COMP 364 - Computer Tools for Life Sciences

Syllabus

Course Syllabus

Lecture Notes

• COMP 364 Survival Kit (Lecture 0): Instructions on how to access a remote computer and various UNIX commands.
• Lecture 1: Introduction to analyzing big data sets. Introduction to the command line.
  • Extra commands: curl, wget
• Lecture 2: The UNIX filesystem: files, paths, permissions and more UNIX commands
• Lecture 3: Removing, Creating and Renaming Files.
• Lecture 4: Intro to Regular Expressions
  • Good resource on the topic: Understanding Regular Expression Syntax
• Lecture 5: Chaining and Nesting Commands
• Lecture 6: Introduction to Python
• Lecture 7: Modules, Functions, Comparators and Lists
  • Reference: Examples from the workshop session.
• Lecture 8: For loop and interation
  • Reference: Output of my Python session
• Lecture 9: If-then-else statements
  • Reference: Analysis the species file
• Lecture 10: Reading and writing to files
  • Reference: Printing lines
• Lecture 11: Reversing the argument list
• Lecture 12: Creating two files based on one.→(The file)
• Lecture 13: Functions in Python
• Lecture 14: Working with Strings
• Lecture 15, 16 and 17: Plotting
  • Reference: File used in class, File used in the lab
• Lecture 18: Extra Plotting
  • Reference: Histograms, Bar Charts
• Lecture 19: Statistics and Plotting
  • Reference: Correlation and other statistics
• Lecture 20: Creating a Bar Chart
• Lecture 21: Heatmaps
  • Reference: Heatmaps
• Lecture 22: Databases
  • Reference: Heatmaps (alternative version)
• Lecture 23 and 24: SQLite Syntax
  • SQLite lab
• Lecture 25: SQLite and Python
• Lecture 26: Python/SQLite example
  • Generate the database, Query the database, Tag file (csv)
• Lecture 27: Python/SQLite Lab
  • SQLite + Python
• Lecture 28: Python conventions