LEARNING OUTCOMES

The module aims to introduce the student to the effective and conscious use of the most common software tools

AIMS AND LEARNING OUTCOMES

The module consists of two parts, of 2 credits each.

The Computer Science part introduces the student to the use of the LibreOffice suite (in particular the Calc spreadsheet), with the aim of making him able to use Calc to process and visualize data, such as those that can be acquired from databases available on the network.

The Bioinformatics part introduces the student to the analysis of biological sequences through computer tools, the use of databases such as ncbi and the visualization of the results obtained with software.

PREREQUISITES

In order to use spreadsheets properly, the student must have basic mathematical skills and reasoning and analytical skills, typically covered by mathematics courses in the first year.

TEACHING METHODS

Teaching takes place over 14-16 weeks, each of which normally includes 3 hours of  lessons and/or guided workshops (students are required to have a laptop, and will receive assistance to install the necessary software)

During the semester there will be an assessment on the first part (with booking and file uploading on AulaWeb).

SYLLABUS/CONTENT

The Computer Science part includes introductory lessons followed by guided workshops on how to find information on the network and process and visualize data using Calc. In detail, the topics covered are:

• basics on operating systems and file systems
• use of compressed archives (zip format)
• general features of spreadsheets
• insertions, import (csv format), editing and formatting of data
• charts for displaying tabular data
• formulas, functions, absolute/relative references, mnemonic names
• filters to hide/rearrange data
• Pivot Tables to create aggregated data
• data analysis tools
• export of sheets in pdf format
• online information: open data, thematic data banks, bibliographic data banks

The Bioinformatics part consists of lectures in which the biological and evolutionary theories underlying the analysis techniques and databases are illustrated, combined with practical sessions in which the techniques taught will be applied. In detail, the topics covered are:

• biological sequences and their importance from a functional and evolutionary point of view
• sequence alignment, BLAST
• replacement matrices
• main databases of biological resources (NCBI, pubmed, nucleotide, protein, genbank)
• multiple alignment of sequences
• concepts of phylogeny: hierarchical clustering, evolutionary distances, linkage
• molecular phylogeny and reconstruction of phylogenetic trees
• calculation of statistical strength indices of trees
• viewing and annotating trees
• "Horizontal" evolution: phylogenetic reconciliation of horizontal gene transfer events

RECOMMENDED READING/BIBLIOGRAPHY

The teaching material (including any video recordings) will be made available on aulaweb.

It is also possible to consult and download the documentation in English on LibreOffice from https://documentation.libreoffice.org/en/english-documentation