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Rahman NT, Meyer C, Thakral D, Cai WL, Chen AT, Obaid R, Garcia-Milian R. Peer Teaching as Bioinformatics Training Strategy: Incentives, Challenges, and Benefits. Med Ref Serv Q 2022; 41:13-25. [PMID: 35225737 DOI: 10.1080/02763869.2022.2020568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Bioinformatics is essential for basic and clinical research. Peer-to-peer (P2P) teaching was used to respond to the bioinformatics training needs at a research-intensive institution. In addition to the data collected from the workshops, personal experiences of the teachers were used to understand incentives, challenges, and benefits of P2P teaching. Developing communication skills such as confidence in teaching, explaining complex concepts, and better understanding of topics benefited P2P teachers. Lack of time and classroom management were identified as major challenges. Hence, P2P teaching can be beneficial not only for bioinformatics trainees but also as a professional development opportunity for peer teachers.
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Affiliation(s)
- Nur-Taz Rahman
- Bioinformatics Support Program, Research and Education Services, Harvey Cushing/John Hay Whitney Medical Library, Yale University, New Haven, Connecticut, USA
| | - Caitlin Meyer
- Bioinformatics Support Program, Research and Education Services, Harvey Cushing/John Hay Whitney Medical Library, Yale University, New Haven, Connecticut, USA
| | - Durga Thakral
- Department of Dermatology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Wesley L Cai
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Ann T Chen
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut, USA
| | - Razib Obaid
- RARAF Radiological Research Accelerator Facility, Nevis Laboratory, Columbia University, Irvington, New York, USA
| | - Rolando Garcia-Milian
- Bioinformatics Support Program, Research and Education Services, Harvey Cushing/John Hay Whitney Medical Library, Yale University, New Haven, Connecticut, USA
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2
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Gatherer D. Reflections on integrating bioinformatics into the undergraduate curriculum: The Lancaster experience. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 48:118-127. [PMID: 31793726 DOI: 10.1002/bmb.21320] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/25/2019] [Accepted: 11/15/2019] [Indexed: 06/10/2023]
Abstract
Bioinformatics is an essential discipline for biologists. It also has a reputation of being difficult for those without a strong quantitative and computer science background. At Lancaster University, we have developed modules for the integration of bioinformatics skills training into our undergraduate biology degree portfolio. This article describes those modules, situating them in the context of the accumulated quarter century of literature on bioinformatics education. The constant evolution of bioinformatics as a discipline is emphasized, drawing attention to the continual necessity to revise and upgrade those skills being taught, even at undergraduate level. Our overarching aim is to equip students both with a portfolio of skills in the currently most essential bioinformatics tools and with the confidence to continue their own bioinformatics skills development at postgraduate or professional level.
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Affiliation(s)
- Derek Gatherer
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, UK
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3
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Govindan B, Pickett S, Riggs B. Fear of the CURE: A Beginner's Guide to Overcoming Barriers in Creating a Course-Based Undergraduate Research Experience. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2020; 21:jmbe-21-48. [PMID: 32528607 PMCID: PMC7243983 DOI: 10.1128/jmbe.v21i2.2109] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/10/2020] [Indexed: 05/21/2023]
Abstract
Over the past decade, growing evidence has shown that there are many benefits to undergraduate students engaging in scientific research, including increased persistence in pursuing STEM careers and successful outcomes in graduate study. With these benefits in mind, there has been a significant push toward providing research opportunities for students in STEM majors. To address this need, an increasing number of undergraduate courses have been developed to provide students with research experiences in a class setting, also known as course-based undergraduate research experiences, or CUREs. Despite the growing success of these courses, a number of barriers remain that deter faculty from developing and implementing CUREs. Here, we will review the perceived challenges of developing a CURE and provide practical strategies to overcome these challenges.
