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OSF as a tool for managing course-embedded research projects

October 10th, 2019,
Posted in: biochemistry, JMU, CURE

Starting out as a first year professor, teaching was a new and exciting endeavour but I lacked experience in the development of curriculum, knowing what students needed to know, and many aspects of the profession of teaching. After a few years of following what others did, I became dissatisfied in my teaching and took the opportunity to take my training as a biochemist into my classroom. In 2014, I started having students participate in my research projects but I needed a way to organize the data and results across several semesters and on the scale of up to 100+ students. My institution did not have effective, on-campus tools to do this and external infrastructure using Google, Evernote, OneNote, etc. lacked the features I wanted. At the suggestion of Yasmeen Shorish, Data Services Coordinator in the JMU Libraries in 2016, I began working with the Open Science Framework and by 2017 had integrated it into my classroom and research lab. I liked that the OSF interface was clean, had integrated storage, a wiki for communication, easy to use version control, and was integrated into the JMU access system so students did not need another login name and password.


In the Biochemistry “lecture” course, students participate in ~5 group projects and 1 individual research project over the semester, all of which are managed on OSF. Despite the course classification, I avoid lecturing about content and instead strive to have students understand biochemistry by solving problems and applying biochemical principles. Many of these projects are based on my own research and sometimes are projects that generate novel results. Each student brings a unique perspective to the project and sometimes students find avenues or develop ideas that I had not considered, which benefits my science and the directions I take. By participating in my course, students are being exposed to authentic, collaborative research experiences while gaining skills in good scientific practice.


The OSF project is organized such that the students and I work in a single, collaborative site with distinct components for each project. I put helpful links or guides to OSF, data management, and figure making in the Home wiki of this component to provide the students with information on the expectations for the projects. To help the students with citations and finding reliable sources of information, Alyssa Valcourt, Science Liaison in the JMU Libraries, has developed activities that are performed in class and provides guides which she posts on the OSF site for later reference.  At the beginning of the semester, I send the link to the OSF site to the students with instructions on how to gain access. With these tools and base knowledge that Alyssa and I provide, the students are ready to begin to collect and manage their data in a file folder within each project component. Over the course of the semester and the 6 projects, students use the wiki feature of OSF to collaboratively report their results and illustrate their work. I typically provide a template to guide their report which helps the students who have little experience with this format to navigate and organize the data. It is fun to see the students explore the full capabilities of the wiki in using videos, gifs, or embedding PDB files and it makes it more fun to assess than just reading a paper document. In addition to the wiki, the students must provide all of their raw and processed data in the OSF storage. Part of the grade for the assignment is how accessible their data are in terms of organization or the use of README files or data dictionaries in an effort to instill good practices in data management and sharing. The projects range from modeling the structure of an uncharacterized protein sequence to building a spectroscope/fluorimeter to analyze the interactions of biomolecules with light to the final individual project which integrates the concepts of the group projects to have students model biomolecule structure and function while also proposing an experimental plan to test their models. This latter activity is much like a scientific grant or business proposal. More recently, I have incorporated OSF into my instructional labs to manage the project which is testing the findings from the lecture course. In this setting, OSF is the electronic notebook for their project and how the students report their results. Being able to use a single platform to manage all of my projects has made integrating my teaching and my scholarship very easy. 


Undertaking a project of this scale and complexity was not without issues that had to be worked out. The first was finding ways to make the wiki useful for a chemist. It was not clear to students how to make chemical equations, mathematical formulas, or figure legends, so I wrote a guide which succinctly shows students how to pull this together. Another is getting students to understand why making data accessible is important. Instructional labs or science courses don’t talk about sharing data, so file naming, data dictionaries, version control, etc. are not aspects that students think of. Admittedly, even I struggle with this issue as I received no formal training in data management. To help the students, I have adapted some of the materials on this topic developed by Yasmeen Shorish and we have discussions in class showing messy desktops with redundant naming or how many students have lost an important file in their downloads folder. Then we talk about taking 10 seconds to give an informative file name can save a lot of time later. These are issues that will constantly need to be addressed until open science and data management practices are more ubiquitous throughout the science curriculum. 


OSF is the central hub around which I can organize, manage, and share data across multiple instructional and research settings. Since using OSF, more than 300 students have collaborated on projects creating knowledge on topics ranging from viral tethering to the enzymatic mechanism of ubiquitination. I allow students to make their work public so that they can develop portfolios of their work to show future employers or admissions committees. Students have presented posters from their findings at ABRCMS and the Virginia Academy of Sciences and since 2014, data produced by this in-class project has contributed 4 peer reviewed publications with another pre-printed article being prepared for publication as of 2019. As I look to the future, I see opportunities to solidify the collaboration between my courses and the possibility of spreading the project among students in very different topics working together to holistically analyze and address scientific questions. Finally, expanding outside of JMU to work regionally, nationally, or globally with this project will not only enhance the quality of science by increasing the diversity of perspectives but also foster the idea that science is a community activity where the more discussion and sharing can lead to more success.


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