[ { "id": "waldin-2019-ccm", "type_id": "journalpaper_notalk", "tu_id": null, "repositum_id": null, "title": "Cuttlefish: Color Mapping for Dynamic Multi‐Scale Visualizations", "date": "2019-03", "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.", "authors_et_al": false, "substitute": null, "main_image": { "description": "Multiple color zoom levels. ", "filetitle": "teaser", "main_file": false, "use_in_gallery": true, "access": "public", "image_width": 509, "image_height": 447, "name": "waldin-2019-ccm-teaser.png", "type": "image/png", "size": 690229, "path": "Publication:waldin-2019-ccm", "url": "https://www.cg.tuwien.ac.at/research/publications/2019/waldin-2019-ccm/waldin-2019-ccm-teaser.png", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2019/waldin-2019-ccm/waldin-2019-ccm-teaser:thumb{{size}}.png" }, "sync_repositum_override": null, "repositum_presentation_id": null, "authors": [ 1339, 1110, 1189, 166, 1365, 1260, 1475, 171 ], "doi": "10.1111/cgf.13611", "journal": "Computer Graphics Forum", "number": "6", "pages_from": "150", "pages_to": "164", "volume": "38", "research_areas": [ "BioVis", "IllVis", "InfoVis" ], "keywords": [ "multiscale visualization", "illustrative visualization", "molecular visualization" ], "weblinks": [ { "href": "https://onlinelibrary.wiley.com/doi/10.1111/cgf.13611", "caption": "Open Access Article in Wiley Online Library", "description": null, "main_file": 1 } ], "files": [ { "description": "Multiple color zoom levels. ", "filetitle": "teaser", "main_file": false, "use_in_gallery": true, "access": "public", "image_width": 509, "image_height": 447, "name": "waldin-2019-ccm-teaser.png", "type": "image/png", "size": 690229, "path": "Publication:waldin-2019-ccm", "url": "https://www.cg.tuwien.ac.at/research/publications/2019/waldin-2019-ccm/waldin-2019-ccm-teaser.png", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2019/waldin-2019-ccm/waldin-2019-ccm-teaser:thumb{{size}}.png" } ], "projects_workgroups": [ "vis", "deskollage" ], "url": "https://www.cg.tuwien.ac.at/research/publications/2019/waldin-2019-ccm/", "__class": "Publication" }, { "id": "Groeller-2017-PTPMD", "type_id": "poster", "tu_id": null, "repositum_id": null, "title": "AnimoAminoMiner: Exploration of Protein Tunnels and their Properties in Molecular Dynamics", "date": "2017-07-24", "abstract": null, "authors_et_al": false, "substitute": null, "main_image": null, "sync_repositum_override": null, "repositum_presentation_id": null, "authors": [ 1254, 1189, 166, 171, 1248 ], "date_from": "2017-07-24", "date_to": "2017-07-24", "event": "BioVis@ISMB 2017", "research_areas": [], "keywords": [], "weblinks": [], "files": [], "projects_workgroups": [ "vis" ], "url": "https://www.cg.tuwien.ac.at/research/publications/2017/Groeller-2017-PTPMD/", "__class": "Publication" }, { "id": "kouril-2017-sccgposter", "type_id": "poster", "tu_id": null, "repositum_id": null, "title": "Maya2cellVIEW: Integrated Tool for Creating Large and Complex Molecular Scenes", "date": "2017-05", "abstract": null, "authors_et_al": false, "substitute": null, "main_image": { "description": null, "filetitle": "teaser", "main_file": false, "use_in_gallery": true, "access": "public", "image_width": 3789, "image_height": 2013, "name": "kouril-2017-sccgposter-teaser.png", "type": "image/png", "size": 285215, "path": "Publication:kouril-2017-sccgposter", "url": "https://www.cg.tuwien.ac.at/research/publications/2017/kouril-2017-sccgposter/kouril-2017-sccgposter-teaser.png", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2017/kouril-2017-sccgposter/kouril-2017-sccgposter-teaser:thumb{{size}}.png" }, "sync_repositum_override": null, "repositum_presentation_id": null, "authors": [ 1383, 1189, 1248, 171 ], "date_from": "2017-05", "date_to": "2017-05", "event": "Spring Conference on Computer Graphics 2017", "research_areas": [ "BioVis", "Modeling" ], "keywords": [], "weblinks": [], "files": [ { "description": null, "filetitle": "poster", "main_file": false, "use_in_gallery": false, "access": "public", "name": "kouril-2017-sccgposter-poster.pdf", "type": "application/pdf", "size": 6909053, "path": "Publication:kouril-2017-sccgposter", "url": "https://www.cg.tuwien.ac.at/research/publications/2017/kouril-2017-sccgposter/kouril-2017-sccgposter-poster.pdf", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2017/kouril-2017-sccgposter/kouril-2017-sccgposter-poster:thumb{{size}}.png" }, { "description": null, "filetitle": "teaser", "main_file": false, "use_in_gallery": true, "access": "public", "image_width": 3789, "image_height": 2013, "name": "kouril-2017-sccgposter-teaser.png", "type": "image/png", "size": 285215, "path": "Publication:kouril-2017-sccgposter", "url": "https://www.cg.tuwien.ac.at/research/publications/2017/kouril-2017-sccgposter/kouril-2017-sccgposter-teaser.png", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2017/kouril-2017-sccgposter/kouril-2017-sccgposter-teaser:thumb{{size}}.png" } ], "projects_workgroups": [ "vis" ], "url": "https://www.cg.tuwien.ac.at/research/publications/2017/kouril-2017-sccgposter/", "__class": "Publication" }, { "id": "LeMuzic_2016_PhD", "type_id": "phdthesis", "tu_id": null, "repositum_id": null, "title": "From Atoms to Cells: Interactive and Illustrative Visualization of Digitally Reproduced Lifeforms", "date": "2016-10-06", "abstract": "Macromolecules, such as proteins, are the building blocks of the machinery of life, and therefore are essential to the comprehension of physiological processes. In physiology, illustrations and animations are often utilized as a mean of communication because they can easily be understood with little background knowledge. However, their realization\nrequires numerous months of manual work, which is both expensive and time consuming.