Lecture notes

This page contains a list of lecture notes. I am not sure if it makes sense to read them here, out of their context, but by keeping them on the web I, at least, know where they are; if anyone else finds them useful that's just an added bonus.

Bioinformatics

Stochastic Models in Bioinformatics (Fall 2007)

• Introducing Mutations to Wright-Fisher — Computer practicals.
• Discrete time molecular Evolution — Computer practicals. (solutions)
• Continuous time molecular Evolution — Computer practicals. (solutions)
• Monte Carlo methods.
• Sampling exercises — Computer practicals. (solutions)

Molecular Evolution (Msc Bioinformatics, Summer 2006)

• Beyond Phylogenies — Computer practicals

Scripting

Scripting (Spring 2005)

• Process Management
• Clustal W Exercises
• Web-services
• NCBI Exercises
• NISC BAC Contig Assembly
• Accessing Databases
• Creating and Modifying Databases
• A Database of Multiple Alignments
• Distributed Systems
• Remote Method Invocation (RMI)
• Threads and Worker Pools

Complex Software Systems (Fall 2003)

• Process Management
• Clustal W Exercises
• Networking
• Searching NCBI Exercises
• CGI Scripts
• CGI Interface to Clustal W
• Wrapping Clustal W and NCBI Searches
• Introduction to SQL and Accessing MySQL from Python
• Database Access to Embl
• Introduction to SQL and Updating MySQL from Python
• A Database of Multiple Alignments
• A Multiple Alignment Database