Bioinformatics in Biomedicine
Code
10776
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
3
Total hours
52
Teaching language
Português
Objectives
To be acquainted with the main trends, and concepts in bioinformatics.
To have a good understanding of the strengths, and limitations of the current bioinformatics tools.
To be able to conjugate several disparate tools/resources into useful protocols.
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.
Some prior knowledge/experience on/with bioinformatics will enhance the student experience.
The students should have an intermediate command of English since most of the presented content is written in this language.
Subject matter
Bioinformatics as a toolbox to address the need for data integration in biomedical research.
Computers, and software as the tools derive information from biological sequences.
Archival of sequence data: notation, format, databases).
Review of the main algorithms to extract information from an isolated sequence.
Review of alignment procedure as a means to derive similarity, and homology information.
The relevance of phylogenetic analysis.
Domain signature notation, and inference about structure/function for amino acid sequences. Ancillary tools, and techniques.
Algorithms for fast sequence matching, and sequence database querying.
Advanced use of the main public databases for biological research (PubMed, INSDC, UniProt).
Integrated data exploitation systems role in retrieving specific datasets (Entrez, SRS, etc).
Bibliography
Pevsner, Jonathan. Bioinformatics and Functional Genomics. 2nd ed. Wiley-Blackwell, 2009.
Lesk A. Introduction to Bioinformatics (2nd Ed.).Oxford University Press, 2005, Oxford.
Orengo C., Jones D., Thornton J. Bioinformatics: Genes, Proteins and Computers. Advanced Text. BIOS Scientific Publishers Limited, 2003, Oxford.
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 supplied protocol. Students are encouraged to practice them back at home given the free availability of both protocols, and associated resources .
Self-tests, and interactive quizzes are supplied through Moodle@FCT.
Lectures may be taught in English provided attendance by foreign students.
Evaluation method
Assessment Items
- Weekly mini tests (group submission) - >=11 pcs
- 30%
- Student groups can exchange two (2) of these tests for a small written Project.
- Individual Test - 1 pcs
- 30 %
- Other aspects
- Spoken participation – 5 %
- Self-assessment check – 5 %
- Balancing personal vs. group performance – 30%
- avg(individualTest,avg(miniTest))-(avg(miniTest)-individualTest)
- Final Exam – 95 % (+ 5 %, self-assessment check)
Eligibility for Assessment
- In accordance with the current rules for the F.C.T.