Virtual reality methods in bioinformatics 1000-718MWR
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
physics
biology
chemistry
mathematics
computer science
Type of course
Learning outcomes
Skills and Competences:
To acquaint students with the basics of 3D visualization theory and technology of virtual reality systems. Acquiring practical skills to apply VR 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.
Knowledge:
Knowledge of the basic theories and technologies of 3D visualization and virtual reality systems (K_W05).
Skills:
Ability 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 and Clinical Medicine of the 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
Additional information (registration calendar, class conductors, localization and schedules of classes), might be available in the USOSweb system: