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Title: Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum

Abstract

Undergraduate life sciences education needs an overhaul, as clearly described in the National Research Council of the National Academies publication BIO 2010: Transforming Undergraduate Education for Future Research Biologists. Among BIO 2010's top recommendations is the need to involve students in working with real data and tools that reflect the nature of life sciences research in the 21st century. Education research studies support the importance of utilizing primary literature, designing and implementing experiments, and analyzing results in the context of a bona fide scientific question in cultivating the analytical skills necessary to become a scientist. Incorporating these basic scientific methodologies in undergraduate education leads to increased undergraduate and post-graduate retention in the sciences. Toward this end, many undergraduate teaching organizations offer training and suggestions for faculty to update and improve their teaching approaches to help students learn as scientists, through design and discovery (e.g., Council of Undergraduate Research [www.cur.org] and Project Kaleidoscope [www.pkal.org]). With the advent of genome sequencing and bioinformatics, many scientists now formulate biological questions and interpret research results in the context of genomic information. Just as the use of bioinformatic tools and databases changed the way scientists investigate problems, it must change how scientists teach to createmore » new opportunities for students to gain experiences reflecting the influence of genomics, proteomics, and bioinformatics on modern life sciences research. Educators have responded by incorporating bioinformatics into diverse life science curricula. While these published exercises in, and guidelines for, bioinformatics curricula are helpful and inspirational, faculty new to the area of bioinformatics inevitably need training in the theoretical underpinnings of the algorithms. Moreover, effectively integrating bioinformatics into courses or independent research projects requires infrastructure for organizing and assessing student work. Here, we present a new platform for faculty to keep current with the rapidly changing field of bioinformatics, the Integrated Microbial Genomes Annotation Collaboration Toolkit (IMG-ACT). It was developed by instructors from both research-intensive and predominately undergraduate institutions in collaboration with the Department of Energy-Joint Genome Institute (DOE-JGI) as a means to innovate and update undergraduate education and faculty development. The IMG-ACT program provides a cadre of tools, including access to a clearinghouse of genome sequences, bioinformatics databases, data storage, instructor course management, and student notebooks for organizing the results of their bioinformatic investigations. In the process, IMG-ACT makes it feasible to provide undergraduate research opportunities to a greater number and diversity of students, in contrast to the traditional mentor-to-student apprenticeship model for undergraduate research, which can be too expensive and time-consuming to provide for every undergraduate. The IMG-ACT serves as the hub for the network of faculty and students that use the system for microbial genome analysis. Open access of the IMG-ACT infrastructure to participating schools ensures that all types of higher education institutions can utilize it. With the infrastructure in place, faculty can focus their efforts on the pedagogy of bioinformatics, involvement of students in research, and use of this tool for their own research agenda. What the original faculty members of the IMG-ACT development team present here is an overview of how the IMG-ACT program has affected our development in terms of teaching and research with the hopes that it will inspire more faculty to get involved.« less

Authors:
; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
Genomics Division
OSTI Identifier:
1048320
Report Number(s):
LBNL-4991E
TRN: US201216%%897
DOE Contract Number:  
DE-AC02-05CH11231
Resource Type:
Journal Article
Journal Name:
PLoS Biology
Additional Journal Information:
Journal Volume: 8; Journal Issue: 8; Related Information: Journal Publication Date: August 10, 2010
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; 99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE; ALGORITHMS; DESIGN; EDUCATION; EDUCATIONAL FACILITIES; MANAGEMENT; ORGANIZING; RECOMMENDATIONS; RETENTION; STORAGE; TRAINING; life sciences, bioinformatics, IMG-ACT, undergraduate education

