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

By Kam Dahlquist

Loyola Marymount University

Resource from the 2015 BioQUEST Summer Workshop

Listed in Teaching Materials | resource by group BioQUEST / HHMI / CaseNet Summer Workshop 2015

Version 1.0 - published on 17 Jan 2018 doi:10.25334/Q46M4X - cite this

Licensed under CC Attribution-NonCommercial-ShareAlike 4.0 International according to these terms


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


BioQUEST / HHMI / CaseNet Summer Workshop 2015

BioQUEST / HHMI / CaseNet Summer Workshop 2015 group image

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