis) and identified by mass spectrometry. We have created 2DE Tandem MS, a computer program designed for use in the biochemistry, proteomics, or bioinformatics classroom. It contains two simulations--2D electrophoresis and tandem mass spectrometry.…

A Course-Based Research Experience: How Benefits Change with Increased Investment in Instructional Time

ERIC Educational Resources Information Center

Shaffer, Christopher D.; Alvarez, Consuelo J.; Bednarski, April E.; Dunbar, David; Goodman, Anya L.; Reinke, Catherine; Rosenwald, Anne G.; Wolyniak, Michael J.; Bailey, Cheryl; Barnard, Daron; Bazinet, Christopher; Beach, Dale L.; Bedard, James E. J.; Bhalla, Satish; Braverman, John; Burg, Martin; Chandrasekaran, Vidya; Chung, Hui-Min; Clase, Kari; DeJong, Randall J.; DiAngelo, Justin R.; Du, Chunguang; Eckdahl, Todd T.; Eisler, Heather; Emerson, Julia A.; Frary, Amy; Frohlich, Donald; Gosser, Yuying; Govind, Shubha; Haberman, Adam; Hark, Amy T.; Hauser, Charles; Hoogewerf, Arlene; Hoopes, Laura L. M.; Howell, Carina E.; Johnson, Diana; Jones, Christopher J.; Kadlec, Lisa; Kaehler, Marian; Key, S. Catherine Silver; Kleinschmit, Adam; Kokan, Nighat P.; Kopp, Olga; Kuleck, Gary; Leatherman, Judith; Lopilato, Jane; MacKinnon, Christy; Martinez-Cruzado, Juan Carlos; McNeil, Gerard; Mel, Stephanie; Mistry, Hemlata; Nagengast, Alexis; Overvoorde, Paul; Paetkau, Don W.; Parrish, Susan; Peterson, Celeste N.; Preuss, Mary; Reed, Laura K.; Revie, Dennis; Robic, Srebrenka; Roecklein-Canfield, Jennifer; Rubin, Michael R.; Saville, Kenneth; Schroeder, Stephanie; Sharif, Karim; Shaw, Mary; Skuse, Gary; Smith, Christopher D.; Smith, Mary A.; Smith, Sheryl T.; Spana, Eric; Spratt, Mary; Sreenivasan, Aparna; Stamm, Joyce; Szauter, Paul; Thompson, Jeffrey S.; Wawersik, Matthew; Youngblom, James; Zhou, Leming; Mardis, Elaine R.; Buhler, Jeremy; Leung, Wilson; Lopatto, David; Elgin, Sarah C. R.

2014-01-01

There is widespread agreement that science, technology, engineering, and mathematics programs should provide undergraduates with research experience. Practical issues and limited resources, however, make this a challenge. We have developed a bioinformatics project that provides a course-based research experience for students at a diverse group of…

Coordinated effort to advance genomes-to-phenomes through the integration of bioinformatics with aquaculture research

USDA-ARS?s Scientific Manuscript database

Aquaculture is the fastest growing food production system in the world. The research program at the USDA-ARS-SNARC strives to improve the efficiency and sustainability of warmwater U.S. aquaculture. SNARC scientists have impacted the catfish (#1 U.S. aquaculture industry), tilapia (#3) and hybrid st...

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

ERIC Educational Resources Information Center

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

2008-01-01

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

A Teaching Approach from the Exhaustive Search Method to the Needleman-Wunsch Algorithm

ERIC Educational Resources Information Center

Xu, Zhongneng; Yang, Yayun; Huang, Beibei

2017-01-01

The Needleman-Wunsch algorithm has become one of the core algorithms in bioinformatics; however, this programming requires more suitable explanations for students with different major backgrounds. In supposing sample sequences and using a simple store system, the connection between the exhaustive search method and the Needleman-Wunsch algorithm…

SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts.

PubMed

Ryan, Michael C; Cleland, James; Kim, RyangGuk; Wong, Wing Chung; Weinstein, John N

2012-09-15

SpliceSeq is a resource for RNA-Seq data that provides a clear view of alternative splicing and identifies potential functional changes that result from splice variation. It displays intuitive visualizations and prioritized lists of results that highlight splicing events and their biological consequences. SpliceSeq unambiguously aligns reads to gene splice graphs, facilitating accurate analysis of large, complex transcript variants that cannot be adequately represented in other formats. SpliceSeq is freely available at http://bioinformatics.mdanderson.org/main/SpliceSeq:Overview. The application is a Java program that can be launched via a browser or installed locally. Local installation requires MySQL and Bowtie. mryan@insilico.us.com Supplementary data are available at Bioinformatics online.

The iconic memory skills of brain injury survivors and non-brain injured controls after visual scanning training.

PubMed

McClure, J T; Browning, R T; Vantrease, C M; Bittle, S T

1994-01-01

Previous research suggests that traumatic brain injury (TBI) results in impairment of iconic memory abilities.We would like to acknowledge the contribution of Jeffrey D. Vantrease, who wrote the software program for the Iconic Memory procedure and measurement. This raises serious implications for brain injury rehabilitation. Most cognitive rehabilitation programs do not include iconic memory training. Instead it is common for cognitive rehabilitation programs to focus on attention and concentration skills, memory skills, and visual scanning skills.This study compared the iconic memory skills of brain-injury survivors and control subjects who all reached criterion levels of visual scanning skills. This involved previous training for the brain-injury survivors using popular visual scanning programs that allowed them to visually scan with response time and accuracy within normal limits. Control subjects required only minimal training to reach normal limits criteria. This comparison allows for the dissociation of visual scanning skills and iconic memory skills.The results are discussed in terms of their implications for cognitive rehabilitation and the relationship between visual scanning training and iconic memory skills.

Employability Skills + Adult Agency Support + Family Support + On-the-Job Support = Successful Employment.

ERIC Educational Resources Information Center

Patton, Patricia Lucey; And Others

1997-01-01

This article describes a comprehensive transition program for students with mild disabilities. The program revolves around a classroom-based employability skills curriculum taught over a semester's duration. Four program components are addressed: employability skills training, family involvement, adult agency referral, and on-the-job support. (CR)

Soccer: Special Olympics Sports Skills Instructional Program.

ERIC Educational Resources Information Center

Joseph P. Kennedy, Jr. Foundation, Washington, DC.

One of five guides in the Sports Skills Instructional Program of the Special Olympics, the booklet describes an approach to teaching soccer skills to mentally retarded persons. An introductory section lists the goals, objectives, and benefits of the program and provides criterion referenced instruments to assess the individual's current…

Perceptions of Preceptors and Students on the Importance of Writing

ERIC Educational Resources Information Center

Fields, Tina T.; Hatala, Jeff J.; Nauert, Richard F.

2014-01-01

Health administration programs vary from other administrative programs based on emphasis in writing. Prior studies about writing skills in professional degree programs show student writing skills are not at a professional level. There is no literature at present that identifies important and essential writing skills related specifically to…

The Skills 2000 Challenge: High Stakes, High Skills.

ERIC Educational Resources Information Center

Ovel, Steve

1999-01-01

Describes the efforts of Iowa's community colleges to meet the need for highly skilled, well-educated workers who can help the state sustain growth, retain companies, and fend off stagnation. Programs developed include partnerships, the establishment of the Iowa Industrial New Jobs Training Program, and the Accelerated Career Education Program.…

Pulmonary and Critical Care Medicine Program Directors' Attitudes toward Training in Medical Education. A Nationwide Survey Study.

PubMed

Richards, Jeremy B; McCallister, Jennifer W; Lenz, Peter H

2016-04-01

Many pulmonary and critical care medicine (PCCM) fellows are interested in improving their teaching skills as well as learning about careers as clinician educators. Educational opportunities in PCCM fellowship programs designed to address these interests have not been well characterized in U.S. training programs. We aimed to characterize educational content and structure for training fellows to teach in PCCM fellowship programs. We evaluated three major domains: (1) existing educational opportunities, (2) PCCM program directors' attitudes toward the importance of teaching fellows how to teach, and (3) potential components of an optimal teaching skills curriculum for PCCM fellows. We surveyed program and associate program directors who were members of the Association of Pulmonary and Critical Care Medicine Program Directors in 2014. Survey domains included existing teaching skills content and structure, presence of a formal medical education curriculum or clinician educator track, perceived barriers to teaching fellows teaching skills, and open-ended qualitative inquiries about the ideal curricula. Data were analyzed both quantitatively and qualitatively. Of 158 invited Association of Pulmonary and Critical Care Medicine Program Directors members, 85 program directors and associate directors responded (53.8% response rate). Annual curricular time dedicated to teaching skills varied widely (median, 3 h; mean, 5.4 h; interquartile range, 2.0-6.3 h), with 17 respondents (20%) allotting no time to teaching fellows to teach and 14 respondents (17%) dedicating more than 10 hours. Survey participants stated that the optimal duration for training fellows in teaching skills was significantly less than what they reported was actually occurring (median optimal duration, 1.5 h/yr; mean, 2.1 h/yr; interquartile range, 1.5-3.5 h/yr; P < 0.001). Only 28 (33.7%) had a formal curriculum for teaching medical education skills. Qualitative analyses identified several barriers to implementing formal teaching skills curricula, including "time," "financial resources," "competing priorities," and "lack of expert faculty." While prior work has demonstrated that fellows are interested in obtaining medical education skills, PCCM program directors and associate directors noted significant challenges to implementing formal educational opportunities to teach fellows these skills. Effective strategies are needed to design, implement, sustain, and assess teaching skills curricula for PCCM fellowships.

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

PubMed

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

2013-09-01

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

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

ERIC Educational Resources Information Center

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…

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

PubMed

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.

Illinois Occupational Skill Standards: Nursing Cluster.

ERIC Educational Resources Information Center

Illinois Occupational Skill Standards and Credentialing Council, Carbondale.

These skill standards, developed through a consortium of educational and industry partners in Illinois, serve as guides to workforce preparation program providers to define content for their programs and to employers to establish the skills and standards necessary for job acquisition and performance. The skill standards include the following…

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

PubMed

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.

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

PubMed

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.

Evaluation of a Classwide Teaching Program for Developing Preschool Life Skills

PubMed Central

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. PMID:17624068

High-Skill Training: Grants from H-1B Visa Fees Meet Specific Workforce Needs, But at Varying Skill Levels. Report to Congressional Requesters.

ERIC Educational Resources Information Center

General Accounting Office, Washington, DC. Education, Workforce, and Income Security Issues.

A study examined the skill grant and scholarship grant programs. Findings indicated skill grantees offered training through various service delivery options to people needing skill upgrading; scholarship grantees provided scholarships to low income students for college degree programs in computer science, mathematics, and engineering. The skill…

Academic Skills Rovers: A Just in Time Peer Support Initiative for Academic Skills and Literacy Development

ERIC Educational Resources Information Center

Copeman, Peter; Keightley, Polly

2014-01-01

In 2013 the University of Canberra (UC) initiated a program of peer-assisted academic skills help, the Academic Skills Rovers program, with the goal of providing drop-in peer learning support to students at campus locations where they congregate to study. The Academic Skills Rovers were initially recruited from the teacher education discipline,…

Evolution of apoptosis-like programmed cell death in unicellular protozoan parasites.

PubMed

Kaczanowski, Szymon; Sajid, Mohammed; Reece, Sarah E

2011-03-25

Apoptosis-like programmed cell death (PCD) has recently been described in multiple taxa of unicellular protists, including the protozoan parasites Plasmodium, Trypanosoma and Leishmania. Apoptosis-like PCD in protozoan parasites shares a number of morphological features with programmed cell death in multicellular organisms. However, both the evolutionary explanations and mechanisms involved in parasite PCD are poorly understood. Explaining why unicellular organisms appear to undergo 'suicide' is a challenge for evolutionary biology and uncovering death executors and pathways is a challenge for molecular and cell biology. Bioinformatics has the potential to integrate these approaches by revealing homologies in the PCD machinery of diverse taxa and evaluating their evolutionary trajectories. As the molecular mechanisms of apoptosis in model organisms are well characterised, and recent data suggest similar mechanisms operate in protozoan parasites, key questions can now be addressed. These questions include: which elements of apoptosis machinery appear to be shared between protozoan parasites and multicellular taxa and, have these mechanisms arisen through convergent or divergent evolution? We use bioinformatics to address these questions and our analyses suggest that apoptosis mechanisms in protozoan parasites and other taxa have diverged during their evolution, that some apoptosis factors are shared across taxa whilst others have been replaced by proteins with similar biochemical activities.