\nComputational biology experts produce everyday large amount of data that is publicly available and that contains valuable information about the structure and also the function of these macromolecules. Instead of relying on manual work to generate illustrative\nvisualizations of the cell biology, we envision a solution that would utilize all the data already available in order to streamline the creation process.\nIn this thesis are presented several contributions that aim at enabling our vision. First, a novel GPU-based rendering pipeline that allows interactive visualization of realistic molecular datasets comprising up to hundreds of millions of macromolecules. The rendering pipeline is embedded into a popular game engine and well known computer graphics optimizations were adapted to support this type of data, such as level-of-detail, instancing and occlusion queries. Secondly, a new method for authoring cutaway views and improving spatial exploration of crowded molecular landscapes. The system relies on the use of clipping objects that are manually placed in the scene and on visibility\nequalizers that allows fine tuning of the visibility of each species present in the scene.\nAgent-based modeling produces trajectory data that can also be combined with structural information in order to animate these landscapes. The snapshots of the trajectories are often played in fast-forward to shorten the length of the visualized sequences, which also renders potentially interesting events occurring at a higher temporal resolution invisible. The third contribution is a solution to visualize time-lapse of agent-based\nsimulations that also reveals hidden information that is only observable at higher temporal resolutions. And finally, a new type of particle-system that utilize quantitative models as input and generate missing spatial information to enable the visualization of molecular trajectories and interactions. The particle-system produces a similar visual output as\ntraditional agent-based modeling tools for a much lower computational footprint and\nallows interactive changing of the simulation parameters, which was not achievable with previous methods.", "authors_et_al": false, "substitute": null, "main_image": { "description": null, "filetitle": "image", "main_file": true, "use_in_gallery": true, "access": "public", "image_width": 261, "image_height": 261, "name": "LeMuzic_2016_PhD-image.jpg", "type": "image/jpeg", "size": 21110, "path": "Publication:LeMuzic_2016_PhD", "url": "https://www.cg.tuwien.ac.at/research/publications/2016/LeMuzic_2016_PhD/LeMuzic_2016_PhD-image.jpg", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2016/LeMuzic_2016_PhD/LeMuzic_2016_PhD-image:thumb{{size}}.png" }, "sync_repositum_override": null, "repositum_presentation_id": null, "authors": [ 1189 ], "date_end": "2016", "date_start": "2013", "matrikelnr": "1326132", "reviewer_1": [ 171 ], "reviewer_2": [ 1399 ], "rigorosum": "2016-11-23", "supervisor": [ 171 ], "research_areas": [ "IllVis" ], "keywords": [], "weblinks": [], "files": [ { "description": null, "filetitle": "image", "main_file": true, "use_in_gallery": true, "access": "public", "image_width": 261, "image_height": 261, "name": "LeMuzic_2016_PhD-image.jpg", "type": "image/jpeg", "size": 21110, "path": "Publication:LeMuzic_2016_PhD", "url": "https://www.cg.tuwien.ac.at/research/publications/2016/LeMuzic_2016_PhD/LeMuzic_2016_PhD-image.jpg", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2016/LeMuzic_2016_PhD/LeMuzic_2016_PhD-image:thumb{{size}}.png" }, { "description": null, "filetitle": "PhD-Thesis", "main_file": true, "use_in_gallery": true, "access": "public", "name": "LeMuzic_2016_PhD-PhD-Thesis.pdf", "type": "application/pdf", "size": 54355957, "path": "Publication:LeMuzic_2016_PhD", "url": "https://www.cg.tuwien.ac.at/research/publications/2016/LeMuzic_2016_PhD/LeMuzic_2016_PhD-PhD-Thesis.pdf", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2016/LeMuzic_2016_PhD/LeMuzic_2016_PhD-PhD-Thesis:thumb{{size}}.png" } ], "projects_workgroups": [ "vis" ], "url": "https://www.cg.tuwien.ac.at/research/publications/2016/LeMuzic_2016_PhD/", "__class": "Publication" }, { "id": "Viola_Ivan_2015_AAM", "type_id": "journalpaper", "tu_id": null, "repositum_id": null, "title": "AnimoAminoMiner: