ID:
501554
Duration (hours):
48
CFU:
6
SSD:
BIOINGEGNERIA ELETTRONICA E INFORMATICA
Year:
2025
Overview
Date/time interval
Primo Semestre (29/09/2025 - 16/01/2026)
Syllabus
Course Objectives
At the end of the course, the student will be able to:
- identify the most appropriate sequencing method, to answer a biological or genetic question;
- use the most appropriate programming environment (Python, R, or a combination of both) to process files and information, and design data analysis;
- apply the suitable bioinformatics tools and online databases to analyse data generated with different methods;
- evaluate and compare the results of the analysis, in order to answer the initial question or take further experimental decisions;
- solve a biological question and communicate bioinformatics results in an integrated and coherent way, using reproducible research methods.
- identify the most appropriate sequencing method, to answer a biological or genetic question;
- use the most appropriate programming environment (Python, R, or a combination of both) to process files and information, and design data analysis;
- apply the suitable bioinformatics tools and online databases to analyse data generated with different methods;
- evaluate and compare the results of the analysis, in order to answer the initial question or take further experimental decisions;
- solve a biological question and communicate bioinformatics results in an integrated and coherent way, using reproducible research methods.
Course Prerequisites
The student will need basic-level knowledge of computers: how to copy files, install basic software, how to use a browser.
The student will be assumed to have basic knowledge of molecular biology and genetics (structure and function of a gene, transcripts, DNA, RNA, transcription and translation processes). Knowledge of biochemistry and cellular biology are not essential but recommended.
Basic knowledge of biostatistics will be useful.
The student will be assumed to have basic knowledge of molecular biology and genetics (structure and function of a gene, transcripts, DNA, RNA, transcription and translation processes). Knowledge of biochemistry and cellular biology are not essential but recommended.
Basic knowledge of biostatistics will be useful.
Teaching Methods
The course will significantly use “blended learning” tools, which assume that one-way information transfer is limited during classes activity. Students will be instead expected to use the Kiro platform for readings and self-evaluation activities.
Class activity will be focused to demonstrations, discussions and problem solving through interaction: demo, group work, quiz and real-time feedback.
Containers (docker), virtual machines and code editors will be used in classes, to improve learning python, R and the other command-line tools used in the course.
The most appropriate inclusive educational methods will be implemented, to meet the needs of specific categories of students defined by the University.
Class activity will be focused to demonstrations, discussions and problem solving through interaction: demo, group work, quiz and real-time feedback.
Containers (docker), virtual machines and code editors will be used in classes, to improve learning python, R and the other command-line tools used in the course.
The most appropriate inclusive educational methods will be implemented, to meet the needs of specific categories of students defined by the University.
Assessment Methods
The student will be assigned a simplified dataset to analyse using the methodologies learned during the course.
Subsequently, the student will be asked to complete a multiple-choice questionnaire on the analysis results and the course content, verifying both analytical skills and the understanding of theoretical foundations.
Subsequently, the student will be asked to complete a multiple-choice questionnaire on the analysis results and the course content, verifying both analytical skills and the understanding of theoretical foundations.
Texts
The course will mostly use freely available material, video and tutorials.
The use of a textbook will be entirely optional, and we suggest the following:
Bioinformatics with Python Cookbook
Tiago Antao
Packt Publishing 2018
R Bioinformatics Cookbook
Dan MacLean
Packt Publishing, 2019
Genomics in the Cloud
Geraldine Van der Auwera & Brian O'Connor
O'Reilly
These textbooks will be made available by the Sciences Library in an e-book version.
The teacher will provide supporting materials and tutorials throughout the classes.
The use of a textbook will be entirely optional, and we suggest the following:
Bioinformatics with Python Cookbook
Tiago Antao
Packt Publishing 2018
R Bioinformatics Cookbook
Dan MacLean
Packt Publishing, 2019
Genomics in the Cloud
Geraldine Van der Auwera & Brian O'Connor
O'Reilly
These textbooks will be made available by the Sciences Library in an e-book version.
The teacher will provide supporting materials and tutorials throughout the classes.
Contents
The course will cover the most common analysis methods, to deal with key applications of next generation sequencing technology.
In particular, students will cover the bases of the following programming environments:
- shell / bas
- python
- R and RStudio GUI
Then, the course will cover the following activities, using the most appropriate computing and programming environments:
- data retrieval from biological databases
- data manipulation and format conversion
- targeted sequencing analyses (germline and somatic)
- analysis of RNAseq data
- bases of data visualization
In particular, students will cover the bases of the following programming environments:
- shell / bas
- python
- R and RStudio GUI
Then, the course will cover the following activities, using the most appropriate computing and programming environments:
- data retrieval from biological databases
- data manipulation and format conversion
- targeted sequencing analyses (germline and somatic)
- analysis of RNAseq data
- bases of data visualization
Course Language
Italian
More information
The teacher will be available via email and for meetings to be agreed on, as well as through collaborative tools: a dedicated channel will be setup on Slack, for interacting with students and discussing different topics.
Degrees
Degrees
EXPERIMENTAL AND APPLIED BIOLOGY
Master’s Degree
2 years
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People
People
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