Docs and links

Required course reading

• Book: Haddock and Dunn, "Practical computing for Biologists"
• Paper: William Stafford Noble, "A quick guide to organising computational biology projects", PLoS Comp Biol, 2009.

Additional course documents

• Ten Simple Rules for the Open Development of Scientific Software (Prlić & Procter, PLoS Comp Biol, 2012)
• Ten Simple Rules for Reproducible Computational Research (Sandve et al., PLoS Comp Bio, 2013).
• So you want to be a computational biologist? (Loman and Watson, Nature Biotech, 2013)
• Best Practices for Scientific Computing (Wilson et al, PLoS Biology, 2014)

For the curious

Here are links if you want to learn more.

• Using named pipes and process substitution in Bioinformatics
• Minimum standards for bioinformatics command line tools by Torsten Seemann.
  • Now also published in the journal GigScience!
• SQLite - Working with large data sets in Python effectively by Sebastian Raschka