Exploration of Protein Tunnels and their Properties in Molecular Dynamics", "date": "2016-01", "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.", "authors_et_al": false, "substitute": null, "main_image": { "description": null, "filetitle": "Image", "main_file": false, "use_in_gallery": false, "access": "public", "image_width": 1576, "image_height": 609, "name": "Viola_Ivan_2015_AAM-Image.jpg", "type": "image/jpeg", "size": 111989, "path": "Publication:Viola_Ivan_2015_AAM", "url": "https://www.cg.tuwien.ac.at/research/publications/2016/Viola_Ivan_2015_AAM/Viola_Ivan_2015_AAM-Image.jpg", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2016/Viola_Ivan_2015_AAM/Viola_Ivan_2015_AAM-Image:thumb{{size}}.png" }, "sync_repositum_override": null, "repositum_presentation_id": null, "authors": [ 1254, 1189, 166, 171, 1248 ], "date_from": "2015-10-25", "date_to": "2015-10-30", "event": "IEEE Vis 2015", "issn": "1077-2626", "journal": "IEEE Transactions on Visualization and Computer Graphics", "lecturer": [ 1254 ], "location": "Illinois, Chicago, USA", "number": "1", "pages_from": "747", "pages_to": "756", "volume": "22", "research_areas": [ "BioVis" ], "keywords": [ "aggregation", "molecular dynamics", "Protein", "interaction", "tunnel" ], "weblinks": [ { "href": "http://dx.doi.org/10.1109/TVCG.2015.2467434", "caption": null, "description": null, "main_file": 0 } ], "files": [ { "description": null, "filetitle": "Image", "main_file": false, "use_in_gallery": false, "access": "public", "image_width": 1576, "image_height": 609, "name": "Viola_Ivan_2015_AAM-Image.jpg", "type": "image/jpeg", "size": 111989, "path": "Publication:Viola_Ivan_2015_AAM", "url": "https://www.cg.tuwien.ac.at/research/publications/2016/Viola_Ivan_2015_AAM/Viola_Ivan_2015_AAM-Image.jpg", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2016/Viola_Ivan_2015_AAM/Viola_Ivan_2015_AAM-Image:thumb{{size}}.png" }, { "description": null, "filetitle": "Paper", "main_file": true, "use_in_gallery": false, "access": "public", "name": "Viola_Ivan_2015_AAM-Paper.pdf", "type": "application/pdf", "size": 1114453, "path": "Publication:Viola_Ivan_2015_AAM", "url": "https://www.cg.tuwien.ac.at/research/publications/2016/Viola_Ivan_2015_AAM/Viola_Ivan_2015_AAM-Paper.pdf", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2016/Viola_Ivan_2015_AAM/Viola_Ivan_2015_AAM-Paper:thumb{{size}}.png" } ], "projects_workgroups": [ "illvisation" ], "url": "https://www.cg.tuwien.ac.at/research/publications/2016/Viola_Ivan_2015_AAM/", "__class": "Publication" }, { "id": "lemuzic-mindek-2016-viseq", "type_id": "journalpaper", "tu_id": null, "repositum_id": null, "title": "Visibility Equalizer: Cutaway Visualization of Mesoscopic Biological Models", "date": "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.", "authors_et_al": false, "substitute": null, "main_image": { "description": null, "filetitle": "Preview", "main_file": false, "use_in_gallery": false, "access": "public", "image_width": 742, "image_height": 663, "name": "lemuzic-mindek-2016-viseq-Preview.png", "type": "image/png", "size": 858868, "path": "Publication:lemuzic-mindek-2016-viseq", "url": "https://www.cg.tuwien.ac.at/research/publications/2016/lemuzic-mindek-2016-viseq/lemuzic-mindek-2016-viseq-Preview.png", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2016/lemuzic-mindek-2016-viseq/lemuzic-mindek-2016-viseq-Preview:thumb{{size}}.png" }, "sync_repositum_override": null, "repositum_presentation_id": null, "authors": [ 1189, 935, 1072, 1260, 1365, 171 ], "date_from": "2016-06-06", "date_to": "2016-06-10", "event": "EuroVis 2016", "journal": "Computer Graphics Forum", "lecturer": [ 935 ], "location": "Groningen, Netherlands", "number": "3", "volume": "35", "research_areas": [ "BioVis", "IllVis" ], "keywords": [ "molecular visualization", "visibility", "occlusion" ], "weblinks": [], "files": [ { "description": null, "filetitle": "Paper", "main_file": true, "use_in_gallery": false, "access": "public", "name": "lemuzic-mindek-2016-viseq-Paper.pdf", "type": "application/pdf", "size": 3971312, "path": "Publication:lemuzic-mindek-2016-viseq", "url": "https://www.cg.tuwien.ac.at/research/publications/2016/lemuzic-mindek-2016-viseq/lemuzic-mindek-2016-viseq-Paper.pdf", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2016/lemuzic-mindek-2016-viseq/lemuzic-mindek-2016-viseq-Paper:thumb{{size}}.png" }, { "description": null, "filetitle": "Preview", "main_file": false, "use_in_gallery": false, "access": "public", "image_width": 742, "image_height": 663, "name": "lemuzic-mindek-2016-viseq-Preview.png", "type": "image/png", "size": 858868, "path": "Publication:lemuzic-mindek-2016-viseq", "url": "https://www.cg.tuwien.ac.at/research/publications/2016/lemuzic-mindek-2016-viseq/lemuzic-mindek-2016-viseq-Preview.png", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2016/lemuzic-mindek-2016-viseq/lemuzic-mindek-2016-viseq-Preview:thumb{{size}}.png" }, { "description": null, "filetitle": "Slides", "main_file": true, "use_in_gallery": false, "access": "public", "name": "lemuzic-mindek-2016-viseq-Slides.pptx", "type": "application/vnd.openxmlformats-officedocument.presentationml.presentation", "size": 