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by Andrew Dalke.
Original Post: NBN lectures
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Feed Description: Writings from the software side of bioinformatics and chemical informatics, with a heaping of Python thrown in for good measure.
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)
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