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Affiliation(s)
- Brinda Govindan
- Department of Biology, San Francisco State University, San Francisco, CA 94132
| | - Sarah Pickett
- Department of Biology, San Francisco State University, San Francisco, CA 94132
- Center for Teaching and Learning, University of California, Berkeley, Berkeley, CA 94720
| | - Blake Riggs
- Department of Biology, San Francisco State University, San Francisco, CA 94132
- Corresponding author. Mailing address: Department of Biology, 1600 Holloway Ave., San Francisco State University, San Francisco, CA 94132. Phone: 415-338-1499. E-mail:
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4
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Choe RC, Scuric Z, Eshkol E, Cruser S, Arndt A, Cox R, Toma SP, Shapiro C, Levis-Fitzgerald M, Barnes G, Crosbie RH. Student Satisfaction and Learning Outcomes in Asynchronous Online Lecture Videos. CBE LIFE SCIENCES EDUCATION 2019; 18:ar55. [PMID: 31675279 PMCID: PMC6829069 DOI: 10.1187/cbe.18-08-0171] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 07/29/2019] [Accepted: 08/08/2019] [Indexed: 05/28/2023]
Abstract
Our study identified online lecture video styles that improved student engagement and satisfaction, while maintaining high learning outcomes in online education. We presented different lecture video styles with standardized material to students and then measured learning outcomes and satisfaction with a survey and summative assessment. We created an iterative qualitative coding scheme, "coding online asynchronous lectures" (COAL), to analyze open-ended student survey responses. Our results reveal that multimedia learning can be satisfying and effective. Students have strong preferences for certain video styles despite their equal learning outcomes, with the Learning Glass style receiving the highest satisfaction ratings. Video styles that were described as impersonal and unfamiliar were rated poorly, while those that were described as personal and engaging and evoked positive affective responses were rated highly. The students in our study rated lecture video styles that aligned with Mayer's multimedia learning principles as highly satisfying, indicating that student feedback can be a valuable resource for course designers to consider as they design their own online courses. Finally, we provide guidelines for creating engaging, effective, and satisfying asynchronous lecture videos to support establishment of best practices in online instruction.
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Affiliation(s)
| | | | - Ethan Eshkol
- Department of Integrative Biology and Physiology
| | | | - Ava Arndt
- Office of the President, University of California, Oakland, Oakland, CA 94607
| | - Robert Cox
- Enrollment Planning and Academic Performance Analysis
| | | | | | | | - Greg Barnes
- Office of the President, University of California, Oakland, Oakland, CA 94607
| | - Rachelle H. Crosbie
- Department of Integrative Biology and Physiology
- Department of Neurology, David Geffen School of Medicine, and
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095
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5
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Anton Feenstra K, Abeln S, Westerhuis JA, Brancos dos Santos F, Molenaar D, Teusink B, Hoefsloot HCJ, Heringa J. Training for translation between disciplines: a philosophy for life and data sciences curricula. Bioinformatics 2018; 34:i4-i12. [PMID: 29950011 PMCID: PMC6022589 DOI: 10.1093/bioinformatics/bty233] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Motivation Our society has become data-rich to the extent that research in many areas has become impossible without computational approaches. Educational programmes seem to be lagging behind this development. At the same time, there is a growing need not only for strong data science skills, but foremost for the ability to both translate between tools and methods on the one hand, and application and problems on the other. Results Here we present our experiences with shaping and running a masters' programme in bioinformatics and systems biology in Amsterdam. From this, we have developed a comprehensive philosophy on how translation in training may be achieved in a dynamic and multidisciplinary research area, which is described here. We furthermore describe two requirements that enable translation, which we have found to be crucial: sufficient depth and focus on multidisciplinary topic areas, coupled with a balanced breadth from adjacent disciplines. Finally, we present concrete suggestions on how this may be implemented in practice, which may be relevant for the effectiveness of life science and data science curricula in general, and of particular interest to those who are in the process of setting up such curricula. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- K Anton Feenstra
- Department of Computer Science, IBIVU Centre for Integrative Bioinformatics Vrije Universiteit Amsterdam, HV Amsterdam, Netherlands
- AIMMS Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, MC Amsterdam, The Netherlands
| | - Sanne Abeln
- Department of Computer Science, IBIVU Centre for Integrative Bioinformatics Vrije Universiteit Amsterdam, HV Amsterdam, Netherlands
- Amsterdam Data Science, GH Amsterdam, The Netherlands
| | - Johan A Westerhuis
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, GE Amsterdam, The Netherlands
