Highlights

Enhancing the Undergraduate Curriculum through Bioinformatics and Research Opportunities

Overview

The ASM/JGI Summer Bioinformatics Institute aims to meet the need for more undergraduate faculty in science, technology, engineering, and math (STEM) disciplines to understand, interpret, and use molecular sequence information to solve problems. The Institute features the analysis of microbial genomes, molecular sequences, and structural data, providing a framework for developing classroom activities and research projects for undergraduate students.

At the completion of the Institute, participants will take home a working knowledge of several key bioinformatics tools and a strengthened ability to connect scientific questions to learning goals and pertinent bioinformatics tools. As participants begin to use the skills and ideas they gain at the Institute back at their home institutions, several measurable outcomes should be generated or enhanced. In terms of students, more of them will:

• Understand the role of scientific research and the process through which it occurs

• Make new connections between virtual and wet-lab components of courses

• Seek out independent research opportunities

Faculty should see increased student engagement in course material and find it easier to incorporate (i) discussions of research into courses and (ii) their own research ideas into courses. All of this increased engagement by students and faculty will allow them to see that educational goals can be met while still generating meaningful scientific results, such as deeply annotated microbial genomes deposited in public databases and functional genomics datasets.

Audience

The Institute is directed to STEM faculty who teach undergraduate courses at community colleges, 4-year colleges, and research universities and who consider themselves true beginners when it comes to understanding and using bioinformatics tools. Preference will be given to faculty with limited or no previous training in bioinformatics and the genomic sciences. Faculty participants will have opportunities to address the following questions:

• You may have done a BLAST search or two, but have you incorporated such searches into multiple, different classroom situations?

• Can you explain how BLAST is based on basic molecular genetics principles?

• Do you know what a Pfam is?

• Can you construct a multiple sequence alignment?

Participation in the Institute is by application. Applicants must be (i) currently teaching full time at U.S.-accredited institutions of higher education and (ii) U.S. citizens or U.S. permanent residents.

Goals

The goals of the program are to:

• Introduce participants to questions related to genomics as they apply to specific teaching situations and to the bioinformatics tools available to address those questions

• Introduce participants to the biological underpinnings of BLAST, how the program works, and how to effectively use it

• Introduce participants to tools involved in weak-pattern searches and other protein analysis tools, comparative genomics, and evolutionary analysis and how to use these tools effectively

• Help participants form a learning network that will continue to foster their future experiences with and uses of bioinformatics tools in their courses

Outcomes

Participants will leave with:

• Working knowledge of BLAST, Pfam, and other bioinformatics tools

• Experience with connecting biological questions of interest to learning concepts, skills training, and bioinformatics tools to address pertinent questions

• Curriculum activities, problem sets, course exercises, and/or research projects that can (i) be incorporated into courses immediately and (ii) engage students

• A network of colleagues to help with brainstorming, troubleshooting, and refining new uses of bioinformatics in undergraduate education

Institute Faculty

Brad Goodner, Hiram College, Hiram, OH

Cheryl Kerfeld, U.S. Department of Energy Joint Genome Institute (DOE-JGI), Walnut Creek, CA

Kathleen (KT) Scott, University of South Florida, Tampa, FL

Sam Donovan, University of Pittsburgh, Pittsburgh, PA

Format

Through the combination of plenary sessions, small-group work, and discussions, the Institute will provide hands-on experience in accessing the Internet for databases, tools, and resources and identifying tools and resources for developing classroom activities and research projects. Discussion, skills training and practice, and pedagogical advice will be provided. All participants will become part of a larger community of practice to advance interdisciplinary training through bioinformatics and genomic sciences.

Requirements for Participation

Upon acceptance to the Institute, participants will be required to:

• Complete three to five pre-Institute readings and assignments

• Participate in a follow-up session within 10 to 18 months after the Institute at the ASM Conference for Undergraduate Educators (ASMCUE)

• Present a poster at ASMCUE about a new bioinformatics curriculum activity within 2 years of completing the Institute

• Submit for publication a curriculum activity enhancing students’ learning about bioinformatics either to the ASM MicrobeLibrary curriculum collection or to another national digital library of peer-reviewed resources

• Participate in longitudinal studies to ascertain the effectiveness of such training

The preparatory work is required, as it provides a solid foundation for enhancing a particpant's training and for benefiting from the Institute. Participants are asked to bring their own laptop computers to the Institute for preparing and sharing their work.

The follow-up work is also required, as it ensures that such professional development results in the advancement of bioinformatics training across the undergraduate curriculum through presentations and publications.

Sponsorship and Credentials

The ASM/DOE-JGI Bioinformatics Institute is managed by the American Society for Microbiology and sponsored by the U.S. Department of Energy Joint Genome Institute and Hiram College.

The American Society for Microbiology is a recipient of the 2000 Carnegie Foundation for the Advancement of Teaching Award and was recognized by President Clinton with the 2000 Presidential Award for Excellence in Mentoring in Science, Mathematics, and Engineering Education for its contribution to education in the sciences and engineering.

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