BASIC Course in Bioinformatics

Conference room Stazione Zoologica Anton Dohrn – 15-18 July

LESSONS SLIDES ARE AVAILABLE HERE 

Monday 15th July
Morning session: 10:00 – 12:30 (Maria Luisa Chiusano)
Introduction.
Overview and basic concepts.

Afternoon session: 14:00 – 16:30 (Maria Luisa Chiusano)
Theory and practice.

Tuesday 16th July
Morning session: 10:00 – 12:30 (Luca
Ambrosino)
Download Material
Sequence alignments (global, local, multiple).
Practice.

Afternoon session: 14:00 – 16:30 (Chiara Colantuono)
Download Material
Introduction to ESTs and RNA-seq.
Practice: Quality Check and Data visualization (IGV, GenomeBrowser).

Wednesday 17th July
Morning session: 10:00 – 12:30 (Luca Ambrosino)
Functional annotation (Interpro, GO, KEGG).
Theory and practice.

Afternoon session: 14:00 – 16:30 (Michael Tangherlini)
Download QIIME virtual machine
Introduction to metagenomics: metabarcoding (QIIME2, workflow and web visualization of results).

Thursday 18th July
Morning session: 10:00 – 12:30 (Michael Tangherlini)
Download the shotgun virtual machine (23GB!!!)
Introduction to metagenomics:  shotgun approaches (workflow).

 

Requirements: you should bring your own laptop, fully charged (there are not many plugs in the conference room); your laptop only needs a browser, while other software will be installed as required during the course; please check that you have admin permissions on your laptop.
The metabarcoding workshop will require participants to install the QIIME2 virtual machine on their own laptop. All the instructions needed to (freely) obtain VirtualBox and the QIIME2 VM can be found at this URL: https://docs.qiime2.org/2019.4/install/virtual/virtualbox/

The shotgun workshop will require the download of a second virtual machine that you can get at https://team.bioinfo.szn.it/s/KBAEFdy7WaLJQL3 (23GB size).

Some of the tools you will use during the course make use of the Java environment, which can be downloaded freely at https://www.java.com/it/download/

For information please contact:
Mara Sangiovanni at BIOINforMA group
– mara.sangiovanni@szn.it / bioinforma@szn.it
081-5833260

Danila Voronov – danila.voronov@szn.it –  081-5833255