| | | | - Douwe Molenaar
- AIMMS Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, MC Amsterdam, The Netherlands
| | - Bas Teusink
- AIMMS Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, MC Amsterdam, The Netherlands
- Amsterdam Data Science, GH Amsterdam, The Netherlands
| | - Huub C J Hoefsloot
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, GE Amsterdam, The Netherlands
| | - Jaap Heringa
- Department of Computer Science, IBIVU Centre for Integrative Bioinformatics Vrije Universiteit Amsterdam, HV Amsterdam, Netherlands
- AIMMS Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, MC Amsterdam, The Netherlands
- Amsterdam Data Science, GH Amsterdam, The Netherlands
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6
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Machluf Y, Gelbart H, Ben-Dor S, Yarden A. Making authentic science accessible-the benefits and challenges of integrating bioinformatics into a high-school science curriculum. Brief Bioinform 2017; 18:145-159. [PMID: 26801769 PMCID: PMC5221422 DOI: 10.1093/bib/bbv113] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 11/19/2015] [Accepted: 12/11/2015] [Indexed: 12/27/2022] Open
Abstract
Despite the central place held by bioinformatics in modern life sciences and related areas, it has only recently been integrated to a limited extent into high-school teaching and learning programs. Here we describe the assessment of a learning environment entitled 'Bioinformatics in the Service of Biotechnology'. Students' learning outcomes and attitudes toward the bioinformatics learning environment were measured by analyzing their answers to questions embedded within the activities, questionnaires, interviews and observations. Students' difficulties and knowledge acquisition were characterized based on four categories: the required domain-specific knowledge (declarative, procedural, strategic or situational), the scientific field that each question stems from (biology, bioinformatics or their combination), the associated cognitive-process dimension (remember, understand, apply, analyze, evaluate, create) and the type of question (open-ended or multiple choice). Analysis of students' cognitive outcomes revealed learning gains in bioinformatics and related scientific fields, as well as appropriation of the bioinformatics approach as part of the students' scientific 'toolbox'. For students, questions stemming from the 'old world' biology field and requiring declarative or strategic knowledge were harder to deal with. This stands in contrast to their teachers' prediction. Analysis of students' affective outcomes revealed positive attitudes toward bioinformatics and the learning environment, as well as their perception of the teacher's role. Insights from this analysis yielded implications and recommendations for curriculum design, classroom enactment, teacher education and research. For example, we recommend teaching bioinformatics in an integrative and comprehensive manner, through an inquiry process, and linking it to the wider science curriculum.
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Affiliation(s)
- Yossy Machluf
- Department of Science Teaching, Weizmann Institute of Science, Rehovot, Israel
| | - Hadas Gelbart
- Department of Science Teaching, Weizmann Institute of Science, Rehovot, Israel
- National Authority for Measurement and Evaluation in Education (RAMA), Ministry of Education, Ramat-Gan, Israel
| | - Shifra Ben-Dor
- Faculty of Biochemistry, Department of Biological Services, Bioinformatics and Biological Computing Unit, Weizmann Institute of Science, Rehovot, Israel
| | - Anat Yarden
- Department of Science Teaching, Weizmann Institute of Science, Rehovot, Israel
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7
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Brown JAL. Evaluating the effectiveness of a practical inquiry-based learning bioinformatics module on undergraduate student engagement and applied skills. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2016; 44:304-13. [PMID: 27161812 DOI: 10.1002/bmb.20954] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 11/20/2015] [Accepted: 12/08/2015] [Indexed: 05/27/2023]
Abstract
A pedagogic intervention, in the form of an inquiry-based peer-assisted learning project (as a practical student-led bioinformatics module), was assessed for its ability to increase students' engagement, practical bioinformatic skills and process-specific knowledge. Elements assessed were process-specific knowledge following module completion, qualitative student-based module evaluation and the novelty, scientific validity and quality of written student reports. Bioinformatics is often the starting point for laboratory-based research projects, therefore high importance was placed on allowing students to individually develop and apply processes and methods of scientific research. Students led a bioinformatic inquiry-based project (within a framework of inquiry), discovering, justifying and exploring individually discovered research targets. Detailed assessable reports were produced, displaying data generated and the resources used. Mimicking research settings, undergraduates were divided into small collaborative groups, with distinctive central themes. The module was evaluated by assessing the quality and originality of the students' targets through reports, reflecting students' use