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 course Computer and Telematic Skills – Bachelor’s Degree in Biological Sciences – will be delivered in self-learning mode: students play an active and central role in their own educational path. The teaching materials are provided in a structured format, but it is the students themselves who manage the timing, methods, and pace of study, thereby developing autonomy and organizational skills. The instructor acts as a guide and support, providing explanations and clarifications when necessary, but without replacing the student’s personal work. The course is made up of 8 lessons, each of which includes slides (in PDF format) and a YouTube video lecture embedded in the DIR platform. For learning purposes, quizzes and exercises will be proposed throughout the course (to be carried out both in the classroom/lab and at home), with automatic correction followed by explanations provided by 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 level of skills acquired in selecting and using the tools presented during the course, with a focus on the main functionalities of the Perl language for solving genomics exercises. The final exam will consist of a computer-based quiz with 16 questions to be completed within a maximum of 30 minutes. The answers are weighted: the correct answer will be scored +1.0, while an obviously incorrect answer will receive a penalty of –0.5. The exam will be considered passed if the student achieves a score of >= 8/16. Learning Outcomes: 1) Knowledge and Understanding – Ability to describe the basic principles for developing small Perl programs applied to biological problems. 2) Skills – Ability to use computational tools to query genomic/proteomic databases, interpret the results, and generate new outputs; ability to apply practical techniques to search for patterns and DNA subsequences. 3) Learning Ability – Ability to study the topics critically and independently, expanding knowledge through textbooks, Perl documentation, and scientific articles.

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. This training program aims to illustrate how computer science intertwines with biology, providing essential tools for the analysis and interpretation of biological data. It begins with the fundamentals of Boolean algebra, which form the logical basis of circuits and algorithms, and moves on to a general introduction to programming languages, highlighting their common principles. An overview of the main paradigms—imperative, functional, object-oriented, and declarative—is presented to understand different approaches and their applications. The course then addresses the fundamental concepts of algorithms through constructs, conditions, and loops, with practical examples. Special attention is given to the Perl language, introducing basic functions, variables, operators, and tools for genomic string manipulation. The program then explores data structures such as arrays, hashes, and suffix trees, analyzing their efficiency in storing and accessing information. The discussion continues with sorting algorithms and techniques for fast searching of genomic patterns within large biological datasets. Finally, methods for parsing and manipulating text files from genomic and proteomic databases are examined, with the goal of learning how to extract, reorganize, and make data usable in the field of bioinformatics.

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.