Incorporating a Collaborative Web-Based Virtual Laboratory in an Undergraduate Bioinformatics Course

Science.gov (United States)

Weisman, David

2010-01-01

Face-to-face bioinformatics courses commonly include a weekly, in-person computer lab to facilitate active learning, reinforce conceptual material, and teach practical skills. Similarly, fully-online bioinformatics courses employ hands-on exercises to achieve these outcomes, although students typically perform this work offsite. Combining a…

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

Science.gov (United States)

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

2017-01-01

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

Progress and challenges in bioinformatics approaches for enhancer identification

KAUST Repository

Kleftogiannis, Dimitrios A.

2017-02-03

Enhancers are cis-acting DNA elements that play critical roles in distal regulation of gene expression. Identifying enhancers is an important step for understanding distinct gene expression programs that may reflect normal and pathogenic cellular conditions. Experimental identification of enhancers is constrained by the set of conditions used in the experiment. This requires multiple experiments to identify enhancers, as they can be active under specific cellular conditions but not in different cell types/tissues or cellular states. This has opened prospects for computational prediction methods that can be used for high-throughput identification of putative enhancers to complement experimental approaches. Potential functions and properties of predicted enhancers have been catalogued and summarized in several enhancer-oriented databases. Because the current methods for the computational prediction of enhancers produce significantly different enhancer predictions, it will be beneficial for the research community to have an overview of the strategies and solutions developed in this field. In this review, we focus on the identification and analysis of enhancers by bioinformatics approaches. First, we describe a general framework for computational identification of enhancers, present relevant data types and discuss possible computational solutions. Next, we cover over 30 existing computational enhancer identification methods that were developed since 2000. Our review highlights advantages, limitations and potentials, while suggesting pragmatic guidelines for development of more efficient computational enhancer prediction methods. Finally, we discuss challenges and open problems of this topic, which require further consideration.

Progress and challenges in bioinformatics approaches for enhancer identification

KAUST Repository

Kleftogiannis, Dimitrios A.; Kalnis, Panos; Bajic, Vladimir B.

2017-01-01

Enhancers are cis-acting DNA elements that play critical roles in distal regulation of gene expression. Identifying enhancers is an important step for understanding distinct gene expression programs that may reflect normal and pathogenic cellular conditions. Experimental identification of enhancers is constrained by the set of conditions used in the experiment. This requires multiple experiments to identify enhancers, as they can be active under specific cellular conditions but not in different cell types/tissues or cellular states. This has opened prospects for computational prediction methods that can be used for high-throughput identification of putative enhancers to complement experimental approaches. Potential functions and properties of predicted enhancers have been catalogued and summarized in several enhancer-oriented databases. Because the current methods for the computational prediction of enhancers produce significantly different enhancer predictions, it will be beneficial for the research community to have an overview of the strategies and solutions developed in this field. In this review, we focus on the identification and analysis of enhancers by bioinformatics approaches. First, we describe a general framework for computational identification of enhancers, present relevant data types and discuss possible computational solutions. Next, we cover over 30 existing computational enhancer identification methods that were developed since 2000. Our review highlights advantages, limitations and potentials, while suggesting pragmatic guidelines for development of more efficient computational enhancer prediction methods. Finally, we discuss challenges and open problems of this topic, which require further consideration.

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

Science.gov (United States)

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

2017-01-01

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

Fundamentals of bioinformatics and computational biology methods and exercises in matlab

CERN Document Server

Singh, Gautam B

2015-01-01

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

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

Science.gov (United States)

Sutcliffe, Iain C.; Cummings, Stephen P.

2007-01-01

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

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

Directory of Open Access Journals (Sweden)

Barbara J. May

2013-02-01

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

Undergraduate Students' Opinions with Regard to Ubiquitous MOOC for Enhancing Cross-Cultural Competence

Science.gov (United States)

Plangsorn, Boonrat; Na-Songkhla, Jaitip; Luetkehans, Lara M.

2016-01-01

The purpose of this study was to study undergraduate students' opinions with regard to the ubiquitous massive open online course (MOOC) for enhancing cross-cultural competence. This descriptive research applied a survey method. The survey data were collected by using survey questionnaires and online questionnaires from 410 undergraduate students…

MACBenAbim: A Multi-platform Mobile Application for searching keyterms in Computational Biology and Bioinformatics.

Science.gov (United States)

Oluwagbemi, Olugbenga O; Adewumi, Adewole; Esuruoso, Abimbola

2012-01-01

Computational biology and bioinformatics are gradually gaining grounds in Africa and other developing nations of the world. However, in these countries, some of the challenges of computational biology and bioinformatics education are inadequate infrastructures, and lack of readily-available complementary and motivational tools to support learning as well as research. This has lowered the morale of many promising undergraduates, postgraduates and researchers from aspiring to undertake future study in these fields. In this paper, we developed and described MACBenAbim (Multi-platform Mobile Application for Computational Biology and Bioinformatics), a flexible user-friendly tool to search for, define and describe the meanings of keyterms in computational biology and bioinformatics, thus expanding the frontiers of knowledge of the users. This tool also has the capability of achieving visualization of results on a mobile multi-platform context. MACBenAbim is available from the authors for non-commercial purposes.

The GMOD Drupal bioinformatic server framework.

Science.gov (United States)

Papanicolaou, Alexie; Heckel, David G

2010-12-15

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

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

Science.gov (United States)

Brown, James A. L.

2016-01-01

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

The GMOD Drupal Bioinformatic Server Framework

Science.gov (United States)

Papanicolaou, Alexie; Heckel, David G.

2010-01-01

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

Best practices in bioinformatics training for life scientists

DEFF Research Database (Denmark)

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

2013-01-01

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

Anticipation of Personal Genomics Data Enhances Interest and Learning Environment in Genomics and Molecular Biology Undergraduate Courses.

Science.gov (United States)

Weber, K Scott; Jensen, Jamie L; Johnson, Steven M

2015-01-01

An important discussion at colleges is centered on determining more effective models for teaching undergraduates. As personalized genomics has become more common, we hypothesized it could be a valuable tool to make science education more hands on, personal, and engaging for college undergraduates. We hypothesized that providing students with personal genome testing kits would enhance the learning experience of students in two undergraduate courses at Brigham Young University: Advanced Molecular Biology and Genomics. These courses have an emphasis on personal genomics the last two weeks of the semester. Students taking these courses were given the option to receive personal genomics kits in 2014, whereas in 2015 they were not. Students sent their personal genomics samples in on their own and received the data after the course ended. We surveyed students in these courses before and after the two-week emphasis on personal genomics to collect data on whether anticipation of obtaining their own personal genomic data impacted undergraduate student learning. We also tested to see if specific personal genomic assignments improved the learning experience by analyzing the data from the undergraduate students who completed both the pre- and post-course surveys. Anticipation of personal genomic data significantly enhanced student interest and the learning environment based on the time students spent researching personal genomic material and their self-reported attitudes compared to those who did not anticipate getting their own data. Personal genomics homework assignments significantly enhanced the undergraduate student interest and learning based on the same criteria and a personal genomics quiz. We found that for the undergraduate students in both molecular biology and genomics courses, incorporation of personal genomic testing can be an effective educational tool in undergraduate science education.

Need Assessment of Enhancing the Weightage of Applied Biochemistry in the Undergraduate Curriculum at MGIMS, Sevagram

Science.gov (United States)

Kumar, Satish; Jena, Lingaraja; Vagha, Jayant

2016-01-01

In order to review the need assessment of enhancing the weightage of Applied Biochemistry in the undergraduate curriculum at Mahatma Gandhi Institute of Medical Sciences (MGIMS), Sevagram, a validated questionnaire was sent to 453 participants which include 387 undergraduate students, 11 interns, 23 postgraduate students, and 32 faculty members. A…

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

Science.gov (United States)

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

2013-09-01

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

Enhancing the Communication and Speaking Skills of Mathematics Undergraduates

OpenAIRE

Groves, James

2012-01-01

In June 2011, the University of Lancaster delivered a substantially-enhanced course in Communication and Presentation Skills to 108 second-year undergraduate mathematicians. The course was delivered jointly by staff in the Department of Mathematics and Statistics and CETAD, the Centre for Training and Development at Lancaster. Funding for the course and its increased staffing requirement came from an MSOR HE Curriculum Innovation Fund grant of £5,000. CETAD is a specialist unit which focuses ...

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

Science.gov (United States)

Lawlor, Brendan; Walsh, Paul

2015-01-01

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

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

Science.gov (United States)

Lawlor, Brendan; Walsh, Paul

2015-01-01

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

An entrepreneurial training model to enhance undergraduate training in biomedical research.

Science.gov (United States)

Kamangar, Farin; Silver, Gillian; Hohmann, Christine; Hughes-Darden, Cleo; Turner-Musa, Jocelyn; Haines, Robert Trent; Jackson, Avis; Aguila, Nelson; Sheikhattari, Payam

2017-01-01

Undergraduate students who are interested in biomedical research typically work on a faculty member's research project, conduct one distinct task (e.g., running gels), and, step by step, enhance their skills. This "apprenticeship" model has been helpful in training many distinguished scientists over the years, but it has several potential drawbacks. For example, the students have limited autonomy, and may not understand the big picture, which may result in students giving up on their goals for a research career. Also, the model is costly and may greatly depend on a single mentor. The NIH Building Infrastructure Leading to Diversity (BUILD) Initiative has been established to fund innovative undergraduate research training programs and support institutional and faculty development of the recipient university. The training model at Morgan State University (MSU), namely " A S tudent- C entered En trepreneurship D evelopment training model" (ASCEND), is one of the 10 NIH BUILD-funded programs, and offers a novel, experimental "entrepreneurial" training approach. In the ASCEND training model, the students take the lead. They own the research, understand the big picture, and experience the entire scope of the research process, which we hypothesize will lead to a greater sense of self-efficacy and research competency, as well as an enhanced sense of science identity. They are also immersed in environments with substantial peer support, where they can exchange research ideas and share experiences. This is important for underrepresented minority students who might have fewer role models and less peer support in conducting research. In this article, we describe the MSU ASCEND entrepreneurial training model's components, rationale, and history, and how it may enhance undergraduate training in biomedical research that may be of benefit to other institutions. We also discuss evaluation methods, possible sustainability solutions, and programmatic challenges that can affect all

A bioinformatics potpourri.

Science.gov (United States)

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

2018-01-19

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

Detection of the "cp4 epsps" Gene in Maize Line NK603 and Comparison of Related Protein Structures: An Advanced Undergraduate Experiment

Science.gov (United States)

Swope, Nicole K.; Fryfogle, Patrick J.; Sivy, Tami L.

2015-01-01

A flexible, rigorous laboratory experiment for upper-level biochemistry undergraduates is described that focuses on the Roundup Ready maize line. The work is appropriate for undergraduate laboratory courses that integrate biochemistry, molecular biology, or bioinformatics. In this experiment, DNA is extracted and purified from maize kernel and…

Data mining for bioinformatics applications

CERN Document Server

Zengyou, He

2015-01-01

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

Course-based undergraduate research experiences in molecular biosciences-patterns, trends, and faculty support.

Science.gov (United States)

Wang, Jack T H

2017-08-15

Inquiry-driven learning, research internships and course-based undergraduate research experiences all represent mechanisms through which educators can engage undergraduate students in scientific research. In life sciences education, the benefits of undergraduate research have been thoroughly evaluated, but limitations in infrastructure and training can prevent widespread uptake of these practices. It is not clear how faculty members can integrate complex laboratory techniques and equipment into their unique context, while finding the time and resources to implement undergraduate research according to best practice guidelines. This review will go through the trends and patterns in inquiry-based undergraduate life science projects with particular emphasis on molecular biosciences-the research-aligned disciplines of biochemistry, molecular cell biology, microbiology, and genomics and bioinformatics. This will provide instructors with an overview of the model organisms, laboratory techniques and research questions that are adaptable for semester-long projects, and serve as starting guidelines for course-based undergraduate research. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

Science.gov (United States)

Grunwald, Sandra K.; Krueger, Katherine J.

2008-01-01

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

Teaching Synthetic Biology, Bioinformatics and Engineering to Undergraduates: The Interdisciplinary Build-a-Genome Course

Science.gov (United States)

Dymond, Jessica S.; Scheifele, Lisa Z.; Richardson, Sarah; Lee, Pablo; Chandrasegaran, Srinivasan; Bader, Joel S.; Boeke, Jef D.

2009-01-01

A major challenge in undergraduate life science curricula is the continual evaluation and development of courses that reflect the constantly shifting face of contemporary biological research. Synthetic biology offers an excellent framework within which students may participate in cutting-edge interdisciplinary research and is therefore an attractive addition to the undergraduate biology curriculum. This new discipline offers the promise of a deeper understanding of gene function, gene order, and chromosome structure through the de novo synthesis of genetic information, much as synthetic approaches informed organic chemistry. While considerable progress has been achieved in the synthesis of entire viral and prokaryotic genomes, fabrication of eukaryotic genomes requires synthesis on a scale that is orders of magnitude higher. These high-throughput but labor-intensive projects serve as an ideal way to introduce undergraduates to hands-on synthetic biology research. We are pursuing synthesis of Saccharomyces cerevisiae chromosomes in an undergraduate laboratory setting, the Build-a-Genome course, thereby exposing students to the engineering of biology on a genomewide scale while focusing on a limited region of the genome. A synthetic chromosome III sequence was designed, ordered from commercial suppliers in the form of oligonucleotides, and subsequently assembled by students into ∼750-bp fragments. Once trained in assembly of such DNA “building blocks” by PCR, the students accomplish high-yield gene synthesis, becoming not only technically proficient but also constructively critical and capable of adapting their protocols as independent researchers. Regular “lab meeting” sessions help prepare them for future roles in laboratory science. PMID:19015540

Deep learning in bioinformatics.

Science.gov (United States)

Min, Seonwoo; Lee, Byunghan; Yoon, Sungroh

2017-09-01

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

Enhancing an Undergraduate Business Statistics Course: Linking Teaching and Learning with Assessment Issues

Science.gov (United States)

Fairfield-Sonn, James W.; Kolluri, Bharat; Rogers, Annette; Singamsetti, Rao

2009-01-01

This paper examines several ways in which teaching effectiveness and student learning in an undergraduate Business Statistics course can be enhanced. First, we review some key concepts in Business Statistics that are often challenging to teach and show how using real data sets assist students in developing deeper understanding of the concepts.…

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

Directory of Open Access Journals (Sweden)

Joanna R. Klein

2012-09-01

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

A Data-enhanced On-line Learning Environment for Undergraduate Earth System Science Education

Science.gov (United States)

di, L.; Deng, M.

2004-12-01

Earth system science (ESS) research often requires integrating, analyzing, and modeling with large amount of multi-disciplinary, multi-source geospatial data. Satellite remote sensing is one of the major sources of such data. Currently, NASA EOSDIS has archived more than three petabytes of Earth remote sensing data. Those data are essential for conducting ESS research. Therefore, training students on how to effectively use large amount of remote sensing data in ESS research is the essential part of their ESS education. However, currently most of undergraduate students have never been trained to handle the huge volume of available data because of lack of resources and suitable teaching technology at ESS colleges. In order to reduce this problem, we are developing a web-based geospatial information system, called GeoBrain, for providing a data-enhanced on-line learning and research environment for ESS education and research. The system makes petabytes of NASA EOS data and information easily accessible to higher-education users. The system allows users to dynamically and collaboratively develop interoperable, web-executable geospatial process and analysis modules and models, and run them on-line against any part of the peta-byte archives for getting back the customized information products rather than raw data. The system makes a data-enhanced ESS learning and research environment, backed by petabytes of NASA EOS data and unavailable to students and professors before, available to them at their desktops. In order to integrate this new learning environment into the undergraduate ESS teaching and research, a NASA EOS Higher Education Alliance (NEHEA), consisting of the GeoBrain development team led by GMU and a group of Earth science educators selected from an open RFP process, has been formed. NEHEA members are incorporating the data enhanced learning environment into their teaching and on-going research and will develop new courses for taking advantages of the

Bringing Web 2.0 to bioinformatics.

Science.gov (United States)

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

2009-01-01

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

How Can Mobile SMS Communication Support and Enhance a First Year Undergraduate Learning Environment?

Science.gov (United States)

Jones, Geraldine; Edwards, Gabriele; Reid, Alan

2009-01-01

In this paper we discuss a case study investigating how the academic and personal development of first year students on an undergraduate sports education degree can be supported and enhanced with mobile SMS (Short Message Service) communication. SMS-based technologies were introduced in response to students' particular needs (in transition to…

Emerging strengths in Asia Pacific bioinformatics.

Science.gov (United States)

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

2008-12-12

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

Best practices in bioinformatics training for life scientists.

KAUST Repository

Via, Allegra

2013-06-25

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

Biggest challenges in bioinformatics.

Science.gov (United States)

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

2013-04-01

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

Biggest challenges in bioinformatics

OpenAIRE

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

2013-01-01

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

Establishing bioinformatics research in the Asia Pacific

Directory of Open Access Journals (Sweden)

Tammi Martti

2006-12-01

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

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

Science.gov (United States)

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

2017-11-27

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

Severe Weather Field Experience: An Undergraduate Field Course on Career Enhancement and Severe Convective Storms

Science.gov (United States)

Godfrey, Christopher M.; Barrett, Bradford S.; Godfrey, Elaine S.

2011-01-01

Undergraduate students acquire a deeper understanding of scientific principles through first-hand experience. To enhance the learning environment for atmospheric science majors, the University of North Carolina at Asheville has developed the severe weather field experience. Participants travel to Tornado Alley in the Great Plains to forecast and…

Preface to Introduction to Structural Bioinformatics

NARCIS (Netherlands)

Feenstra, K. Anton; Abeln, Sanne

2018-01-01

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

COMPARISON OF POPULAR BIOINFORMATICS DATABASES

OpenAIRE

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

2016-01-01

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

Computational biology and bioinformatics in Nigeria.

Science.gov (United States)

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

2014-04-01

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

Computational biology and bioinformatics in Nigeria.

Directory of Open Access Journals (Sweden)

Segun A Fatumo

2014-04-01

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

Establishing bioinformatics research in the Asia Pacific

OpenAIRE

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

2006-01-01

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

Peer Learning and Support of Technology in an Undergraduate Biology Course to Enhance Deep Learning

Science.gov (United States)

Tsaushu, Masha; Tal, Tali; Sagy, Ornit; Kali, Yael; Gepstein, Shimon; Zilberstein, Dan

2012-01-01

This study offers an innovative and sustainable instructional model for an introductory undergraduate course. The model was gradually implemented during 3 yr in a research university in a large-lecture biology course that enrolled biology majors and nonmajors. It gives priority to sources not used enough to enhance active learning in higher…

Generalized Centroid Estimators in Bioinformatics

Science.gov (United States)

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

2011-01-01

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

Introduction to bioinformatics.

Science.gov (United States)

Can, Tolga

2014-01-01

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

Bioinformatics clouds for big data manipulation.

Science.gov (United States)

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

2012-11-28

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

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

Science.gov (United States)

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

2016-12-22

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

Designing XML schemas for bioinformatics.

Science.gov (United States)

Bruhn, Russel Elton; Burton, Philip John

2003-06-01

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

Bioinformatics

DEFF Research Database (Denmark)

Baldi, Pierre; Brunak, Søren

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

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

Science.gov (United States)

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

2016-01-01

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

Bioinformatics clouds for big data manipulation

Directory of Open Access Journals (Sweden)

Dai Lin

2012-11-01

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

Bioinformatics clouds for big data manipulation

KAUST Repository

Dai, Lin

2012-11-28

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

Undergraduate Biocuration: Developing Tomorrow's Researchers While Mining Today's Data.

Science.gov (United States)

Mitchell, Cassie S; Cates, Ashlyn; Kim, Renaid B; Hollinger, Sabrina K

2015-01-01

Biocuration is a time-intensive process that involves extraction, transcription, and organization of biological or clinical data from disjointed data sets into a user-friendly database. Curated data is subsequently used primarily for text mining or informatics analysis (bioinformatics, neuroinformatics, health informatics, etc.) and secondarily as a researcher resource. Biocuration is traditionally considered a Ph.D. level task, but a massive shortage of curators to consolidate the ever-mounting biomedical "big data" opens the possibility of utilizing biocuration as a means to mine today's data while teaching students skill sets they can utilize in any career. By developing a biocuration assembly line of simplified and compartmentalized tasks, we have enabled biocuration to be effectively performed by a hierarchy of undergraduate students. We summarize the necessary physical resources, process for establishing a data path, biocuration workflow, and undergraduate hierarchy of curation, technical, information technology (IT), quality control and managerial positions. We detail the undergraduate application and training processes and give detailed job descriptions for each position on the assembly line. We present case studies of neuropathology curation performed entirely by undergraduates, namely the construction of experimental databases of Amyotrophic Lateral Sclerosis (ALS) transgenic mouse models and clinical data from ALS patient records. Our results reveal undergraduate biocuration is scalable for a group of 8-50+ with relatively minimal required resources. Moreover, with average accuracy rates greater than 98.8%, undergraduate biocurators are equivalently accurate to their professional counterparts. Initial training to be completely proficient at the entry-level takes about five weeks with a minimal student time commitment of four hours/week.

Interdisciplinary Introductory Course in Bioinformatics

Science.gov (United States)

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

2010-01-01

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

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

Science.gov (United States)

Campbell, Chad E.; Nehm, Ross H.

2013-01-01

The growing importance of genomics and bioinformatics methods and paradigms in biology has been accompanied by an explosion of new curricula and pedagogies. An important question to ask about these educational innovations is whether they are having a meaningful impact on students’ knowledge, attitudes, or skills. Although assessments are necessary tools for answering this question, their outputs are dependent on their quality. Our study 1) reviews the central importance of reliability and construct validity evidence in the development and evaluation of science assessments and 2) examines the extent to which published assessments in genomics and bioinformatics education (GBE) have been developed using such evidence. We identified 95 GBE articles (out of 226) that contained claims of knowledge increases, affective changes, or skill acquisition. We found that 1) the purpose of most of these studies was to assess summative learning gains associated with curricular change at the undergraduate level, and 2) a minority (<10%) of studies provided any reliability or validity evidence, and only one study out of the 95 sampled mentioned both validity and reliability. Our findings raise concerns about the quality of evidence derived from these instruments. We end with recommendations for improving assessment quality in GBE. PMID:24006400

Undergraduate courses for enhancing design ability in naval architecture

Directory of Open Access Journals (Sweden)

Kyu-Yeul Lee

2013-09-01

Full Text Available Contemporary lectures in undergraduate engineering courses typically focus on teaching major technical knowledge-based theories in a limited time. Therefore, most lectures do not allow the students to gain understanding of how the theories are applied, especially in Naval Architecture and Ocean Engineering departments. Shipyards require students to acquire practical ship design skills in undergraduate courses. To meet this requirement, two lectures are organized by the authors; namely, “Planning Procedure of Naval Architecture & Ocean Engineering” (PNAOE and “Innovative Ship Design” (ISD. The concept of project-based and collaborative learning is applied in these two lectures. In the PNAOE lecture, sophomores receive instruction in the designing and building of model ships, and the students' work is evaluated in a model ship contest. This curriculum enables students to understand the concepts of ship design and production. In the ISD lecture, seniors learn how to develop their creative ideas about ship design and communicate with members of group. They are encouraged to cooperate with others and understand the ship design process. In the capstone design course, students receive guidance to facilitate understanding of how the knowledge from their sophomore or junior classes, such as fluid mechanics, statics, and dynamics, can be applied to practical ship design. Students are also encouraged to compete in the ship design contest organized by the Society of Naval Architects of Korea. Moreover, the effectiveness of project-based and collaborative learning for enhancing interest in the shipbuilding Industry and understanding the ship design process is demonstrated by citing the PNAOE and ISD lectures as examples.

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

Science.gov (United States)

Brazas, Michelle D; Ouellette, B F Francis

2013-09-01

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

Taking Bioinformatics to Systems Medicine.

Science.gov (United States)

van Kampen, Antoine H C; Moerland, Perry D

2016-01-01

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

Crowdsourcing for bioinformatics.

Science.gov (United States)

Good, Benjamin M; Su, Andrew I

2013-08-15

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

The Development and Validation of a Rubric to Enhance Performer Feedback for Undergraduate Vocal Solo Performance

Science.gov (United States)

Herrell, Katherine A.

2014-01-01

This is a study of the development and validation of a rubric to enhance performer feedback for undergraduate vocal solo performance. In the literature, assessment of vocal performance is under-represented, and the value of feedback from the assessment of musical performances, from the point of view of the performer, is nonexistent. The research…

Rising Strengths Hong Kong SAR in Bioinformatics.

Science.gov (United States)

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

2017-06-01

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

EURASIP journal on bioinformatics & systems biology

National Research Council Canada - National Science Library

2006-01-01

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

Virtual Bioinformatics Distance Learning Suite

Science.gov (United States)

Tolvanen, Martti; Vihinen, Mauno

2004-01-01

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

OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows

Science.gov (United States)

2013-01-01

Background Biomedical ontologies are key elements for building up the Life Sciences Semantic Web. Reusing and building biomedical ontologies requires flexible and versatile tools to manipulate them efficiently, in particular for enriching their axiomatic content. The Ontology Pre Processor Language (OPPL) is an OWL-based language for automating the changes to be performed in an ontology. OPPL augments the ontologists’ toolbox by providing a more efficient, and less error-prone, mechanism for enriching a biomedical ontology than that obtained by a manual treatment. Results We present OPPL-Galaxy, a wrapper for using OPPL within Galaxy. The functionality delivered by OPPL (i.e. automated ontology manipulation) can be combined with the tools and workflows devised within the Galaxy framework, resulting in an enhancement of OPPL. Use cases are provided in order to demonstrate OPPL-Galaxy’s capability for enriching, modifying and querying biomedical ontologies. Conclusions Coupling OPPL-Galaxy with other bioinformatics tools of the Galaxy framework results in a system that is more than the sum of its parts. OPPL-Galaxy opens a new dimension of analyses and exploitation of biomedical ontologies, including automated reasoning, paving the way towards advanced biological data analyses. PMID:23286517

The 2016 Bioinformatics Open Source Conference (BOSC).

Science.gov (United States)

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

2016-01-01

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

Microwave-Enhanced Organic Syntheses for the Undergraduate Laboratory: Diels-Alder Cycloaddition, Wittig Reaction, and Williamson Ether Synthesis

Science.gov (United States)

Baar, Marsha R.; Falcone, Danielle; Gordon, Christopher

2010-01-01

Microwave heating enhanced the rate of three reactions typically performed in our undergraduate organic chemistry laboratory: a Diels-Alder cycloaddition, a Wittig salt formation, and a Williamson ether synthesis. Ninety-minute refluxes were shortened to 10 min using a laboratory-grade microwave oven. In addition, yields improved for the Wittig…

The use of podcasts to enhance research-teaching linkages in undergraduate nursing students.

Science.gov (United States)

Strickland, Karen; Gray, Colin; Hill, Gordon

2012-07-01

An understanding of research is important to enable nurses to provide evidence-based care. However, undergraduate nursing students often find research a challenging subject. The purpose of this paper is to present an evaluation of the introduction of podcasts in an undergraduate research module to enhance research-teaching linkages between the theoretical content and research in practice and improve the level of student support offered in a blended learning environment. Two cohorts of students (n=228 and n=233) were given access to a series of 5 "guest speaker" podcasts made up of presentations and interviews with research experts within Edinburgh Napier. These staff would not normally have contact with students on this module, but through the podcasts were able to share their research expertise and methods with our learners. The main positive results of the podcasts suggest the increased understanding achieved by students due to the multi-modal delivery approach, a more personal student/tutor relationship leading to greater engagement, and the effective use of materials for revision and consolidation purposes. Negative effects of the podcasts centred around problems with the technology, most often difficulty in downloading and accessing the material. This paper contributes to the emerging knowledge base of podcasting in nurse education by demonstrating how podcasts can be used to enhance research-teaching linkages and raises the question of why students do not exploit the opportunities for mobile learning. Copyright © 2012 Elsevier Ltd. All rights reserved.

Bioinformatics in translational drug discovery.

Science.gov (United States)

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

2017-08-31

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

Navigating the changing learning landscape: perspective from bioinformatics.ca

OpenAIRE

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

2013-01-01

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

Bioinformatics for cancer immunotherapy target discovery

DEFF Research Database (Denmark)

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

2014-01-01

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

Bioinformatics for Exploration

Science.gov (United States)

Johnson, Kathy A.

2006-01-01

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

The 2015 Bioinformatics Open Source Conference (BOSC 2015).

Science.gov (United States)

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

2016-02-01

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

Component-Based Approach for Educating Students in Bioinformatics

Science.gov (United States)

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

2009-01-01

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

Phylogenetic trees in bioinformatics

Energy Technology Data Exchange (ETDEWEB)

Burr, Tom L [Los Alamos National Laboratory

2008-01-01

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

A Mathematical Optimization Problem in Bioinformatics

Science.gov (United States)

Heyer, Laurie J.

2008-01-01

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

Bioinformatics and Cancer

Science.gov (United States)

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

Biology in 'silico': The Bioinformatics Revolution.

Science.gov (United States)

Bloom, Mark

2001-01-01

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

Undergraduate Biocuration: Developing Tomorrow’s Researchers While Mining Today’s Data

Science.gov (United States)

Mitchell, Cassie S.; Cates, Ashlyn; Kim, Renaid B.; Hollinger, Sabrina K.

