@article{miao_nar_2020, title = "Adenita: interactive 3D modelling and visualization of DNA nanostructures", author = "Elisa De Llano and Haichao Miao and Yasaman Ahmadi and Armanda J Wilson and Morgan Beeby and Ivan Viola and Ivan Barisic", year = "2020", month = jul, doi = "10.1093/nar/gkaa593", journal = "Nucleic Acids Research", URL = "https://www.cg.tuwien.ac.at/research/publications/2020/miao_nar_2020/", } @article{Halladjian_2020, title = "ScaleTrotter: Illustrative Visual Travels Across Negative Scales", author = "Sarkis Halladjian and Haichao Miao and David Kou\v{r}il and Eduard Gr\"{o}ller and Ivan Viola and Tobias Isenberg", year = "2020", month = jan, journal = "IEEE Transactions on Visualization and Computer Graphics", volume = "26", number = "1", URL = "https://www.cg.tuwien.ac.at/research/publications/2020/Halladjian_2020/", } @phdthesis{klein_2019_PHD, title = "Instant Construction of Atomistic Models for Visualization in Integrative Cell Biology", author = "Tobias Klein", year = "2019", abstract = "AbstractComputational models have advanced research of integrative cell biology in variousways. Especially in the biological mesoscale, the scale between atoms and cellularenvironments, computational models improve the understanding and qualitative anal-ysis. The mesoscale is an important range, since it represents the range of scalesthat are not fully accessible to a single experimental technique. Complex molecularassemblies within this scale have been visualized with x-ray crystallography, thoughonly in isolation. Mesoscale models shows how molecules are assembled into morecomplex subcelluar environments that orchestrate the processes of life. The skillfulcombination of the results of imaging and experimental techniques provides a glimpseof the processes, which are happening here. Only recently, biologists have startedto unify the various sources of information. They have begun to computationallyassemble and subsequently visualize complex environments, such as viruses or bacteria.Currently, we live in an opportune time for researching integrative structural biologydue to several factors. First and foremost, the wealth of data, driven through sourceslike online databases, makes structural information about biological entities publiclyavailable. In addition to that, the progress of parallel processors builds the foundationto instantly construct and render large mesoscale environments in atomistic detail.Finally, new scientific advances in visualization allow the efficient rendering of complexbiological phenomena with millions of structural units.In this cumulative thesis, we propose several novel techniques that facilitate the instantconstruction of mesoscale structures. The common methodological strategy of thesetechniques and insight from this thesis is “compute instead of store”. This approacheliminates the storage and memory management complexity, and enables instantchanges of the constructed models. Combined, our techniques are capable of instantlyconstructing large-scale biological environments using the basic structural buildingblocks of cells. These building blocks are mainly nucleic acids, lipids, and solubleproteins. For the generation of long linear polymers formed by nucleic acids, wepropose a parallel construction technique that makes use of a midpoint displacementalgorithm. The efficient generation of lipid membranes is realized through a texturesynthesis approach that makes use of the Wang tiling concept. For the population ofsoluble proteins, we present a staged algorithm, whereby each stage is processed inparallel. We have integrated the instant construction approach into a visual environmentin order to improve several aspects. First, it allows immediate feedback on the createdix structures and the results of parameter changes. Additionally, the integration ofconstruction in visualization builds the foundation for visualization systems that striveto construct large-scale environments on-the-fly. Lastly, it advances the qualitativeanalysis of biological mesoscale environments, where a multitude of synthesized modelsis required. In order to disseminate the physiology of biological mesoscale models,we propose a novel concept that simplifies the creation of multi-scale proceduralanimations. ", month = nov, address = "Favoritenstrasse 9-11/E193-02, A-1040 Vienna, Austria", school = "Research Unit of Computer Graphics, Institute of Visual Computing and Human-Centered Technology, Faculty of Informatics, TU Wien ", URL = "https://www.cg.tuwien.ac.at/research/publications/2019/klein_2019_PHD/", } @article{klein_2019_PGG, title = "Parallel Generation and Visualization of Bacterial Genome Structures", author = "Tobias Klein and Peter Mindek and Ludovic Autin and David Goodsell and Arthur Olson and Eduard Gr\"{o}ller and Ivan Viola", year = "2019", abstract = "Visualization of biological mesoscale models provides a glimpse at the inner workings of living cells. One of the most complex components of these models is DNA, which is of fundamental importance for all forms of life. Modeling the 3D structure of genomes has previously only been attempted by sequential approaches. We present the first parallel approach for the instant construction of DNA structures. Traditionally, such structures are generated with algorithms like random walk, which have inherent sequential constraints. These algorithms result in the desired structure, are easy to control, and simple to formulate. Their execution, however, is very time-consuming, as they are not designed to exploit parallelism. We propose an approach to parallelize the process, facilitating an implementation on the GPU.", month = nov, journal = "Computer Graphics Forum", volume = "38", number = "7", doi = "10.1111/cgf.13816", pages = "57--68", URL = "https://www.cg.tuwien.ac.at/research/publications/2019/klein_2019_PGG/", } @article{amirkhanov-2019-manylands, title = "ManyLands: A Journey Across 4D Phase Space of Trajectories", author = "Aleksandr Amirkhanov and Ilona Kosiuk and Peter Szmolyan and Artem Amirkhanov and Gabriel Mistelbauer and Eduard Gr\"{o}ller and Renata Raidou", year = "2019", abstract = "Mathematical models of ordinary differential equations are used to describe and understand biological phenomena. These models are dynamical systems that often describe the time evolution of more than three variables, i.e., their dynamics take place in a multi-dimensional space, called the phase space. Currently, mathematical domain scientists use plots of typical trajectories in the phase space to analyze the qualitative behavior of dynamical systems. These plots are called phase portraits and they perform well for 2D and 3D dynamical systems. However, for 4D, the visual exploration of trajectories becomes challenging, as simple subspace juxtaposition is not sufficient. We propose ManyLands to support mathematical domain scientists in analyzing 4D models of biological systems. By describing the subspaces as Lands, we accompany domain scientists along a continuous journey through 4D HyperLand, 3D SpaceLand, and 2D FlatLand, using seamless transitions. The Lands are also linked to 1D TimeLines. We offer an additional dissected view of trajectories that relies on small-multiple compass-alike pictograms for easy navigation across subspaces and trajectory segments of interest. We show three use cases of 4D dynamical systems from cell biology and biochemistry. An informal evaluation with mathematical experts confirmed that ManyLands helps them to visualize and analyze complex 4D dynamics, while facilitating mathematical experiments and simulations.", month = oct, journal = "Computer Graphics Forum", volume = "38", number = "7", doi = "10.1111/cgf.13828", pages = "191--202", keywords = "Visual analytics, Web-based interaction", URL = "https://www.cg.tuwien.ac.at/research/publications/2019/amirkhanov-2019-manylands/", } @inproceedings{Sbardellati-2019-vcbm, title = "Interactive Exploded Views for Molecular Structures", author = "Maximilian Sbardellati and Haichao Miao and Hsiang-Yun Wu and Eduard Gr\"{o}ller and Ivan Barisic and Ivan Viola", year = "2019", abstract = "We propose an approach to interactively create exploded views of molecular structures with the goal to help domain experts in their design process and provide them with a meaningful visual representation of component relationships. Exploded views are excellently suited to manage visual occlusion of structure components, which is one of the main challenges when visualizing complex 3D data. In this paper, we discuss four key parameters of an exploded view: explosion distance, direction, order, and the selection of explosion components. We propose two strategies, namely the structure-derived exploded view and the interactive free-form exploded view, for computing these four parameters systematically. The first strategy allows scientists to automatically create exploded views by computing the parameters from the given object structures. The second strategy further supports them to design and customize detailed explosion paths through user interaction. Our approach features the possibility to animate exploded views, to incorporate ease functions into these animations and to display the explosion path of components via arrows. Finally, we demonstrate three use cases with various challenges that we investigated in collaboration with a domain scientist. Our approach, therefore, provides interesting new ways of investigating and presenting the design layout and composition of complex molecular structures.", month = sep, event = "VCBM 2019", booktitle = "Proceedings of the 9th Eurographics Workshop on Visual Computing for Biology and Medicine", pages = "103--112", URL = "https://www.cg.tuwien.ac.at/research/publications/2019/Sbardellati-2019-vcbm/", } @phdthesis{miao_thesis_2019, title = "Geometric Abstraction for Effective Visualization and Modeling", author = "Haichao Miao", year = "2019", abstract = "In this cumulative thesis, I describe geometric abstraction as a strategy to create an integrated visualization system for spatial scientific data. The proposed approach creates a multitude of representations of spatial data in two dominant ways. Along the spatiality axis, it gradually removes spatial details and along the visual detail axis, the features are increasingly aggregated and represented by different visual objects. These representations are then integrated into a conceptual abstraction space that enables users to efficiently change the representation to adjust the abstraction level to a task in mind. To enable the expert to perceive correspondence between these representations, controllable animated transitions are provided. Finally, the abstraction space can record user interactions and provides visual indications to guide the expert towards interesting representations for a particular task and data set. Mental models of the experts play a crucial role in the understanding of the abstract representations and are considered in the design of the visualization system to keep the cognitive load low on the user’s side. This approach is demonstrated in two distinct fields of placenta research and in silico design of DNA nanostructures. For both fields geometric abstraction facilitates effective visual inspection and modeling. The Adenita toolkit, a software for the design of novel DNA nanostructures, implements the proposed visualization concepts. This toolkit, together with the proposed visualization concepts, is currently deployed to several research groups to help them in nanotechnology research.", month = aug, address = "Favoritenstrasse 9-11/E193-02, A-1040 Vienna, Austria", school = "Research Unit of Computer Graphics, Institute of Visual Computing and Human-Centered Technology, Faculty of Informatics, TU Wien ", URL = "https://www.cg.tuwien.ac.at/research/publications/2019/miao_thesis_2019/", } @article{klein_2019_PMP, title = "Multi-Scale Procedural Animations of Microtubule Dynamics Based on Measured Data", author = "Tobias Klein and Ivan Viola and Eduard Gr\"{o}ller and Peter Mindek", year = "2019", abstract = "Biologists often use computer graphics to visualize structures, which due to physical limitations are not possible to imagewith a microscope. One example for such structures are microtubules, which are present in every eukaryotic cell. They are part ofthe cytoskeleton maintaining the shape of the cell and playing a key role in the cell division. In this paper, we propose a scientifically-accurate multi-scale procedural model of microtubule dynamics as a novel application scenario for procedural animation, which cangenerate visualizations of their overall shape, molecular structure, as well as animations of the dynamic behaviour of their growth anddisassembly. The model is spanning from tens of micrometers down to atomic resolution. All the aspects of the model are driven byscientific data. The advantage over a traditional, manual animation approach is that when the underlying data change, for instance dueto new evidence, the model can be recreated immediately. The procedural animation concept is presented in its generic form, withseveral novel extensions, facilitating an easy translation to other domains with emergent multi-scale behavior.", month = aug, journal = "IEEE Transactions on Visualization and Computer Graphics", volume = "26", number = "1", doi = "10.1109/TVCG.2019.2934612", pages = "622--632", URL = "https://www.cg.tuwien.ac.at/research/publications/2019/klein_2019_PMP/", } @incollection{raidou_2019_springer, title = "Visual Analytics for the Representation, Exploration and Analysis of High-Dimensional, Multi-Faceted Medical Data", author = "Renata Raidou", year = "2019", abstract = "Medicine is among research fields with a significant impact on humans and their health. Already for decades, medicine has established a tight coupling with the visualization domain, proving the importance of developing visualization techniques, designed exclusively for this research discipline. However, medical data is steadily increasing in complexity with the appearance of heterogeneous, multi-modal, multiparametric, cohort or population, as well as uncertain data. To deal with this kind of complex data, the field of Visual Analytics has emerged. In this chapter, we discuss the many dimensions and facets of medical data. Based on this classification, we provide a general overview of state-of-the-art visualization systems and solutions dealing with highdimensional, multi-faceted data. Our particular focus will be on multimodal, multi-parametric data, on data from cohort or population studies and on uncertain data, especially with respect to Visual Analytics applications for the representation, exploration, and analysis of highdimensional, multi-faceted medical data.", month = jul, booktitle = "Biomedical Visualisation", chapter = "10", doi = "https://doi.org/10.1007/978-3-030-14227-8_10", editor = "Springer", note = "https://www.springer.com/gp/book/9783030142261", publisher = "Springer", volume = "2", URL = "https://www.cg.tuwien.ac.at/research/publications/2019/raidou_2019_springer/", } @article{byska-2019-mdfc, title = "Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization", author = "Jan Byska and Thomas Trautner and Sergio Marques and Jiri Damborsky and Barbora Kozlikova and Manuela Waldner", year = "2019", abstract = "Analyzing molecular dynamics (MD) simulations is a key aspect to understand protein dynamics and function. With increasing computational power, it is now possible to generate very long and complex simulations, which are cumbersome to explore using traditional 3D animations of protein movements. Guided by requirements derived from multiple focus groups with protein engineering experts, we designed and developed a novel interactive visual analysis approach for long and crowded MD simulations. In this approach, we link a dynamic 3D focus+context visualization with a 2D chart of time series data to guide the detection and navigation towards important spatio-temporal events. The 3D visualization renders elements of interest in more detail and increases the temporal resolution dependent on the time series data or the spatial region of interest. In case studies with different MD simulation data sets and research questions, we found that the proposed visual analysis approach facilitates exploratory analysis to generate, confirm, or reject hypotheses about causalities. Finally, we derived design guidelines for interactive visual analysis of complex MD simulation data.", month = jun, journal = "Computer Graphics Forum", volume = "38", number = "3", doi = "10.1111/cgf.13701", pages = "441--453", keywords = "scientific visualization, user centered design", URL = "https://www.cg.tuwien.ac.at/research/publications/2019/byska-2019-mdfc/", } @misc{miao_nantech_2019, title = "Interactive Visual Analysis for the Design of DNA Nanostructures", author = "Haichao Miao and Elisa De Llano and Ivan Viola and Ivan Barisic", year = "2019", month = may, event = "NANTECH 2019 – Nucleic Acid Nanotechnology: From Algorithmic Design to Biochemical Applications – Espoo, Finland", Conference date = "Poster presented at NANTECH 2019 – Nucleic Acid Nanotechnology: From Algorithmic Design to Biochemical Applications – Espoo, Finland (2019-05-27--2019-05-29)", URL = "https://www.cg.tuwien.ac.at/research/publications/2019/miao_nantech_2019/", } @article{wu-2019-bmc, title = "Metabopolis: Scalable Network Layout for Biological Pathway Diagrams in Urban Map Style", author = "Hsiang-Yun Wu and Martin N\"{o}llenburg and Filipa L. Sousa and Ivan Viola", year = "2019", abstract = "Background Biological pathways represent chains of molecular interactions in biological systems that jointly form complex dynamic networks. The network structure changes from the significance of biological experiments and layout algorithms often sacrifice low-level details to maintain high-level information, which complicates the entire image to large biochemical systems such as human metabolic pathways. Results Our work is inspired by concepts from urban planning since we create a visual hierarchy of biological pathways, which is analogous to city blocks and grid-like road networks in an urban area. We automatize the manual drawing process of biologists by first partitioning the map domain into multiple sub-blocks, and then building the corresponding pathways by routing edges schematically, to maintain the global and local context simultaneously. Our system incorporates constrained floor-planning and network-flow algorithms to optimize the layout of sub-blocks and to distribute the edge density along the map domain. We have developed the approach in close collaboration with domain experts and present their feedback on the pathway diagrams based on selected use cases. Conclusions We present a new approach for computing biological pathway maps that untangles visual clutter by decomposing large networks into semantic sub-networks and bundling long edges to create space for presenting relationships systematically.", month = may, doi = "http://doi.org/10.1186/s12859-019-2779-4", journal = "BMC Bioinformatics", number = "187", volume = "20", pages = "1--20", keywords = "Biological pathways, Graph drawing, Mapmetaphor, Orthogonallayout, Floorplanning, Edgerouting", URL = "https://www.cg.tuwien.ac.at/research/publications/2019/wu-2019-bmc/", } @techreport{wu-2019-report, title = "From Cells to Atoms - Biological Information