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Estudia a la UdG

Dades generals

Curs acadèmic:
2020
Descripció:
Eines bioinformàtiques via web. Accés a bases de dades biològics. Filogènia molecular. Identificació de gens.
Crèdits ECTS:
3

Grups

Grup BT

Durada:
Semestral, 2n semestre
Professorat:
LUIS BLANCAFORT SAN JOSE  / FERRAN FEIXAS GERONES  / JUDITH OLLE VILANOVA  / NURIA PEREZ BIELSA  / PEDRO SALVADOR SEDANO
Idioma de les classes:
Anglès (100%)

Competències

  • Capacitat per analitzar críticament a partir de la recollida d'informació i la interpretació de dades , situacions complexes i dissenyar estratègies creatives i innovadores per resoldre-les.
  • Saber comunicar-se oralment i per escrit en l'àmbit científic i professional , utilitzant les llengües pròpies i l'anglès.
  • Treballar en equip contribuint a l'elaboració de projectes específics i multidisciplinaris.
  • Planificar i avaluar la pròpia activitat i el propi aprenentatge i elaborar estratègies per millorar-los aplicant criteris de qualitat.
  • Capacitat per actuar, generar propostes i prendre decisions en la investigació i en l'activitat professional amb criteris ètics i de sostenibilitat.
  • Utilitzar i aplicar de forma segura la instrumentació i les metodologies experimentals pròpies de la disciplina.
  • Utilitzar programes informàtics específics per al tractament complex de dades.
  • Identificar i entendre , a nivell estructural i funcional , les bases moleculars de les estructures i els processos biològics , les seves aplicacions i els mecanismes de regulació.
  • Identificar i interpretar la informació continguda en bases de dades sobre molècules amb activitat biològica i aplicar les eines bioinformàtiques bàsiques.

Continguts

1. Introduction. Definition and work setting. Bioinformatics resource portals (EBI-EMBL, NCBI, Expasy).

2. Databases and sequence formats in bioinformatics. Introduction to SRS (Sequence Retrieval System). Retrieving basic data from online databases. Bibliographic information. Genic information.

3. Sequence search and analysis. Similar sequences (homologous and non-homologous). Most common sequence formats (FASTA).

4. Gene annotation. Advanced DNA sequence search in databases. Gene mapping and transcript identification

5. Multiple alignment and phylogenetic trees reconstruction. Multiple Sequence Alignment by ClustalW. Phylogenetic tree methods: (a) maximum parsimony; (b) neighbor-joining; (c) maximum likelihood. Bootstrap confidence levels. Primer design.

6. Advanced gene annotation. Genome browsing: Genome Data Viewer. Gene Ontology.

7. Protein structure and function. Protein-ligand interaction. Molecular modeling with Chimera.

8. Docking and Molecular Dynamics techniques (DOCK6 and GROMACS).

Activitats

Tipus d’activitat Hores amb professor Hores sense professor Hores virtuals amb professor Total
Anàlisi / estudi de casos 0 2,00 0 2,00
Prova d'avaluació 0 39,00 0 39,00
Sessió participativa 24,00 0 0 24,00
Sessió pràctica 0 10,00 0 10,00
Total 24,00 51,00 0 75

Bibliografia

  • Attwood, Teresa K (2002). Introducción a la bioinformática. Madrid [etc.]: Prentice Hall. Catàleg
  • Ramsden, Jeremy (2015). Bioinformatics : (3rd. ed.). London: Springer. Catàleg
  • Higgs, Paul G (2005). Bioinformatics and molecular evolution. Oxford: Blackwell. Catàleg
  • Dear, Paul H (2007). Bioinformatics. Bloxham: Scion. Catàleg
  • Mount, David W (2004). Bioinformatics : (2nd ed.). New York: Cold Spring Harbor Laboratory Press. Catàleg
  • Bueno Torrens, David (2015). 100 gens que ens fan humans :. Valls: Cossetània. Catàleg

Avaluació i qualificació

Activitats d'avaluació:

Descripció de l'activitat Avaluació de l'activitat % Recuperable
Continuous assessment Continuous assessment activities ? The course comprises a series of short tasks including information searching, problem solving and presenting, and computer simulation. 50
Project Presentation of a final project. Its assessment will depend on scientific rigor, quality of the results and their discussion. 50

Qualificació

The 50% of the grade will be achieved by presenting a final project, which will consist of a scientific report developed by a team of two students. During the first weeks of the course, a gene and a protein will be randomly assigned to each pair of students. Both parts (gene and protein) require a minimum grade of 4,6 points in order to contribute to the total grade of the final project, which must be of at least 5 points. Students who fail one or both parts will be able to retake them, and in that case, the maximum grade for the part will be 6 points.

Continuous assessment activities will consist of a total of 7 tasks distributed throughout the course, and they will equal and represent the remaining 50% of the grade. The average grade must be of at least 5 points. Those students with an average under 5 will be able to retake the failed activities by presenting a specific task along with the final project. This conditions will only apply to those students with an average of continuous assessment activities under 5 points. Therefore, it is not possible to retake a single task if the average grade is 5 or more points.

In order to pass the course both parts (project and continuous assesment) must have a minimum punctuation of 5.

Criteris específics de la nota «No Presentat»:
No delivery of the final Project.

Avaluació única:
Under particular circumstances authorized by Science Department of UdG, students will be able to request to invoke a unique examination. That assessment will require the student to develop individually the final project, which will contain additional parts in order to cover the topics evaluated in the continuous assessment activities.

Requisits mínims per aprovar:
The minimum score required to pass is an average final grade of 5 points.

The minimum score required to pass the continuous assessment activities is a minimum average score of five points.

The minimum score required to pass the final project is a minimum average score of five points, and a minimum of 4,6 points must be obtained for each part.

Attendance is mandatory.

Tutoria

The students will be able to set up private tutorials by email request.

Comunicacio i interacció amb l'estudiantat

For each topic there will be forums available.

Observacions

Totally practical course. This course is de training part of Fonaments de Bioinformàtica.

Assignatures recomanades

  • Fonaments de bioinformàtica

Modificació del disseny

Modificació de les activitats:
Blended learning course scenario.
Half of the activities will be offered on-site in the informatics classroom and the remaining will be performed online with the support materials provided by the teachers.

Lockdown scenario.
All the activities and tasks will be performed online, and the teaching support materials will be adapted to this new scenario.

Handling of vulnerable students or students under temporal quarantine.
We will provide these students with the same teaching supporting materials adapted to the lockdown scenario and/or live streaming of the lectures.

Modificació de l'avaluació:
The assessment criteria will remain the same in all scenarios. The 50% of the final grade will depend on the final project and the other 50%, on the average grade of the 7 continuous assessment tasks.

Tutoria i comunicació:
If needed, private tutorials will be conducted online via Google Meet or Microsoft Teams