2015-01-01

Biocuration is a time-intensive process that involves extraction, transcription, and organization of biological or clinical data from disjointed data sets into a user-friendly database. Curated data is subsequently used primarily for text mining or informatics analysis (bioinformatics, neuroinformatics, health informatics, etc.) and secondarily as a researcher resource. Biocuration is traditionally considered a Ph.D. level task, but a massive shortage of curators to consolidate the ever-mounting biomedical “big data” opens the possibility of utilizing biocuration as a means to mine today’s data while teaching students skill sets they can utilize in any career. By developing a biocuration assembly line of simplified and compartmentalized tasks, we have enabled biocuration to be effectively performed by a hierarchy of undergraduate students. We summarize the necessary physical resources, process for establishing a data path, biocuration workflow, and undergraduate hierarchy of curation, technical, information technology (IT), quality control and managerial positions. We detail the undergraduate application and training processes and give detailed job descriptions for each position on the assembly line. We present case studies of neuropathology curation performed entirely by undergraduates, namely the construction of experimental databases of Amyotrophic Lateral Sclerosis (ALS) transgenic mouse models and clinical data from ALS patient records. Our results reveal undergraduate biocuration is scalable for a group of 8–50+ with relatively minimal required resources. Moreover, with average accuracy rates greater than 98.8%, undergraduate biocurators are equivalently accurate to their professional counterparts. Initial training to be completely proficient at the entry-level takes about five weeks with a minimal student time commitment of four hours/week. PMID:26557796

Bioinformatics research in the Asia Pacific: a 2007 update.

Science.gov (United States)

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

2008-01-01

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

When cloud computing meets bioinformatics: a review.

Science.gov (United States)

Zhou, Shuigeng; Liao, Ruiqi; Guan, Jihong

2013-10-01

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

Application of machine learning methods in bioinformatics

Science.gov (United States)

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

2018-05-01

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

Using Quantitative Literacy to Enhance Critical Thinking Skills in Undergraduate Nursing Students.

Science.gov (United States)

Asknes, Edna

2017-04-01

Critical thinking and quantitative literacy (QL) are similarly grounded: both focus on analyzing and evaluating evidence, identifying implications and consequences, drawing inferences, and communicating information. This teaching strategy was based on those commonalities and was designed so that undergraduate nursing students would enhance their critical thinking skills as they used their QL skills. QL skills are most effective when taught, learned, and used to solve significant, pertinent problems. Using the principles of learner-centered, team-based learning, QL was integrated into the curriculum of the Maternal-Newborn Nursing course at an urban community college with a diverse student population. Students were engaged and demonstrated enhanced and ongoing development of their critical thinking and problem-solving skills. They also reported a better understanding of data interpretation and use. The positive outcome of this project revealed further opportunities for incorporating QL into nursing curricula and highlighted the need for research on the use of QL in nursing education. [J Nurs Educ. 2017;56(4):240-242.]. Copyright 2017, SLACK Incorporated.

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

DEFF Research Database (Denmark)

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

2010-01-01

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

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

DEFF Research Database (Denmark)

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

2012-01-01

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

Planning bioinformatics workflows using an expert system

Science.gov (United States)

Chen, Xiaoling; Chang, Jeffrey T.

2017-01-01

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

Continuing Education Workshops in Bioinformatics Positively Impact Research and Careers.

Science.gov (United States)

Brazas, Michelle D; Ouellette, B F Francis

2016-06-01

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

Using "Arabidopsis" Genetic Sequences to Teach Bioinformatics

Science.gov (United States)

Zhang, Xiaorong

2009-01-01

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

A semantic web approach applied to integrative bioinformatics experimentation: a biological use case with genomics data.

NARCIS (Netherlands)

Post, L.J.G.; Roos, M.; Marshall, M.S.; van Driel, R.; Breit, T.M.

2007-01-01

The numerous public data resources make integrative bioinformatics experimentation increasingly important in life sciences research. However, it is severely hampered by the way the data and information are made available. The semantic web approach enhances data exchange and integration by providing

Development of Bioinformatics Infrastructure for Genomics Research.

Science.gov (United States)

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

2017-06-01

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

Fuzzy Logic in Medicine and Bioinformatics

Directory of Open Access Journals (Sweden)

Angela Torres

2006-01-01

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

Online Bioinformatics Tutorials | Office of Cancer Genomics

Science.gov (United States)

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

The Geosciences Division of the Council on Undergraduate Research (GeoCUR): Supporting Faculty that Mentor Undergraduate Researchers

Science.gov (United States)

Fox, L. K.; Guertin, L. A.; Manley, P. L.; Fortner, S. K.

2012-12-01

Undergraduate research is a proven effective pedagogy that has a number of benefits including: enhancing student learning through mentoring relationships with faculty; increasing retention; increasing enrollment in graduate programs; developing critical thinking, creativity, problem solving and intellectual independence; and, developing an understanding of research methodology. Undergraduate research also has been demonstrated in preparing students for careers. In addition to developing disciplinary and technical expertise, participation in undergraduate research helps students improve communication skills (written, oral, and graphical) and time management. Early involvement in undergraduate research improves retention and, for those engaged at the 2YC level, helps students successfully transfers to 4YC. The Geosciences Division of the Council on Undergraduate Research (GeoCUR) supports faculty in their development of undergraduate research programs at all levels. GeoCUR leads workshops for new and future faculty covering all aspects of undergraduate research including incorporating research into coursework, project design, mentoring students, sustaining programs, and funding sources. GeoCUR members support new faculty by providing a range of services including: peer-review of grant proposals; advice on establishing an undergraduate research program; balancing teaching and research demands; and networking with other geoscientist. GeoCUR has also developed web resources that support faculty and departments in development of undergraduate research programs (http://serc.carleton.edu/NAGTWorkshops/undergraduate_research/index.html). This presentation will describe the services provided by GeoCUR and highlight examples of programs and resources available to geoscientists in all career stages for effective undergraduate research mentoring and development.

Development of Web-Based Learning Environment Model to Enhance Cognitive Skills for Undergraduate Students in the Field of Electrical Engineering

Science.gov (United States)

Lakonpol, Thongmee; Ruangsuwan, Chaiyot; Terdtoon, Pradit

2015-01-01

This research aimed to develop a web-based learning environment model for enhancing cognitive skills of undergraduate students in the field of electrical engineering. The research is divided into 4 phases: 1) investigating the current status and requirements of web-based learning environment models. 2) developing a web-based learning environment…

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

Science.gov (United States)

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

2018-02-01

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

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

Science.gov (United States)

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

2018-01-01

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

OpenHelix: bioinformatics education outside of a different box.

Science.gov (United States)

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

2010-11-01

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

Analyzing the Existing Undergraduate Engineering Leadership Skills

Directory of Open Access Journals (Sweden)

Hamed M. Almalki

2016-12-01

Full Text Available Purpose: Studying and analyzing the undergraduate engineering students' leadership skills to discover their potential leadership strengths and weaknesses. This study will unveil potential ways to enhance the ways we teach engineering leadership. The research has great insights that might assist engineering programs to improve curricula for the purpose of better engineering preparation to meet industry's demands. Methodology and Findings: 441 undergraduate engineering students have been surveyed in two undergraduate engineering programs to discover their leadership skills. The results in both programs were revealing that undergraduate engineering students are lacking behind in the visionary leadership skills compared to directing, including and cultivating leadership styles. Recommendation: A practical framework has been proposed to enhance the lacking leadership skills by utilizing the Matrix of Change (MOC, and the Balanced Scorecard BSC to capture the best leadership scenarios to design virtual simulation environment as per the lacking leadership skills which is the visionary leadership skills in this case. After that, the virtual simulation will be used to provide an experiential learning by replacing human beings with avatars that can be managed or dramatized by real people to enable the creation of live, practical, measurable, and customizable leadership development programs.

Translational Bioinformatics and Clinical Research (Biomedical) Informatics.

Science.gov (United States)

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

2015-06-01

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

Development of a cloud-based Bioinformatics Training Platform.

Science.gov (United States)

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

2017-05-01

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

Analyzing the Existing Undergraduate Engineering Leadership Skills

OpenAIRE

Hamed M. Almalki; Luis Rabelo; Charles Davis; Hammad Usmani; Debra Hollister; Alfonso Sarmiento

2016-01-01

Purpose: Studying and analyzing the undergraduate engineering students' leadership skills to discover their potential leadership strengths and weaknesses. This study will unveil potential ways to enhance the ways we teach engineering leadership. The research has great insights that might assist engineering programs to improve curricula for the purpose of better engineering preparation to meet industry's demands. Methodology and Findings: 441 undergraduate engineering students have been s...

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

Science.gov (United States)

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

2017-01-01

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

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

Directory of Open Access Journals (Sweden)

Thomas K. Karikari

2015-09-01

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

Interdisciplinary Collaborative Learning: Using Decision Analysts to Enhance Undergraduate International Management Education

Science.gov (United States)

Palocsay, Susan W.; White, Marion M.; Zimmerman, D. Kent

2004-01-01

This article describes an experiential learning activity designed to promote the development of decision-making skills in international management students at the undergraduate level. Students from an undergraduate management science course in decision analysis served as consultants on a case assigned to teams in an international management class.…

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

Science.gov (United States)

Ranganathan, Shoba; Eisenhaber, Frank; Tong, Joo Chuan; Tan, Tin Wee

2009-12-03

The 2009 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation dating back to 1998, was organized as the 8th International Conference on Bioinformatics (InCoB), Sept. 7-11, 2009 at Biopolis, Singapore. Besides bringing together scientists from the field of bioinformatics in this region, InCoB has actively engaged clinicians and researchers from the area of systems biology, to facilitate greater synergy between these two groups. InCoB2009 followed on from a series of successful annual events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand), Busan (South Korea), New Delhi (India), Hong Kong and Taipei (Taiwan), with InCoB2010 scheduled to be held in Tokyo, Japan, Sept. 26-28, 2010. The Workshop on Education in Bioinformatics and Computational Biology (WEBCB) and symposia on Clinical Bioinformatics (CBAS), the Singapore Symposium on Computational Biology (SYMBIO) and training tutorials were scheduled prior to the scientific meeting, and provided ample opportunity for in-depth learning and special interest meetings for educators, clinicians and students. We provide a brief overview of the peer-reviewed bioinformatics manuscripts accepted for publication in this supplement, grouped into thematic areas. In order to facilitate scientific reproducibility and accountability, we have, for the first time, introduced minimum information criteria for our pubilcations, including compliance to a Minimum Information about a Bioinformatics Investigation (MIABi). As the regional research expertise in bioinformatics matures, we have delineated a minimum set of bioinformatics skills required for addressing the computational challenges of the "-omics" era.

Microsoft Biology Initiative: .NET Bioinformatics Platform and Tools

Science.gov (United States)

Diaz Acosta, B.

2011-01-01

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

PyPedia: using the wiki paradigm as crowd sourcing environment for bioinformatics protocols.

Science.gov (United States)

Kanterakis, Alexandros; Kuiper, Joël; Potamias, George; Swertz, Morris A

2015-01-01

Today researchers can choose from many bioinformatics protocols for all types of life sciences research, computational environments and coding languages. Although the majority of these are open source, few of them possess all virtues to maximize reuse and promote reproducible science. Wikipedia has proven a great tool to disseminate information and enhance collaboration between users with varying expertise and background to author qualitative content via crowdsourcing. However, it remains an open question whether the wiki paradigm can be applied to bioinformatics protocols. We piloted PyPedia, a wiki where each article is both implementation and documentation of a bioinformatics computational protocol in the python language. Hyperlinks within the wiki can be used to compose complex workflows and induce reuse. A RESTful API enables code execution outside the wiki. Initial content of PyPedia contains articles for population statistics, bioinformatics format conversions and genotype imputation. Use of the easy to learn wiki syntax effectively lowers the barriers to bring expert programmers and less computer savvy researchers on the same page. PyPedia demonstrates how wiki can provide a collaborative development, sharing and even execution environment for biologists and bioinformaticians that complement existing resources, useful for local and multi-center research teams. PyPedia is available online at: http://www.pypedia.com. The source code and installation instructions are available at: https://github.com/kantale/PyPedia_server. The PyPedia python library is available at: https://github.com/kantale/pypedia. PyPedia is open-source, available under the BSD 2-Clause License.

Concepts and introduction to RNA bioinformatics

DEFF Research Database (Denmark)

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

2014-01-01

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

Adapting bioinformatics curricula for big data

Science.gov (United States)

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

2016-01-01

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

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

Science.gov (United States)

Rein, Diane C

2006-07-01

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

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

Science.gov (United States)

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

2012-07-19

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

Concepts Of Bioinformatics And Its Application In Veterinary ...

African Journals Online (AJOL)

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

Efficient Feature Selection and Classification of Protein Sequence Data in Bioinformatics

Science.gov (United States)

Faye, Ibrahima; Samir, Brahim Belhaouari; Md Said, Abas

2014-01-01

Bioinformatics has been an emerging area of research for the last three decades. The ultimate aims of bioinformatics were to store and manage the biological data, and develop and analyze computational tools to enhance their understanding. The size of data accumulated under various sequencing projects is increasing exponentially, which presents difficulties for the experimental methods. To reduce the gap between newly sequenced protein and proteins with known functions, many computational techniques involving classification and clustering algorithms were proposed in the past. The classification of protein sequences into existing superfamilies is helpful in predicting the structure and function of large amount of newly discovered proteins. The existing classification results are unsatisfactory due to a huge size of features obtained through various feature encoding methods. In this work, a statistical metric-based feature selection technique has been proposed in order to reduce the size of the extracted feature vector. The proposed method of protein classification shows significant improvement in terms of performance measure metrics: accuracy, sensitivity, specificity, recall, F-measure, and so forth. PMID:25045727

Enhancing Undergraduate Education with NASA Resources

Science.gov (United States)

Manning, James G.; Meinke, Bonnie; Schultz, Gregory; Smith, Denise Anne; Lawton, Brandon L.; Gurton, Suzanne; Astrophysics Community, NASA

2015-08-01

://nightsky.jpl.nasa.gov/news-display.cfm?News_ID=611.These resources help enhance the Science, Technology, Engineering, and Mathematics (STEM) experiences of undergraduates, and will be described with access information provided.

Mentored undergraduate research in the geosciences

Science.gov (United States)

Judge, Shelley; Pollock, Meagen; Wiles, Greg; Wilson, Mark

2012-09-01

There is little argument about the merits of undergraduate research, but it can seem like a complex, resource-intensive endeavor [e.g., Laursen et al., 2010; Lopatto, 2009; Hunter et al., 2006]. Although mentored undergraduate research can be challenging, the authors of this feature have found that research programs are strengthened when students and faculty collaborate to build new knowledge. Faculty members in the geology department at The College of Wooster have conducted mentored undergraduate research with their students for more than 60 years and have developed a highly effective program that enhances the teaching, scholarship, and research of our faculty and provides life-changing experiences for our students. Other colleges and universities have also implemented successful mentored undergraduate research programs in the geosciences. For instance, the 18 Keck Geology Consortium schools (http://keckgeology.org/), Princeton University, and other institutions have been recognized for their senior capstone experiences by U.S. News & World Report.

NSU Undergraduate Academic Advising Center

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College of Psychology Dr. Kiran C. Patel College of Allopathic Medicine Dr. Kiran C. Patel College of , dentistry, law, and psychology. Certificate Receive a graduate level certificate to enhance your skills Institute Core Services & Equipment HPD Research Undergraduate Research Community Community Outreach

Undergraduate Events | Nova Southeastern University

Science.gov (United States)

College of Psychology Dr. Kiran C. Patel College of Allopathic Medicine Dr. Kiran C. Patel College of , dentistry, law, and psychology. Certificate Receive a graduate level certificate to enhance your skills Institute Core Services & Equipment HPD Research Undergraduate Research Community Community Outreach

BioWarehouse: a bioinformatics database warehouse toolkit.

Science.gov (United States)

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

2006-03-23

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

Bioinformatics approaches for identifying new therapeutic bioactive peptides in food

Directory of Open Access Journals (Sweden)

Nora Khaldi

2012-10-01

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

Adapting bioinformatics curricula for big data.

Science.gov (United States)

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

2016-01-01

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

Application of Bioinformatics in Chronobiology Research

Directory of Open Access Journals (Sweden)

Robson da Silva Lopes

2013-01-01

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

National Genome Research Initiative: A New Paradigm For Teaching Research To Undergraduates In South America

Directory of Open Access Journals (Sweden)

Rafael Ovalle

2012-05-01

Full Text Available Introduction: From 2007 to 2011, the Howard Hughes Medical Institute (HHMI recruited professors across the US to test a new paradigm in undergraduate education: the National Genome Research Initiative (NGRI. Undergraduates were taught to isolate bacteriophages, characterize their findings, and report to the scientific community.Objective: The educational goal of the NGRI program was to expose science undergraduates to an authentic research experience to increase graduation rates. The scientific goal was to isolate mycobacteriophages to be used as therapeutic agents against disease-causing mycobacteria.Materials and Methods: In a one-semester lab course undergraduates are taught to find, grow, and purify bacteriophages. In the second semester, students use bioinformatic software to annotate sequences of their bacteriophages.Results: Ahead of data on student graduation rates, the NGRI program has generated expanded productivity for US undergraduates. Over a four year period, thousands of participants were taught to collect bacteriophages, annotate sequences, and present their findings. Those undergraduates will have isolated 2300+ phages, annotated 250+ sequences, presented hundreds of posters at conferences across the US, and are co-authors on papers published by labs participating in the NGRI program.Discussion: Many professors in the US academic community are convinced that the NGRI program will have lasting impact on the US educational system. Several professors have banded together to form the Phage Galaxy Consortium to continue HHMI’s goal of implementation of the NGRI program at all US colleges.Conclusions: HHMI’s paradigm is ready for distribution to Central and South America.

Undergraduate medical students' empathy: current perspectives

Directory of Open Access Journals (Sweden)

Quince T

2016-08-01

Full Text Available Thelma Quince, Pia Thiemann, John Benson, Sarah Hyde Primary Care Unit, Department of Public Health and Primary Care, Institute of Public Health, University of Cambridge, Cambridge, UK Abstract: Empathy is important to patient care. It enhances patients’ satisfaction, comfort, self-efficacy, and trust which in turn may facilitate better diagnosis, shared decision making, and therapy adherence. Empathetic doctors experience greater job satisfaction and psychological well-being. Understanding the development of empathy of tomorrow's health care professionals is important. However, clinical empathy is poorly defined and difficult to measure, while ways to enhance it remain unclear. This review examines empathy among undergraduate medical students, focusing upon three main questions: How is empathy measured? This section discusses the problems of assessing empathy and outlines the utility of the Jefferson Scale of Empathy – Student Version and Davis's Interpersonal Reactivity Index. Both have been used widely to assess medical students' empathy. Does empathy change during undergraduate medical education? The trajectory of empathy during undergraduate medical education has been and continues to be debated. Potential reasons for contrasting results of studies are outlined. What factors may influence the development of empathy? Although the influence of sex is widely recognized, the impact of culture, psychological well-being, and aspects of undergraduate curricula are less well understood. This review identifies three interrelated issues for future research into undergraduate medical students' empathy. First, the need for greater clarity of definition, recognizing that empathy is multidimensional. Second, the need to develop meaningful ways of measuring empathy which include its component dimensions and which are relevant to patients' experiences. Medical education research has generally relied upon single, self-report instruments, which have

Scientific Visualization Tools for Enhancement of Undergraduate Research

Science.gov (United States)

Rodriguez, W. J.; Chaudhury, S. R.

2001-05-01

Undergraduate research projects that utilize remote sensing satellite instrument data to investigate atmospheric phenomena pose many challenges. A significant challenge is processing large amounts of multi-dimensional data. Remote sensing data initially requires mining; filtering of undesirable spectral, instrumental, or environmental features; and subsequently sorting and reformatting to files for easy and quick access. The data must then be transformed according to the needs of the investigation(s) and displayed for interpretation. These multidimensional datasets require views that can range from two-dimensional plots to multivariable-multidimensional scientific visualizations with animations. Science undergraduate students generally find these data processing tasks daunting. Generally, researchers are required to fully understand the intricacies of the dataset and write computer programs or rely on commercially available software, which may not be trivial to use. In the time that undergraduate researchers have available for their research projects, learning the data formats, programming languages, and/or visualization packages is impractical. When dealing with large multi-dimensional data sets appropriate Scientific Visualization tools are imperative in allowing students to have a meaningful and pleasant research experience, while producing valuable scientific research results. The BEST Lab at Norfolk State University has been creating tools for multivariable-multidimensional analysis of Earth Science data. EzSAGE and SAGE4D have been developed to sort, analyze and visualize SAGE II (Stratospheric Aerosol and Gas Experiment) data with ease. Three- and four-dimensional visualizations in interactive environments can be produced. EzSAGE provides atmospheric slices in three-dimensions where the researcher can change the scales in the three-dimensions, color tables and degree of smoothing interactively to focus on particular phenomena. SAGE4D provides a navigable

Tissue Banking, Bioinformatics, and Electronic Medical Records: The Front-End Requirements for Personalized Medicine

Science.gov (United States)

Suh, K. Stephen; Sarojini, Sreeja; Youssif, Maher; Nalley, Kip; Milinovikj, Natasha; Elloumi, Fathi; Russell, Steven; Pecora, Andrew; Schecter, Elyssa; Goy, Andre

2013-01-01

Personalized medicine promises patient-tailored treatments that enhance patient care and decrease overall treatment costs by focusing on genetics and “-omics” data obtained from patient biospecimens and records to guide therapy choices that generate good clinical outcomes. The approach relies on diagnostic and prognostic use of novel biomarkers discovered through combinations of tissue banking, bioinformatics, and electronic medical records (EMRs). The analytical power of bioinformatic platforms combined with patient clinical data from EMRs can reveal potential biomarkers and clinical phenotypes that allow researchers to develop experimental strategies using selected patient biospecimens stored in tissue banks. For cancer, high-quality biospecimens collected at diagnosis, first relapse, and various treatment stages provide crucial resources for study designs. To enlarge biospecimen collections, patient education regarding the value of specimen donation is vital. One approach for increasing consent is to offer publically available illustrations and game-like engagements demonstrating how wider sample availability facilitates development of novel therapies. The critical value of tissue bank samples, bioinformatics, and EMR in the early stages of the biomarker discovery process for personalized medicine is often overlooked. The data obtained also require cross-disciplinary collaborations to translate experimental results into clinical practice and diagnostic and prognostic use in personalized medicine. PMID:23818899

Skate Genome Project: Cyber-Enabled Bioinformatics Collaboration

Science.gov (United States)

Vincent, J.

2011-01-01

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

Systems Engineering Initiative: Undergraduate Education Enhancement in a Regional Education Network

International Nuclear Information System (INIS)

Kurwitz, R. C.; Peddicord, K.; Poston, J.; Yang, X.; Bostanci, H.

2016-01-01

Full text: The Systems Engineering Initiative (SEI) is an experience based education enhancement programme that forms teams of undergraduate students with faculty and industry mentors to solve problems of interest to industry. This model of innovation creates a new learning paradigm that is outside the traditional classroom based model and fits more of the Master-apprentice model as applied to engineering teams. The SEI programme is currently administered by the Nuclear Power Institute (NPI), a regional nuclear education network, and is being carried out at three partner universities. Previous nuclear related projects have benefited industry and are of high technical quality with publications in peer-reviewed journals and awards for presentations in various forums. Students within the programme have benefited through development of soft skills outside the traditional curriculum, understanding of how their knowledge fits into a nuclear organization, and exposure to career opportunities. Industry and other NPI stakeholders benefit from the development of capable engineers and technicians, positive outreach to the community, and most importantly, knowledge transfer to the next generation of nuclear professionals. (author

BioWarehouse: a bioinformatics database warehouse toolkit

Directory of Open Access Journals (Sweden)

Stringer-Calvert David WJ

2006-03-01

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

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

Science.gov (United States)

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

2005-09-01

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

Undergraduate medical students’ empathy: current perspectives

Science.gov (United States)

Quince, Thelma; Thiemann, Pia; Benson, John; Hyde, Sarah

2016-01-01

Empathy is important to patient care. It enhances patients’ satisfaction, comfort, self-efficacy, and trust which in turn may facilitate better diagnosis, shared decision making, and therapy adherence. Empathetic doctors experience greater job satisfaction and psychological well-being. Understanding the development of empathy of tomorrow’s health care professionals is important. However, clinical empathy is poorly defined and difficult to measure, while ways to enhance it remain unclear. This review examines empathy among undergraduate medical students, focusing upon three main questions: How is empathy measured? This section discusses the problems of assessing empathy and outlines the utility of the Jefferson Scale of Empathy – Student Version and Davis’s Interpersonal Reactivity Index. Both have been used widely to assess medical students’ empathy. Does empathy change during undergraduate medical education? The trajectory of empathy during undergraduate medical education has been and continues to be debated. Potential reasons for contrasting results of studies are outlined. What factors may influence the development of empathy? Although the influence of sex is widely recognized, the impact of culture, psychological well-being, and aspects of undergraduate curricula are less well understood. This review identifies three interrelated issues for future research into undergraduate medical students’ empathy. First, the need for greater clarity of definition, recognizing that empathy is multidimensional. Second, the need to develop meaningful ways of measuring empathy which include its component dimensions and which are relevant to patients’ experiences. Medical education research has generally relied upon single, self-report instruments, which have utility across large populations but are limited. Finally, there is a need for greater methodological rigor in investigating the possible determinants of clinical empathy in medical education. Greater

Collaborating with Undergraduates To Contribute to Biochemistry Community Resources.

Science.gov (United States)

Haas, Kathryn L; Heemstra, Jennifer M; Medema, Marnix H; Charkoudian, Louise K

2018-01-30

Course-based undergraduate research experiences (CUREs) have gained traction as effective ways to expand the impact of undergraduate research while fulfilling pedagogical goals. In this Perspective, we present innovative ways to incorporate fundamental benefits and principles of CUREs into a classroom environment through information/technology-based research projects that lead to student-generated contributions to digital community resources (CoRes). These projects represent an attractive class of CUREs because they are less resource-intensive than laboratory-based CUREs, and the projects align with the expectations of today's students to create rapid and publicly accessible contributions to society. We provide a detailed discussion of two example types of CoRe projects that can be implemented in courses to impact research and education at the chemistry-biology interface: bioinformatics annotations and development of educational tools. Finally, we present current resources available for faculty interested in incorporating CUREs or CoRe projects into their pedagogical practices. In sharing these stories and resources, we hope to lower the barrier for widespread adoption of CURE and CoRe approaches and generate discussions about how to utilize the classroom experience to make a positive impact on our students and the future of the field of biochemistry.

Evaluating an Inquiry-Based Bioinformatics Course Using Q Methodology

Science.gov (United States)

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

2008-01-01

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

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

Science.gov (United States)

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

2005-01-01

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

An Overview of Bioinformatics Tools and Resources in Allergy.

Science.gov (United States)

Fu, Zhiyan; Lin, Jing

2017-01-01

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

Researching with undergraduate students

DEFF Research Database (Denmark)

Wulf-Andersen, Trine Østergaard; Mogensen, Kevin; Hjort-Madsen, Peder

2013-01-01

The article presents a particular case of undergraduate students working on subprojects within the framework of their supervisors' (the authors') research project during Autumn Semester 2012 and Spring Semester 2013. The article's purpose is to show that an institutionalized focus on students...... as "research learners" rather than merely curriculum learners proves productive for both research and teaching. We describe the specific university learning context and the particular organization of undergraduate students' supervision and assistantships. The case builds on and further enhances a well......-established and proven university model of participant-directed, problem-oriented project work. We explore students' and researchers' experiences of being part of the collaboration, focusing on learning potentials and dilemmas associated with the multiple roles of researcher and student that characterized...

Recent developments in life sciences research: Role of bioinformatics

African Journals Online (AJOL)

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

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

African Journals Online (AJOL)

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

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

Science.gov (United States)

Smith, David Roy

2015-07-01

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

Mathematics and evolutionary biology make bioinformatics education comprehensible

Science.gov (United States)

Weisstein, Anton E.

2013-01-01

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

Mathematics and evolutionary biology make bioinformatics education comprehensible.

Science.gov (United States)

Jungck, John R; Weisstein, Anton E

2013-09-01

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

Bioinformatics of cardiovascular miRNA biology.

Science.gov (United States)

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

2015-12-01

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

An innovative approach for testing bioinformatics programs using metamorphic testing

Directory of Open Access Journals (Sweden)

Liu Huai

2009-01-01

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

Video Bioinformatics Analysis of Human Embryonic Stem Cell Colony Growth

Science.gov (United States)

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

2010-01-01

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

MOWServ: a web client for integration of bioinformatic resources

Science.gov (United States)

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

2010-01-01

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

Bioinformatics-Aided Venomics

Directory of Open Access Journals (Sweden)

Quentin Kaas

2015-06-01

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

A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection.