Visualization (in Chinese)", author = "Hsiang-Yun Wu and Haichao Miao and Ivan Viola", year = "2019", month = mar, number = "TR-193-02-2019-1", address = "Favoritenstrasse 9-11/E193-02, A-1040 Vienna, Austria", institution = "Research Unit of Computer Graphics, Institute of Visual Computing and Human-Centered Technology, Faculty of Informatics, TU Wien ", note = "human contact: technical-report@cg.tuwien.ac.at", URL = "https://www.cg.tuwien.ac.at/research/publications/2019/wu-2019-report/", } @article{waldin-2019-ccm, title = "Cuttlefish: Color Mapping for Dynamic Multi‐Scale Visualizations", author = "Nicholas Waldin and Manuela Waldner and Mathieu Le Muzic and Eduard Gr\"{o}ller and David Goodsell and Ludovic Autin and Arthur Olson and Ivan Viola", year = "2019", abstract = "Visualizations of hierarchical data can often be explored interactively. For example, in geographic visualization, there are continents, which can be subdivided into countries, states, counties and cities. Similarly, in models of viruses or bacteria at the highest level are the compartments, and below that are macromolecules, secondary structures (such as α‐helices), amino‐acids, and on the finest level atoms. Distinguishing between items can be assisted through the use of color at all levels. However, currently, there are no hierarchical and adaptive color mapping techniques for very large multi‐scale visualizations that can be explored interactively. We present a novel, multi‐scale, color‐mapping technique for adaptively adjusting the color scheme to the current view and scale. Color is treated as a resource and is smoothly redistributed. The distribution adjusts to the scale of the currently observed detail and maximizes the color range utilization given current viewing requirements. Thus, we ensure that the user is able to distinguish items on any level, even if the color is not constant for a particular feature. The coloring technique is demonstrated for a political map and a mesoscale structural model of HIV. The technique has been tested by users with expertise in structural biology and was overall well received.", month = mar, doi = "10.1111/cgf.13611", journal = "Computer Graphics Forum", number = "6", volume = "38", pages = "150--164", keywords = "multiscale visualization, illustrative visualization, molecular visualization", URL = "https://www.cg.tuwien.ac.at/research/publications/2019/waldin-2019-ccm/", } @article{Weissenboeck_2019, title = "Dynamic Volume Lines: Visual Comparison of 3D Volumes through Space-filling Curves", author = "Johannes Weissenb\"{o}ck and Bernhard Fr\"{o}hler and Eduard Gr\"{o}ller and Johann Kastner and Christoph Heinzl", year = "2019", abstract = "The comparison of many members of an ensemble is difficult, tedious, and error-prone, which is aggravated by often justsubtle differences. In this paper, we introduceDynamic Volume Linesfor the interactive visual analysis and comparison of sets of 3Dvolumes. Each volume is linearized along a Hilbert space-filling curve into a 1D Hilbert line plot, which depicts the intensities over theHilbert indices. We present a nonlinear scaling of these 1D Hilbert line plots based on the intensity variations in the ensemble of 3Dvolumes, which enables a more effective use of the available screen space. The nonlinear scaling builds the basis for our interactivevisualization techniques. An interactive histogram heatmap of the intensity frequencies serves as overview visualization. When zoomingin, the frequencies are replaced by detailed 1D Hilbert line plots and optional functional boxplots. To focus on important regions of thevolume ensemble, nonlinear scaling is incorporated into the plots. An interactive scaling widget depicts the local ensemble variations.Our brushing and linking interface reveals, for example, regions with a high ensemble variation by showing the affected voxels ina 3D spatial view. We show the applicability of our concepts using two case studies on ensembles of 3D volumes resulting fromtomographic reconstruction. In the first case study, we evaluate an artificial specimen from simulated industrial 3D X-ray computedtomography (XCT). In the second case study, a real-world XCT foam specimen is investigated. Our results show thatDynamic VolumeLinescan identify regions with high local intensity variations, allowing the user to draw conclusions, for example, about the choice ofreconstruction parameters. Furthermore, it is possible to detect ring artifacts in reconstructions volumes.I", month = jan, journal = "IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS", number = "1", volume = "25", pages = "1040--1049", keywords = "Ensemble data, comparative visualization, visual analysis, Hilbert curve, nonlinear scaling, X-ray computed tomography", URL = "https://www.cg.tuwien.ac.at/research/publications/2019/Weissenboeck_2019/", } @article{Miao_2019, title = "Multiscale Molecular Visualization", author = "Haichao Miao and Tobias Klein and David Kou\v{r}il and Peter Mindek and Karsten Schatz and Eduard Gr\"{o}ller and Barbora Kozlikova and Tobias Isenberg and Ivan Viola", year = "2019", abstract = "We provide a high-level survey of multiscale molecular visualization techniques, with a focus on application-domain questions, challenges, and tasks. We provide a general introduction to molecular visualization basicsand describe a number of domain-specific tasks that drive this work. These tasks, in turn, serve as the generalstructure of the following survey. First, we discuss methods that support the visual analysis of moleculardynamics simulations. We discuss, in particular, visual abstraction and temporal aggregation. In the secondpart, we survey multiscale approaches that support the design, analysis, and manipulation of DNAnanostructures and related concepts for abstraction, scale transition, scale-dependent modeling, andnavigation of the resulting abstraction spaces. In the third part of the survey, we showcase approaches thatsupport interactive exploration within large structural biology assemblies up to the size of bacterial cells.We describe fundamental rendering techniques as well as approaches for element instantiation, visibilitymanagement, visual guidance, camera control, and support of depth perception. We close the survey with abrief listing of important tools that implement many of the discussed approaches and a conclusion thatprovides some research challenges in the field.", month = jan, doi = "10.1016/j.jmb.2018.09.004.", journal = "Journal of Molecular Biology", number = "31", volume = "6", pages = "1049--1070", keywords = "molecular visualization, molecular dynamics, modelitics, DNA nanotechnology, visual abstraction", URL = "https://www.cg.tuwien.ac.at/research/publications/2019/Miao_2019/", } @article{raidou2018visualflatter, title = "VisualFlatter - Visual Analysis of Distortions in the Projection of Biomedical Structures", author = "Nicolas Grossmann and Thomas K\"{o}ppel and Eduard Gr\"{o}ller and Renata Raidou", year = "2018", abstract = "Projections of complex anatomical or biological structures from 3D to 2D are often used by visualization and domain experts to facilitate inspection and understanding. Representing complex structures, such as organs or molecules, in a simpler 2D way often requires less interaction, while enabling comparability. However, the most commonly employed projection methods introduce size or shape distortions, in the resulting 2D representations. While simple projections display known distortion patterns, more complex projection algorithms are not easily predictable.We propose the VisualFlatter, a visual analysis tool that enables visualization and domain experts to explore and analyze projection-induced distortions, in a structured way. Our tool provides a way to identify projected regions with semantically relevant distortions and allows users to comparatively analyze distortion outcomes, either from alternative projection methods or due to different setups through the projection pipeline. The user is given the ability to improve the initial projection configuration, after comparing different setups. We demonstrate the functionality of our tool using four scenarios of 3D to 2D projections, conducted with the help of domain or visualization experts working on different application fields. We also performed a wider evaluation with 13 participants, familiar with projections, to assess the usability and functionality of the Visual Flatter.", month = sep, journal = "Eurographics Proceedings", URL = "https://www.cg.tuwien.ac.at/research/publications/2018/raidou2018visualflatter/", } @misc{Miao2018FDN, title = "A Preview to Adenita: Visualization and Modeling of DNA Nanostructures", author = "Elisa De Llano and Haichao Miao and Tobias Isenberg and Eduard Gr\"{o}ller and Ivan Viola and Ivan Barisic", year = "2018", abstract = "We present Adenita, an open-source software that aims to provide an integrated in silico design toolkit for DNA Nanostructures. It facilitates the modular assembly of pre-existing and de novo designs, regardless of the used approach. Adenita is being developed in the context of the MARA project [1], a highly ambitious project aiming to produce a DNA nanorobot capable of targeted cell lyses. Currently, the existing design and visualization tools are insufficient to solve the specific challenges in our project. We aim to overcome these limitations with Adenita, a new semi-automated approach that we are developing as the MARA project advances. Adenita integrates visualizations [2] with user interactions and algorithms in a semi-manual approach. At the core, we use a hierarchical data model that enables us to combine both a top-down (DAEDALUS [3]) and a bottom-up (caDNAno [4]) design approach