Bioinformatics

Course Information
TitleΒΙΟΠΛΗΡΟΦΟΡΙΚΗ / Bioinformatics
CodeABA3
FacultySciences
SchoolBiology
Cycle / Level2nd / Postgraduate
Teaching PeriodWinter
CoordinatorZacharias Skouras
CommonNo
StatusInactive
Course ID40003395
Class Information
Academic Year2018 – 2019
Class PeriodWinter
Faculty Instructors
Class ID
600132818
Course Type 2016-2020
  • Scientific Area
  • Skills Development
Course Type 2011-2015
Specific Foundation / Core
Mode of Delivery
  • Face to face
Digital Course Content
Language of Instruction
  • Greek (Instruction, Examination)
  • English (Instruction, Examination)
Learning Outcomes
Familiarization with biological sequences, databases and data retrieval. Familiarization with the organization of transcriptional units in prokaryotes, eukaryotes and viruses and with relevant analysis using appropriate software and internet tools. Study of the basic biological databases and their types of information and training on search strategies and data retrieval. Study of the basic operational principles of online tools and standalone packages used for DNA and amino-acid sequence analysis, determination of transcriptional unit, restriction enzyme analysis, primer design for PCR, genome analysis, prediction of protein structure. Introduction to genomics/metagenomics and biological networks. Training on pairwise and multiple sequence alignment using BLAST and Clustalw. Training on the basic steps and methods of phylogenetic tree construction.
General Competences
  • Retrieve, analyse and synthesise data and information, with the use of necessary technologies
  • Work in an interdisciplinary team
Course Content (Syllabus)
Lectures: The basics of the operation and use of the computer room. Definition, design and structure of biological databases. Search strategies. Analysis and evaluation of search results. DNA and amino-acid sequence analysis. Determination of transcriptional units. Primer design. Genome structure, function and evolution. Biological networks. Alignment algorithms. Models of molecular evolution. Construction and evaluation of phylogenetic trees. Mega-scale phylogenetic analyses and new tools. Future bioinformatics and applications. Practicals: Statistical analysis. Use of computer room. Biological databases and search strategies. DNA and amino-acid sequence analysis. Determination of transcriptional unit. Sequence alignment and motif discovery. Construction of phylogenetic trees.
Educational Material Types
  • Slide presentations
  • Multimedia
  • 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
  • Use of ICT in Student Assessment
Course Organization
ActivitiesWorkloadECTSIndividualTeamworkErasmus
Lectures✓✓
Seminars✓✓
Laboratory Work✓✓
Reading Assigment✓✓
Tutorial✓✓
Interactive Teaching in Information Center✓✓
Total
Student Assessment
Description
Group assignments and presentations (marking scale: 0-10, passing grade: 6).
Student Assessment methods
  • Written Assignment (Formative, Summative)
  • Oral Exams (Formative, Summative)
  • Performance / Staging (Formative, Summative)
  • Labortatory Assignment (Formative, Summative)
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
01-12-2015