First cycle
degree courses
Second cycle
degree courses
Single cycle
degree courses
School of Agricultural Sciences and Veterinary Medicine
BIOTECHNOLOGIES FOR FOOD SCIENCE
Course unit
APPLIED BIOINFORMATICS
AVP5073517, A.A. 2017/18

Information concerning the students who enrolled in A.Y. 2017/18

Information on the course unit
Degree course Second cycle degree in
BIOTECHNOLOGIES FOR FOOD SCIENCE (Ord. 2017)
IF0362, Degree course structure A.Y. 2017/18, A.Y. 2017/18
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Degree course track BIOTECHNOLOGIES FOR FOOD SCIENCE [002LE]
Number of ECTS credits allocated 10.0
Type of assessment Mark
Course unit English denomination APPLIED BIOINFORMATICS
Website of the academic structure http://www.agrariamedicinaveterinaria.unipd.it/
Department of reference Department of Comparative Biomedicine and Food Science
Mandatory attendance No
Language of instruction English
Branch LEGNARO (PD)
Single Course unit The Course unit can be attended under the option Single Course unit attendance
Optional Course unit The Course unit can be chosen as Optional Course unit

Lecturers
Teacher in charge CRISTIAN TACCIOLI BIO/11
Other lecturers ENRICO MASSIMILIANO NEGRISOLO BIO/05
ENRICO MASSIMILIANO NEGRISOLO BIO/05

ECTS: details
Type Scientific-Disciplinary Sector Credits allocated
Educational activities in elective or integrative disciplines BIO/05 Zoology 4.0
Core courses BIO/11 Molecular Biology 6.0

Mode of delivery (when and how)
Period First semester
Year 1st Year
Teaching method frontal

Organisation of didactics
Type of hours Credits Hours of
teaching
Hours of
Individual study
Shifts
Practice 2.0 16 34.0 No turn
Laboratory 1.0 8 17.0 No turn
Lecture 7.0 56 119.0 No turn

Calendar
Start of activities 02/10/2017
End of activities 19/01/2018

Examination board
Board From To Members of the board
1 Commissione A.A. 2016/17 01/12/2016 30/11/2017 TACCIOLI CRISTIAN (Presidente)
NEGRISOLO ENRICO MASSIMILIANO (Membro Effettivo)

Syllabus
Prerequisites: The students need to know the main characteristics of DNA structure, amino acids, genes and genomes. A basic knowledge of personal computers is also required (Windows, Mac or Linux).
Target skills and knowledge: The students will acquire a broad knowledge on the bioinformatics tools currently available that are relevant for the Biotechnologist for food Science and the basics of Python programming.
Examination methods: There will be a written Bioinformatics examination at the end of the course.
Assessment criteria: The student will be evaluated on the basis of the knowledge and the ability to use/create the programs presented in class and to perform bioinformatic analyses.
Course unit contents: PRINCIPLES OF BIOINFORMATICS USING PYTHON

Basics of Python programming (for/while loop, if/else statements, lists, tuples, dictionaries, regular expressions, lambda functions, list comprehensions, open/read files, directories, classes and objects). How to use Numpy, Scipy, matplotlib and Biopython. Parsing data files. Introduction to Alignment algorithms, Clustering and PCA.


MOLECULAR EVOLUTION, PHYLOGENETICS AND PHYLOGENOMICS

Principles of molecular evolution, phylogenetics and phylogenomics. Multiple alignments: a phylogenetic context. Methods of phylogenetic reconstruction: the main computer packages. Types of selection acting at DNA and amino acid level: local and web bioinformatic tools. Prediction of RNA and protein structures and their usage in molecular evolution, phylogenetics and phylogenomics. Bioinformatics approaches to species identification included the analysis of gene orders.
Planned learning activities and teaching methods: The course includes lectures and practical of bioinformatics, for a total of 80 hours.
Additional notes about suggested reading: The material used for the course will be made available to students through the Moodle platform of the School at:
- https://elearning.unipd.it/scuolaamv/login/index.php

Furthermore, a manual of "Python programming language for Genomics" will be made available to the students registered to this course.
Textbooks (and optional supplementary readings)
  • Pevsner, Jonathan, Bioinformatics and functional genomics. Hoboken: NJ, Wiley-Blackwell, 2015. Cerca nel catalogo
  • Kinser, Jason, Python for Bioinformatics. Sudbury - Massachusetts: Jones and Bartlett, 2008. Cerca nel catalogo