of the DNA Nanostructure. From the DNA data model, we create smooth visualizations that depict the structure in multiple scales from its atomic details to a highlevel geometric representation of the target shape. In addition, we employ different layouts for the same structure [5]: 3D structural representations, 2D caDNAno-style diagrams, and 1D display of the linear sequences. Creators enable the parametrized generation of structural motifs, while Manipulators facilitate the advanced modifications of the structural properties, such as connecting components and adding bridging strands. Analysis of the designs is still in a preliminary phase, but it already enables the straightforward estimation of distances and the melting temperatures [6] of binding regions. The first DNA nanostructures that we designed with the new tool are now under experimental evaluation. ", month = jun, location = "Rome", event = "3rd Functional DNA Nanotechnology Workshop", Conference date = "Poster presented at 3rd Functional DNA Nanotechnology Workshop (2018-06-06--2018-06-08)", URL = "https://www.cg.tuwien.ac.at/research/publications/2018/Miao2018FDN/", } @article{miao2018Dimsum, title = "DimSUM: Dimension and Scale Unifying Maps for Visual Abstraction of DNA Origami Structures", author = "Haichao Miao and Elisa De Llano and Tobias Isenberg and Eduard Gr\"{o}ller and Ivan Barisic and Ivan Viola", year = "2018", month = jun, journal = "Computer Graphics Forum", volume = "37", number = "3", URL = "https://www.cg.tuwien.ac.at/research/publications/2018/miao2018Dimsum/", } @misc{wu-2018-metabo, title = "A Visual Comparison of Hand-Drawn and Machine-Generated Human Metabolic Pathways", author = "Hsiang-Yun Wu and Martin N\"{o}llenburg and Ivan Viola", year = "2018", abstract = "This poster abstract presents a visual comparison between three hand-drawn and one machine-generated human metabolic pathway diagrams. The human metabolic pathways, which describe significant biochemical reactions in the human body, have been increasingly investigated due to the development of analysis processes and are compiled into pathway diagrams to provide an overview of reaction in the human body. This complex network includes about 5,000 metabolites and 7,500 reactions, which are hierarchically nested and difficult to visualize. We collect and analyze well-known human metabolic pathway diagrams, and summarize the design choices of these diagrams, respectively. Together with a machine-generated diagram, we can understand the visual complexity of three hand-drawn and one machine-generated diagrams. ", month = jun, event = "EuroVis", Conference date = "Poster presented at EuroVis (2018-06-04--2018-06-08)", URL = "https://www.cg.tuwien.ac.at/research/publications/2018/wu-2018-metabo/", } @article{Furmanova_2018, title = "COZOID: contact zone identifier for visual analysis of protein-protein interactions", author = "Katar\'{i}na Furmanov\'{a} and Jan Byska and Eduard Gr\"{o}ller and Ivan Viola and Jan J. Pale\v{c}ek and Barbora Kozlikova", year = "2018", abstract = "Background: Studying the patterns of protein-protein interactions (PPIs) is fundamental for understanding thestructure and function of protein complexes. The exploration of the vast space of possible mutual configurations ofinteracting 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 guidedexploration of PPI configuration space. It helps proteomic experts to select the most relevant configurations andexplore their contact zones at different levels of detail. The system integrates a set of methods that follow and supportthe workflow of proteomics experts. The first visual abstraction method, the Matrix view, is based on customizedinteractive heat maps and provides the users with an overview of all possible residue-residue contacts in all PPIconfigurations and their interactive filtering. In this step, the user can traverse all input PPI configurations and obtain anoverview of their interacting amino acids. Then, the models containing a particular pair of interacting amino acids canbe selectively picked and traversed. Detailed information on the individual amino acids in the contact zones and theirproperties is presented in the Contact-Zone list-view. The list-view provides a comparative tool to rank the best modelsbased on the similarity of their contacts to the template-structure contacts. All these techniques are interactivelylinked with other proposed methods, the Exploded view and the Open-Book view, which represent individualconfigurations in three-dimensional space. These representations solve the high overlap problem associated withmany configurations. Using these views, the structural alignment of the best models can also be visually confirmed.", month = apr, doi = " 10.1186/s12859-018-2113-6", journal = "BMC Bioinformatics", number = "19:125 ", pages = "1--25", URL = "https://www.cg.tuwien.ac.at/research/publications/2018/Furmanova_2018/", } @article{miao_tvcg_2018, title = "Multiscale Visualization and Scale-adaptive Modification of DNA Nanostructures", author = "Haichao Miao and Elisa De Llano and Johannes Sorger and Yasaman Ahmadi and Tadija Kekic and Tobias Isenberg and Eduard Gr\"{o}ller and Ivan Barisic and Ivan Viola", year = "2018", month = jan, journal = "IEEE Transactions on Visualization and Computer Graphics", volume = "24", number = "1", URL = "https://www.cg.tuwien.ac.at/research/publications/2018/miao_tvcg_2018/", } @article{klein_2017_IM, title = "Instant Construction and Visualization of Crowded Biological Environments", author = "Tobias Klein and Ludovic Autin and Barbora Kozlikova and David Goodsell and Arthur Olson and Eduard Gr\"{o}ller and Ivan Viola", year = "2018", abstract = "We present the first approach to integrative structural modeling of the biological mesoscale within an interactive visual environment. These complex models can comprise up to millions of molecules with defined atomic structures, locations, and interactions. Their construction has previously been attempted only within a non-visual and non-interactive environment. Our solution unites the modeling and visualization aspect, enabling interactive construction of atomic resolution mesoscale models of large portions of a cell. We present a novel set of GPU algorithms that build the basis for the rapid construction of complex biological structures. These structures consist of multiple membrane-enclosed compartments including both soluble molecules and fibrous structures. The compartments are defined using volume voxelization of triangulated meshes. For membranes, we present an extension of the Wang Tile concept that populates the bilayer with individual lipids. Soluble molecules are populated within compartments using the Halton sequence for their distribution. Fibrous structures, such as RNA or actin filaments, are created by self-avoiding random walks. Resulting overlaps of molecules are resolved by a forced-based system. Our approach opens new possibilities to the world of interactive construction of cellular compartments. We demonstrate its effectiveness by showcasing scenes of different scale and complexity that comprise blood plasma, mycoplasma, and HIV.", journal = "IEEE Transactions on Visualization and Computer Graphics", doi = "10.1109/TVCG.2017.2744258", URL = "https://www.cg.tuwien.ac.at/research/publications/2018/klein_2017_IM/", } @techreport{wu-2017-dagstuhl, title = "Mapifying the Genome, Scalable Set Visualizations (Dagstuhl Seminar 17332)", author = "Radu Jianu and Martin Krzywinski and Luana Micallef and Hsiang-Yun Wu", year = "2018", number = "TR-193-02-2018-2", address = "Favoritenstrasse 9-11/E193-02, A-1040 Vienna, Austria", institution = "Institute of Computer Graphics and Algorithms, Vienna University of Technology ", note = "human contact: technical-report@cg.tuwien.ac.at", URL = "https://www.cg.tuwien.ac.at/research/publications/2018/wu-2017-dagstuhl/", } @phdthesis{sorger-2017-thesis, title = "Integration Strategies in the Visualization of Multifaceted Spatial Data", author = "Johannes Sorger", year = "2017", abstract = "Visualization designers have several visual channels at their disposal for encoding data into visual representations, e.g., position, size, shape, orientation, color, texture, brightness, as well as motion. The mapping of attributes to visual channels can be chosen by the designer. In theory, any data attribute can be represented by any of these visual channels or by a combination of multiple of these channels. In practice, the optimal mapping and the most suitable type of visualization strongly depend on the data as well as on the user's task. In the visualization of spatial data, the mapping of spatial attributes to visual channels is inherently given by the data. Multifaceted spatial data possesses a wide range of additional (non-spatial) attributes without a given mapping. The data's given spatial context is often important for successfully fulfilling a task. The design space in spatial data visualization can therefore be heavily constrained when trying to choose an optimal mapping for other attributes within the spatial context. To solve an exploration or presentation task in the domain of multifaceted spatial data, special strategies have to be employed in order to integrate the essential information from the various data facets in an appropriate representation form with the spatial context. This thesis explores visualization integration strategies for multifaceted spatial data. The first part of this thesis describes the design space of integration in terms of two aspects: visual and functional integration. Visual integration describes how representations of the different data facets can be visually composed within a spatial context. Functional