Science.gov (United States)

Goodacre, Norman; Aljanahi, Aisha; Nandakumar, Subhiksha; Mikailov, Mike; Khan, Arifa S

2018-01-01

Detection of distantly related viruses by high-throughput sequencing (HTS) is bioinformatically challenging because of the lack of a public database containing all viral sequences, without abundant nonviral sequences, which can extend runtime and obscure viral hits. Our reference viral database (RVDB) includes all viral, virus-related, and virus-like nucleotide sequences (excluding bacterial viruses), regardless of length, and with overall reduced cellular sequences. Semantic selection criteria (SEM-I) were used to select viral sequences from GenBank, resulting in a first-generation viral database (VDB). This database was manually and computationally reviewed, resulting in refined, semantic selection criteria (SEM-R), which were applied to a new download of updated GenBank sequences to create a second-generation VDB. Viral entries in the latter were clustered at 98% by CD-HIT-EST to reduce redundancy while retaining high viral sequence diversity. The viral identity of the clustered representative sequences (creps) was confirmed by BLAST searches in NCBI databases and HMMER searches in PFAM and DFAM databases. The resulting RVDB contained a broad representation of viral families, sequence diversity, and a reduced cellular content; it includes full-length and partial sequences and endogenous nonretroviral elements, endogenous retroviruses, and retrotransposons. Testing of RVDBv10.2, with an in-house HTS transcriptomic data set indicated a significantly faster run for virus detection than interrogating the entirety of the NCBI nonredundant nucleotide database, which contains all viral sequences but also nonviral sequences. RVDB is publically available for facilitating HTS analysis, particularly for novel virus detection. It is meant to be updated on a regular basis to include new viral sequences added to GenBank. IMPORTANCE To facilitate bioinformatics analysis of high-throughput sequencing (HTS) data for the detection of both known and novel viruses, we have

NSU Undergraduate Student Tuition and Fees

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College of Psychology Dr. Kiran C. Patel College of Allopathic Medicine Dr. Kiran C. Patel College of , dentistry, law, and psychology. Certificate Receive a graduate level certificate to enhance your skills Institute Core Services & Equipment HPD Research Undergraduate Research Community Community Outreach

The development and validation of the Blended Socratic Method of Teaching (BSMT: An instructional model to enhance critical thinking skills of undergraduate business students

Directory of Open Access Journals (Sweden)

Eugenia Arazo Boa

2018-01-01

Full Text Available Enhancing critical thinking skills is one of the paramount goals of many educational institutions. This study presents the development and validation of the Blended Socratic Method of Teaching (BSMT, a teaching model intended to foster critical thinking skills of business students in the undergraduate level. The main objectives of the study were to 1 to survey the critical thinking skills of undergraduate business students, and 2 to develop and validate the BSMT model designed to enhance critical thinking skills. The research procedure comprised of two phases related to the two research objectives: 1 surveying the critical thinking skills of 371 undergraduate business students at Naresuan University International College focusing on the three critical thinking competencies of the RED model—recognize assumptions, evaluate arguments, and draw conclusion, and the determination of the level of their critical thinking; and 2 developing the instructional model followed by validation of the model by five experts. The results of the study were: 1 the undergraduate business students have deficient critical thinking based on the RED Model competencies as they scored “below average” on the critical thinking appraisal, and 2 the developed model comprised six elements: focus, syntax, principles of reaction, the social system, the support system, and application. The experts were in complete agreement that the model is “highly appropriate” in improving the critical thinking skills of the business students. The main essence of the model is the syntax comprising of five steps: group assignment, analysis and writing of case studies; group presentation of the business case analysis in class; Socratic discussion/questioning in class; posting of the case study on the class Facebook account; and online Socratic discussion/questioning. The BSMT model is an authentic and comprehensive model combining the Socratic method of teaching, information and

A Bioinformatics Facility for NASA

Science.gov (United States)

Schweighofer, Karl; Pohorille, Andrew

2006-01-01

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

Comprehensive decision tree models in bioinformatics.

Directory of Open Access Journals (Sweden)

Gregor Stiglic

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

Comprehensive decision tree models in bioinformatics.

Science.gov (United States)

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

2012-01-01

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

When process mining meets bioinformatics

NARCIS (Netherlands)

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

2011-01-01

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

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

CERN Document Server

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

2015-01-01

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

Bioconductor: open software development for computational biology and bioinformatics

DEFF Research Database (Denmark)

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

2004-01-01

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

Peer Mentoring for Bioinformatics presentation

OpenAIRE

Budd, Aidan

2014-01-01

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

PubData: search engine for bioinformatics databases worldwide

OpenAIRE

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

2016-01-01

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

Guidelines for the undergraduate psychology major: Version 2.0.

Science.gov (United States)

2016-01-01

The APA Guidelines for the Undergraduate Psychology Major: Version 2.0 (henceforth Guidelines 2.0; APA, 2013) represents a national effort to describe and develop high-quality undergraduate programs in psychology. The task force charged with the revision of the original guidelines for the undergraduate major examined the success of the document's implementation and made changes to reflect emerging best practices and to integrate psychology's work with benchmarking scholarship in higher education. Guidelines 2.0 abandoned the original distinction drawn between psychology-focused skills and psychology skills that enhance liberal arts development. Instead, Guidelines 2.0 describes five inclusive goals for the undergraduate psychology major and two developmental levels of student learning outcomes. Suggestions for assessment planning are provided for each of the five learning goals. (c) 2016 APA, all rights reserved).

Improving STEM Undergraduate Education with Efficient Learning Design

DEFF Research Database (Denmark)

Godsk, Mikkel

2018-01-01

The project investigates the potential of Learning Design for efficiently improving STEM undergraduate education with technology. In order to investigate this potential, the project consists of two main studies at Aarhus University: a study of the perspectives of the main stakeholders on Learning...... Design uptake. The project concludes that it is possible to improve STEM undergraduate education with Learning Design for technology-enhanced learning efficiently and that Efficient Learning Design provides a useful concept for qualifying educational decisions....... provided by technology-enhanced learning based on Learning Design, and in particular students’ learning was of a high common interest. However, only the educators were directly interested in Learning Design and its support for design, reuse in their practice and to inform pedagogy. A holistic concept...

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

African Journals Online (AJOL)

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

Assessment of Data Reliability of Wireless Sensor Network for Bioinformatics

Directory of Open Access Journals (Sweden)

Ting Dong

2017-09-01

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

Reproducible Bioinformatics Research for Biologists

Science.gov (United States)

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

Bioinformatics of genomic association mapping

NARCIS (Netherlands)

Vaez Barzani, Ahmad

2015-01-01

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

Bioinformatic tools for PCR Primer design

African Journals Online (AJOL)

ES

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

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

NARCIS (Netherlands)

Wanders, B.

2012-01-01

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

Generative Topic Modeling in Image Data Mining and Bioinformatics Studies

Science.gov (United States)

Chen, Xin

2012-01-01

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

Taking Bioinformatics to Systems Medicine

NARCIS (Netherlands)

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

2016-01-01

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

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

Science.gov (United States)

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

2016-09-29

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

Bioinformatics Education in Pathology Training: Current Scope and Future Direction

Directory of Open Access Journals (Sweden)

Michael R Clay

2017-04-01

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

Field Research in the Teaching of Undergraduate Soil Science

Science.gov (United States)

Brevik, Eric C.; Senturklu, Songul; Landblom, Douglas

2015-04-01

Several studies have demonstrated that undergraduate students benefit from research experiences. Benefits of undergraduate research include 1) personal and intellectual development, 2) more and closer contact with faculty, 3) the use of active learning techniques, 4) creation of high expectations, 5) development of creative and problem-solving skills, 6) greater independence and intrinsic motivation to learn, and 7) exposure to practical skills. The scientific discipline also benefits, as studies have shown that undergraduates who engage in research experiences are more likely to remain science majors and finish their degree program (Lopatto, 2007). Research experiences come as close as possible to allowing undergraduates to experience what it is like to be an academic or research member of their profession working to advance their discipline. Soils form in the field, therefore, field experiences are very important in developing a complete and holistic understanding of soil science. Combining undergraduate research with field experiences can provide extremely beneficial outcomes to the undergraduate student, including increased understanding of and appreciation for detailed descriptions and data analysis as well as an enhanced ability to see how various parts of their undergraduate education come together to understand a complex problem. The experiences of the authors in working with undergraduate students on field-based research projects will be discussed, along with examples of some of the undergraduate research projects that have been undertaken. In addition, student impressions of their research experiences will be presented. Reference Lopatto, D. 2007. Undergraduate research experiences support science career decisions and active learning. CBE -- Life Sciences Education 6:297-306.

Agonist Binding to Chemosensory Receptors: A Systematic Bioinformatics Analysis

Directory of Open Access Journals (Sweden)

Fabrizio Fierro

2017-09-01

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

Teaching Bioinformatics and Neuroinformatics by Using Free Web-Based Tools

Science.gov (United States)

Grisham, William; Schottler, Natalie A.; Valli-Marill, Joanne; Beck, Lisa; Beatty, Jackson

2010-01-01

This completely computer-based module's purpose is to introduce students to bioinformatics resources. We present an easy-to-adopt module that weaves together several important bioinformatic tools so students can grasp how these tools are used in answering research questions. Students integrate information gathered from websites dealing with…

Bioinformatics meets user-centred design: a perspective.

Directory of Open Access Journals (Sweden)

Katrina Pavelin

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

Bioinformatics on the Cloud Computing Platform Azure

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

2014-01-01

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

Formative assessment promotes learning in undergraduate clinical ...

African Journals Online (AJOL)

Introduction. Clinical clerkships, typically situated in environments lacking educational structure, form the backbone of undergraduate medical training. The imperative to develop strategies that enhance learning in this context is apparent. This study explored the impact of longitudinal bedside formative assessment on ...

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

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

2015-01-01

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

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

NARCIS (Netherlands)

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

2014-01-01

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

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

Science.gov (United States)

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

BioStar: an online question & answer resource for the bioinformatics community

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Although the era of big data has produced many bioinformatics tools and databases, using them effectively often requires specialized knowledge. Many groups lack bioinformatics expertise, and frequently find that software documentation is inadequate and local colleagues may be overburdened or unfamil...

The Instructional Network: Using Facebook to Enhance Undergraduate Mathematics Instruction

Science.gov (United States)

Gregory, Peter; Gregory, Karen; Eddy, Erik

2014-01-01

Facebook is a website with over one billion users worldwide that is synonymous with social-networking. However, in this study, Facebook is used as an "instructional network". Two sections of an undergraduate calculus course were used to study the effects of participating in a Facebook group devoted solely to instruction. One section was…

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

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

2014-01-01

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

Dynamic Undergraduate Climate Change Affinity Program: University of Delaware Climate Program for Undergraduates (CPUG)

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Merrill, J.

2017-12-01

Multidisciplinary undergraduate climate change education is critical for students entering any sector of the workforce. The University of Delaware has developed a new interdisciplinary affinity program—UD Climate Program for Undergraduates (CPUG)—open to undergraduate students of all majors to provide a comprehensive educational experience designed to educate skilled climate change problem-solvers for a wide range of professional careers. The program is designed to fulfill all General Education requirements, and includes a residential community commitment and experiential learning in community outreach and problem solving. Seminars will introduce current popular press and research materials and provide practice in confirming source credibility, communications training, and psychological support, as well as team building. As undergraduates, members of the UD CPUG team will define, describe, and develop a solution or solutions for a pressing local climate challenge that has the potential for global impact. The choice of a challenge and approach to addressing it will be guided by the student's advisor. Students are expected to develop a practical, multidisciplinary solution to address the challenge as defined, using their educational and experiential training. Solutions will be presented to the UD community during the spring semester of their senior year, as a collaborative team solution, with enhancement through individual portfolios from each team member. The logic model, structure, curricular and co-curricular supports for the CPUG will be provided. Mechanisms of support available through University administration will also be discussed.

Using Mobile Technology to Enhance Undergraduate Student Digital Information Literacy Skills: A Canadian Case Study

Directory of Open Access Journals (Sweden)

Alice Schmidt Hanbidge

2015-08-01

Full Text Available Learning essential information literacy skills through the use of mobile phones is an innovative mlearning pilot project that was collaboratively undertaken in a Canadian university college over the course of two academic terms by faculty and the library staff. The research pilot project involved ninety one undergraduate students in five different classes majoring in psychology, social work, education or social development studies in an attempt to determine the effectiveness of using mobile technology to enhance students’ information literacy skills and learning experiences. Pre and post-test measures, and survey questionnaires generated quantitative and qualitative data that was analyzed to determine the degree of changes in frequency of mobile device information literacy access and fluency in digital literacy skills. The article highlights the Mobile Information Literacy innovation and includes the development and design of the mobile lessons, interactive exercises, and its applications. The study’s main results and conclusions are also discussed. Additionally, the successes and challenges of the pilot to support anytime, anywhere student mobile information literacy eLearning training that engages mobile learners and enhances their learning experience are identified and critically reflected upon to improve the innovation for stage two of the project.

The growing need for microservices in bioinformatics

Directory of Open Access Journals (Sweden)

Christopher L Williams

2016-01-01

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

The growing need for microservices in bioinformatics.

Science.gov (United States)

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

2016-01-01

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

The growing need for microservices in bioinformatics

Science.gov (United States)

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

2016-01-01

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

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

Science.gov (United States)

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

2016-01-01

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

Engaging Undergraduates through Interdisciplinary Research in Nanotechnology

Science.gov (United States)

Goonewardene, Anura U.; Offutt, Christine; Whitling, Jacqueline; Woodhouse, Donald

2012-01-01

To recruit and retain more students in all science disciplines at our small (5,000 student) public university, we implemented an interdisciplinary strategy focusing on nanotechnology and enhanced undergraduate research. Inherently interdisciplinary, the novelty of nanotechnology and its growing career potential appeal to students. To engage…

Sustainability Matters for Undergraduate Teaching and Learning

Science.gov (United States)

Fry, Catherine L.; Wei, Cynthia A.

2015-01-01

A growing body of evidence shows that infusing sustainability into undergraduate courses and programs can simultaneously benefit institutional goals, student learning outcomes, and society at large. In addition to being a globally relevant and urgent topic, sustainability can enhance learning of disciplinary concepts and development of broad…

Chapter 16: text mining for translational bioinformatics.

Science.gov (United States)

Cohen, K Bretonnel; Hunter, Lawrence E

2013-04-01

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

Time to Engage? Texting to Support and Enhance First Year Undergraduate Learning

Directory of Open Access Journals (Sweden)

Geraldine Jones

2009-04-01

Full Text Available In this paper we discuss a case study investigating how the academic and personal development of first year students on an undergraduate sports education degree can be supported and enhanced with mobile SMS communication. SMS-based technologies were introduced in response to students’ particular needs (in transition to Higher Education and characteristics (‘digital natives’. Despite being unaccustomed to using their mobile phones for academic study, students willingly participated in SMS communication with their tutor via a texting management service. Drawing on evidence from two student surveys, focus groups and a tutor’s journal, we illustrate the potential that mobile SMS communication has to link and establish continuity between face to face teaching sessions and online learning activities in the Virtual Learning Environment (VLE. Many students perceived the SMS communication to have had a positive impact on their management of study time. We link our findings with the existing literature and argue that mobile text based communication has the potential to support the development of time management skills, an important component of self regulatory learning, a skill which has been shown to be key in making a successful transition.

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

Science.gov (United States)

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

2012-07-01

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

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

Science.gov (United States)

Shachak, Aviv; Ophir, Ron; Rubin, Eitan

2005-01-01

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

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

Science.gov (United States)

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

2015-06-02

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

SPECIES DATABASES AND THE BIOINFORMATICS REVOLUTION.

Science.gov (United States)

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

BioSmalltalk: a pure object system and library for bioinformatics.

Science.gov (United States)

Morales, Hernán F; Giovambattista, Guillermo

2013-09-15

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

Bioclipse: an open source workbench for chemo- and bioinformatics

Directory of Open Access Journals (Sweden)

Wagener Johannes

2007-02-01

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

The Genomics Education Partnership: Successful Integration of Research into Laboratory Classes at a Diverse Group of Undergraduate Institutions

Science.gov (United States)

Shaffer, Christopher D.; Alvarez, Consuelo; Bailey, Cheryl; Barnard, Daron; Bhalla, Satish; Chandrasekaran, Chitra; Chandrasekaran, Vidya; Chung, Hui-Min; Dorer, Douglas R.; Du, Chunguang; Eckdahl, Todd T.; Poet, Jeff L.; Frohlich, Donald; Goodman, Anya L.; Gosser, Yuying; Hauser, Charles; Hoopes, Laura L.M.; Johnson, Diana; Jones, Christopher J.; Kaehler, Marian; Kokan, Nighat; Kopp, Olga R.; Kuleck, Gary A.; McNeil, Gerard; Moss, Robert; Myka, Jennifer L.; Nagengast, Alexis; Morris, Robert; Overvoorde, Paul J.; Shoop, Elizabeth; Parrish, Susan; Reed, Kelynne; Regisford, E. Gloria; Revie, Dennis; Rosenwald, Anne G.; Saville, Ken; Schroeder, Stephanie; Shaw, Mary; Skuse, Gary; Smith, Christopher; Smith, Mary; Spana, Eric P.; Spratt, Mary; Stamm, Joyce; Thompson, Jeff S.; Wawersik, Matthew; Wilson, Barbara A.; Youngblom, Jim; Leung, Wilson; Buhler, Jeremy; Mardis, Elaine R.; Lopatto, David

2010-01-01

Genomics is not only essential for students to understand biology but also provides unprecedented opportunities for undergraduate research. The goal of the Genomics Education Partnership (GEP), a collaboration between a growing number of colleges and universities around the country and the Department of Biology and Genome Center of Washington University in St. Louis, is to provide such research opportunities. Using a versatile curriculum that has been adapted to many different class settings, GEP undergraduates undertake projects to bring draft-quality genomic sequence up to high quality and/or participate in the annotation of these sequences. GEP undergraduates have improved more than 2 million bases of draft genomic sequence from several species of Drosophila and have produced hundreds of gene models using evidence-based manual annotation. Students appreciate their ability to make a contribution to ongoing research, and report increased independence and a more active learning approach after participation in GEP projects. They show knowledge gains on pre- and postcourse quizzes about genes and genomes and in bioinformatic analysis. Participating faculty also report professional gains, increased access to genomics-related technology, and an overall positive experience. We have found that using a genomics research project as the core of a laboratory course is rewarding for both faculty and students. PMID:20194808

Community annotation and bioinformatics workforce development in concert--Little Skate Genome Annotation Workshops and Jamborees.

Science.gov (United States)

Wang, Qinghua; Arighi, Cecilia N; King, Benjamin L; Polson, Shawn W; Vincent, James; Chen, Chuming; Huang, Hongzhan; Kingham, Brewster F; Page, Shallee T; Rendino, Marc Farnum; Thomas, William Kelley; Udwary, Daniel W; Wu, Cathy H

2012-01-01

Recent advances in high-throughput DNA sequencing technologies have equipped biologists with a powerful new set of tools for advancing research goals. The resulting flood of sequence data has made it critically important to train the next generation of scientists to handle the inherent bioinformatic challenges. The North East Bioinformatics Collaborative (NEBC) is undertaking the genome sequencing and annotation of the little skate (Leucoraja erinacea) to promote advancement of bioinformatics infrastructure in our region, with an emphasis on practical education to create a critical mass of informatically savvy life scientists. In support of the Little Skate Genome Project, the NEBC members have developed several annotation workshops and jamborees to provide training in genome sequencing, annotation and analysis. Acting as a nexus for both curation activities and dissemination of project data, a project web portal, SkateBase (http://skatebase.org) has been developed. As a case study to illustrate effective coupling of community annotation with workforce development, we report the results of the Mitochondrial Genome Annotation Jamborees organized to annotate the first completely assembled element of the Little Skate Genome Project, as a culminating experience for participants from our three prior annotation workshops. We are applying the physical/virtual infrastructure and lessons learned from these activities to enhance and streamline the genome annotation workflow, as we look toward our continuing efforts for larger-scale functional and structural community annotation of the L. erinacea genome.

Community annotation and bioinformatics workforce development in concert—Little Skate Genome Annotation Workshops and Jamborees

Science.gov (United States)

Wang, Qinghua; Arighi, Cecilia N.; King, Benjamin L.; Polson, Shawn W.; Vincent, James; Chen, Chuming; Huang, Hongzhan; Kingham, Brewster F.; Page, Shallee T.; Farnum Rendino, Marc; Thomas, William Kelley; Udwary, Daniel W.; Wu, Cathy H.

2012-01-01

Recent advances in high-throughput DNA sequencing technologies have equipped biologists with a powerful new set of tools for advancing research goals. The resulting flood of sequence data has made it critically important to train the next generation of scientists to handle the inherent bioinformatic challenges. The North East Bioinformatics Collaborative (NEBC) is undertaking the genome sequencing and annotation of the little skate (Leucoraja erinacea) to promote advancement of bioinformatics infrastructure in our region, with an emphasis on practical education to create a critical mass of informatically savvy life scientists. In support of the Little Skate Genome Project, the NEBC members have developed several annotation workshops and jamborees to provide training in genome sequencing, annotation and analysis. Acting as a nexus for both curation activities and dissemination of project data, a project web portal, SkateBase (http://skatebase.org) has been developed. As a case study to illustrate effective coupling of community annotation with workforce development, we report the results of the Mitochondrial Genome Annotation Jamborees organized to annotate the first completely assembled element of the Little Skate Genome Project, as a culminating experience for participants from our three prior annotation workshops. We are applying the physical/virtual infrastructure and lessons learned from these activities to enhance and streamline the genome annotation workflow, as we look toward our continuing efforts for larger-scale functional and structural community annotation of the L. erinacea genome. PMID:22434832

Pattern of Smartphones Utilisation among Engineering Undergraduates

Directory of Open Access Journals (Sweden)

Muliati Sedek

2014-04-01

Full Text Available The smartphones ownership among the undergraduates in Malaysia was recorded as high. However, little was known about its utilization patterns, thus, the focus of this research was to determine the utilisation patterns of smartphones based on the National Education Technology Standard for Students (NETS.S among engineering undergraduates in Malaysia. This study was based on a quantitative research and the population comprised undergraduates from four Malaysian Technical Universities. A total of 400 questionnaires were analyzed. Based on the results, the undergraduates’ utilisation level of smartphones for communication and collaboration tool was at a high level. Meanwhile, utilisation for operations and concepts tool and research and information fluency tool were at moderate level. Finally, smartphones utilisation as digital citizenship tool and critical thinking, problem solving and creativity tool were both at a low level. Hence, more training and workshops should be given to the students in order to encourage them to fully utilise smartphones in enhancing the higher order thinking skills.

Enhancing Undergraduates' Capabilities through Team-Based Competitions: The Edward Jones Challenge

Science.gov (United States)

Umble, Elisabeth J.; Umble, Michael; Artz, Kendall

2008-01-01

The Edward Jones Company recently initiated financial sponsorship of team-based competitions in six undergraduate business core classes at Baylor University. The challenges were chosen to take place in an introductory freshman business class, Managerial Accounting, Principles of Marketing, Corporate Finance, Operations Management, and Strategic…

Bioinformatics in New Generation Flavivirus Vaccines

Directory of Open Access Journals (Sweden)

Penelope Koraka

2010-01-01

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

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

Science.gov (United States)

Wren, Jonathan D

2016-09-01

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

Bioinformatic analysis of neurotropic HIV envelope sequences identifies polymorphisms in the gp120 bridging sheet that increase macrophage-tropism through enhanced interactions with CCR5

International Nuclear Information System (INIS)

Mefford, Megan E.; Kunstman, Kevin; Wolinsky, Steven M.; Gabuzda, Dana

2015-01-01

Macrophages express low levels of the CD4 receptor compared to T-cells. Macrophage-tropic HIV strains replicating in brain of untreated patients with HIV-associated dementia (HAD) express Envs that are adapted to overcome this restriction through mechanisms that are poorly understood. Here, bioinformatic analysis of env sequence datasets together with functional studies identified polymorphisms in the β3 strand of the HIV gp120 bridging sheet that increase M-tropism. D197, which results in loss of an N-glycan located near the HIV Env trimer apex, was detected in brain in some HAD patients, while position 200 was estimated to be under positive selection. D197 and T/V200 increased fusion and infection of cells expressing low CD4 by enhancing gp120 binding to CCR5. These results identify polymorphisms in the HIV gp120 bridging sheet that overcome the restriction to macrophage infection imposed by low CD4 through enhanced gp120–CCR5 interactions, thereby promoting infection of brain and other macrophage-rich tissues. - Highlights: • We analyze HIV Env sequences and identify amino acids in beta 3 of the gp120 bridging sheet that enhance macrophage tropism. • These amino acids at positions 197 and 200 are present in brain of some patients with HIV-associated dementia. • D197 results in loss of a glycan near the HIV Env trimer apex, which may increase exposure of V3. • These variants may promote infection of macrophages in the brain by enhancing gp120–CCR5 interactions

Bioinformatic analysis of neurotropic HIV envelope sequences identifies polymorphisms in the gp120 bridging sheet that increase macrophage-tropism through enhanced interactions with CCR5

Energy Technology Data Exchange (ETDEWEB)

Mefford, Megan E., E-mail: megan_mefford@hms.harvard.edu [Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA (United States); Kunstman, Kevin, E-mail: kunstman@northwestern.edu [Northwestern University Medical School, Chicago, IL (United States); Wolinsky, Steven M., E-mail: s-wolinsky@northwestern.edu [Northwestern University Medical School, Chicago, IL (United States); Gabuzda, Dana, E-mail: dana_gabuzda@dfci.harvard.edu [Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA (United States); Department of Neurology (Microbiology and Immunobiology), Harvard Medical School, Boston, MA (United States)

2015-07-15

Macrophages express low levels of the CD4 receptor compared to T-cells. Macrophage-tropic HIV strains replicating in brain of untreated patients with HIV-associated dementia (HAD) express Envs that are adapted to overcome this restriction through mechanisms that are poorly understood. Here, bioinformatic analysis of env sequence datasets together with functional studies identified polymorphisms in the β3 strand of the HIV gp120 bridging sheet that increase M-tropism. D197, which results in loss of an N-glycan located near the HIV Env trimer apex, was detected in brain in some HAD patients, while position 200 was estimated to be under positive selection. D197 and T/V200 increased fusion and infection of cells expressing low CD4 by enhancing gp120 binding to CCR5. These results identify polymorphisms in the HIV gp120 bridging sheet that overcome the restriction to macrophage infection imposed by low CD4 through enhanced gp120–CCR5 interactions, thereby promoting infection of brain and other macrophage-rich tissues. - Highlights: • We analyze HIV Env sequences and identify amino acids in beta 3 of the gp120 bridging sheet that enhance macrophage tropism. • These amino acids at positions 197 and 200 are present in brain of some patients with HIV-associated dementia. • D197 results in loss of a glycan near the HIV Env trimer apex, which may increase exposure of V3. • These variants may promote infection of macrophages in the brain by enhancing gp120–CCR5 interactions.

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

Science.gov (United States)

Fristensky, Brian

2007-01-01

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

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

Directory of Open Access Journals (Sweden)

Fristensky Brian

2007-02-01

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

mORCA: sailing bioinformatics world with mobile devices.

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

2018-03-01

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

p3d--Python module for structural bioinformatics.

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Fufezan, Christian; Specht, Michael

2009-08-21

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

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

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

2017-08-29

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

Bioinformatic tools for PCR Primer design

African Journals Online (AJOL)

ES

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

Realizing Student, Faculty, and Institutional Outcomes at Scale: Institutionalizing Undergraduate Research, Scholarship, and Creative Activity within Systems and Consortia

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Malachowski, Mitchell; Osborn, Jeffrey M.; Karukstis, Kerry K.; Ambos, Elizabeth L.

2015-01-01

This chapter reviews the evidence for the effectiveness of undergraduate research as a student, faculty, and institutional success pathway, and provides the context for the Council on Undergraduate Research's support for developing and enhancing undergraduate research in systems and consortia. The chapter also provides brief introductions to each…

Advance in structural bioinformatics

CERN Document Server

Wei, Dongqing; Zhao, Tangzhen; Dai, Hao

2014-01-01

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

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

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

2017-09-15

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

Enhancing Critical Thinking across the Undergraduate Experience: An Exemplar from Engineering

Science.gov (United States)

Ralston, Patricia A.; Bays, Cathy L.

2013-01-01

Faculty in a large, urban school of engineering designed a longitudinal study to assess the critical thinking skills of undergraduate students as they progressed through the engineering program. The Paul-Elder critical thinking framework was used to design course assignments and develop a holistic assessment rubric. The curriculum was re-designed…

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

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

2001-01-01

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

Use of electronic information resources among the undergraduate ...

African Journals Online (AJOL)

... among the undergraduate students in academic libraries in a recessed economy. ... and simple percentages were used to analyze the data for the research question. ... it also promoted their learning abilities and enhanced the development of research ... It was recommended that the management should make available ...

"Extreme Programming" in a Bioinformatics Class

Science.gov (United States)

Kelley, Scott; Alger, Christianna; Deutschman, Douglas

2009-01-01

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

Modern bioinformatics meets traditional Chinese medicine.

Science.gov (United States)

Gu, Peiqin; Chen, Huajun

2014-11-01

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

The SUPER Program: A Research-based Undergraduate Experience

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Ernakovich, J. G.; Boone, R. B.; Boot, C. M.; Denef, K.; Lavallee, J. M.; Moore, J. C.; Wallenstein, M. D.