Evolution of apoptosis-like programmed cell death in unicellular protozoan parasites

PubMed Central

2011-01-01

Apoptosis-like programmed cell death (PCD) has recently been described in multiple taxa of unicellular protists, including the protozoan parasites Plasmodium, Trypanosoma and Leishmania. Apoptosis-like PCD in protozoan parasites shares a number of morphological features with programmed cell death in multicellular organisms. However, both the evolutionary explanations and mechanisms involved in parasite PCD are poorly understood. Explaining why unicellular organisms appear to undergo 'suicide' is a challenge for evolutionary biology and uncovering death executors and pathways is a challenge for molecular and cell biology. Bioinformatics has the potential to integrate these approaches by revealing homologies in the PCD machinery of diverse taxa and evaluating their evolutionary trajectories. As the molecular mechanisms of apoptosis in model organisms are well characterised, and recent data suggest similar mechanisms operate in protozoan parasites, key questions can now be addressed. These questions include: which elements of apoptosis machinery appear to be shared between protozoan parasites and multicellular taxa and, have these mechanisms arisen through convergent or divergent evolution? We use bioinformatics to address these questions and our analyses suggest that apoptosis mechanisms in protozoan parasites and other taxa have diverged during their evolution, that some apoptosis factors are shared across taxa whilst others have been replaced by proteins with similar biochemical activities. PMID:21439063

Interactive software tool to comprehend the calculation of optimal sequence alignments with dynamic programming.

PubMed

Ibarra, Ignacio L; Melo, Francisco

2010-07-01

Dynamic programming (DP) is a general optimization strategy that is successfully used across various disciplines of science. In bioinformatics, it is widely applied in calculating the optimal alignment between pairs of protein or DNA sequences. These alignments form the basis of new, verifiable biological hypothesis. Despite its importance, there are no interactive tools available for training and education on understanding the DP algorithm. Here, we introduce an interactive computer application with a graphical interface, for the purpose of educating students about DP. The program displays the DP scoring matrix and the resulting optimal alignment(s), while allowing the user to modify key parameters such as the values in the similarity matrix, the sequence alignment algorithm version and the gap opening/extension penalties. We hope that this software will be useful to teachers and students of bioinformatics courses, as well as researchers who implement the DP algorithm for diverse applications. The software is freely available at: http:/melolab.org/sat. The software is written in the Java computer language, thus it runs on all major platforms and operating systems including Windows, Mac OS X and LINUX. All inquiries or comments about this software should be directed to Francisco Melo at fmelo@bio.puc.cl.

Visual gene developer: a fully programmable bioinformatics software for synthetic gene optimization.

PubMed

Jung, Sang-Kyu; McDonald, Karen

2011-08-16

Direct gene synthesis is becoming more popular owing to decreases in gene synthesis pricing. Compared with using natural genes, gene synthesis provides a good opportunity to optimize gene sequence for specific applications. In order to facilitate gene optimization, we have developed a stand-alone software called Visual Gene Developer. The software not only provides general functions for gene analysis and optimization along with an interactive user-friendly interface, but also includes unique features such as programming capability, dedicated mRNA secondary structure prediction, artificial neural network modeling, network & multi-threaded computing, and user-accessible programming modules. The software allows a user to analyze and optimize a sequence using main menu functions or specialized module windows. Alternatively, gene optimization can be initiated by designing a gene construct and configuring an optimization strategy. A user can choose several predefined or user-defined algorithms to design a complicated strategy. The software provides expandable functionality as platform software supporting module development using popular script languages such as VBScript and JScript in the software programming environment. Visual Gene Developer is useful for both researchers who want to quickly analyze and optimize genes, and those who are interested in developing and testing new algorithms in bioinformatics. The software is available for free download at http://www.visualgenedeveloper.net.

Visual gene developer: a fully programmable bioinformatics software for synthetic gene optimization

PubMed Central

2011-01-01

Background Direct gene synthesis is becoming more popular owing to decreases in gene synthesis pricing. Compared with using natural genes, gene synthesis provides a good opportunity to optimize gene sequence for specific applications. In order to facilitate gene optimization, we have developed a stand-alone software called Visual Gene Developer. Results The software not only provides general functions for gene analysis and optimization along with an interactive user-friendly interface, but also includes unique features such as programming capability, dedicated mRNA secondary structure prediction, artificial neural network modeling, network & multi-threaded computing, and user-accessible programming modules. The software allows a user to analyze and optimize a sequence using main menu functions or specialized module windows. Alternatively, gene optimization can be initiated by designing a gene construct and configuring an optimization strategy. A user can choose several predefined or user-defined algorithms to design a complicated strategy. The software provides expandable functionality as platform software supporting module development using popular script languages such as VBScript and JScript in the software programming environment. Conclusion Visual Gene Developer is useful for both researchers who want to quickly analyze and optimize genes, and those who are interested in developing and testing new algorithms in bioinformatics. The software is available for free download at http://www.visualgenedeveloper.net. PMID:21846353

Cancer Bioinformatics for Updating Anticancer Drug Developments and Personalized Therapeutics.

PubMed

Lu, Da-Yong; Qu, Rong-Xin; Lu, Ting-Ren; Wu, Hong-Ying

2017-01-01

Last two to three decades, this world witnesses a rapid progress of biomarkers and bioinformatics technologies. Cancer bioinformatics is one of such important omics branches for experimental/clinical studies and applications. Same as other biological techniques or systems, bioinformatics techniques will be widely used. But they are presently not omni-potent. Despite great popularity and improvements, cancer bioinformatics has its own limitations and shortcomings at this stage of technical advancements. This article will offer a panorama of bioinformatics in cancer researches and clinical therapeutic applications-possible advantages and limitations relating to cancer therapeutics. A lot of beneficial capabilities and outcomes have been described. As a result, a successful new era for cancer bioinformatics is waiting for us if we can adhere on scientific studies of cancer bioinformatics in malignant- origin mining, medical verifications and clinical diagnostic applications. Cancer bioinformatics gave a great significance in disease diagnosis and therapeutic predictions. Many creative ideas and future perspectives are highlighted. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Career Skills Enhancement Program (CSEP). A National Workplace Literacy Program, Final Report To Cover Activities April 1, 1990-September 30, 1991.

ERIC Educational Resources Information Center

Gray, Brenda

The Career Skills Enhancement Program (CSEP) was a National Workplace Literacy Program offered to Santa Clara County (California) Office of Education (COE) employees. A job skills study involved personal interviews, job shadowing, and examination of job descriptions and materials used by employees. Based on the study and initial needs assessment,…

Improving oncology nurses' communication skills for difficult conversations.

PubMed

Baer, Linda; Weinstein, Elizabeth

2013-06-01

When oncology nurses have strong communication skills, they play a pivotal role in influencing patient satisfaction, adherence to plans of care, and overall clinical outcomes. However, research studies indicate that nurses tend to keep communication with patients and families at a superficial, nontherapeutic level. Processes for teaching goals-of-care communication skills and for implementing skills into clinical practice are not clearly defined. Nurses at a large comprehensive cancer center recognized the need for help with this skill set and sought out communication experts to assist in providing the needed education. An educational project was developed to improve therapeutic communication skills in oncology nurses during goals-of-care discussions and giving bad news. The program was tailored to nurses and social workers providing care to patients in a busy, urban, academic, outpatient oncology setting. Program topics included exploring the patient's world, eliciting hopes and concerns, and dealing with conflict about goals. Sharing and discussing specific difficult questions and scenarios were encouraged throughout the program. The program was well attended and well received by oncology nurses and social workers. Participants expressed interest in the continuation of communication programs to further enhance skills.

Training basic teaching skills to community and institutional support staff for people with severe disabilities: a one-day program.

PubMed

Parsons, M B; Reid, D H; Green, C W

1996-01-01

Shortcomings in the technology for training support staff in methods of teaching people with severe disabilities recently have resulted in calls to improve the technology. We evaluated a program for training basic teaching skills within one day. The program entailed classroom-based verbal and video instruction, practice, and feedback followed by on-the-job feedback. In Study I, four undergraduate interns participated in the program, and all four met the mastery criterion for teaching skills. Three teacher aides participated in Study 2, with results indicating that when the staff applied their newly acquired teaching skills, students with profound disabilities made progress in skill acquisition. Clinical replications occurred in Study 3, involving 17 staff in school classrooms, group homes, and an institution. Results of Studies 2 and 3 also indicated staff were accepting of the program and improved their verbal skills. Results are discussed regarding advantages of training staff in one day. Future research suggestions are offered, focusing on identifying means of rapidly training other teaching skills in order to develop the most effective, acceptable, and efficient technology for staff training.

Illinois Occupational Skill Standards: Physical Therapist Assistant Cluster.

ERIC Educational Resources Information Center

Illinois Occupational Skill Standards and Credentialing Council, Carbondale.

These skill standards, developed through a consortium of educational and industry partners in Illinois, serve as guides to workforce preparation program providers to define content for their programs and to employers to establish the skills and standards necessary for job acquisition and performance. The skill standards include the following…

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

ERIC Educational Resources Information Center

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…

Illinois Occupational Skill Standards: Medical Office Cluster.

ERIC Educational Resources Information Center

Illinois Occupational Skill Standards and Credentialing Council, Carbondale.

These skill standards, developed through a consortium of educational and industry partners in Illinois, serve as guides to workforce preparation program providers to define content for their programs and to employers to establish the skills and standards necessary for job acquisition and performance. The skill standards include the following…

Illinois Occupational Skill Standards: Press Operations Cluster.

ERIC Educational Resources Information Center

Illinois Occupational Skill Standards and Credentialing Council, Carbondale.

These skill standards, developed through a consortium of educational and industry partners in Illinois, serve as guides to workforce preparation program providers to define content for their programs and to employers to establish the skills and standards necessary for job acquisition and performance. The skill standards include the following…

Hospitality Occupational Skills Training Cooperative. Project HOST Curriculum Guide.

ERIC Educational Resources Information Center

Northwest Educational Cooperative, Des Plaines, IL.

This curriculum guide provides instructional materials for an 8-week training program, entitled Hospitality Occupational Skills Training (HOST) Cooperative. It offers an alternative skills training program to meet the needs of disadvantaged, minority populations and of employers who must recruit more highly skilled workers from those populations.…

The Impact of Diagnosing Skill Deficiencies and Assessment-Based Communication Training on Managerial Performance.

ERIC Educational Resources Information Center

Papa, Michael J.; Graham, Elizabeth E.

1991-01-01

Evaluates an organizational diagnosis program that assesses managerial communication skills and provides the frame for follow-up training programs. Finds that managers participating in follow-up communication skills training performed significantly higher on interpersonal skills, problem-solving ability, and productivity over three long-term…

75 FR 55801 - Medicare Program; Prospective Payment System and Consolidated Billing for Skilled Nursing...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-14

... 0938-AP87 Medicare Program; Prospective Payment System and Consolidated Billing for Skilled Nursing... Payment System and Consolidated Billing for Skilled Nursing Facilities for FY 2011.'' DATES: Effective... illustrate the skilled nursing facility (SNF) prospective payment system (PPS) payment rate computations for...

Illinois Occupational Skill Standards: Retail Garden Center Cluster.

ERIC Educational Resources Information Center

Illinois Occupational Skill Standards and Credentialing Council, Carbondale.

These skill standards, developed through a consortium of educational and industry partners in Illinois, serve as guides to workforce preparation program providers to define content for their programs and to employers to establish the skills and standards necessary for job acquisition and performance. The skill standards include the following…

Soft Skills Training: An Annotated Guide to Selected Programs.

ERIC Educational Resources Information Center

Leigh, Wilhelmina A.; Lee, Deitra H.; Lindquist, Malinda A.

This guidebook presents data from a two-part study that reviewed existing literature on soft work skills, defined soft skills, and determined their importance to employers. The study also identified programs that were teaching those skills. Researchers contacted 90 organizations, asking for detailed written materials about themselves. The 53 that…

A De Novo-Assembly Based Data Analysis Pipeline for Plant Obligate Parasite Metatranscriptomic Studies

PubMed Central

Guo, Li; Allen, Kelly S.; Deiulio, Greg; Zhang, Yong; Madeiras, Angela M.; Wick, Robert L.; Ma, Li-Jun

2016-01-01

Current and emerging plant diseases caused by obligate parasitic microbes such as rusts, downy mildews, and powdery mildews threaten worldwide crop production and food safety. These obligate parasites are typically unculturable in the laboratory, posing technical challenges to characterize them at the genetic and genomic level. Here we have developed a data analysis pipeline integrating several bioinformatic software programs. This pipeline facilitates rapid gene discovery and expression analysis of a plant host and its obligate parasite simultaneously by next generation sequencing of mixed host and pathogen RNA (i.e., metatranscriptomics). We applied this pipeline to metatranscriptomic sequencing data of sweet basil (Ocimum basilicum) and its obligate downy mildew parasite Peronospora belbahrii, both lacking a sequenced genome. Even with a single data point, we were able to identify both candidate host defense genes and pathogen virulence genes that are highly expressed during infection. This demonstrates the power of this pipeline for identifying genes important in host–pathogen interactions without prior genomic information for either the plant host or the obligate biotrophic pathogen. The simplicity of this pipeline makes it accessible to researchers with limited computational skills and applicable to metatranscriptomic data analysis in a wide range of plant-obligate-parasite systems. PMID:27462318

Wrapping up BLAST and other applications for use on Unix clusters.