140149203, "path": "Publication:lemuzic-mindek-2016-viseq", "url": "https://www.cg.tuwien.ac.at/research/publications/2016/lemuzic-mindek-2016-viseq/lemuzic-mindek-2016-viseq-Slides.pptx", "thumb_image_sizes": [] } ], "projects_workgroups": [ "illvisation" ], "url": "https://www.cg.tuwien.ac.at/research/publications/2016/lemuzic-mindek-2016-viseq/", "__class": "Publication" }, { "id": "Reisacher2016", "type_id": "inproceedings", "tu_id": null, "repositum_id": null, "title": "CellPathway: A Simulation Tool for Illustrative Visualization of Biochemical Networks", "date": "2016", "abstract": "The molecular knowledge about complex biochemical reaction networks in biotechnology is crucial and has received a lot\nof attention lately. As a consequence, multiple visualization programs have been already developed to illustrate the anatomy\nof a cell. However, since a real cell performs millions of reactions every second to sustain live, it is necessary to move from\nanatomical to physiological illustrations to communicate knowledge about the behavior of a cell more accurately. In this thesis I\npropose a reaction system including a collision detection algorithm, which is able to work at the level of single atoms, to enable\nprecise simulation of molecular interactions. To visually explain molecular activities during the simulation process, a real-time\nglow effect in combination with a clipping object have been implemented. Since intracellular processes are performed with a\nset of chemical transformations, a hierarchical structure is used to illustrate the impact of one reaction on the entire simulation.\nThe CellPathway system integrates acceleration techniques to render large datasets containing millions of atoms in real-time,\nwhile the reaction system is processed directly on the GPU to enable simulation with more than 1000 molecules. Furthermore,\na graphical user interface has been implemented to allow the user to control parameters during simulation interactively.", "authors_et_al": false, "substitute": null, "main_image": { "description": null, "filetitle": "image", "main_file": false, "use_in_gallery": true, "access": "public", "image_width": 400, "image_height": 400, "name": "Reisacher2016-image.jpg", "type": "image/jpeg", "size": 135376, "path": "Publication:Reisacher2016", "url": "https://www.cg.tuwien.ac.at/research/publications/2016/Reisacher2016/Reisacher2016-image.jpg", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2016/Reisacher2016/Reisacher2016-image:thumb{{size}}.png" }, "sync_repositum_override": null, "repositum_presentation_id": null, "authors": [ 1267, 1189, 171 ], "booktitle": "Proceedings of WSCG", "lecturer": [ 1189 ], "location": "Pilsen, Czech Republic", "research_areas": [ "BioVis", "IllVis" ], "keywords": [], "weblinks": [], "files": [ { "description": null, "filetitle": "image", "main_file": false, "use_in_gallery": true, "access": "public", "image_width": 400, "image_height": 400, "name": "Reisacher2016-image.jpg", "type": "image/jpeg", "size": 135376, "path": "Publication:Reisacher2016", "url": "https://www.cg.tuwien.ac.at/research/publications/2016/Reisacher2016/Reisacher2016-image.jpg", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2016/Reisacher2016/Reisacher2016-image:thumb{{size}}.png" }, { "description": null, "filetitle": "paper", "main_file": true, "use_in_gallery": false, "access": "public", "name": "Reisacher2016-paper.pdf", "type": "application/pdf", "size": 1151123, "path": "Publication:Reisacher2016", "url": "https://www.cg.tuwien.ac.at/research/publications/2016/Reisacher2016/Reisacher2016-paper.pdf", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2016/Reisacher2016/Reisacher2016-paper:thumb{{size}}.png" } ], "projects_workgroups": [ "illvisation" ], "url": "https://www.cg.tuwien.ac.at/research/publications/2016/Reisacher2016/", "__class": "Publication" }, { "id": "Waldin_Nicholas_2016_Chameleon", "type_id": "inproceedings", "tu_id": null, "repositum_id": null, "title": "Chameleon Dynamic Color Mapping for Multi-Scale Structural Biology Models", "date": "2016", "abstract": "Visualization of structural biology data uses color to categorize or separate dense structures into particular semantic units. In\nmultiscale models of viruses or bacteria, there are atoms on the finest level of detail, then amino-acids, secondary structures,\nmacromolecules, up to the compartment level and, in all these levels, elements can be visually distinguished by color. However,\ncurrently only single scale coloring schemes are utilized that show information for one particular scale only. We present a novel\ntechnology which adaptively, based on the current scale level, adjusts the color scheme to depict or distinguish the currently\nbest visible structural information. We treat the color as a visual resource that is distributed given a particular demand. The\nchanges of the color scheme are seamlessly interpolated between the color scheme from the previous views into a given new one.