Topic outline

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  General

  • BCH2203 Introduction to Programming in Python (Winter 2022)

    In this course students will be instructed in how to program in Python. Ultimately students will learn how to use Python to analyze, process and visualize data. This course is designed for students with little to no experience in programming. 

    This is a graduate course that can be taken for by UofT Biochemistry graduate students. Those students should enrol using ACORN/ROSI.
    

    Teacher: Ramses van Zon

    Start date: 12 Jan 2022

    End date: 15 Apr 2023

    Scientific Computing Credits: 9

    Data Science Credits: 9

    : 1
  • Syllabus Page
  • Forum for questions regarding the course material
  • Announcements Forum
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  Lectures Slides

  • Lecture 1: Intro File
  • Lecture 2: Lists and I/O in Python File
  • Lecture 3: Dictionaries, functions, modules... File
  • Lecture 4: Arrays File
  • Lecture 5: Regular expressions and dataframes File
  • Lecture 6: Review and Visualization with Matplotlib File
  • Lecture 7: Biopython File
  • Lecture 8: Sequence Alignment with BLAST and BioPython File
  • Lecture 9: Performance File
  • Lecture 10: Machine Learning File
  • Lecture 11: Randomness File
  • Lecture 12: Structure File
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  Recordings

  • Lecture 1: About the course and Python File
  • Lecture 2: Lists and I/O in Python File
  • Lecture 3: Dictionaries, functions and modules File
  • Lecture 4 Recording (lists. strings, numpy) missing. File 54.6MB Video file (MP4) Uploaded 2/02/22, 13:29

    Due to technical difficulties, recording of the lecture on Feb 2, 2022 failed.  What's posted here is a very similar lecture from 2020.  Please consider the pdf slides above as the definite reference of what was covered in the Feb 2 lecture.

  • Lecture 5: Dataframes and regular expressions File
  • Lecture 6: Review and Matplotlib Visualization File
  • Lecture 7: Biopython File
  • Lecture 8: Sequence Alignment with BLAST and BioPython File
  • Lecture 9: Performance File
  • Lecture 10: Machine Learning File
  • Lecture 11: Randomness and stats File
  • Lecture 12: Protein Structures File
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  Assignments

  • 1. Survey Analysis Assignment

    Opened: Wednesday, 19 January 2022, 12:00 AM

    Due: Wednesday, 26 January 2022, 11:59 PM
  • 2. Survey Analysis Improved Assignment

    Opened: Wednesday, 2 February 2022, 1:30 PM

    Due: Wednesday, 9 February 2022, 11:59 PM
  • 3: Pandas and zombies Assignment

    Opened: Wednesday, 16 February 2022, 12:00 AM

    Due: Wednesday, 2 March 2022, 11:59 PM
  • 4. Rotten eggs Assignment

    Opened: Thursday, 10 March 2022, 12:00 AM

    Due: Thursday, 17 March 2022, 11:59 PM
  • 5. Seeds classification Assignment

    Opened: Wednesday, 23 March 2022, 12:59 AM

    Due: Wednesday, 30 March 2022, 11:59 PM
  • 6. Classify downloaded protein structures Assignment

    Opened: Sunday, 10 April 2022, 12:00 AM

    Due: Sunday, 17 April 2022, 11:59 PM
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  Additional material

  • dna.fasta - DNA sequence used in the example in lecture 8 (alignment) File