Adjunct associate professor
Publications
2017
![[PDF]](https://vis.uib.no/wp-content/plugins/papercite/img/pdf.png)
[Bibtex] @ARTICLE {Furmanova2017Ligand,
author = "Furmanov{\'a}, Katar{\'\i}na and Jare{\v{s}}ov{\'a}, Miroslava and By{\v{s}}ka, Jan and Jur{\v{c}}{\'i}k, Adam and Parulek, J{\'u}lius and Hauser, Helwig and Kozl{\'i}kov{\'a}, Barbora",
title = "Interactive exploration of ligand transportation through protein tunnels",
journal = "BMC Bioinformatics",
year = "2017",
volume = "18(Suppl 2)",
number = "22",
month = "feb",
abstract = "Background: Protein structures and their interaction with ligands have been in the focus of biochemistry andstructural biology research for decades. The transportation of ligand into the protein active site is often complexprocess, driven by geometric and physico-chemical properties, which renders the ligand path full of jitter andimpasses. 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 amulti-scale simplification model. It helps to navigate the user to the most interesting parts of the ligand trajectory byexploring different attributes of the ligand and its movement, such as its distance to the active site, changes of aminoacids lining the ligand, or ligand ââ¬Åstucknessââ¬?. The process is supported by three linked views ââ¬â 3D representation of thesimplified 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 domainexperts. The tool was tested by the domain experts from protein engineering and the results confirm that it helps tonavigate the user to the most interesting parts of the ligand trajectory and to understand the ligand behavior",
pdf = "pdfs/Furmanova2017.pdf",
images = "images/Furmanova2016Interactive.png",
thumbnails = "images/Furmanova2016Interactive.png",
note = "https://doi.org/10.1186/s12859-016-1448-0"
}@ARTICLE {Kocincova2017SS,
author = "Kocincov{\'a}, Lucia and Jare{\v{s}}ov{\'a}, Miroslava and By{\v{s}}ka, Jan and Parulek, J{\'u}lius and Hauser, Helwig and Kozl{\'i}kov{\'a}, Barbora",
title = "Comparative visualization of protein secondary structures",
journal = "BMC Bioinformatics",
year = "2017",
volume = "18(Suppl 2)",
number = "23",
month = "feb",
abstract = "Background: Protein function is determined by many factors, namely by its constitution, spatial arrangement, anddynamic behavior. Studying these factors helps the biochemists and biologists to better understand the proteinbehavior and to design proteins with modified properties. One of the most common approaches to these studies is tocompare the protein structure with other molecules and to reveal similarities and differences in their polypeptidechains.Results: We support the comparison process by proposing a new visualization technique that bridges the gapbetween traditionally used 1D and 3D representations. By introducing the information about mutual positions ofprotein chains into the 1D sequential representation the users are able to observe the spatial differences between theproteins without any occlusion commonly present in 3D view. Our representation is designed to serve namely forcomparison of multiple proteins or a set of time steps of molecular dynamics simulation.Conclusions: The novel representation is demonstrated on two usage scenarios. The first scenario aims to compare aset of proteins from the family of cytochromes P450 where the position of the secondary structures has a significantimpact on the substrate channeling. The second scenario focuses on the protein flexibility when by comparing a setof time steps our representation helps to reveal the most dynamically changing parts of the protein chain.",
pdf = "pdfs/Kocincova2017.pdf",
images = "images/Lucia2016Comparative.png",
thumbnails = "images/Lucia2016Comparative.png",
note = "https://doi.org/10.1186/s12859-016-1449-z"
}2016
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[Bibtex] @ARTICLE {Michael2016Visual,
author = "Michael Krone and Barbora Kozlikova and Norbert Lindow and Marc Baaden and Daniel Baum, and Julius Parulek and Hans-Christian Hege and Ivan Viola",
title = "Visual Analysis of Biomolecular Cavities: State of the Art",
journal = "Computer Graphics Forum",
year = "2016",
abstract = "In this report we review and structure the branch of molecular visualization that is concerned with the visual analysis of cavities in macromolecular protein structures. First the necessary background, the domain terminology, and the goals of analytical reasoning are introduced. Based on a comprehensive collection of relevant research works, we present a novel classification for cavity detection approaches and structure them into four distinct classes: grid-based, Voronoi-based, surface-based, and probe-based methods. The subclasses are then formed by their combinations. We match these approaches with corresponding visualization technologies starting with direct 3D visualization, followed with non-spatial visualization techniques that for example abstract the interactions between structures into a relational graph, straighten the cavity of interest to see its profile in one view, or aggregate the time sequence into a single contour plot. We also discuss the current state of methods for the visual analysis of cavities in dynamic data such as molecular dynamics simulations. Finally, we give an overview of the most common tools that are actively developed and used in the structural biology and biochemistry research. Our report is concluded by an outlook on future challenges in the field.",
