BIOINFORMATICS
| Title | ΒΙΟΠΛΗΡΟΦΟΡΙΚΗ / BIOINFORMATICS |
| Code | ΜΝΝ301 |
| Faculty | Sciences |
| School | Physics |
| Cycle / Level | 2nd / Postgraduate |
| Teaching Period | Winter |
| Common | No |
| Status | Active |
| Course ID | 40000168 |
| Academic Year | 2020 – 2021 |
| Class Period | Winter |
| Faculty Instructors | |
| Weekly Hours | 3 |
| Class ID | 600178963
|
Course Type 2016-2020
- Scientific Area
Course Type 2011-2015
Specific Foundation / Core
Mode of Delivery
- Face to face
Digital Course Content
- e-Study Guide https://qa.auth.gr/en/class/1/600178963
- At the Website of the School: http://nn.physics.auth.gr/index.php?option=com_content&view=category&layout=blog&id=43&Itemid=88&lang=el
Language of Instruction
- Greek (Instruction, Examination)
- English (Instruction, Examination)
Prerequisites
Required Courses
- ΜΝΝ103 MOLECULAR BIOLOGY AND GENETIC ENGINEERING
Learning Outcomes
Familiarization with the basic biological databases, their type of information/data, and the search strategies and data retrieval. Basic organization of the transcriptional unit. Study and use of online analysis programs and standalone software for the analysis of DNA and protein sequences, the determination of transcriptional unit, restriction enzyme analysis, primer design for the polymerase chain reaction, the analysis of genomes, secondary structure prediction etc. Familiarization with methods for pairwise and multiple sequence alignment (BLAST, Clustalw). Methods and strategies for phylogeny reconstruction.
General Competences
- Apply knowledge in practice
- Retrieve, analyse and synthesise data and information, with the use of necessary technologies
- Work autonomously
- Work in teams
- Work in an international context
- Work in an interdisciplinary team
- Generate new research ideas
- Be critical and self-critical
- Advance free, creative and causative thinking
Course Content (Syllabus)
Protein and nucleic acids sequences. Sequence alignment and homology. Internet–Databases-Software. Structure prediction. Genetic algorithms. Transcriptional unit. Primer design. Familiarization with DNA and protein databases. Structure-function prediction. Phylogenetic trees. Virtual lab.
Keywords
Bioinformatics, computational biology, sequence databases, alignment, phylogeny
Educational Material Types
- Slide presentations
- Interactive excersises
Use of Information and Communication Technologies
Use of ICT
- Use of ICT in Course Teaching
- Use of ICT in Laboratory Teaching
- Use of ICT in Communication with Students
Description
Power point presentations, use of computer room and electronic communication with the students.
Course Organization
| Activities | Workload | ECTS | Individual | Teamwork | Erasmus |
|---|---|---|---|---|---|
| Lectures | 30 | 1 | ✓ | ||
| Laboratory Work | 20 | 0.7 | ✓ | ||
| Interactive Teaching in Information Center | 10 | 0.3 | ✓ | ||
| Written assigments | 15 | 0.5 | ✓ | ||
| Total | 75 | 2.5 |
Student Assessment
Description
Group assignments and presentations.
Student Assessment methods
- Written Assignment (Summative)
- Oral Exams (Summative)
- Performance / Staging (Formative)
Bibliography
Course Bibliography (Eudoxus)
Baxevanis A.D. & Ouellette F. (Ελληνική έκδοση). 2004. Βιοπληροφορική. Επιστημονικές Εκδόσεις Παρισιάνου Α.Ε. Αθήνα (Επιμέλεια ελληνικής έκδοσης: Ευάγγελος Ν. Μουδριανάκης, Σταύρος Ι. Χαμόδρακας).
Additional bibliography for study
β1. Ηλεκτρονικό υλικό στο Blackboard
β2. Χρήσιμες ιστοσελίδες
- National Center for Biotechnology Information (NCBI)
http://www.ncbi.nlm.nih.gov/
- European Bioinformatics Institute (EBI)
http://www.ebi.ac.uk/
- Ensembl Genome Browser
http://www.ensembl.org/index.html
- PubMed
http://www.ncbi.nlm.nih.gov/pubmed
- Bionformatics (Oxford Journals)
http://bioinformatics.oxfordjournals.org/
- Nucleic Acids Research (Oxford Journals)
http://nar.oxfordjournals.org/
- Sequence Retrieval System (SRS)
http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+srsq2+-noSession
- Codon Usage Database
http://www.kazusa.or.jp/codon/
- The Restriction Enzyme Database (REBASE)
http://rebase.neb.com/rebase/rebase.html
- Genomatix Software Suite
http://www.genomatix.de/cgi-bin/tools/tools.pl
- Bioweb (Institut Pasteur)
http://bioweb2.pasteur.fr/
- The GENSCAN Web Server at MIT
http://genes.mit.edu/GENSCAN.html
- Softberry
http://linux1.softberry.com/berry.phtml
- Phylogeny Programs
http://evolution.genetics.washington.edu/phylip/software.html
Last Update
30-07-2013
