Our paper’s completion has probably been delayed till September or so pending some (in my opinion puzzling) organizational issues within a group that works with us. My research work is also pending due to the fact that I’m waiting for someone to prepare a “data matrix” for me, and the person doesn’t seem to know that leaving other people hanging is somewhat impolite.
So, I decided that as a person that works in bioinformatics I could learn something new. That is why I’ve decided to learn Python. The fact that it forces you to use proper indentation and its syntax seems ideal for me, who has little programming experience save bash shell scripting and a few PHP (terrible). I’ve found a nice tutorial for it and so far it’s going OK.
I’ve taken a look at the Biopython project as a reference for future work, but it mostly deals with sequence analysis, which is not my field. I wonder if there are Python tools for microarray data analysis, because I really don’t like R (it’s slow and it’s more of an environment than a programming language) and the only ones I know are from the Bioconductor project, in R, as I wrote. Not only that, but I work on proprietary high density oligonucleotide arrays, not the most common two-color (Cy3 + Cy5) variants.
If that’s not the case, I could look into annotation, probably, which is something I do extensively to filter out biologically non relevant data (always a problem when you deal with complex algorithms). Still, there’s more time before I get to doing something relevant to my work, so the chances are that I’ll find something by then.
Luca Beltrame SCIENCE