BIOINFORMATICS
| Title | ΒΙΟΠΛΗΡΟΦΟΡΙΚΗ / BIOINFORMATICS |
| Code | GM.MGB.6.7 |
| Faculty | Sciences |
| School | Biology |
| Cycle / Level | 1st / Undergraduate |
| Teaching Period | Spring |
| Coordinator | Ilias Kappas |
| Common | No |
| Status | Active |
| Course ID | 40001171 |
Programme of Study: PPS Tmīma Viologías (2017-sīmera)
Registered students: 112
| Orientation | Attendance Type | Semester | Year | ECTS |
|---|---|---|---|---|
| Moriakī Viología, Genetikī kai Viotechnología | Elective Courses | 6 | 3 | 6 |
| Perivallontikī Viología | Elective Courses | 6 | 3 | 6 |
| Genikī | Elective Courses | 6 | 3 | 6 |
| Academic Year | 2021 – 2022 |
| Class Period | Spring |
| Faculty Instructors | |
| Weekly Hours | 3 |
| Class ID | 600193271
|
Course Type 2016-2020
- Scientific Area
- Skills Development
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/1/600193271
- At the Website of the School: http://www.bio.auth.gr/course/viopliroforiki
- eLearning (Moodle):
Erasmus
The course is also offered to exchange programme students.
Language of Instruction
- Greek (Instruction, Examination)
- English (Instruction, Examination)
Prerequisites
General Prerequisites
Molecular Biology, Genetics, Evolution and Population Genetics.
Learning Outcomes
Familiarization with the application of informatics on the organization and understanding of biological information. Training on the use and analysis of molecular data for biological inference. Acquisition of technical skills on the use of several biological databases available in the internet. Familiarization with tools for retrieval, comparison and analysis of biological data. Training on the use of various software and online servers for homology establishment, genetic analysis, genome analysis, determination of 3D macromolecular structure, phylogenetic analysis of DNA and amino-acid sequences. Theoretical background on evolutionary models and training on the basic steps and applications of phylogenetic analysis.
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
Course Content (Syllabus)
Lectures: Definition, design and structure of biological databases. Search strategies. Analysis and evaluation of search results. DNA and amino-acid sequence analysis. Protein structure prediction. Analysis of motifs. Primer design. Sequence alignment and establishment of homology. Models of molecular evolution. Construction and evaluation of phylogenetic trees. Future bioinformatics and developments in computational biology.
Practicals: Use of biological databases and search strategies. Analysis of DNA and amino-acid sequences. Sequence alignment. Use of online tools for the establishment of homology. Construction of phylogenetic trees.
Keywords
Bioinformatics, Computational biology, Sequence alignment, Phylogeny, Biological database
Educational Material Types
- Slide presentations
- Interactive excersises
- Book
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
- Use of ICT in Student Assessment
Description
Power Point presentations, use of computer room and electronic communication with the students.
Course Organization
| Activities | Workload | ECTS | Individual | Teamwork | Erasmus |
|---|---|---|---|---|---|
| Lectures | 30 | 1.2 | ✓ | ||
| Seminars | 2 | 0.1 | ✓ | ||
| Laboratory Work | 20 | 0.8 | ✓ | ||
| Reading Assigment | 60 | 2.4 | |||
| Tutorial | 2 | 0.1 | ✓ | ||
| Interactive Teaching in Information Center | 12 | 0.5 | ✓ | ||
| Exams | 24 | 1.0 | |||
| Total | 150 | 6 |
Student Assessment
Description
1. Written exams on theory (75% of final mark). Evaluation through multiple choice tests and questions on knowledge/reasoning.
2. Practical exams (25% of final mark). Evaluation of group assignment.
Student Assessment methods
- Written Exam with Multiple Choice Questions (Summative)
- Written Exam with Short Answer Questions (Summative)
- Written Exam with Extended Answer Questions (Summative)
- Written Assignment (Formative, Summative)
- Written Exam with Problem Solving (Summative)
Bibliography
Course Bibliography (Eudoxus)
Βιοπληροφορική & Λειτουργική Γονιδιωματική, Jonathan Pevsner. Ακαδημαϊκές Εκδόσεις Ι. Μπάσδρα & ΣΙΑ Ο.Ε., Έκδοση 3η.
Additional bibliography for study
β1. Νικολάου Χ. 2016. Υπολογιστική Βιολογία. Ελληνικά Ακαδημαϊκά Ηλεκτρονικά Συγγράμματα και Βοηθήματα (www.kallipos.gr).
β2. Ηλεκτρονικό υλικό στο Blackboard
β3. 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
12-10-2021
