Course outline


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<h3>Productivity and Reproducibility in Ecology & Evolution</h3> <h4>Instructors: Jason Pither (UBC, Okanagan campus), Gavin Simpson (U. Regina), and postdocs from the Living Data Project</h4> <p><strong>Course Description</strong><br> This course aims to transform the way that ecologists and evolutionary biologists work: to increase productivity, improve accountability, and meet new requirements for research reproducibility. Trainees will learn how to integrate open science best practices into their individual and collaborative research workflows, and use digital platforms and tools to facilitate collaboration, ensure transparency, enable pre-registrations, and implement version control and provenance tracking. </p> <p><strong>Meeting Times:</strong> <br> 9:00-10:30am PST (11:00am-12:30pm CST, noon-1:30pm EST)<br> Week 1: Tues Sept 28, Thurs Oct 1<br> Week 2: Tues Oct 6, Thurs Oct 8<br> Week 3: Tues Oct 13, Thurs Oct 15<br> MID-TERM BREAK (U. Montréal)<br> Week 4: Tues Oct 27, Thurs Oct 29 </p> <p><strong>Pre-requisites</strong><br> - Graduate-level thesis in Ecology or Evolutionary Biology - Introductory R programming experience (i.e. base R)</p> <p><strong>Delivery format</strong><br> - 8 sessions, 1.5 hours per session - Sessions are delivered as mini-workshops, typically including an introductory lecture component, followed by hands-on activities </p> <p><strong>Online Resources:</strong><br> All materials for this and associated courses will be available on the wiki pages the <a href="" rel="nofollow">OSF site</a> for the Living Data Project. Here you can find pre-read materials, additional resources, and details on how to coordinate and communicate with your groups. </p> <p><strong>Assessment</strong> - Hands-on assignments (30%) - Group project (70%) </p> <p>The assignments and project will aim to ensure students gain experience and skills necessary for designing and implementing reproducible workflows, and for fostering productive and open collaborations.</p> <p>We anticipate the outside class time commitment to be approximately 1 to 1.5 hours per session. This will include readings in advance of sessions. </p> <p><strong>Required materials</strong><br> - Personal computer with videoconferencing ability - Internet access </p> <p><strong>Additional Resources</strong><br> Some online open resources that inform our instructional materials include:<br> - <a href="" rel="nofollow">Reproducibility in Science</a><br> - <a href="" rel="nofollow">The Practice of Reproducible Research</a><br> - <a href="" rel="nofollow">Software Carpentry</a><br> - <a href="" rel="nofollow">Open Science MOOC</a> </p> <p><strong>NOTE</strong>: We focus on the use of open-source and free software and tools to maximize accessibility </p> <hr> <h3>Tentative schedule of topics and activities (each week has 2 sessions)</h3> <h4><strong>Week 1</strong></h4> <ul> <li>Overview of the course and expectations </li> <li>The Reproducibility crisis and the Open Science movement</li> <li>Overview of the core components of Open Science </li> </ul> <p><strong>Activities</strong><br> - Explore Virtual Research Environments (VREs)<br> - Set up OSF account, explore key features <br> - Create Zotero account<br> - Install R/RStudio<br> - Create Git / Github account </p> <h4><strong>Week 2</strong></h4> <ul> <li>What are the barriers to reproducibility, at individual, institutional, and other levels? </li> <li>Overview of Questionable Research Practices (QRPs) and their impacts </li> </ul> <p><strong>Activities</strong><br> - Connect Zotero & Github as "add-ons" to OSF<br> - Explore other OSF add-ons like Figshare<br> - Create R Markdown document and practice push/pull to Github<br> - Install <code>rosf</code> R package and practice upload / download to OSF </p> <h4><strong>Week 3</strong></h4> <ul> <li>What are pre-registrations and registered reports? What are their benefits? </li> <li>How to integrate Open Science best practices throughout the research workflow </li> </ul> <p><strong>Activities</strong><br> - Create and submit mock manuscript in R-Markdown including figures and citations <br> - Optionally use journal Markdown template </p> <h4><strong>Week 4</strong></h4> <ul> <li>What is meant by Open Access, and what variations exist? </li> <li>What are preprints and why might you use them? </li> <li>How can Open Science improve Equity, Diversity, and Inclusion </li> </ul> <p><strong>Activities</strong><br> - Github and OSF project management & web hosting </p> <h3>Group project: Pre-register a replication study</h3> <p>Through the 4 weeks, groups will prepare and submit a pre-registration or registered report for a replication study. The groups will use OSF, Zotero, and Github to manage and organize all materials. </p>
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