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Open science, open data, open source projects for undergraduate research experiences

By Kam Dahlquist

Loyola Marymount University

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Abstract

This resource has been updated - find the current version here: https://qubeshub.org/publications/314

Description:
In this workshop, I will demonstrate a suite of open source tools that students use in my courses to conduct original research in my courses.  In a team-taught, cross-listed Biological Databases course, students use the XMLPipeDB suite to create a gene database for a microorganism and use it to analyze published DNA microarray data.  In a team-taught, cross-listed Biomathematical Modeling course, students use the GRNmap software to perform differential equations modeling of a medium-scale gene regulatory network and the GRNsight software to visualize the results.  Each of these courses is taught "in the open" on a publicly-accessible course wiki.  The results of student research are published on the web for the scientific community.  There is a special emphasis in the courses on interdisciplinary teamwork, computer literacy, data literacy, and information literacy.

i will discuss how you can adopt and adapt these exercises and/or framework in your courses.

additional resources:

Mathematical modelling open source software

Visualization open source software

XMLPipeDB website

Biological Databases course website

Biomathematical Modeling course website

Bioinformatics Laboratory course website

Cite this work

Researchers should cite this work as follows:

  • Kam Dahlquist (2015), "Open science, open data, open source projects for undergraduate research experiences," https://qubeshub.org/resources/445.

    BibTex | EndNote

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