PřF:C2150 Information proc. ch & bioch. - Course Information

C2150 Information processing and visualization in chemistry and biochemistry

Extent and Intensity

0/2/0. 2 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).
In-person direct teaching

Teacher(s)

RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Július Zemaník (seminar tutor)

Guaranteed by

RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science

Prerequisites

The course is held in a computer lab equipped with workstations running the Linux operating system, specifically the Ubuntu distribution. Completing the course C2110 UNIX Operating System and Programming Basics is recommended but not a prerequisite. Basic user-level knowledge of any operating system, such as MS Windows, MacOS, or Linux, is sufficient for successful participation. The course aims to introduce students to visualization software, which is typically also available in MS Windows or MacOS environments.

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

• Bioinformatics (programme PřF, B-BIC)

Course objectives

The course is intended for anyone who wants to get a basic overview of visualizations in molecular modelling and their practical application in chemistry, biochemistry and structural biology. Students are gradually introduced to approaches for obtaining data on biomolecular structures from public databases such as Protein Data Bank (PDB) or PubChem and methods for visualizing chemical and biological structures. Emphasis is placed on working effectively with software tools to analyse and visualise biomolecules such as proteins, nucleic acids and small molecules.
In addition to basic visualization skills, the course includes the creation of graphical output, including graphs, diagrams, and illustrations of molecular interactions. These skills are expanded to include preparing complex scientific communications such as presentations, poster presentations, or schematics for publications. Students learn how to effectively interpret and present data in the context of scientific research and how to select the appropriate graphical format for different types of scientific communication.
The course also introduces the use of visualization tools in the study of biomolecules' structural properties, interactions, and dynamics, which are key aspects of modern structural biology. Emphasis is placed on linking theoretical knowledge with practical application so that graduates can apply the skills acquired in a wide range of scientific disciplines.

Learning outcomes

On successful completion of the course, a learner will be able to: get a molecular structure data from database; visualize a structure using programs for visualization of molecules; use molecular structure data to solve simple scientific problems; visualize chemical data using simple graphs and schemes;

Syllabus

• 1. Introduction to the course: Focus and objectives of the course; Introduction to the WOLF computer cluster; Basics of the scientific method and working with information; Forms of scientific communication: articles, presentations, posters; Overview of software tools used; Requirements for the final project.
• 2. Basics of visualization of molecules: Chemical formula and its representation; Reaction schemes; Overview of tools for 2D graphical representation of molecules.
• 3. Working with 3D structures of molecules.
• 4. Visualization of molecules in 3D: Work in VMD, PyMOL, ChimeraX. Creating high-quality 3D models for publications.
• 5. 3D printing in chemistry and biochemistry: Overview of 3D printing applications; Preparation of data for 3D printing of molecular structures; Demonstration of 3D model realization.
• 6. Data analysis and graph visualization: Generation and editing of graphs in Gnuplot and matplotlib; Presentation and interpretation of results in scientific communications.
• 8. Graphical editing of scientific materials: Graphics editors: GIMP: working with raster graphics, Inkscape: creating vector graphics. Practical tips for preparing publications and presentations.
• 9. Creating professional documents in LaTeX. Advanced tools: packages, formatting, inserting graphic elements.
• 10. Working with citation managers: the importance of citation managers for scientific work, Working with Zotero software: import/export of citations, Organization and management of references, Integration with  LaTeX and text editors.
• 11. Final project: Design and implementation of a comprehensive scholarly output (presentation or poster), Creation of a scholarly communication (ongoing during the semester), Presentation at a simulated conference.

Literature

• Molecular modeling of proteins. Edited by Andreas Kukol. Totowa: Humana Press, 2008, xi, 390. ISBN 9781588298645. info
• HÖLTJE, Hans-Dieter and Gerd FOLKERS. Molecular modelling :basic principles and applications. Edited by Thomas Beier - Wofgang Sippl - Didier Rognan. Weinheim: VCH Verlagsgesellschaft, 1997, xii, 194 s. ISBN 3-527-29384-1. info
• Molecular modeling of nucleic acids. Edited by Neocles B. Leontis - John SantaLucia. Washington: American Chemical Society, 1998, x, 435 s. ISBN 0-8412-3541-4. info
• http://www.ks.uiuc.edu/Research/vmd/

Teaching methods

Practical computer exercises. Presentation during a simulated conference.

Assessment methods

The student will prepare a short presentation or poster communication, either based on his/her own data or a summary of already published results. This will then be presented at a simulated conference at the end of the course.

Language of instruction

Czech

Further Comments

Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.

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