Publications
2025
Who Let the Guards Out: Visual Support for Patrolling Games
IEEE Transactions on Visualization and Computer Graphics
Effective security patrol management is critical for ensuring safety in diverse environments such as art galleries, airports, and factories. The behavior of patrols in these situations can be modeled by patrolling games. They simulate the behavior of the patrol and adversary in the building, which is modeled as a graph of interconnected nodes representing rooms. The designers of algorithms solving the game face the problem of analyzing complex graph layouts with temporal dependencies. Therefore, appropriate visual support is crucial for them to work effectively. In this paper, we present a novel tool that helps the designers of patrolling games explore the outcomes of the proposed algorithms and approaches, evaluate their success rate, and propose modifications that can improve their solutions. Our tool offers an intuitive and interactive interface, featuring a detailed exploration of patrol routes and probabilities of taking them, simulation of patrols, and other requested features. In close collaboration with experts in designing patrolling games, we conducted three case studies demonstrating the usage and usefulness of our tool.
10.1109/tvcg.2024.3456306
Visual Support for the Loop Grafting Workflow on Proteins
Filip Opálený, Pavol Ulbrich, Joan Planas-Iglesias, Jan Byška, Jan Stourac, David Bednář, Katarína Furmanová, Barbora Kozlikova
IEEE Transactions on Visualization and Computer Graphics
In understanding and redesigning the function of proteins in modern biochemistry, protein engineers are increasingly focusing on exploring regions in proteins called loops. Analyzing various characteristics of these regions helps the experts design the transfer of the desired function from one protein to another. This process is denoted as loop grafting. We designed a set of interactive visualizations that provide experts with visual support through all the loop grafting pipeline steps. The workflow is divided into several phases, reflecting the steps of the pipeline. Each phase is supported by a specific set of abstracted 2D visual representations of proteins and their loops that are interactively linked with the 3D View of proteins. By sequentially passing through the individual phases, the user shapes the list of loops that are potential candidates for loop grafting. Finally, the actual in-silico insertion of the loop candidates from one protein to the other is performed, and the results are visually presented to the user. In this way, the fully computational rational design of proteins and their loops results in newly designed protein structures that can be further assembled and tested through in-vitro experiments. We showcase the contribution of our visual support design on a real case scenario changing the enantiomer selectivity of the engineered enzyme. Moreover, we provide the readers with the experts' feedback.
10.1109/tvcg.2024.3456401
The Language of Infographics: Toward Understanding Conceptual Metaphor Use in Scientific Storytelling
Hana Pokojná, Tobias Isenberg, Stefan Bruckner, Barbora Kozlíková, Laura Garrison
IEEE Transactions on Visualization and Computer Graphics
10.1109/tvcg.2024.3456327Immersive and Interactive Learning With eDIVE: A Solution for Creating Collaborative VR Education Experiences
Vojtěch Brůža, Alžběta Šašinková, Čeněk Šašinka, Zdeněk Stachoň, Barbora Kozlíková, Jiří Chmelík
Computer Graphics Forum
10.1111/cgf.700012024
Interactive Diagrams for Software Documentation
IEEE Working Conference on Software Visualization (VISSOFT)
Getting acquainted with a large codebase can be a daunting task for software developers, both new and seasoned. The description of a codebase and its development should be the purpose of its documentation. However, software documentation, if it exists at all, is usually textual and accompanied only by simple static diagrams. It is also time-consuming to maintain manually. Even an API reference, which can be generated automatically from the codebase itself, has many drawbacks. It is limited to what it can extract from the codebase, is cumbersome to navigate, and fails to capture the interwoven nature of code. We explore an alternative approach centered around a node-link diagram representing the structure of a codebase. The diagram is interactive and filterable, providing details on demand. It is designed for automation, relying on static analysis of the codebase, and thus produces results quickly and offers a viable alternative to missing or outdated documentation. To evaluate this approach, we implemented a prototype named Helveg that is able to analyze and visualize C# code. Testing with five professional programmers provided feedback on the approach's benefits and challenges, which we discuss in detail.
10.1109/vissoft64034.2024.00012Design and evaluation of alphabetic and numeric input methods for virtual reality
David Kuťák, Danielle Langlois, Roman Rozič, Jan Byška, Haichao Miao, Simone Kriglstein, Barbora Kozlíková
Computers & Graphics
10.1016/j.cag.2024.103955
ProjectAnatomy : a handy tool for learning forearm anatomy with augmented physicalisations
Behaviour & Information Technology
ProjectAnatomy combines tangible objects with video projections that show the anatomy of the human forearm intended for learning through its eye-catching appearance. The prototype was shown to three target groups: non-experts, trainee medical students, and anatomy experts to provide qualitative and quantitative feedback. The study and observation of the users in the first two groups were carried out ‘in the wild’ where the users would come in contact with this type of visualisation to collect data on how it should be adjusted to their needs. The results have shown that the non-experts find it most helpful in learning anatomy, contrary to the experts who find it less useful yet very interesting and see its educational potential. The trainee medical students scored it the lowest; however, they would find it helpful to complement dissection classes. We conclude that this visual installation could be used in science centers and, when enriched with more details, for beginning medical students. Our study contributes specifically to the field of physical visualisation using 3D printed objects combined with projections that can be adjusted to the level of detail suitable for the target audience.