and understanding of concepts and tools required to generate their data. Furthermore, evaluation of the bioinformatic module was assessed semi-quantitatively using pre- and post-module quizzes (a non-assessable activity, not contributing to their grade), which incorporated process- and content-specific questions (indicative of their use of the online tools). Qualitative assessment of the teaching intervention was performed using post-module surveys, exploring student satisfaction and other module specific elements. Overall, a positive experience was found, as was a post module increase in correct process-specific answers. In conclusion, an inquiry-based peer-assisted learning module increased students' engagement, practical bioinformatic skills and process-specific knowledge. © 2016 by The International Union of Biochemistry and Molecular Biology, 44:304-313 2016.
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Affiliation(s)
- James A L Brown
- Department of Biochemistry, School of Natural Sciences, National University of Ireland Galway, Ireland and Discipline of Surgery, School of Medicine, Lambe Institute for Translational Research, National University of Ireland Galway, Ireland
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8
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Zaaijer S, Erlich Y. Using mobile sequencers in an academic classroom. eLife 2016; 5. [PMID: 27054412 PMCID: PMC4869913 DOI: 10.7554/elife.14258] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 04/06/2016] [Indexed: 11/13/2022] Open
Abstract
The advent of mobile DNA sequencers has made it possible to generate DNA sequencing data outside of laboratories and genome centers. Here, we report our experience of using the MinION, a mobile sequencer, in a 13-week academic course for undergraduate and graduate students. The course consisted of theoretical sessions that presented fundamental topics in genomics and several applied hackathon sessions. In these hackathons, the students used MinION sequencers to generate and analyze their own data and gain hands-on experience in the topics discussed in the theoretical classes. The manuscript describes the structure of our class, the educational material, and the lessons we learned in the process. We hope that the knowledge and material presented here will provide the community with useful tools to help educate future generations of genome scientists. DOI:http://dx.doi.org/10.7554/eLife.14258.001
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Affiliation(s)
- Sophie Zaaijer
- Department of Computer Science, Fu Foundation School of Engineering, Columbia University, New York, United States.,New York Genome Center, New York, United States
| | | | - Yaniv Erlich
- Department of Computer Science, Fu Foundation School of Engineering, Columbia University, New York, United States.,New York Genome Center, New York, United States.,Department of Systems Biology, Center for Computational Biology and Bioinformatics, Columbia University, New York, United States
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9
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Bowling BV, Schultheis PJ, Strome ED. Implementation and assessment of a yeast orphan gene research project: involving undergraduates in authentic research experiences and progressing our understanding of uncharacterized open reading frames. Yeast 2015; 33:43-53. [PMID: 26460164 DOI: 10.1002/yea.3139] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 10/02/2015] [Accepted: 10/08/2015] [Indexed: 01/07/2023] Open
Abstract
Saccharomyces cerevisiae was the first eukaryotic organism to be sequenced; however, little progress has been made in recent years in furthering our understanding of all open reading frames (ORFs). From October 2012 to May 2015 the number of verified ORFs had only risen from 75.31% to 78%, while the number of uncharacterized ORFs had decreased from 12.8% to 11% (representing > 700 genes still left in this category; http://www.yeastgenome.org/genomesnapshot). Course-based research has been shown to increase student learning while providing experience with real scientific investigation; however, implementation in large, multi-section courses presents many challenges. This study sought to test the feasibility and effectiveness of incorporating authentic research into a core genetics course, with multiple instructors, to increase student learning and progress our understanding of uncharacterized ORFs. We generated a module-based annotation toolkit and utilized easily accessible bioinformatics tools to predict gene function for uncharacterized ORFs within the Saccharomyces Genome Database (SGD). Students were each assigned an uncharacterized ORF, which they annotated using contemporary comparative genomics methodologies, including multiple sequence alignment, conserved domain identification, signal peptide prediction and cellular localization algorithms. Student learning outcomes were measured by quizzes, project reports and presentations, as well as a post-project questionnaire. Our results indicate that the authentic research experience had positive impacts on students' perception of their learning and their confidence to conduct future research. Furthermore, we believe that creation of an online repository and adoption and/or adaptation of this project across multiple researchers and institutions could speed the process of gene function prediction.