PubMed

Hokamp, Karsten; Shields, Denis C; Wolfe, Kenneth H; Caffrey, Daniel R

2003-02-12

We have developed two programs that speed up common bioinformatic applications by spreading them across a UNIX cluster.(1) BLAST.pm, a new module for the 'MOLLUSC' package. (2) WRAPID, a simple tool for parallelizing large numbers of small instances of programs such as BLAST, FASTA and CLUSTALW. The packages were developed in Perl on a 20-node Linux cluster and are provided together with a configuration script and documentation. They can be freely downloaded from http://wolfe.gen.tcd.ie/wrapper.

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

PubMed

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 design. © 2014 John Wiley & Sons Ltd.

Training Verbal and Nonverbal Communication Interview Skills to Adolescents

ERIC Educational Resources Information Center

Olszewski, Abbie; Panorska, Anna; Gillam, Sandra Laing

2017-01-01

Adolescents' verbal and nonverbal communication skills were compared before and after training in a workforce readiness training program, Language for Scholars (LFS), and a study skills program, Ideal Student Workshop (ISW). A cross-over design was used, ensuring that 44 adolescents received both programs and acted as their own control. The LFS…

A Career-Oriented Foreign Language Program for Keystone Oaks School District, Pittsburgh, Pennsylvania.

ERIC Educational Resources Information Center

Grubesky, Marcia R.

A career-oriented foreign language program is discussed that takes into account marketable skills of foreign language majors for a number of careers. The program is threefold. First, it recognizes the need for language skills to supplement technical, business, and professional skills to expand educational knowledge; capabilities in diplomacy and…

Summer Education Program for Neurologically and Physically Handicapped Children. Summer 1975. Evaluation Report.

ERIC Educational Resources Information Center

Ellis, Ronald S.

Evaluated was the Summer Education Program for Neurologically and Physically Handicapped Children, designed to improve the performance of 145 children (6-16 years old) in the following areas--gross motor skills, swimming, fine motor skills, socialization with nonhandicapped peers, and independent daily living skills. The program included the…

The Cognitive Domain: The Last Frontier. Final Report of the Regional Study Award Project.

ERIC Educational Resources Information Center

Clary, Joan; Mahaffy, John

The theoretical foundations of thinking skills models differ. One category of thinking skills programs uses the cognitive process approach on the premise that thinking abilities depend upon certain fundamental processes. Thinking skills programs that present a strategic approach to thinking are called heuristics-oriented programs, and focus on an…

An Examination of Community College Occupational Programs and Their Role in Equipping Students with the Necessary Skills to Supply the Demand for High-Demand Middle-Skill Jobs

ERIC Educational Resources Information Center

Blackman, Orville G.

2009-01-01

This study addresses the fundamental question, "Are Kentucky's public community and technical colleges training enough students with the relevant skills to fill job openings in Kentucky's middle-skill jobs?" By examining student interests in occupational programs, labor market demand for trained middle-skill employees, and their…

Employment training for disadvantaged or dependent populations.

PubMed

Stern, H

1982-01-01

The vocational rehabilitation process is viewed as having two dominant work-related components: the actual work-training experience and employability skills. The paper argues that both components are critical and must be integrated. The major role of the vocational rehabilitation agency is viewed as that of provider of employability (or job-seeking) skills programs. These programs consist of: (1) employability skills courses, (2) work performance demand standard setting, and (3) on-the-job rotational task schemes. Actual work skills can only be provided in the "real world" of work. Centralized work-training programs are viewed as creating inappropriate socialization and only moderately transferable skills.

Learning Skills Profiles of master's students in nursing administration: assessing the impact of problem-based learning.

PubMed

Baker, Constance M; McDaniel, Anna M; Pesut, Daniel J; Fisher, Mary L

2007-01-01

Attempts to compare graduate student performances before and after introducing new curricula are rare; yet faculties need outcome measures to justify program costs and demonstrate effectiveness. Boyatzis and Kolb's Learning Skills Profile is used to assess the outcomes of a problem-based learning MSN program. Increases were demonstrated among all 12 learning skills; statistically significant increases were found in eight of the personal learning skills and six of the job skill demands. Comparisons are made between scores of students in the MSN program and scores of master's students in business administration.

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

ERIC Educational Resources Information Center

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…

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

ERIC Educational Resources Information Center

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…

Illinois Occupational Skill Standards: Lodging Cluster.

ERIC Educational Resources Information Center

Illinois Occupational Skill Standards and Credentialing Council, Carbondale.

This document of skill standards for the lodging cluster serves as a guide to workforce preparation program providers in defining content for their programs and to employers to establish the skills and standards necessary for job acquisition. These 28 occupational skill standards describe what people should know and be able to do in an…

Illinois Occupational Skill Standards: Greenhouse/Nursery Cluster.

ERIC Educational Resources Information Center

Illinois Occupational Skill Standards and Credentialing Council, Carbondale.

This document of skill standards for the greenhouse/nursery cluster serves as a guide to workforce preparation program providers in defining content for their programs and to employers to establish the skills and standards necessary for job acquisition. These 23 occupational skill standards describe what people should know and be able to do in an…

Description of an Introductory Learning Strategies Course for the Job Skills Educational Program.

ERIC Educational Resources Information Center

Murphy, Debra Ann; Derry, Sharon J.

The Job Skills Educational Program (JSEP), currently under development for the Army Research Institute, embeds learner strategies training within the context of a basic skills computer-assisted instruction curriculum. The curriculum is designed for low-ability soldiers, and consists largely of instruction in the domain of intellectual skills. An…

Illinois Occupational Skill Standards: Landscape Technician Cluster.

ERIC Educational Resources Information Center

Illinois Occupational Skill Standards and Credentialing Council, Carbondale.

This document of skill standards for the landscape technician cluster serves as a guide to workforce preparation program providers in defining content for their programs and to employers to establish the skills and standards necessary for job acquisition. These 19 occupational skill standards describe what people should know and be able to do in…

Designing and Evaluating a Personal Skills Development Program for Management Education

ERIC Educational Resources Information Center

Pang, Elvy; Hung, Humphry

2012-01-01

Success in preparing business students for professional careers requires these students to develop a set of well-defined personal skills. The present study examined 145 business students to assess the effectiveness of a personal skills development (PSD) program by measuring the impact of the training on the students' attitudes in skill development…

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

ERIC Educational Resources Information Center

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…

Skills for Action. What Works Clearinghouse Intervention Report

ERIC Educational Resources Information Center

What Works Clearinghouse, 2006

2006-01-01

"Skills for Action," a program to build positive character values and life and citizenship skills for students in grades 9-12, includes classroom lessons and service learning. The program, with more than 100 lessons focused around 26 personal, social, and thinking skills, ranges from one semester to four years in length. Students explore…

Salt Lake Skills Center Handicapped Advocacy Program. Summary Report.

ERIC Educational Resources Information Center

Hall, Bo; Armstrong, Terry L.

The Handicapped Advocacy Program (HAP) is an advocacy service for individuals with disabilities who are sponsored in skills training by the Utah Division of Rehabilitation Services (DRS). It has developed a system whereby DRS clients can be tracked throughout their tenure at the Salt Lake Skills Center. Other services include Skills Center…

Incorporating Skills into Social Studies Programs, K-12.

ERIC Educational Resources Information Center

Gregory, George, Ed.

Designed to assist schools in implementing developmental skills in the social studies programs for grades K-12, this guide is divided into seven sections. The first section, a literature review, cites publications on social studies skills. Section 2 gives an interdisciplinary view of shared skills in the New York state curriculum. Three skill…

Defining College-Level Skills. Report of the Task Force on Definition of College-Level Skills.

ERIC Educational Resources Information Center

Minnesota Higher Education Coordinating Board, St. Paul.

Recommendations concerning the reading, writing, and mathematics skills that are needed by students entering degree programs in Minnesota postsecondary institutions are offered by a Minnesota Higher Education Coordinating Board task force. In addition to describing reading skills that students need for most college degree programs, conditions…

ReGaTE: Registration of Galaxy Tools in Elixir

PubMed Central

Mareuil, Fabien; Deveaud, Eric; Kalaš, Matúš; Soranzo, Nicola; van den Beek, Marius; Grüning, Björn; Ison, Jon; Ménager, Hervé

2017-01-01

Abstract Background: Bioinformaticians routinely use multiple software tools and data sources in their day-to-day work and have been guided in their choices by a number of cataloguing initiatives. The ELIXIR Tools and Data Services Registry (bio.tools) aims to provide a central information point, independent of any specific scientific scope within bioinformatics or technological implementation. Meanwhile, efforts to integrate bioinformatics software in workbench and workflow environments have accelerated to enable the design, automation, and reproducibility of bioinformatics experiments. One such popular environment is the Galaxy framework, with currently more than 80 publicly available Galaxy servers around the world. In the context of a generic registry for bioinformatics software, such as bio.tools, Galaxy instances constitute a major source of valuable content. Yet there has been, to date, no convenient mechanism to register such services en masse. Findings: We present ReGaTE (Registration of Galaxy Tools in Elixir), a software utility that automates the process of registering the services available in a Galaxy instance. This utility uses the BioBlend application program interface to extract service metadata from a Galaxy server, enhance the metadata with the scientific information required by bio.tools, and push it to the registry. Conclusions: ReGaTE provides a fast and convenient way to publish Galaxy services in bio.tools. By doing so, service providers may increase the visibility of their services while enriching the software discovery function that bio.tools provides for its users. The source code of ReGaTE is freely available on Github at https://github.com/C3BI-pasteur-fr/ReGaTE. PMID:28402416

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

PubMed Central

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

George W. Wingate High School Multilingual Survival Skills Program, 1985-1986. OEA Evaluation Report.

ERIC Educational Resources Information Center

New York City Board of Education, Brooklyn. Office of Educational Assessment.

The Multilingual Survival Skills Program, in its final year of a three-year funding cycle, provided instructional and support services to 350 Haitian and Hispanic students of limited English proficiency (LEP) at George Wingate High School (Brooklyn, New York). The program emphasized the acquisition of English language skills, using students'…

Procedures and Reasoning for Skill Proficiency Testing in Physical Education Teacher Education Programs

ERIC Educational Resources Information Center

Baghurst, Timothy; Richard, Kevin; Mwavita, Mwarumba; Ramos, Nilo

2015-01-01

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…

Electrician Cluster, STEP Training Plan. Skills Training and Education Program.

ERIC Educational Resources Information Center

Alabama State Dept. of Postsecondary Education, Montgomery.

This guide is a training plan for the electrical skills cluster of the Skills Training and Education Program (STEP), an open-entry, open-exit program funded by the Job Training Partnership Act (JTPA). In the STEP training plan, each task has its own lesson plan guide. This manual contains the following information: definitions, instructions for…

Clerical Cluster, STEP Training Plan. Skills Training and Education Program.

ERIC Educational Resources Information Center

Alabama State Dept. of Postsecondary Education, Montgomery.

This guide is a training plan for the clerical skills cluster of the Skills Training and Education Program (STEP), an open-entry, open-exit program funded by the Job Training Partnership Act (JTPA). In the STEP training plan, each task has its own lesson plan guide. This manual contains the following information: definitions, instructions for…

Project COMPAS [Consortium for Operating and Managing Programs for the Advancment of Skills]: A Design for Change.

ERIC Educational Resources Information Center

Schermerhorn, Leora L., Ed.; And Others

Descriptive and evaluative information is provided in this report on Project COMPAS (Consortium for Operating and Managing Programs for the Advancement of Skills), a cooperative effort between seven community colleges which developed cognitive skills programs for entry-level freshmen. Chapter I reviews the unique features of Project COMPAS,…

California Community College Handbook: Teaching Basic Skills in Vocational Education. Model Programs.

ERIC Educational Resources Information Center

Evaluation and Training Inst., Los Angeles, CA.

This handbook was produced as a result of a project that studied California community college programs that teach basic skills in vocational education programs. The project included a literature review, a telephone survey, and 12 site visits. The handbook contains four sections: (1) steps for integrating basic skills and vocational instruction;…

Preschool Social-Emotional Skills Training: A Controlled Pilot Test of the Making Choices and Strong Families Programs

ERIC Educational Resources Information Center

Conner, Natalie W.; Fraser, Mark W.

2011-01-01

Objective: The purpose of this study was to pilot test a multicomponent program designed to prevent aggressive behavior in preschool children. The first program component was comprised of social-emotional skills training. It focused on improving the social information processing and emotional-regulation skills of children. The second component was…

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

ERIC Educational Resources Information Center

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…

Development of an Information Literacy Program for the Degree Completion Program at Philadelphia College of Bible.

