Cipher: 2207
Nomenclature: INFORMATION tools in molecular biosciences
Study programme: Molecular biosciences
Module: Bioinformatics
Case holder:

Assoc. Prof. Dr. Sc. Paško Konjevoda, zn. adviser
Institution of the case holder:

Ruđer Boskovic Institute
Contributors - Contractors:
Subject status: Electoral College
The year in which the case is submitted: Year I
The semester in which the case is submitted: Semester II
Subject objective:

Introduce students to basic IT tools used in computational biology and their application in molecular biology, pharmaceutical industry and biotechnology.
Case contents:

Theoretical part
Field of computational biology and bioinformatics. Application of computational biology and bioinformatics in molecular biology, pharmaceutical industry and biotechnology. Biological databases. Stacking sequences. Phylogenetic analysis. Transcriptomics. Proteomics. Metabolomics. Biochemical dynamics. Systemic biology. Programming languages. Open-source data analysis programs. Commercial data analysis programs. The most common errors in data analysis.

Practical part - working with Unipro UGENE
Introduction to the graphical interface. Loading sequences. Annotation sequences. Loading and viewing 3D structures. Stacking sequences. Phylogenetic analysis. Use of BLAST. Prediction of the secondary structure.

Seminars
Practical application of computational biology in molecular biology, pharmaceutical industry and biotechnology.
Learning outcomes: competences, knowledge, skills that the subject develops:

1. Propose the use of COMPUTER biology and bioinformatics itineraries in molecular biology, pharmaceutical industry and biotechnology.
2. Apply basic computer platforms and operating systems.
3. Use programs to analyze data from different databases and formats.
4. Work with the integrated Unipro UGENE data analysis system.
ECTS Credits 6
Lectures 5
Seminars (IS) 5
Exercises (E) 20
Altogether 30
The way of teaching and acquiring knowledge:

Attendance and active participation in seminars.
Ways of teaching and acquiring knowledge: (notes)
Monitoring and evaluating students (mark in fat printing only relevant categories) Teaching activities, Mandatory seminar work
Rating method: Oral exam, Essay/Seminar, Continuous examination of knowledge in the course of teaching
Mandatory literature:

1. Hodgman TC, French A, Westhead DR. BIOS Instant Notes Bioinformatics. 2nd edition, Taylor & Francis, Abingdon, 2009.
2. Unipro UGENE Manual Version 1.20.0 (http://ugene.net/)
Supplementary (recommended) literature:

1. Claverie J-M, Notredame C. Bioinformatics for Dummies. 2nd edition, Wiley, Hoboken, 2007.
2. Haddock S, Dunn C. Practical Computing For Biologists. Sinauer Associates, 2010.
3. Wünschiers R. Computational Biology. 2nd edition, Springer-Verlag, Berlin, 2013.
4. Flower DR. Bioinformatics for vaccinology, Wiley-Blackwell, Hoboken, 2007.
How to monitor the quality and performance performance (evaluation):

The success of the course will be evaluated annually by the joint expert committee of the Rudjer Boskovic Institute, the University of Dubrovnik and the University of Osijek, and the leaders will receive information from the participants about the adequacy of the program and performance by the leadership through the survey.