Citation Formats

Ditty, Jayna L, Kvaal, Christopher A, Goodner, Brad, Freyermuth, Sharyn K, Bailey, Cheryl, Britton, Robert A, Gordon, Stuart G, Heinhorst, Sabine, Reed, Kelynne, Xu, Zhaohui, Sanders-Lorenz, Erin R, Axen, Seth, Kim, Edwin, Johns, Mitrick, Scott, Kathleen, and Kerfeld, Cheryl A. Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum. United States: N. p., 2011. Web.
Ditty, Jayna L, Kvaal, Christopher A, Goodner, Brad, Freyermuth, Sharyn K, Bailey, Cheryl, Britton, Robert A, Gordon, Stuart G, Heinhorst, Sabine, Reed, Kelynne, Xu, Zhaohui, Sanders-Lorenz, Erin R, Axen, Seth, Kim, Edwin, Johns, Mitrick, Scott, Kathleen, & Kerfeld, Cheryl A. Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum. United States.
Ditty, Jayna L, Kvaal, Christopher A, Goodner, Brad, Freyermuth, Sharyn K, Bailey, Cheryl, Britton, Robert A, Gordon, Stuart G, Heinhorst, Sabine, Reed, Kelynne, Xu, Zhaohui, Sanders-Lorenz, Erin R, Axen, Seth, Kim, Edwin, Johns, Mitrick, Scott, Kathleen, and Kerfeld, Cheryl A. Mon . "Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum". United States. https://www.osti.gov/servlets/purl/1048320.
@article{osti_1048320,
title = {Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum},
author = {Ditty, Jayna L and Kvaal, Christopher A and Goodner, Brad and Freyermuth, Sharyn K and Bailey, Cheryl and Britton, Robert A and Gordon, Stuart G and Heinhorst, Sabine and Reed, Kelynne and Xu, Zhaohui and Sanders-Lorenz, Erin R and Axen, Seth and Kim, Edwin and Johns, Mitrick and Scott, Kathleen and Kerfeld, Cheryl A},
abstractNote = {Undergraduate life sciences education needs an overhaul, as clearly described in the National Research Council of the National Academies publication BIO 2010: Transforming Undergraduate Education for Future Research Biologists. Among BIO 2010's top recommendations is the need to involve students in working with real data and tools that reflect the nature of life sciences research in the 21st century. Education research studies support the importance of utilizing primary literature, designing and implementing experiments, and analyzing results in the context of a bona fide scientific question in cultivating the analytical skills necessary to become a scientist. Incorporating these basic scientific methodologies in undergraduate education leads to increased undergraduate and post-graduate retention in the sciences. Toward this end, many undergraduate teaching organizations offer training and suggestions for faculty to update and improve their teaching approaches to help students learn as scientists, through design and discovery (e.g., Council of Undergraduate Research [www.cur.org] and Project Kaleidoscope [www.pkal.org]). With the advent of genome sequencing and bioinformatics, many scientists now formulate biological questions and interpret research results in the context of genomic information. Just as the use of bioinformatic tools and databases changed the way scientists investigate problems, it must change how scientists teach to create new opportunities for students to gain experiences reflecting the influence of genomics, proteomics, and bioinformatics on modern life sciences research. Educators have responded by incorporating bioinformatics into diverse life science curricula. While these published exercises in, and guidelines for, bioinformatics curricula are helpful and inspirational, faculty new to the area of bioinformatics inevitably need training in the theoretical underpinnings of the algorithms. Moreover, effectively integrating bioinformatics into courses or independent research projects requires infrastructure for organizing and assessing student work. Here, we present a new platform for faculty to keep current with the rapidly changing field of bioinformatics, the Integrated Microbial Genomes Annotation Collaboration Toolkit (IMG-ACT). It was developed by instructors from both research-intensive and predominately undergraduate institutions in collaboration with the Department of Energy-Joint Genome Institute (DOE-JGI) as a means to innovate and update undergraduate education and faculty development. The IMG-ACT program provides a cadre of tools, including access to a clearinghouse of genome sequences, bioinformatics databases, data storage, instructor course management, and student notebooks for organizing the results of their bioinformatic investigations. In the process, IMG-ACT makes it feasible to provide undergraduate research opportunities to a greater number and diversity of students, in contrast to the traditional mentor-to-student apprenticeship model for undergraduate research, which can be too expensive and time-consuming to provide for every undergraduate. The IMG-ACT serves as the hub for the network of faculty and students that use the system for microbial genome analysis. Open access of the IMG-ACT infrastructure to participating schools ensures that all types of higher education institutions can utilize it. With the infrastructure in place, faculty can focus their efforts on the pedagogy of bioinformatics, involvement of students in research, and use of this tool for their own research agenda. What the original faculty members of the IMG-ACT development team present here is an overview of how the IMG-ACT program has affected our development in terms of teaching and research with the hopes that it will inspire more faculty to get involved.},
doi = {},
journal = {PLoS Biology},
number = 8,
volume = 8,
place = {United States},
year = {2011},
month = {8}
}