ERIC Educational Resources Information Center

Brown, Lyn S.; Ryan, G. Jeremiah

One of the major requirements in the degree completion program at Philadelphia College of Bible (Pennsylvania) is the completion of a major research paper. The paper is designed to develop research skills, sharpen writing skills, encourage critical thinking, and promote problem-solving skills. Students were not adequately prepared by either the…

Evaluation of the Preschool Life Skills Program in Head Start Classrooms: A Systematic Replication

ERIC Educational Resources Information Center

Hanley, Gregory P.; Fahmie, Tara A.; Heal, Nicole A.

2014-01-01

In an attempt to address risk factors associated with extensive nonfamilial child care, we implemented the preschool life skills (PLS) program (Hanley, Heal, Tiger, & Ingvarsson, 2007) in two community-based Head Start classrooms. A multiple baseline design across classrooms, repeated across skills, showed that the program resulted in a 5-fold…

The Prevalence of Anxiety and Pro-Social Behaviors in Child-Centered and Basic Skills Preschool Classrooms.

ERIC Educational Resources Information Center

Reio, Thomas G., Jr.; Maciolek, C. Lynn; Weiss, Erin M.

Although there is considerable evidence that kindergartners in child-centered programs have more opportunities to increase prosocial behavior and are more internally motivated than children in basic skills programs, the efficacy of child-centered versus basic skills programs with regard to prosocial behavior has not been examined among preschool…

The role of life skills promotion in substance abuse prevention: a mediation analysis.

PubMed

Bühler, Anneke; Schröder, Elke; Silbereisen, Rainer K

2008-08-01

Research has shown that life skills programs are the most effective single activity in school-based substance abuse prevention. However, little is known about the processes through which they are effective. This study examines whether an evidence-based prevention program targeting general competence is effective through the promotion of knowledge about life skills and enhanced related behaviors. Based on a sample of 442 fifth graders participating in a quasi-experimental prevention study, as expected, mediation analyses revealed that increased knowledge about life skills paralleled an increase in students' distant attitudes toward alcohol and nicotine use. Unexpectedly, behaviors manifesting enhanced life skills were found not only among program participants who remained experimental/non-smokers or stopped smoking but also among smokers. In general, findings suggest that favorable prevention outcomes may be influenced through building knowledge about general life skills. The notion of uniform mechanisms of effectiveness in prevention programs is discussed.

Computer Simulation of Embryonic Systems: What can a virtual embryo teach us about developmental toxicity? (LA Conference on Computational Biology & Bioinformatics)

EPA Science Inventory

This presentation will cover work at EPA under the CSS program for: (1) Virtual Tissue Models built from the known biology of an embryological system and structured to recapitulate key cell signals and responses; (2) running the models with real (in vitro) or synthetic (in silico...

An Innovative Plant Genomics and Gene Annotation Program for High School, Community College, and University Faculty

ERIC Educational Resources Information Center

Hacisalihoglu, Gokhan; Hilgert, Uwe; Nash, E. Bruce; Micklos, David A.

2008-01-01

Today's biology educators face the challenge of training their students in modern molecular biology techniques including genomics and bioinformatics. The Dolan DNA Learning Center (DNALC) of Cold Spring Harbor Laboratory has developed and disseminated a bench- and computer-based plant genomics curriculum for biology faculty. In 2007, a five-day…

Determining the Skills Gap: A Study of the Perceptions of Entry-Level Skills of Recent Career and Technology Education Completers

ERIC Educational Resources Information Center

Green, Lee C.

2015-01-01

This study examined the perceptions of community employers as to the skill levels of graduates from Career and Technology Education (CTE) programs. This study also examined the perceptions of former students of CTE programs. The skill level is the skills that the job market deem necessary to be successful in a particular industry. This study also…

Improving Narrative Writing Skills, Composition Skills, and Related Attitudes among Second Grade Students by Integrating Word Processing, Graphic Organizers, and Art into a Process Approach to Writing.

ERIC Educational Resources Information Center

Gallick-Jackson, Sheryl A.

A practicum program was developed and implemented to improve narrative writing skills, composition skills, and related attitudes among the targeted second grade students. Objectives for the program were for: 75% of the students to increase their narrative writing skills by at least one proficiency level; 75% of the students to increase their…

Assessing the Content and Quality of Commercially Available Reading Software Programs: Do They Have the Fundamental Structures to Promote the Development of Early Reading Skills in Children?

ERIC Educational Resources Information Center

Grant, Amy; Wood, Eileen; Gottardo, Alexandra; Evans, Mary Ann; Phillips, Linda; Savage, Robert

2012-01-01

The current study developed a taxonomy of reading skills and compared this taxonomy with skills being trained in 30 commercially available software programs designed to teach emergent literacy or literacy-specific skills for children in preschool, kindergarten, and Grade 1. Outcomes suggest that, although some skills are being trained in a…

Toward genome-enabled mycology.

PubMed

Hibbett, David S; Stajich, Jason E; Spatafora, Joseph W

2013-01-01

Genome-enabled mycology is a rapidly expanding field that is characterized by the pervasive use of genome-scale data and associated computational tools in all aspects of fungal biology. Genome-enabled mycology is integrative and often requires teams of researchers with diverse skills in organismal mycology, bioinformatics and molecular biology. This issue of Mycologia presents the first complete fungal genomes in the history of the journal, reflecting the ongoing transformation of mycology into a genome-enabled science. Here, we consider the prospects for genome-enabled mycology and the technical and social challenges that will need to be overcome to grow the database of complete fungal genomes and enable all fungal biologists to make use of the new data.

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

ERIC Educational Resources Information Center

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…

Medicare Program; Prospective Payment System and Consolidated Billing for Skilled Nursing Facilities for FY 2017, SNF Value-Based Purchasing Program, SNF Quality Reporting Program, and SNF Payment Models Research. Final rule.

PubMed

2016-08-05

This final rule updates the payment rates used under the prospective payment system (PPS) for skilled nursing facilities (SNFs) for fiscal year (FY) 2017. In addition, it specifies a potentially preventable readmission measure for the Skilled Nursing Facility Value-Based Purchasing Program (SNF VBP), and implements requirements for that program, including performance standards, a scoring methodology, and a review and correction process for performance information to be made public, aimed at implementing value-based purchasing for SNFs. Additionally, this final rule includes additional polices and measures in the Skilled Nursing Facility Quality Reporting Program (SNF QRP). This final rule also responds to comments on the SNF Payment Models Research (PMR) project.

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

PubMed

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.

SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts

PubMed Central

Ryan, Michael C.; Cleland, James; Kim, RyangGuk; Wong, Wing Chung; Weinstein, John N.

2012-01-01

Summary: SpliceSeq is a resource for RNA-Seq data that provides a clear view of alternative splicing and identifies potential functional changes that result from splice variation. It displays intuitive visualizations and prioritized lists of results that highlight splicing events and their biological consequences. SpliceSeq unambiguously aligns reads to gene splice graphs, facilitating accurate analysis of large, complex transcript variants that cannot be adequately represented in other formats. Availability and implementation: SpliceSeq is freely available at http://bioinformatics.mdanderson.org/main/SpliceSeq:Overview. The application is a Java program that can be launched via a browser or installed locally. Local installation requires MySQL and Bowtie. Contact: mryan@insilico.us.com Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:22820202

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

ERIC Educational Resources Information Center

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…

An Exploration of a Community-Based LEGO® Social-Skills Program for Youth with Autism Spectrum Disorder

ERIC Educational Resources Information Center

MacCormack, Jeffrey W. H.; Matheson, Ian A.; Hutchinson, Nancy L.

2015-01-01

Clinical interventions have been effective at increasing social skills of youth with autism spectrum disorder (ASD). However, generalization of those skills to non-clinical environments is often low. To reduce this generalization gap, community-based programs have been designed to help youth develop social skills in naturalistic settings. This…

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

PubMed

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 teaching medical students how to communicate effectively with patients and colleagues.

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

PubMed Central

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 faculties in designing a proper program for teaching medical students how to communicate effectively with patients and colleagues. PMID:26767096

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

ERIC Educational Resources Information Center

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…

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

ERIC Educational Resources Information Center

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.…

The Effectiveness of the Master Thinker Program in Developing Critical Thinking Skills of 11th Grade Students in Bahrain

ERIC Educational Resources Information Center

Alnabhan, Mousa; Alhamdan, Najat; Darwish, Ahmed

2014-01-01

The current study aimed at investigating the effect of the Master Thinker program on developing critical thinking skills of 11th grade students in Bahrain. Specifically, this research attempts to examine the hypothesis: Teaching the Master Thinker program will be significantly effective in developing critical thinking and its skills (inference,…

Evaluation of a Life Skills Program to Prevent Adolescent Alcohol Use in Two European Countries: One-Year Follow-Up

ERIC Educational Resources Information Center

Giannotta, Fabrizia; Weichold, Karina

2016-01-01

Background: Life skills programs are effective tools to combat youth substance use. However there is a lack of studies concerning their effectiveness in Europe. Objective: This study investigated the 1 year follow up effects and the program implementation of a life skills school-based intervention (IPSY: Information + Psychosocial…

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

ERIC Educational Resources Information Center

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.…

Take a New Bearing: Skills and Sensitive Strategies for Sharing Spiders, Stars, Shelters, Safety, and Solitude.

ERIC Educational Resources Information Center

Ford, Phyllis M.

This book is the leader handbook of the American Camping Association's (Indiana) Outdoor Living Skills Program. The purpose of this program is the development of outdoor living skills that emphasize environmental values. The program is divided into five levels and participants can enter at any point depending on their maturity and existing camping…

Evaluation of the ARDESOS Program: An Initiative to Improve Critical Thinking Skills

ERIC Educational Resources Information Center

Saiz, Carlos; Rivas, Silvia F.

2011-01-01

It is desirable that reasoning, problem-solving and decision-making skills should form an integral part of our private and professional lives. Here we show how these skills can be improved through the use of the ARDESOS program. To test the effect of the program, we have also developed an assessment test (PENCRISAL). Our results are going in the…

A School-Wide Three-Tiered Program of Social Skills Intervention: Results of a Three-Year Cohort Study

ERIC Educational Resources Information Center

Albrecht, Susan Fread; Mathur, Sarup R.; Jones, Ruth E.; Alazemi, Saad

2015-01-01

The purpose of this paper was to summarize the implementation of a schoolwide tiered intervention program in three Midwestern U.S. elementary schools over a period of three years. The program, Social Skills Training and Aggression Reduction Techniques plus Time-Away (START[superscript Plus]) includes components of social skills training at the…

Communication and Research Skills in the Information Systems Curriculum: A Method of Assessment

ERIC Educational Resources Information Center

Lazarony, Paul J.; Driscoll, Donna A.

2010-01-01

Assessment of learning goals has become the norm in business programs in higher education across the country. This paper offers a methodology for the assessment of both communication skills and research skills within a curriculum of the Bachelor of Science in Information Systems Program. Program level learning goals assessed in this paper are: (1)…

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

ERIC Educational Resources Information Center

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…

hm Science Study Skills Program: People, Energy, and Appropriate Technology. Student Text.

ERIC Educational Resources Information Center

Wilson, Carol; Krasnow, Gary

This program includes 14 activity-oriented units which integrate instruction in science study skills with hands-on learning about energy and appropriate technology. The program is suitable for use in a wide range of science curricula in grades 7 to 10. Unit topics and the corresponding skills fostered (in parentheses) in part one focus on: the…

Budgeting Skills: Functional Living Skills for Adolescents and Adults with Mild and Moderate Disabilities.

ERIC Educational Resources Information Center

Nishioka-Evans, Vicki; And Others

Intended primarily for parents of teenagers or young adults with mild and moderate mental disabilities, this guide offers a specific program to teach basic budgeting skills. The program is differentiated for teenagers who either can count money or who have trouble reading and counting money. The program for teenagers who can count money begins…

Perceptions of the use of critical thinking teaching methods.

PubMed

Kowalczyk, Nina; Hackworth, Ruth; Case-Smith, Jane

2012-01-01

To identify the perceived level of competence in teaching and assessing critical thinking skills and the difficulties facing radiologic science program directors in implementing student-centered teaching methods. A total of 692 program directors received an invitation to complete an electronic survey soliciting information regarding the importance of critical thinking skills, their confidence in applying teaching methods and assessing student performance, and perceived obstacles. Statistical analysis included descriptive data, correlation coefficients, and ANOVA. Responses were received from 317 participants indicating program directors perceive critical thinking to be an essential element in the education of the student; however, they identified several areas for improvement. A high correlation was identified between the program directors' perceived level of skill and their confidence in critical thinking, and between their perceived level of skill and ability to assess the students' critical thinking. Key barriers to implementing critical thinking teaching strategies were identified. Program directors value the importance of implementing critical thinking teaching methods and perceive a need for professional development in critical thinking educational methods. Regardless of the type of educational institution in which the academic program is located, the level of education held by the program director was a significant factor regarding perceived confidence in the ability to model critical thinking skills and the ability to assess student critical thinking skills.

