Category Archives: laboratory

Submission e Valutazione Progetti

Carissimi, vi comunichiamo la data di consegna dei vostri progetti: il 20 maggio alle 23.00. Cogliamo l’occasione per anticiparvi i criteri di valutazione.

Ricordatevi di iscrivere il vostro gruppo come spiegato in questa pagina.

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laboratory 06

Today we split the tasks into two categories:

LAB06: Abandon all hope, ye who enter here

LAB06: Abandon all hope, ye who enter here

Nello scorso laboratorio abbiamo visto due cose molto importanti: come ricevere parametri dalla shell e come leggere file. Nonostante la spiegazione anti-caos preventiva, sembra che molti di voi le trovino problematiche e quindi oggi cercheremo di fare degli esercizi mirati su questi argomenti nuovi, che sono fondamentali per raggiungere gli scopi del corso (fare un programma perl che c’entri qualcosa con la genomica).

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LAB05: Some real programming!

Lab05: Some real programming!

In the exercises until now we worked with input values that were written in the beginning of the programs. This is not how real programs work. Since we now know how to read files and pass parameters, we can start writing useful programs, that work in the same way as the shell commands we saw: taking their input from files.

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Lab04: welcome back, we missed you

This is the landing page for the fourth laboratory, here at the Paolotti. We missed you!

Remember to keep this page updated regularly, as we are going to put some updates in here.

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hw2 solution

This post shows the solution for the homework coded hw2.
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Lab03: Cribi Crash Course

Today we met at the Vallisneri to play with the foundamentals of Perl (slides below).
Now you have some time to practice with Perl, so if you want to start from the basics here you are a step-by-step guide.
As always remember to “appello Nome Cognome” before starting, and say “goodbye” before leaving.

Screenshot 2014-04-03 13.59.43PDF of Perl slides

LAB02 – bourne again shell!

Today we are going to:

  1. Refresh some shell commands, and maybe learning new ones
  2. Start using bioinformatics programs, in addition to the standard Linux commands
  3. Meet Perl for the first time. Nice to meet you!

Read this page (to the end) before starting the practical.

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Lab02/3: first steps with Perl

This post is a part of the second laboratory session. Please refer to the main post. 

Ready to start programming? We hope so. This post will teach you the very first things 🙂

What a Perl program is

As we already said in class, a Perl program (or script, better), is a plain text file, as a FASTQ or SAM file is. It contains a set of instructions that the computer can execute. Unlike human beings, computers love repetitive tasks…

We are going to give you an actual lesson of Perl next Friday, but we think it is a good idea to make you touch it in advance.

Every programming language has:

  • variables: basically they are a piece of memory that can store an information, and has a name.
  • conditionals: we execute an instruction IF some condition is verified.
  • loops: we execute a set of instruction as many times as needed. Example: for every sequence in a FASTA file, calculate the reverse complement and print it.

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Lab02/2: first bioinformatics programs

This post is a part of the second laboratory session. Please refer to the main post.

Linux commands like ls and grep are just programs, but they are special because any UNIX like terminal will ship them (for free :).

Now we are going to use a Perl script and an alignment program to perform two tasks:

  • simulate a whole genome shotgun
  • align the reads produced from the shotgun

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