HRT 841 : Plants and Python

September 01, 2020

Michigan State University, East Lansing, Michigan
Link to the course page  

Plants and Python JupyterBook   This is an interactive, online book based on the course material developed by the instructors, Dr. Dan Chitwood and Dr. Robert VanBuren.
The content is available in both English and Spanish.

This is a graduate level class offered every year in Fall, and open to students from all departments. The objective of the course is to teach students how to apply computational modeling to plant biology. It introduces students to data analysis, algorithmic thinking, model building, bioinformatics, and molecular biology using coding and computational resources. The course assumes no prior experience in plant biology or coding; rather, this course selects specific examples in which mathematical, modeling, and bioinformatic approaches intersect with the biology of plants. Students apply learned objectives to a course research project. Specific topics covered in the course include:

• Using Jupyter notebooks for education, coding, and research.
• Coding from scratch: indexing, loops, dictionaries, functions.
• Data visualization.
• Using mathematics and code to model biological phenomena.
• Using high performance computing (HPC) resources.
• Using Biopython for reading, storing, writing, and manipulating sequences.
• Comparative genomics.
• Short read analysis.
• Applying learned concepts to student-led research questions.
• Communicating research and scientific writing.