NBN lectures

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NBN lectures

It's been a pretty intense 6 weeks. I taught another Python course at the NBN in Cape Town, South Africa. I was here in early 1994 to teach a beginning course. This time it was an improvers level course. The student skill levels were rather diverse. All of the students had done some programming before, but many were at the beginning level. Some were more advanced and a few came into bioinformatics from computer science.

The lectures notes are available. Here's an index of what I covered:

Parsing FASTA files
Parsing BLAST
Using Biopython to do BLAST searches
Using matplotlib to make a hydrophobicity plot
List comprehensions and generators
Introduction to HTML, leading up to using CherryPy to make a simple web app
XML and XML-RPC
Clustering with PyCluster

The course was 2 hours per day. The hardest part of the lectures for me was coming up with good assignments. I wanted ones that were biologically and technologically interesting and open to experimentation. Because of the range of backgrounds I ended up having some more advanced exercise that were optional only for the beginning students.

At the end of the course I reviewed the assignments as a 1-on-1 code-review. Each one took between 45 minutes and 2 hours.

I also offered to teach two days on usability. The first day was an overview with an in-class assignment (suggested by Rachel Smith) on designing a microwave oven control. The second day was a full day spent designing a BLAST interface, using Ruediger Braeuning from the NBN as the customer representative and test subject.

The teacher for proteomics wasn't able to make it so I offered to teach a chemical informatics course instead. I covered the basics of:

Nomenclature systems, up to SMILES and SMARTS
Fingerprints
Similarity searches (based on John Barnard's excellent notes)
Chemical databases