Some TA-ing at UNIL, including in Biostatistics/R and Bioinformatics. Here are two of the practicals I prepared:

• Introduction to microarray analysis: Three hour practical for 3rd year Biology students at UNIL. Download some normalized affy data, blindly use Limma to find significant genes, cluster them with TMEV, conduct GO analysis of one cluster... conclude about confounding factors in experimental design.
• Introduction to BLAST: Two hour practical for 2nd year biology students. Calculate score & evalue of an alignment by hand... compare with true Blast results obtained on NCBI, see that blastp and blastn have different sensitivities. Check some new NCBI blast features.

Semester programming projects:

• Programming project: for introduction to python/biopython class. Determining Codon Adaptation Index in ants. Required datafiles: sequence fasta file and blastx report (also available from fourmidable).
• Programming project: for introduction to python/biopython class. Improved protein sequences for non-model organisms.

Introduction to bioinformatics & bioruby @ (2010/10/31)