Teaching code

4S009830

Credits

12

Coordinator

Rosalba Giugno

Language

English

Scientific Disciplinary Sector (SSD)

INF/01 - INFORMATICS

Courses Single

Authorized

Moodle Seminars 0

The teaching is organized as follows:

Learning objectives

Knowledge and understanding The course aims to provide students with the knowledge and understanding of the paradigms and advanced programming tools for the management of biomedical / bioinformatic data and information. Applying knowledge and understanding The student will therefore be able to a) apply the paradigms and advanced programming tools for the analysis of genomic, transcriptomics and proteomics data; b) apply the code performance analysis and identify critical issues and their optimization. Making judgements Ability to independently propose effective and efficient solutions for the biomedical and bioinformatics application domain; ability to identify critical issues for the treatment of complex bioinformatics problems. Communication The student will also be able to interact with various interlocutors in a multidisciplinary biomedical and bioinformatics context, to interact with colleagues in the performance of group work, and to interact with the interlocutors in the working or research environment. Lifelong learning skills Ability to understand scientific literature in the process of interpreting the results or proposed solution, and to carry out individual and group in-depth studies aimed at tackling problems from the research and business world.

Prerequisites and basic notions

Basic notion of programming

Program

R Programming
Basic constructs: variables, operators, control structures (if, for, while).
Input/Output (I/O): reading and writing files (CSV, Excel), interaction with the environment.
Functions: definition, arguments, return values, anonymous functions.
Data structures: vectors, lists, matrices, data frames, factors.
Python Programming
Basic constructs: variables, data types, operators, control structures (if, for, while).
Input/Output (I/O): reading and writing files (txt, CSV), handling keyboard input.
Functions: definition, parameters, return values, lambda functions.
Data structures: lists, tuples, dictionaries, sets.
Programming with Bioconductor
Bioconductor fundamentals: installation and package management.
Main data structures: SummarizedExperiment, GRanges, SingleCellExperiment.
Omics data analysis: import, normalization, and manipulation of genomic and transcriptomic data.
RNA-Seq Data Analysis
Introduction:
NGS technologies and experimental design principles
Overview of R, Python, and web-based tools
Data preprocessing:
From FASTQ to BAM
Reference genome indexing
Read mapping to the genome
Alignment sorting and indexing
Mapping quality control
Advanced analysis:
Variant discovery and call set refinement
Differential gene expression analysis
Using DESeq2 for RNA-Seq data
Practical applications:
Exercises on coding and non-coding RNA
Integrated workflows in R and Python

Didactic methods

Students will attend lectures and exercises, the content of which will be provided via notebooks. Students will install and use software related to the chosen topics and analyze real-world cases.

Learning assessment procedures

he exam consists of a written part (A) and the development of a project (B). (A) consists in developing during the test day exercises and theoretical questions on the course program. (B) is the development of a project agreed upon with the teacher to be developed i class and/or at home (this depends on project's typology) (the project is valid throughout the academic year).

Evaluation criteria

Voting for parts A and B is expressed in thirty.

Criteria for the composition of the final grade

The final vote is calculated as min (31, ((A + B) / 2) + C).
C is expressed in the interval [-4, + 4] and reflects the maturation and scientific autonomy acquired during the development of the tests and the project, in the exposure and in the interpretation of the scientific literature and the scientific context of the project.

Exam language

English