@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/", } @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/", } @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/", } @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/", } @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{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/", } @misc{lemuzic_2014_ipv, title = "Illustrative Visualization of Biochemical Processes Featuring Multiple Temporal Scales", author = "Mathieu Le Muzic and Julius Parulek and Manuela Waldner and Ivan Viola", year = "2014", abstract = "Scientific illustrators are commonly using structural description of molecular compounds when depicting complex biochemical processes. However, computational biology also provides procedural models describing the function of biological processes which are not currently used in the production pipeline. Instead, animators utilize scientific knowledge to manually animate and reproduce the functioning of cellular biology. We would like to explore the use of such models in order to generate explanatory illustrations that would show how molecular machinery works. Particle-based simulations provide the means for spatially representing the dynamics of biochemical processes. They compute the positions of each single particle and are supposed to mimic a realistic behaviour of the metabolites. Current mesoscale visualization also allows to directly show the results of such simulations by mapping the positions of particles in a virtual 3D environment. Nevertheless, some biochemical processes, like the DNA repair for instance, exhibit temporal multiscale aspects because they comprise diffusion rates which are much greater in comparison with reaction rates. As a result, it is challenging to produce a clear and coherent visualization out of this type of simulation. Indeed, when viewing the process at the pace which would let us see the reactions, it becomes impossible for the human eye to keep track of individual elements because of the very large diffusion displacements. On the other hand, if one would playback the simulation slow enough to be see a steady motion of individual elements, then only a very few number of reactions would occur in a reasonable amount of time. In this work we propose to solve the problem associated with multiple temporal scales by providing means for spatial. With this approach we aim at showing the two different temporal scale at the same time by using advanced trajectory smoothing mechanism. This would allow us to see individual elements while showing a world full of reactions, hence enabling us to communicate complex biological processes and molecular machineries in a comprehensive way. ", event = "Eurographics Workshop on Visual Computing for Biology", Conference date = "Poster presented at Eurographics Workshop on Visual Computing for Biology (2014-09-04--2014-09-05)", URL = "https://www.cg.tuwien.ac.at/research/publications/2014/lemuzic_2014_ipv/", }