This course provides essential training in modern research tools and methods that are fundamental to conducting reproducible, efficient, and collaborative research in the biological and health sciences.
The course syllabus is shown below.
Course title and instructors
Title: BIO390: Research Tools and Methods
Semester: Fall 2025
Credit Hours: 1
Meeting Time: Once per week for 1 hour
Course Director: Michael E. DeWitt, MS
Email: medewitt@wakehealth.edu or dewime23@wfu.edu
Course description
This course introduces students to essential computational tools and methods used in modern scientific research. The course emphasizes hands-on learning and practical application of tools that enhance research reproducibility, collaboration, and efficiency. Students will learn version control systems, plain text editing and markup languages, knowledge management and reference management tools, data storage methods, and best practices for organizing and managing research projects. The course is designed for students who are preparing for research careers and need foundational skills in computational research methods. No prior programming experience is required, though familiarity with basic computer operations is expected.
Learning outcomes
Upon successful completion of this course, students will be able to:
- Use version control systems (Git) to track changes, collaborate, and manage research projects
- Create and edit documents using plain text markup languages (Markdown, LaTeX)
- Use knowledge management systems (Obsidian, Zotero) for organizing research notes and managing references
- Understand different data storage formats and methods appropriate for various research contexts
- Organize research projects following best practices for reproducibility
- Apply computational tools to enhance research workflow efficiency
- Understand the principles of reproducible research and data management
- Navigate command-line interfaces for file management and tool execution
Textbook and other resources
There is no required textbook for this course. All materials will be provided through course handouts, online resources, and documentation. The following resources are recommended for reference:
- Pro Git by Scott Chacon and Ben Straub (available online at https://git-scm.com/book)
- The Markdown Guide (available online at https://www.markdownguide.org)
- The LaTeX Companion by Frank Mittelbach et al. (available online through university library)
- Reproducible Research with R and R Studio by Christopher Gandrud
Additional online resources and documentation will be provided throughout the course for specific tools and topics.
Course structure and schedule
This course meets once per week for one hour over 15 weeks. Each session will combine brief instruction with hands-on practice. Students are expected to bring a laptop to each class session. All software used in this course is free and open-source.
| Week | Topic | Date | Instructor |
|---|---|---|---|
| 1 | Introduction to research tools and reproducibility | TBD | DeWitt |
| 2 | Command line basics: navigating the file system | TBD | DeWitt |
| 3 | Plain text editing: Introduction to Markdown | TBD | DeWitt |
| 4 | Plain text editing: Advanced Markdown and document generation | TBD | DeWitt |
| 5 | Plain text editing: Introduction to LaTeX for scientific writing | TBD | DeWitt |
| 6 | Knowledge management: Obsidian and Zotero for reference management | TBD | DeWitt |
| 7 | Version control: Git basics, workflows, branching, and merging | TBD | DeWitt |
| 8 | Version control: Collaborating with Git and GitHub | TBD | DeWitt |
| 9 | Data storage: File formats, organization, and naming conventions | TBD | DeWitt |
| 10 | Data storage: Introduction to relational databases | TBD | DeWitt |
| 11 | Data storage: NoSQL databases and cloud storage options | TBD | DeWitt |
| 12 | Data management: Best practices for research data | TBD | DeWitt |
| 13 | Reproducible research: Virtual environments and containers | TBD | DeWitt |
| 14 | Integration: Project organization and putting it all together | TBD | DeWitt |
| 15 | Final project presentations and course wrap-up | TBD | DeWitt |
Note: Specific dates will be provided at the beginning of the semester. Topics may be adjusted based on class progress and student interests.
Grades and assignments
Students’ evaluation will be based on their attendance, participation in class activities, completion of weekly practice exercises, and a final project that demonstrates proficiency with the tools covered in the course.
| Activity | Weight |
|---|---|
| Attendance and participation | 20% |
| Weekly practice exercises | 50% |
| Final project | 30% |
Weekly practice exercises: Each week, students will complete a brief exercise applying the tools and concepts covered in class. These exercises are designed to reinforce learning and will be submitted via the course learning management system.
Final project: Students will create a small research project (or adapt an existing project) that demonstrates the use of version control, plain text editing, and appropriate data storage methods. Projects will be presented during the final class session. Detailed project guidelines will be provided mid-semester.
Course policies
Attendance: Regular attendance is expected and essential for success in this course. Each class builds on previous material, and hands-on practice during class time is crucial. Please alert the instructor if you are unable to attend for any reason.
Late/Makeup work: Weekly exercises are due one week after they are assigned. Unless otherwise stated, assignments are due on those days. We recognize that there are sometimes extenuating circumstances (i.e., life happens) and as such we will allow you to submit assignments up to 2 days late without any penalty. If there is a valid reason for requiring an extension, please contact the instructor as soon as possible and before the due date. We can evaluate late work on a case-by-case basis.
Software and equipment: Students are required to bring a laptop to each class session. All software used in this course is free and open-source. Installation instructions will be provided during the first class session. If you do not have access to a laptop, please contact the instructor immediately to discuss alternatives.
Collaboration: Students are encouraged to work together and help each other learn the material. However, each student must submit their own work for weekly exercises. For the final project, collaboration may be permitted with prior approval from the instructor.
Artificial intelligence: Artificial intelligence tools and large language models such as ChatGPT, Claude, and Gemini are now part of the academic and professional landscape and we encourage you to find ways to use them to enhance your learning. However, if you use these tools, you must cite your sources and provide a detailed description of the tools you used to complete the assignment. In no way can these tools take the place of your own work and understanding of the material. They should be used to supplement your learning, not replace it. You are ultimately responsible for your work including content and the use of valid citations and references. Using these tools without proper attribution is plagiarism and will be treated as such.
Department/School/University policies
Academic Integrity: Wake Forest University is committed to a culture of academic integrity. As a part of this community, you share the responsibility for creating a place of honesty, intellectual curiosity, and individual accountability. As you committed to with your honor pledge signature, you agree “not to deceive any member of the community; not to steal, cheat, or plagiarize on academic work; and not to engage in any other form of academic misconduct.” If you have questions about documenting your work, working with external sources, working with peers on assigned work, etc., consult with me as soon as possible. Instances of academic dishonesty will be referred to the Honor and Ethics Council.
Accessibility: Wake Forest University provides reasonable accommodations to students with disabilities. If you are in need of an accommodation, then please contact me privately as early in the term as possible. Retroactive accommodations will not be provided. Students requiring accommodations must also consult the Center for Learning, Access, and Student Success (118 Reynolda Hall, 336-758-5929, class.wfu.edu).
Accommodations for Religious or Spiritual Practices: Wake Forest University benefits from the multitude of faiths and spiritual identities held by members of our learning community. Our institution values this religious and spiritual diversity and supports providing academic accommodations to students for religious or spiritual observations. The Office of Diversity and Inclusion has developed a calendar of common Holy Days observed by many individuals on our campus. Should you need such accommodations this semester, you should email me as soon as possible to ensure we have time to develop equitable alternatives. You are encouraged to use this template, developed by the Office of the Chaplain, to make these requests.
Class recordings In case any class recordings are provided they are reserved only for students in this class for educational purposes and are protected under FERPA. The recordings should not be shared outside the class in any form. Violation of this restriction by a student could lead to Student Misconduct proceedings.
Syllabus change notice
This syllabus and the dates herein are subject to change.