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

PubMed

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.

Bioinformatics research in the Asia Pacific: a 2007 update.

PubMed

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.

Employability Planning Process. STIP II (Skill Training Improvement Programs Round II).

ERIC Educational Resources Information Center

Los Angeles Community Coll. District, CA.

Four reports are presented detailing procedures for improving the employability of students enrolled in the Los Angeles Community College District's Skill Training Improvement Programs (STIP II). Each report was submitted by one of the four STIP II programs: Los Angeles Southwest College's program for computer programming; the programs for…

The Military Accessions Vital to National Interest Program: What It Is and How It Can Be Made Relevant

DTIC Science & Technology

2011-05-19

recruited through the MAVNI program possess language skills and cultural expertise that can help the commander make sense of what is going on around him...made; (1) further development of the MAVNI program in order to better leverage the language skills and cultural expertise of the Soldiers recruited...describe and direct. Soldiers recruited through the MAVNI program possess language skills and cultural expertise that can help the commander make

A motivation-focused weight loss maintenance program is an effective alternative to a skill-based approach.

PubMed

West, D S; Gorin, A A; Subak, L L; Foster, G; Bragg, C; Hecht, J; Schembri, M; Wing, R R

2011-02-01

Maintaining weight loss is a major challenge in obesity treatment. Individuals often indicate that waning motivation prompts cessation of effective weight management behaviors. Therefore, a novel weight loss maintenance program that specifically targets motivational factors was evaluated. Overweight women (N=338; 19% African American) with urinary incontinence were randomized to lifestyle obesity treatment or control and followed for 18 months. All participants in lifestyle (N=226) received the same initial 6-month group behavioral obesity treatment and were then randomized to (1) a novel motivation-focused maintenance program (N=113) or (2) a standard skill-based maintenance approach (N=113). Weight assessed at baseline, 6 and 18 months. Both treatment groups (motivation-focused and skill-based) achieved comparable 18-month weight losses (-5.48% for motivation-focused vs -5.55% in skill-based, P=0.98), and both groups lost significantly more than controls (-1.51%; P=0.0012 in motivation-focused and P=0.0021 in skill-based). A motivation-focused maintenance program offers an alternative, effective approach to weight maintenance expanding available evidence-based interventions beyond traditional skill-based programs.

A National Survey on Teaching and Assessing Technical Proficiency in Vascular Surgery in Canada.

PubMed

Drudi, Laura; Hossain, Sajjid; Mackenzie, Kent S; Corriveau, Marc-Michel; Abraham, Cherrie Z; Obrand, Daniel I; Vassiliou, Melina; Gill, Heather; Steinmetz, Oren K

2016-05-01

This survey aims to explore trainees' perspectives on how Canadian vascular surgery training programs are using simulation in teaching and assessing technical skills through a cross-sectional national survey. A 10-min online questionnaire was sent to Program Directors of Canada's Royal College of Physicians and Surgeons' of Canada approved training programs in vascular surgery. This survey was distributed among residents and fellows who were studying in the 2013-2014 academic year. Twenty-eight (58%) of the 48 Canadian vascular surgery trainees completed the survey. A total of 68% of the respondents were part of the 0 + 5 integrated vascular surgery training program. The use of simulation in the assessment of technical skills at the beginning of training was reported by only 3 (11%) respondents, whereas 43% reported that simulation was used in their programs in the assessment of technical skills at some time during their training. Training programs most often provided simulation as a method of teaching and learning endovascular abdominal aortic or thoracic aneurysm repair (64%). Furthermore, 96% of trainees reported the most common resource to learn and enhance technical skills was dialog with vascular surgery staff. Surveyed vascular surgery trainees in Canada report that simulation is rarely used as a tool to assess baseline technical skills at the beginning of training. Less than half of surveyed trainees in vascular surgery programs in Canada report that simulation is being used for skills acquisition. Currently, in Canadian training programs, simulation is most commonly used to teach endovascular skills. Copyright © 2016 Elsevier Inc. All rights reserved.

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

PubMed

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 < 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. 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.

7 CFR 785.3 - Annual certification of State mediation programs.

Code of Federal Regulations, 2010 CFR

2010-01-01

... program; (ii) An identification of issues available for mediation under the program; (iii) Management of... requirements for mediators including: (A) Training in mediation skills and in USDA programs; (B) Identification... mediation program provides for training of mediators in mediation skills and in all issues covered by the...

Implementation and evaluation of the Johns Hopkins University School of Medicine leadership program for women faculty.

PubMed

Levine, Rachel B; González-Fernández, Marlís; Bodurtha, Joann; Skarupski, Kimberly A; Fivush, Barbara

2015-05-01

Women continue to be underrepresented in top leadership roles in academic medicine. Leadership training programs for women are designed to enhance women's leadership skills and confidence and increase overall leadership diversity. The authors present a description and evaluation of a longitudinal, cohort-based, experiential leadership program for women faculty at the Johns Hopkins University School of Medicine. We compared pre- and post-program self-assessed ratings of 11 leadership skills and specific negotiation behaviors from 3 cohorts of leadership program participants (n=134) from 2010 to 2013. Women reported significant improvements in skills across 11 domains with the exceptions of 2 domains, Public Speaking and Working in Teams, both of which received high scores in the pre-program assessment. The greatest improvement in rankings occurred within the domain of negotiation skills. Although women reported an increase in their negotiation skills, we were not able to demonstrate an increase in the number of times that women negotiated for salary, space, or promotion following participation in the program. The Johns Hopkins School of Medicine Leadership Program for Women Faculty has demonstrable value for the professional development of participants and addresses institutional strategies to enhance leadership diversity and the advancement of women.

Innovative cardiopulmonary resuscitation and automated external defibrillator programs in schools: Results from the Student Program for Olympic Resuscitation Training in Schools (SPORTS) study.

PubMed

Vetter, Victoria L; Haley, Danielle M; Dugan, Noreen P; Iyer, V Ramesh; Shults, Justine

2016-07-01

Bystander cardiopulmonary resuscitation (CPR) rates are low. Our study objective was to encourage Philadelphia high school students to develop CPR/AED (automated external defibrillator) training programs and to assess their efficacy. The focus was on developing innovative ways to learn the skills of CPR/AED use, increasing willingness to respond in an emergency, and retention of effective psychomotor resuscitation skills. Health education classes in 15 Philadelphia School District high schools were selected, with one Control and one Study Class per school. Both completed CPR/AED pre- and post-tests to assess cognitive knowledge and psychomotor skills. After pre-tests, both were taught CPR skills and AED use by their health teacher. Study Classes developed innovative programs to learn, teach, and retain CPR/AED skills. The study culminated with Study Classes competing in multiple CPR/AED skills events at the CPR/AED Olympic event. Outcomes included post-tests, Mock Code, and presentation scores. All students' cognitive and psychomotor skills improved with standard classroom education (p<0.001). Competition with other schools at the CPR/AED Olympics and the development of their own student-directed education programs resulted in remarkable retention of psychomotor skill scores in the Study Class (88%) vs the Control Class (79%) (p<0.001). Olympic participants averaged 93.1% on the Mock Code with 10 of 12 schools ≥94%. Students who developed creative and novel methods of teaching and learning resuscitation skills showed outstanding application of these skills in a Mock Code with remarkable psychomotor skill retention, potentially empowering a new generation of effectively trained CPR bystanders. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Communication skills training in orthopaedics.

PubMed

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.

Emerging strengths in Asia Pacific bioinformatics.

PubMed

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.

Emerging strengths in Asia Pacific bioinformatics

PubMed Central

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

2008-01-01

The 2008 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998, was organized as the 7th International Conference on Bioinformatics (InCoB), jointly with the Bioinformatics and Systems Biology in Taiwan (BIT 2008) Conference, Oct. 20–23, 2008 at Taipei, Taiwan. Besides bringing together scientists from the field of bioinformatics in this region, InCoB is actively involving researchers from the area of systems biology, 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. PMID:19091008

Development, Implementation, and Evaluation of a Professional Skills Development Program: The Case of Concordia University's GradProSkills

ERIC Educational Resources Information Center

Venkatesh, Vivek; Rabah, Jihan; Lamoureux-Scholes, Laurie; Pelczer, Ildiko; Urbaniak, Kathryn; Martin, Frédérica

2014-01-01

The Graduate and Professional Skills (GradProSkills) program is an initiative developed and run by Concordia University's School of Graduate Studies and the university's Office of the Vice-President, Research and Graduate Studies. This paper presents a case study in which we describe the development, implementation, and evaluative components of…

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

ERIC Educational Resources Information Center

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…

Generalization of Skills through the Addition of Individualized Coaching: Development and Evaluation of a Social Skills Training Program in a Rural Setting

ERIC Educational Resources Information Center

Gottlieb, Jennifer D.; Pryzgoda, Jayde; Neal, Andrea; Schuldberg, David

2005-01-01

There has been recent interest in adding interventions that aid in skill generalization to standard social skills training programs for schizophrenia. Some of these adjunctive interventions are very comprehensive and clearly promising (e.g., IVAST; Liberman, Glynn, Blair, Ross, & Marder, 2002), but their overall cost-effectiveness and feasibility…

The Effects of Social Skills Groups for Young Children with Social Delays

ERIC Educational Resources Information Center

Koyama, Takanori

2011-01-01

This study was conducted as a program evaluation of an existing social skills program. A review of literature identified a limited number of empirical studies on group-based social skills training for young children with social delays. The purpose of this study was to examine the effects of social skills groups as well as the effects of homework…

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

ERIC Educational Resources Information Center

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…

A Multi-Faceted Approach for the Development of the Army's Functional Basic Skills Education Program (BSEP).

ERIC Educational Resources Information Center

Begland, Robert R.

In reviewing the Army Continuing Education System in 1979, the Assistant Secretary of the Army found a basic skills program based on traditional academic level goals was inadequate to meet the Army's requirement to provide functional, job-related basic skill education. Combining the shrinking manpower pool and projected basic skill deficiencies of…

Pennsylvania Blue Shield's Job Linked Skills Program. A Basic Skills Education Program. Final Performance Report.

ERIC Educational Resources Information Center

Pennsylvania Blue Shield, Camp Hill.

A project developed a model curriculum to be delivered by computer-based instruction to teach the required literacy skills for entry workers in the health insurance industry. Literacy task analyses were performed for the targeted jobs and then validated with focus groups. The job tasks and related basic skills were divided into modules. The job…

Evaluation of the dating skills program for improving heterosocial interactions in people with mental retardation.

PubMed

Valenti-Hein, D C; Yarnold, P R; Mueser, K T

1994-01-01

The effectiveness of a social skills training program for improving heterosocial interactions in persons with mental retardation was examined. Moderate to borderline mentally retarded subjects were selected based on problems with social anxiety and social skill deficits. Subjects were then randomly assigned to either a 12-session Dating Skills Program (DSP) or a wait list control (WLC) group. Assessments of social skills in a role-play test, knowledge about social/sexual situations, and social anxiety were obtained for all subjects at baseline, posttreatment, and at an 8-week follow-up. In addition, naturalistic observations were made of interactions of subjects in the DSP group. Subjects who participated in the DSP showed improvements in social skill and social/sexual knowledge at posttest and at follow-up compared to subjects in the WLC group. Social anxiety did not change over time for either group of subjects. Subjects who received the DSP increased interactions with persons of the opposite gender over time, while same-gender interactions decreased. The results replicate and extend previous research on the Dating Skills Program, and suggest that social skills training interventions may improve the heterosocial interactions of adults with mental retardation.

Evaluative Assessment for NASA/GSFC Equal Opportunity Programs Office Sponsored Programs

NASA Technical Reports Server (NTRS)

Jarrell, H. Judith

1995-01-01

The purpose of PREP (Pre-College Minority Engineering Program) is to upgrade skills of minority students who have shown an interest in pursuing academic degrees in electrical engineering. The goal is to upgrade skills needed for successful completion of the rigorous curriculum leading to a Bachelor of Science degree in engineering through a comprehensive upgrade of academic, study and interpersonal skills.

The Feasibility and Effects of a Parent-Facilitated Social Skills Training Program on Social Engagement of Children with Autism Spectrum Disorders

ERIC Educational Resources Information Center

Radley, Keith C.; Jenson, William R.; Clark, Elaine; O'Neill, Robert E.