images = "images/STARcavities2016.png",
thumbnails = "images/STARcavities2016.png",
publisher = "The Eurographics Association and John Wiley \& Sons Ltd.",
issn = "1467-8659",
doi = "10.1111/cgf.12928",
project = "physioillustration"
} [Bibtex]
@INPROCEEDINGS {Kolesar2016VCBM,
author = "Ivan Kolesar and Jan By\v{s}ka and Julius Parulek and Helwig Hauser and Barbora Kozl\'{i}kov\'{a}",
title = "Unfolding and Interactive Exploration of Protein Tunnels andtheir Dynamics",
booktitle = "Eurographics Workshop on Visual Computing for Biology and Medicine",
year = "2016",
pages = "1--10",
month = "sep",
abstract = "The presence of tunnels in protein structures substantially influences their reactivity with other molecules. Therefore, studying their properties and changes over time has been in the scope of biochemists for decades. In this paper we introduce a novel approach for comparative visualization and exploration of ensembles of tunnels. Our goal is to overcome occlusion problems present in traditional tunnel representations while providing users a quick way to navigate through the input dataset to identify potentially interesting tunnels. First, we unfold the input tunnels to a 2D representation enabling to observe the mutual position of amino acids forming the tunnel surface and the amount of surface they influence. These 2D images are subsequently described by image moments commonly used in image processing. This way we are able to detect similarities and outliers in the dataset, which are visualized as clusters in a scatterplot graph. The same coloring scheme is used in the linked bar chart enabling to detect the position of the cluster members over time. These views provide a way to select a subset of potentially interesting tunnels that can be further explored in detail using the 2D unfolded view and also traditional 3D representation. The usability of our approach is demonstrated on case studies conducted by the domain experts.",
images = "images/Kolesar-2016-VCBM.png",
thumbnails = "images/Kolesar-2016-VCBM-thumbnail.jpg",
proceedings = "Proceedings of Eurographics Workshop on Visual Computing in Biology and Medicine",
keywords = "unfolding, storytelling, game visualization",
location = "Bergen, Norway",
project = "physioillustration"
}2015
[Bibtex] @INPROCEEDINGS {eurovisstar20151112,
author = "Kozlikova, Barbora and Krone, Michael and Lindow, Norbert and Falk, Martin and Baaden, Marc and Baum, Daniel and Viola, Ivan and Parulek, Julius and Hege, Hans-Christian",
title = "Visualization of Biomolecular Structures: State of the Art",
booktitle = "Eurographics Conference on Visualization (EuroVis) - STARs",
year = "2015",
editor = "R. Borgo and F. Ganovelli and I. Viola",
volume = "-",
publisher = "The Eurographics Association",
abstract = "Structural properties of molecules are of primary concern in many fields. This report provides a comprehensiveoverview on techniques that have been developed in the fields of molecular graphics and visualization with a focuson applications in structural biology. The field heavily relies on computerized geometric and visual representationsof three-dimensional, complex, large, and time-varying molecular structures. The report presents a taxonomy thatdemonstrates which areas of molecular visualization have already been extensively investigated and where the fieldis currently heading. It discusses visualizations for molecular structures, strategies for efficient display regardingimage quality and frame rate, covers different aspects of level of detail, and reviews visualizations illustrating thedynamic aspects of molecular simulation data. The report concludes with an outlook on promising and importantresearch topics to enable further success in advancing the knowledge about interaction of molecular structures.",
images = "images/molvis_star.png",
thumbnails = "images/molvis_star.png",
proceedings = "Eurographics Conference on Visualization (EuroVis) - STARs",
doi = "10.2312/eurovisstar.20151112",
journal = "-",
number = "-",
keywords = "-",
project = "physioillustration"
} [Bibtex]
@INPROCEEDINGS {cellVIEW_2015,
author = "Mathieu Le Muzic and Ludovic Autin and Julius Parulek and Ivan Viola",
title = "cellVIEW: a Tool for Illustrative and Multi-Scale Rendering of Large Biomolecular Datasets",
booktitle = "EG Workshop on Visual Computing for Biology and Medicine",
year = "2015",
month = "sep",
