Database systems for bioinformatics (2015/2016)

Course code
Carlo Combi
Academic sector
Language of instruction
Teaching is organised as follows:
Activity Credits Period Academic staff Timetable
Teoria 6 I semestre Alberto Belussi
Tecnologie per le basi di dati 3 II semestre Carlo Combi
Laboratorio 3 II semestre Roberto Posenato

Lesson timetable

Learning outcomes

This course provides the student with the required knowledge for the design and implementation of databases and related applications.
In particular, attention will be paid on methodologies for conceptual and logical database design, on the implementation of databases through widely known (relational) database management systems. Both theoretical and "practical" query languages will be introduced, as relational algebra and SQL.
After an introduction of the basic concepts of computer networks, the course will deal with methodologies and technologies for the design and implementation of data-centric web sites, with an emphasis on the storage and query of bioinformatics data.


* Introduction of data base management systems. Architecture and functionalities of a database system.
* Data models for database systems. The relational data model.
* Interacting with a database: languages for the definition, manipulation, and query of a database. Relational algebra. The SQL language.
* Database design. The methodology. The Entity-Relationship (ER) data model. Logical database design: the logical schema of a database. Translating conceptual schemata in relational schemata.
* The internal architecture of a database management system: the relevance of transactional systems. The ACID transaction properties. Physical data organisation: sequential data structures and indexes (B-trees and hashing).
* Data centric web applications and bioinformatics. Basic concepts of computer networks. Semistructured data models; XML for bioinformatics. Interaction of web servers and data base management systems. Design methodologies for data-centric web applications. The MVC model. Design of data-centric web-based bioinformatics applications.

Assessment methods and criteria

The exam consists of a written examination with exercises on the different topics of the course (theory) lasting about 2 and a half hours. A lab examination about a web system dealing with bioinformatics data will be proposed for the lab part of the course.

Reference books
Activity Author Title Publisher Year ISBN Note
Teoria P. Atzeni, S. Ceri, P. Fraternali, S. Paraboschi, R. Torlone Basi di dati (Edizione 4) McGraw-Hill 2014 978-88-386-6587-5
Teoria E. Baralis, A. Belussi, G. Psaila Basi di dati - Temi d'esame svolti (Edizione 1) Progetto Leonardo Società Editrice Esculapio Bologna 1999 B135655713
Teoria R. Elmasri, S.H. Navathe Sistemi di Basi di Dati: Fondamenti (Edizione 6) Pearson 2011 978-88-7192-628-5
Tecnologie per le basi di dati P. Atzeni, S. Ceri, P. Fraternali, S. Paraboschi, R. Torlone Basi di dati (Edizione 4) McGraw-Hill 2014 978-88-386-6587-5