Database systems for bioinformatics (2014/2015)

Course code
Carlo Combi
Other available courses
Other available courses
    Academic sector
    Language of instruction
    Teaching is organised as follows:
    Activity Credits Period Academic staff Timetable
    Teoria 6 I sem. Carlo Combi
    Tecnologie per le basi di dati 3 II sem. Carlo Combi
    Laboratorio 3 II sem. Pietro Sala

    Lesson timetable

    I sem.
    Activity Day Time Type Place Note
    Teoria Monday 11:30 AM - 1:30 PM lesson Lecture Hall A  
    Teoria Tuesday 11:30 AM - 1:30 PM lesson Lecture Hall D  
    II sem.
    Activity Day Time Type Place Note
    Tecnologie per le basi di dati Monday 11:30 AM - 1:30 PM lesson Lecture Hall B  
    Tecnologie per le basi di dati Tuesday 10:30 AM - 12:30 PM lesson Lecture Hall B  
    Laboratorio Wednesday 1:30 PM - 4:30 PM laboratorio Laboratory Delta  

    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 project on a web system dealing with bioinformatics data is assigned 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 R. Elmasri, S.H. Navathe Sistemi di Basi di Dati: Fondamenti (Edizione 6) Pearson 2011 978-88-7192-628-5