| Activity | Credits | Period | Academic staff | Timetable |
|---|---|---|---|---|
| Teoria | 4 | II semestre | Alberto Castellini | |
| Laboratorio | 2 | II semestre | Alberto Castellini |
The aim of this course is to provide languages and formalisms for dealing with some typical problems in bioinformatics, such as the analysis of biological data, the representation of biological systems by suitable models and the simulation of such systems. The analysis of some case studies and laboratory classes will enable to understand how languages presented during the course can be used in practice.
TEORY
OUTLINES OF JAVA PROGRAMMING LANGUAGE
Main elements of the Java programming language. Polymorphism and inheritance. Overloading. Abstract classes and methods. Interfaces. Main classes, interfaces and data structures available in Java. Exception management (hints). Input/output streams and files.
BIOJAVA
Main classes provided by the BioJava library for the implementation of bioapplications. (alphabets, symbols, symbol lists, sequences). Basic operations on sequences (transcription, complement, reverse, translation). Input/output of sequences from files in the main bioinformatic formats (Fasta, GenBank,…). Classes for the representation of sequence annotations. Classes for the statistical analysis of sequences (hints).
MATLAB BIOINFORMATICS TOOLBOX
Outlines of Matlab programming language main elements. Cell arrays. Characters and text variables. Structures. Matlab programming: scripts and functions. Introduction to Bioinformatics toolbox: data formats and functions for connecting to bioinformatics databases; functions and tools for sequence analysis.
PYTHON E BIOPYTHON
Main elements of the Python language and main features of Biopython (hints).
FORMALISMS AND MODELS FOR ANALYSIS AND REPRESENTATION OF BIOLOGICAL SYSTEMS
Biological network analysis. Outlines of genetic programming for the synthesis of metabolic pathways.
LABORATORY
JAVA
Development of a Java framework for the representation and transformation of DNA, RNA and amino acid sequences. Analysis of data structures for the representation of dynamical models of metabolic systems.
BIOJAVA
Usage of the main elements of BioJava library and implementation of codes employing BioJava interfaces and classes.
MATLAB BIOINFORMATICS TOOLBOX
Usage of the main functions provided by the Matlab Bioinformatics toolbox for statistical analysis and alignment of biological sequences.
The exam consists of a project and an oral test. The project concerns the study and the presentation of an advanced topic or the implementation of a technique explained during the course. The oral test concerns the topics presented during the course.
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