2014-01-01

Due to impairments in social interactions and communication, children with autism spectrum disorders (ASD) have a need for effective social skills training programs. However, many programs fail due to a lack of acquisition, maintenance, and generalization of target skills. The primary purpose of this study was to evaluate the feasibility and…

The Effectiveness of the Life Skills Program IPSY for the Prevention of Adolescent Tobacco Use: The Mediating Role of Yielding to Peer Pressure

ERIC Educational Resources Information Center

Weichold, Karina; Tomasik, Martin J.; Silbereisen, Rainer K.; Spaeth, Michael

2016-01-01

In this study, the effectiveness of a life skills program to impede tobacco use in early adolescence was scrutinized. The focus was on the mediating role of yielding to peer pressure. The universal school-based life skills program IPSY (Information + Psychosocial Competence = Protection) against adolescent substance use was implemented over 3…

A survey of physical assessment techniques performed by RNs: lessons for nursing education.

PubMed

Giddens, Jean F

2007-02-01

There is ongoing concern about the adequacy of the educational preparation of nursing graduates; at the same time, there is concern regarding excessive content within nursing curricula. The purpose of this study was to identify physical examination skills performed by practicing nurses to better understand the competencies needed by graduates of nursing programs. A sample of 193 nurses completed a survey indicating the frequency they performed various physical assessment techniques. Thirty skills routinely performed by nurses were identified; the remaining skills were reportedly performed occasionally or were not performed. The fact that only 30 skills were reportedly performed regularly by the sample raises questions about the depth at which examinations should be conducted in the clinical setting and the depth at which physical examination skills should be taught in nursing programs. Nurse educators should assess the skills currently taught in nursing programs and consider what skills graduates actually need to enter nursing practice.

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

PubMed

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.

BioQueue: a novel pipeline framework to accelerate bioinformatics analysis.

PubMed

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

eSBMTools 1.0: enhanced native structure-based modeling tools.

PubMed

Lutz, Benjamin; Sinner, Claude; Heuermann, Geertje; Verma, Abhinav; Schug, Alexander

2013-11-01

Molecular dynamics simulations provide detailed insights into the structure and function of biomolecular systems. Thus, they complement experimental measurements by giving access to experimentally inaccessible regimes. Among the different molecular dynamics techniques, native structure-based models (SBMs) are based on energy landscape theory and the principle of minimal frustration. Typically used in protein and RNA folding simulations, they coarse-grain the biomolecular system and/or simplify the Hamiltonian resulting in modest computational requirements while achieving high agreement with experimental data. eSBMTools streamlines running and evaluating SBM in a comprehensive package and offers high flexibility in adding experimental- or bioinformatics-derived restraints. We present a software package that allows setting up, modifying and evaluating SBM for both RNA and proteins. The implemented workflows include predicting protein complexes based on bioinformatics-derived inter-protein contact information, a standardized setup of protein folding simulations based on the common PDB format, calculating reaction coordinates and evaluating the simulation by free-energy calculations with weighted histogram analysis method or by phi-values. The modules interface with the molecular dynamics simulation program GROMACS. The package is open source and written in architecture-independent Python2. http://sourceforge.net/projects/esbmtools/. alexander.schug@kit.edu. Supplementary data are available at Bioinformatics online.

New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation.

PubMed

Antczak, Maciej; Popenda, Mariusz; Zok, Tomasz; Zurkowski, Michal; Adamiak, Ryszard W; Szachniuk, Marta

2018-04-15

Understanding the formation, architecture and roles of pseudoknots in RNA structures are one of the most difficult challenges in RNA computational biology and structural bioinformatics. Methods predicting pseudoknots typically perform this with poor accuracy, often despite experimental data incorporation. Existing bioinformatic approaches differ in terms of pseudoknots' recognition and revealing their nature. A few ways of pseudoknot classification exist, most common ones refer to a genus or order. Following the latter one, we propose new algorithms that identify pseudoknots in RNA structure provided in BPSEQ format, determine their order and encode in dot-bracket-letter notation. The proposed encoding aims to illustrate the hierarchy of RNA folding. New algorithms are based on dynamic programming and hybrid (combining exhaustive search and random walk) approaches. They evolved from elementary algorithm implemented within the workflow of RNA FRABASE 1.0, our database of RNA structure fragments. They use different scoring functions to rank dissimilar dot-bracket representations of RNA structure. Computational experiments show an advantage of new methods over the others, especially for large RNA structures. Presented algorithms have been implemented as new functionality of RNApdbee webserver and are ready to use at http://rnapdbee.cs.put.poznan.pl. mszachniuk@cs.put.poznan.pl. Supplementary data are available at Bioinformatics online.

Big data for big questions: it is time for data analysts to act

PubMed Central

Moscato, Pablo

2015-01-01

Pablo Moscato speaks to Francesca Lake, Managing Editor Australian Research Council Future Fellow Prof. Pablo Moscato was born in 1964 in La Plata, Argentina. Obtaining his B.Sc. in Physics at University of La Plata, his PhD was defended at UNICAMP, Brazil. While at the California Institute of Technology Concurrent Computation Program he developed, in collaboration with Michael Norman, the first application of a methodology later called ‘memetic algorithms’, which is now widely used internationally. He is the founding co-director of the Priority Research Centre for Bioinformatics, Biomarker Discovery and Information-based Medicine (CIBM) (2006–present) and the funding director of the Newcastle Bioinformatics Initiative (2002–2006) of The University of Newcastle (Australia). He is also Chief Investigator of the Australian Research Council Centre in Bioinformatics. He is one of Australia's most cited computer scientists. Over the past 7 years, he has introduced a unifying hallmark of cancer progression based on the changes of information theory quantifiers, and developed a novel mathematical model and an associated solution procedure based on combinatorial optimization techniques to identify drug combinations for cancer therapeutics. In addition, he has identified proteomic signatures to predict the clinical symptoms of Alzheimer's disease, among other ‘firsts’. He is a member of the Editorial Board of Future Science OA. PMID:28031895

An architecture for genomics analysis in a clinical setting using Galaxy and Docker

PubMed Central

Digan, W; Countouris, H; Barritault, M; Baudoin, D; Laurent-Puig, P; Blons, H; Burgun, A

2017-01-01

Abstract Next-generation sequencing is used on a daily basis to perform molecular analysis to determine subtypes of disease (e.g., in cancer) and to assist in the selection of the optimal treatment. Clinical bioinformatics handles the manipulation of the data generated by the sequencer, from the generation to the analysis and interpretation. Reproducibility and traceability are crucial issues in a clinical setting. We have designed an approach based on Docker container technology and Galaxy, the popular bioinformatics analysis support open-source software. Our solution simplifies the deployment of a small-size analytical platform and simplifies the process for the clinician. From the technical point of view, the tools embedded in the platform are isolated and versioned through Docker images. Along the Galaxy platform, we also introduce the AnalysisManager, a solution that allows single-click analysis for biologists and leverages standardized bioinformatics application programming interfaces. We added a Shiny/R interactive environment to ease the visualization of the outputs. The platform relies on containers and ensures the data traceability by recording analytical actions and by associating inputs and outputs of the tools to EDAM ontology through ReGaTe. The source code is freely available on Github at https://github.com/CARPEM/GalaxyDocker. PMID:29048555

An architecture for genomics analysis in a clinical setting using Galaxy and Docker.

PubMed

Digan, W; Countouris, H; Barritault, M; Baudoin, D; Laurent-Puig, P; Blons, H; Burgun, A; Rance, B

2017-11-01

Next-generation sequencing is used on a daily basis to perform molecular analysis to determine subtypes of disease (e.g., in cancer) and to assist in the selection of the optimal treatment. Clinical bioinformatics handles the manipulation of the data generated by the sequencer, from the generation to the analysis and interpretation. Reproducibility and traceability are crucial issues in a clinical setting. We have designed an approach based on Docker container technology and Galaxy, the popular bioinformatics analysis support open-source software. Our solution simplifies the deployment of a small-size analytical platform and simplifies the process for the clinician. From the technical point of view, the tools embedded in the platform are isolated and versioned through Docker images. Along the Galaxy platform, we also introduce the AnalysisManager, a solution that allows single-click analysis for biologists and leverages standardized bioinformatics application programming interfaces. We added a Shiny/R interactive environment to ease the visualization of the outputs. The platform relies on containers and ensures the data traceability by recording analytical actions and by associating inputs and outputs of the tools to EDAM ontology through ReGaTe. The source code is freely available on Github at https://github.com/CARPEM/GalaxyDocker. © The Author 2017. Published by Oxford University Press.

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

PubMed

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.

A Meta-analysis of universal mental health prevention programs for higher education students.

PubMed

Conley, Colleen S; Durlak, Joseph A; Kirsch, Alexandra C

2015-05-01

This meta-analysis investigated the effectiveness of universal mental health prevention programs for higher education students on a range of adjustment outcomes. A systematic literature search identified 103 controlled published and unpublished interventions involving college, graduate, or professional students. As hypothesized, skill-training programs that included a supervised practice component were significantly more effective overall (mean effect size = 0.45, confidence interval (CI) = 0.39 to 0.52) compared to skill-training programs without supervised practice (0.11, CI = -0.01 to 0.22) and psychoeducational (information-only) programs (0.13, CI = 0.06 to 0.21). When comparisons on specific outcomes were possible, skill-training programs including supervised practice were significantly more effective than the other two groups of programs in reducing symptoms of depression, anxiety, stress, and general psychological distress, and in improving social-emotional skills, self-perceptions, and academic behaviors and performance. The magnitude of effects achieved in several outcome areas is comparable to or higher than that reported in other reviews of universal programs, suggesting that skill-training programs for higher education students that incorporate supervised practice now join the ranks of other effective preventive mental health interventions. This review offers several recommendations to improve the experimental rigor of future research.

Palliative Care Education in Emergency Medicine Residency Training: A Survey of Program Directors, Associate Program Directors, and Assistant Program Directors.

PubMed

Kraus, Chadd K; Greenberg, Marna R; Ray, Daniel E; Dy, Sydney Morss

2016-05-01

Emergency medicine (EM) residents perceive palliative care (PC) skills as important and want training, yet there is a general lack of formal PC training in EM residency programs. A clearer definition of the PC educational needs of EM trainees is a research priority. To assess PC competency education in EM residency programs. This was a mixed-mode survey of residency program directors, associate program directors, and assistant program directors at accredited EM residency programs, evaluating four educational domains: 1) importance of specific competencies for senior EM residents, 2) senior resident skills in PC competencies, 3) effectiveness of educational methods, and 4) barriers to training. Response rate was 50% from more than 100 residency programs. Most respondents (64%) identified PC competencies as important for residents to learn, and 59% reported that they teach7 PC skills in their residency program. In Domains 1 and 2, crucial conversations, management of pain, and management of the imminently dying had the highest scores for importance and residents' skill. In Domain 3, bedside teaching, mentoring from hospice and palliative medicine faculty, and case-based simulation were the most effective educational methods. In Domain 4, lack of PC expertise among faculty and lack of interest by faculty and residents were the greatest barriers. There were differences between competency importance and senior resident skill level for management of the dying child, withdrawal/withholding of nonbeneficial interventions, and ethical/legal issues. There are specific barriers and opportunities for PC competency training and gaps in resident skill level. Specifically, there are discrepancies in competency importance and residency skill in the management of the dying child, nonbeneficial interventions, and ethical and legal issues that could be a focus for educational interventions in PC competency training in EM residencies. Copyright © 2016 American Academy of Hospice and Palliative Medicine. Published by Elsevier Inc. All rights reserved.

20 CFR 672.105 - What are the purposes of the YouthBuild program?

Code of Federal Regulations, 2012 CFR

2012-04-01

... program has as goals: (1) To promote leadership skills development and community service activities. YouthBuild programs will foster the development of leadership skills and a commitment to community...

20 CFR 672.105 - What are the purposes of the YouthBuild program?

Code of Federal Regulations, 2014 CFR

2014-04-01

... program has as goals: (1) To promote leadership skills development and community service activities. YouthBuild programs will foster the development of leadership skills and a commitment to community...

20 CFR 672.105 - What are the purposes of the YouthBuild program?

Code of Federal Regulations, 2013 CFR

2013-04-01

... program has as goals: (1) To promote leadership skills development and community service activities. YouthBuild programs will foster the development of leadership skills and a commitment to community...

Wanted: A Developmentally Oriented Alcohol Prevention Program.

ERIC Educational Resources Information Center

Spoth, Richard; Rosenthal, David

1980-01-01

Describes an alcohol prevention program with a comprehensive developmental skills orientation. The program includes values clarification, decision making, career planning and communication skills, assertiveness and relaxation training, and relationship with parents and peers. (Author/JAC)

Maine's Employability Skills Program

ERIC Educational Resources Information Center

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…

Volleyball: Special Olympics Sports Skills Instructional Program.

ERIC Educational Resources Information Center

Special Olympics, Inc., Washington, DC.

One of seven booklets on Special Olympics Sports Skills Instructional Programs, this guide presents an instructional program for volleyball coaches working with mentally retarded persons. The instructional program presents information on the following topics: long term goals; short term objectives; modifications and adaptations of equipment, sport…

Constructive Alternatives to Punishment.