integration, describes how events that have been triggered, for instance, through user interaction, can be coordinated across the various visually integrated representations. The second part of this thesis describes contributions to the field of visualization in the context of concrete integration applications for exploration and presentation scenarios. The first scenario addresses a set of challenges in the exploratory analysis of multifaceted spatial data in the scope of a decision making scenario in lighting design. The user's task is to find an optimal lighting solution among dozens or even hundreds of potential candidates. In the scope of a design study, the challenges in lighting design are addressed with LiteVis, a system that integrates representations of the simulation parameter space with representations of all relevant aspects of the simulation output. The integration of these heterogeneous aspects together with a novel ranking visualization are thereby the key to enabling an efficient exploration and comparison of lighting parametrizations. In presentation scenarios, the generation of insights often cannot rely on user interaction and therefore needs a different approach. The challenge is to generate visually appealing, yet information-rich representations for mainly passive observation. In this context, this thesis addresses two different challenges in the domain of molecular visualization. The first challenge concerns the conveying of relations between two different representations of a molecular data set, such as a virus. The relation is established via animated transitions - a temporal form of integration between two representations. The proposed solution features a novel technique for creating such transitions that are re-usable for different data sets, and can be combined in a modular fashion. Another challenge in presentation scenarios of multifaceted spatial data concerns the presentation of the transition between development states of molecular models, where the actual biochemical process of the transition is not exactly known or it is too complex to represent. A novel technique applies a continuous abstraction of both model representations to a level of detail at which the relationship between them can be accurately conveyed, in order to overcome a potential indication of false relationship information. Integration thereby brings the different abstraction levels and the different model states into relation with each other. The results of this thesis clearly demonstrate that integration is a versatile tool in overcoming key challenges in the visualization of multifaceted spatial data. ", month = sep, address = "Favoritenstrasse 9-11/E193-02, A-1040 Vienna, Austria", school = "Institute of Computer Graphics and Algorithms, Vienna University of Technology ", URL = "https://www.cg.tuwien.ac.at/research/publications/2017/sorger-2017-thesis/", } @inproceedings{Gehrer-2017-molmach, title = "Visualization of molecular machinery using agent-based animation", author = "Daniel Gehrer and Ivan Viola", year = "2017", month = may, event = "Spring Conference on Computer Graphics", booktitle = "Proceedings of SCCG 2017", URL = "https://www.cg.tuwien.ac.at/research/publications/2017/Gehrer-2017-molmach/", } @misc{kouril-2017-sccgposter, title = "Maya2cellVIEW: Integrated Tool for Creating Large and Complex Molecular Scenes", author = "David Kou\v{r}il and Mathieu Le Muzic and Barbora Kozlikova and Ivan Viola", year = "2017", month = may, event = "Spring Conference on Computer Graphics 2017", Conference date = "Poster presented at Spring Conference on Computer Graphics 2017 (2017-05)", URL = "https://www.cg.tuwien.ac.at/research/publications/2017/kouril-2017-sccgposter/", } @inproceedings{sorger_2017_metamorphers, title = "Metamorphers: Storytelling Templates For Illustrative Animated Transitions in Molecular Visualization", author = "Johannes Sorger and Peter Mindek and Peter Rautek and Eduard Gr\"{o}ller and Graham Johnson and Ivan Viola", year = "2017", abstract = "In molecular biology, illustrative animations are used to convey complex biological phenomena to broad audiences. However, such animations have to be manually authored in 3D modeling software, a time consuming task that has to be repeated from scratch for every new data set, and requires a high level of expertise in illustration, animation, and biology. We therefore propose metamorphers: a set of operations for defining animation states as well as the transitions to them in the form of re-usable story telling templates. The re-usability is two-fold. Firstly, due to their modular nature, metamorphers can be re-used in different combinations to create a wide range of animations. Secondly, due to their abstract nature, metamorphers can be re-used to re-create an intended animation for a wide range of compatible data sets. Metamorphers thereby mask the low level complexity of explicit animation specifications by exploiting the inherent properties of the molecular data, such as the position, size, and hierarchy level of a semantic data subset.", month = may, location = "Mikulov, Czech Republic", booktitle = "Proceedings of the Spring Conference on Computer Graphics 2017", pages = "27--36", keywords = "animated transitions, storytelling, molecular visualization", URL = "https://www.cg.tuwien.ac.at/research/publications/2017/sorger_2017_metamorphers/", } @article{Kolesar-Fractional-2016, title = "A Fractional Cartesian Composition Model for Semi-Spatial ComparativeVisualization Design", author = "Ivan Koles\'{a}r and Stefan Bruckner and Ivan Viola and Helwig Hauser", year = "2017", month = jan, journal = "IEEE Transactions on Visualization and Computer Graphics", volume = "23", number = "1", doi = "10.1109/TVCG.2016.2598870", pages = "851-860", URL = "https://www.cg.tuwien.ac.at/research/publications/2017/Kolesar-Fractional-2016/", } @article{mindek-2017-marion, title = "Visualization Multi-Pipeline for Communicating Biology", author = "Peter Mindek and David Kou\v{r}il and Johannes Sorger and David Toloudis and Blair Lyons and Graham Johnson and Eduard Gr\"{o}ller and Ivan Viola", year = "2017", abstract = "We propose a system to facilitate biology communication by developing a pipeline to support the instructional visualization of heterogeneous biological data on heterogeneous user-devices. Discoveries and concepts in biology are typically summarized with illustrations assembled manually from the interpretation and application of heterogenous data. The creation of such illustrations is time consuming, which makes it incompatible with frequent updates to the measured data as new discoveries are made. Illustrations are typically non-interactive, and when an illustration is updated, it still has to reach the user. Our system is designed to overcome these three obstacles. It supports the integration of heterogeneous datasets, reflecting the knowledge that is gained from different data sources in biology. After pre-processing the datasets, the system transforms them into visual representations as inspired by scientific illustrations. As opposed to traditional scientific illustration these representations are generated in real-time - they are interactive. The code generating the visualizations can be embedded in various software environments. To demonstrate this, we implemented both a desktop application and a remote-rendering server in which the pipeline is embedded. The remote-rendering server supports multi-threaded rendering and it is able to handle multiple users simultaneously. This scalability to different hardware environments, including multi-GPU setups, makes our system useful for efficient public dissemination of biological discoveries. ", journal = "IEEE Transactions on Visualization and Computer Graphics", volume = "24", number = "1", keywords = "Biological visualization, remote rendering, public dissemination", URL = "https://www.cg.tuwien.ac.at/research/publications/2017/mindek-2017-marion/", } @inproceedings{vad_viktor-2017-WVE, title = "Watergate: Visual Exploration of Water Trajectories in Protein Dynamics", author = "Viktor Vad and Jan Byska and Adam Jurcik and Ivan Viola and Eduard Gr\"{o}ller and Helwig Hauser and Sergio M. Margues and Jiri Damborsky and Barbora Kozlikova", year = "2017", abstract = "The function of proteins is tightly related to their interactions with other molecules. The study of such interactions often requires to track the molecules that enter or exit specific regions of the proteins. This is investigated with molecular dynamics simulations, producing the trajectories of thousands of water molecules during hundreds of thousands of time steps. To ease the exploration of such rich spatio-temporal data, we propose a novel workflow for the analysis and visualization of large sets of water-molecule trajectories. Our solution consists of a set of visualization techniques, which help biochemists to classify, cluster, and filter the trajectories and to explore the properties and behavior of selected subsets in detail. Initially, we use an interactive histogram and a time-line visualization to give an overview of all water trajectories and select the interesting ones for further investigation. Further, we depict clusters of trajectories in a novel 2D representation illustrating the flows of water molecules. These views are interactively linked with a 3D representation where we show individual paths, including their simplification, as well as extracted statistical information displayed by isosurfaces. The proposed solution has been designed in tight collaboration with experts to support specific tasks in their scientific workflows. They also conducted several case studies to evaluate the usability and effectiveness