TEORY
- Introduction
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OUTLINES OF JAVA PROGRAMMING LANGUAGE AND BIOJAVA
Main elements of the Java programming language. Object oriented programming. Polymorphism and inheritance. Overloading. Abstract classes and methods. Interfaces and abstract classes. Main classes, interfaces and data structures available in Java. 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).
- BioJava official website
- Netbeans
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MATLAB AND MATLAB BIOINFORMATICS TOOLBOX
Outlines of Matlab programming language main elements. Variables. Matrices and arrays. Operators. Cell arrays. Characters and text variables. Structures. Charts and graphics. Scripts and functions. Flow control and loops. Data analysis. Introduction to Bioinformatics toolbox: data formats and functions for connecting to bioinformatics databases; functions and tools for sequence analysis.
- Official website
- Matlab 7 - Getting started guide
- Matlab 7 – Data Analysis guide
- List of pdf guides
- Mathworks documentation
- Statistics Toolbox 7 – User’s Guide (pdf)
- Statistics toolbox guide (online)
- Matlab introductory tutorial
- Bioinformatics toolbox 3 - User's guide
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PYTHON E BIOPYTHON
The Python interpreter. Main elements of the Python programming language. Numbers, strings, lists, tuples, sequences, dictionaries. Loops, functions, scripts, modules, input/output. Classes. Errors and exceptions (hints). Main features of Biopython. Sequences and alphabets. Sequence objects: nucleotide frequencies, concatenation, complement, transcription, translation. MutableSeq, UnknownSeq and SeqRecord objects.
- Python official website
- Python tutorial
- Python documentation
- Biopython official website
- Biopython tutorial and cookbook
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OTHER APPLICATIONS FOR STATISTICAL DATA ANALYSIS
Brief introduction to some of the main software for statistical analysis: Excel/Calc, R, SAS JMP, SPSS. Main functionalities and application fields.
Resources:
Resources:
Exercises:
Resources:
- Java. Dai fondamenti alla programmazione avanzata. Karsten Samaschke. Apogeo. 2005.
- References reported as links in the syllabus above.