For Students Defended theses

Defended theses

Doctoral theses

Partial atomic charges in proteins (Ondřej Schindler, 2024)
Visualization of biomacromolecules (David Sehnal, 2023)
Validation of molecular 3D structures (Vladimír Horský, 2022)
Annotation and visualization of protein secondary structures (Adam Midlik, 2022)

Master theses

Annotation of ligands in protein families (Kamil Jelínek, 2026)
Comparison of data management systems for research data (Filip Fábry, 2026)
Web Search Component for Dynamic Metadata-Based Search and Filtering (Michal Mikuš, 2026)
Configurable De-identification and Export of Experimental DICOM Data for Research Repositories (Juraj Kulich, 2026)
Extension for Automated Workflow Processing in the National Repository Platform (Filip Kollár, 2026)
DAREG Data Processing Workflow Component Integration (Filip Bugoš, 2026)
Predicted 3D structures as a source of potential novel sugar-interacting proteins (Kateřina Nazarčuková, 2026)
Refactoring Mol* Volumes & Segmentations 2.0 into a Standalone Library (Daniel Kříž, 2026)
Lightweight Visualisation and Annotation of Volumetric and Segmentation Data in Mol* (Dominik Tichý, 2026)
Acquisition of research data from specialised instruments (David Konečný, 2025)
Calculations of partial atomic charges by machine learning methods (Jan Bříza, 2025)
Design and implementation of a new architecture for the ACC II (Martin Pilát, 2025)
Design and implementation of automatic data storage in ChannelsDB (Ján Kučera, 2025)
Structural Bioinformatics Application Platform (Eduard Ruisl, 2025)
Automatic updates for the protein similarity search application (Jakub Oršula, 2024)
API for a web application Atomic Charge Calculator II (Lenka Ptáčníková, 2023)

Bachelor theses

Visualization and Analytics Components for Molecular Dynamics Data Repository (Oliver Blščák, 2026)
Virtual Research Environment for Molecular Dynamics Simulation Experiments (Filip Krása, 2026)
Advancing Automated VM Image Orchestration for Federated Clouds (Lukas Móder, 2026)
User Interface for Molecular Dynamics Data Repository (Filip Múdry, 2026)
Implementation of a Deployment Method to Kubernetes for Electronic Laboratory Notebook Software (Drahomír Malota, 2026)
Implementation of unattended mode and optimization of DAREG Lab Client (Matej Barna, 2026)
Design and implementation of a new version of 2DProts database web pages (Mario Mičulka, 2026)
Repairing protein structures from AlphaFold DB (Lukáš Bohuš, 2025)
Analysis of IDR in transcriptome (Margarita Marsova, 2025)
GOLEM application back end (Jakub Plhal, 2025)
VRML to STL mesh format converter for Mol* VS (Marek Eibel, 2025)
Data downsampling for Mol* VS (Patrik Roháč, 2025)
Making data stored in the Onedata system available by application for Windows (Andrej Gáfrik, 2025)
Extending Metadata Annotations with Identification of Biomolecules in Simulation Data (Tomáš Pavlík, 2025)
Visualisation of tunnels in ChannelsDB using Mol* (Dušan Veľký, 2024)
Anonymizing experimental data in the MAFIL laboratory (Filip Kovářík, 2024)
Enhancing the FAIRness of Gromacs software: Adding support to extract metadata in JSON/YAML formats (Róbert Randiak, 2024)
Deployment of the OMERO system as part of the data workflow in the CELLIM laboratory (Barbora Juríčková, 2024)
Acquisition protocol templates and compliance verification in the MAFIL laboratory (Boris Engler, 2024)
Software tools for analysis of ring 3D structure (Michal Oleksik, 2024)
Modern visualization of partial atomic charges in Mol* (Dominik Tichý, 2023)
Comparison of machine-learning approaches for calculating partial atomic charges (Jan Bříza, 2023)
Interactive data system to record the process of neurological measurements of volunteers (Maxmilián Šeffer, 29. 6. 2023)
System for ensuring the registration and safety of MR measurements in the MAFIL laboratory (Lukáš Kratochvíl, 2023)
Automated setup of the experiment parameters on magnetic resonance device and following acquiring measured data from PACS (Matúš Pavlásek, 2023)
Visualization of protein families using 2D diagrams (Amálie Švehlová, 2023)