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Affiliation(s)
- Bethany V Bowling
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY, USA
| | - Patrick J Schultheis
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY, USA
| | - Erin D Strome
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY, USA
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10
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Magana AJ, Taleyarkhan M, Alvarado DR, Kane M, Springer J, Clase K. A survey of scholarly literature describing the field of bioinformatics education and bioinformatics educational research. CBE LIFE SCIENCES EDUCATION 2014; 13:607-23. [PMID: 25452484 PMCID: PMC4255348 DOI: 10.1187/cbe.13-10-0193] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 08/20/2014] [Accepted: 09/05/2014] [Indexed: 05/22/2023]
Abstract
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 potential advancement of research and development in complex biomedical systems has created a need for an educated workforce in bioinformatics. However, effectively integrating bioinformatics education through formal and informal educational settings has been a challenge due in part to its cross-disciplinary nature. In this article, we seek to provide an overview of the state of bioinformatics education. This article identifies: 1) current approaches of bioinformatics education at the undergraduate and graduate levels; 2) the most common concepts and skills being taught in bioinformatics education; 3) pedagogical approaches and methods of delivery for conveying bioinformatics concepts and skills; and 4) assessment results on the impact of these programs, approaches, and methods in students' attitudes or learning. Based on these findings, it is our goal to describe the landscape of scholarly work in this area and, as a result, identify opportunities and challenges in bioinformatics education.
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Affiliation(s)
- Alejandra J Magana
- *Department of Computer and Information Technology, Purdue University, West Lafayette, IN 47906 *Department of Computer and Information Technology, Purdue University, West Lafayette, IN 47906
| | - Manaz Taleyarkhan
- *Department of Computer and Information Technology, Purdue University, West Lafayette, IN 47906
| | - Daniela Rivera Alvarado
- *Department of Computer and Information Technology, Purdue University, West Lafayette, IN 47906
| | - Michael Kane
- *Department of Computer and Information Technology, Purdue University, West Lafayette, IN 47906
| | - John Springer
- *Department of Computer and Information Technology, Purdue University, West Lafayette, IN 47906
| | - Kari Clase
- Department of Technology, Leadership and Innovation, Purdue University, West Lafayette, IN 47906
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11
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Luo J. Teaching the ABCs of bioinformatics: a brief introduction to the Applied Bioinformatics Course. Brief Bioinform 2013; 15:1004-13. [PMID: 24008274 PMCID: PMC4239802 DOI: 10.1093/bib/bbt065] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
With the development of the Internet and the growth of online resources, bioinformatics training for wet-lab biologists became necessary as a part of their education. This article describes a one-semester course ‘Applied Bioinformatics Course’ (ABC, http://abc.cbi.pku.edu.cn/) that the author has been teaching to biological graduate students at the Peking University and the Chinese Academy of Agricultural Sciences for the past 13 years. ABC is a hands-on practical course to teach students to use online bioinformatics resources to solve biological problems related to their ongoing research projects in molecular biology. With a brief introduction to the background of the course, detailed information about the teaching strategies of the course are outlined in the ‘How to teach’ section. The contents of the course are briefly described in the ‘What to teach’ section with some real examples. The author wishes to share his teaching experiences and the online teaching materials with colleagues working in bioinformatics education both in local and international universities.
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