10.1080/0144929x.2024.2413161
Cartography of Touch: Transformation of Touch through Anatomical Projections
Hana Pokojná
Leonardo
10.1162/leon_a_02403
Antarstick: Extracting Snow Height From Time‐Lapse Photography
Matěj Lang, Radoslav Mráz, Marek Trtík, Sergej Stoppel, Jan Byška, Barbora Kozlíková
Computer Graphics Forum
10.1111/cgf.15088BioMedical Visualization: Past Work, Current Trends, and Open Challenges
Katarína Furmanová, Barbora Kozlikova, Thomas Höllt, M. Eduard Gröller, Bernhard Preim, Renata Georgia Raidou
This book provides an overview of the many visualization strategies that have been proposed in recent decades for solving problems within the disciplines of medicine and biology. It also evaluates which visualization techniques applied to various areas of biomedicine have been the most impactful and which challenges can be considered solved using visualization. The topics covered in this book include visualization research in omics, interaction networks and pathways, biological structures, tumor diagnosis and treatment, vasculature, brain, surgery, educational contexts, therapy and rehabilitation, electronic health records, and public health. One chapter is dedicated to general visualization techniques commonly used for biomedical data, such as surface and volume rendering, as well as abstract and illustrative approaches. For each of these areas, the past and present research trends are discussed, highlighting the influential works. Furthermore, the book explains how research is affected by developments in technology, data availability, and domain practice. Individual sections also summarize the typical target users, the nature of the data, and the typical tasks addressed in the given domain. With a uniquely broad scope, the book identifies research trends in biomedical visualization using a manually curated and searchable repository of more than 3,800 publications. The resultant trends are further categorized according to the application field and using natural language processing. The book also utilizes 16 interviews conducted with researchers in the field of biomedical visualization for the purpose of soliciting their opinions regarding the evolution and trends in the domain.
10.1007/978-3-031-66789-3
Make Some Energy: Tangible and Interactive Chemical Reactions
Hana Pokojná, Barbora Kozlíková, Simone Kriglstein, Daniel Echeverri
Proceedings of the Expanded 2024 Conference on Animation and Interactive Art
10.5281/zenodo.13382838Co-authored publications (2024)
Stories with Style: Narrative, Virtual, and Imaginary Spaces of Reading Fiction in Virtual Reality
10.1145/3701571.3701601The challenge of chromatin model comparison and validation - a project from the first international 4D Nucleome Hackathon
Jędrzej Kubica, Sevastianos Korsak, Ariana Brenner Clerkin, David Kouřil, Dvir Schirman, Anurupa Devi Yadavalli, Krzysztof Banecki, Michał Kadlof, Ben Busby, Dariusz Plewczynski
10.1101/2024.10.02.616241InVADo: Interactive Visual Analysis of Molecular Docking Data
Marco Schäfer, Nicolas Brich, Jan Byška, Sérgio M. Marques, David Bednář, Philipp Thiel, Barbora Kozlíková, Michael Krone
10.1109/tvcg.2023.3337642Who benefits and who doesn't in virtual reality learning: An experimental study comparing two types of school
Radovan Šikl, Karla Brücknerová, Hana Švedová, Filip Děchtěrenko, Pavel Ugwitz, Jiří Chmelík, Hana Pokorná, Vojtěch Juřík
10.1111/jcal.12973VRET ENVIRONMENTS ARCHITECTURE: ADJUSTING IMMERSIVE VIRTUAL ENVIRONMENTS FOR PSYCHOTHERAPEUTIC TRAINING
Vojtěch Juřík, Kristína Varšová, Jiří Chmelík, Oto Janoušek
10.21125/inted.2024.12902023
Molecumentary: Adaptable Narrated Documentaries Using Molecular Visualization
David Kouril, Ondrej Strnad, Peter Mindek, Sarkis Halladjian, Tobias Isenberg, M. Eduard Groller, Ivan Viola
IEEE Transactions on Visualization and Computer Graphics
10.1109/tvcg.2021.3130670
State of the Art of Molecular Visualization in Immersive Virtual Environments
David Kuťák, Pere‐Pau Vázquez, Tobias Isenberg, Michael Krone, Marc Baaden, Jan Byška, Barbora Kozlíková, Haichao Miao
Computer Graphics Forum
10.1111/cgf.14738
Seeing the unseen: Comparison study of representation approaches for biochemical processes in education
PLOS ONE
The representations of biochemical processes must balance visual portrayals with descriptive content to be an effective learning tool. To determine what type of representation is the most suitable for education, we designed five different representations of adenosine triphosphate (ATP) synthesis and examined how they are perceived. Our representations consisted of an overview of the process in a detailed and abstract illustrative format, continuous video formats with and without narration, and a combined illustrative overview with dynamic components. The five representations were evaluated by non-experts who were randomly assigned one of them and experts who viewed and compared all five representations. Subsequently, we conducted a focus group on the outcomes of these evaluations, which gave insight into possible explanations of our results, where the non-experts preferred the detailed static representation and found the narrated video least helpful, in contradiction to the experts who favored the narrated video the most.
10.1371/journal.pone.0293592
xOpat: eXplainable Open Pathology Analysis Tool
Jiří Horák, Katarína Furmanová, Barbora Kozlikova, Tomáš Brázdil, Petr Holub, Martin Kačenga, Matej Gallo, Rudolf Nenutil, Jan Byška, Vit Rusnak
Computer Graphics Forum
Histopathology research quickly evolves thanks to advances in whole slide imaging (WSI) and artificial intelligence (AI). However, existing WSI viewers are tailored either for clinical or research environments, but none suits both. This hinders the adoption of new methods and communication between the researchers and clinicians. The paper presents xOpat, an open-source, browser- based WSI viewer that addresses these problems. xOpat supports various data sources, such as tissue images, pathologists’ annotations, or additional data produced by AI models. Furthermore, it provides efficient rendering of multiple data layers, their visual representations, and tools for annotating and presenting findings. Thanks to its modular, protocol-agnostic, and extensible architecture, xOpat can be easily integrated into different environments and thus helps to bridge the gap between research and clinical practice. To demonstrate the utility of xOpat, we present three case studies, one conducted with a developer of AI algorithms for image segmentation and two with a research pathologist.