\nWith such dynamic multi-scale color mapping we ensure that the viewer is able to distinguish structural detail that is shown\non any given scale. This technique has been tested by users with an expertise in structural biology and has been overall well\nreceived.", "authors_et_al": false, "substitute": null, "main_image": { "description": null, "filetitle": "Overview", "main_file": false, "use_in_gallery": false, "access": "public", "image_width": 378, "image_height": 472, "name": "Waldin_Nicholas_2016_Chameleon-Overview.png", "type": "image/png", "size": 488060, "path": "Publication:Waldin_Nicholas_2016_Chameleon", "url": "https://www.cg.tuwien.ac.at/research/publications/2016/Waldin_Nicholas_2016_Chameleon/Waldin_Nicholas_2016_Chameleon-Overview.png", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2016/Waldin_Nicholas_2016_Chameleon/Waldin_Nicholas_2016_Chameleon-Overview:thumb{{size}}.png" }, "sync_repositum_override": null, "repositum_presentation_id": null, "authors": [ 1461, 1189, 1110, 166, 1365, 1260, 171 ], "booktitle": "Eurographics Workshop on Visual Computing for Biology and Medicine", "event": "VCBM", "lecturer": [ 1339 ], "research_areas": [], "keywords": [], "weblinks": [ { "href": "https://diglib.eg.org/handle/10.2312/vcbm20161266", "caption": null, "description": null, "main_file": 0 } ], "files": [ { "description": null, "filetitle": "Overview", "main_file": false, "use_in_gallery": false, "access": "public", "image_width": 378, "image_height": 472, "name": "Waldin_Nicholas_2016_Chameleon-Overview.png", "type": "image/png", "size": 488060, "path": "Publication:Waldin_Nicholas_2016_Chameleon", "url": "https://www.cg.tuwien.ac.at/research/publications/2016/Waldin_Nicholas_2016_Chameleon/Waldin_Nicholas_2016_Chameleon-Overview.png", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2016/Waldin_Nicholas_2016_Chameleon/Waldin_Nicholas_2016_Chameleon-Overview:thumb{{size}}.png" }, { "description": null, "filetitle": "paper", "main_file": true, "use_in_gallery": false, "access": "public", "name": "Waldin_Nicholas_2016_Chameleon-paper.pdf", "type": "application/pdf", "size": 25172411, "path": "Publication:Waldin_Nicholas_2016_Chameleon", "url": "https://www.cg.tuwien.ac.at/research/publications/2016/Waldin_Nicholas_2016_Chameleon/Waldin_Nicholas_2016_Chameleon-paper.pdf", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2016/Waldin_Nicholas_2016_Chameleon/Waldin_Nicholas_2016_Chameleon-paper:thumb{{size}}.png" }, { "description": null, "filetitle": "zoomed A", "main_file": false, "use_in_gallery": false, "access": "public", "image_width": 378, "image_height": 472, "name": "Waldin_Nicholas_2016_Chameleon-zoomed A.png", "type": "image/png", "size": 462676, "path": "Publication:Waldin_Nicholas_2016_Chameleon", "url": "https://www.cg.tuwien.ac.at/research/publications/2016/Waldin_Nicholas_2016_Chameleon/Waldin_Nicholas_2016_Chameleon-zoomed A.png", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2016/Waldin_Nicholas_2016_Chameleon/Waldin_Nicholas_2016_Chameleon-zoomed A:thumb{{size}}.png" }, { "description": null, "filetitle": "zoomed B", "main_file": false, "use_in_gallery": false, "access": "public", "image_width": 380, "image_height": 474, "name": "Waldin_Nicholas_2016_Chameleon-zoomed B.png", "type": "image/png", "size": 360850, "path": "Publication:Waldin_Nicholas_2016_Chameleon", "url": "https://www.cg.tuwien.ac.at/research/publications/2016/Waldin_Nicholas_2016_Chameleon/Waldin_Nicholas_2016_Chameleon-zoomed B.png", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2016/Waldin_Nicholas_2016_Chameleon/Waldin_Nicholas_2016_Chameleon-zoomed B:thumb{{size}}.png" } ], "projects_workgroups": [ "vis", "deskollage" ], "url": "https://www.cg.tuwien.ac.at/research/publications/2016/Waldin_Nicholas_2016_Chameleon/", "__class": "Publication" }, { "id": "cellVIEW_2015", "type_id": "inproceedings", "tu_id": null, "repositum_id": null, "title": "cellVIEW: a Tool for Illustrative and Multi-Scale Rendering of Large Biomolecular Datasets", "date": "2015-09", "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.", "authors_et_al": false, "substitute": null, "main_image": { "description": null, "filetitle": "", "main_file": true, "use_in_gallery": true, "access": "public", "image_width": 1264, "image_height": 796, "name": "cellVIEW_2015-.png", "type": "image/png", "size": 1483300, "path": "Publication:cellVIEW_2015", "url": "https://www.cg.tuwien.ac.at/research/publications/2015/cellVIEW_2015/cellVIEW_2015-.png", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2015/cellVIEW_2015/cellVIEW_2015-:thumb{{size}}.png" }, "sync_repositum_override": null, "repositum_presentation_id": null, "authors": [ 1189, 1260, 1143, 171 ], "booktitle": "Eurographics Workshop on Visual Computing for Biology and Medicine", "date_from": "2015-09-14", "date_to": "2015-09-15", "editor": "Katja