2014-12-01

Producing undergraduates capable of broad, independent thinking is one of the grand challenges in science education. Experience-based learning, specifically hands-on research, is one mechanism for increasing students' ability to think critically. With this in mind, we created a two-semester long research program called SUPER (Skills for Undergraduate Participation in Ecological Research) aimed at teaching students to think like scientists and enhancing the student research experience through instruction and active-learning about the scientific method. Our aim was for students to gain knowledge, skills, and experience, and to conduct their own research. In the first semester, we hosted active-learning workshops on "Forming Hypotheses", "Experimental Design", "Collecting and Managing Data", "Analysis of Data", "Communicating to a Scientific Audience", "Reading Literature Effectively", and "Ethical Approaches". Each lesson was taught by different scientists from one of many ecological disciplines so that students were exposed to the variation in approach that scientists have. In the second semester, students paired with a scientific mentor and began doing research. To ensure the continued growth of the undergraduate researcher, we continued the active-learning workshops and the students attended meetings with their mentors. Thus, the students gained technical and cognitive skills in parallel, enabling them to understand both "the how" and "the why" of what they were doing in their research. The program culminated with a research poster session presented by the students. The interest in the program has grown beyond our expectations, and we have now run the program successfully for two years. Many of the students have gone on to campus research jobs, internships and graduate school, and have attributed part of their success in obtaining their positions to their experience with the SUPER program. Although common in other sciences, undergraduate research experiences are

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

Directory of Open Access Journals (Sweden)

Ernest Rossi

2006-01-01

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

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

Directory of Open Access Journals (Sweden)

Ernest Rossi

2006-01-01

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

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

Science.gov (United States)

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

2012-01-01

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

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

Science.gov (United States)

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

2016-06-13

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

A Quick Guide for Building a Successful Bioinformatics Community

Science.gov (United States)

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

2015-01-01

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

Undergraduate Research in Physics as an Educational Tool

Science.gov (United States)

Hakim, Toufic M.; Garg, Shila

2001-03-01

The National Science Foundation's 1996 report "Shaping the Future: New Expectations for Undergraduate Education in Science, Mathematics, Engineering and Technology" urged that in order to improve SME&T education, decisive action must be taken so that "all students have access to excellent undergraduate education in science .... and all students learn these subjects by direct experience with the methods and processes of inquiry." Research-related educational activities that integrate education and research have been shown to be valuable in improving the quality of education and enhancing the number of majors in physics departments. Student researchers develop a motivation to continue in science and engineering through an appreciation of how science is done and the excitement of doing frontier research. We will address some of the challenges of integrating research into the physics undergraduate curriculum effectively. The departmental and institutional policies and infrastructure required to help prepare students for this endeavor will be discussed as well as sources of support and the establishment of appropriate evaluation procedures.

Enhancing interdisciplinary, mathematics, and physical science in an undergraduate life science program through physical chemistry.

Science.gov (United States)

Pursell, David P

2009-01-01

BIO2010 advocates enhancing the interdisciplinary, mathematics, and physical science components of the undergraduate biology curriculum. The Department of Chemistry and Life Science at West Point responded by developing a required physical chemistry course tailored to the interests of life science majors. To overcome student resistance to physical chemistry, students were enabled as long-term stakeholders who would shape the syllabus by selecting life science topics of interest to them. The initial 2 yr of assessment indicates that students have a positive view of the course, feel they have succeeded in achieving course outcome goals, and that the course is relevant to their professional future. Instructor assessment of student outcome goal achievement via performance on exams and labs is comparable to that of students in traditional physical chemistry courses. Perhaps more noteworthy, both student and instructor assessment indicate positive trends from year 1 to year 2, presumably due to the student stakeholder effect.

New Link in Bioinformatics Services Value Chain: Position, Organization and Business Model

Directory of Open Access Journals (Sweden)

Mladen Čudanov

2012-11-01

Full Text Available This paper presents development in the bioinformatics services industry value chain, based on cloud computing paradigm. As genome sequencing costs per Megabase exponentially drop, industry needs to adopt. Paper has two parts: theoretical analysis and practical example of Seven Bridges Genomics Company. We are focused on explaining organizational, business and financial aspects of new business model in bioinformatics services, rather than technical side of the problem. In the light of that we present twofold business model fit for core bioinformatics research and Information and Communication Technologie (ICT support in the new environment, with higher level of capital utilization and better resistance to business risks.

Bioinformatics in High School Biology Curricula: A Study of State Science Standards

Science.gov (United States)

Wefer, Stephen H.; Sheppard, Keith

2008-01-01

The proliferation of bioinformatics in modern biology marks a modern revolution in science that promises to influence science education at all levels. This study analyzed secondary school science standards of 49 U.S. states (Iowa has no science framework) and the District of Columbia for content related to bioinformatics. The bioinformatics…

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

Science.gov (United States)

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

2006-11-06

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

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

Science.gov (United States)

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

2006-01-01

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

On the Strategies of Graduation Thesis Writing Teaching of Translation Major Undergraduates Based on Eco-Translatology

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Lin, Wang

2017-01-01

Graduation thesis is an indispensible procedure for each undergraduate, which is crucial for successful graduation, employment, further study and even further development. However, due to most undergraduates' ignorance of academic writing and the deficiency of current thesis writing course, thesis writing ability can hardly be enhanced and…

Genomics and bioinformatics resources for translational science in Rosaceae.

Science.gov (United States)

Jung, Sook; Main, Dorrie

2014-01-01

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

A Study of the Vocational Education Preferences and Interests of the Indian Undergraduate Students

Directory of Open Access Journals (Sweden)

P.A. Reddy

2011-05-01

Full Text Available The study identifies the priorities of vocational educational courses and interests of the Indian undergraduate students. The study was conducted in S.V. University area covering 300 undergraduate students of Arts, Commerce and Science streams. The study identified the more prominent, prominent and less prominent vocational educational courses. Further, studies the association between vocational education interests and the background of the students (sex, caste, stream of study, year of study and area. The difference between various groups of students belonging to above groups in their vocational education interests of the undergraduate students was also identified. The study provided a suggestive list of vocational educational courses for undergraduate students for enhancing their employability.

Implementing bioinformatic workflows within the bioextract server

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

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

Science.gov (United States)

Loucif, Samia

2014-01-01

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

Combining medical informatics and bioinformatics toward tools for personalized medicine.

Science.gov (United States)

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

2003-01-01

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

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

Science.gov (United States)

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

2015-04-01

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

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

Science.gov (United States)

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

2015-01-01

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

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

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Geraint Duck

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

The Potential to use Publication of Undergraduate Research as a Teaching Tool

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Brevik, Eric C.; Lindbo, David L.; Belcher, Christopher

2015-04-01

Several studies crossing numerous disciplinary boundaries have demonstrated that undergraduate students benefit from research experiences. These benefits include personal and intellectual development, more and closer contact with faculty, the use of active learning techniques, the creation of high expectations, the development of creative and problem-solving skills, and the development of greater independence and intrinsic motivation to learn. The discipline also gains in that studies show undergraduates who engage in research experiences are more likely to remain science majors and finish their degree program. Research experiences come as close as possible to allowing undergraduates to experience what it is like to be an academic or research member of their profession working to advance their discipline, therefore enhancing their professional socialization into their chosen field. If the goals achieved by undergraduate research include introducing these students to the advancement of their chosen field, it stands to reason the ultimate ending to this experience would be the publication of a peer-reviewed paper. While not all undergraduate projects will end with a product worthy of peer-reviewed publication, some definitely do, and the personal experience of the authors indicates that undergraduate students who achieve publication get great satisfaction and a sense of personal achievement from that publication. While a top-tier international journal probably isn't going to be the ultimate destination for many of these projects, there are several appropriate outlets. The SSSA journal Soil Horizons has published several undergraduate projects in recent years, and good undergraduate projects can often be published in state academy of science journals. Journals focused expressly on publishing undergraduate research include the Journal of Undergraduate Research and Scholarly Excellence, Reinvention, and the American Journal of Undergraduate Research. Case studies of

Relax with CouchDB--into the non-relational DBMS era of bioinformatics.

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

2012-07-01

With the proliferation of high-throughput technologies, genome-level data analysis has become common in molecular biology. Bioinformaticians are developing extensive resources to annotate and mine biological features from high-throughput data. The underlying database management systems for most bioinformatics software are based on a relational model. Modern non-relational databases offer an alternative that has flexibility, scalability, and a non-rigid design schema. Moreover, with an accelerated development pace, non-relational databases like CouchDB can be ideal tools to construct bioinformatics utilities. We describe CouchDB by presenting three new bioinformatics resources: (a) geneSmash, which collates data from bioinformatics resources and provides automated gene-centric annotations, (b) drugBase, a database of drug-target interactions with a web interface powered by geneSmash, and (c) HapMap-CN, which provides a web interface to query copy number variations from three SNP-chip HapMap datasets. In addition to the web sites, all three systems can be accessed programmatically via web services. Copyright © 2012 Elsevier Inc. All rights reserved.

Using registries to integrate bioinformatics tools and services into workbench environments

DEFF Research Database (Denmark)

Ménager, Hervé; Kalaš, Matúš; Rapacki, Kristoffer

2016-01-01

The diversity and complexity of bioinformatics resources presents significant challenges to their localisation, deployment and use, creating a need for reliable systems that address these issues. Meanwhile, users demand increasingly usable and integrated ways to access and analyse data, especially......, a software component that will ease the integration of bioinformatics resources in a workbench environment, using their description provided by the existing ELIXIR Tools and Data Services Registry....

Undergraduate Research as a Primary Pathway to STEM Careers: Perspectives from the Council on Undergraduate Research

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Manley, P. L.; Ambos, E. L.

2012-12-01

Undergraduate research (UR) is one of the most authentic and effective ways to promote student learning, and is a high-impact educational practice that can lead to measurable gains in student retention and graduation rates, as well as career aspirations. In recent years, UR has expanded from intensive summer one-on-one faculty-student mentored experiences to application in a variety of educational settings, including large lower division courses. The Council on Undergraduate Research (CUR), founded in 1978, is a national organization of individual (8000) and institutional members (650) within a divisional structure that includes geosciences, as well as 10 other thematic areas. CUR's main mission is to support and promote high-quality undergraduate student-faculty collaborative research and scholarship that develops learning through research. CUR fulfills this mission through extensive publication offerings, faculty and student-directed professional development events, and outreach and advocacy activities that share successful models and strategies for establishing, institutionalizing, and sustaining undergraduate research programs. Over the last decade, CUR has worked with hundreds of academic institutions, including two-year colleges, to develop practices to build undergraduate research into campus cultures and operations. As documented in CUR publications such as Characteristics of Excellence in Undergraduate Research (COEUR), strategies institutions may adopt to enhance and sustain UR often include: (1) the establishment of a central UR campus office, (2) extensive student and faculty participation in campus-based, as well as regional UR celebration events, (3) development of a consistent practice of assessment of UR's impact on student success, and, (4) establishment of clear policies for recognizing and rewarding faculty engagement in UR, particularly with respect to mentorship and publication with student scholars. Three areas of current focus within the

DOE EPSCoR Initiative in Structural and computational Biology/Bioinformatics

Energy Technology Data Exchange (ETDEWEB)

Wallace, Susan S.

2008-02-21

The overall goal of the DOE EPSCoR Initiative in Structural and Computational Biology was to enhance the competiveness of Vermont research in these scientific areas. To develop self-sustaining infrastructure, we increased the critical mass of faculty, developed shared resources that made junior researchers more competitive for federal research grants, implemented programs to train graduate and undergraduate students who participated in these research areas and provided seed money for research projects. During the time period funded by this DOE initiative: (1) four new faculty were recruited to the University of Vermont using DOE resources, three in Computational Biology and one in Structural Biology; (2) technical support was provided for the Computational and Structural Biology facilities; (3) twenty-two graduate students were directly funded by fellowships; (4) fifteen undergraduate students were supported during the summer; and (5) twenty-eight pilot projects were supported. Taken together these dollars resulted in a plethora of published papers, many in high profile journals in the fields and directly impacted competitive extramural funding based on structural or computational biology resulting in 49 million dollars awarded in grants (Appendix I), a 600% return on investment by DOE, the State and University.

Bioinformatics approaches to single-cell analysis in developmental biology.

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Yalcin, Dicle; Hakguder, Zeynep M; Otu, Hasan H

2016-03-01

Individual cells within the same population show various degrees of heterogeneity, which may be better handled with single-cell analysis to address biological and clinical questions. Single-cell analysis is especially important in developmental biology as subtle spatial and temporal differences in cells have significant associations with cell fate decisions during differentiation and with the description of a particular state of a cell exhibiting an aberrant phenotype. Biotechnological advances, especially in the area of microfluidics, have led to a robust, massively parallel and multi-dimensional capturing, sorting, and lysis of single-cells and amplification of related macromolecules, which have enabled the use of imaging and omics techniques on single cells. There have been improvements in computational single-cell image analysis in developmental biology regarding feature extraction, segmentation, image enhancement and machine learning, handling limitations of optical resolution to gain new perspectives from the raw microscopy images. Omics approaches, such as transcriptomics, genomics and epigenomics, targeting gene and small RNA expression, single nucleotide and structural variations and methylation and histone modifications, rely heavily on high-throughput sequencing technologies. Although there are well-established bioinformatics methods for analysis of sequence data, there are limited bioinformatics approaches which address experimental design, sample size considerations, amplification bias, normalization, differential expression, coverage, clustering and classification issues, specifically applied at the single-cell level. In this review, we summarize biological and technological advancements, discuss challenges faced in the aforementioned data acquisition and analysis issues and present future prospects for application of single-cell analyses to developmental biology. © The Author 2015. Published by Oxford University Press on behalf of the European

Transition from Traditional to ICT-Enhanced Learning Environments in Undergraduate Chemistry Courses

Science.gov (United States)

Barak, Miri

2007-01-01

This paper describes a three-year study conducted among chemistry instructors (professors and teaching assistants) at a post-secondary institution. The goal was to explore the integration process of information and communication technologies (ICT) into traditional teaching. Four undergraduate chemistry courses incorporated a course website, an…

p3d – Python module for structural bioinformatics

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Fufezan Christian

2009-08-01

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

A comparison of common programming languages used in bioinformatics.

Science.gov (United States)

Fourment, Mathieu; Gillings, Michael R

2008-02-05

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

Bioinformatics process management: information flow via a computational journal

Directory of Open Access Journals (Sweden)

Lushington Gerald

2007-12-01

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

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

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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.

Fostering successful interprofessional teamwork through an undergraduate student placement in a secondary school.

Science.gov (United States)

Fortugno, Mariella; Chandra, Smriti; Espin, Sherry; Gucciardi, Enza

2013-07-01

This exploratory case study examined an interprofessional placement of undergraduate students from nutrition, nursing, early childhood education, and child and youth care who collaborated to develop and deliver four healthy-living modules to secondary school students in Canada. An inductive thematic analysis was used to describe the teamwork that occurred between students. Data collected included focus groups with undergraduate students and preceptors, undergraduate students' reflections and secondary school students' evaluations of the modules delivered. Two major themes that emerged from all data sources were "team functioning" and "shift in perspectives". The undergraduate students identified several ways that facilitated their successful and positive teamwork with one another and also expressed how the placement experience improved their interprofessional skills. Findings from this study are discussed in relation to contact theory (Allport, 1954) and self-presentation theory (Goffman, 1963). This study suggests that providing undergraduate students with interprofessional placements in an educational setting can enhance interprofessional teamwork opportunities for students of various disciplines.

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

Science.gov (United States)

Cazals, Frédéric; Dreyfus, Tom

2017-04-01

Software in structural bioinformatics has mainly been application driven. To favor practitioners seeking off-the-shelf applications, but also developers seeking advanced building blocks to develop novel applications, we undertook the design of the Structural Bioinformatics Library ( SBL , http://sbl.inria.fr ), a generic C ++/python cross-platform software library targeting complex problems in structural bioinformatics. Its tenet is based on a modular design offering a rich and versatile framework allowing the development of novel applications requiring well specified complex operations, without compromising robustness and performances. The SBL involves four software components (1-4 thereafter). For end-users, the SBL provides ready to use, state-of-the-art (1) applications to handle molecular models defined by unions of balls, to deal with molecular flexibility, to model macro-molecular assemblies. These applications can also be combined to tackle integrated analysis problems. For developers, the SBL provides a broad C ++ toolbox with modular design, involving core (2) algorithms , (3) biophysical models and (4) modules , the latter being especially suited to develop novel applications. The SBL comes with a thorough documentation consisting of user and reference manuals, and a bugzilla platform to handle community feedback. The SBL is available from http://sbl.inria.fr. Frederic.Cazals@inria.fr. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

What do medical students understand by research and research skills? Identifying research opportunities within undergraduate projects.

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Murdoch-Eaton, Deborah; Drewery, Sarah; Elton, Sarah; Emmerson, Catherine; Marshall, Michelle; Smith, John A; Stark, Patsy; Whittle, Sue

2010-01-01

Undergraduate research exposure leads to increased recruitment into academic medicine, enhanced employability and improved postgraduate research productivity. Uptake of undergraduate research opportunities is reported to be disappointing, and little is known about how students perceive research. To investigate opportunities for undergraduate participation in research, recognition of such opportunities, and associated skills development. A mixed method approach, incorporating student focus and study groups, and documentary analysis at five UK medical schools. Undergraduates recognised the benefits of acquiring research skills, but identified practical difficulties and disadvantages of participating. Analysis of 905 projects in four main research skill areas - (1) research methods; (2) information gathering; (3) critical analysis and review; (4) data processing - indicated 52% of projects provided opportunities for students to develop one or more skills, only 13% offered development in all areas. In 17%, project descriptions provided insufficient information to determine opportunities. Supplied with information from a representative sample of projects (n = 80), there was little consensus in identifying skills among students or between students and researchers. Consensus improved dramatically following guidance on how to identify skills. Undergraduates recognise the benefits of research experience but need a realistic understanding of the research process. Opportunities for research skill development may not be obvious. Undergraduates require training to recognise the skills required for research and enhanced transparency in potential project outcomes.

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

OpenAIRE

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

2016-01-01

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

Rough-fuzzy pattern recognition applications in bioinformatics and medical imaging

CERN Document Server

Maji, Pradipta

2012-01-01

Learn how to apply rough-fuzzy computing techniques to solve problems in bioinformatics and medical image processing Emphasizing applications in bioinformatics and medical image processing, this text offers a clear framework that enables readers to take advantage of the latest rough-fuzzy computing techniques to build working pattern recognition models. The authors explain step by step how to integrate rough sets with fuzzy sets in order to best manage the uncertainties in mining large data sets. Chapters are logically organized according to the major phases of pattern recognition systems dev

Bioinformatics and moonlighting proteins

Directory of Open Access Journals (Sweden)

Sergio eHernández

2015-06-01

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

Research on Improving the Training Quality of Undergraduate Communists in Independent Colleges

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Lina Jiang

2014-02-01

Full Text Available Problems which undergraduate communists have in their motivations, ideal and faith to be members of Chinese Communist Party attach new trend and situation to the education and cultivation of undergraduate communists. The author has surveyed students of 14 departments in Beijing Normal University Zhuhai Campus. The questionnaire which is to learn the problems faced in the recruiting, cultivation and education of undergraduate communists, mainly concentrates on 5 aspects—motivations to be a party member, requirements for a party member, activities in students’ party branches, education of communists and recruiting of party members. At last, based on the analysis of the results and according to different groups, Beijing Normal University Zhuhai Campus, as an independent college, carries on multi-level party classes, delegates the authority of party class teaching and adopts popular mode of party classes. At the same time, she combines the classes with social work, enhances the evaluating work of party members and arouses the awareness of undergraduate communists, and also promotes the training quality of undergraduate communists.

Best practices in bioinformatics training for life scientists.

KAUST Repository

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

2013-01-01

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

Integrating numerical computation into the undergraduate education physics curriculum using spreadsheet excel

Science.gov (United States)

Fauzi, Ahmad

2017-11-01

Numerical computation has many pedagogical advantages: it develops analytical skills and problem-solving skills, helps to learn through visualization, and enhances physics education. Unfortunately, numerical computation is not taught to undergraduate education physics students in Indonesia. Incorporate numerical computation into the undergraduate education physics curriculum presents many challenges. The main challenges are the dense curriculum that makes difficult to put new numerical computation course and most students have no programming experience. In this research, we used case study to review how to integrate numerical computation into undergraduate education physics curriculum. The participants of this research were 54 students of the fourth semester of physics education department. As a result, we concluded that numerical computation could be integrated into undergraduate education physics curriculum using spreadsheet excel combined with another course. The results of this research become complements of the study on how to integrate numerical computation in learning physics using spreadsheet excel.

Privacy Preserving PCA on Distributed Bioinformatics Datasets

Science.gov (United States)

Li, Xin

2011-01-01

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

Rise and demise of bioinformatics? Promise and progress.

Directory of Open Access Journals (Sweden)

Christos A Ouzounis

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

Meeting review: 2002 O'Reilly Bioinformatics Technology Conference.

Science.gov (United States)

Counsell, Damian

2002-01-01

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

Enhancing Teaching and Learning Wi-Fi Networking Using Limited Resources to Undergraduates

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Sarkar, Nurul I.

2013-01-01

Motivating students to learn Wi-Fi (wireless fidelity) wireless networking to undergraduate students is often difficult because many students find the subject rather technical and abstract when presented in traditional lecture format. This paper focuses on the teaching and learning aspects of Wi-Fi networking using limited hardware resources. It…

Enhancing the Undergraduate Industrial Engineering Curriculum: Defining Desired Characteristics and Emerging Topics

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Eskandari, Hamidreza; Sala-Diakanda, Serge; Furterer, Sandra; Rabelo, Luis; Crumpton-Young, Lesia; Williams, Kent

2007-01-01

Purpose: This paper aims to present the results of an initial research study conducted to identify the desired professional characteristics of an industrial engineer with an undergraduate degree and the emerging topic areas that should be incorporated into the curriculum to prepare industrial engineering (IE) graduates for the future workforce.…

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

Directory of Open Access Journals (Sweden)

Cieślik Marcin

2011-02-01

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

Endovascular Device Testing with Particle Image Velocimetry Enhances Undergraduate Biomedical Engineering Education

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Nair, Priya; Ankeny, Casey J.; Ryan, Justin; Okcay, Murat; Frakes, David H.

2016-01-01

We investigated the use of a new system, HemoFlow™, which utilizes state of the art technologies such as particle image velocimetry to test endovascular devices as part of an undergraduate biomedical engineering curriculum. Students deployed an endovascular stent into an anatomical model of a cerebral aneurysm and measured intra-aneurysmal flow…

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

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Anjali Srivastava

2017-09-01

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

Bioinformatics: A History of Evolution "In Silico"

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Ondrej, Vladan; Dvorak, Petr

2012-01-01

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

Protein raftophilicity. How bioinformatics can help membranologists

DEFF Research Database (Denmark)

Nielsen, Henrik; Sperotto, Maria Maddalena

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

Development and implementation of a bioinformatics online ...

African Journals Online (AJOL)

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

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

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

2016-01-01

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

The Current Use of Social Media in Undergraduate Nursing Education: A Review of the Literature.

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Ross, Jennifer Gunberg; Myers, Shannon Marie

2017-07-01

Social media, including blogs, Twitter, wikis, Facebook, YouTube, and Ning, provides an opportunity for nurse educators to engage undergraduate nursing students who are members of the millennial generation in active learning while enhancing knowledge and fostering communication. Despite the rise of social media usage in undergraduate nursing education, there is a significant deficiency of empirical evidence supporting the efficacy and outcomes of these teaching strategies. This article provides an overview of social media use in undergraduate nursing education and a review of the existing research related to social media use in prelicensure nursing education. Overall, undergraduate nursing students respond positively to social media use in nursing education; however, no outcome measures are available to determine the effect of these teaching strategies on student learning.

Does the Pedagogy for the Teaching of First Year Undergraduate Laboratory Practicals Still Meet the Needs of the Curriculum?

OpenAIRE

Ann Hopper

2014-01-01

This work examines the teaching approach for chemistry laboratory practicals for first year undergraduate students to determine if the underpinning pedagogical strategy meets the requirements for these students for the remainder of their undergraduate programme. This is based on the knowledge, skills, content and learning outcomes for undergraduate chemistry courses. This work aims to enhance the first year experience of chemistry education by facilitating greater student engagement and “deep...

Teaching Strategies for Personality Assessment at the Undergraduate Level.

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Roche, Michael J; Jacobson, Nicholas C; Roche, Carley A

2017-01-01

Personality assessment is a crucial component of clinical practice, and the training and proficiency criteria to develop competence are complex and multifaceted. Like many advanced topics, the field of personality assessment would benefit from early exposure in undergraduate classroom settings. This research evaluates how an undergraduate personality course can be enhanced through 2 enrichment activities (self-assessments and a personality project). Students completed several self-assessments of their personality and wrote a comprehensive and integrative personality assessment about themselves. Results demonstrated that these activities increased interest in personality assessment, deepened understanding of course material, and promoted student growth and self-exploration. We discuss the benefits of these enrichment activities for the student, instructor, and field of personality science.

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

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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.

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

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Balqis, Widodo, Lukiati, Betty; Amin, Mohamad

2017-05-01

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

A BIOINFORMATIC STRATEGY TO RAPIDLY CHARACTERIZE CDNA LIBRARIES

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

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

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

2012-01-01

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

Exploring Cystic Fibrosis Using Bioinformatics Tools: A Module Designed for the Freshman Biology Course

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Zhang, Xiaorong

2011-01-01

We incorporated a bioinformatics component into the freshman biology course that allows students to explore cystic fibrosis (CF), a common genetic disorder, using bioinformatics tools and skills. Students learn about CF through searching genetic databases, analyzing genetic sequences, and observing the three-dimensional structures of proteins…

2nd Colombian Congress on Computational Biology and Bioinformatics

CERN Document Server

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

2014-01-01

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

Biowep: a workflow enactment portal for bioinformatics applications.

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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

Biowep: a workflow enactment portal for bioinformatics applications

Directory of Open Access Journals (Sweden)

Romano Paolo

2007-03-01

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

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

Science.gov (United States)

Oshita, Kazuki; Arakawa, Kazuharu; Tomita, Masaru

2011-04-29

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

KBWS: an EMBOSS associated package for accessing bioinformatics web services

Directory of Open Access Journals (Sweden)

Tomita Masaru

2011-04-01

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

Undergraduate Research as a Process for STEM Teaching and Learning Systemic Change: Lessons Learned from the Council on Undergraduate Research NSF CCLI and TUES Projects

Science.gov (United States)

Ambos, E. L.; Havholm, K. G.; Malachowski, M.; Osborn, J.; Karukstis, K.

2013-12-01

For more than seven years, the Council on Undergraduate Research (CUR), the primary organization supporting programs, services, and advocacy for undergraduate research, has been working with support from the NSF's Division of Undergraduate Education (DUE) to enhance, sustain, and institutionalize undergraduate research in diverse STEM disciplines and higher education settings. The Council on Undergraduate Research comprises more than 9000 individual and 670 institutional members within a divisional structure that includes geosciences, as well as 11 other thematic areas. Through its most recent grant: 'Transformational Learning through Undergraduate Research: Comprehensive Support for Faculty, Institutions, State Systems and Consortia' (NSF DUE CCLI III Award #09-20275), CUR has been collaborating with six higher education systems, each selected after a rigorous national application process in 2010 and 2011. These six systems, which collectively represent 79 individual institutions, are the Council of Public Liberal Arts Colleges (COPLAC), University of Wisconsin System (UWS), California State University System (CSU), City University of New York (CUNY), Great Lakes Colleges Association (GLCA), and Pennsylvania State System of Higher Education (PASSHE). The more than 350 participants of faculty and senior-level administrators from the six systems are engaged in shared multi-faceted and multi-year professional development experiences. Teams from each system attended customized institutes facilitated by CUR experts in 2011-2012, during which the teams developed specific action plans focused on institutionalizing undergraduate research on their campus and within their system. The systems were reconvened as a group a year after the first institute, to chart progress toward achieving their goals. Based on interviews and surveys with participants, campus teams are making substantial progress toward implementation of robust undergraduate research programs, and are making

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

Science.gov (United States)

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

2018-01-01

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

Statistical modelling in biostatistics and bioinformatics selected papers

CERN Document Server

Peng, Defen

2014-01-01

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

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

Science.gov (United States)

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

2013-01-01

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

Air, Ocean and Climate Monitoring Enhancing Undergraduate Training in the Physical, Environmental and Computer Sciences

Science.gov (United States)

Hope, W. W.; Johnson, L. P.; Obl, W.; Stewart, A.; Harris, W. C.; Craig, R. D.

2000-01-01

Faculty in the Department of Physical, Environmental and Computer Sciences strongly believe in the concept that undergraduate research and research-related activities must be integrated into the fabric of our undergraduate Science and Technology curricula. High level skills, such as problem solving, reasoning, collaboration and the ability to engage in research, are learned for advanced study in graduate school or for competing for well paying positions in the scientific community. One goal of our academic programs is to have a pipeline of research activities from high school to four year college, to graduate school, based on the GISS Institute on Climate and Planets model.

CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community.

Science.gov (United States)

Connor, Thomas R; Loman, Nicholas J; Thompson, Simon; Smith, Andy; Southgate, Joel; Poplawski, Radoslaw; Bull, Matthew J; Richardson, Emily; Ismail, Matthew; Thompson, Simon Elwood-; Kitchen, Christine; Guest, Martyn; Bakke, Marius; Sheppard, Samuel K; Pallen, Mark J

2016-09-01

The increasing availability and decreasing cost of high-throughput sequencing has transformed academic medical microbiology, delivering an explosion in available genomes while also driving advances in bioinformatics. However, many microbiologists are unable to exploit the resulting large genomics datasets because they do not have access to relevant computational resources and to an appropriate bioinformatics infrastructure. Here, we present the Cloud Infrastructure for Microbial Bioinformatics (CLIMB) facility, a shared computing infrastructure that has been designed from the ground up to provide an environment where microbiologists can share and reuse methods and data.

Bioboxes: standardised containers for interchangeable bioinformatics software.

Science.gov (United States)

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

2015-01-01

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

Comparative Proteome Bioinformatics: Identification of Phosphotyrosine Signaling Proteins in the Unicellular Protozoan Ciliate Tetrahymena

DEFF Research Database (Denmark)

Gammeltoft, Steen; Christensen, Søren Tvorup; Joachimiak, Marcin

2005-01-01

Tetrahymena, bioinformatics, cilia, evolution, signaling, TtPTK1, PTK, Grb2, SH-PTP 2, Plcy, Src, PTP, PI3K, SH2, SH3, PH......Tetrahymena, bioinformatics, cilia, evolution, signaling, TtPTK1, PTK, Grb2, SH-PTP 2, Plcy, Src, PTP, PI3K, SH2, SH3, PH...

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

DEFF Research Database (Denmark)

Kouskoumvekaki, Irene; Shublaq, Nour; Brunak, Søren

2014-01-01

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

Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator

Directory of Open Access Journals (Sweden)

Thoraval Samuel

2005-04-01

Full Text Available Abstract Background Computational methods for problem solving need to interleave information access and algorithm execution in a problem-specific workflow. The structures of these workflows are defined by a scaffold of syntactic, semantic and algebraic objects capable of representing them. Despite the proliferation of GUIs (Graphic User Interfaces in bioinformatics, only some of them provide workflow capabilities; surprisingly, no meta-analysis of workflow operators and components in bioinformatics has been reported. Results We present a set of syntactic components and algebraic operators capable of representing analytical workflows in bioinformatics. Iteration, recursion, the use of conditional statements, and management of suspend/resume tasks have traditionally been implemented on an ad hoc basis and hard-coded; by having these operators properly defined it is possible to use and parameterize them as generic re-usable components. To illustrate how these operations can be orchestrated, we present GPIPE, a prototype graphic pipeline generator for PISE that allows the definition of a pipeline, parameterization of its component methods, and storage of metadata in XML formats. This implementation goes beyond the macro capacities currently in PISE. As the entire analysis protocol is defined in XML, a complete bioinformatic experiment (linked sets of methods, parameters and results can be reproduced or shared among users. Availability: http://if-web1.imb.uq.edu.au/Pise/5.a/gpipe.html (interactive, ftp://ftp.pasteur.fr/pub/GenSoft/unix/misc/Pise/ (download. Conclusion From our meta-analysis we have identified syntactic structures and algebraic operators common to many workflows in bioinformatics. The workflow components and algebraic operators can be assimilated into re-usable software components. GPIPE, a prototype implementation of this framework, provides a GUI builder to facilitate the generation of workflows and integration of heterogeneous

Analyzing the field of bioinformatics with the multi-faceted topic modeling technique.

Science.gov (United States)

Heo, Go Eun; Kang, Keun Young; Song, Min; Lee, Jeong-Hoon

2017-05-31

Bioinformatics is an interdisciplinary field at the intersection of molecular biology and computing technology. To characterize the field as convergent domain, researchers have used bibliometrics, augmented with text-mining techniques for content analysis. In previous studies, Latent Dirichlet Allocation (LDA) was the most representative topic modeling technique for identifying topic structure of subject areas. However, as opposed to revealing the topic structure in relation to metadata such as authors, publication date, and journals, LDA only displays the simple topic structure. In this paper, we adopt the Tang et al.'s Author-Conference-Topic (ACT) model to study the field of bioinformatics from the perspective of keyphrases, authors, and journals. The ACT model is capable of incorporating the paper, author, and conference into the topic distribution simultaneously. To obtain more meaningful results, we use journals and keyphrases instead of conferences and bag-of-words.. For analysis, we use PubMed to collected forty-six bioinformatics journals from the MEDLINE database. We conducted time series topic analysis over four periods from 1996 to 2015 to further examine the interdisciplinary nature of bioinformatics. We analyze the ACT Model results in each period. Additionally, for further integrated analysis, we conduct a time series analysis among the top-ranked keyphrases, journals, and authors according to their frequency. We also examine the patterns in the top journals by simultaneously identifying the topical probability in each period, as well as the top authors and keyphrases. The results indicate that in recent years diversified topics have become more prevalent and convergent topics have become more clearly represented. The results of our analysis implies that overtime the field of bioinformatics becomes more interdisciplinary where there is a steady increase in peripheral fields such as conceptual, mathematical, and system biology. These results are

Engaging Undergraduates in Economics

Science.gov (United States)

Gajwani, Kiran; Miron, Jeffrey

2015-01-01

Siegfried and Stock (2007) explore the undergraduate training of PhD economists. Their findings show that among U.S. undergraduate economics programs, the Harvard University Economics Department produces many eventual economics PhD recipients. In this article, the authors discuss Harvard's undergraduate economics program and highlight some key…

Graduate teaching assistants' perceptions of teaching competencies required for work in undergraduate science labs

Science.gov (United States)

Deacon, Christopher; Hajek, Allyson; Schulz, Henry

2017-11-01

Many post-secondary institutions provide training and resources to help GTAs fulfil their teaching roles. However, few programmes focus specifically on the teaching competencies required by GTAs who work with undergraduate students in laboratory settings where learning tends to be more active and inquiry based than in classroom settings. From a review of 8 GTA manuals, we identified 20 competencies and then surveyed faculty and lab coordinators (FIS) and GTAs from a Faculty of Science at a comprehensive Canadian university to identify which of those competencies are required of GTAs who work in undergraduate science labs. GTAs and FIS did not significantly differ in the competencies they view as required for GTAs to work effectively in undergraduate labs. But, when comparing the responses of GTAs and FIS to TA manuals, 'Clearly and effectively communicates ideas and information with students' was the only competency for which there was agreement on the level of requirement. We also examined GTAs' self-efficacy for each of the identified competencies and found no overall relationship between self-efficacy and demographic characteristics, including experience and training. Our results can be used to inform the design of training programmes specifically for GTAs who work in undergraduate science labs, for example, programmes should provide strategies for GTAs to obtain feedback which they can use to enhance their teaching skills. The goal of this study is to improve undergraduate lab instruction in faculties of science and to enhance the teaching experience of GTAs by better preparing them for their role.

Structuring an Undergraduate Mathematics Seminar Dealing with Options and Hedging

Science.gov (United States)

Prevot, K. J.

2006-01-01

Offering mathematics majors the opportunity to engage in current, real-world applications can be an important enhancement to their undergraduate course curriculum. Instead of focusing on the traditional topic areas in pure and/or applied mathematics, one may structure a seminar course for senior mathematics majors by concentrating on a specific…

libcov: A C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny

OpenAIRE

Butt, Davin; Roger, Andrew J; Blouin, Christian

2005-01-01

Background An increasing number of bioinformatics methods are considering the phylogenetic relationships between biological sequences. Implementing new methodologies using the maximum likelihood phylogenetic framework can be a time consuming task. Results The bioinformatics library libcov is a collection of C++ classes that provides a high and low-level interface to maximum likelihood phylogenetics, sequence analysis and a data structure for structural biological methods. libcov can be used ...

The impacts and "best practices" of undergraduate - graduate student mentoring relationships in undergraduate research experiences

Science.gov (United States)

Campanile, Megan Faurot

With the growth of undergraduate research in the U.S., over the past two decades, faculty are more often assigning graduate students to mentor undergraduate students than providing the one-on-one mentoring themselves. A critical gap that exists in the literature is how undergraduate -- graduate student mentoring relationships in undergraduate research influences both students' academic and career paths. The research questions that framed this study were: (1) What, if any, changes occur in the academic and career paths of undergraduate and graduate students who participate in undergraduate research experiences? and (2) Are there variables that constitute "best practices" in the mentoring relationships in undergraduate research experiences and, if so, what are they? The study context was the National Science Foundation Research Experiences for Undergraduates program at Illinois Institute of Technology and the 113 undergraduate researchers and 31 graduate student mentors who participated from 2006 -- 2014. Surveys and interviews were administered to collect pre- and post-program data and follow-up data during the 2014 -- 2015 academic year. Descriptive statistics, content analysis method, and constant comparative method were used to analyze the data. Key findings on the undergraduate researchers were their actual earned graduate degree types (Ph.D. 20%, M.D. 20%, M.S. 48%, other 12%) and fields (STEM 57%, medical 35%, other 8%) and the careers they were pursuing or working in. All the graduate student mentors were pursuing or working in the STEM fields (academia 50%, industry 40%, government 10%). More than 75% of both the undergraduate and graduate students reported that their mentoring relationships had a somewhat to extremely influential impact on their academic and career paths. A set of "best practices" of mentoring were developed for both the undergraduate and graduate students and focused on the mentoring experiences related to learning and teaching about

Bioinformatics for whole-genome shotgun sequencing of microbial communities.

Directory of Open Access Journals (Sweden)

Kevin Chen

2005-07-01

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

Educational Aspects of Undergraduate Research on Smartphone Application Development

Directory of Open Access Journals (Sweden)

Joseph Gibson

2013-12-01

Full Text Available Smartphones have become commonplace in today's society. There seems to be a mobile application for every conceivable use, expect one. Smartphones have been conspicuously absent in higher education. This research examines the use of mobile applications (apps in the higher education setting. In addition, it evaluates the potential for including smartphone application development in undergraduate computer science curriculum. This paper will present a variety of smartphone apps that were developed by undergraduate researchers for use for use by students and faculty in a university environment, and apps developed to enhance the educational experience in the classroom. We also study the efficacy of the inclusion of smartphone app development in the computer science curriculum and modes for its inclusion.

Promoting synergistic research and education in genomics and bioinformatics.

Science.gov (United States)

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

2008-01-01

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

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

Science.gov (United States)

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

2017-06-30

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

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

Science.gov (United States)

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

2018-05-14

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

Bioinformatics and Microarray Data Analysis on the Cloud.

Science.gov (United States)

Calabrese, Barbara; Cannataro, Mario

2016-01-01

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

Protecting innovation in bioinformatics and in-silico biology.

Science.gov (United States)

Harrison, Robert

2003-01-01

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

Pay-as-you-go data integration for bio-informatics

NARCIS (Netherlands)

Wanders, B.

2012-01-01

Scientific research in bio-informatics is often data-driven and supported by numerous biological databases. A biological database contains factual information collected from scientific experiments and computational analyses about areas including genomics, proteomics, metabolomics, microarray gene

BioShaDock: a community driven bioinformatics shared Docker-based tools registry [version 1; referees: 2 approved

Directory of Open Access Journals (Sweden)

François Moreews

2015-12-01

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

RNA Secondary Structure Prediction by Using Discrete Mathematics: An Interdisciplinary Research Experience for Undergraduate Students

Science.gov (United States)

Ellington, Roni; Wachira, James

2010-01-01

The focus of this Research Experience for Undergraduates (REU) project was on RNA secondary structure prediction by using a lattice walk approach. The lattice walk approach is a combinatorial and computational biology method used to enumerate possible secondary structures and predict RNA secondary structure from RNA sequences. The method uses discrete mathematical techniques and identifies specified base pairs as parameters. The goal of the REU was to introduce upper-level undergraduate students to the principles and challenges of interdisciplinary research in molecular biology and discrete mathematics. At the beginning of the project, students from the biology and mathematics departments of a mid-sized university received instruction on the role of secondary structure in the function of eukaryotic RNAs and RNA viruses, RNA related to combinatorics, and the National Center for Biotechnology Information resources. The student research projects focused on RNA secondary structure prediction on a regulatory region of the yellow fever virus RNA genome and on an untranslated region of an mRNA of a gene associated with the neurological disorder epilepsy. At the end of the project, the REU students gave poster and oral presentations, and they submitted written final project reports to the program director. The outcome of the REU was that the students gained transferable knowledge and skills in bioinformatics and an awareness of the applications of discrete mathematics to biological research problems. PMID:20810968

RNA secondary structure prediction by using discrete mathematics: an interdisciplinary research experience for undergraduate students.

Science.gov (United States)

Ellington, Roni; Wachira, James; Nkwanta, Asamoah

2010-01-01

The focus of this Research Experience for Undergraduates (REU) project was on RNA secondary structure prediction by using a lattice walk approach. The lattice walk approach is a combinatorial and computational biology method used to enumerate possible secondary structures and predict RNA secondary structure from RNA sequences. The method uses discrete mathematical techniques and identifies specified base pairs as parameters. The goal of the REU was to introduce upper-level undergraduate students to the principles and challenges of interdisciplinary research in molecular biology and discrete mathematics. At the beginning of the project, students from the biology and mathematics departments of a mid-sized university received instruction on the role of secondary structure in the function of eukaryotic RNAs and RNA viruses, RNA related to combinatorics, and the National Center for Biotechnology Information resources. The student research projects focused on RNA secondary structure prediction on a regulatory region of the yellow fever virus RNA genome and on an untranslated region of an mRNA of a gene associated with the neurological disorder epilepsy. At the end of the project, the REU students gave poster and oral presentations, and they submitted written final project reports to the program director. The outcome of the REU was that the students gained transferable knowledge and skills in bioinformatics and an awareness of the applications of discrete mathematics to biological research problems.

Nispero: a cloud-computing based Scala tool specially suited for bioinformatics data processing

OpenAIRE

Evdokim Kovach; Alexey Alekhin; Eduardo Pareja Tobes; Raquel Tobes; Eduardo Pareja; Marina Manrique

2014-01-01

Nowadays it is widely accepted that the bioinformatics data analysis is a real bottleneck in many research activities related to life sciences. High-throughput technologies like Next Generation Sequencing (NGS) have completely reshaped the biology and bioinformatics landscape. Undoubtedly NGS has allowed important progress in many life-sciences related fields but has also presented interesting challenges in terms of computation capabilities and algorithms. Many kinds of tasks related with NGS...

An Adaptive Hybrid Multiprocessor technique for bioinformatics sequence alignment

KAUST Repository

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

2012-01-01

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

Developing Effective Undergraduate Research Experience

Science.gov (United States)

Evans, Michael; Ilie, Carolina C.

2011-03-01

Undergraduate research is a valuable educational tool for students pursuing a degree in physics, but these experiences can become problematic and ineffective if not handled properly. Undergraduate research should be planned as an immersive learning experience in which the student has the opportunity to develop his/her skills in accordance with their interests. Effective undergraduate research experiences are marked by clear, measurable objectives and frequent student-professor collaboration. These objectives should reflect the long and short-term goals of the individual undergraduates, with a heightened focus on developing research skills for future use. 1. Seymour, E., Hunter, A.-B., Laursen, S. L. and DeAntoni, T. (2004), ``Establishing the benefits of research experiences for undergraduates in the sciences: First findings from a three-year study''. Science Education, 88: 493--534. 2. Behar-Horenstein, Linda S., Johnson, Melissa L. ``Enticing Students to Enter Into Undergraduate Research: The Instrumentality of an Undergraduate Course.'' Journal of College Science Teaching 39.3 (2010): 62-70.

Ethics education in undergraduate pre-health programs. The contribution of undergraduate colleges and universities to the ethical and moral development of future doctors in the medical and dental professions.

Science.gov (United States)

Erratt, Tamie D

2011-08-01

There are many barriers to ethics education of students attending medical and dental schools. The question is asked, "Should more attention be given to addressing students' ethics education during their undergraduate years of preparation for professional healthcare programs?" This qualitative study utilizes digitally recorded personal interviews with two undergraduate pre-healthcare students, one medical student, one recently matriculated dental student, one undergraduate pre-healthcare faculty member, three dental school faculty members, and three medical school faculty members. Interview participants discuss areas of personal knowledge and experience concerning: the admissions process and screening of potential medical/dental students for ethical traits and behaviors, influences on student ethical development, undergraduate pre-healthcare ethics training, and preferred college major for pre-healthcare students. The study concludes that undergraduate pre-healthcare programs should take the initiative to be proactive and deliberate in strengthening the positive influences on students. Strategies include: 1) humanities curricula to broaden perspectives and increase non-prejudice; 2) mentoring and modeling by older students, faculty, and community and professional volunteers; 3) ethical case study discussions in class or extracurricular activities; and 4) volunteer/service learning activities. Additionally, curriculum learning is enhanced by the use of reflection and writing, discussions, and media.

A bioinformatics-based overview of protein Lys-Ne-acetylation

Science.gov (United States)

Among posttranslational modifications, there are some conceptual similarities between Lys-N'-acetylation and Ser/Thr/Tyr O-phosphorylation. Herein we present a bioinformatics-based overview of reversible protein Lys-acetylation, including some comparisons with reversible protein phosphorylation. T...

jORCA: easily integrating bioinformatics Web Services.

Science.gov (United States)

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

2010-02-15

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

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

Science.gov (United States)

Nehm, Ross H.; Budd, Ann F.

2006-01-01

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

Easy computer assisted teaching method for undergraduate surgery

OpenAIRE

Agrawal, Vijay P

2015-01-01

Use of computers to aid or support the education or training of people has become commonplace in medical education. Recent studies have shown that it can improve learning outcomes in diagnostic abilities, clinical skills and knowledge across different learner levels from undergraduate medical education to continuing medical education. It also enhance the educational process by increasing access to learning materials, standardising the educational process, providing opportunities for asynchron...

G2LC: Resources Autoscaling for Real Time Bioinformatics Applications in IaaS

Directory of Open Access Journals (Sweden)

Rongdong Hu

2015-01-01

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

Penalized feature selection and classification in bioinformatics

OpenAIRE

Ma, Shuangge; Huang, Jian

2008-01-01

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

Toward Personalized Pressure Ulcer Care Planning: Development of a Bioinformatics System for Individualized Prioritization of Clinical Pratice Guideline

Science.gov (United States)

2016-10-01

AWARD NUMBER: W81XWH-15-1-0342 TITLE: Toward Personalized Pressure Ulcer Care Planning: Development of a Bioinformatics System for Individualized...Planning: Development of a Bioinformatics System for Individualized Prioritization of Clinical Pratice Guideline 5a. CONTRACT NUMBER 5b. GRANT...recommendations of CPG has been identified by experts in the field. We will use bioinformatics to enable data extraction, storage, and analysis to support

Architecture exploration of FPGA based accelerators for bioinformatics applications

CERN Document Server

Varma, B Sharat Chandra; Balakrishnan, M

2016-01-01

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

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

Directory of Open Access Journals (Sweden)

James F. Aiton

1994-01-01

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

Undergraduate surgical nursing preparation and guided operating room experience: A quantitative analysis.

Science.gov (United States)

Foran, Paula

2016-01-01

The aim of this research was to determine if guided operating theatre experience in the undergraduate nursing curricula enhanced surgical knowledge and understanding of nursing care provided outside this specialist area in the pre- and post-operative surgical wards. Using quantitative analyses, undergraduate nurses were knowledge tested on areas of pre- and post-operative surgical nursing in their final semester of study. As much learning occurs in nurses' first year of practice, participants were re-tested again after their Graduate Nurse Program/Preceptorship year. Participants' results were compared to the model of operating room education they had participated in to determine if there was a relationship between the type of theatre education they experienced (if any) and their knowledge of surgical ward nursing. Findings revealed undergraduates nurses receiving guided operating theatre experience had a 76% pass rate compared to 56% with non-guided or no experience (p nurses achieved a 100% pass rate compared to 53% with non-guided or no experience (p research informs us that undergraduate nurses achieve greater learning about surgical ward nursing via guided operating room experience as opposed to surgical ward nursing experience alone. Copyright © 2015 Elsevier Ltd. All rights reserved.

Staff Scientist - RNA Bioinformatics | Center for Cancer Research

Science.gov (United States)

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

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

Science.gov (United States)

Vetrivel, Umashankar; Pilla, Kalabharath

2008-01-01

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

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

African Journals Online (AJOL)

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

Virginia Bioinformatics Institute to expand cyberinfrastructure education and outreach project

OpenAIRE

Whyte, Barry James

2008-01-01

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

6th International Conference on Practical Applications of Computational Biology & Bioinformatics

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Luscombe, Nicholas; Fdez-Riverola, Florentino; Rodríguez, Juan; Practical Applications of Computational Biology & Bioinformatics

2012-01-01

The growth in the Bioinformatics and Computational Biology fields over the last few years has been remarkable.. The analysis of the datasets of Next Generation Sequencing needs new algorithms and approaches from fields such as Databases, Statistics, Data Mining, Machine Learning, Optimization, Computer Science and Artificial Intelligence. Also Systems Biology has also been emerging as an alternative to the reductionist view that dominated biological research in the last decades. This book presents the results of the  6th International Conference on Practical Applications of Computational Biology & Bioinformatics held at University of Salamanca, Spain, 28-30th March, 2012 which brought together interdisciplinary scientists that have a strong background in the biological and computational sciences.

Peer Learning and Support of Technology in an Undergraduate Biology Course to Enhance Deep Learning

Science.gov (United States)

Tsaushu, Masha; Tal, Tali; Sagy, Ornit; Kali, Yael; Gepstein, Shimon; Zilberstein, Dan

2012-01-01

This study offers an innovative and sustainable instructional model for an introductory undergraduate course. The model was gradually implemented during 3 yr in a research university in a large-lecture biology course that enrolled biology majors and nonmajors. It gives priority to sources not used enough to enhance active learning in higher education: technology and the students themselves. Most of the lectures were replaced with continuous individual learning and 1-mo group learning of one topic, both supported by an interactive online tutorial. Assessment included open-ended complex questions requiring higher-order thinking skills that were added to the traditional multiple-choice (MC) exam. Analysis of students’ outcomes indicates no significant difference among the three intervention versions in the MC questions of the exam, while students who took part in active-learning groups at the advanced version of the model had significantly higher scores in the more demanding open-ended questions compared with their counterparts. We believe that social-constructivist learning of one topic during 1 mo has significantly contributed to student deep learning across topics. It developed a biological discourse, which is more typical to advanced stages of learning biology, and changed the image of instructors from “knowledge transmitters” to “role model scientists.” PMID:23222836

Peer learning and support of technology in an undergraduate biology course to enhance deep learning.

Science.gov (United States)

Tsaushu, Masha; Tal, Tali; Sagy, Ornit; Kali, Yael; Gepstein, Shimon; Zilberstein, Dan

2012-01-01

This study offers an innovative and sustainable instructional model for an introductory undergraduate course. The model was gradually implemented during 3 yr in a research university in a large-lecture biology course that enrolled biology majors and nonmajors. It gives priority to sources not used enough to enhance active learning in higher education: technology and the students themselves. Most of the lectures were replaced with continuous individual learning and 1-mo group learning of one topic, both supported by an interactive online tutorial. Assessment included open-ended complex questions requiring higher-order thinking skills that were added to the traditional multiple-choice (MC) exam. Analysis of students' outcomes indicates no significant difference among the three intervention versions in the MC questions of the exam, while students who took part in active-learning groups at the advanced version of the model had significantly higher scores in the more demanding open-ended questions compared with their counterparts. We believe that social-constructivist learning of one topic during 1 mo has significantly contributed to student deep learning across topics. It developed a biological discourse, which is more typical to advanced stages of learning biology, and changed the image of instructors from "knowledge transmitters" to "role model scientists."

Mentoring as a Learning Tool: Enhancing the Effectiveness of an Undergraduate Business Mentoring Program

Science.gov (United States)

D'Abate, Caroline P.; Eddy, Erik R.

2008-01-01

Mentoring can be used as a pedagogical alternative both to extend and augment the educational experience of business students. This article addresses a gap in the literature regarding the use and effectiveness of mentoring in undergraduate business education by examining improvements to an existing mentoring program. After reviewing the mentoring…

Multimedia as a Means to Enhance Teaching Technical Vocabulary to Physics Undergraduates in Rwanda

Science.gov (United States)

Rusanganwa, Joseph

2013-01-01

This study investigates whether the integration of ICT in education can facilitate teaching and learning. An example of such integration is computer assisted language learning (CALL) of English technical vocabulary by undergraduate physics students in Rwanda. The study draws on theories of cognitive load and multimedia learning to explore learning…

Undergraduate Program Review Processes: A Case Study in Opportunity for Academic Libraries

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Costella, John; Adam, Tom; Gray, Fran; Nolan, Nicole; Wilkins, Catherine

2013-01-01

How can an academic library most effectively participate and expand its contributions to program reviews at the institutional level? By becoming involved in undergraduate reviews, college and university libraries can articulate new and enhanced roles for themselves on campus. Academic libraries have always contributed to a variety of institutional…

Transforming the Learning Environment of Undergraduate Physics Laboratories to Enhance Physics Inquiry Processes

Directory of Open Access Journals (Sweden)

Gregory P. Thomas

2017-04-01

Full Text Available Concerns persist regarding the lack of promotion of students’ scientific inquiry processes in undergraduate physics laboratories. The consensus in the literature is that, especially in the early years of undergraduate physics programs, students’ laboratory work is characterized by recipe type, step-by-step instructions for activities where the aim is often confirmation of an already well-established physics principle or concept. In response to evidence reflecting these concerns at their university, the authors successfully secured funding for this study. A mixed-method design was employed. In the 2011/2012 academic year baseline data were collected. A quantitative survey, the Undergraduate Physics Laboratory Learning Environment Scale (UPLLES was developed, validated, and used to explore students’ perceptions of their physics laboratory environments. Analysis of data from the UPLLES and from interviews confirmed the concerns evident in the literature and in a previous evaluation of laboratories undertaken in 2002. To address these concerns the activities that students were to perform in the laboratory section of the course/s were re/designed to engage students in more inquiry oriented thinking and activity. In Fall 2012, the newly developed laboratory activities and tutorials, were implemented for the first time in PHYS124; a first year course. These changes were accompanied by structured training of teaching assistants and changes to the structure of the evaluation of students’ laboratory performance. At the end of that term the UPLLES was administered (n = 266 and interviews with students conducted (n = 16 to explore their perceptions of their laboratory environments. Statistically significant differences (p<.001 between the students in the PHYS 124 classes of 2011/2012 and 2012/2013 across all dimensions were found. Effect sizes of 0.82 to 1.3, between the views of students in the first semester physics classes of 2011/2012 and 2012

Using Interactive Data Visualizations for Exploratory Analysis in Undergraduate Genomics Coursework: Field Study Findings and Guidelines

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Kumar, Anuj; Nong, Paige; Su, Gang; Meng, Fan

2016-01-01

Life scientists increasingly use visual analytics to explore large data sets and generate hypotheses. Undergraduate biology majors should be learning these same methods. Yet visual analytics is one of the most underdeveloped areas of undergraduate biology education. This study sought to determine the feasibility of undergraduate biology majors conducting exploratory analysis using the same interactive data visualizations as practicing scientists. We examined 22 upper level undergraduates in a genomics course as they engaged in a case-based inquiry with an interactive heat map. We qualitatively and quantitatively analyzed students’ visual analytic behaviors, reasoning and outcomes to identify student performance patterns, commonly shared efficiencies and task completion. We analyzed students’ successes and difficulties in applying knowledge and skills relevant to the visual analytics case and related gaps in knowledge and skill to associated tool designs. Findings show that undergraduate engagement in visual analytics is feasible and could be further strengthened through tool usability improvements. We identify these improvements. We speculate, as well, on instructional considerations that our findings suggested may also enhance visual analytics in case-based modules. PMID:26877625

Framing the Undergraduate Research Experience: Discovery Involvement in Retailing Undergraduate Education

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Sternquist, Brenda; Huddleston, Patricia; Fairhurst, Ann

2018-01-01

We provide an overview of ways to involve undergraduate business and retailing students in faculty research projects and discuss advantages of these student-faculty collaborations. We use Kolb's experiential learning cycle to provide a framework for creating an effective and engaging undergraduate research experience and use it to classify types…

Organization of an undergraduate research group

International Nuclear Information System (INIS)

Hill, J.; Noteboom, E.

1995-01-01

Traditionally, research groups consist of senior physicists, staff members, and graduate students. The physics department at Creighton University has formed a Relativistic Heavy Ion physics research group consisting primarily of undergraduate students. Although senior staff and graduate students are actively involved, undergraduate research and the education of undergraduates is the focus of the group. The presentation, given by two undergraduate members of the group, will outline progress made in the group's organization, discuss the benefits to the undergraduate group members, and speak to the balance which must be struck between education concerns and research goals

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

African Journals Online (AJOL)

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

To promote the engineering innovative abilities of undergraduates by taking projects as the guidance and competitions as the promotion

Science.gov (United States)

Xu, Yishen; Wu, Di; Chen, Daqing; Gu, Jihua; Gao, Lei

2017-08-01

According to the inherent requirements of education for talents' knowledge, quality and comprehensive ability and the major training goals of optoelectronics information science and engineering, in order to enhance the undergraduates' comprehensive practical ability and consciousness of innovation, we carried out the reforms of teaching method and teaching mode, which took the training programs of innovation and entrepreneurship for undergraduates, extracurricular academic research fund, "Chun-Tsung Scholar" program or research projects of their tutors as the guidance, and took the all levels of relevant discipline competitions as the promotion. And the training mainline of engineering innovation talents as "undergraduate's tutorial system ->innovative training program or tutor's research project ->academic competition ->graduation projects (thesis)" was constructed stage by stage by combining the undergraduates' graduation projects and their participated academic competition into one for improving the quality of the graduation projects (thesis). The practical results of the last several years illuminate that the proposed training model can effectively stimulate the students' awareness of autonomous learning, enhance their comprehensive ability of analyzing and solving problems and improve their ability of engineering practice and innovation as well as their teamwork spirit.

Bioinformatics analysis and detection of gelatinase encoded gene in Lysinibacillussphaericus

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

2016-11-01

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

Attitudes towards transferable skills in medical undergraduates.

