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BIOL 432

Computation and Big Data in Biology

3.0 units · Undergraduate

Winter 2025

Topics

  • Introduction to machine learning concepts and principal
  • Working with DNA data files and the BLAST search in R
  • DNA Alignments and phylogenetic trees in R
  • Fundamentals of RNA sequencing and transcriptome
  • Interpret and write original regular expressions to efficiently modify biological data files (e.g
  • Training

Readings

  • Required: NONE Optional Course Textbooks Course Textbooks Edition(s) Publisher
  • Supplemental: Resource Resource Type Access Further Information Practical Computing for Biologists by Haddock & Dunn Other Bookstore Oxford University Press Bioinformatics Data Skills by Vince Buffalo Other Bookstore O’Reilly
Fall 2025

Topics

  • Introduction to Machine Learning and Principal Components Analysis
  • Support Vectors and Decision Trees
  • Phylogenetics
  • Bioinformatics
  • Biostatistics
  • DNA
  • RNA

Readings

  • Listed material: R Machine Learning for Biologists
  • Listed material: Before Lecture:
  • Listed material: During Lecture Session:
  • Listed material: During Tutorial/Help Sessions:
  • Listed material: Review feedback and prepare for next week. Assessments
  • Listed material: 20% Weekly Assignments – usually due 24 to 48 hours after lecture
  • Listed material: 10% Participation and Peer-Review – peer evaluations of group work
  • Listed material: 20% Final Group Project – a multi-week open-ended group project and presentation
  • Listed material: 40% Final Exam – a very simple, hand-written exam to Support & Flexibility
  • Listed material: Grace period: Typically 24 to 48 hours for assignments—no need to ask.
  • Required: Course Textbooks Edition(s) Publisher
2023 · Syllabus

Topics

  • DNA sequence data and alignments

Readings

  • Listed material: Bioinformatics for Biologists by Robert I. Colautti.
  • Listed material: Practical Computing for Biologists by Haddock & Dunn (Oxford University Press).
  • Listed material: Bioinformatics Data Skills by Vince Buffalo (O’Reilly).
Winter 2022

Topics

  • DNA
  • RNA
  • Phylogenetics
  • Development
  • Problem-solving

Readings

  • Listed material: None Required. Suggested: R for Data Science by Hadley Wickham Practical Computing for Biologists by Haddock & Dunn (Oxford University Press) Bioinformatics Data Skills by Buffalo (O’Reilly)
2020-2021

Topics

  • Development
  • Problem-solving

Readings

  • Listed material: None Required Useful reference books: Practical Computing for Biologists by Haddock & Dunn (Oxford University Press) Bioinformatics Data Skills by Buffalo (O’Reilly)
2019-2020

Topics

  • Development
  • Problem-solving

Readings

  • Listed material: None Required Useful reference books: Practical Computing for Biologists by Haddock & Dunn (Oxford University Press) Bioinformatics Data Skills by Buffalo (O’Reilly)
2018-2019

Readings

  • Listed material: None Required Useful reference books: Practical Computing for Biologists by Haddock & Dunn (Oxford University Press) Bioinformatics Data Skills by Buffalo (O’Reilly). BioStars Handbook by Albert (independent). Online: https://www.biostarhandbook.com
Sources