Hands-on experience in computational genomics

Grant:

Instructional Development Fund (IDF)

Academic Year:

2015 - 2016 (June 1, 2015 through May 31, 2016)

Funding Requested:

$500.00

Project Dates:

Tue, 01/05/2016 - Thu, 04/14/2016

Applicant(s):

jmkidd

kitzmanj

Overview of the Project:

Advances in data generation have revolutionized all aspects of biology. In particular, the advent of affordable high-throughput sequencing has transformed biological research into a data-intensive, quantitative field. There is a large and growing need to train researchers and other professionals in the basic, practical skills necessary to meet this challenge. Toward these ends, we have developed a new course, Human Genetics 551: Computational Genomics, targeted towards graduate (masters and Ph.D level) students without an existing background in computer programming or statistics. This is a population of students that is not well served by existing classes. This audience will benefit immensely from practical, hands-on experience analyzing real-world genomic data sets. We are requesting $500 to facilitate usage of the FLUX computer cluster for course projects focused on analysis of real data. The FLUX system is a campus-wide computing resource and features a pay-as-you-go usage model. We anticipate that most students will utilize FLUX in their own future research endeavors, thus necessitating the incorporation of FLUX into our course design. If awarded, the $500 grant will be used to purchase ‘on-demand’ computing resources for student use during the semester. Please see http://arc-ts.umich.edu/resources/compute-resources/ for more information on the FLUX environment.

Final Report Fields

Project Objectives:

We have developed a new course, Human Genetics 551: Computational Genomics, targeted towards graduate (masters and Ph.D level) students without an existing background in computer programming or statistics. This is a population of students that is not well served by existing classes that would benefit immensely from practical, hands-on experience analyzing real-world genomic data sets. In addition to teaching foundational topics in computational genomics, enrolled students will complete final course project involving the reanalysis of published data sets using the tools and concepts covered in the course.

Project Achievements:

HG551 was taught for the first time in Winter 2016 with 19 students enrolled. The class was reviewed extremely favorably by students based on course reviews and will be expanded to three credits in Winter 2017. Six final projects were completed by groups of students, two of which involved computational analysis of data previously generated by the students themselves. This course directly addresses a deficiency in our curriculum identified by a recent external review of the department and provides initial exposure to a critical skill required for all biomedical researchers.

Continuation:

Yes, this project will continue as we are building on our experiences using the FLUX system to teach computational genomics in future offerings of HG551. We additionally plan to advertise and expand the number of students enrolled in the class and, ultimately, further integrate these concepts into the broader genomics curriculum.

Dissemination:

We have shared our experiences with computational staff and also with other colleagues considering use of the FLUX resource in future classes.

Advice to your Colleagues:

We experienced problems with m-tokens and student logins, but these should be resolved in large part by infrastructure changes being completed this summer. We also were overly ambitious in terms of the time and background knowledge initially required, but were able to quickly adjust our planned exercises.

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