Bühler and Lars Linsen and Nigel W. John", "isbn": "978-3-905674-82-8", "issn": "2070-5786", "lecturer": [ 1189 ], "location": "Chester, United Kingdom", "organization": "EG Digital Library", "pages_from": "61", "pages_to": "70", "publisher": "The Eurographics Association", "research_areas": [ "BioVis", "IllVis" ], "keywords": [], "weblinks": [], "files": [ { "description": null, "filetitle": "", "main_file": true, "use_in_gallery": true, "access": "public", "image_width": 1264, "image_height": 796, "name": "cellVIEW_2015-.png", "type": "image/png", "size": 1483300, "path": "Publication:cellVIEW_2015", "url": "https://www.cg.tuwien.ac.at/research/publications/2015/cellVIEW_2015/cellVIEW_2015-.png", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2015/cellVIEW_2015/cellVIEW_2015-:thumb{{size}}.png" }, { "description": "the paper", "filetitle": "paper", "main_file": true, "use_in_gallery": false, "access": "public", "name": "cellVIEW_2015-paper.pdf", "type": "application/pdf", "size": 14485825, "path": "Publication:cellVIEW_2015", "url": "https://www.cg.tuwien.ac.at/research/publications/2015/cellVIEW_2015/cellVIEW_2015-paper.pdf", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2015/cellVIEW_2015/cellVIEW_2015-paper:thumb{{size}}.png" } ], "projects_workgroups": [ "illvisation" ], "url": "https://www.cg.tuwien.ac.at/research/publications/2015/cellVIEW_2015/", "__class": "Publication" }, { "id": "lemuzic_2015_timelapse", "type_id": "inproceedings", "tu_id": null, "repositum_id": null, "title": "Illustrative Timelapse: A Technique for Illustrative Visualization of Particle Simulations on the Mesoscale Level", "date": "2015-04", "abstract": "Animated movies are a popular way to communicate complex phenomena\nin cell biology to the broad audience. Animation artists\napply sophisticated illustration techniques to communicate a story,\nwhile trying to maintain a realistic representation of a complex dynamic\nenvironment. Since such hand-crafted animations are timeconsuming\nand cost-intensive to create, our goal is to formalize\nillustration techniques used by artists to facilitate the automatic\ncreation of visualizations generated from mesoscale particle-based\nmolecular simulations. Our technique Illustrative Timelapse supports\nvisual exploration of complex biochemical processes in dynamic\nenvironments by (1) seamless temporal zooming to observe\nphenomena in different temporal resolutions, (2) visual abstraction\nof molecular trajectories to ensure that observers are able to visually\nfollow the main actors, (3) increased visual focus on events of interest,\nand (4) lens effects to preserve a realistic representation of the\nenvironment in the context. Results from a first user study indicate\nthat visual abstraction of trajectories improves the ability to follow\na story and is also appreciated by users. Lens effects increased the\nperceived amount of molecular motion in the environment while\ntrading off traceability of individual molecules.", "authors_et_al": false, "substitute": null, "main_image": { "description": null, "filetitle": "screenshot", "main_file": true, "use_in_gallery": true, "access": "public", "image_width": 1804, "image_height": 810, "name": "lemuzic_2015_timelapse-screenshot.jpg", "type": "image/jpeg", "size": 238322, "path": "Publication:lemuzic_2015_timelapse", "url": "https://www.cg.tuwien.ac.at/research/publications/2015/lemuzic_2015_timelapse/lemuzic_2015_timelapse-screenshot.jpg", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2015/lemuzic_2015_timelapse/lemuzic_2015_timelapse-screenshot:thumb{{size}}.png" }, "sync_repositum_override": null, "repositum_presentation_id": null, "authors": [ 1189, 1110, 1143, 171 ], "booktitle": "Visualization Symposium (PacificVis), 2015 IEEE Pacific", "date_from": "2015-04-14", "date_to": "2015-04-17", "lecturer": [ 1189 ], "location": "Zijingang Campus, Zhejiang University, Hangzhou, China", "organization": "8th IEEE Pacific Visualization Symposium (PacificVis 2015)", "pages_from": "247", "pages_to": "254", "publisher": "IEEE", "research_areas": [ "BioVis", "IllVis" ], "keywords": [], "weblinks": [], "files": [ { "description": "the paper", "filetitle": "paper", "main_file": true, "use_in_gallery": false, "access": "public", "name": "lemuzic_2015_timelapse-paper.pdf", "type": "application/pdf", "size": 1414681, "path": "Publication:lemuzic_2015_timelapse", "url": "https://www.cg.tuwien.ac.at/research/publications/2015/lemuzic_2015_timelapse/lemuzic_2015_timelapse-paper.pdf", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2015/lemuzic_2015_timelapse/lemuzic_2015_timelapse-paper:thumb{{size}}.png" }, { "description": null, "filetitle": "screenshot", "main_file": true, "use_in_gallery": true, "access": "public", "image_width": 1804, "image_height": 810, "name": "lemuzic_2015_timelapse-screenshot.jpg", "type": "image/jpeg", "size": 238322, "path": "Publication:lemuzic_2015_timelapse", "url": "https://www.cg.tuwien.ac.at/research/publications/2015/lemuzic_2015_timelapse/lemuzic_2015_timelapse-screenshot.jpg", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2015/lemuzic_2015_timelapse/lemuzic_2015_timelapse-screenshot:thumb{{size}}.png" } ], "projects_workgroups": [ "illvisation" ], "url": "https://www.cg.tuwien.ac.at/research/publications/2015/lemuzic_2015_timelapse/", "__class": "Publication" }, { "id": "waldner-2014-af", "type_id": "journalpaper", "tu_id": null, "repositum_id": null, "title": " Attractive Flicker: Guiding Attention in Dynamic Narrative Visualizations", "date": "2014-12", "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.", "authors_et_al": false, "substitute": null, "main_image": { "description": null, "filetitle": "", "main_file": false, "use_in_gallery": false, "access": "public", "image_width": 600, "image_height": 605, "name": "waldner-2014-af-.png", "type": "image/png", "size": 232715, "path": "Publication:waldner-2014-af", "url": "https://www.cg.tuwien.ac.at/research/publications/2014/waldner-2014-af/waldner-2014-af-.png", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2014/waldner-2014-af/waldner-2014-af-:thumb{{size}}.png" }, "sync_repositum_override": null, "repositum_presentation_id": null, "authors": [ 1110, 1189, 660, 190, 171 ], "date_from": "2014-11-09", "date_to": "2014-11-14", "event": "IEEE VIS 2014", "journal": "IEEE Transactions on Visualization and Computer Graphics", "lecturer": [ 1110 ], "location": "Paris, France", "number": "12", "pages_from": "2456", "pages_to": "2465", "volume": "20", "research_areas": [ "BioVis", "Perception" ], "keywords": [ "Narrative Visualization", "Flicker", "Visual Attention" ], "weblinks": [ { "href": "http://dx.doi.org/10.1109/TVCG.2014.2346352", "caption": null, "description": null, "main_file": 0 } ], "files": [ { "description": null, "filetitle": "", "main_file": false, "use_in_gallery": false, "access": "public", "image_width": 600, "image_height": 605, "name": "waldner-2014-af-.png", "type": "image/png", "size": 232715, "path": "Publication:waldner-2014-af", "url": "https://www.cg.tuwien.ac.at/research/publications/2014/waldner-2014-af/waldner-2014-af-.png", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2014/waldner-2014-af/waldner-2014-af-:thumb{{size}}.png" }, { "description": "Screenshot of the large molecular scene used in the final experiment", "filetitle": "molecularScene", "main_file": false, "use_in_gallery": false, "access": "public", "image_width": 7597, "image_height": 1327, "name": "waldner-2014-af-molecularScene.png", "type": "image/png", "size": 3805356, "path": "Publication:waldner-2014-af", "url": "https://www.cg.tuwien.ac.at/research/publications/2014/waldner-2014-af/waldner-2014-af-molecularScene.png", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2014/waldner-2014-af/waldner-2014-af-molecularScene:thumb{{size}}.png" }, { "description": null, "filetitle": "paper", "main_file": true, "use_in_gallery": false, "access": "public", "name": "waldner-2014-af-paper.pdf", "type": "application/pdf", "size": 6413298, "path": "Publication:waldner-2014-af", "url": "https://www.cg.tuwien.ac.at/research/publications/2014/waldner-2014-af/waldner-2014-af-paper.pdf", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2014/waldner-2014-af/waldner-2014-af-paper:thumb{{size}}.png" }, { "description": null, "filetitle": "Preview video", "main_file": true, "use_in_gallery": false, "access": "public", "preview_image_width": 1280, "preview_image_height": 720, "name": "waldner-2014-af-Preview video.mp4", "type": "video/mp4", "size": 16497882, "path": "Publication:waldner-2014-af", "preview_name": "waldner-2014-af-Preview video:preview.png", "preview_type": "image/jpeg", "preview_size": 14964, "url": "https://www.cg.tuwien.ac.at/research/publications/2014/waldner-2014-af/waldner-2014-af-Preview video.mp4", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2014/waldner-2014-af/waldner-2014-af-Preview video:thumb{{size}}.png", "video_mp4": "https://www.cg.tuwien.ac.at/research/publications/2014/waldner-2014-af/waldner-2014-af-Preview video:video.mp4" }, { "description": null, "filetitle": "Submission video", "main_file": true, "use_in_gallery": false, "access": "public", "preview_image_width": 1280, "preview_image_height": 720, "name": "waldner-2014-af-Submission video.mp4", "type": "video/mp4", "size": 23904054, "path": "Publication:waldner-2014-af", "preview_name": "waldner-2014-af-Submission video:preview.png", "preview_type": "image/jpeg", "preview_size": 48929, "url": "https://www.cg.tuwien.ac.at/research/publications/2014/waldner-2014-af/waldner-2014-af-Submission video.mp4", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2014/waldner-2014-af/waldner-2014-af-Submission video:thumb{{size}}.png", "video_mp4": "https://www.cg.tuwien.ac.at/research/publications/2014/waldner-2014-af/waldner-2014-af-Submission video:video.mp4" } ], "projects_workgroups": [ "illvisation" ], "url": "https://www.cg.tuwien.ac.at/research/publications/2014/waldner-2014-af/", "__class": "Publication" }, { "id": "lemuzic-2014-ivm", "type_id": "journalpaper", "tu_id": null, "repositum_id": null, "title": "Illustrative