Virtual reality methods in bioinformatics 1100-4PM21
Learning content:
1. Principles of 3D visualization. VR technology overview. Virtual reality methods in studies of the structure and dynamics of complex systems.
2. Basic elements of the specialized VisNow platform (https://visnow.icm.edu.pl) for the analysis and manipulation of three-dimensional objects, with particular emphasis on (bio)molecular and (bio)medical systems, as well as on molecular fields. Practical exercises using this environment.
3. Molecular forces at the microscopic (atomic resolution) and mesoscopic level (using effective potentials for whole molecular groups). Fundamentals of the NAMD/VMD modeling environment for the visualization and manipulation of (bio)molecular structures (see: https://www.ks.uiuc.edu/Research/namd/, https://www.ks.uiuc.edu/Research/vmd/). Fundamentals of the Steered (interactive) Molecular Dynamics model taking into account forces generated by the researcher. Controlled molecular dynamics in practical applications.
4. Practical applications of a specialized virtual reality system based on 3D-systems manipulators (https://www.3dsystems.com/haptics-devices/touch/).
5. Basics of 3D printing technology. Practical applications in printing complex (bio)molecular systems. Other applications of VR methods.
Main fields of studies for MISMaP
chemistry
computer science
biology
biotechnology
physics
Learning outcomes
Skills and Competences:
To acquaint students with the basics of 3D visualization theory and the technology of virtual reality systems. Acquiring practical skills to apply VR techniques in the study of the structure and function of (bio) molecular systems and in other applications, important from the point of view of the development of modern methods of bioinformatics and systems biology.
Knowledge:
He/she knows the basic theories and technologies of 3D visualization and virtual reality systems (K_W05).
Skills:
Is able to use 3D visualization and virtual reality techniques in the study of the structure and functions of (bio) molecular systems and in other applications, important from the point of view of the development of modern methods of bioinformatics and systems biology
(K_U08).
Assessment criteria
Exam in the form of a written test.
Practical placement
Internships can be held at the Bioinformatics Laboratory of the Institute of Experimental Medicine, Polish Academy of Sciences.
Bibliography
Collective work, ed. B. Lesyng, "Virtual reality methods in modeling of biomolecular systems and nanosystems". Didactic course at the University of Warsaw for 2nd-degree studies in natural sciences (lectures and exercises).
NAMD user's guide
http://www.ks.uiuc.edu/Research/namd/2.9/ug/
VMD User's guide
https://www.ks.uiuc.edu/Research/vmd/current/ug/
Additional information
Information on level of this course, year of study and semester when the course unit is delivered, types and amount of class hours - can be found in course structure diagrams of apropriate study programmes. This course is related to the following study programmes:
Additional information (registration calendar, class conductors, localization and schedules of classes), might be available in the USOSweb system: