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ΒΙΟΠΛΗΡΟΦΟΡΙΚΗ

Course Information

Title ΒΙΟΠΛΗΡΟΦΟΡΙΚΗ / Bioinformatics
Code ABA3
Faculty Sciences
School Biology
Cycle / Level 2nd / Postgraduate
Teaching Period Winter
Coordinator Zacharias Skouras
Common No
Status Active
Course ID 40003395

Class Information

Academic Year 2016 – 2017
Class Period Winter
Faculty Instructors
Class ID
600039467
Type of the Course
  • Scientific Area
  • Skills Development
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
Activities WorkloadTotal hours of student effort for the semester. Includes lectures, labs, field etc. ECTSThe credit units (ECTS) of the respective teaching activity. Each unit correponds to X hours of student workload. IndividualFor the learning activity cooperation between students is not requisite TeamworkFor the learning activity the students cooperate in teams ErasmusThe learning activity is available to students of exchange programmes
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 (FormativeFormative assessment is a range of formal and informal assessment procedures employed by teachers during the learning process in order to modify teaching and learning activities to improve student attainment., SummativeSummative assessment refers to the assessment of the learning and summarizes the development of learners at a particular time.)
  • Oral Exams (FormativeFormative assessment is a range of formal and informal assessment procedures employed by teachers during the learning process in order to modify teaching and learning activities to improve student attainment., SummativeSummative assessment refers to the assessment of the learning and summarizes the development of learners at a particular time.)
  • Performance / Staging (FormativeFormative assessment is a range of formal and informal assessment procedures employed by teachers during the learning process in order to modify teaching and learning activities to improve student attainment., SummativeSummative assessment refers to the assessment of the learning and summarizes the development of learners at a particular time.)
  • Labortatory Assignment (FormativeFormative assessment is a range of formal and informal assessment procedures employed by teachers during the learning process in order to modify teaching and learning activities to improve student attainment., SummativeSummative assessment refers to the assessment of the learning and summarizes the development of learners at a particular time.)
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

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