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Whittle, S R; Eaton, D G

2001-02-01

Changes to the style of medical teaching will place a greater responsibility on individual medical students to manage their own learning, highlighting the need for students to develop good so-called 'transferable' skills at an early stage in their undergraduate career. To assess the attitudes of first year undergraduates towards transferable skills, and investigate the gender difference in these attitudes. To assess the contribution of their first year course to skills development. First year students, enrolled on a traditional-style course. A questionnaire asking the students to consider: (a) the importance of named transferable skills for medicine; (b) their own ability in these areas; and (c) the influence of their first year course. All students, irrespective of gender, regarded transferable skills as very important to medicine, rating organizational skills and self-learning skills as most important. Overall, students have a high level of confidence in their own skills. Male students rated their overall level of skills more highly than women. In particular they rated their information handling, managing self-learning and technical skills more highly. Students feel that their first year course has enhanced their skills in most areas. Our results suggest that students will feel equipped to succeed in a learning system which places the onus on them to take responsibility for their own learning. They clearly believe that they have the necessary skills for independent learning. The study highlights the need to enhance students' self-evaluation skills.

Integration of Proteomics, Bioinformatics, and Systems Biology in Traumatic Brain Injury Biomarker Discovery

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Guingab-Cagmat, J.D.; Cagmat, E.B.; Hayes, R.L.; Anagli, J.

2013-01-01

Traumatic brain injury (TBI) is a major medical crisis without any FDA-approved pharmacological therapies that have been demonstrated to improve functional outcomes. It has been argued that discovery of disease-relevant biomarkers might help to guide successful clinical trials for TBI. Major advances in mass spectrometry (MS) have revolutionized the field of proteomic biomarker discovery and facilitated the identification of several candidate markers that are being further evaluated for their efficacy as TBI biomarkers. However, several hurdles have to be overcome even during the discovery phase which is only the first step in the long process of biomarker development. The high-throughput nature of MS-based proteomic experiments generates a massive amount of mass spectral data presenting great challenges in downstream interpretation. Currently, different bioinformatics platforms are available for functional analysis and data mining of MS-generated proteomic data. These tools provide a way to convert data sets to biologically interpretable results and functional outcomes. A strategy that has promise in advancing biomarker development involves the triad of proteomics, bioinformatics, and systems biology. In this review, a brief overview of how bioinformatics and systems biology tools analyze, transform, and interpret complex MS datasets into biologically relevant results is discussed. In addition, challenges and limitations of proteomics, bioinformatics, and systems biology in TBI biomarker discovery are presented. A brief survey of researches that utilized these three overlapping disciplines in TBI biomarker discovery is also presented. Finally, examples of TBI biomarkers and their applications are discussed. PMID:23750150

The Undergraduate Teaching Assistant Experience Offers Opportunities Similar to the Undergraduate Research Experience†

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Schalk, Kelly A.; McGinnis, J. Randy; Harring, Jeffrey R.; Hendrickson, Amy; Smith, Ann C.

2009-01-01

There has been a growing concern in higher education about our failure to produce scientifically trained workers and scientifically literate citizens. Active-learning and research-oriented activities are posited as ways to give students a deeper understanding of science. We report on an undergraduate teaching assistant (UTA) experience and suggest that students who participate as a UTA obtain benefits analogous to those who participate as an undergraduate research assistant (URA). We examined the experiences of 24 undergraduates acting as UTAs in a general microbiology course. Self-reported gains by the UTAs were supported by observational data from undergraduates in the course who were mentored by the UTAs and by the graduate teaching assistants (GTAs) with whom the UTAs worked. Specifically, data from the UTAs’ journals and self-reported Likert scales and rubrics indicated that our teaching assistants developed professional characteristics such as self-confidence and communication and leadership skills, while they acquired knowledge of microbiology content and laboratory skills. Data from the undergraduate Likert scale as well as the pre- and post-GTA rubrics further confirmed our UTA’s data interpretations. These findings are significant because they offer empirical data to support the suggestion that the UTA experience is an effective option for developing skills and knowledge in undergraduates that are essential for careers in science. The UTA experience provides a valuable alternative to the URA experience. PMID:23653688

The Undergraduate Teaching Assistant Experience Offers Opportunities Similar to the Undergraduate Research Experience

Directory of Open Access Journals (Sweden)

Kelly A. Schalk

2009-12-01

Full Text Available There has been a growing concern in higher education about our failure to produce scientifically trained workers and scientifically literate citizens. Active-learning and research-oriented activities are posited as ways to give students a deeper understanding of science. We report on an undergraduate teaching assistant (UTA experience and suggest that students who participate as a UTA obtain benefits analogous to those who participate as an undergraduate research assistant (URA. We examined the experiences of 24 undergraduates acting as UTAs in a general microbiology course. Self-reported gains by the UTAs were supported by observational data from undergraduates in the course who were mentored by the UTAs and by the graduate teaching assistants (GTAs with whom the UTAs worked. Specifically, data from the UTAs’ journals and self-reported Likert scales and rubrics indicated that our teaching assistants developed professional characteristics such as self-confidence and communication and leadership skills, while they acquired knowledge of microbiology content and laboratory skills. Data from the undergraduate Likert scale as well as the pre- and post-GTA rubrics further confirmed our UTA’s data interpretations. These findings are significant because they offer empirical data to support the suggestion that the UTA experience is an effective option for developing skills and knowledge in undergraduates that are essential for careers in science. The UTA experience provides a valuable alternative to the URA experience.

Successful Undergraduate Research: Creating Win-Win-Win

Science.gov (United States)

Guswa, A. J.; Rhodes, A. L.

2003-12-01

Undergraduate involvement in research has the potential to advance science, enhance education, strengthen the research community, and raise general awareness of the importance and impact of scientific understanding. Rather than being competing objectives, these goals are synergistic. Effective research experiences are those that create win-win-win situations: benefits to the student, benefits to the project, and benefits to the scientific community. When structured appropriately, undergraduate research fits into a learner-centered paradigm that puts emphasis on student learning, rather than instructor teaching. Under such a paradigm the student and professor learn together, constructing knowledge by integrating information with critical-thinking and problem-solving skills, and use this knowledge to address issues in real-life contexts. Creating such a learning environment requires that the professor be vested in the outcome of the research, that the student take a meta-cognitive approach to the project and work at a level appropriate to her abilities, and that the student understand how her contribution fits into the project and the larger field. All of these factors lead to greater independence, confidence, and productivity on the part of the student. By providing undergraduates with these experiences, we introduce not only future scientists but also non-scientists to the excitement of discovery and the value of scientific research. Currently, we involve undergraduates in our research on the hydrology and geochemistry of a tropical montane cloud forest in Monteverde, Costa Rica. At the start of each student's involvement, we provide her with the big picture: our project goals, the relevant social issues, and the importance of watershed research. Each student then articulates her own educational and project objectives. Together, we choose tasks that match her skills and interests with our scholarly work. Specific activities range from literature review to

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

African Journals Online (AJOL)

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

The "art" of science communication in undergraduate research training

Science.gov (United States)

Fatemi, F. R.; Stockwell, J.; Pinheiro, V.; White, B.

2016-12-01

Student creation of well-designed and engaging visuals in science communication can enhance their deep learning while streamlining the transmission of information to their audience. However, undergraduate research training does not frequently emphasize the design aspect of science communication. We devised and implemented a new curricular component to the Lake Champlain NSF Research Experiences for Undergraduates (REU) program in Vermont. We took a holistic approach to communication training, with a targeted module in "art and science". Components to the module included: 1) an introduction to environmental themes in fine art, 2) a photography assignment in research documentation, 3) an overview of elements of design (e.g., color, typography, hierarchy), 4) a graphic design workshop using tools in Powerpoint, and 5) an introduction to scientific illustration. As part of the REU program, students were asked to document their work through photographs, and develop an infographic or scientific illustration complementary to their research. The "art and science" training culminated with a display and critique of their visual work. We report on student responses to the "art and science" training from exit interviews and survey questions. Based on our program, we identify a set of tools that mentors can use to enhance their student's ability to engage with a broad audience.

mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking.

Science.gov (United States)

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

2016-01-01

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

How to engage undergraduate students in Soil Science: some strategies to enhance their motivation

Science.gov (United States)

Zornoza, Raúl; Lozano-García, Beatriz; Acosta, Jose A.; Martínez-Martínez, Silvia; Parras-Alcántara, Luis; Faz, Angel

2017-04-01

Teaching soil science can be a challenge in those degrees where students are not familiar with the soil system and do not understand the importance of soil science for their future career. This is the case of students of Biology, Agronomy or Environmental Science, who normally consider soil as a mere substrate for vegetation development, with no interest about how soil determines productivity and quality of terrestrial ecosystems. Thus, students lack of initial motivation to study Soil Science, and just attend lectures and practical lessons as mandatory procedure to get the degree. To engage undergraduate students from Biology, Agronomy and Environmental Sciences in Soil Science, we developed a strategy to enhance their motivation by means of making them participants of the selection of the soils and analyses used for their training. By means of dichotomous keys, students, grouped in pairs, first select the main purpose of their study from different options (land productivity, soil biodiversity, soil fertility, effectiveness of restoration, effect of land use, effect of management, etc). Once objective is decided, we give them some information about sampling strategies, so that they select how soil sampling is going to be performed, and the number of samples to be taken. In terms of the initial objective, they also decide from a given list the properties they should measure. In a practical basis, from the list of selected properties to be measured, professors decide the ones they can really develop in terms of timing, resources and space demand. After that, they are aware about the fact that they have an experimental design developed by them to achieve the goal they meant. Under this perspective, their motivation is enhanced since students are the ones deciding what to study in terms of their personal and professional interests, so that learning is more effective. The negative aspect of this strategy is that it involves many hours of tutorials for the professor

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

Directory of Open Access Journals (Sweden)

Sarah Torres

2010-06-01

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

Bioinformatics in the Netherlands : The value of a nationwide community

NARCIS (Netherlands)

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

2017-01-01

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

Elucidating Bioethics with Undergraduates.

Science.gov (United States)

Hoskins, Betty B.; Shannon, Thomas A.

1977-01-01

Discusses the importance of developing bioethics programs for undergraduate students. Two aspects are considered: (1) current areas of concern and sources of bibliographic information; and (2) problems encountered in undergraduate projects. A list of references is provided. (HM)

Service-learning: an integral part of undergraduate public health.

Science.gov (United States)

Cashman, Suzanne B; Seifer, Sarena D

2008-09-01

In 2003, the Institute of Medicine (IOM) described public health as "an essential part of the training of citizens," a body of knowledge needed to achieve a public health literate citizenry. To achieve that end, the IOM recommended that "all undergraduates should have access to education in public health." Service-learning, a type of experiential learning, is an effective and appropriate vehicle for teaching public health and developing public health literacy. While relatively new to public health, service-learning has its historical roots in undergraduate education and has been shown to enhance students' understanding of course relevance, change student and faculty attitudes, encourage support for community initiatives, and increase student and faculty volunteerism. Grounded in collaborative relationships, service-learning grows from authentic partnerships between communities and educational institutions. Through emphasizing reciprocal learning and reflective practice, service-learning helps students develop skills needed to be effective in working with communities and ultimately achieve social change. With public health's enduring focus on social justice, introducing undergraduate students to public health through the vehicle of service-learning as part of introductory public health core courses or public health electives will help ensure that our young people are able to contribute to developing healthy communities, thus achieving the IOM's vision.

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

International Nuclear Information System (INIS)

Taylor, Ronald C.

2010-01-01

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

Learning Genetics through an Authentic Research Simulation in Bioinformatics

Science.gov (United States)

Gelbart, Hadas; Yarden, Anat

2006-01-01

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

The Undergraduate ALFALFA Team: Outcomes for Over 250 Undergraduate Participants

Science.gov (United States)

Troischt, Parker; Koopmann, Rebecca A.; Haynes, Martha P.; ALFALFA Team

2016-01-01

The NSF-sponsored Undergraduate ALFALFA (Arecibo Legacy Fast ALFA) Team (UAT) is a consortium of 19 institutions founded to promote undergraduate research and faculty development within the extragalactic ALFALFA HI blind survey project and follow-up programs. In this talk we present outcomes for the more than 250 undergraduate students who have who have participated in the program during the 8 years of funding. 40% of these students have been women and members of underrepresented groups. To date 148 undergraduate students have attended annual workshops at Arecibo Observatory, interacting with faculty, graduate students, their peers, and Arecibo staff in lectures, group activities, tours, and observing runs. Team faculty have supervised 159 summer research projects and 120 academic year (e.g., senior thesis) projects. 68 students have traveled to Arecibo Observatory for observing runs and 55 have presented their results at national meetings such as the AAS. Through participation in the UAT, students are made aware of career paths they may not have previously considered. More than 90% of alumni are attending graduate school and/or pursuing a career in STEM. 42% of those pursuing graduate degrees in Physics or Astronomy are women. This work has been supported by NSF grants AST-0724918/0902211, AST-075267/0903394, AST-0725380, and AST-1211005

Atlas – a data warehouse for integrative bioinformatics

Directory of Open Access Journals (Sweden)

Yuen Macaire MS

2005-02-01

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

Defining Quality in Undergraduate Education

Directory of Open Access Journals (Sweden)

Alison W. Bowers

2018-01-01

Full Text Available Objectives: This research brief explores the literature addressing quality in undergraduate education to identify what previous research has said about quality and to offer future directions for research on quality in undergraduate education. Method: We conducted a scoping review to provide a broad overview of existing research. Using targeted search terms in academic databases, we identified and reviewed relevant academic literature to develop emergent themes and implications for future research. Results: The exploratory review of the literature revealed a range of thoughtful discussions and empirical studies attempting to define quality in undergraduate education. Many publications highlighted the importance of including different stakeholder perspectives and presented some of the varying perceptions of quality among different stakeholders. Conclusions: While a number of researchers have explored and written about how to define quality in undergraduate education, there is not a general consensus regarding a definition of quality in undergraduate education. Past research offers a range of insights, models, and data to inform future research. Implication for Theory and/or Practice: We provide four recommendations for future research to contribute to a high quality undergraduate educational experience. We suggest more comprehensive systematic reviews of the literature as a next step.

E-MSD: an integrated data resource for bioinformatics.

Science.gov (United States)

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

2005-01-01

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

Intrageneric Primer Design: Bringing Bioinformatics Tools to the Class

Science.gov (United States)

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

2006-01-01

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

Individual Supervision to Enhance Reflexivity and the Practice of Patient-Centered Care: Experience at the Undergraduate Level.

Science.gov (United States)

Berney, Alexandre; Bourquin, Céline

2017-12-22

This article reports on what is at work during individual supervision of medical students in the context of teaching breaking bad news (BBN). Surprisingly, there is a relative lack of research and report on the topic of supervision, even though it is regularly used in medical training. Building on our research and teaching experience on BBN at the undergraduate level, as well as interviews of supervisors, the following key elements have been identified: learning objectives (e.g., raising student awareness of structural elements of the interview, emotion (patients and students) handling), pedagogical approach (being centered on student's needs and supportive to promote already existing competences), essentials (e.g., discussing skills and examples from the clinical practice), and enhancing reflexivity while discussing specific issues (e.g., confusion between the needs of the patient and those of the student). Individual supervision has been identified as crucial and most satisfactory by students to provide guidance and to foster a reflexive stance enabling them to critically apprehend their communication style. Ultimately, the challenge is to teach medical students to not only connect with the patient but also with themselves.

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

Indian Academy of Sciences (India)

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

Undergraduate experiments on statistical optics

International Nuclear Information System (INIS)

Scholz, Ruediger; Friege, Gunnar; Weber, Kim-Alessandro

2016-01-01

Since the pioneering experiments of Forrester et al (1955 Phys. Rev. 99 1691) and Hanbury Brown and Twiss (1956 Nature 177 27; Nature 178 1046), along with the introduction of the laser in the 1960s, the systematic analysis of random fluctuations of optical fields has developed to become an indispensible part of physical optics for gaining insight into features of the fields. In 1985 Joseph W Goodman prefaced his textbook on statistical optics with a strong commitment to the ‘tools of probability and statistics’ (Goodman 2000 Statistical Optics (New York: John Wiley and Sons Inc.)) in the education of advanced optics. Since then a wide range of novel undergraduate optical counting experiments and corresponding pedagogical approaches have been introduced to underpin the rapid growth of the interest in coherence and photon statistics. We propose low cost experimental steps that are a fair way off ‘real’ quantum optics, but that give deep insight into random optical fluctuation phenomena: (1) the introduction of statistical methods into undergraduate university optical lab work, and (2) the connection between the photoelectrical signal and the characteristics of the light source. We describe three experiments and theoretical approaches which may be used to pave the way for a well balanced growth of knowledge, providing students with an opportunity to enhance their abilities to adapt the ‘tools of probability and statistics’. (paper)

"Not Necessarily a Bad Thing ...": A Study of Online Plagiarism amongst Undergraduate Students

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Selwyn, Neil

2008-01-01

Whilst the copying, falsification and plagiarism of essays and assignments has long been a prevalent form of academic misconduct amongst undergraduate students, the increasing use of the internet in higher education has raised concern over enhanced levels of online plagiarism and new types of "cyber-cheating". Based on a self-report…

Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development.

Science.gov (United States)

Kaczor-Urbanowicz, Karolina Elzbieta; Kim, Yong; Li, Feng; Galeev, Timur; Kitchen, Rob R; Gerstein, Mark; Koyano, Kikuye; Jeong, Sung-Hee; Wang, Xiaoyan; Elashoff, David; Kang, So Young; Kim, Su Mi; Kim, Kyoung; Kim, Sung; Chia, David; Xiao, Xinshu; Rozowsky, Joel; Wong, David T W

2018-01-01

Analysis of RNA sequencing (RNA-Seq) data in human saliva is challenging. Lack of standardization and unification of the bioinformatic procedures undermines saliva's diagnostic potential. Thus, it motivated us to perform this study. We applied principal pipelines for bioinformatic analysis of small RNA-Seq data of saliva of 98 healthy Korean volunteers including either direct or indirect mapping of the reads to the human genome using Bowtie1. Analysis of alignments to exogenous genomes by another pipeline revealed that almost all of the reads map to bacterial genomes. Thus, salivary exRNA has fundamental properties that warrant the design of unique additional steps while performing the bioinformatic analysis. Our pipelines can serve as potential guidelines for processing of RNA-Seq data of human saliva. Processing and analysis results of the experimental data generated by the exceRpt (v4.6.3) small RNA-seq pipeline (github.gersteinlab.org/exceRpt) are available from exRNA atlas (exrna-atlas.org). Alignment to exogenous genomes and their quantification results were used in this paper for the analyses of small RNAs of exogenous origin. dtww@ucla.edu. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Nanoinformatics: an emerging area of information technology at the intersection of bioinformatics, computational chemistry and nanobiotechnology

Directory of Open Access Journals (Sweden)

Fernando González-Nilo

2011-01-01

Full Text Available After the progress made during the genomics era, bioinformatics was tasked with supporting the flow of information generated by nanobiotechnology efforts. This challenge requires adapting classical bioinformatic and computational chemistry tools to store, standardize, analyze, and visualize nanobiotechnological information. Thus, old and new bioinformatic and computational chemistry tools have been merged into a new sub-discipline: nanoinformatics. This review takes a second look at the development of this new and exciting area as seen from the perspective of the evolution of nanobiotechnology applied to the life sciences. The knowledge obtained at the nano-scale level implies answers to new questions and the development of new concepts in different fields. The rapid convergence of technologies around nanobiotechnologies has spun off collaborative networks and web platforms created for sharing and discussing the knowledge generated in nanobiotechnology. The implementation of new database schemes suitable for storage, processing and integrating physical, chemical, and biological properties of nanoparticles will be a key element in achieving the promises in this convergent field. In this work, we will review some applications of nanobiotechnology to life sciences in generating new requirements for diverse scientific fields, such as bioinformatics and computational chemistry.

CROSSWORK for Glycans: Glycan Identificatin Through Mass Spectrometry and Bioinformatics

DEFF Research Database (Denmark)

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

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

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

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Lewis, Jamie; Bartlett, Andrew; Atkinson, Paul

2016-01-01

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

A middleware-based platform for the integration of bioinformatic services

Directory of Open Access Journals (Sweden)

Guzmán Llambías

2015-08-01

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

A Survey on Evolutionary Algorithm Based Hybrid Intelligence in Bioinformatics

Directory of Open Access Journals (Sweden)

Shan Li

2014-01-01

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

Writing toward a Scientific Identity: Shifting from Prescriptive to Reflective Writing in Undergraduate Biology

Science.gov (United States)

Otfinowski, Rafael; Silva-Opps, Marina

2015-01-01

Analytical writing enhances retention of science learning and is integral to student-centered classrooms. Despite this, scientific writing in undergraduate programs is often presented as a series of sentence-level conventions of grammar, syntax, and citation formats, reinforcing students' perceptions of its highly prescriptive nature. The authors…

Undergraduate Chemistry Education: A Workshop Summary

Science.gov (United States)

Sawyer, Keegan; Alper, Joe

2014-01-01

"Undergraduate Chemistry Education" is the summary of a workshop convened in May 2013 by the Chemical Science Roundtable of the National Research Council to explore the current state of undergraduate chemistry education. Research and innovation in undergraduate chemistry education has been done for many years, and one goal of this…

Introducing bioinformatics, the biosciences' genomic revolution

CERN Document Server

Zanella, Paolo

1999-01-01

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

Online Lectures in Undergraduate Medical Education: Scoping Review.

Science.gov (United States)

Tang, Brandon; Coret, Alon; Qureshi, Aatif; Barron, Henry; Ayala, Ana Patricia; Law, Marcus

2018-04-10

The adoption of the flipped classroom in undergraduate medical education calls on students to learn from various self-paced tools-including online lectures-before attending in-class sessions. Hence, the design of online lectures merits special attention, given that applying multimedia design principles has been shown to enhance learning outcomes. The aim of this study was to understand how online lectures have been integrated into medical school curricula, and whether published literature employs well-accepted principles of multimedia design. This scoping review followed the methodology outlined by Arksey and O'Malley (2005). Databases, including MEDLINE, PsycINFO, Education Source, FRANCIS, ERIC, and ProQuest, were searched to find articles from 2006 to 2016 related to online lecture use in undergraduate medical education. In total, 45 articles met our inclusion criteria. Online lectures were used in preclinical and clinical years, covering basic sciences, clinical medicine, and clinical skills. The use of multimedia design principles was seldom reported. Almost all studies described high student satisfaction and improvement on knowledge tests following online lecture use. Integration of online lectures into undergraduate medical education is well-received by students and appears to improve learning outcomes. Future studies should apply established multimedia design principles to the development of online lectures to maximize their educational potential. ©Brandon Tang, Alon Coret, Aatif Qureshi, Henry Barron, Ana Patricia Ayala, Marcus Law. Originally published in JMIR Medical Education (http://mededu.jmir.org), 10.04.2018.

Emergent Computation Emphasizing Bioinformatics

CERN Document Server

Simon, Matthew

2005-01-01

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

Neonatal Informatics: Transforming Neonatal Care Through Translational Bioinformatics

Science.gov (United States)

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

2012-01-01

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

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

Science.gov (United States)

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

2012-03-19

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

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

Science.gov (United States)

2012-01-01

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

Multiobjective optimization in bioinformatics and computational biology.

Science.gov (United States)

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

2007-01-01

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

The secondary metabolite bioinformatics portal

DEFF Research Database (Denmark)

Weber, Tilmann; Kim, Hyun Uk

2016-01-01

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

Blended learning pedagogy designed for communication module among undergraduate nursing students: A quasi-experimental study.

Science.gov (United States)

Shorey, Shefaly; Kowitlawakul, Yanika; Devi, M Kamala; Chen, Hui-Chen; Soong, Swee Kit Alan; Ang, Emily

2018-02-01

Effective communication is important for nurse and patient outcomes. Nursing students often feel unprepared to communicate effectively with patients and other healthcare workers within the clinical environment. Blended learning pedagogy-based communication skills training can provide an alternative to traditional methods of teaching to enhance students' satisfaction and self-efficacy levels in communicating with others. To examine the effectiveness of blended learning pedagogy in a redesigned communication module among nursing undergraduates in enhancing their satisfaction levels and attitudes towards learning communication module as well as self-efficacy in communication. A single group pre-test and post-test quasi-experimental design was adopted. Data were collected from August 2016 to November 2016 from 124 nursing undergraduates from a leading nursing school. Blended learning pedagogy was adopted to redesign a communication module that offered a wide array of learning opportunities via face-to-face classroom and online sessions. Validated and reliable instruments were used to measure satisfaction levels with blended learning pedagogy, attitudes towards learning communication, and communication self-efficacy. Descriptive and inferential statistics were used to analyze the data. Participants had enhanced satisfaction levels with blended learning pedagogy, better attitudes in learning communication skills, and improved communication self-efficacies at posttest (week 13 of the semester) when compared with their pre-test scores (week one of the semester). Participants scored higher in the Blended Learning Satisfaction Scale, the Communication Skills Attitude Scale, and the communication skills subscale of the Nursing Students Self-Efficacy Scale. Blended learning pedagogy can be effectively used in facilitating communication modules and enhancing student outcomes among nursing undergraduates. The long-term effectiveness of using blended learning pedagogy in

Predicting Supervisor Capacities to Foster Higher Forms of Learning through Undergraduate Medical Student Research

Science.gov (United States)

MacDougall, Margaret

2014-01-01

The credibility of short-term undergraduate research as a paradigm for effective learning within Medicine has been recognized. With a view to strengthening this paradigm and enhancing research-teaching linkages, this study explores whether particular types of research supervisor are pre-disposed to providing supportive learning environments.…

Online Video Tutorials Increase Learning of Difficult Concepts in an Undergraduate Analytical Chemistry Course

Science.gov (United States)

He, Yi; Swenson, Sandra; Lents, Nathan

2012-01-01

Educational technology has enhanced, even revolutionized, pedagogy in many areas of higher education. This study examines the incorporation of video tutorials as a supplement to learning in an undergraduate analytical chemistry course. The concepts and problems in which students faced difficulty were first identified by assessing students'…

MLH1 Promoter Methylation and Prediction/Prognosis of Gastric Cancer: A Systematic Review and Meta and Bioinformatic Analysis.

Science.gov (United States)

Shen, Shixuan; Chen, Xiaohui; Li, Hao; Sun, Liping; Yuan, Yuan

2018-01-01

Background: The promoter methylation of MLH1 gene and gastric cancer (GC)has been investigated previously. To get a more credible conclusion, we performed a systematic review and meta and bioinformatic analysis to clarify the role of MLH1 methylation in the prediction and prognosis of GC. Methods: Eligible studies were targeted after searching the PubMed, Web of Science, Embase, BIOSIS, CNKI and Wanfang Data to collect the information of MLH1 methylation and GC. The link strength between the two was estimated by odds ratio with its 95% confidence interval. The Newcastle-Ottawa scale was used for quantity assessment . Subgroup and sensitivity analysis were conducted to explore sources of heterogeneity. The Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) were employed for bioinformatics analysis on the correlation between MLH1 methylation and GC risk, clinicopathological behavior as well as prognosis. Results: 2365 GC and 1563 controls were included in the meta-analysis. The pooled OR of MLH1 methylation in GC was 4.895 (95% CI: 3.149-7.611, PMLH1 methylation enhanced GC risk but might not related with GC clinicopathological features and prognosis. Conclusion: MLH1 methylation is an alive biomarker for the prediction of GC and it might not affect GC behavior. Further study could be conducted to verify the impact of MLH1 methylation on GC prognosis.

A program for undergraduate research into the mechanisms of sensory coding and memory decay

Energy Technology Data Exchange (ETDEWEB)

Calin-Jageman, R J

2010-09-28

This is the final technical report for this DOE project, entitltled "A program for undergraduate research into the mechanisms of sensory coding and memory decay". The report summarizes progress on the three research aims: 1) to identify phyisological and genetic correlates of long-term habituation, 2) to understand mechanisms of olfactory coding, and 3) to foster a world-class undergraduate neuroscience program. Progress on the first aim has enabled comparison of learning-regulated transcripts across closely related learning paradigms and species, and results suggest that only a small core of transcripts serve truly general roles in long-term memory. Progress on the second aim has enabled testing of several mutant phenotypes for olfactory behaviors, and results show that responses are not fully consistent with the combinitoral coding hypothesis. Finally, 14 undergraduate students participated in this research, the neuroscience program attracted extramural funding, and we completed a successful summer program to enhance transitions for community-college students into 4-year colleges to persue STEM fields.

Computational Lipidomics and Lipid Bioinformatics: Filling In the Blanks.

Science.gov (United States)

Pauling, Josch; Klipp, Edda

2016-12-22

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

A review of bioinformatic methods for forensic DNA analyses.

Science.gov (United States)

Liu, Yao-Yuan; Harbison, SallyAnn

2018-03-01

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

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

Science.gov (United States)

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

2017-10-30

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

Kubernetes as an approach for solving bioinformatic problems.

OpenAIRE

Markstedt, Olof

2017-01-01

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

Project-Based Learning Using Discussion and Lesson-Learned Methods via Social Media Model for Enhancing Problem Solving Skills

Science.gov (United States)

Jewpanich, Chaiwat; Piriyasurawong, Pallop

2015-01-01

This research aims to 1) develop the project-based learning using discussion and lesson-learned methods via social media model (PBL-DLL SoMe Model) used for enhancing problem solving skills of undergraduate in education student, and 2) evaluate the PBL-DLL SoMe Model used for enhancing problem solving skills of undergraduate in education student.…

Integrating Clinical Neuropsychology into the Undergraduate Curriculum.

Science.gov (United States)

Puente, Antonio E.; And Others

1991-01-01

Claims little information exists in undergraduate education about clinical neuropsychology. Outlines an undergraduate neuropsychology course and proposes ways to integrate the subject into existing undergraduate psychology courses. Suggests developing specialized audio-visual materials for telecourses or existing courses. (NL)

Data mining in bioinformatics using Weka.

Science.gov (United States)

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

2004-10-12

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

Inter-Institutional Partnerships Propel A Successful Collaborative Undergraduate Degree Program In Chemistry.

