Notes from MPUG, October 2013

Finally, here are my notes from the Melbourne Python User Group meeting in October.

We had over twenty people and three speakers.

Claire Sloggett, a bioinformatician at the VLSCI, gave a great introduction to Python for Genomics, starting with the “quick!” explanation of how life works, moving on to Python for genomics and then Python for managing pipelines.

I had not heard of The Rosalind Project, which is the the bioinformatics equivalent of Project Euler.

Tools that Claire uses in her work include:

  • ipython
  • scipy, numpy & matplotlib
  • biopython, pysam, pyBed
  • pandas & pytables
  • rpy2 (for accessing R code)
  • lots of wrappers around various C libraries

The pipeline discussion focused on Ruffus, which Claire uses to manage pipelines for SAM to BAM conversion work.

Lex Hider (@lexualchocolate) talked about “how to be truly lazy” by using Salt Stack. This was a revisit of Lex’s talk at PyCon AU this year, and the video is online and well worth watching to get a good overview of Salt.

Bianca Gibson gave a update on Linux Australia, including 2014, which is in Perth in early January, StixCamp Gembrook, and some of the aspects of Linux Australia that people may not be aware of, including the grants program, the various subcommittees and the new community newsletter.

This entry was posted in Python. Bookmark the permalink.