COMPUTER AND BIOINFORMATIC SKILLS
cod. 1004679

Academic year 2023/24
3° year of course - Second semester
Professor
- Giulia MORI
Academic discipline
Biochimica (BIO/10)
Field
Attività formative affini o integrative
Type of training activity
Related/supplementary
60 hours
of face-to-face activities
6 credits
hub: PARMA
course unit
in ITALIAN

Learning objectives

At the end of the training activity the student should have acquired basic theoretical and practical knowledge related to the management of files, use of software for word processing, spreadsheets, and presentations, interrogation of biological databases, and use of bioinformatics tools.
In particular, the student should have acquired:
D1. Knowledge and ability to understand. The course is mainly aimed at acquiring practical skills in the use of computers in the biological field. Basic theoretical concepts necessary for the understanding of computer and bioinformatics applications will be provided.
D2. Ability to apply knowledge. Through practical exercises under the guidance of the teacher, students will have the opportunity to acquire practical skills on the use of "individual productivity" programs and on the use of the most important bioinformatics programs.
D3. Autonomy of judgement. Evaluate and interpret experimental data; use scientific literature data critically. Evaluate computational and experimental methodologies that allow optimal resolution of a biological problem.
D4. Communicative skills. Through examples, students will be shown how to report the results of bioinformatics analyses in a document consisting of text and images, and how to organize the same results in a presentation.
D5. Learning ability. The course aims to help students to autonomously consult scientific literature and databases, and to become self-taught in the use of software. Critical discussion and interactive participation will be stimulated in order to acquire a study methodology that allows the continuation of university education, or the achievement of the skills required for placement in professional activities at the end of the three-year course.

Prerequisites

Basic knowledge of biochemistry and molecular biology. Basics of computer use.

Course unit content

The course consists of two parts. The first part will address basic concepts about the use of computer and file management, as well as practical notions on the use of operating systems with graphical interface. Exercises will be carried out on applications for word processing, spreadsheets, multimedia presentations. The second part will introduce the areas of bioinformatics and discuss the analysis of the sequences and structures of DNA and proteins. Students will be made familiar with the main databases of biological macromolecules and the most common techniques of bioinformatics analysis

Full programme

Computer Skills
Basic concepts: meaning and scope of computer science.
Computer usage and file management: practical notions of using operating systems with a graphical interface.
General-purpose applications: practical word processing concepts, spreadsheets use, multimedia presentation preparation.
Computer networks: practical uses of the World Wide Web.

Bioinformatics skills
Introduction to bioinformatics: meaning and areas of bioinformatics. Objects of bioinformatics: DNA and protein sequences, DNA and protein structures. Evolution of biological information over time.
Biological sequences databases: definition and purpose of the databases; major DNA (GenBank, DDBJ, EMBL) and protein (UniProt) databases. Questioning and consulting of the databases. Syntax of sequence FASTA format.
Comparison of sequences: meaning and purpose of sequence alignment; Pairs alignment. Local and global algorithms alignment. Calculation of the alignment score. Penalty for gap insertion and gap extension. Amino acid substitution matrices.
Search for homology: meaning of homology. Measurements of the significance of the alignment. Database homology research tools. Use of Blast program and interpretation of the homology search result.
Multiple sequence alignment and phylogeny: construction of multiple alignment using the ClustalX program. Observation and analysis of multiple alignment using the GeneDoc program.
Consensus, pattern, and profiles built from multiple alignments.
Phylogenetic reconstruction with the neighbor-joining algorithm implemented in ClustalX. Observation and analysis of phylogenetic trees with the FigTree program.
Prediction of the biochemical characteristics of proteins: chemical-physical properties, functional properties, structural properties. Prediction of chemical-physical properties using the ProtParam program. Prediction of protein cellular localization using PSort and SignalP programs. Protein structure prediction by homology modeling or de novo prediction with AlphaFold.

Bibliography

FONDAMENTI DI BIOINFORMATICA
Manuela Helmer Citterich, Fabrizio Ferrè, Giulio Graziano Pesole, Chiara Romualdi, Ed. Zanichelli

Teaching methods

The lessons of computer skills will be carried out mainly through practical exercises involving the use of computers by students. Students will learn the use of software for personal productivity: word processing, spreadsheets, and multimedia presentations. Part of the lectures on bioinformatics skills will focus on theoretical arguments through a discussion of the basic concepts of the subject. The lectures will be interposed with practical exercises directed to the use of the most common bioinformatics applications. During these lessons, students will be trained to search for biological information in the databases and to solve the most common problems of sequence analysis. During the practical exercises students will be able to follow step by step the use of the computer by the teacher and to replicate operations and controls on individual workstations.

Assessment methods and criteria

To check the general skills of the students, each student will present to the teacher a scientific report including text and figures, a spreadsheet table, and a short multimedia presentation.
Bioinformatics skills will be verified through an individual computer test that includes solving 5 biological problems through bioinformatics applications, plus 4 tests (1 hour). The understanding of the basic concepts of bioinformatics will be verified through a short oral interview, consisting in 3 to 8 theoretical and practical questions, in which will be evaluated: the understanding of the theoretical aspects, the understanding of the analyses carried out and the clarity in the exposure of the results and their interpretation. The final rank is up to thirty.

Other information

The course makes use of a classroom for the practical calculation equipped with 128 workstations connected to the Internet and equipped with general and bioinformatics programs discussed during the course. Only applications and programs in the public domain will be used during the course.