Science.gov (United States)

D'Souza, Malcolm J; Wang, Qiquan

2012-10-01

Small private liberal arts colleges are increasingly tuition-dependent and mainly attract students by creating student-centered learning communities. On the other hand, larger universities tend to be trendsetters where its faculty tend to seek intellectual independence and are involved in career focused cutting-edge research. The Institutional Development Awards (IDeA) and Experimental Program to Stimulate Competitive Research (EPSCoR) are federal-state-university partnerships that builds basic research infrastructure and coax the state-wide higher education institutions to collaborate with each other in order to enhance their competitiveness. As a result in Delaware, Wesley College instituted curricular and operational changes to launch an undergraduate program in biological chemistry where its students take three upper division chemistry courses and can choose to participate in annual summer undergraduate internships at nearby Delaware State University.

Teaching medical ethics to undergraduate students in post-apartheid South Africa, 2003 2006.

Science.gov (United States)

Moodley, Keymanthri

2007-11-01

The apartheid ideology in South Africa had a pervasive influence on all levels of education including medical undergraduate training. The role of the health sector in human rights abuses during the apartheid era was highlighted in 1997 during the Truth and Reconciliation Commission hearings. The Health Professions Council of South Africa (HPCSA) subsequently realised the importance of medical ethics education and encouraged the introduction of such teaching in all medical schools in the country. Curricular reform at the University of Stellenbosch in 1999 presented an unparalleled opportunity to formally introduce ethics teaching to undergraduate students. This paper outlines the introduction of a medical ethics programme at the Faculty of Health Sciences from 2003 to 2006, with special emphasis on the challenges encountered. It remains one of the most comprehensive undergraduate medical ethics programmes in South Africa. However, there is scope for expanding the curricular time allocated to medical ethics. Integrating the curriculum both horizontally and vertically is imperative. Implementing a core curriculum for all medical schools in South Africa would significantly enhance the goals of medical education in the country.

A Social Capital Perspective on the Mentoring of Undergraduate Life Science Researchers: An Empirical Study of Undergraduate-Postgraduate-Faculty Triads.

Science.gov (United States)

Aikens, Melissa L; Sadselia, Sona; Watkins, Keiana; Evans, Mara; Eby, Lillian T; Dolan, Erin L

2016-01-01

Undergraduate researchers at research universities are often mentored by graduate students or postdoctoral researchers (referred to collectively as "postgraduates") and faculty, creating a mentoring triad structure. Triads differ based on whether the undergraduate, postgraduate, and faculty member interact with one another about the undergraduate's research. Using a social capital theory framework, we hypothesized that different triad structures provide undergraduates with varying resources (e.g., information, advice, psychosocial support) from the postgraduates and/or faculty, which would affect the undergraduates' research outcomes. To test this, we collected data from a national sample of undergraduate life science researchers about their mentoring triad structure and a range of outcomes associated with research experiences, such as perceived gains in their abilities to think and work like scientists, science identity, and intentions to enroll in a PhD program. Undergraduates mentored by postgraduates alone reported positive outcomes, indicating that postgraduates can be effective mentors. However, undergraduates who interacted directly with faculty realized greater outcomes, suggesting that faculty interaction is important for undergraduates to realize the full benefits of research. The "closed triad," in which undergraduates, postgraduates, and faculty all interact directly, appeared to be uniquely beneficial; these undergraduates reported the highest gains in thinking and working like a scientist. © 2016 M. L. Aikens et al. CBE—Life Sciences Education © 2016 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Vigna subterranea ammonium transporter gene (VsAMT1: Some bioinformatics insights

Directory of Open Access Journals (Sweden)

Adewole T. Adetunji

2015-12-01

Full Text Available Ammonium transporters (AMTs play a role in the uptake of ammonium, the form in which nitrogen is preferentially absorbed by plants. Vigna subterranea (VsAMT1 and Solanum tuberosum (StAMT1 AMT1s were characterized using molecular biology and bioinformatics methods. AMT1-specific primers were designed and used to amplify the AMT1 internal regions. Nucleotide sequencing, alignment and phylogenetic analysis assigned VsAMT1 and StAMT1 to the AMT1 family. The deduced amino acid sequences showed that VsAMT1 is 92% and 89% similar to Phaseolus vulgaris PvAMT1.1 and Glycine max AMT1 respectively, while StAMT1 is 92% similar to Solanum lycopersicum LeAMT1.1, and correspond to the 5th–10th trans-membrane domains. Residues VsAMT1 D23 and StAMT1 D15 are predicted to be essential for ammonium transport, while mutations of VsAMT1 W1A-L and S87A and StAMT1 S76A may further enhance ammonium transport. In addition to nitrogen uptake from the roots, VsAMT1 may also contribute to interactions with rhizobia.

Bioinformatics and structural characterization of a hypothetical protein from Streptococcus mutans

DEFF Research Database (Denmark)

Nan, Jie; Brostromer, Erik; Liu, Xiang-Yu

2009-01-01

. From the interlinking structural and bioinformatics studies, we have concluded that SMU.440 could be involved in polyketide-like antibiotic resistance, providing a better understanding of this hypothetical protein. Besides, the combination of multiple methods in this study can be used as a general...

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

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Vamathevan, J; Birney, E

2017-08-01

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

Teaching and Research at Undergraduate Institutions

Science.gov (United States)

Garg, Shila

2006-03-01

My own career path has been non-traditional and I ended up at a primarily undergraduate institution by pure accident. However, teaching at a small college has been extremely rewarding to me, since I get to know and interact with my students, have an opportunity to work with them one-on-one and promote their intellectual growth and sense of social responsibility. One of the growing trends at undergraduate institutions in the past decade has been the crucial role of undergraduate research as part of the teaching process and the training of future scientists. There are several liberal arts institutions that expect research-active Faculty who can mentor undergraduate research activities. Often faculty members at these institutions consider their roles as teacher-scholars with no boundary between these two primary activities. A researcher who is in touch with the developments in his/her own field and contributes to new knowledge in the field is likely to be a more exciting teacher in the classroom and share the excitement of discovery with the students. At undergraduate institutions, there is generally very good support available for faculty development projects in both teaching and research. Often, there is a generous research leave program as well. For those who like advising and mentoring undergraduates and a teaching and learning centered paradigm, I will recommend a career at an undergraduate institution. In my presentation, I will talk about how one can prepare for such a career.

Design-Oriented Enhanced Robotics Curriculum

Science.gov (United States)

Yilmaz, M.; Ozcelik, S.; Yilmazer, N.; Nekovei, R.

2013-01-01

This paper presents an innovative two-course, laboratory-based, and design-oriented robotics educational model. The robotics curriculum exposed senior-level undergraduate students to major robotics concepts, and enhanced the student learning experience in hybrid learning environments by incorporating the IEEE Region-5 annual robotics competition…

Predicting Physical Activity and Healthy Nutrition Behaviors Using Social Cognitive Theory: Cross-Sectional Survey among Undergraduate Students in Chongqing, China.

Science.gov (United States)

Xu, Xianglong; Pu, Yang; Sharma, Manoj; Rao, Yunshuang; Cai, Yilin; Zhao, Yong

2017-11-05

(1) Background: Generally suggested public health measures to reduce obesity were to limit television (TV) viewing, enhance daily physical activities, enable the consumption of fruit and vegetables, and reduce sugar-sweetened beverage intake. This study analyzed the extent to which selected social cognitive theory constructs can predict these behaviors among Chinese undergraduate students. (2) Methods: This cross-sectional study included 1976 undergraduate students from six universities in Chongqing, China. A self-administered five-point Likert common physical activity and nutrition behavior scale based on social cognitive theory was utilized. (3) Results: This study included 687 (34.77%) males and 1289 (65.23%) females. A total of 60.14% of the students engaged in exercise for less than 30 min per day. Approximately 16.5%of the participants spent at least 4 h watching TV and sitting in front of a computer daily. Approximately 79% of the participants consumed less than five cups of fruit and vegetables daily. Undergraduate students who had high self-efficacy scores had more leisure time physical activities. Those who have high expectation scores had considerable time watching TV and sitting in front of a computer. Undergraduate students who had high expectation and self-efficacy scores had substantially low consumption of sugar-sweetened beverages. Those who had high self-efficacy scores consumed considerable amounts of fruit and vegetables. Furthermore, the type of university, BMI group, gender, age, lack of siblings, and grade level were associated with the aforementioned four behaviors. (4) Conclusion: Physical inactivity and unhealthy nutrition behaviors are common among undergraduate students. This study used social cognitive theory to provide several implications for limiting the TV viewing, enhancing daily physical activities, consuming fruit and vegetables, and reducing sugar-sweetened beverage intake among undergraduate students.

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

Science.gov (United States)

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

2015-02-01

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

Databases and Associated Bioinformatic Tools in Studies of Food Allergens, Epitopes and Haptens – a Review

Directory of Open Access Journals (Sweden)

Bucholska Justyna

2018-06-01

Full Text Available Allergies and/or food intolerances are a growing problem of the modern world. Diffi culties associated with the correct diagnosis of food allergies result in the need to classify the factors causing allergies and allergens themselves. Therefore, internet databases and other bioinformatic tools play a special role in deepening knowledge of biologically-important compounds. Internet repositories, as a source of information on different chemical compounds, including those related to allergy and intolerance, are increasingly being used by scientists. Bioinformatic methods play a signifi cant role in biological and medical sciences, and their importance in food science is increasing. This study aimed at presenting selected databases and tools of bioinformatic analysis useful in research on food allergies, allergens (11 databases, epitopes (7 databases, and haptens (2 databases. It also presents examples of the application of computer methods in studies related to allergies.

Bioinformatics prediction of swine MHC class I epitopes from Porcine Reproductive and Respiratory Syndrome Virus

DEFF Research Database (Denmark)

Welner, Simon; Nielsen, Morten; Lund, Ole

an effective CTL response against PRRSV, we have taken a bioinformatics approach to identify common PRRSV epitopes predicted to react broadly with predominant swine MHC (SLA) alleles. First, the genomic integrity and sequencing method was examined for 334 available complete PRRSV type 2 genomes leaving 104...... by the PopCover algorithm, providing a final list of 54 epitopes prioritized according to maximum coverage of PRRSV strains and SLA alleles. This bioinformatics approach provides a rational strategy for selecting peptides for a CTL-activating vaccine with broad coverage of both virus and swine diversity...

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

Science.gov (United States)

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

2017-01-01

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

Engineering Students: Enhancing Employability Skills through PBL

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H, Othman; Mat Daud K., A.; U, Ewon; Salleh B, Mohd; Omar N., H.; Baser J, Abd; Ismail M., E.; A, Sulaiman

2017-05-01

As a developing country, Malaysia faces challenging tasks to develop her economy just like many other countries. Nowadays, change involves many aspects like the economy from agriculture to manufacturing, technology from modern to more advanced ones; mindset from traditional to advanced and so on. Previous studies show that one of the major issues facing local graduates is the lack of employability skills. This problem concerns not only the government but undergraduates and institutions alike. From the pedagogical aspect, one of the more effective ways to improve this is through instructional delivery and in this case the use of Problem-based Learning (PBL). The need to adopt PBL should involved applied subjects undertaken by engineering students. Studies have shown that the use of PBL has been proven to make learning more attractive and effective. In this research, we studied the effectiveness of PBL towards enhancing employability skills among engineering undergraduates. This study adopted a combination of qualitative and quantitative approaches. Data was collected using documents analysis. Student samples comprised manufacturing engineering undergraduates from public institutions of higher learning in Malaysia. The results show that student’s employability skills can be enhanced using PBL. In addition, students become more competitive towards making them more relevance with the needs of the industry with regard to employability skills. In conclusion, PBL is a very effective catalyst towards raising the employability skills among engineering undergraduates and should be adopted in all engineering education.

EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats

Science.gov (United States)

Ison, Jon; Kalaš, Matúš; Jonassen, Inge; Bolser, Dan; Uludag, Mahmut; McWilliam, Hamish; Malone, James; Lopez, Rodrigo; Pettifer, Steve; Rice, Peter

2013-01-01

Motivation: Advancing the search, publication and integration of bioinformatics tools and resources demands consistent machine-understandable descriptions. A comprehensive ontology allowing such descriptions is therefore required. Results: EDAM is an ontology of bioinformatics operations (tool or workflow functions), types of data and identifiers, application domains and data formats. EDAM supports semantic annotation of diverse entities such as Web services, databases, programmatic libraries, standalone tools, interactive applications, data schemas, datasets and publications within bioinformatics. EDAM applies to organizing and finding suitable tools and data and to automating their integration into complex applications or workflows. It includes over 2200 defined concepts and has successfully been used for annotations and implementations. Availability: The latest stable version of EDAM is available in OWL format from http://edamontology.org/EDAM.owl and in OBO format from http://edamontology.org/EDAM.obo. It can be viewed online at the NCBO BioPortal and the EBI Ontology Lookup Service. For documentation and license please refer to http://edamontology.org. This article describes version 1.2 available at http://edamontology.org/EDAM_1.2.owl. Contact: jison@ebi.ac.uk PMID:23479348

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

Science.gov (United States)

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

2015-02-28

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

Exploring perceptions of the educational environment among undergraduate physiotherapy students.

Science.gov (United States)

Palmgren, Per J; Lindquist, Ingrid; Sundberg, Tobias; Nilsson, Gunnar H; Laksov, Klara B

2014-07-19

The aim of this study was to explore areas of strength and weakness in the educational environment as perceived by undergraduate physiotherapy students and to investigate these areas in relation to the respondents' demographic characteristics. This study utilized a cross-sectional study design and employed the Dundee Ready Education Environment Measure, a 50-item, self-administered inventory relating to a variety of topics directly pertinent to educational environments. Convenience sampling was used, and the scores were compared across demographic variables. All undergraduate physiotherapy students in their first five terms of the programme in a major Swedish university were invited to participate in the study. A total of 222 students (80%) completed the inventory. With an overall score of 150/200 (75%), the students rated the educational environment in this institution as "more positive than negative". Two items consistently received deprived scores - authoritarian teachers and teaching with an overemphasis on factual learning. Students in term 4 differed significantly from others, and students with earlier university education experience perceived the atmosphere more negatively than their counterparts. There were no significant differences with regards to other demographic variables. This study provides valuable insight into how undergraduate physiotherapy students perceive their educational environment. In general, students perceived that their educational programme fostered a sound educational environment. However, some areas require remedial measures in order to enhance the educational experience.

Host-parasite interactions and ecology of the malaria parasite-a bioinformatics approach.

Science.gov (United States)

Izak, Dariusz; Klim, Joanna; Kaczanowski, Szymon

2018-04-25

Malaria remains one of the highest mortality infectious diseases. Malaria is caused by parasites from the genus Plasmodium. Most deaths are caused by infections involving Plasmodium falciparum, which has a complex life cycle. Malaria parasites are extremely well adapted for interactions with their host and their host's immune system and are able to suppress the human immune system, erase immunological memory and rapidly alter exposed antigens. Owing to this rapid evolution, parasites develop drug resistance and express novel forms of antigenic proteins that are not recognized by the host immune system. There is an emerging need for novel interventions, including novel drugs and vaccines. Designing novel therapies requires knowledge about host-parasite interactions, which is still limited. However, significant progress has recently been achieved in this field through the application of bioinformatics analysis of parasite genome sequences. In this review, we describe the main achievements in 'malarial' bioinformatics and provide examples of successful applications of protein sequence analysis. These examples include the prediction of protein functions based on homology and the prediction of protein surface localization via domain and motif analysis. Additionally, we describe PlasmoDB, a database that stores accumulated experimental data. This tool allows data mining of the stored information and will play an important role in the development of malaria science. Finally, we illustrate the application of bioinformatics in the development of population genetics research on malaria parasites, an approach referred to as reverse ecology.

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

Science.gov (United States)

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

2010-09-15

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

Undergraduate students' perceived academic environmental ...

African Journals Online (AJOL)

This study examined the relationship between undergraduates' perception of the academic environment, their attitude to academic work and achievement. A total of 348 undergraduates who formed the sample were drawn from five departments in three universities in Nigeria. The study revealed that four dimensions of the ...

Integrating undergraduate research into the electro-optics and laser engineering technology program at Indiana University of Pennsylvania

Science.gov (United States)

Zhou, Andrew F.

2014-07-01

Bringing research into an undergraduate curriculum is a proven and powerful practice with many educational benefits to students and the professional rewards to faculty mentors. In recent years, undergraduate research has gained national prominence as an effective problem-based learning strategy. Developing and sustaining a vibrant undergraduate research program of high quality and productivity is an outstanding example of the problem-based learning. To foster student understanding of the content learned in the classroom and nurture enduring problem-solving and critical-thinking abilities, we have created a collaborative learning environment by building research into the Electro-Optics curriculum for the first- and second-year students. The teaching methodology is described and examples of the research projects are given. Such a research-integrated curriculum effectively enhances student learning and critical thinking skills, and strengthens the research culture for the first- and second-year students.

MicroRNA from tuberculosis RNA: A bioinformatics study

OpenAIRE

Wiwanitkit, Somsri; Wiwanitkit, Viroj

2012-01-01

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

Integration of NASA Research into Undergraduate Education in Math, Science, Engineering and Technology at North Carolina A&T State University

Science.gov (United States)

Monroe, Joseph; Kelkar, Ajit

2003-01-01

The NASA PAIR program incorporated the NASA-Sponsored research into the undergraduate environment at North Carolina Agricultural and Technical State University. This program is designed to significantly improve undergraduate education in the areas of mathematics, science, engineering, and technology (MSET) by directly benefiting from the experiences of NASA field centers, affiliated industrial partners and academic institutions. The three basic goals of the program were enhancing core courses in MSET curriculum, upgrading core-engineering laboratories to compliment upgraded MSET curriculum, and conduct research training for undergraduates in MSET disciplines through a sophomore shadow program and through Research Experience for Undergraduates (REU) programs. Since the inception of the program nine courses have been modified to include NASA related topics and research. These courses have impacted over 900 students in the first three years of the program. The Electrical Engineering circuit's lab is completely re-equipped to include Computer controlled and data acquisition equipment. The Physics lab is upgraded to implement better sensory data acquisition to enhance students understanding of course concepts. In addition a new instrumentation laboratory in the department of Mechanical Engineering is developed. Research training for A&T students was conducted through four different programs: Apprentice program, Developers program, Sophomore Shadow program and Independent Research program. These programs provided opportunities for an average of forty students per semester.

Undergraduate Convexity

DEFF Research Database (Denmark)

Lauritzen, Niels

Based on undergraduate teaching to students in computer science, economics and mathematics at Aarhus University, this is an elementary introduction to convex sets and convex functions with emphasis on concrete computations and examples. Starting from linear inequalities and Fourier-Motzkin elimin......Based on undergraduate teaching to students in computer science, economics and mathematics at Aarhus University, this is an elementary introduction to convex sets and convex functions with emphasis on concrete computations and examples. Starting from linear inequalities and Fourier......-Motzkin elimination, the theory is developed by introducing polyhedra, the double description method and the simplex algorithm, closed convex subsets, convex functions of one and several variables ending with a chapter on convex optimization with the Karush-Kuhn-Tucker conditions, duality and an interior point...... algorithm....

Bioinformatics for Next Generation Sequencing Data

Directory of Open Access Journals (Sweden)

Alberto Magi

2010-09-01

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

Frames for undergraduates

CERN Document Server

Han, Deguang; Larson, David; Weber, Eric

2007-01-01

Frames for Undergraduates is an undergraduate-level introduction to the theory of frames in a Hilbert space. This book can serve as a text for a special-topics course in frame theory, but it could also be used to teach a second semester of linear algebra, using frames as an application of the theoretical concepts. It can also provide a complete and helpful resource for students doing undergraduate research projects using frames. The early chapters contain the topics from linear algebra that students need to know in order to read the rest of the book. The later chapters are devoted to advanced topics, which allow students with more experience to study more intricate types of frames. Toward that end, a Student Presentation section gives detailed proofs of fairly technical results with the intention that a student could work out these proofs independently and prepare a presentation to a class or research group. The authors have also presented some stories in the Anecdotes section about how this material has moti...

Undergraduate Students' Information Search Practices

Science.gov (United States)

Nikolopoulou, Kleopatra; Gialamas, Vasilis

2011-01-01

This paper investigates undergraduate students' information search practices. The subjects were 250 undergraduate students from two university departments in Greece, and a questionnaire was used to document their search practices. The results showed that the Web was the primary information system searched in order to find information for…

Undergraduate study in psychology: Curriculum and assessment.

Science.gov (United States)

Norcross, John C; Hailstorks, Robin; Aiken, Leona S; Pfund, Rory A; Stamm, Karen E; Christidis, Peggy

2016-01-01

The undergraduate curriculum in psychology profoundly reflects and shapes the discipline. Yet, reliable information on the undergraduate psychology curriculum has been difficult to acquire due to insufficient research carried out on unrepresentative program samples with disparate methods. In 2014, APA launched the first systematic effort in a decade to gather national data on the psychology major and program outcomes. We surveyed a stratified random sample of department chairs/coordinators of accredited colleges and universities in the United States that offer undergraduate courses and programs in psychology. A total of 439 undergraduate psychology programs (45.2%) completed the survey. This article summarizes, for both associate and baccalaureate programs, the results of the Undergraduate Study in Psychology. Current practices concerning the introductory course, the courses offered, core requirements, the psychology minor, and tracks/concentrations are presented. The frequency of formal program reviews and program-level assessment methods are also addressed. By extending prior research on the undergraduate curriculum, we chronicle longitudinal changes in the psychology major over the past 20 years. (c) 2016 APA, all rights reserved).

Shared Bioinformatics Databases within the Unipro UGENE Platform

Directory of Open Access Journals (Sweden)

Protsyuk Ivan V.

2015-03-01

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

Teaching medical ethics to undergraduate students in post‐apartheid South Africa, 2003–2006

Science.gov (United States)

Moodley, Keymanthri

2007-01-01

The apartheid ideology in South Africa had a pervasive influence on all levels of education including medical undergraduate training. The role of the health sector in human rights abuses during the apartheid era was highlighted in 1997 during the Truth and Reconciliation Commission hearings. The Health Professions Council of South Africa (HPCSA) subsequently realised the importance of medical ethics education and encouraged the introduction of such teaching in all medical schools in the country. Curricular reform at the University of Stellenbosch in 1999 presented an unparalleled opportunity to formally introduce ethics teaching to undergraduate students. This paper outlines the introduction of a medical ethics programme at the Faculty of Health Sciences from 2003 to 2006, with special emphasis on the challenges encountered. It remains one of the most comprehensive undergraduate medical ethics programmes in South Africa. However, there is scope for expanding the curricular time allocated to medical ethics. Integrating the curriculum both horizontally and vertically is imperative. Implementing a core curriculum for all medical schools in South Africa would significantly enhance the goals of medical education in the country. PMID:17971474

Can a tablet device alter undergraduate science students' study behavior and use of technology?

Science.gov (United States)

Morris, Neil P; Ramsay, Luke; Chauhan, Vikesh

2012-06-01

This article reports findings from a study investigating undergraduate biological sciences students' use of technology and computer devices for learning and the effect of providing students with a tablet device. A controlled study was conducted to collect quantitative and qualitative data on the impact of a tablet device on students' use of devices and technology for learning. Overall, we found that students made extensive use of the tablet device for learning, using it in preference to laptop computers to retrieve information, record lectures, and access learning resources. In line with other studies, we found that undergraduate students only use familiar Web 2.0 technologies and that the tablet device did not alter this behavior for the majority of tools. We conclude that undergraduate science students can make extensive use of a tablet device to enhance their learning opportunities without institutions changing their teaching methods or computer systems, but that institutional intervention may be needed to drive changes in student behavior toward the use of novel Web 2.0 technologies.

Researching Undergraduate Social Science Research

Science.gov (United States)

Rand, Jane

2016-01-01

The experience(s) of undergraduate research students in the social sciences is under-represented in the literature in comparison to the natural sciences or science, technology, engineering and maths (STEM). The strength of STEM undergraduate research learning environments is understood to be related to an apprenticeship-mode of learning supported…

Complexity of comprehensive care treatments in undergraduate dental programs: The benefits of observing and assisting experienced faculty members

Directory of Open Access Journals (Sweden)

Moataz Elgezawi

2017-10-01

Conclusions: Exposing students to manage complex oral rehabilitation including procedures like sinus lifting and bone augmentation, through an evidence-based interdisciplinary approach during the undergraduate comprehensive clinical dentistry course enhances their confidence and clinical acumen as an independent practitioner.

Using Mobile Technology to Enhance Undergraduate Student Digital Information Literacy Skills: A Canadian Case Study

OpenAIRE

Alice Schmidt Hanbidge; Nicole Sanderson; Tony Tin

2015-01-01

Learning essential information literacy skills through the use of mobile phones is an innovative mlearning pilot project that was collaboratively undertaken in a Canadian university college over the course of two academic terms by faculty and the library staff. The research pilot project involved ninety one undergraduate students in five different classes majoring in psychology, social work, education or social development studies in an attempt to determine the effectiveness of us...

National Writing Project's Multimodal Literacies and Teacher Collaboration: Enhanced Student Learning on Global Social Issues

Science.gov (United States)

Iyengar, Kalpana; Hood, Caleb

2016-01-01

Iyengar and Hood, both teacher consultants with the San Antonio Writing Project (SAWP), and instructors of an undergraduate society and social issues class, collaborated to enhance their undergraduate students' writing experiences using the National Writing Project model (Lieberman & Wood, 2003). Iyengar and Hood used strategies such as…

Undergraduate Program: Philadelphia

Science.gov (United States)

Betsock, Lori

2008-08-01

Undergraduate chemical science students—join us in Philadelphia on August 17 and 18, 2008, for an educational and career-oriented program designed specifically for you. Attend symposia about global climate change and clean energy; hear Nobel Laureate F. Sherwood Rowland speak about his fascinating career, "A Life in Tracer Chemistry". Weigh options for your future by attending the Graduate School Reality Check and graduate school recruiting events. All events will take place in the Sheraton Philadelphia City Center at 17th and Race Streets, except the Undergraduate Poster Sessions and Sci-Mix, which will be held in the Pennsylvania Convention Center.

Robust Bioinformatics Recognition with VLSI Biochip Microsystem

Science.gov (United States)

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

2006-01-01

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

Microbial bioinformatics 2020.

Science.gov (United States)

Pallen, Mark J

2016-09-01

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

Tissue damage in organic rainbow trout muscle investigated by proteomics and bioinformatics

DEFF Research Database (Denmark)

Wulff, Tune; Silva, T.; Nielsen, Michael Engelbrecht

2013-01-01

and magnitude of the cellular response, in the context of a regenerative process. Using a bioinformatics approach, the main biological function of these proteins were assigned, showing the regulation of proteins involved in processes like apoptosis, iron homeostasis and regulation of muscular structure...

Perceptions of Undergraduate Students and Faculty Regarding the Impact of Electronic Communication on the Written-Communication Skills of Undergraduate Students

Science.gov (United States)

Houser, Laura Ann Camlet

2012-01-01

This narrative-qualitative study investigated the perceived impact that electronic communication has on the written-communication skills of undergraduate students. Open-ended survey questions queried the experiences of undergraduate students who use electronic communication, as well as the perceptions of faculty who teach undergraduate students.…

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

Science.gov (United States)

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

2011-01-01

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

A conference experience for undergraduates

International Nuclear Information System (INIS)

Collins, L.A.; Magee, N.H.; Bryant, H.C.; Zeilik, M.

1999-01-01

Programs launched by many universities and the federal government expose many undergraduate students in the physical sciences to research early in their careers. However, in their research experiences, undergraduates are not usually introduced to the modes by which scientific knowledge, which they may have helped gather, is communicated and evaluated by working scientists. Nor is it always made clear where the research frontiers really lie. To this end, we guided a selected group of undergraduates through a national scientific conference, followed by a week of tutorials and discussions to help them better understand what had transpired. The program complemented the basic undergraduate research endeavors by emphasizing the importance of disseminating results both to other scientists and to society in general. Tutors and discussion leaders in the second week were experts in their fields and included some of the invited speakers from the main meeting. A considerable improvement in the understanding of the issues and prospects for a career in physics was discernible among the students after their two-week experience. copyright 1999 American Association of Physics Teachers

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

Science.gov (United States)

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

2010-01-01

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

Making developmental biology relevant to undergraduates in an era of economic rationalism in Australia.

Science.gov (United States)

Key, Brian; Nurcombe, Victor

2003-01-01

This report describes the road map we followed at our university to accommodate three main factors: financial pressure within the university system; desire to enhance the learning experience of undergraduates; and motivation to increase the prominence of the discipline of developmental biology in our university. We engineered a novel, multi-year undergraduate developmental biology program which was "student-oriented," ensuring that students were continually exposed to the underlying principles and philosophy of this discipline throughout their undergraduate career. Among its key features are introductory lectures in core courses in the first year, which emphasize the relevance of developmental biology to tissue engineering, reproductive medicine, therapeutic approaches in medicine, agriculture and aquaculture. State-of-the-art animated computer graphics and images of high visual impact are also used. In addition, students are streamed into the developmental biology track in the second year, using courses like human embryology and courses shared with cell biology, which include practicals based on modern experimental approaches. Finally, fully dedicated third-year courses in developmental biology are undertaken in conjunction with stand-alone practical courses where students experiencefirst-hand work in a research laboratory. Our philosophy is a "cradle-to-grave" approach to the education of undergraduates so as to prepare highly motivated, enthusiastic and well-educated developmental biologists for entry into graduate programs and ultimately post-doctoral research.

[Undergraduate education of medical technologists to promote scientific and technological literacy].

