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ELEMENTS OF INFORMATICS AND BIOINFORMATICS

CODE 57279
ACADEMIC YEAR 2023/2024
CREDITS
  • 4 cfu during the 2nd year of 8762 SCIENZE BIOLOGICHE (L-13) - GENOVA
    		•
    SCIENTIFIC DISCIPLINARY SECTOR INF/01
    LANGUAGE Italian
    TEACHING LOCATION
  • GENOVA
    		•
    SEMESTER 1° Semester
    PREREQUISITES
    Prerequisites
    You can take the exam for this unit if you passed the following exam(s):
    • Biological Sciences 8762 (coorte 2022/2023)
    • INSTITUTIONS OF MATHEMATICS 52344
    TEACHING MATERIALS AULAWEB

    AIMS AND CONTENT

    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, that use software tools with interface and documentation in English.

    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 could 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 (optional)
    • 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

    TEACHERS AND EXAM BOARD

    LESSONS

    LESSONS START

    For the timetable go to the link: https://easyacademy.unige.it/portalestudenti/

    Please check the module Aulaweb for timetable updates dependent on the sanitary and epidemic situation.

    Class schedule

    ELEMENTS OF INFORMATICS AND BIOINFORMATICS

    EXAMS

    EXAM DESCRIPTION

    The exam consists of two independent parts:

    • the Computer Science part consists in the analysis by Calc of data provided by the lecturer (those who passed the assessment in the semester are exempted).
    • The Bioinformatics part requires to carry out a series of analyzes on a biological sequence provided by the lecturer.

    The exam is passed only when the marks on the last two submission of the Computer Science and Bioinformatics parts are at least 18/30.  In this case the final mark is the average of the two marks rounded up.

    ASSESSMENT METHODS

    The Computer Science part verifies the ability to properly use the Calc spreadsheet.

    The Bioinformatics part verifies the ability to analyze biological sequences.