Universidade Nova de Lisboa

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Faculdade de Ciências e Tecnologia

Bioinformatics

Code

7626

Academic unit

Faculdade de Ciências e Tecnologia

Department

Departamento de Ciências da Vida

Credits

6.0

Teacher in charge

João Manuel Gonçalves Couceiro Feio de Almeida

Weekly hours

4

Total hours

59

Teaching language

Português

Objectives

The main goal is to present a panorama of the bioinformatics tool available today and their rational utilization.
The students will acquire knowledge and proficiency in several bioinformatic tools: sequence internal and comparative analysis; database search; and content visualisation.
All the tool presented are freely accessible through user interfaces in the World Wide Web.
Basic concepts from the fields of informatics (hardware, software, and networking) and bioinformatics (information, notation, annotation, alignment, similarity, public databases, search engines, electronic benches, and algorithms) are taught.
Student informatics skills are levelled before introducing more sophisticated topics. Most topics are to be object of hands-on lab sessions.

Prerequisites

The students must understand the basic concepts on molecular biology and have knowledge on the related techniques. Prior knowledge on biology and biochemistry are needed.

 

The students should have some acquaintance with PC-type computers running a Microsoft Windows environment.

 The students should have an intermediate command of English since most of the presented content is written in this language.

Subject matter

Basic concepts on informatics (hardware, software categories, networking and Internet, database structure and tools, licensing).
Biological sequences: production (sequencing techniques, notation, formats), internal analysis (statistics, repeats, dominion detection), comparative analysis (homology, similarity, substitution matrix, alignment).
Public databases: stored data (bibliographic citations, nucleotide and proteic sequences, annotation), level of data processing, structure (logical vs. physical) and entry ownership versus curation. Associated search systems (Entrez, SRS) and dataset exploration.
Electronic benches (Taverna).
Phylogenetic analysis tools and basic concepts.
Brief introduction to image acquisition, process and analysis.
Other topics: biological systems modelling and simulation, and evolutionary studies through artificial life.

Bibliography

 

Lesk A. Introduction to Bioinformatics (2nd Ed.).Oxford University Press, 2005, Oxford. (ISBN 0 19 927787 7)

Orengo C., Jones D., Thornton J. Bioinformatics: Genes, Proteins and Computers. Advanced Text. BIOS Scientific Publishers Limited, 2003, Oxford. (ISBN 1 85996 054 5)

Claverie J.-M., Notredame, C. Bioinformatics for Dummies. Advanced Text. For Dummies, 2003, ?. (ISBN 0 76451 696 5)

Bergeron B. Bioinformatics Computing. PTR, Prentice Hall, 2003, New Jersey. (ISBN 0 13 100825 0)

Lacroix Z., Critchlow T. Bioinformatics, Managing Scientific Data. Morgan Kaufmann Publishers, 2003, San Francisco. (ISBN 1 55860 829 X)

Web content available through selected hyperlinks.

Teaching method

The main concepts are presented in lectures. Presentation and source material are made available to the students through the WWW.Hands-on sessions where students follow a given protocol and are faced a final self-evaluation test.

Evaluation method

Assessment items:

  • Tests - 2 (40% to 70% of the final mark)
  • Final exam - 2 periods (40% to 100% of the final mark)
  • Questionnaires - 11 minimum (30% of the final mark)
  • Written assignment - optional (30% of the final mark)

 

Available assessment flows:

  •  First time students (opções) - [30%+70%; 30%+40%+30%]
    1. Questionnaires (10) - Tests (2) – Exam, 2nd period (if necessary) - Written assignment (optional)
    2. Questionnaires - Exam, 1st period – Exam, 2nd period (if necessary) - Written assignment (optional)
  • Other students - [100%]
    1. Exam, 1st period – Exam, 2nd period (if necessary)
    2. Tests (2) – Exam, 2nd period (if necessary)

Students trying to improve their final mark will never be considered as first time students, even if they are in their first enrollement in the course.

Students with more than two (2) enrollements in this course will be considered as first time students.

First time students will have to declare their intended assessment flow útil the first test.

The student assiduity will be managed according to the faculty rules.

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