Science.gov (United States)

Yamaguchi, Hiroyuki; Akizawa, Hirotsugu

2010-07-01

It is becoming increasingly important for today's medical technologists to receive proper training on the safety of medical treatment and healthcare in order to accommodate the rapid changes and advancement in medical technology. In particular, because of the increase of hospital-acquired infections, the role of medical technologists involved in infection control has become much more important. In addition, particularly in Japan, the career options available to students graduating with a degree in medical technology have become much more diverse, ranging from research laboratories to clinical services; however, undergraduate education for medical technologists is limited. It is therefore deemed necessary for undergraduate students to be provided with adequate training from their universities by offering a wider selection of classes in this subject area. In this paper, we summarize our preliminary findings on the trial lessons that are offered to medical technology students in their microbiology class. These lessons are designed to enhance students' academic potential and to engage their interest.

Bioinformatic analysis of functional differences between the immunoproteasome and the constitutive proteasome

DEFF Research Database (Denmark)

Kesmir, Can; van Noort, V.; de Boer, R.J.

2003-01-01

not yet been quantified how different the specificity of two forms of the proteasome are. The main question, which still lacks direct evidence, is whether the immunoproteasome generates more MHC ligands. Here we use bioinformatics tools to quantify these differences and show that the immunoproteasome...

In-depth analysis of the adipocyte proteome by mass spectrometry and bioinformatics

DEFF Research Database (Denmark)

Adachi, Jun; Kumar, Chanchal; Zhang, Yanling

2007-01-01

, mitochondria, membrane, and cytosol of 3T3-L1 adipocytes. We identified 3,287 proteins while essentially eliminating false positives, making this one of the largest high confidence proteomes reported to date. Comprehensive bioinformatics analysis revealed that the adipocyte proteome, despite its specialized...

Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN.

Science.gov (United States)

He, Yongqun; Xiang, Zuoshuang

2010-09-27

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

G-DOC Plus - an integrative bioinformatics platform for precision medicine.

Science.gov (United States)

Bhuvaneshwar, Krithika; Belouali, Anas; Singh, Varun; Johnson, Robert M; Song, Lei; Alaoui, Adil; Harris, Michael A; Clarke, Robert; Weiner, Louis M; Gusev, Yuriy; Madhavan, Subha

2016-04-30

G-DOC Plus is a data integration and bioinformatics platform that uses cloud computing and other advanced computational tools to handle a variety of biomedical BIG DATA including gene expression arrays, NGS and medical images so that they can be analyzed in the full context of other omics and clinical information. G-DOC Plus currently holds data from over 10,000 patients selected from private and public resources including Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA) and the recently added datasets from REpository for Molecular BRAin Neoplasia DaTa (REMBRANDT), caArray studies of lung and colon cancer, ImmPort and the 1000 genomes data sets. The system allows researchers to explore clinical-omic data one sample at a time, as a cohort of samples; or at the level of population, providing the user with a comprehensive view of the data. G-DOC Plus tools have been leveraged in cancer and non-cancer studies for hypothesis generation and validation; biomarker discovery and multi-omics analysis, to explore somatic mutations and cancer MRI images; as well as for training and graduate education in bioinformatics, data and computational sciences. Several of these use cases are described in this paper to demonstrate its multifaceted usability. G-DOC Plus can be used to support a variety of user groups in multiple domains to enable hypothesis generation for precision medicine research. The long-term vision of G-DOC Plus is to extend this translational bioinformatics platform to stay current with emerging omics technologies and analysis methods to continue supporting novel hypothesis generation, analysis and validation for integrative biomedical research. By integrating several aspects of the disease and exposing various data elements, such as outpatient lab workup, pathology, radiology, current treatments, molecular signatures and expected outcomes over a web interface, G-DOC Plus will continue to strengthen precision medicine research. G-DOC Plus is available

Bioinformatics: Cheap and robust method to explore biomaterial from Indonesia biodiversity

Science.gov (United States)

Widodo

2015-02-01

Indonesia has a huge amount of biodiversity, which may contain many biomaterials for pharmaceutical application. These resources potency should be explored to discover new drugs for human wealth. However, the bioactive screening using conventional methods is very expensive and time-consuming. Therefore, we developed a methodology for screening the potential of natural resources based on bioinformatics. The method is developed based on the fact that organisms in the same taxon will have similar genes, metabolism and secondary metabolites product. Then we employ bioinformatics to explore the potency of biomaterial from Indonesia biodiversity by comparing species with the well-known taxon containing the active compound through published paper or chemical database. Then we analyze drug-likeness, bioactivity and the target proteins of the active compound based on their molecular structure. The target protein was examined their interaction with other proteins in the cell to determine action mechanism of the active compounds in the cellular level, as well as to predict its side effects and toxicity. By using this method, we succeeded to screen anti-cancer, immunomodulators and anti-inflammation from Indonesia biodiversity. For example, we found anticancer from marine invertebrate by employing the method. The anti-cancer was explore based on the isolated compounds of marine invertebrate from published article and database, and then identified the protein target, followed by molecular pathway analysis. The data suggested that the active compound of the invertebrate able to kill cancer cell. Further, we collect and extract the active compound from the invertebrate, and then examined the activity on cancer cell (MCF7). The MTT result showed that the methanol extract of marine invertebrate was highly potent in killing MCF7 cells. Therefore, we concluded that bioinformatics is cheap and robust way to explore bioactive from Indonesia biodiversity for source of drug and another

OralCard: a bioinformatic tool for the study of oral proteome.

Science.gov (United States)

Arrais, Joel P; Rosa, Nuno; Melo, José; Coelho, Edgar D; Amaral, Diana; Correia, Maria José; Barros, Marlene; Oliveira, José Luís

2013-07-01

The molecular complexity of the human oral cavity can only be clarified through identification of components that participate within it. However current proteomic techniques produce high volumes of information that are dispersed over several online databases. Collecting all of this data and using an integrative approach capable of identifying unknown associations is still an unsolved problem. This is the main motivation for this work. We present the online bioinformatic tool OralCard, which comprises results from 55 manually curated articles reflecting the oral molecular ecosystem (OralPhysiOme). It comprises experimental information available from the oral proteome both of human (OralOme) and microbial origin (MicroOralOme) structured in protein, disease and organism. This tool is a key resource for researchers to understand the molecular foundations implicated in biology and disease mechanisms of the oral cavity. The usefulness of this tool is illustrated with the analysis of the oral proteome associated with diabetes melitus type 2. OralCard is available at http://bioinformatics.ua.pt/oralcard. Copyright © 2013 Elsevier Ltd. All rights reserved.

Enhancing first year chemistry student's participation in practical ...

African Journals Online (AJOL)

In this study, enhancing student's participation in practical analytical ... The data were collected from I year chemistry undergraduate students of class size 56 of ... learning practical Chemistry were mainly due to problems in preparing a flow ...

Learning Nucleic Acids Solving by Bioinformatics Problems

Science.gov (United States)

Nunes, Rhewter; de Almeida Júnior, Edivaldo Barbosa; de Menezes, Ivandilson Pessoa Pinto; Malafaia, Guilherme

2015-01-01

The article describes the development of a new approach to teach molecular biology to undergraduate biology students. The 34 students who participated in this research belonged to the first period of the Biological Sciences teaching course of the Instituto Federal Goiano at Urutaí Campus, Brazil. They were registered in Cell Biology in the first…

Eating Disorders and Body Image of Undergraduate Men

Science.gov (United States)

Ousley, Louise; Cordero, Elizabeth Diane; White, Sabina

2008-01-01

Eating disorders and body dissatisfaction among undergraduate men are less documented and researched than are eating disorders and body dissatisfaction among undergraduate women. Objective and Participants: In this study, the authors examined these issues in undergraduate men to identify similarities and differences between this population and…

Identification of Enhancers In Human: Advances In Computational Studies

KAUST Repository

Kleftogiannis, Dimitrios A.

2016-03-24

Roughly ~50% of the human genome, contains noncoding sequences serving as regulatory elements responsible for the diverse gene expression of the cells in the body. One very well studied category of regulatory elements is the category of enhancers. Enhancers increase the transcriptional output in cells through chromatin remodeling or recruitment of complexes of binding proteins. Identification of enhancer using computational techniques is an interesting area of research and up to now several approaches have been proposed. However, the current state-of-the-art methods face limitations since the function of enhancers is clarified, but their mechanism of function is not well understood. This PhD thesis presents a bioinformatics/computer science study that focuses on the problem of identifying enhancers in different human cells using computational techniques. The dissertation is decomposed into four main tasks that we present in different chapters. First, since many of the enhancer’s functions are not well understood, we study the basic biological models by which enhancers trigger transcriptional functions and we survey comprehensively over 30 bioinformatics approaches for identifying enhancers. Next, we elaborate more on the availability of enhancer data as produced by different enhancer identification methods and experimental procedures. In particular, we analyze advantages and disadvantages of existing solutions and we report obstacles that require further consideration. To mitigate these problems we developed the Database of Integrated Human Enhancers (DENdb), a centralized online repository that archives enhancer data from 16 ENCODE cell-lines. The integrated enhancer data are also combined with many other experimental data that can be used to interpret the enhancers content and generate a novel enhancer annotation that complements the existing integrative annotation proposed by the ENCODE consortium. Next, we propose the first deep-learning computational

Enhancing Hispanic Minority Undergraduates' Botany Laboratory Experiences: Implementation of an Inquiry-Based Plant Tissue Culture Module Exercise

Science.gov (United States)

Siritunga, Dimuth; Navas, Vivian; Diffoot, Nanette

2012-01-01

Early involvement of students in hands-on research experiences are known to demystify research and promote the pursuit of careers in science. But in large enrollment departments such opportunities for undergraduates to participate in research are rare. To counteract such lack of opportunities, inquiry-based laboratory module in plant tissue…

Pattern of Smartphones Utilisation among Engineering Undergraduates

OpenAIRE

Muliati Sedek

2014-01-01

The smartphones ownership among the undergraduates in Malaysia was recorded as high. However, little was known about its utilization patterns, thus, the focus of this research was to determine the utilisation patterns of smartphones based on the National Education Technology Standard for Students (NETS.S) among engineering undergraduates in Malaysia. This study was based on a quantitative research and the population comprised undergraduates from four Malaysian Technical Universities. A total ...

Single-Cell Transcriptomics Bioinformatics and Computational Challenges

Directory of Open Access Journals (Sweden)

Lana Garmire

2016-09-01

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

Life Science Professional Societies Expand Undergraduate Education Efforts

Science.gov (United States)

Matyas, Marsha Lakes; Ruedi, Elizabeth A.; Engen, Katie; Chang, Amy L.

2017-01-01

The "Vision and Change in Undergraduate Biology Education" reports cite the critical role of professional societies in undergraduate life science education and, since 2008, have called for the increased involvement of professional societies in support of undergraduate education. Our study explored the level of support being provided by…

An assessment of student experiences and learning based on a novel undergraduate e-learning resource.

Science.gov (United States)

Mehta, S; Clarke, F; Fleming, P S

2016-08-12

Purpose/objectives The aims of this study were to describe the development of a novel e-learning resource and to assess its impact on student learning experiences and orthodontic knowledge.Methods Thirty-two 4th year dental undergraduate students at Queen Mary University of London were randomly allocated to receive electronic access to e-learning material covering various undergraduate orthodontic topics over a 6-week period. Thirty-one control students were not given access during the study period. All students were asked to complete electronic quizzes both before (T0) and after (T1) the study period and a general questionnaire concerning familiarity with e-learning. The test group also completed a user satisfaction questionnaire at T1. Two focus groups were also undertaken to explore learners' experiences and suggestions in relation to the resource.Results The mean quiz result improved by 3.9% and 4.5% in the control and test groups, respectively. An independent t-test, however, demonstrated a lack of statistical significance in knowledge gain between control and test groups (P = 0.941). The qualitative feedback indicated that students believed that use of the resource enhanced knowledge and basic understanding with students expressing a wish to ingrain similar resources in other areas of undergraduate teaching.Conclusions Use of the novel orthodontic e-resource by 4th year undergraduate students over a 6-week period did not result in a significant improvement in subject knowledge. However, the e-learning has proven popular among undergraduates and the resources will continue to be refined.

Undergraduate Convexity

DEFF Research Database (Denmark)

Lauritzen, Niels

Based on undergraduate teaching to students in computer science, economics and mathematics at Aarhus University, this is an elementary introduction to convex sets and convex functions with emphasis on concrete computations and examples. Starting from linear inequalities and Fourier-Motzkin elimin...

Promoting Clinical Reasoning in Undergraduate Physical Therapy Education: A Review of Strategies and Approaches

DEFF Research Database (Denmark)

Brekke, Anders Falk

2015-01-01

Title: Promoting Clinical Reasoning in Undergraduate Physical Therapy Education: A Review of Strategies and Approaches Juneja H1, Brekke A F2 1,2 Physical Therapy Education, University College Zealand, Denmark Background: Clinical reasoning (CR) also referred to as “critical thinking” or “decision....... It is imperative that physical therapy educators utilize innovative pedagogical methods to facilitate learning of reasoning skills in students. Purpose: The review is an attempt to highlight and discuss selected pedagogical strategies and approaches to enhance clinical reasoning skills in undergraduate physical...... programs was shortlisted for the review. References of pertinent literature were scanned to identify further relevant citations. Results: The review provides a detailed insight into the interwoven nature of pedagogical techniques to promote clinical reasoning being used by different physical therapy...

May I see your ID, please? An explorative study of the professional identity of undergraduate medical education leaders.

Science.gov (United States)

Sundberg, Kristina; Josephson, Anna; Reeves, Scott; Nordquist, Jonas

2017-02-01

The mission of undergraduate medical education leaders is to strive towards the enhancement of quality of medical education and health care. The aim of this qualitative study is, with the help of critical perspectives, to contribute to the research area of undergraduate medical education leaders and their identity formation; how can the identity of undergraduate medical education leaders be defined and further explored from a power perspective? In this explorative study, 14 educational leaders at a medical programme in Scandinavia were interviewed through semi-structured interviews. The data was analysed through Moustakas' structured, phenomenological analysis approach and then pattern matched with Gee's power-based identity model. Educational leaders identify themselves more as mediators than leaders and do not feel to any larger extent that their professional identity is authorised by the university. These factors potentially create difficulties when trying to communicate with medical teachers, often also with a weaker sense of professional identity, about medical education. The perceptions of the professional identity of undergraduate medical education leaders provide us with important notions on the complexities on executing their important mission to develop medical education: their perceptions of ambiguity towards the process of trying to lead teachers toward educational development and a perceived lack of authorisation of their work from the university level. These are important flaws to observe and correct when improving the context in which undergraduate medical education leaders are trying to develop and improve undergraduate medical programmes. A practical outcome of the results of this study is the facilitation of design of faculty development programmes for educational leaders in undergraduate medial education.

Exploring the Relationship between Campus Leadership Development and Undergraduate Student Motivation to Lead among a Malaysian Sample

Science.gov (United States)

Krauss, Steven Eric; Hamid, Jamaliah Abdul

2015-01-01

Despite the number of studies investigating the perceived effectiveness of campus-based leadership development programming among undergraduates, most have focused on programme outcomes and few have investigated the role of the campus environment in enhancing students' motivation to lead, particularly in non-Western contexts. To address these gaps,…

Feasibility and outcomes of paid undergraduate student nurse positions.

Science.gov (United States)

Gamroth, Lucia; Budgen, Claire; Lougheed, Mary

2006-09-01

new graduates and to retain existing nurses. Stakeholder groups were administrators, labour organizations, professional associations, educators and government. One idea to support job readiness and retention focussed on the feasibility of implementing cooperative education for nursing students. The effort was unsuccessful owing to lack of funding, but resulted in a review of the literature on cooperative education and other work-study programs. Cooperative education connects classroom learning with paid work experience for the purpose of enhancing students' education (Fitt and Heverly 1990; Heinemann and De Falco 1992; Ryder 1987). Reported benefits for students were improved job preparation and graduate retention (Ishida et al. 1998), additional staffing and reduction in orientation time (Cusack 1990; Ishida et al. 1998), increased practice judgment (Cusack 1990; Siedenberg 1989) and better workload management (Ross and Marriner 1985). A work-study model reported in the literature offered benefits similar to those of cooperative education, with greater flexibility in design. An example was the University of Texas Health Science Center at Houston's collaborative work-study scholarship program with local hospitals (Kee and Ryser 2001). Students in second clinical semesters were employed as unlicensed personnel by hospitals. The students, as unlicensed personnel, worked to the level of their nursing preparation. Reported benefits for students were academic credit, financial assistance, interaction with multidisciplinary teams, opportunity to refine clinical skills, understanding of nurses' roles and guaranteed interview for positions on graduation (Kee and Ryser 2001). Benefits for practice organizations were skilled help, the opportunity to recruit new nurses and increased interaction with a university nursing program. While nurse education stakeholders in British Columbia were exploring options, the concept of undergraduate student nurse employment was initiated by a

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

Czech Academy of Sciences Publication Activity Database

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

2004-01-01

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

Bioinformatics analysis identifies several intrinsically disordered human E3 ubiquitin-protein ligases

DEFF Research Database (Denmark)

Boomsma, Wouter Krogh; Nielsen, Sofie Vincents; Lindorff-Larsen, Kresten

2016-01-01

conduct a bioinformatics analysis to examine >600 human and S. cerevisiae E3 ligases to identify enzymes that are similar to San1 in terms of function and/or mechanism of substrate recognition. An initial sequence-based database search was found to detect candidates primarily based on the homology...

An intensive primary-literature-based teaching program directly benefits undergraduate science majors and facilitates their transition to doctoral programs.

Science.gov (United States)

Kozeracki, Carol A; Carey, Michael F; Colicelli, John; Levis-Fitzgerald, Marc; Grossel, Martha

2006-01-01

UCLA's Howard Hughes Undergraduate Research Program (HHURP), a collaboration between the College of Letters and Science and the School of Medicine, trains a group of highly motivated undergraduates through mentored research enhanced by a rigorous seminar course. The course is centered on the presentation and critical analysis of scientific journal articles as well as the students' own research. This article describes the components and objectives of the HHURP and discusses the results of three program assessments: annual student evaluations, interviews with UCLA professors who served as research advisors for HHURP scholars, and a survey of program alumni. Students indicate that the program increased their ability to read and present primary scientific research and to present their own research and enhanced their research experience at UCLA. After graduating, they find their involvement in the HHURP helped them in securing admission to the graduate program of their choice and provided them with an advantage over their peers in the interactive seminars that are the foundation of graduate education. On the basis of the assessment of the program from 1998-1999 to 2004-2005, we conclude that an intensive literature-based training program increases student confidence and scientific literacy during their undergraduate years and facilitates their transition to postgraduate study.

Combining multiple decisions: applications to bioinformatics

International Nuclear Information System (INIS)

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

2008-01-01

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

Establishing Common Course Objectives for Undergraduate Exercise Physiology

Science.gov (United States)

Simonson, Shawn R.

2015-01-01

Undergraduate exercise physiology is a ubiquitous course in undergraduate kinesiology/exercise science programs with a broad scope and depth of topics. It is valuable to explore what is taught within this course. The purpose of the present study was to facilitate an understanding of what instructors teach in undergraduate exercise physiology, how…

Bioinformatics Analysis Reveals Genes Involved in the Pathogenesis of Ameloblastoma and Keratocystic Odontogenic Tumor.

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Santos, Eliane Macedo Sobrinho; Santos, Hércules Otacílio; Dos Santos Dias, Ivoneth; Santos, Sérgio Henrique; Batista de Paula, Alfredo Maurício; Feltenberger, John David; Sena Guimarães, André Luiz; Farias, Lucyana Conceição

2016-01-01

Pathogenesis of odontogenic tumors is not well known. It is important to identify genetic deregulations and molecular alterations. This study aimed to investigate, through bioinformatic analysis, the possible genes involved in the pathogenesis of ameloblastoma (AM) and keratocystic odontogenic tumor (KCOT). Genes involved in the pathogenesis of AM and KCOT were identified in GeneCards. Gene list was expanded, and the gene interactions network was mapped using the STRING software. "Weighted number of links" (WNL) was calculated to identify "leader genes" (highest WNL). Genes were ranked by K-means method and Kruskal-Wallis test was used (Preview data was used to corroborate the bioinformatics data. CDK1 was identified as leader gene for AM. In KCOT group, results show PCNA and TP53 . Both tumors exhibit a power law behavior. Our topological analysis suggested leader genes possibly important in the pathogenesis of AM and KCOT, by clustering coefficient calculated for both odontogenic tumors (0.028 for AM, zero for KCOT). The results obtained in the scatter diagram suggest an important relationship of these genes with the molecular processes involved in AM and KCOT. Ontological analysis for both AM and KCOT demonstrated different mechanisms. Bioinformatics analyzes were confirmed through literature review. These results may suggest the involvement of promising genes for a better understanding of the pathogenesis of AM and KCOT.

Secretome Analysis of Lipid-Induced Insulin Resistance in Skeletal Muscle Cells by a Combined Experimental and Bioinformatics Workflow

DEFF Research Database (Denmark)

Deshmukh, Atul S; Cox, Juergen; Jensen, Lars Juhl

2015-01-01

, in principle, allows an unbiased and comprehensive analysis of cellular secretomes; however, the distinction of bona fide secreted proteins from proteins released upon lysis of a small fraction of dying cells remains challenging. Here we applied highly sensitive MS and streamlined bioinformatics to analyze......-resistant conditions. Our study demonstrates an efficient combined experimental and bioinformatics workflow to identify putative secreted proteins from insulin-resistant skeletal muscle cells, which could easily be adapted to other cellular models....

Undergraduate Research as Engaged Student Learning

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Wolf, Lorraine W.

2018-01-01

This chapter discusses the impact of undergraduate research as a form of engaged student learning. It summarizes the gains reported in post-fellowship assessment essays acquired from students participating in the Auburn University Undergraduate Research Fellowship Program. The chapter also discusses the program's efforts to increase opportunities…

Teaching Old French Literature to Undergraduates.

Science.gov (United States)

Stewart, Harry E.

As a prelude to graduate-level work for French majors, medieval studies are proposed for undergraduate students. Problems inherent in the establishment of the undergraduate program are identified with some suggested solutions. Concepts related to historical grammar, teaching materials, literature, and linguistics are developed. A logical course…

Teamwork education improves trauma team performance in undergraduate health professional students.

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Baker, Valerie O'Toole; Cuzzola, Ronald; Knox, Carolyn; Liotta, Cynthia; Cornfield, Charles S; Tarkowski, Robert D; Masters, Carolynn; McCarthy, Michael; Sturdivant, Suzanne; Carlson, Jestin N

2015-01-01

Effective trauma resuscitation requires efficient and coordinated care from a team of providers; however, providers are rarely instructed on how to be effective members of trauma teams. Team-based learning using Team Strategies and Tools to Enhance Performance and Patient Safety (TeamSTEPPS) has been shown to improve team dynamics among practicing professionals, including physicians and nurses. The impact of TeamSTEPPS on students being trained in trauma management in an undergraduate health professional program is currently unknown. We sought to determine the impact of TeamSTEPPS on team dynamics among undergraduate students being trained in trauma resuscitation. We enrolled teams of undergraduate health professional students from four programs: nursing, physician assistant, radiologic science, and respiratory care. After completing an online training on trauma resuscitation principles, the participants completed a trauma resuscitation scenario. The participants then received teamwork training using TeamSTEPPS and completed a second trauma resuscitation scenario identical to the first. All resuscitations were recorded and scored offline by two blinded research assistants using both the Team Emergency Assessment Measure (TEAM) and Trauma Team Performance Observation Tool (TPOT) scoring systems. Pre-test and post-test TEAM and TPOT scores were compared. We enrolled a total of 48 students in 12 teams. Team leadership, situational monitoring, and overall communication improved with TeamSTEPPS training (P=0.04, P=0.02, and P=0.03, respectively), as assessed by the TPOT scoring system. TeamSTEPPS also improved the team's ability to prioritize tasks and work together to complete tasks in a rapid manner (P<0.01 and P=0.02, respectively) as measured by TEAM. Incorporating TeamSTEPPS into trauma team education leads to improved TEAM and TPOT scores among undergraduate health professionals.

Teamwork education improves trauma team performance in undergraduate health professional students

Directory of Open Access Journals (Sweden)

Valerie O’Toole Baker

2015-06-01

Full Text Available Purpose: Effective trauma resuscitation requires efficient and coordinated care from a team of providers; however, providers are rarely instructed on how to be effective members of trauma teams. Team-based learning using Team Strategies and Tools to Enhance Performance and Patient Safety (TeamSTEPPS has been shown to improve team dynamics among practicing professionals, including physicians and nurses. The impact of TeamSTEPPS on students being trained in trauma management in an undergraduate health professional program is currently unknown. We sought to determine the impact of TeamSTEPPS on team dynamics among undergraduate students being trained in trauma resuscitation. Methods: We enrolled teams of undergraduate health professional students from four programs: nursing, physician assistant, radiologic science, and respiratory care. After completing an online training on trauma resuscitation principles, the participants completed a trauma resuscitation scenario. The participants then received teamwork training using TeamSTEPPS and completed a second trauma resuscitation scenario identical to the first. All resuscitations were recorded and scored offline by two blinded research assistants using both the Team Emergency Assessment Measure (TEAM and Trauma Team Performance Observation Tool (TPOT scoring systems. Pre-test and post-test TEAM and TPOT scores were compared. Results: We enrolled a total of 48 students in 12 teams. Team leadership, situational monitoring, and overall communication improved with TeamSTEPPS training (P=0.04, P=0.02, and P=0.03, respectively, as assessed by the TPOT scoring system. TeamSTEPPS also improved the team’s ability to prioritize tasks and work together to complete tasks in a rapid manner (P<0.01 and P=0.02, respectively as measured by TEAM. Conclusions: Incorporating TeamSTEPPS into trauma team education leads to improved TEAM and TPOT scores among undergraduate health professionals.

Cognitive diversity in undergraduate engineering: Dyslexia

Science.gov (United States)

Fitzpatrick, Velvet R.

In the United States, institutions have established multiple programs and initiatives aimed at increasing the diversity of both faculty and students in engineering as means to produce a workforce that will better serve society. However, there are two major problems in addressing engineering student diversity. First, the engineering education research community has paid little attention to date as to how engineering education research characterizes diversity in its broadest sense. Second, research on persons with disabilities in undergraduates engineering, a population of interests within diversity, is minimal. Available disability studies tend to be skewed toward physical disabilities, leading to a neglect of cognitive differences such as learning disabilities (LD). In addition, disability research questions and study designs are inherently steeped in ability bias. The purpose of this dissertation is to explore the meaning of ability for students with dyslexia while in undergraduate engineering and establish the significance of cognitive diversity, focusing on LD and more specifically dyslexia, in undergraduate engineering education and answer the following research question: How do undergraduate engineering students with dyslexia experience ability while pursuing and persisting in engineering? The motivation was to lay the groundwork for future engineering education studies on undergraduate students with LD in general but dyslexia in specific. The first goal was to conduct a critical literature review pertaining to the academic strengths of undergraduate students with LD, specifically, dyslexia and the second goal was to describe how undergraduate engineering students with dyslexia experience ability. The intent was not to redefine dyslexia or disability. The intent is to provide an inclusive account of dyslexia, weakness and strengths, within the field of engineering education. This study was conducted from a qualitative inquiry approach, within the social

Matrix groups for undergraduates

CERN Document Server

Tapp, Kristopher

2005-01-01

Matrix groups touch an enormous spectrum of the mathematical arena. This textbook brings them into the undergraduate curriculum. It makes an excellent one-semester course for students familiar with linear and abstract algebra and prepares them for a graduate course on Lie groups. Matrix Groups for Undergraduates is concrete and example-driven, with geometric motivation and rigorous proofs. The story begins and ends with the rotations of a globe. In between, the author combines rigor and intuition to describe basic objects of Lie theory: Lie algebras, matrix exponentiation, Lie brackets, and maximal tori.

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

Science.gov (United States)

Campbell, Chad E.; Nehm, Ross H.

2013-01-01

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

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

DEFF Research Database (Denmark)

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

2015-01-01

During 11–12 August 2014, a Protein Bioinformatics and Community Resources Retreat was held at the Wellcome Trust Genome Campus in Hinxton, UK. This meeting brought together the principal investigators of several specialized protein resources (such as CAZy, TCDB and MEROPS) as well as those from...... protein databases from the large Bioinformatics centres (including UniProt and RefSeq). The retreat was divided into five sessions: (1) key challenges, (2) the databases represented, (3) best practices for maintenance and curation, (4) information flow to and from large data centers and (5) communication...

Integrating ICT with education: using computer games to enhance ...

African Journals Online (AJOL)

Integrating ICT with education: using computer games to enhance learning mathematics at undergraduate level. ... This research seeks to look into ways in which computer games as ICT tools can be used to ... AJOL African Journals Online.

Imitation in Undergraduate Teaching and Learning

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Zhou, Jiangyuan; Guo, Wei

2016-01-01

Research in developmental psychology and neuroscience has demonstrated the critical role of imitation in human learning. Self-report questionnaires collected from 456 undergraduate students in two U.S. institutions and one Chinese institution demonstrated that undergraduate students from both U.S. and Chinese cultures used various imitations in…

A Review of Undergraduate Mentoring Programs

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Gershenfeld, Susan

2014-01-01

This review summarizes published studies on undergraduate mentoring programs from 2008 to 2012. Twenty studies met the inclusion criteria, which included empirical research on formal mentoring programs with undergraduate students as mentees or mentors. Each study was assessed based on limitations identified in two earlier reviews of the mentoring…