of our new solution with respect to their research scenarios. These confirmed that our proposed solution helps in analyzing water trajectories and in extracting the essential information out of the large amount of input data.", location = "September, 2017 Bremen, Germany", booktitle = "Eurographics Workshop on Visual Computing for Biology and Medicine 2017", pages = "33--42", URL = "https://www.cg.tuwien.ac.at/research/publications/2017/vad_viktor-2017-WVE/", } @article{Kozlikova-Visualization-2016b, title = "Visualization of Biomolecular Structures: State of the Art Revisited", author = "Barbora Kozlikova and Michael Krone and Martin Falk and Norbert Lindow and Daniel Baum and Ivan Viola and Marc Baaden and Julius Parulek and Hans-Christian Hege", year = "2016", month = nov, doi = "10.1111/cgf.13072", journal = "Computer Graphics Forum", number = "XX", URL = "https://www.cg.tuwien.ac.at/research/publications/2016/Kozlikova-Visualization-2016b/", } @inproceedings{sorger-2016-fowardabstraction, title = "Illustrative Transitions in Molecular Visualization via Forward and Inverse Abstraction Transform", author = "Johannes Sorger and Peter Mindek and Tobias Klein and Graham Johnson and Ivan Viola", year = "2016", abstract = "A challenging problem in biology is the incompleteness of acquired information when visualizing biological phenomena. Structural biology generates detailed models of viruses or bacteria at different development stages, while the processes that relate one stage to another are often not clear. Similarly, the entire life cycle of a biological entity might be available as a quantitative model, while only one structural model is available. If the relation between two models is specified at a lower level of detail than the actual models themselves, the two models cannot be interpolated correctly. We propose a method that deals with the visualization of incomplete data information in the developmental or evolutionary states of biological mesoscale models, such as viruses or microorganisms. The central tool in our approach is visual abstraction. Instead of directly interpolating between two models that show different states of an organism, we gradually forward transform the models into a level of visual abstraction that matches the level of detail of the modeled relation between them. At this level, the models can be interpolated without conveying false information. After the interpolation to the new state, we apply the inverse transformation to the model’'s original level of abstraction. To show the flexibility of our approach, we demonstrate our method on the basis of molecular data, in particular data of the HIV virion and the mycoplasma bacterium.", month = sep, organization = "Eurographics", location = "Bergen", editor = "S. Bruckner, B. Preim, and A. Vilanova", booktitle = "Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM)", pages = "21--30", keywords = "I.3.3 [Computer Graphics]: Picture/Image Generation-Display algorithms", URL = "https://www.cg.tuwien.ac.at/research/publications/2016/sorger-2016-fowardabstraction/", } @article{Viola_Ivan_2015_AAM, title = "AnimoAminoMiner: Exploration of Protein Tunnels and their Properties in Molecular Dynamics", author = "Jan Byska and Mathieu Le Muzic and Eduard Gr\"{o}ller and Ivan Viola and Barbora Kozlikova", year = "2016", abstract = "In this paper we propose a novel method for the interactive exploration of protein tunnels. The basic principle of our approach is that we entirely abstract from the 3D/4D space the simulated phenomenon is embedded in. A complex 3D structure and its curvature information is represented only by a straightened tunnel centerline and its width profile. This representation focuses on a key aspect of the studied geometry and frees up graphical estate to key chemical and physical properties represented by surrounding amino acids. The method shows the detailed tunnel profile and its temporal aggregation. The profile is interactively linked with a visual overview of all amino acids which are lining the tunnel over time. In this overview, each amino acid is represented by a set of colored lines depicting the spatial and temporal impact of the amino acid on the corresponding tunnel. This representation clearly shows the importance of amino acids with respect to selected criteria. It helps the biochemists to select the candidate amino acids for mutation which changes the protein function in a desired way. The AnimoAminoMiner was designed in close cooperation with domain experts. Its usefulness is documented by their feedback and a case study, which are included.", month = jan, journal = "IEEE Transactions on Visualization and Computer Graphics", volume = "22", number = "1", issn = "1077-2626", pages = "747--756", keywords = "aggregation, molecular dynamics, Protein, interaction, tunnel", URL = "https://www.cg.tuwien.ac.at/research/publications/2016/Viola_Ivan_2015_AAM/", } @article{lemuzic-mindek-2016-viseq, title = "Visibility Equalizer: Cutaway Visualization of Mesoscopic Biological Models", author = "Mathieu Le Muzic and Peter Mindek and Johannes Sorger and Ludovic Autin and David Goodsell and Ivan Viola", year = "2016", abstract = "In scientific illustrations and visualization, cutaway views are often employed as an effective technique for occlusion management in densely packed scenes.We propose a novel method for authoring cutaway illustrations of mesoscopic biological models. In contrast to the existing cutaway algorithms, we take advantage of the specific nature of the biological models. These models consist of thousands of instances with a comparably smaller number of different types. Our method constitutes a two stage process. In the first step, clipping objects are placed in the scene, creating a cutaway visualization of the model. During this process, a hierarchical list of stacked bars inform the user about the instance visibility distribution of each individual molecular type in the scene. In the second step, the visibility of each molecular type is fine-tuned through these bars, which at this point act as interactive visibility equalizers. An evaluation of our technique with domain experts confirmed that our equalizer-based approach for visibility specification is valuable and effective for both, scientific and educational purposes.", journal = "Computer Graphics Forum", volume = "35", number = "3", keywords = "molecular visualization, visibility, occlusion", URL = "https://www.cg.tuwien.ac.at/research/publications/2016/lemuzic-mindek-2016-viseq/", } @article{vad-2016-bre, title = "Generalized box-plot for root growth ensembles", author = "Viktor Vad and Douglas Cedrim and Wolfgang Busch and Peter Filzmoser and Ivan Viola", year = "2016", abstract = "Background In the field of root biology there has been a remarkable progress in root phenotyping, which is the efficient acquisition and quantitative description of root morphology. What is currently missing are means to efficiently explore, exchange and present the massive amount of acquired, and often time dependent root phenotypes. Results In this work, we present visual summaries of root ensembles by aggregating root images with identical genetic characteristics. We use the generalized box plot concept with a new formulation of data depth. In addition to spatial distributions, we created a visual representation to encode temporal distributions associated with the development of root individuals. Conclusions The new formulation of data depth allows for much faster implementation close to interactive frame rates. This allows us to present the statistics from bootstrapping that characterize the root sample set quality. As a positive side effect of the new data-depth formulation we are able to define the geometric median for the curve ensemble, which was well received by the domain experts.", journal = "BMC Bioinformatics", URL = "https://www.cg.tuwien.ac.at/research/publications/2016/vad-2016-bre/", } @article{Krone2016VABC, title = "Visual Analysis of Biomolecular Cavities: State of the Art", 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", 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.", journal = "Computer Graphics Forum", volume = "35", number = "3", pages = "527--551", URL = "https://www.cg.tuwien.ac.at/research/publications/2016/Krone2016VABC/", } @inproceedings{Reisacher2016, title = "CellPathway: A Simulation Tool for Illustrative Visualization of Biochemical Networks", author = "Matthias Reisacher and Mathieu Le Muzic and Ivan Viola", year = "2016", abstract = "The molecular knowledge about complex biochemical reaction networks in biotechnology is crucial and has received a lot of attention lately. As a consequence, multiple visualization programs have been already developed to illustrate the anatomy of a cell. However, since a real cell performs millions of reactions every second to sustain live, it is necessary to move from anatomical to physiological illustrations to communicate knowledge about the behavior of a cell more accurately. In this thesis I propose a reaction system including a collision detection algorithm, which is able to work at the level of single atoms, to enable precise simulation of molecular interactions. To visually explain molecular activities during the simulation process, a real-time glow effect in combination with a clipping object have been implemented. Since intracellular processes are performed with a set of chemical transformations, a hierarchical structure is used to illustrate the impact of one reaction on the entire simulation. The CellPathway system integrates acceleration techniques to render large datasets containing millions of atoms in real-time, while the reaction system is processed directly on