10.1111/cgf.14812
sMolBoxes: Dataflow Model for Molecular Dynamics Exploration
Pavol Ulbrich, Manuela Waldner, Katarína Furmanová, Sérgio Manuel Marques, David Bednář, Barbora Kozlikova, Jan Byška
IEEE Transactions on Visualization and Computer Graphics
We present sMolBoxes, a dataflow representation for the exploration and analysis of long molecular dynamics (MD) simulations. When MD simulations reach millions of snapshots, a frame-by-frame observation is not feasible anymore. Thus, biochemists rely to a large extent only on quantitative analysis of geometric and physico-chemical properties. However, the usage of abstract methods to study inherently spatial data hinders the exploration and poses a considerable workload. sMolBoxes link quantitative analysis of a user-defined set of properties with interactive 3D visualizations. They enable visual explanations of molecular behaviors, which lead to an efficient discovery of biochemically significant parts of the MD simulation. sMolBoxes follow a node-based model for flexible definition, combination, and immediate evaluation of properties to be investigated. Progressive analytics enable fluid switching between multiple properties, which facilitates hypothesis generation. Each sMolBox provides quick insight to an observed property or function, available in more detail in the bigBox View. The case studies illustrate that even with relatively few sMolBoxes, it is possible to express complex analytical tasks, and their use in exploratory analysis is perceived as more efficient than traditional scripting-based methods.
10.1109/tvcg.2022.3209411
A multimodal smartwatch-based interaction concept for immersive environments
Matěj Lang, Clemens Strobel, Felix Weckesser, Danielle Langlois, Enkelejda Kasneci, Barbora Kozlíková, Michael Krone
Computers & Graphics
10.1016/j.cag.2023.10.010
Effect of the Rings: A Visual Story Design Comparing Three Chemical Characters
Hana Pokojná, Farhan Rasheed, Konrad J. Shönborn
Biomedical Visualization
10.1007/978-3-031-41652-1_6Co-authored publications (2023)
Nanotilus: Generator of Immersive Guided-Tours in Crowded 3D Environments
Ruwayda Alharbi, Ondrej Strnad, Laura R. Luidolt, Manuela Waldner, David Kouril, Ciril Bohak, Tobias Klein, Eduard Groller, Ivan Viola
10.1109/tvcg.2021.3133592Who benefits and who doesn't in virtual reality learning: An experimental study comparing two types of school
Radovan Sikl, Karla Brücknerová, Hana Švedová, Filip Dechterenko, Pavel Ugwitz, Jiří Chmelík, Hana Svatoňová, Vojtěch Juřík
10.31234/osf.io/74puz
EbAcraft: Engaging Local Communities in Learning About Ecosystem-Based Adaptation for Coastal Cities in Europe
Ítalo de Sena, Chiara Cocco, Vojtěch Brůža, Pierre Lenicolais, Saul Crowley, Francesco Pilla
10.1109/e-science58273.2023.102549412022
Vivern–A Virtual Environment for Multiscale Visualization and Modeling of DNA Nanostructures
David Kutak, Matias Nicolas Selzer, Jan Byska, Maria Lujan Ganuza, Ivan Barisic, Barbora Kozlikova, Haichao Miao
IEEE Transactions on Visualization and Computer Graphics
10.1109/tvcg.2021.3106328
CATANA: an online modelling environment for proteins and nucleic acid nanostructures
Nucleic Acids Research
<jats:title>Abstract</jats:title>
<jats:p>In the last decade, significant advances have been made towards the rational design of proteins, DNA, and other organic nanostructures. The emerging possibility to precisely engineer molecular structures resulted in a wide range of new applications in fields such as biotechnology or medicine. The complexity and size of the artificial molecular systems as well as the number of interactions are greatly increasing and are manifesting the need for computational design support. In addition, a new generation of AI-based structure prediction tools provides researchers with completely new possibilities to generate recombinant proteins and functionalized DNA nanostructures. In this study, we present Catana, a web-based modelling environment suited for proteins and DNA nanostructures. User-friendly features were developed to create and modify recombinant fusion proteins, predict protein structures based on the amino acid sequence, and manipulate DNA origami structures. Moreover, Catana was jointly developed with the novel Unified Nanotechnology Format (UNF). Therefore, it employs a state-of-the-art coarse-grained data model, that is compatible with other established and upcoming applications. A particular focus was put on an effortless data export to allow even inexperienced users to perform in silico evaluations of their designs by means of molecular dynamics simulations. Catana is freely available at http://catana.ait.ac.at/.</jats:p>
10.1093/nar/gkac350
The transparent minds: methods of creation of 3D digital models from patient specific data
Hana Pokojná, Caroline Erolin, Christopher Henstridge
Journal of Visual Communication in Medicine
10.1080/17453054.2021.2008230
LoopGrafter: a web tool for transplanting dynamical loops for protein engineering
Nucleic Acids Research
<jats:title>Abstract</jats:title>
<jats:p>The transplantation of loops between structurally related proteins is a compelling method to improve the activity, specificity and stability of enzymes. However, despite the interest of loop regions in protein engineering, the available methods of loop-based rational protein design are scarce. One particular difficulty related to loop engineering is the unique dynamism that enables them to exert allosteric control over the catalytic function of enzymes. Thus, when engaging in a transplantation effort, such dynamics in the context of protein structure need consideration. A second practical challenge is identifying successful excision points for the transplantation or grafting. Here, we present LoopGrafter (https://loschmidt.chemi.muni.cz/loopgrafter/), a web server that specifically guides in the loop grafting process between structurally related proteins. The server provides a step-by-step interactive procedure in which the user can successively identify loops in the two input proteins, calculate their geometries, assess their similarities and dynamics, and select a number of loops to be transplanted. All possible different chimeric proteins derived from any existing recombination point are calculated, and 3D models for each of them are constructed and energetically evaluated. The obtained results can be interactively visualized in a user-friendly graphical interface and downloaded for detailed structural analyses.</jats:p>
10.1093/nar/gkac249Co-authored publications (2022)
Multiscale Unfolding: Illustratively Visualizing the Whole Genome at a Glance
Sarkis Halladjian, David Kouril, Haichao Miao, M. Eduard Groller, Ivan Viola, Tobias Isenberg
