Ateneo - UPO

Bioinformatics is the discipline dedicated to analyzing and attributing biological significance to the vast amount of biomolecular data available to date. It is an essential tool in biochemical, molecular biological, biomedical, and biotechnological research and basic activities.

This course aims to provide useful tools for understanding the fundamentals of programming, with a particular focus on the use of the PERL programming language. The foundational knowledge provided will be beneficial for tackling topics such as data analysis and visualization (especially genomic strings), with further insights to explore bioinformatics or computational biology subjects in the future.

1) Pascarella, Paiardini - 'Bioinformatics: from sequence to protein structure', Ed. Zanichelli 2010
2) James Tisdall, Beginning Perl for Bioinformatics - An Introduction to Perl for Biologists. Ed. O'Reilly Media, February 2009
3) Online PERL documentation
4) YouTube video lectures + PDF slides provided by the lecturer during the course

The course aims to equip students with the knowledge and skills to understand and utilize the most common computational tools used today in bioinformatic analyses of protein and nucleic acid structures, while also providing insight into their functionalities.

Specifically, the course will cover the PERL programming language, applied to genomic and metagenomic problems such as DNA and mRNA sequences, pattern recognition, score sorting, and the filtering and processing of data from genomic and proteomic databases.

The course is scheduled for the second semester of the second year. To successfully follow and benefit from the course, students should possess:

1. Knowledge of Molecular Biology (concept of gene, genome, structure of nucleic acids, regulation of gene expression)
2. Basic understanding of mathematics and statistics, including trigonometric functions and probability theory (probability, probability distribution, statistical tests)
3. Proficiency in using computers and internet navigation

Students with physical disabilities, Learning Disabilities or Special Education Needs can request specific services and tools via the Staff Sviluppo e Coordinamento Carriere e Servizi alle Studentesse e agli Studenti, consulting the University webpage: https://www.uniupo.it/en/services/services-students-physical-or-learning-disabilities Students with disabilities, learning disabilities or special education needs, once they have contacted the University Staff, can refer to the tutor in charge of the course to define the examination modalities, concerning academic aspects.

The Computer and Telematic Skills course, part of the three-year degree program in Biological Sciences, will be conducted in a self-learning format. The course consists of 8 lessons, each including PDF slides and an embedded YouTube video lecture on the DIR page.

To facilitate learning, quizzes and exercises will be provided throughout the course. These activities, which can be completed both in the classroom/laboratory and at home, will feature automatic correction followed by explanations from the instructor.

The slides presented by the instructor during the lectures are available in the DIR section.

The instructor will provide detailed information regarding the schedule (days and times) for any laboratory exercises. In the theoretical part of the course (classroom lessons or self-study), exercises and proposed solutions will be reviewed, discussed, and analyzed.

The instructor will only respond to signed emails sent from the university domain: nome.cognome@uniupo.it

Students with physical disabilities, Learning Disabilities or Special Education Needs can request specific services and tools via the Staff Sviluppo e Coordinamento Carriere e Servizi alle Studentesse e agli Studenti, consulting the University webpage: https://www.uniupo.it/en/services/services-students-physical-or-learning-disabilities Students with disabilities, learning disabilities or special education needs, once they have contacted the University Staff, can refer to the tutor in charge of the course to define the examination modalities, concerning academic aspects.

The exam aims to assess the student's proficiency in selecting and using the tools covered during the course, with a particular focus on the main functionalities of the PERL language for solving genomic exercises.

The final exam will be a computer-based quiz consisting of 16 questions, with a maximum duration of 30 minutes. The answers are weighted: the correct answer will have a weight of +1.0, while an obviously incorrect answer will have a negative weight of -0.5.

The exam will be considered passed, and the candidate deemed qualified if they achieve a score of at least 8 out of 16.

1. Relationship between Biology and Computer Science
2. Introduction to Boolean Algebra
3. Introduction to Programming Languages
4. Overview (imperative, functional, object-oriented, declarative languages, etc.)
5. Introduction to Algorithms with Key Constructs and Loops
6. PERL: Basic Functions, Scalar Variables, Logical and Comparison Operators, Genomic String Functions
7. Data Structures: Arrays, Hashes, and Suffix Trees
8. Sorting Algorithms and Efficient Search of Genomic Patterns
9. Parsing and Manipulating Text Files Extracted from Genomic/Proteomic Databases

1. Knowledge and Understanding: The student will understand the mechanisms underlying the development of small PERL programs for solving biological problems.
2. Skills: The student will be able to use computational tools to query and interact with genomic/proteomic databases, interpret the results, and produce new outputs using the PERL programming language. Additionally, the theoretical foundation in molecular biology techniques will facilitate laboratory activities that involve these techniques. The practical experience will also enable the student to independently manage the main basic techniques for searching patterns and DNA subsequences within files from genomic databases.
3. Learning Ability: The student will develop the ability to use the provided educational material for a critical and reasoned study of the topics covered. Furthermore, the student will be able to independently deepen and update their knowledge through reading texts, PERL language documentation, and scientific articles related to the topics discussed during the course.