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Revising Class materials for BIO720

This is just a place to keep track of notes and suggestions for things to add/substract or change, based on feedback etc..

General things

  • Should we do (like 708) a one hour lecture and 2 hour tutorial (across two days)

  • Definitely need to have this formally scheduled as the number of students is too great.

Some additional UNIX, life at the shell topics to add

  • More introduction to sed and awk for manipulating simple text files.

    • Maybe reformating and selecting a few columns from BED and GTF files as an example.

  • Process managements (to go along with submitting long jobs and shell scripts).

    • Did BG introduce screen or tmux in 2018?

  • More command line tools for genomics

    • seqtk, bioawk, samtools, bedtools, tabix. I think we only barely used fastQC , trimmomatic and bwa

  • More on common genomics file formats?

Suggestions from Bio720 students (2018)

This does not include every suggestion that was made to Brian and Ian, but the subset of realistic ones to consider. Some (allowing groups to work on individual assignments) are not sensible for the class model we are using. Even still I am not sure all suggestions are feasible for this graduate class, but here is the list.

  • DataCamp assignments. Too many? Some way to make at least some optional like we did at the end.

  • More timely feedback.

  • Slow down on the fundamentals, with more detailed examples or in class problems.

    • i.e. fundamentals of computational thinking, not just practical skills.

  • More detailed course outline.

  • More consistent assignment schedule

  • Specific office hours.

  • Use coloured cards for in class help (one colour for technical help, a different colour for help help.)

  • Some felt it was too much content this year. However, we actually went slower than in previous years. Given that this is effectively a remedial computational skills class, I am not sure I would advise this.