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Python and C

In early October 2006 I lectured at the University of Stellenbosch on how to make C and Python work together, various ways to parse files, and more.

Modern Web Applications Development for Bioinformatics

At the end of July 2006 I taught an intense two week NBN course titled "Modern Web Applications Development for Bioinformatics" and based on the TurboGears framework. Here are the lecture notes.

Programming for Bioinformatics in Python

In August-September of 2005 I taught an intermediate level programming course at the NBN (National Bioinformatics Network) in South Africa. Here are the various notes and assignments for the course.

Introduction to Programming for Bioinformatics in Python

In February 2004 I taught an introductary programming course at the NBN (National Bioinformatics Network) in South Africa. It was part of an intense and impressive 7 week training session for bioinformatics research with topics including bioinfomatics theory, algorithms, databases, software, unix, programming and even grant writing.

The portion I taught was two hours a day, six days a week for the first two weeks. I started off with a translation of a introductory Perl course Lincoln Stein taught but after the first day I realized that most of the people in the class had very little programming experience so I started the next day with the basics and lots of slides.

Some of the students already knew how to program so I made a wide range of exercises with the expectation that the beginning students would only get through the first few in each problem set while the most advanced ones would still be challenged with the harder ones. Judging from the feedback it worked out pretty well.

Here are all the slides in PDF and PowerPoint format. I made them using Apple's Keynote but that format is verbose and requires directories so too much work to put it on-line. Contact me if you need them.

  • Introduction to Python [html]
  • Strings in Python [PDF|PPT]
  • Variables and References in Python [PDF|PPT]
  • Lists and the 'for' loop [PDF|PPT]
  • Stepping through a 'for' loop [PDF|PPT]
  • The if statement and files [PDF|PPT]
  • Working on exercises (a few notes first) [PDF|PPT]
  • Code Blocks and Indentation [PDF|PPT]
  • Functions [PDF|PPT]
  • Why? [PDF|PPT]
  • Dictionaries [PDF|PPT]
  • Advanced Exercises [PDF|PPT]
  • Sorting and Modules [PDF|PPT]
  • Searching and Regular Expressions [PDF|PPT]
  • Important modules: Biopython, SQL & COM [PDF|PPT]
  • "Everything Else" [PDF|PPT]
  • Answers to all the exercises

Some of the exercises used data files. I think this is the complete list. If missing I note why.

I really enjoyed teaching the course. It was a lot of work but the result was seeing many people really get into it and faces light up with understanding and achievement.

To the whole class, best wishes and good luck for the future!

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