The University of Iowa IMSD: Iowa Biosciences Academy

NIH RePORTER · NIH · R25 · $85,119 · view on reporter.nih.gov ↗

Abstract

PROJECT SUMMARY Bioinformatics and computational skills are no longer “elective” but must be part of the core competency for the next generation of biomedical researchers. However, existing curricula on these areas have significant deficiencies, including a lack of introductory, biology-focused courses that are suitable for undergraduate biology majors and graduate students in the biological disciplines, and a lack of emphasis on good computational practices that ensure robust and reproducible computational studies. This proposal supplement describes strategies. This proposal supplement describes strategies for building on existing curricula at the University of Iowa to quickly generate courses that will help students at every level become knowledgeable, articulate and facile in manipulating large biomedical datasets to extract meaningful insights. Aim 1 concerns adapting a newly deployed semester-length course called “Introduction to Scientific Computing” which includes topics such as reproducibility in computational projects, version control, command-line interface, remote computing, and general and statistical programming to a 4-6 week long summer workshop format. The summer workshop format makes the course available to a broader community, which includes undergraduate students from the UI IMSD program, nearby 4-year colleges doing research in the summer at the university, high school students and teachers in the local area seeking to gain skills in computational research. Aim 2 concerns expansion of an existing Introductory level Bioinformatics course to incorporate hands-on manipulation, analysis and graphic visualization of multiple genome/transcriptome sized datasets pertinent to the biological theme of the course in any given semester. A second goal of Aim 2 is to develop a course pipeline in which genomic and transcriptomic data is generated in-house, allowing students the opportunity to bring biomedically relevant datasets from their raw format through the steps needed to generate value-added conclusions. Fungal genomes have been selected for this purpose based on their relatively small genome size, compelling biological diversity and estimated 1.5 million species, 300 of which can cause primary or opportunistic infections in humans and only a fraction of which currently have publicly available genome sequences. Fungi are also involved in the industrial processing of many of the most profitable products used in human medicine. For example, some members of the Penicillium genus produce the antibiotic, penicillin. In summary, these aims create a cadre of UI students with the qualifications and ambitions to pursue careers involving analysis of biomedical datasets so central to the future of health and medicine in today's challenging environment.

Key facts

NIH application ID
10145902
Project number
3R25GM058939-19S1
Recipient
UNIVERSITY OF IOWA
Principal Investigator
LORI C ADAMS-PHILLIPS
Activity code
R25
Funding institute
NIH
Fiscal year
2020
Award amount
$85,119
Award type
3
Project period
1999-04-01 → 2022-01-31