10.1109/tvcg.2021.3065443Collaborative and individual learning of geography in immersive virtual reality: An effectiveness study
Michal Sedlák, Stefano Triberti, Čeněk Šašinka, Zdeněk Stachoň, Jiří Chmelík, Milan Doležal
10.1371/journal.pone.0276267Geography Education in a Collaborative Virtual Environment: A Qualitative Study on Geography Teachers
Kateřina Jochecová, Michal Černý, Zdeněk Stachoň, Hana Švedová, Natálie Káčová, Jiří Chmelík, Vojtěch Brůža, Ondřej Kvarda, Pavel Ugwitz, Alžběta Šašinková, Nicola Catherine Fořtová, Čeněk Šašinka
10.3390/ijgi11030180
Understanding the impact of statistical and machine learning choices on predictive models for radiotherapy
10.2312/vcbm.202211882021
HyperLabels: Browsing of Dense and Hierarchical Molecular 3D Models
David Kouril, Tobias Isenberg, Barbora Kozlikova, Miriah Meyer, M. Eduard Groller, Ivan Viola
IEEE Transactions on Visualization and Computer Graphics
10.1109/tvcg.2020.2975583
Unified Nanotechnology Format: One Way to Store Them All
David Kuťák, Erik Poppleton, Haichao Miao, Petr Šulc, Ivan Barišić
Molecules
<jats:p>The domains of DNA and RNA nanotechnology are steadily gaining in popularity while proving their value with various successful results, including biosensing robots and drug delivery cages. Nowadays, the nanotechnology design pipeline usually relies on computer-based design (CAD) approaches to design and simulate the desired structure before the wet lab assembly. To aid with these tasks, various software tools exist and are often used in conjunction. However, their interoperability is hindered by a lack of a common file format that is fully descriptive of the many design paradigms. Therefore, in this paper, we propose a Unified Nanotechnology Format (UNF) designed specifically for the biomimetic nanotechnology field. UNF allows storage of both design and simulation data in a single file, including free-form and lattice-based DNA structures. By defining a logical and versatile format, we hope it will become a widely accepted and used file format for the nucleic acid nanotechnology community, facilitating the future work of researchers and software developers. Together with the format description and publicly available documentation, we provide a set of converters from existing file formats to simplify the transition. Finally, we present several use cases visualizing example structures stored in UNF, showcasing the various types of data UNF can handle.</jats:p>
10.3390/molecules27010063
PREVIS: Predictive visual analytics of anatomical variability for radiotherapy decision support
Katarína Furmanová, Ludvig P Muren, Oscar Casares-Magaz, Vitali Moiseenko, John P Einck, Sara Pilskog, Renata G Raidou
Computers & Graphics
Radiotherapy (RT) requires meticulous planning prior to treatment, where the RT plan is optimized with organ delineations on a pre-treatment Computed Tomography (CT) scan of the patient. The conventionally fractionated treatment usually lasts several weeks. Random changes (e.g., rectal and bladder filling in prostate cancer patients) and systematic changes (e.g., weight loss) occur while the patient is being treated. Therefore, the delivered dose distribution may deviate from the planned. Modern technology, in particular image guidance, allows to minimize these deviations, but risks for the patient remain. We present PREVIS: a visual analytics tool for (i) the exploration and prediction of changes in patient anatomy during the upcoming treatment, and (ii) the assessment of treatment strategies, with respect to the anticipated changes. Records of during-treatment changes from a retrospective imaging cohort with complete data are employed in PREVIS, to infer expected anatomical changes of new incoming patients with incomplete data, using a generative model. Abstracted representations of the retrospective cohort partitioning provide insight into an underlying automated clustering, showing main modes of variation for past patients. Interactive similarity representations support an informed selection of matching between new incoming patients and past patients. A Principal Component Analysis (PCA)-based generative model describes the predicted spatial probability distributions of the incoming patient’s organs in the upcoming weeks of treatment, based on observations of past patients. The generative model is interactively linked to treatment plan evaluation, supporting the selection of the optimal treatment strategy. We present a usage scenario, demonstrating the applicability of PREVIS in a clinical research setting, and we evaluate our visual analytics tool with eight clinical researchers.
10.1016/j.cag.2021.04.010
ChemVA: Interactive Visual Analysis of Chemical Compound Similarity in Virtual Screening
IEEE Transactions on Visualization and Computer Graphics
10.1109/tvcg.2020.3030438LoopGrafter: Visual Support for the Grafting Workflow of Protein Loops
IEEE Transactions on Visualization and Computer Graphics
10.1109/tvcg.2021.3114755
VRdeo: Creating engaging educational material for asynchronous student-teacher exchange using virtual reality
Computers & Graphics
10.1016/j.cag.2021.06.009Co-authored publications (2021)
A Comparison of Monoscopic and Stereoscopic 3D Visualizations: Effect on Spatial Planning in Digital Twins
Lukáš Herman, Vojtěch Juřík, Dajana Snopková, Jiří Chmelík, Pavel Ugwitz, Zdeněk Stachoň, Čeněk Šašinka, Tomáš Řezník
10.3390/rs13152976Exploring tilting methods for typing under water
Cejka, Jan, Chmelik, Jiri, Liarokapis, Fotis
10.1007/s11042-020-09305-72020
Taggle: Combining overview and details in tabular data visualizations
Katarína Furmanová, Samuel Gratzl, Holger Stitz, Thomas Zichner, Miroslava Jarešová, Alexander Lex, Marc Streit
Information Visualization
Most tabular data visualization techniques focus on overviews, yet many practical analysis tasks are concerned with investigating individual items of interest. At the same time, relating an item to the rest of a potentially large table is important. In this work, we present Taggle, a tabular visualization technique for exploring and presenting large and complex tables. Taggle takes an item-centric, spreadsheet-like approach, visualizing each row in the source data individually using visual encodings for the cells. At the same time, Taggle introduces data-driven aggregation of data subsets. The aggregation strategy is complemented by interaction methods tailored to answer specific analysis questions, such as sorting based on multiple columns and rich data selection and filtering capabilities. We demonstrate Taggle by a case study conducted by a domain expert on complex genomics data analysis for the purpose of drug discovery.
