Computer lab

This page contains a short overview of what we are going to do at the Computer Lab, and some links to useful resources.


The “Aula Informatica di Biologia” is located in the Paolotti Building. Click here to see it in Google Maps.


  1. Please… reset all the bad behaviours of the “laurea trienniale“, such as considering the instructions a recipe to follow without thinking. Your goal is not to “finish” (what..?) but to learn something.
  2. Take your time, Google what you don’t know about computers, ask Andrea and Elisa proper questions. This means try to formulate the right question rather than “what I’m supposed to do now?”.
  3. The mandatory skill any scientist must have is problem solving. If you spend some time to try to isolate, understand and overcome your issues,… you’ll make big steps forward. Much better than just “finishing” the lab soon.
  4. Time table: don’t ask. We tend to consider 6pm as a good exit time. Should you need some extra time it’s okay for us to stay till 6.30pm… But you choose when to exit, so don’t ask us because we simply don’t know. And, please, don’t even mention any fu** train 🙂
  5. If you follow instructions very precisely (saving the files in the directory you were told) you’ll get some extra points at the end.

Provisional Program (6 May – 10 May)

Monday – Introduction to Linux and the shell and something more
How to survive in a terminal. Key concepts:

  • Files and directories
  • Tab for autocompletion
  • What a “simple text” file is
  • Simple commands…
  • …and how to “pipe” them

Tuesday – Command line BLAST and PASS
We’ll learn how to use BLAST via command line (this allows to use custom databases, perform thousand queries and much more…), and also PASS, a faster program designed for short reads alignment printing output in SAM format.

Wednesday – BLAST output and how to classify bugs with it

Thursday – Comparing classification via gDNA or rRNA

Friday – MEGAN



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