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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.
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