10.1177/1473871619878085
DockVis: Visual Analysis of Molecular Docking Trajectories
Katarína Furmanová, Ondrej Vavra, Barbora Kozlikova, Jiri Damborsky, Vojtěch Vonásek, David Bednář, Jan Byška
Computer Graphics Forum
Computation of trajectories for ligand binding and unbinding via protein tunnels and channels is important for predicting possible protein-ligand interactions. These highly complex processes can be simulated by several software tools, which provide biochemists with valuable information for drug design or protein engineering applications. This paper focuses on aiding this exploration process by introducing the DockVis visual analysis tool. DockVis operates with the multivariate output data from one of the latest available tools for the prediction of ligand transport, CaverDock. DockVis provides the users with several linked views, combining the 2D abstracted depictions of ligands and their surroundings and properties with the 3D view. In this way,we enable the users to perceive the spatial configurations of ligand passing through the protein tunnel. The users are initially visually directed to the most relevant parts of ligand trajectories, which can be then explored in higher detail by the follow-up analyses. DockVis was designed in tight collaboration with protein engineers developing the CaverDock tool. However, the concept of DockVis can be extended to any other tool predicting ligand pathways by the molecular docking. DockVis will be made available to the wide user community as part of the Caver Analyst 3.0 software package (www.caver.cz).
10.1111/cgf.14048
Multiscale Visual Drilldown for the Analysis of Large Ensembles of Multi-Body Protein Complexes
IEEE Transactions on Visualization and Computer Graphics
When studying multi-body protein complexes, biochemists use computational tools that can suggest hundreds or thousands of their possible spatial configurations. However, it is not feasible to experimentally verify more than only a very small subset of them. In this paper, we propose a novel multiscale visual drilldown approach that was designed in tight collaboration with proteomic experts, enabling a systematic exploration of the configuration space. Our approach takes advantage of the hierarchical structure of the data – from the whole ensemble of protein complex configurations to the individual configurations, their contact interfaces, and the interacting amino acids. Our new solution is based on interactively linked 2D and 3D views for individual hierarchy levels and at each level, we offer a set of selection and filtering operations enabling the user to narrow down the number of configurations that need to be manually scrutinized. Furthermore, we offer a dedicated filter interface, which provides the users with an overview of the applied filtering operations and enables them to examine their impact on the explored ensemble. This way, we maintain the history of the exploration process and thus enable the user to return to an earlier point of the exploration. We demonstrate the effectiveness of our approach on two case studies conducted by collaborating proteomic experts.
10.1109/tvcg.2019.2934333VAPOR: Visual Analytics for the Exploration of Pelvic Organ Variability in Radiotherapy.
Katarína Furmanová, Nicolas Grossmann, Ludvig P. Muren, Oscar Casares-Magaz, Vitali Moiseenko, John P. Einck, Eduard M. Gröller, Renata G. Raidou
Computers & Graphics
In radiation therapy (RT) for prostate cancer, changes in patient anatomy during treatment might lead to inadequate tumor coverage and higher irradiation of healthy tissues in the nearby pelvic organs. Exploring and analyzing anatomical variability throughout the course of RT can support the design of more robust treatment strategies, while identifying patients that are prone to radiation-induced toxicity. We present VAPOR, a novel application for the exploration of pelvic organ variability in a cohort of patients, across the entire treatment process. Our application addresses: (i) the global exploration and analysis of anatomical variability in an abstracted tabular view, (ii) the local exploration and analysis thereof in anatomical 2D/3D views, where comparative and ensemble visualizations are integrated, and (iii) the correlation of anatomical variability with radiation doses and potential toxicity. The workflow is based on available retrospective cohort data, which include segmentations of the bladder, the prostate, and the rectum through the entire treatment period. VAPOR is applied to four usage scenarios, which were conducted with two medical physicists. Our application provides clinical researchers with promising support in demonstrating the significance of treatment adaptation to anatomical changes.
10.1016/j.cag.2020.07.001Visual Analysis of Protein–Protein Interaction Docking Models Using COZOID Tool
Protein-Protein Interaction Networks
Networks of protein–protein interactions (PPI) constitute either stable or transient complexes in every cell. Most of the cellular complexes keep their function, and therefore stay similar, during evolution. The evolutionary constraints preserve most cellular functions via preservation of protein structures and interactions. The evolutionary conservation information is utilized in template-based approaches, like protein structure modeling or docking. Here we use the combination of the template-free docking method with conservation-based selection of the best docking model using our newly developed COZOID tool. We describe a step-by-step protocol for visual selection of docking models, based on their similarity to the original protein complex structure. Using the COZOID tool, we first analyze contact zones of the original complex structure and select contact amino acids for docking restraints. Then we model and dock the homologous proteins. Finally, we utilize different analytical modes of our COZOID tool to select the docking models most similar to the original complex structure.
