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	Curriculum vitae

Alberto Castellini

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• Lesson timetable, educational objectives, exam methods.

TEORY

• Introduction

• 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.

  • Exercise 02/05/2011: A Java data structure for modeling biochemical processes.

• 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 AND 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.

  • Exercises 05/04/2011 and 12/04/2011
  • Solutions 5-04-2011 (NetBeans project)
  • BioinformaticsFinal

  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.

  • BioJavaLib
  • Exercise 10/05/2011
  • Exercise 17/05/2011
  • Solutions to Exercise 10/05/2011 and 17/05/2011(NetBeans prject)

• MATLAB BIOINFORMATICS TOOLBOX

  Usage of the main functions provided by the Matlab Bioinformatics toolbox for statistical analysis and alignment of biological sequences.

  • Exercise 24/05/2011
  • Exercise 31/05/2011

• Java. Dai fondamenti alla programmazione avanzata. Karsten Samaschke. Apogeo. 2005.
• References reported as links in the syllabus above

• Presentation topics