abstract = "In this article we introduce cellVIEW, a new system to interactively visualize large biomolecular datasets on the atomic level. Our tool is unique and has been specifically designed to match the ambitions of our domain experts to model and interactively visualize structures comprised of several billions atom. The cellVIEW system integrates acceleration techniques to allow for real-time graphics performance of 60 Hz display rate on datasets representing large viruses and bacterial organisms. Inspired by the work of scientific illustrators, we propose a level-of-detail scheme which purpose is two-fold: accelerating the rendering and reducing visual clutter. The main part of our datasets is made out of macromolecules, but it also comprises nucleic acids strands which are stored as sets of control points. For that specific case, we extend our rendering method to support the dynamic generation of DNA strands directly on the GPU. It is noteworthy that our tool has been directly implemented inside a game engine. We chose to rely on a third party engine to reduce software development work-load and to make bleeding-edge graphics techniques more accessible to the end-users. To our knowledge cellVIEW is the only suitable solution for interactive visualization of large bimolecular landscapes on the atomic level and is freely available to use and extend.",
images = "images/cellview2015.png",
thumbnails = "images/cellview2015.png",
proceedings = "Proceedings of Eurographics Workshop on Visual Computing in Biology and Medicine",
project = "physioillustration"
}@INPROCEEDINGS {7156384,
author = "Le Muzic, Mathieu and Waldner, Manuela and Parulek, Julius and Viola, Ivan",
title = "Illustrative Timelapse: A technique for illustrative visualization of particle-based simulations",
booktitle = "Visualization Symposium (PacificVis), 2015 IEEE Pacific",
year = "2015",
pages = "247-254",
month = "April",
abstract = "Animated movies are a popular way to communicate complex phenomena in cell biology to the broadaudience. Animation artists apply sophisticated illustration techniques to communicate a story, while trying to maintain a realistic representation of a complex dynamic environment. Since suchhand-crafted animations are time-consuming and cost-intensive to create, our goal is to formalizeillustration techniques used by artists to facilitate the automatic creation of visualizations generated from mesoscale particle-based molecular simulations. Our technique Illustrative Timelapse supports visual exploration of complex biochemical processes in dynamic environments by(1) seamless temporal zooming to observe phenomena in different temporal resolutions, (2) visualabstraction of molecular trajectories to ensure that observers are able to visually follow themain actors, (3) increased visual focus on events of interest, and (4) lens effects to preserve arealistic representation of the environment in the context. Results from a first user studyindicate that visual abstraction of trajectories improves the ability to follow a story and isalso appreciated by users. Lens effects increased the perceived amount of molecular motion in theenvironment while trading off traceability of individual molecules.",
images = "images/illustrative_timelapse.png",
thumbnails = "images/illustrative_timelapse.png",
proceedings = "Proceedings of IEEE Pacific Visualization",
keywords = "Biological system modeling;Data models;Data visualization;Lenses;Trajectory;Videos;Visualization;I.3.7[COMPUTER GRAPHICS]: Three-Dimensional Graphics and Realismââ¬âAnimation;I.6.3 [SIMULATION AND MODELING]: Applicationsââ¬â",
doi = "10.1109/PACIFICVIS.2015.7156384",
project = "physioillustration"
}2014
[Bibtex] @ARTICLE {Natali14Rapid,
author = "Mattia Natali and Julius Parulek and Daniel Patel",
title = "Rapid Modelling of Interactive Geological Illustrations with Faults and Compaction",
journal = "Proceedings of Spring Conference on Computer Graphics (SCCG)",
year = "2014",
abstract = "In this paper, we propose new methods for building geological illustrations and animations. We focus on allowing geologists to create their subsurface models by means of sketches, to quickly communicate concepts and ideas rather than detailed information. The result of our sketch-based modelling approach is a layer-cake volume representing geological phenomena, where each layer is rock material which has accumulated due to a user-defined depositional event. Internal geological structures can be inspected by different visualization techniques that we employ. Faulting and compaction of rock layers are important processes in geology. They can be modelled and visualized with our technique. Our representation supports non-planar faults that a user may define by means of sketches. Real-time illustrative animations are achieved by our GPU accelerated approach.",
pdf = "pdfs/Natali14Rapid.pdf",
images = "images/Natali2014Rapid0.png, images/Natali2014Rapid1.png",
thumbnails = "images/Natali2014Rapid0.png, images/Natali2014Rapid1.png",
url = "http://dx.doi.org/10.1145/2643188.2643201",
project = "geoillustrator"
}![[VID]](https://vis.uib.no/wp-content/papercite-data/images/video.png)
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