the GPU to enable simulation with more than 1000 molecules. Furthermore, a graphical user interface has been implemented to allow the user to control parameters during simulation interactively.", location = "Pilsen, Czech Republic", booktitle = "Proceedings of WSCG", URL = "https://www.cg.tuwien.ac.at/research/publications/2016/Reisacher2016/", } @inproceedings{cellVIEW_2015, title = "cellVIEW: a Tool for Illustrative and Multi-Scale Rendering of Large Biomolecular Datasets", author = "Mathieu Le Muzic and Ludovic Autin and Julius Parulek and Ivan Viola", year = "2015", 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.", month = sep, isbn = "978-3-905674-82-8", publisher = "The Eurographics Association", organization = "EG Digital Library", location = "Chester, United Kingdom", issn = "2070-5786", editor = "Katja B\"{u}hler and Lars Linsen and Nigel W. John", booktitle = "Eurographics Workshop on Visual Computing for Biology and Medicine", pages = "61--70", URL = "https://www.cg.tuwien.ac.at/research/publications/2015/cellVIEW_2015/", } @article{Viola_Ivan_2015_MCT, title = "MoleCollar and Tunnel Heat Map Visualizations for Conveying Spatio-Temporo-Chemical Properties Across and Along Protein Voids", author = "Jan Byska and Adam Jurcik and Eduard Gr\"{o}ller and Ivan Viola and Barbora Kozlikova", year = "2015", abstract = "Studying the characteristics of proteins and their inner void space, including their geometry, physico-chemical properties and dynamics are instrumental for evaluating the reactivity of the protein with other small molecules. The analysis of long simulations of molecular dynamics produces a large number of voids which have to be further explored and evaluated. In this paper we propose three new methods: two of them convey important properties along the long axis of a selected void during molecular dynamics and one provides a comprehensive picture across the void. The first two proposed methods use a specific heat map to present two types of information: an overview of all detected tunnels in the dynamics and their bottleneck width and stability over time, and an overview of a specific tunnel in the dynamics showing the bottleneck position and changes of the tunnel length over time. These methods help to select a small subset of tunnels, which are explored individually and in detail. For this stage we propose the third method, which shows in one static image the temporal evolvement of the shape of the most critical tunnel part, i.e., its bottleneck. This view is enriched with abstract depictions of different physicochemical properties of the amino acids surrounding the bottleneck. The usefulness of our newly proposed methods is demonstrated on a case study and the feedback from the domain experts is included. The biochemists confirmed that our novel methods help to convey the information about the appearance and properties of tunnels in a very intuitive and comprehensible manner.", month = may, journal = "Computer Graphics Forum", volume = "3", number = "34", note = "EuroVis 2015 - Conference Proceedings", pages = "1--10", URL = "https://www.cg.tuwien.ac.at/research/publications/2015/Viola_Ivan_2015_MCT/", } @inproceedings{Viola_Ivan_2015_VBS, title = "Visualization of Biomolecular Structures: State of the Art", author = "Barbora Kozlikova and Michael Krone and Norbert Lindow and Martin Falk and Marc Baaden and Daniel Baum and Ivan Viola and Julius Parulek and Hans-Christian Hege", year = "2015", abstract = "Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three-dimensional, complex, large, and time-varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate, covers different aspects of level of detail, and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The report concludes with an outlook on promising and important research topics to enable further success in advancing the knowledge about interaction of molecular structures.", month = may, publisher = "The Eurographics Association", location = "Cagliari, Italy", event = "Eurographics Conference on Visualization (EuroVis) (2015)", editor = "R. Borgo and F. Ganovelli and I. Viola", booktitle = "Eurographics Conference on Visualization (EuroVis) - STARs", pages = "061--081", URL = "https://www.cg.tuwien.ac.at/research/publications/2015/Viola_Ivan_2015_VBS/", } @inproceedings{lemuzic_2015_timelapse, title = "Illustrative Timelapse: A Technique for Illustrative Visualization of Particle Simulations on the Mesoscale Level", author = "Mathieu Le Muzic and Manuela Waldner and Julius Parulek and Ivan Viola", year = "2015", abstract = "Animated movies are a popular way to communicate complex phenomena in cell biology to the broad audience. Animation artists apply sophisticated illustration techniques to communicate a story, while trying to maintain a realistic representation of a complex dynamic environment. Since such hand-crafted animations are timeconsuming and cost-intensive to create, our goal is to formalize illustration 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) visual abstraction of molecular trajectories to ensure that observers are able to visually follow the main actors, (3) increased visual focus on events of interest, and (4) lens effects to preserve a realistic representation of the environment in the context. Results from a first user study indicate that visual abstraction of trajectories improves the ability to follow a story and is also appreciated by users. Lens effects increased the perceived amount of molecular motion in the environment while trading off traceability of individual molecules.", month = apr, publisher = "IEEE", organization = "8th IEEE Pacific Visualization Symposium (PacificVis 2015)", location = "Zijingang Campus, Zhejiang University, Hangzhou, China", booktitle = "Visualization Symposium (PacificVis), 2015 IEEE Pacific", pages = "247--254", URL = "https://www.cg.tuwien.ac.at/research/publications/2015/lemuzic_2015_timelapse/", } @article{waldner-2014-af, title = " Attractive Flicker: Guiding Attention in Dynamic Narrative Visualizations", author = "Manuela Waldner and Mathieu Le Muzic and Matthias Bernhard and Werner Purgathofer and Ivan Viola", year = "2014", abstract = "Focus+context techniques provide visual guidance in visualizations by giving strong visual prominence to elements of interest while the context is suppressed. However, finding a visual feature to enhance for the focus to pop out from its context in a large dynamic scene, while leading to minimal visual deformation and subjective disturbance, is challenging. This paper proposes Attractive Flicker, a novel technique for visual guidance in dynamic narrative visualizations. We first show that flicker is a strong visual attractor in the entire visual field, without distorting, suppressing, or adding any scene elements. The novel aspect of our Attractive Flicker technique is that it consists of two signal stages: The first “orientation stage” is a short but intensive flicker stimulus to attract the attention to elements of interest. Subsequently, the intensive flicker is reduced to a minimally disturbing luminance oscillation (“engagement stage”) as visual support to keep track of the focus elements. To find a good trade-off between attraction effectiveness and subjective annoyance caused by flicker, we conducted two perceptual studies to find suitable signal parameters. We showcase Attractive Flicker with the parameters obtained from the perceptual statistics in a study of molecular interactions. With Attractive Flicker, users were able to easily follow the narrative of the visualization on a large display, while the flickering of focus elements was not disturbing when observing the context.", month = dec, journal = "IEEE Transactions on Visualization and Computer Graphics", volume = "20", number = "12", pages = "2456--2465", keywords = "Narrative Visualization, Flicker, Visual Attention", URL = "https://www.cg.tuwien.ac.at/research/publications/2014/waldner-2014-af/", } @article{Viola_Ivan_IIP, title = "Interactively illustrating polymerization using three-level model fusion", author = "Ivan Koles\'{a}r and Julius Parulek and Ivan Viola and Stefan Bruckner and Anne-Kristin Stavrum and Helwig Hauser", year = "2014", abstract = "Background: Research in cell biology is steadily contributing new knowledge about many aspects of physiological processes, both with respect to the involved molecular structures as well as their related function. llustrations of the spatio-temporal development of such processes are not only used in biomedical education, but also can serve scientists as an additional platform for in-silico experiments. Results: In this paper, we contribute a new, three-level modeling approach to illustrate physiological processes from the class of polymerization at different time scales. We integrate physical and empirical modeling, according to which approach best suits the different involved levels of detail, and we additionally enable a form of interactive steering, while the process is illustrated. We demonstrate the suitability of our approach in the context of several polymerization processes and report from a first evaluation with domain experts. Conclusion: We conclude that our approach provides a new, hybrid modeling approach for illustrating the process of emergence in physiology, embedded in a densely filled environment. Our approach of a complementary fusion of three systems combines the strong points from the different modeling approaches and is capable to bridge different spatial and temporal scales.", month = oct, issn = "1471-2105", journal = "BMC Bioinformatics 2014", number = "345", volume = "15", pages = "1--16", keywords = "Multi-agent modeling, L-system modeling, Biochemical visualization, Visualization