66557 - BIOMEDICAL DATA BASES

Learning outcomes

The student will be trained on the major biologically and medically oriented public data bases. Major tools accessible from specific data bases will be also utilized in order to facilitate information retrieval and data analysis. At the end of the course, the student acquires expertise in retrieving and extracting information for problem solving.

Course contents

Introduction to the NCBI Entrez system.
General overview and usage of the NCBI databases: Genbank, Refseq, dbSNP, dbEST, UniGene, Genomes, PubMed/MeSH, OMIM, MMDB, CCD.
Alignment algorithms, general features of FASTA and BLAST, usage of the BLAST algorithms at NCBI.
Usage of molecular visualization software: RasTop and DeepView. Sequence versus structural alignment.
Homology modeling using both the DeepView software and the Swiss Modeller server.
General overview and usage of the molecular structure database PDB at RCSB
Introduction to the Gene Ontology database.
General overview and usage of the EnsEMBL Genome database.

Readings/Bibliography

"Introduction to Bioinformatics", Arthur Lesk, Oxford University Press.
Online materials and other suggested readings will be indicated during the course.

Teaching methods

Both lectures and practical activities in the informatics laboratory.

Assessment methods

The exam at the end of the course aims at assessing the achievement of the main learning objectives of the course:

• Knowledge of the main public biomedical databases and of their content.
  
• Knowledge of the main information retrieval systems available on the web.
• Ability to use several types of software for information retrieval from databases and information processing.

The written test will comprise 6-8 separate problems of information retrieval and
information processing, to be solved in class within 3 hours.
The final score will be based on the average of the marks obtained by the students
in the separate problems and on their oral discussion.

Teaching tools

Video projector, PC with internet connection, informatics laboratory.
Slides of all the lectures will be available as PowerPoint files.

Office hours

See the website of Maria Paola Turina