ERIC Educational Resources Information Center

Reclaiming Children and Youth: Journal of Emotional and Behavioral Problems, 1997

1997-01-01

Provides examples of programs that teach children positive behavior skills for success in life rather than resorting to traditional punishment. Looks at the Positive Education Program, Boys Town, the Westerly School District, and the New Opportunities Program. Such programs help children learn appropriate skills that replace problem behaviors.…

MicroRNAs as Potential Regulators of Glutathione Peroxidases Expression and Their Role in Obesity and Related Pathologies.

PubMed

Matoušková, Petra; Hanousková, Barbora; Skálová, Lenka

2018-04-14

Glutathione peroxidases (GPxs) belong to the eight-member family of phylogenetically related enzymes with different cellular localization, but distinct antioxidant function. Several GPxs are important selenoproteins. Dysregulated GPx expression is connected with severe pathologies, including obesity and diabetes. We performed a comprehensive bioinformatic analysis using the programs miRDB, miRanda, TargetScan, and Diana in the search for hypothetical microRNAs targeting 3'untranslated regions (3´UTR) of GPxs. We cross-referenced the literature for possible intersections between our results and available reports on identified microRNAs, with a special focus on the microRNAs related to oxidative stress, obesity, and related pathologies. We identified many microRNAs with an association with oxidative stress and obesity as putative regulators of GPxs. In particular, miR-185-5p was predicted by a larger number of programs to target six GPxs and thus could play the role as their master regulator. This microRNA was altered by selenium deficiency and can play a role as a feedback control of selenoproteins' expression. Through the bioinformatics analysis we revealed the potential connection of microRNAs, GPxs, obesity, and other redox imbalance related diseases.

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome.

PubMed

McDonald, Daniel; Clemente, Jose C; Kuczynski, Justin; Rideout, Jai Ram; Stombaugh, Jesse; Wendel, Doug; Wilke, Andreas; Huse, Susan; Hufnagle, John; Meyer, Folker; Knight, Rob; Caporaso, J Gregory

2012-07-12

We present the Biological Observation Matrix (BIOM, pronounced "biome") format: a JSON-based file format for representing arbitrary observation by sample contingency tables with associated sample and observation metadata. As the number of categories of comparative omics data types (collectively, the "ome-ome") grows rapidly, a general format to represent and archive this data will facilitate the interoperability of existing bioinformatics tools and future meta-analyses. The BIOM file format is supported by an independent open-source software project (the biom-format project), which initially contains Python objects that support the use and manipulation of BIOM data in Python programs, and is intended to be an open development effort where developers can submit implementations of these objects in other programming languages. The BIOM file format and the biom-format project are steps toward reducing the "bioinformatics bottleneck" that is currently being experienced in diverse areas of biological sciences, and will help us move toward the next phase of comparative omics where basic science is translated into clinical and environmental applications. The BIOM file format is currently recognized as an Earth Microbiome Project Standard, and as a Candidate Standard by the Genomic Standards Consortium.

Critical Television Viewing Skills: Fitting Them into the Curriculum.

ERIC Educational Resources Information Center

Carpenter, Lee

1982-01-01

The need for teaching critical television viewing skills is seen as part of a greater need for a sequential media skills program and continued support for reactive art, music, and physical education programs in the schools. Twenty-eight references are listed. (Author/LLS)

Illinois Occupational Skill Standards: Telecommunications Technician Cluster.

ERIC Educational Resources Information Center

Illinois Occupational Skill Standards and Credentialing Council, Carbondale.

This document, which is intended as a guide for workforce preparation program providers, details the Illinois Occupational Skill Standards for programs preparing students for employment in the telecommunications technician occupational cluster. The document begins with a brief overview of the Illinois perspective on occupational skills standards…

Edge Bioinformatics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lo, Chien-Chi

2015-08-03

Edge Bioinformatics is a developmental bioinformatics and data management platform which seeks to supply laboratories with bioinformatics pipelines for analyzing data associated with common samples case goals. Edge Bioinformatics enables sequencing as a solution and forward-deployed situations where human-resources, space, bandwidth, and time are limited. The Edge bioinformatics pipeline was designed based on following USE CASES and specific to illumina sequencing reads. 1. Assay performance adjudication (PCR): Analysis of an existing PCR assay in a genomic context, and automated design of a new assay to resolve conflicting results; 2. Clinical presentation with extreme symptoms: Characterization of a known pathogen ormore » co-infection with a. Novel emerging disease outbreak or b. Environmental surveillance« less

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

ERIC Educational Resources Information Center

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…

Analysis of Prospective Mathematics Teachers’ Basic Teaching Skills (a Study of Mathematics Education Departement Students’ Field Experience Program at STKIP Garut)

NASA Astrophysics Data System (ADS)

Rahayu, D. V.

2017-02-01

This study was intended to figure out basic teaching skills of Mathematics Department Students of STKIP Garut at Field Experience Program in academic year 2014/2015. This study was qualitative research with analysis descriptive technique. Instrument used in this study was observation sheet to measure basic teaching mathematics skills. The result showed that ability of content mastery and explaining skill were in average category. Questioning skill, conducting variations skill and conducting assessment skill were in good category. Managing classroom skill and giving motivation skill were in poor category. Based on the result, it can be concluded that the students’ basic teaching skills weren’t optimal. It is recommended for the collegians to get lesson with appropriate strategy so that they can optimize their basic teaching skills.

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

PubMed

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.

Bioinformatics goes back to the future.

PubMed

Miller, Crispin J; Attwood, Teresa K

2003-02-01

The need to turn raw data into knowledge has led the bioinformatics field to focus increasingly on the manipulation of information. By drawing parallels with both cryptography and artificial intelligence, we can develop an understanding of the changes that are occurring in bioinformatics, and how these changes are likely to influence the bioinformatics job market.

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

ERIC Educational Resources Information Center

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'…

Component-Based Approach for Educating Students in Bioinformatics

ERIC Educational Resources Information Center

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…

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

ERIC Educational Resources Information Center

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…

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

ERIC Educational Resources Information Center

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.…

Computational biology and bioinformatics in Nigeria.

PubMed

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.

Computational Biology and Bioinformatics in Nigeria

PubMed Central

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

2014-01-01

Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in the biological data generated by the scientific community. The critical need to process and analyze such a deluge of data and turn it into useful knowledge has caused bioinformatics to gain prominence and importance. Bioinformatics is an interdisciplinary research area that applies techniques, methodologies, and tools in computer and information science to solve biological problems. In Nigeria, bioinformatics has recently played a vital role in the advancement of biological sciences. As a developing country, the importance of bioinformatics is rapidly gaining acceptance, and bioinformatics groups comprised of biologists, computer scientists, and computer engineers are being constituted at Nigerian universities and research institutes. In this article, we present an overview of bioinformatics education and research in Nigeria. We also discuss professional societies and academic and research institutions that play central roles in advancing the discipline in Nigeria. Finally, we propose strategies that can bolster bioinformatics education and support from policy makers in Nigeria, with potential positive implications for other developing countries. PMID:24763310

Preparing Refugees for Skilled Employment: Methods and Materials for Coordinated Instruction in Vocational Skills, English as a Second Language, Mathematics, Work Orientation and Independent Job Search.

ERIC Educational Resources Information Center

Jewish Employment and Vocational Service, Philadelphia, PA. Center for Career Services.

This manual serves as a guide for the evaluation, design, administration, and teaching of vocational training programs for limited-English-proficient (LEP) students, based on a coordinated vocational skills curriculum developed for refugee clients. The vocational focus of the program is woodworking and skilled assembly, but the principles of…

The Secret Agent Society Social Skills Program for Children with High-Functioning Autism Spectrum Disorders: A Comparison of Two School Variants

ERIC Educational Resources Information Center

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…

Washington State's Integrated Basic Education and Skills Training Program (I-BEST): New Evidence of Effectiveness. CCRC Working Paper No. 20

ERIC Educational Resources Information Center

Zeidenberg, Matthew; Cho, Sung-Woo; Jenkins, Davis

2010-01-01

To increase the rate at which adult basic skills students advance to and succeed in college-level occupational programs, the Washington State Board for Community and Technical Colleges (SBCTC) developed the Integrated Basic Education and Skills Training, or I-BEST. In the I-BEST model, a basic skills instructor and an occupational instructor team…

Returning nurses to the workforce: developing a fast track back program.

PubMed

Burns, Helen K; Sakraida, Teresa J; Englert, Nadine C; Hoffmann, Rosemary L; Tuite, Patricia; Foley, Susan M

2006-01-01

Fast Track Back: Re-entry into Nursing Practice program. Describes the development, implementation, and evaluation of a state-of-the-art re-entry program facilitating the return of licensed nonpracticing RNs to the workforce through a quality education program that retools them for the workforce in the areas of pharmacology, skill development using the latest technology, practice standards, and nursing issues. The program consists of didactic content taught via classroom, Internet, skills laboratory, and high fidelity human simulated technology and a clinical component. The program is a mechanism that enables re-entry nurses to improve skills and competencies necessary to practice in today's healthcare environment.

The effectiveness of a sex education program facilitating social skills for people with intellectual disability in Japan.

PubMed

Hayashi, Mayumi; Arakida, Mikako; Ohashi, Kazutomo

2011-03-01

Sex education should include social skills, such as those that allow individuals to relate, socialize, and communicate with others, to assist people with intellectual disability (ID) to live life fully in the community. We administered and investigated the effects of a program involving 8 interactive sex education sessions that were aimed at improving the social skills of people with ID. Participants were 17 people with ID and 17 control group participants in Japan. The evaluation was conducted with a questionnaire based on KiSS-18 (Kikuchi's Scale of Social Skills: 18 items; Kikuchi, 2007 ). The score of KiSS-18 in the experimental group was 55.4 ± 12.9 before the administration of the program, as compared to a mean of 61.8 ± 13.2 after the program. A significant increase was identified. There was no significant difference between the first and second average score in the control group. The sex education program involving social skills training for people with ID had significant effects.

To what extent are medical interviewing skills teachable?

PubMed

Kraan, H F; Crijnen, A A; de Vries, M W; Zuidweg, J; Imbos, T; Van der Vleuten, C P

1990-01-01

Growth patterns of medical interviewing skills during a 6-year undergraduate curriculum are assessed by studying 563 medical students taken from five year-groups, interviewing simulated patients. In a cross-sectional, quasi-experimental design their skills are rated by means of the Maastricht History-taking and Advice Checklist (MAAS), an observation instrument which measures five categories of interviewing skills pertaining to initial medical consultations. The findings suggest that the skills for 'history-taking', 'presenting solutions' and 'structuring of the interview' are effectively learned. These learning effects result from a continuous small group teaching program with expert and peer review of videotaped encounters with simulated patients. The teaching effects of this program seem less for the skills pertinent to the phase of 'exploring the reasons for encounter' and to the 'basic interviewing skills', because the students' growing medical knowledge and the increasing ability to solve medical problems exert a counteracting influence on the acquisition of these easily deteriorating skills. The results might be helpful to curriculum planners in order to make their programs for medical interviewing skills more effective.

Middlesex Community College Software Technical Writing Program.

ERIC Educational Resources Information Center

Middlesex Community Coll., Bedford, MA.

This document describes the Software Technical Writing Program at Middlesex Community College (Massachusetts). The program is a "hands-on" course designed to develop job-related skills in three major areas: technical writing, software, and professional skills. The program was originally designed in cooperation with the Massachusetts High…

Communication skills training on how to break bad news for Japanese nurses in oncology: effects of training on nurses' confidence and perceived effectiveness.

PubMed

Fukui, Sakiko; Ogawa, Keiko; Fukui, Naoshi

2010-03-01

Delivering bad news is an important communication skill for oncology nurses. No Asian study has developed a communication skills training program. We investigated the effect of such a program on the confidence and practical competence of Japanese oncology nurses. Thirty-one nurses participated, based on Western work in a 6-h workshop; the effect was assessed for 3 months. We evaluated the program effect by measuring nurse-rated confidence regarding communication with patients three times (before, immediately after, and 3 months after the program), in addition to interviewing them on the perception of the program at T3. On nurse-rated confidence in communication, 16/21 items were significantly increased 3 months after the program, and almost all nurses were positive about the course effectiveness. Communication skills training increased Japanese nurses' confidence as well as being perceived as effective.

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

ERIC Educational Resources Information Center

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…

Outdoor Leadership Skills: A Program Perspective

ERIC Educational Resources Information Center

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…

Illinois Occupational Skill Standards: Chemical Process Technical Operators.

ERIC Educational Resources Information Center

Illinois Occupational Skill Standards and Credentialing Council, Carbondale.

This document, which is intended for workforce preparation program providers, details the Illinois Occupational Skill Standards for programs preparing students for employment as chemical process technical operators. The document begins with a brief overview of the Illinois perspective on occupational skill standards and credentialing, the process…

Illinois Occupational Skill Standards: Automotive Technician Cluster.