of physiology, Polymerization", URL = "https://www.cg.tuwien.ac.at/research/publications/2014/Viola_Ivan_IIP/", } @inproceedings{kolesar-ivan-2014-polymers, title = "Illustrating Polymerization using Three-level Model Fusion", author = "Ivan Koles\'{a}r and Julius Parulek and Ivan Viola and Stefan Bruckner and Anne-Kristin Stavrum and Helwig Hauser", year = "2014", abstract = "Research in cell biology is steadily contributing new knowledge about many di?erent aspects of physiological processes like polymerization, both with respect to the involved molecular structures as well as their related function. Illustrations of the spatio-temporal development of such processes are not only used in biomedical education, but also can serve scientists as an additional platform for in-silico experiments. In this paper, we contribute a new, three-level modeling approach to illustrate physiological processes from the class of polymerization at di?erent time scales. We integrate physical and empirical modeling, according to which approach suits the di?erent involved levels of detail best, and we additionally enable a simple form of interactive steering while the process is illustrated. We demonstrate the suitability of our approach in the context of several polymerization processes and report from a ?rst evaluation with domain experts.", month = jul, publisher = "IEEE Digital Library", organization = "4th Symposium on Biological Data Visualization (in Conjunction with the International Conference on Intelligent Systems for Molecular Biology (ISMB 2014)) ", location = "Boston, USA", booktitle = "Proceedings of IEEE BioVis 2014", pages = "1--22", URL = "https://www.cg.tuwien.ac.at/research/publications/2014/kolesar-ivan-2014-polymers/", } @article{lemuzic-2014-ivm, title = "Illustrative Visualization of Molecular Reactions using Omniscient Intelligence and Passive Agents ", author = "Mathieu Le Muzic and Julius Parulek and Anne-Kristin Stavrum and Ivan Viola", year = "2014", abstract = "In this paper we propose a new type of a particle systems, tailored for illustrative visualization purposes, in particular for visualizing molecular reactions in biological networks. Previous visualizations of biochemical processes were exploiting the results of agent-based modeling. Such modeling aims at reproducing accurately the stochastic nature of molecular interactions. However, it is impossible to expect events of interest happening at a certain time and location, which is impractical for storytelling. To obtain the means of controlling molecular interactions, we propose to govern passive agents with an omniscient intelligence, instead of giving to the agents the freedom of initiating reaction autonomously. This makes it possible to generate illustrative animated stories that communicate the functioning of the molecular machinery. The rendering performance delivers for interactive framerates of massive amounts of data, based on the dynamic tessellation capabilities of modern graphics cards. Finally, we report an informal expert feedback we obtained from the potential users.", month = jun, journal = "Computer Graphics Forum", volume = "33", number = "3", note = "Article first published online: 12 JUL 2014", pages = "141--150", URL = "https://www.cg.tuwien.ac.at/research/publications/2014/lemuzic-2014-ivm/", } @article{Viola_Ivan_CLD, title = "Continuous Levels-of-Detail and Visual Abstraction for Seamless Molecular Visualization", author = "Julius Parulek and Daniel J\"{o}nsson and Timo Ropinski and Stefan Bruckner and Anders Ynnerman and Ivan Viola", year = "2014", abstract = "Molecular visualization is often challenged with rendering of large molecular structures in real time. We introduce a novel approach that enables us to show even large protein complexes. Our method is based on the level-of-detail concept, where we exploit three different abstractions combined in one visualization. Firstly, molecular surface abstraction exploits three different surfaces, solvent-excluded surface (SES), Gaussian kernels and van der Waals spheres, combined as one surface by linear interpolation. Secondly, we introduce three shading abstraction levels and a method for creating seamless transitions between these representations. The SES representation with full shading and added contours stands in focus while on the other side a sphere representation of a cluster of atoms with constant shading and without contours provide the context. Thirdly, we propose a hierarchical abstraction based on a set of clusters formed on molecular atoms. All three abstraction models are driven by one importance function classifying the scene into the near-, mid- and far-field. Moreover, we introduce a methodology to render the entire molecule directly using the A-buffer technique, which further improves the performance. The rendering performance is evaluated on series of molecules of varying atom counts.", month = may, issn = "0167-7055", journal = "Computer Graphics Forum", number = "6", volume = "33", pages = "276--287", keywords = "clustering, implicit surfaces, level of detail algorithms, scientific visualization, Computer Applications", URL = "https://www.cg.tuwien.ac.at/research/publications/2014/Viola_Ivan_CLD/", } @article{Viola_Ivan_2013_VCA, title = "Visual cavity analysis in molecular simulations", author = "Julius Parulek and Cagatay Turkay and Nathalie Reuter and Ivan Viola", year = "2013", abstract = "Molecular surfaces provide a useful mean for analyzing interactions between biomolecules; such as identification and characterization of ligand binding sites to a host macromolecule. We present a novel technique, which extracts potential binding sites, represented by cavities, and characterize them by 3D graphs and by amino acids. The binding sites are extracted using an implicit function sampling and graph algorithms. We propose an advanced cavity exploration technique based on the graph parameters and associated amino acids. Additionally, we interactively visualize the graphs in the context of the molecular surface. We apply our method to the analysis of MD simulations of Proteinase 3, where we verify the previously described cavities and suggest a new potential cavity to be studied.", month = nov, issn = "1471-2105", journal = "BMC Bioinformatics", number = "Suppl 19:S4 ", volume = "14", pages = "1--15", URL = "https://www.cg.tuwien.ac.at/research/publications/2013/Viola_Ivan_2013_VCA/", } @inproceedings{sorger-2013-neuromap, title = "neuroMAP - Interactive Graph-Visualization of the Fruit Fly's Neural Circuit", author = "Johannes Sorger and Katja B\"{u}hler and Florian Schulze and Tianxiao Liu and Barry Dickson", year = "2013", abstract = "Neuroscientists study the function of neural circuits in the brain of the common fruit fly Drosophila melanogaster to discover how complex behavior is generated. To establish models of neural information processing, knowledge about potential connections between individual neurons is required. Connections can occur when the arborizations of two neurons overlap. Judging connectivity by analyzing overlaps using traditional volumetric visualization is difficult since the examined objects occlude each other. A more abstract form of representation is therefore desirable. In collaboration with a group of neuroscientists, we designed and implemented neuroMap, an interactive two-dimensional graph that renders the brain and its interconnections in the form of a circuit-style wiring diagram. neuroMap provides a clearly structured overview of all possible connections between neurons and offers means for interactive exploration of the underlying neuronal database. In this paper, we discuss the design decisions that formed neuroMap and evaluate its application in discussions with the scientists.", month = oct, publisher = "IEEE", location = "Atlanta", booktitle = "Biological Data Visualization (BioVis), 2013 IEEE Symposium on ", pages = "73--80", URL = "https://www.cg.tuwien.ac.at/research/publications/2013/sorger-2013-neuromap/", } @inproceedings{Viola_Ivan_2013_SVA, title = "Seamless Visual Abstraction of Molecular Surfaces", author = "Julius Parulek and Timo Ropinski and Ivan Viola", year = "2013", abstract = "Molecular visualization is often challenged with rendering of large sequences of molecular simulations in real time. We introduce a novel approach that enables us to show even large protein complexes over time in real-time. Our method is based on the level-ofdetail concept, where we exploit three different molecular surface models, solvent excluded surface (SES), Gaussian kernels and van der Waals spheres combined in one visualization. We introduce three shading levels that correspond to their geometric counterparts and a method for creating seamless transition between these representations. The SES representation with full shading and added contours stands in focus while on the other side a sphere representation with constant shading and without contours provide the context. Moreover, we introduce a methodology to render the entire molecule directly using the A-buffer technique, which further improves the performance. The rendering performance is evaluated on series of molecules of varying atom counts.", month = may, isbn = "978-80-223-3377-1", series = " SCCG '13", publisher = "ACM Publishing House", organization = "Comenius University, Bratislava", location = "Smolenice, Slovak Republic", editor = "Roman Durikovi\v{c}, Holly Rushmeier", booktitle = "SCCG 2013 - 29th Proceedings Spring conference on Computer Graphics", pages = "120--127", keywords = "Implicit Surfaces, Level-of-detail, Visualization of Molecular Surfaces", URL = "https://www.cg.tuwien.ac.at/research/publications/2013/Viola_Ivan_2013_SVA/", }