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NBN notes

I was in South Africa for almost 3 months. I'm now back to Sweden. While in South Africa I taught a intensive course for the NBN on Modern Web Applications Development for Bioinformatics using TurboGears and SQLObject. It includes examples of setting up a TurboGears 0.9 quickstart and various examples centered around the NCBI taxonomy data set.

In late September I went to the Pretoria node of the NBN, the Bioinformatics and Computational Biology Unit. I helped get a prototype web-baseded LIMS for sequence and literature databases, including wikipedia-style annotations on records. It used TurboGears, SQLAlchemy, XML-RPC and more, but there are no notes. At some point in the future they will have code available, I think.

After two weeks in Pretoria I went to Stellenbosch and did some lectures and hands-on help with the Triple-J group doing systems biology. That is, they do systems biology. I talked about Python. They know what they are doing and the lectures covered some pretty advanced topics: ctypes, C extensions, SWIG basics, parsing SBML with ElementTree (Systems Biology Markup Language), writing a tokenizer and parser manually, using PLY, and threads.


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