Bioinformatics in undergraduate education: Practical examples

Boyle, John A.

doi:10.1002/bmb.2004.494032040376

Cited by 37 publications

(21 citation statements)

References 3 publications

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“…Locating and understanding documentation are essential bioinformatics skills, and an introductory course should provide ample opportunities to develop those skills. Such an approach is broadly consistent with learning through guided inquiry, and has been considered by other bioinformatics instructors [2,3,10,11]. A second argument against producing detailed cookbooks is that the constant evolution of bioinformatic software makes these documents quickly obsolete, thereby requiring a large and open-ended maintenance effort by the instructor.…”

Section: Discussionmentioning

confidence: 76%

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

Weisman

2010

Biochem Molecular Bio Educ

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Face-to-face bioinformatics courses commonly include a weekly, in-person computer lab to facilitate active learning, reinforce conceptual material, and teach practical skills. Similarly, fully-online bioinformatics courses employ hands-on exercises to achieve these outcomes, although students typically perform this work offsite. Combining a face-to-face lecture course with a web-based virtual laboratory presents new opportunities for collaborative learning of the conceptual material, and for fostering peer support of technical bioinformatics questions. To explore this combination, an in-person lecture-only undergraduate bioinformatics course was augmented with a remote web-based laboratory, and tested with a large class. This study hypothesized that the collaborative virtual lab would foster active learning and peer support, and tested this hypothesis by conducting a student survey near the end of the semester. Respondents broadly reported strong benefits from the online laboratory, and strong benefits from peer-provided technical support. In comparison with traditional inperson teaching labs, students preferred the virtual lab by a factor of two. Key aspects of the course architecture and design are described to encourage further experimentation in teaching collaborative online bioinformatics laboratories.

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Section: Discussionmentioning

confidence: 76%

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

Weisman

2010

Biochem Molecular Bio Educ

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“…In a report by the National Academy of Sciences entitled BIO 2010: Transforming Undergraduate Education for Future Research Biologists, a key recommendation was the "need to involve students in working with real data and tools that reflect the nature of life sciences research in the 21 st century" (as cited in Ditty et al, 2010, p. 1). Similarly, the American Society for Biochemistry and Molecular Biology (ASBMB) endorsed the use of bioinformatics and related data resources as a core competency for students in molecular biology courses (Boyle, 2004;Voet et al, 2003). Bednarski, Elgin and Pakrasi (2005) were among the earliest to incorporate bioinformatics data into undergraduate courses.…”

Section: Literature Reviewmentioning

confidence: 99%

Developing data literacy competencies to enhance faculty collaborations

MacMillan

2015

LIBER

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In order to align information literacy (IL) instruction with changing faculty and student needs, librarians must expand their skills and competencies beyond traditional information sources. In the sciences, this increasingly means integrating the data resources used by researchers into instruction for undergraduate students. Open access data repositories allow students to work with more primary data than ever before, but only if they know how and where to look. This paper will describe the development of two IL workshops designed to scaffold student learning in the biological sciences across two second-year courses, detailing the long-term collaboration between a librarian and an instructor that now serves over 500 students per semester. In each workshop, students are guided through the discovery and analysis of life sciences data from multiple sites, encouraged to integrate text and data sources, and supported in completing research assignments.

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“…Bioinformatics is the science that has emerged in response to the development of genomics so it could handle, manage and analyze large data sets in short time with high speed and accuracy. Due to its importance, teaching bioinformatics at the undergraduate level in a biology laboratory program using customized, interactive and problembased approaches has become an essential requirement in life and biomedical science curricula in the last two decades [5], [15], [16], [17], [18], [19], [20]. They all established guidelines for the contents and format of undergraduate bioinformatics courses and training programmes using customized software and tools with hyperlinks to web applications.…”

Section: Determination Of the Intron Splice Junctionsmentioning

confidence: 99%

“…Additionally, using computers as essential tools in scientific education and research will strengthen the skills of graduates in using computers to access databases, manipulate and store specific information and communicate effectively. All these skills are essential requirements for modern graduates who are seeking good career opportunities [18].…”

Section: Determination Of the Intron Splice Junctionsmentioning

confidence: 99%

Development of a Local Entomological Database for Education and Research using Simulation (Virtual) Methods

Khater¹,

Mahmoud²,

Ghallab³

et al. 2014

IJACSA

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Abstract-Bioinformatics has been regarded as one of the rapidly-evolving fields with enormous impact on the history of life and biomedical sciences. It is an interdisciplinary science that integrates life sciences, mathematics and computer science in order to extract meaningful biological insights from large data sets of raw DNA and protein sequences. Our objective was the development of an entomogenomics database (provisionally named EntomDB) for education and research in entomology (entomology is the science of insects). This DB includes DNA/protein sequence data selected from genomes of major insect models of importance in biology and biomedical research. EntomDB will represent a customized easy, interactive and selflearning resource tool for beginner users in poor-resource settings. This will enable the users to learn basic skills in bioinformatics and genomics, needlessly to search through the numerous databases currently available on the World-Wide Web with their complex interfaces and contents. EntomDB will help students and young researchers in studying the primary structure, splicing, and translation and predict function of different genes by using simple simulation methods. It is also designed to be adaptable to work off-line, in case no internet connection is available. EntomDB is primarily designed for entomology discipline; however, it can easily be adapted for other disciplines in life and biomedical sciences. EntomDB will have important educational and developmental outcomes in promoting bioinformatics learning in the developing world and provide affordable first-level training for advanced degree and research levels.

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Bioinformatics in undergraduate education: Practical examples

Cited by 37 publications

References 3 publications

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

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

Developing data literacy competencies to enhance faculty collaborations

Development of a Local Entomological Database for Education and Research using Simulation (Virtual) Methods

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