10.1007/978-1-4939-9873-9_7
PINGU: Principles of Interactive Navigation for Geospatial Understanding
Zoltán Orémuš, Kahin Akram Hassan, Jiří Chmelík, Michaela Kňažková, Jan Byška, Renata Georgia Raidou, Barbora Kozlíková
IEEE PacificVis 2020
10.1109/pacificvis48177.2020.7567Co-authored publications (2020)
The 3D hype: Evaluating the potential of real 3D visualization in geo-related applications
Vojtěch Juřík, Vincent Lecours, Lukáš Herman, Dajana Snopková, Adrianne John Galang, Zdeněk Stachoň, Jiří Chmelík, Petr Kubíček, Čeněk Šašinka
10.1371/journal.pone.0233353Lessons learnt from developing visual analytics applications for adaptive prostate cancer radiotherapy
Renata Georgia Raidou, Katarína Furmanová, Nicolas Grossmann, Oscar Casares-Magaz, Vitali Moiseenko, John P Einck, Eduard Gröller, Ludvig P Muren
10.2312/visgap.20201110Intrinsic-Extrinsic Convolution and Pooling for Learning on 3D Protein Structures
Pedro Hermosilla, Marco Schäfer, Matěj Lang, Gloria Fackelmann, Pere Pau Vázquez, Barbora Kozlíková, Michael Krone, Tobias Ritschel, Timo Ropinski
10.48550/arxiv.2007.06252
Dynamics-function relationship in the catalytic domains of N-terminal acetyltransferases
Angèle Abboud, Pierre Bédoucha, Jan Byška, Thomas Arnesen, Nathalie Reuter
10.1016/j.csbj.2020.02.017
Visual exploration of large normal mode spaces to study protein flexibility
Pierre Bedoucha, Nathalie Reuter, Helwig Hauser, Jan Byška
10.1016/j.cag.2020.05.025
The Moving Target of Visualization Software for an Ever More Complex World
Guido Reina, Hank Childs, Krešimir Matković, Katja Bühler, Manuela Waldner, David Pugmire, Barbora Kozlíková, Timo Ropinski, Patric Ljung, Takayuki Itoh, Eduard Gröller, Michael Krone
10.1016/j.cag.2020.01.0052019
An Interactive and Multimodal Virtual Mind Map for Future Workplace
David Kuťák, Milan Doležal, Bojan Kerous, Zdenek Eichler, Jiří Vašek, Fotis Liarokapis
Frontiers in ICT
10.3389/fict.2019.00014
DockVis: Visual Analysis of Molecular Docking Data
Eurographics Workshop on Visual Computing for Biology and Medicine
Molecular docking is one of the key mechanisms for predicting possible interactions between ligands and proteins. This highly complex task can be simulated by several software tools, providing the biochemists with possible ligand trajectories, which have to be subsequently explored and evaluated for their biochemical relevance. This paper focuses on aiding this exploration process by introducing DockVis visual analysis tool. DockVis operates primarily with the multivariate output data from one of the latest available tools for molecular docking, CaverDock. CaverDock output consists of several parameters and properties, which have to be subsequently studied and understood. DockVis was designed in tight collaboration with protein engineers using the CaverDock tool. However, we believe that the concept of DockVis can be extended to any other molecular docking tool providing the users with corresponding computation results.
10.2312/vcbm.20191238Visual Analysis of Ligand Trajectories in Molecular Dynamics
Adam Jurčík, Katarína Furmanová, Jan Byška, Vojtěch Vonásek, Ondrej Vavra, Pavol Ulbrich, Helwig Hauser, Barbora Kozlikova
IEEE Pacific Visualization Symposium 2019
In many cases, protein reactions with other small molecules (ligands) occur in a deeply buried active site. When studying these types of reactions, it is crucial for biochemists to examine trajectories of ligand motion. These trajectories are predicted with in-silico methods that produce large ensembles of possible trajectories. In this paper, we propose a novel approach to the interactive visual exploration and analysis of large sets of ligand trajectories, enabling the domain experts to understand protein function based on the trajectory properties. The proposed solution is composed of multiple linked 2D and 3D views, enabling the interactive exploration and filtering of trajectories in an informed way. In the workflow, we focus on the practical aspects of the interactive visual analysis specific to ligand trajectories. We adapt the small multiples principle to resolve an overly large number of trajectories into smaller chunks that are easier to analyze. We describe how drill-down techniques can be used to create and store selections of the trajectories with desired properties, enabling the comparison of multiple datasets. In appropriately designed 2D and 3D views, biochemists can either observe individual trajectories or choose to aggregate the information into a functional boxplot or density visualization. Our solution is based on a tight collaboration with the domain experts, aiming to address their needs as much as possible. The usefulness of our novel approach is demonstrated by two case studies, conducted by the collaborating protein engineers.
