Genome Solver Annotation Workshops

The Human Microbiome Project (HMP) has created a wealth of new questions for scientists. However, the current rate of microbial DNA sequencing far outpaces the ability of experts to analyze the genomes and metagenomes that have resulted from the HMP, creating a need for additional hands and minds to deal with the myriad of questions. This need in turn creates an opportunity for undergraduates to get involved in research on the HMP. Through the National Science Foundation (NSF) TUES (Transforming Undergraduate Education in Science, Technology, Engineering and Mathematics) program funding, we propose to generate a community of new microbial genome analysts within classrooms, within and between schools by teaching faculty how to teach their students t o do the analysis, by giving faculty support for curricular reforms, by creating an atmosphere in which authentic research experiences for students can be created (from development of hypotheses to publication), and by assessing the effectiveness of the program.

Our project goals align with the need for students to be trained in practices with currency in scientific research, especially interdisciplinary research. Importantly, we are proposing practices which can be integrated into a wide range of courses and so answering the call for a diversity of approaches which bring students to the original research problems. These goals highlight the challenges: training faculty who may have been educated in the "pre-omics" era, and integrating curricular pieces in pedagogically meaningful ways. We intend to address these goals by providing faculty training and access to the latest Bioinformatics research tools developed at the J. Craig Venter Institute (JCVI) and other open source genome analysis tools. We propose to create a framework for faculty training that will impact student learning, and develop a community of practice (COP) for both faculty and students to collaborate on specific projects developed from genome sequence data available via the HMP.

Course Details

Through this project we are conducting genome analysis workshops to train faculty. Workshop attendees will learn about general methodologies, standards, and processes used to annotate and analyze microbial genomes. The workshop contents will be available to aid the faculty in developing teaching modules. In addition, extensive documentation on methodologies and tools will be available via the online environment created for this project. On online web portal Genome Solver (www.genomesolver.org) will be a virtual space for development and sustaining of community. Genome Solver will assist faculty with technical issues and curricular design, as well as an online environment for the ongoing sharing of information including publication of student work. The intellectual merit, broader Impact and effectiveness of the program in terms of faculty satisfaction and student learning will be measured from data obtained through online surveys and quizzes.

Faculty will gain experience with and access to tools for microbial analysis, allowing for involvement of students in authentic research projects for wider dissemination to the scientific community. Students involved in these projects will be exposed to current techniques in genomics research as well as to practices of science including collaboration, communication, and critique. This will prepare them for entry into the research community by fostering the requisite habits of mind and practices. Bioinformatics resources and tools, training materials, and curricular information is available via workshops at JCVI and to all via the online community. We anticipate that the online community — because of the faculty discussions and student publications available there — will sustain and broaden this project especially with specific efforts to recruit individuals from minority serving institutions.

Funding

National Science Foundation TUES Program (Transforming Undergraduate Education in Science, Technology, Engineering and Mathematics)