Cipher: 2202
Nomenclature: Visualization in bioinformatics
Study programme: Molecular biosciences
Module: Bioinformatics
Case holder:

The headline prof.dr.sc. The scale, zn. advisor-permanent choice
Prof.dr.sc. Irena Galić
Institution of the case holder:

Rudjer Boskovic Institute, Zagreb
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:

Create a coherent programming unit within the generic module bioinformatics by applying new techniques and technology in multidisciplinary scientific research and professional work.
Case contents:

Lecture Content
Human-computer interface and visualization. Computer-supported scientific visualization technique. Multimedia graphic communications. Elements of web graphical interfaces. Methods of distributed bioinformatics. Grid computing and data visualization. Methods of collecting, segmenting, filtering and displaying visual data. Consideration of the application of different visualization techniques and technology in the analysis of sequential data, categorical data and numerical data. Programmer techniques for the development of graphic data and their visualization. 3D structural bioinformatic visualization. Multidimensional visualization tools. Digital processing and statistical methods of analyzing information in an image. Statistical visual analysis. Classification and recognition of image content. Spatial statistical model. Spatial frequencies, correlations and structural extraction. Methods of analysis of the image of DNA micronises (microarrays). Design and implementation of bioinformatic visualization system. Visual network integration technology. Presentation of multimedia teleconference, telemedicine and VO (Virtual Organization) as an application of network cooperation in medicine and research.
Content of the exercises:
Practical work using Matlab on specific tasks. Application of NMR and modern microscopic instrumentation as part of practical tasks. Exercises on bioinformatic Grid applications, using EGEE e-Science infrastructure. The work takes place in smaller groups on concrete tasks on modern Grid (computer-mute) infrastructure.
Learning outcomes: competences, knowledge, skills that the subject develops:

1. Use new visualization techniques and technologies and modern software tools.
2. Design proposals for solutions to specific problems in medicine and computational biology.
3. Apply modern ICST technologies to the Grid platform within the ERA (European Research Area).
4. Valorize the use of new techniques and technology in multidisciplinary scientific research and professional work.
ECTS Credits 6
Lectures 5
Seminars (IS) 5
Exercises (E) 20
Altogether 30
The way of teaching and acquiring knowledge:

all forms of teaching and other activities according to a pre-published criterion.
Ways of teaching and acquiring knowledge: (notes)

Scientific equipment for visualization from the scientific research program and Grid infrastructures in the ERA system will be used.
Monitoring and evaluating students (mark in fat printing only relevant categories) Attendance, Mandatory seminar work
Rating method: Written exam, Oral exam, Continuous examination of knowledge in the course of teaching, Practical work
Mandatory literature:

[1] K.Skala, Optoelectronic Systems,2003.
[2] Bryan Bergeron, Bioinformatics Computing,HMD, 2003.
[3] Multimedia Referral Center URL: www.carnet.hr/obrazovni/referalni/imme 2004
Supplementary (recommended) literature:

[4] Zoe Lacroix, Bioinformatics: Managing the dana, 2004.
[5] Cynthia Gibas, Per Jambeck, Developing Bioinformatics Computer Skills, 2003
How to monitor the quality and performance performance (evaluation):

As part of WebCT, tests, surveys.
The success of the course will be evaluated annually by the joint expert committee of the Ruđer Boskovic Institute, the University of Dubrovnik and the University of Josip Juraj Strossmayer in Osijek based on exam success and surveys.