Visualization of Molecular Reactions using Omniscient Intelligence and Passive Agents ", "date": "2014-06", "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.", "authors_et_al": false, "substitute": null, "main_image": { "description": null, "filetitle": "image", "main_file": false, "use_in_gallery": true, "access": "public", "image_width": 1027, "image_height": 1027, "name": "lemuzic-2014-ivm-image.jpg", "type": "image/jpeg", "size": 399463, "path": "Publication:lemuzic-2014-ivm", "url": "https://www.cg.tuwien.ac.at/research/publications/2014/lemuzic-2014-ivm/lemuzic-2014-ivm-image.jpg", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2014/lemuzic-2014-ivm/lemuzic-2014-ivm-image:thumb{{size}}.png" }, "sync_repositum_override": null, "repositum_presentation_id": null, "authors": [ 1189, 1143, 1190, 171 ], "date_from": "2014-06-09", "date_to": "2014-06-13", "event": "EuroVis", "journal": "Computer Graphics Forum", "lecturer": [ 1189 ], "location": "Swansea, Wales, UK", "note": "Article first published online: 12 JUL 2014", "number": "3", "pages_from": "141", "pages_to": "150", "volume": "33", "research_areas": [ "BioVis", "IllVis" ], "keywords": [], "weblinks": [ { "href": "http://onlinelibrary.wiley.com/doi/10.1111/cgf.12370/abstract", "caption": null, "description": null, "main_file": 0 } ], "files": [ { "description": null, "filetitle": "image", "main_file": false, "use_in_gallery": true, "access": "public", "image_width": 1027, "image_height": 1027, "name": "lemuzic-2014-ivm-image.jpg", "type": "image/jpeg", "size": 399463, "path": "Publication:lemuzic-2014-ivm", "url": "https://www.cg.tuwien.ac.at/research/publications/2014/lemuzic-2014-ivm/lemuzic-2014-ivm-image.jpg", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2014/lemuzic-2014-ivm/lemuzic-2014-ivm-image:thumb{{size}}.png" }, { "description": null, "filetitle": "paper", "main_file": true, "use_in_gallery": false, "access": "public", "name": "lemuzic-2014-ivm-paper.pdf", "type": "application/pdf", "size": 2888693, "path": "Publication:lemuzic-2014-ivm", "url": "https://www.cg.tuwien.ac.at/research/publications/2014/lemuzic-2014-ivm/lemuzic-2014-ivm-paper.pdf", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2014/lemuzic-2014-ivm/lemuzic-2014-ivm-paper:thumb{{size}}.png" }, { "description": null, "filetitle": "video", "main_file": true, "use_in_gallery": false, "access": "public", "preview_image_width": 1920, "preview_image_height": 1080, "name": "lemuzic-2014-ivm-video.mp4", "type": "video/mp4", "size": 288142406, "path": "Publication:lemuzic-2014-ivm", "preview_name": "lemuzic-2014-ivm-video:preview.png", "preview_type": "image/jpeg", "preview_size": 33186, "url": "https://www.cg.tuwien.ac.at/research/publications/2014/lemuzic-2014-ivm/lemuzic-2014-ivm-video.mp4", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2014/lemuzic-2014-ivm/lemuzic-2014-ivm-video:thumb{{size}}.png", "video_mp4": "https://www.cg.tuwien.ac.at/research/publications/2014/lemuzic-2014-ivm/lemuzic-2014-ivm-video:video.mp4" } ], "projects_workgroups": [ "illvisation" ], "url": "https://www.cg.tuwien.ac.at/research/publications/2014/lemuzic-2014-ivm/", "__class": "Publication" }, { "id": "lemuzic_2014_ipv", "type_id": "poster", "tu_id": null, "repositum_id": null, "title": "Illustrative Visualization of Biochemical Processes Featuring Multiple Temporal Scales", "date": "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 \nmimic 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.\n", "authors_et_al": false, "substitute": null, "main_image": { "description": null, "filetitle": "", "main_file": false, "use_in_gallery": false, "access": "public", "name": "lemuzic_2014_ipv-.pdf", "type": "application/pdf", "size": 823052, "path": "Publication:lemuzic_2014_ipv", "url": "https://www.cg.tuwien.ac.at/research/publications/2014/lemuzic_2014_ipv/lemuzic_2014_ipv-.pdf", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2014/lemuzic_2014_ipv/lemuzic_2014_ipv-:thumb{{size}}.png" }, "sync_repositum_override": null, "repositum_presentation_id": null, "authors": [ 1189, 1143, 1110, 171 ], "date_from": "2014-09-04", "date_to": "2014-09-05", "event": "Eurographics Workshop on Visual Computing for Biology", "research_areas": [ "IllVis" ], "keywords": [], "weblinks": [], "files": [ { "description": null, "filetitle": "", "main_file": false, "use_in_gallery": false, "access": "public", "name": "lemuzic_2014_ipv-.pdf", "type": "application/pdf", "size": 823052, "path": "Publication:lemuzic_2014_ipv", "url": "https://www.cg.tuwien.ac.at/research/publications/2014/lemuzic_2014_ipv/lemuzic_2014_ipv-.pdf", "thumb_image_sizes": [ 16, 64, 100, 175, 300, 600 ], "thumb_url": "https://www.cg.tuwien.ac.at/research/publications/2014/lemuzic_2014_ipv/lemuzic_2014_ipv-:thumb{{size}}.png" } ], "projects_workgroups": [ "vis" ], "url": "https://www.cg.tuwien.ac.at/research/publications/2014/lemuzic_2014_ipv/", "__class": "Publication" } ]