Workflows and computing!

Biology is increasingly data intensive!

Command line skills are the new pipetting!

The most important skill to develop is the confidence that the solution is out there and you can find it. Everybody learns something new every day they do data analysis!

Why are we using the cloud??

  • easy install of software!
  • big compute power and disk.
  • general skills that “travel” - not specific to one location or computer type.

Why do we teach command line??

Workflows, and responsible conduct of computational research

The basic goals:

  • readers and reviewers of your work should be able to discover what you did to analyze your data, starting from the raw data and going all the way to your final figures.

  • if you can automate the entire process, this will serve the above purpose and also lead to efficiency gains for yourself in updating analyses.

  • automating small data analyses will seem unnecessary, but the skills you gain in doing this will enable you to handle much larger data analyses much more easily.

    Think - could you do a particular task on 1 data set? 5 data sets? 50 data sets? 5000 data sets?

Reading material

Computing Workflows for Biologists: A Roadmap

Repeatability considerations - see 2016 Oslo workshop