ERIC Educational Resources Information Center

Illinois Occupational Skill Standards and Credentialing Council, Carbondale.

This document, which is intended as a guide for work force preparation program providers, details the Illinois occupational skill standards for programs preparing students for employment in occupations in the automotive technician cluster. The document begins with overviews of the Illinois perspective on occupational skill standards and…

Illinois Occupational Skill Standards. Meeting Professional Cluster.

ERIC Educational Resources Information Center

Illinois Occupational Skill Standards and Credentialing Council, Carbondale.

This document, which is intended as a guide for workforce preparation program providers, details the Illinois occupational skill standards for programs preparing students for employment in the meeting professional occupational cluster. It begins with a brief overview of the Illinois perspective on occupational skill standards and credentialing,…

Illinois Occupational Skill Standards. Beef Production Cluster.

ERIC Educational Resources Information Center

Illinois Occupational Skill Standards and Credentialing Council, Carbondale.

This document, which is intended as a guide for workforce preparation program providers, details the Illinois occupational skill standards for programs preparing students for employment in occupations in the beef production cluster. The document begins with a brief overview of the Illinois perspective on occupational skill standards and…

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

PubMed

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.

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

PubMed

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.

ReGaTE: Registration of Galaxy Tools in Elixir.

PubMed

Doppelt-Azeroual, Olivia; Mareuil, Fabien; Deveaud, Eric; Kalaš, Matúš; Soranzo, Nicola; van den Beek, Marius; Grüning, Björn; Ison, Jon; Ménager, Hervé

2017-06-01

Bioinformaticians routinely use multiple software tools and data sources in their day-to-day work and have been guided in their choices by a number of cataloguing initiatives. The ELIXIR Tools and Data Services Registry (bio.tools) aims to provide a central information point, independent of any specific scientific scope within bioinformatics or technological implementation. Meanwhile, efforts to integrate bioinformatics software in workbench and workflow environments have accelerated to enable the design, automation, and reproducibility of bioinformatics experiments. One such popular environment is the Galaxy framework, with currently more than 80 publicly available Galaxy servers around the world. In the context of a generic registry for bioinformatics software, such as bio.tools, Galaxy instances constitute a major source of valuable content. Yet there has been, to date, no convenient mechanism to register such services en masse. We present ReGaTE (Registration of Galaxy Tools in Elixir), a software utility that automates the process of registering the services available in a Galaxy instance. This utility uses the BioBlend application program interface to extract service metadata from a Galaxy server, enhance the metadata with the scientific information required by bio.tools, and push it to the registry. ReGaTE provides a fast and convenient way to publish Galaxy services in bio.tools. By doing so, service providers may increase the visibility of their services while enriching the software discovery function that bio.tools provides for its users. The source code of ReGaTE is freely available on Github at https://github.com/C3BI-pasteur-fr/ReGaTE . © The Author 2017. Published by Oxford University Press.

Training oncology and palliative care clinical nurse specialists in psychological skills: evaluation of a pilot study.

PubMed

Clark, Jane E; Aitken, Susan; Watson, Nina; McVey, Joanne; Helbert, Jan; Wraith, Anita; Taylor, Vanessa; Catesby, Sarah

2015-06-01

National guidelines in the United Kingdom recommend training Clinical Nurse Specialists in psychological skills to improve the assessment and intervention with psychological problems experienced by people with a cancer diagnosis (National Institute for Health and Clinical Excellence, 2004). This pilot study evaluated a three-day training program combined with supervision sessions from Clinical Psychologists that focused on developing skills in psychological assessment and intervention for common problems experienced by people with cancer. Questionnaires were developed to measure participants' levels of confidence in 15 competencies of psychological skills. Participants completed these prior to the program and on completion of the program. Summative evaluation was undertaken and results were compared. In addition, a focus group interview provided qualitative data of participants' experiences of the structure, process, and outcomes of the program. Following the program, participants rated their confidence in psychological assessment and skills associated with providing psychological support as having increased in all areas. This included improved knowledge of psychological theories, skills in assessment and intervention and accessing and using supervision appropriately. The largest increase was in providing psycho-education to support the coping strategies of patients and carers. Thematic analysis of interview data identified two main themes including learning experiences and program enhancements. The significance of the clinical supervision sessions as key learning opportunities, achieved through the development of a community of practice, emerged. Although this pilot study has limitations, the results suggest that a combined teaching and supervision program is effective in improving Clinical Nurse Specialists' confidence level in specific psychological skills. Participants' experiences highlighted suggestions for refinement and development of the program. Opportunities for further research and developments in this area are discussed.

Cook It Up! A community-based cooking program for at-risk youth: overview of a food literacy intervention.

PubMed

Thomas, Heather Mc; Irwin, Jennifer D

2011-11-15

In Canada, there are limited occasions for youth, and especially at-risk youth, to participate in cooking programs. The paucity of these programs creates an opportunity for youth-focused cooking programs to be developed, implemented, and evaluated with the goal of providing invaluable life skills and food literacy to this potentially vulnerable group. Thus, an 18-month community-based cooking program for at-risk youth was planned and implemented to improve the development and progression of cooking skills and food literacy. This paper provides an overview of the rationale for and implementation of a cooking skills intervention for at-risk youth. The manuscript provides information about the process of planning and implementing the intervention as well as the evaluation plan. Results of the intervention will be presented elsewhere. Objectives of the intervention included the provision of applied food literacy and cooking skills education taught by local chefs and a Registered Dietitian, and augmented with fieldtrips to community farms to foster an appreciation and understanding of food, from 'gate to plate'. Eight at-risk youth (five girls and three boys, mean age = 14.6) completed the intervention as of November 2010. Pre-test cooking skills assessments were completed for all participants and post-test cooking skills assessments were completed for five of eight participants. Post intervention, five of eight participants completed in-depth interviews about their experience. The Cook It Up! program can provide an effective template for other agencies and researchers to utilize for enhancing existing programs or to create new applied cooking programs for relevant vulnerable populations. There is also a continued need for applied research in this area to reverse the erosion of cooking skills in Canadian society.

Cook It Up! A community-based cooking program for at-risk youth: overview of a food literacy intervention

PubMed Central

2011-01-01

Background In Canada, there are limited occasions for youth, and especially at-risk youth, to participate in cooking programs. The paucity of these programs creates an opportunity for youth-focused cooking programs to be developed, implemented, and evaluated with the goal of providing invaluable life skills and food literacy to this potentially vulnerable group. Thus, an 18-month community-based cooking program for at-risk youth was planned and implemented to improve the development and progression of cooking skills and food literacy. Findings This paper provides an overview of the rationale for and implementation of a cooking skills intervention for at-risk youth. The manuscript provides information about the process of planning and implementing the intervention as well as the evaluation plan. Results of the intervention will be presented elsewhere. Objectives of the intervention included the provision of applied food literacy and cooking skills education taught by local chefs and a Registered Dietitian, and augmented with fieldtrips to community farms to foster an appreciation and understanding of food, from 'gate to plate'. Eight at-risk youth (five girls and three boys, mean age = 14.6) completed the intervention as of November 2010. Pre-test cooking skills assessments were completed for all participants and post-test cooking skills assessments were completed for five of eight participants. Post intervention, five of eight participants completed in-depth interviews about their experience. Discussion The Cook It Up! program can provide an effective template for other agencies and researchers to utilize for enhancing existing programs or to create new applied cooking programs for relevant vulnerable populations. There is also a continued need for applied research in this area to reverse the erosion of cooking skills in Canadian society. PMID:22085523

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

PubMed

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 program conditions and context, creating opportunities for choice and new experiences, and adopting a facilitating and enabling role (coaching and capitalizing on teachable moments).

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

PubMed

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 < 0.001) and by 23.44% in non-randomized studies (95% CI, 13.98%-32.90%; P < 0.001). Few adverse events occurred during training; however, compared with a control group, evidence was insufficient to support the effectiveness of powered wheelchair 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.

Study of a Nongraded Supplementary Group Communication Skills Program: Rationale, Pupil Personal-Social Characteristics, and Program Effects.

ERIC Educational Resources Information Center

Stumpe, Doris M.

The purposes of this study were to design an experimental communications skills improvement program for low-achieving middle-grade pupils, to investigate certain assumed pupil personal-social characteristics on which the program was based, and to assess the effectiveness of the program. Two basic features incorporated into the new program were (1)…

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

PubMed

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

2012-01-01

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. 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. 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%). 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 year of residency training or later. Gathering data from residency program directors provides support for developing new assessment tools in high-stakes licensing examinations.

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

PubMed Central

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 year of residency training or later. Conclusions Gathering data from residency program directors provides support for developing new assessment tools in high-stakes licensing examinations. PMID:22833698

Versatile and declarative dynamic programming using pair algebras.

PubMed

Steffen, Peter; Giegerich, Robert

2005-09-12

Dynamic programming is a widely used programming technique in bioinformatics. In sharp contrast to the simplicity of textbook examples, implementing a dynamic programming algorithm for a novel and non-trivial application is a tedious and error prone task. The algebraic dynamic programming approach seeks to alleviate this situation by clearly separating the dynamic programming recurrences and scoring schemes. Based on this programming style, we introduce a generic product operation of scoring schemes. This leads to a remarkable variety of applications, allowing us to achieve optimizations under multiple objective functions, alternative solutions and backtracing, holistic search space analysis, ambiguity checking, and more, without additional programming effort. We demonstrate the method on several applications for RNA secondary structure prediction. The product operation as introduced here adds a significant amount of flexibility to dynamic programming. It provides a versatile testbed for the development of new algorithmic ideas, which can immediately be put to practice.

Increasing team skills: an evaluation of program effectiveness.

PubMed

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.

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

PubMed Central

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

2017-01-01

Background 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. Objective 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. Methods 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. Results 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. The mean number of interactive program activities that participants engaged in was 15.5 (SD 13.3) out of a total of 39 possible activities. Follow-up assessments were completed by 436 of the 877 (49.7%) participants. GEE analyses revealed decreased perceived stress (odds ratio, OR=0.93; 95% CI 0.87-0.99; P=.03) and increases in several life skills addressed between baseline and the follow-up assessment. The proportion of adolescents with at-risk alcohol use declined from 20.2% at baseline to 15.5% at follow-up (OR 0.70, 95% CI 0.53-0.93; P=.01), whereas no significant changes were obtained for tobacco (OR 0.94, 95% CI 0.65-1.36; P=.76) or cannabis use (OR 0.91, 95% CI 0.67-1.24; P=.54). Conclusions These results reveal high-level acceptance and promising effectiveness of this interventional approach, which could be easily and economically implemented. A reasonable next step would be to test the efficacy of this program within a controlled trial. PMID:28978498

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.

PubMed

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. The mean number of interactive program activities that participants engaged in was 15.5 (SD 13.3) out of a total of 39 possible activities. Follow-up assessments were completed by 436 of the 877 (49.7%) participants. GEE analyses revealed decreased perceived stress (odds ratio, OR=0.93; 95% CI 0.87-0.99; P=.03) and increases in several life skills addressed between baseline and the follow-up assessment. The proportion of adolescents with at-risk alcohol use declined from 20.2% at baseline to 15.5% at follow-up (OR 0.70, 95% CI 0.53-0.93; P=.01), whereas no significant changes were obtained for tobacco (OR 0.94, 95% CI 0.65-1.36; P=.76) or cannabis use (OR 0.91, 95% CI 0.67-1.24; P=.54). These results reveal high-level acceptance and promising effectiveness of this interventional approach, which could be easily and economically implemented. A reasonable next step would be to test the efficacy of this program within a controlled trial. ©Severin Haug, Raquel Paz Castro, Christian Meyer, Andreas Filler, Tobias Kowatsch, Michael P Schaub. Originally published in JMIR Mhealth and Uhealth (http://mhealth.jmir.org), 04.10.2017.

The 2017 Bioinformatics Open Source Conference (BOSC)

PubMed Central

Harris, Nomi L.; Cock, Peter J.A.; Chapman, Brad; Fields, Christopher J.; Hokamp, Karsten; Lapp, Hilmar; Munoz-Torres, Monica; Tzovaras, Bastian Greshake; Wiencko, Heather

2017-01-01

The Bioinformatics Open Source Conference (BOSC) is a 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. The 18th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2017) took place in Prague, Czech Republic in July 2017. The conference brought together nearly 250 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, open and reproducible science, and this year’s theme, open data. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community, called the OBF Codefest. PMID:29118973

The 2017 Bioinformatics Open Source Conference (BOSC).

PubMed

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

2017-01-01

The Bioinformatics Open Source Conference (BOSC) is a 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. The 18th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2017) took place in Prague, Czech Republic in July 2017. The conference brought together nearly 250 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, open and reproducible science, and this year's theme, open data. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community, called the OBF Codefest.