Ateneo - UPO

Bioinformatics is the discipline that deals with the analysis and attribution of biological meaning to the mass of biomolecular data available to date and represents an indispensable tool in
basic and research biochemical, molecular-biological, biomedical and biotechnological activities.
The course will aim to provide useful tools for understanding the basics of programming, with particular attention and help of the PERL programming language. The bases provided will be
useful to address issues such as analysis and data visualization (in particular genomic strings), as well as hints to deepen, in the future, bioinformatics or computational biology topics.

1) Pascarella, Paiardini – "Bioinformatica: dalla sequenza alla struttura delle proteine", Ed. Zanichelli 2010
2) James Tisdall, Beginning Perl for Bioinformatics - An Introduction to Perl for Biologists. Ed. O'Reilly Media, February 2009
3) Documentazione PERL online
4) Video-lezioni YouTube + slides in PDF fornite dal docente durante il corso

The course aims to introduce the biology student to the use of the most common computational tools in use today in the bioinformatics analysis of protein and nucleic acid structures and to
the acquisition of notions on how they work.
In particular, the PERL programming language will be treated, applied to genomic and metagenomic problems such as DNA sequences, mRNA, pattern search, scores sorting, filtering and
processing of data from genomic and proteomic databases.

The elective course is placed in the second semester of the second year. To take it profitably, the student must possess:
1) Notions of Molecular Biology (concept of gene, genome, structure of nucleic acids, regulation of gene expression).
2) Basic knowledge of mathematics and statistics, trigonometric functions, probability theory (probability, probability distribution, statistical tests)
3) Basic knowledge of computer use and internet navigation.

The Computer Skills and Telematics course - CdL triennale in Biological Sciences, will be set in self-study mode. The course consists of 8 lessons, each of which includes slides (in PDF format) and a YouTube video lesson "embedded" in the DIR page.
For learning purposes, during the course will be proposed quizzes and exercises (to be carried out both in the classroom / laboratory and at home) with automatic correction and subsequent
explanation by the teacher.

The slides projected by the lecturer during the lecture are available in the DIR section.
The teacher will give detailed information regarding the time organization (days and hours) for any laboratory exercises. In the theoretical part of the course (classroom lectures or self-study),
the exercises and the proposed solutions will be commented, discussed and analyzed.
The teacher answers only to signed e-mails coming from the upo-university domain.
nome.cognome@uniupo.it

The exam aims to verify the level of ability acquired in selecting and using the tools illustrated during the course, focusing on the main functionalities of the PERL language for the solution of genomics exercises.
Final exam will be a quiz composed of 16 questions to be taken on computer with a maximum duration of 30 minutes. The answers are weighted: the only right answer will have a weight of
+1.0, while the obviously wrong answer will have a negative weight of -0.5.
The exam will be considered passed and the candidate eligible upon achieving a score >=8/16.

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,.)
5) Introduction to algorithms with main constructs and loops
6) PERL: Basic functions, scalar variables, logical and comparison operators, functions on genomic strings
7) Array, Hash and Suffix Tree data structures
8) Sorting algorithms and efficient search of genomic patterns
9) Parsing and manipulation of text files extracted from genomic/proteomic databases

1) Knowledge and Understanding: will know the mechanisms underlying the development of small PERL programs for solving biological problems.
2) Skills: he/she will be able to use computer tools to query and interact with genomic/proteomic databases, interpret results, and output new results using the PERL programming language.
In addition, the theoretical basis of molecular biology techniques will facilitate him/her in laboratory activities involving the use of such techniques. Moreover the practical activity will make
the student able to manage autonomously the main basic techniques used to search for DNA patterns and subsequences contained in files from genomic databases.
3) Learning ability: the student will acquire the ability to use the didactic material provided for a critical and reasoned study of the topics covered and also will be able to deepen and update independently, through reading of texts, documentation of PERL language and scientific articles related to all topics covered during the course.