10.1109/pacificvis.2019.00032
Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization
Jan Byška, Thomas Trautner, Sérgio Manuel Marques, Jiří Damborský, Barbora Kozlíková, Manuela Waldner
Computer Graphics Forum
10.1111/cgf.13701
Labels on Levels: Labeling of Multi-Scale Multi-Instance and Crowded 3D Biological Environments
David Kouřil, Ladislav Čmolík, Barbora Kozlíková, Hsiang-Yun Wu, Graham Johnson, David S. Goodsell, Arthur Olson, Eduard M. Groeller, Ivan Viola
IEEE Transactions on Visualization and Computer Graphics
10.1109/tvcg.2018.2864491Co-authored publications (2019)
Digital restoration of fragmentary human skeletal remains: Testing the feasibility of virtual reality
Jurda, Mikolas, Urbanova, Petra, Chmelik, Jiri
10.1016/j.jflm.2019.06.005
Sampling-based Motion Planning for Tracking Evolution of Dynamic Tunnels in Molecular Dynamics Simulations
10.1007/s10846-018-0877-6
Visualization of Large Molecular Trajectories
David Duran, Pedro Hermosilla, Timo Ropinski, Barbora Kozlíková, Álvar Vinacua, Pere-Pau Vazquez
10.1109/tvcg.2018.2864851
Multiscale Molecular Visualization
Haichao Miao, Tobias Klein, David Kouřil, Peter Mindek, Karsten Schatz, Eduard M. Gröller, Barbora Kozlíková, Tobias Isenberg, Ivan Viola
10.1016/j.jmb.2018.09.0042018
CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories
Adam Jurčík, David Bednář, Jan Byška, Sérgio Manuel Marques, Katarína Furmanová, Lukáš Daniel, Piia Pauliina Kokkonen, Jan Brezovský, Ondřej Strnad, Jan Stourac, Antonín Pavelka, Martin Manak, Jiri Damborsky, Barbora Kozlikova
Bioinformatics
Motivation: Studying the transport paths of ligands, solvents, or ions in transmembrane proteins and proteins with buried binding sites is fundamental to the understanding of their biological function. A detailed analysis of the structural features influencing the transport paths is also important for engineering proteins for biomedical and biotechnological applications. Results: CAVER Analyst 2.0 is a software tool for quantitative analysis and real-time visualization of tunnels and channels in static and dynamic structures. This version provides the users with many new functions, including advanced techniques for intuitive visual inspection of the spatiotemporal behavior of tunnels and channels. Novel integrated algorithms allow an efficient analysis and data reduction in large protein structures and molecular dynamic simulations. Availability and implementation: CAVER Analyst 2.0 is a multi-platform standalone Java-based application. Binaries and documentation are freely available at www.caver.cz.
10.1093/bioinformatics/bty386
COZOID: COntact ZOne IDentifier for visual analysis of protein-protein interactions
BMC Bioinformatics
BACKGROUND: Studying the patterns of protein-protein interactions (PPIs) is fundamental for understanding the structure and function of protein complexes. The exploration of the vast space of possible mutual configurations of interacting proteins and their contact zones is very time consuming and requires the proteomic expert knowledge. RESULTS: In this paper, we propose a novel tool containing a set of visual abstraction techniques for the guided exploration of PPI configuration space. It helps proteomic experts to select the most relevant configurations and explore their contact zones at different levels of detail. The system integrates a set of methods that follow and support the workflow of proteomics experts. The first visual abstraction method, the Matrix view, is based on customized interactive heat maps and provides the users with an overview of all possible residue-residue contacts in all PPI configurations and their interactive filtering. In this step, the user can traverse all input PPI configurations and obtain an overview of their interacting amino acids. Then, the models containing a particular pair of interacting amino acids can be selectively picked and traversed. Detailed information on the individual amino acids in the contact zones and their properties is presented in the Contact-Zone list-view. The list-view provides a comparative tool to rank the best models based on the similarity of their contacts to the template-structure contacts. All these techniques are interactively linked with other proposed methods, the Exploded view and the Open-Book view, which represent individual configurations in three-dimensional space. These representations solve the high overlap problem associated with many configurations. Using these views, the structural alignment of the best models can also be visually confirmed. CONCLUSIONS: We developed a system for the exploration of large sets of protein-protein complexes in a fast and intuitive way. The usefulness of our system has been tested and verified on several docking structures covering the three major types of PPIs, including coiled-coil, pocket-string, and surface-surface interactions. Our case studies prove that our tool helps to analyse and filter protein-protein complexes in a fraction of the time compared to using previously available techniques.
10.1186/s12859-018-2113-6Co-authored publications (2018)
Collaborative Immersive Virtual Environments for Education in Geography
Čeněk Šašinka, Zdeněk Stachoň, Michal Sedlák, Jiří Chmelík, Lukáš Herman, Petr Kubíček, Alžběta Šašinková, Milan Doležal, Hynek Tejkl, Tomáš Urbánek, Hana Svatoňová, Pavel Ugwitz, Vojtěch Juřík
10.3390/ijgi8010003
Instant Construction and Visualization of Crowded Biological Environments
Tobias Klein, Ludovic Autin, Barbora Kozlíková, David S. Goodsell, Arthur Olson, Eduard M. Gröller, Ivan Viola
10.1109/tvcg.2017.27442582017
AnthroVis: Visual Analysis of 3D Mesh Ensembles for Forensic Anthropology
Proceedings of the 33rd Spring Conference on Computer Graphics
Digital approaches to shape comparison and analysis play a very important role in forensic anthropology. New methods are still emerging and the whole area is experiencing a shift from traditional 2D image data to processing of 3D meshes. Therefore, the visual exploration of 3D meshes and methods for their visual comparison play a crucial role in the anthropological research. In our paper we present a novel AnthroVis tool for visual analysis of 3D mesh ensembles, which was designed in tight cooperation with the domain experts. It aims to enhance their workflow by introducing several visualizations that help to understand the similarities and differences between 3D meshes. AnthroVis in general consists of three methods, which serve as a guidance in the process of the comparison of two or more mesh ensembles. The first method, based on the idea of interactive heat plots, provides an overview of pairwise comparisons in a set of analyzed meshes and enables their filtering and sorting. The second method consists of anthropologically relevant cross-cuts indicating the variability through the set of meshes. The last method uses superimposition principle for pairs of meshes equipped with several visual enhancements indicating local mesh differences in three-dimensional space. The domain expert evaluation was performed primarily on facial images, but the tool proved to be applicable to other areas of forensic anthropology as well. Its usefulness is demonstrated by three case studies describing the real situations and problems encountered by anthropologists in forensic casework.
