HRT 841: Foundations in Computational and Plant Sciences

Course Code: HRT 841

Credits: 3

Credits and Offerings

  • 3 credits (approximately 3 hours lecture each week)
  • Fall semester every year
  • Open to students from all departments

Course Description

Computational modeling applied to plant biology. Data analysis, algorithmic thinking, model building, bioinformatics, and molecular biology using coding and computational resources.

Course Objectives

This 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.

Course Materials

The course materials can be found online at https://github.com/DanChitwood/PlantsAndPython

Topics

  • 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

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