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Information

Title The eLearning course for Food Microbial Bioinformatician - Module 2: Bioinformatics pathway (FULL)
Type Fad e-learning (FAD)
Provider IZS dell'Abruzzo e del Molise "G. Caporale"
Edition1
ECM event No
Municipality / foreign state of development -
Place of delivery -
Starting date 29/03/2021
Ending date 15/12/2021
Participation fee -

Course introduction

This module provides with an introduction to programming languages and to WGS data, deals with the various phases of the Dry Lab, as WGS data and comparative analysis, and related bioinformatic tools. Units: 2.1 Priming on Linux 2.2 WGS data 2.3 Data analysis 2.4 Visualization tools Duration: 300 hours

Learning objectives

Learning objectives
  • Acquisire competenze per l'analisi e la risoluzione dei problemi nei vari contesti
  • Acquisire conoscenze teoriche e aggiornamenti

Job profiles

  • Veterinario - Tutte le discipline
  • Biologo - Biologo
  • Medico chirurgo - Tutte le discipline
  • Tecnico sanitario di laboratorio biomedico - Tecnico sanitario di laboratorio biomedico

Scientific coordinators

Surname and Name Qualifications Job Profile
Pomilio FrancescoReparto Igiene e Tecnologie degli AlimentiVeterinario Dirigente Responsabile

Tutors' panel

Surname and Name Role Job Profile Discipline (or qualification) Substitute
Di Pasquale AdrianoDocente / Esperto di contenuto FAD e-learningAltre professioniNot specifiedN/A
Mangone IolandaDocente / Esperto di contenuto FAD e-learningBiologoBiologoN/A
Rinaldi AntonioDocente / Esperto di contenuto FAD e-learningAltre professioniNot specifiedN/A
chiaverini alexandraDocente / Esperto di contenuto FAD e-learningVeterinarioIgiene, prod, trasf, commercializ conserv e trasporto alimenti di origine animale e derivatiN/A
Radomski NicolasDocente / Esperto di contenuto FAD e-learningAltre professioniNot specifiedN/A
DI MARCANTONIO LISADocente / Esperto di contenuto FAD e-learningBiologoBiologoN/A
Garofolo GiulianoDocente / Esperto di contenuto FAD e-learningVeterinarioSanità animaleN/A
Torresi MarinaDocente / Esperto di contenuto FAD e-learningBiologoBiologoN/A
KRASTEVA IVANKA MARINOVADocente / Esperto di contenuto FAD e-learningAltre professioniNot specifiedN/A
LUCIANI MIRELLADocente / Esperto di contenuto FAD e-learningBiologoBiologoN/A

Summary of the programme

Unit

Contents

Unit 2.1

Priming on Linux

Learning objectives

At the end of the unit, the student will know:

  • Linux computing environment and programminglanguages
    • how to use existing tools to solve common bioinformaticsproblems
    • how to reformat data with regularexpressions
  • how to use program like grep and cat to handle text files through Unix commandlines
    • how to carry out combining and automatinganalyses
    • how to install software on own pc and relativedependancies
      • how to work on remotecomputers
    • basic programming with UNIX andPython
    • how to manage adatabase

Topics

Index Intro

Introduction to Linux information system Introduction to Shell

Text files management Installing software

Working on remote computers Programming with Unix and Python

 

Database management system. Basic concepts In depth contents

Summary Test

Unit 2.2

WGS data

Learning objectives

At the end of the unit, the student will know:

  • several outputs and formats of the WGSdata
  • how to manipulate information anddata
  • how to download a sequence from publicdatabases

Topics

Index Intro

Data format Data storage

Access to public databases In depth contents Summary

Test

Unit 2.3

Data analysis

Learning objectives

At the end of the unit, the student will know principles and tools:

  • for quality assessment andtrimming
  • forassembly
  • for alignment or sequencesearching
  • formapping
  • for assemblyrefinement
  • for assembly statistics and qualityassessment
  • for species and subtypingidentification
  • forannotation
  • for virulence geneprediction
  • for antimicrobial resistancegenes
  • for variantcalling
  • for phylogeneticanalysis

 

  • for comparative genomictools
  • for 16S dataanalysis
  • for shotgun dataanalysis
  • for trascriptomics dataanalysis
  • for proteomics dataanalysis

Topics

Index Intro

WGS Data analysis Comparative analysis Metagenomics Data analysis Transcriptomics data analysis Proteomics data analysis

In depth contents Summary

Test

Unit 2.4

Visualization tools

Learning objectives

At the end of the unit, the student will be able to use several programs for visualisation of analysis outputs

Topics

Index Intro

Several programs for visualization of analysis outputs In depth contents

Summary Test

Detailed information

Language English
Simultaneous translation No
Learning materials Nessuno
Learning assessment procedures Questionario con quesiti a scelta quadrupla con singola risposta esatta
Total training length (hh:mm) 300:00
Minimum attendance 90%

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