10.1145/3154353.3154363
Interactive Exploration of Ligand Transportation through Protein Tunnels
Katarína Furmanová, Miroslava Jarešová, Jan Byška, Adam Jurčík, Julius Parulek, Helwig Hauser, Barbora Kozlikova
BMC Bioinformatics
Background: Protein structures and their interaction with ligands have been in the focus of biochemistry and structural biology research for decades. The transportation of ligand into the protein active site is often complex process, driven by geometric and physico-chemical properties, which renders the ligand path full of jitter and impasses. This prevents understanding of the ligand transportation and reasoning behind its behavior along the path. Results: To address the needs of the domain experts we design an explorative visualization solution based on a multi-scale simplification model. It helps to navigate the user to the most interesting parts of the ligand trajectory by exploring different attributes of the ligand and its movement, such as its distance to the active site, changes of amino acids lining the ligand, or ligand “stuckness”. The process is supported by three linked views – 3D representation of the simplified trajectory, scatterplot matrix, and bar charts with line representation of ligand-lining amino acids. Conclusions: The usage of our tool is demonstrated on molecular dynamics simulations provided by the domain experts. The tool was tested by the domain experts from protein engineering and the results confirm that it helps to navigate the user to the most interesting parts of the ligand trajectory and to understand the ligand behavior.
10.1186/s12859-016-1448-0
Visualization of Biomolecular Structures: State of the Art Revisited
Barbora Kozlíková, Michael Krone, Martin Falk, Norbert Lindow, Marc Baaden, Daniel Baum, Ivan Viola, Julius Parulek, Hans-Christian Hege
Computer Graphics Forum
10.1111/cgf.13072Co-authored publications (2017)
3D MODELLING AND MAPPING FOR VIRTUAL EXPLORATION OF UNDERWATER ARCHAEOLOGY ASSETS
Liarokapis, F., Kouril, P., Agrafiotis, P., Demesticha, S., Chmelik, J., Skarlatos, D.
10.5194/isprs-archives-xlii-2-w3-425-2017
Comparative Visualization of Protein Secondary Structures
Lucia Kocincová, Miroslava Jarešová, Jan Byška, Julius Parulek, Helwig Hauser, Barbora Kozlíková
10.1186/s12859-016-1449-z
Watergate: Visual Exploration of Water Trajectories in Protein Dynamics
Viktor Vad, Jan Byška, Adam Jurčík, Ivan Viola, Eduard M. Gröller, Helwig Hauser, Sérgio Manuel Marques, Jiří Damborský, Barbora Kozlíková
10.2312/vcbm.20171235
Protein Tunnel Reprojection for Physico-Chemical Property Analysis
Jan Malzahn, Barbora Kozlíková, Timo Ropinski
10.2312/vcbm.201712312016
AnimoAminoMiner: Exploration of Protein Tunnels and their Properties in Molecular Dynamics
Jan Byška, Mathieu Le Muzic, Eduard Gröller, Ivan Viola, Barbora Kozlíková
IEEE Transactions on Visualization and Computer Graphics
10.1109/tvcg.2015.2467434
Accelerated Visualization of Transparent Molecular Surfaces in Molecular Dynamics
Adam Jurčík, Julius Parulek, Jiří Sochor, Barbora Kozlíková
IEEE Pacific Visualization Symposium 2016
10.1109/pacificvis.2016.7465258Co-authored publications (2016)
CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules
Antonín Pavelka, Eva Šebestová, Barbora Kozlíková, Jan Brezovský, Jiří Sochor, Jiří Damborský
10.1109/tcbb.2015.2459680
Visual Analysis of Biomolecular Cavities: State of the Art
Michael Krone, Barbora Kozlíková, Norbert Lindow, Marc Baaden, Daniel Baum, Julius Parulek, Hans-Christian Hege, Ivan Viola
10.1111/cgf.12928
Application of Sampling-based Path Planning for Tunnel Detection in Dynamic Protein Structures
Vojtěch Vonásek, Barbora Kozlíková
10.1109/mmar.2016.7575276
Unfolding and Interactive Exploration of Protein Tunnels and their Dynamics
Ivan Kolesár, Jan Byška, Julius Parulek, Helwig Hauser, Barbora Kozlíková
10.2312/vcbm.201612652015
Visibility-Based Approach to Surface Detection of Tunnels in Proteins
Adam Jurčík, Jan Byška, Jiří Sochor, Barbora Kozlíková
31st Proceedings of Spring Conference on Computer Graphics
10.1145/2788539.2788548
Path-planning algorithm for transportation of molecules through protein tunnel bottlenecks
Jan Byška, Ivana Kolingerová, Barbora Kozlíková, Jiří Sochor
31st Proceedings of Spring Conference on Computer Graphics
10.1145/2788539.2788550
MoleCollar and Tunnel Heat Map Visualizations for Conveying Spatio-Temporo-Chemical Properties Across and Along Protein Voids
Jan Byška, Adam Jurčík, Eduard M. Gröller, Ivan Viola, Barbora Kozlíková
Computer Graphics Forum
10.1111/cgf.12612
Visualization of Biomolecular Structures: State of the Art
Barbora Kozlíková, Michael Krone, Norbert Lindow, Martin Falk, Marc Baaden, Daniel Baum, Ivan Viola, Julius Parulek, Hans-Christian Hege
Eurographics Conference on Visualization (EuroVis) – STARs
10.2312/eurovisstar.20151112Co-authored publications (2015)
Generation of variable human faces from 3D scan dataset
10.1109/vs-games.2015.7295777Automated facial landmark detection, comparison and visualization
10.1145/2788539.27885402014
CAVER Analyst 1.0: Graphic tool for interactive visualization and analysis of tunnels and channels in protein structures
Barbora Kozlíková, Eva Šebestová, Vilém Šustr, Jan Brezovský, Ondřej Strnad, Lukáš Daniel, David Bednář, Antonín Pavelka, Martin Maňák, Martin Bezděka, Petr Beneš, Matúš Kotry, Artur Wiktor Gora, Jiří Damborský, Jiří Sochor
Bioinformatics
10.1093/bioinformatics/btu364