PhysioIllustration

The focus of the project is is to develop novel graphics data representations, visual representations, occlusion handling, visual guidance and storytel-ling, zooming, interaction and integration of physiological models and medical imaging. The visualization technology will be developed and evaluated on multiple scale levels, from molecular machines, up to the organ level.

Our Resilient Genome

Our Resilient Genome is a short science animation by filmmaker Pina Kingman. It was developed as part of the PhysioIllustration Project with the Visualization Group, Department of Informatics at the University of Bergen. The aim of this project is to research novel visual communication techniques and advance knowledge translation methods, specifically in the field of molecular and cellular biology. This research culminated in the creation of a short film describing DNA Repair and is intended for the general public. In addition to showcasing our novel visual communication methods, the film also highlights research undertaken by the Department of Molecular Biology, UiB. The film tells the story of our DNA, how it is constantly breaking and rebuilding over and over again to keep us alive, and provides a glimpse into the fascinating world of cellular biology.

St. Tropez International Film Festival in Nice, France

The Nice in South of France International Film and Television Festival of World Cinema held in the South of France at the same time as the World famous Cannes film festival, in its 4th year is a global industry event that will reach out to the many filmmakers who always place film at the centre of our acts as a truly international film industry event, being held a week before the Cannes International film festival so filmmakers can be in the south of France for both events bringing together films from around the world.

We have built a small but exceptional professional network of industry professional that will look at all films entered and will give business and commercial advice, in some cases the distributors attending will make offers to the filmmakers for their work and to work together to put your movies in the market place, we have the people and skills in our professional team to make this happen, if the professional attending feel there is a market for your movie, they will as with many films over the years of our other festival make it happen. We are unique in the amount of platforms and festival we offer filmmakers, we can create a ripple for your movie to be seen around the world, it all starts here by entering your movie.

Generally, to take nothing into account other than the art of film and the pre-eminence of artistic talent, and finally to facilitate transmission, so that tomorrow’s Festival can continue the adventure with the combined strengths of experience and modernity, for those that enter the Festival will truly be the future filmmakers of the film industry.

Acknowledgements

Funding and Support for this project comes from NFR (project #218023), The Bergen University Fund (Universitetsfondet), and BEK/ Bergen senter for elektronisk kunst http://www.bek.no.

Related links

Interactive molecular illustration

Physiological processes are of the temporal and spatial multi-scale and ranges from molecular level to the whole organism. Many of the processes have their begining in the molecular scale. Important processes such as polymerization, diffusion, reactions are all happening in the crowded environment full of different molecules. Also those processes have vast temporal range from nanoseconds (diffusion) to seconds (polymerization). Our first focus is therefore on the illustrative visualization of physiological processes in the molecular scale to provide intuitive visual representation, which the user can observe and interact with.

Illustrating Polymerization using Three-level Model Fusion

Feel free to download the unity prototype of our current research project here: UnityProject. It contains Unity project, which can be opened by the Unity Editor. In the prototype project hierarchy there are models and materials used to create scenes and simulation, 7 scenes which covers the demonstration bundle of project and the scripts.

The demonstration bundle consist of 7 unity scenes. Three of the scenes: parp, cellulose and tubulin, are biological examples of our prototype described in the paper. For additional demonstration of approach there are examples: starpolymer, copolymer and showcase. StarPolymer scene demonstrates the creation of star polymer with our approach, copolymer on the other hand presents the creation of block linear copolymer. Showcase demonstration is described in more detail in the paper. The last scene demonstrates more advanced visualization of our system mentioned in the Discussion section of the paper.

Every scene have predefined GameObjects for important parts pf the system: LSystem and Agent system (see Fig. 1). Those objects contains their respective scripts, which handles the initialization and update of systems. For managing and setting the parameters of those system, there is provided Editor custom GUI in the Inspector panel.

LSystem GUI is divided to three parts. First is the part managing the alphabet of the L-System. Here are specified symbols, which are later used to define the rules and the axiom. The description and semantic meaning of those rules are detaily described in the paper. Second part manages the axiom, which is the starting point of the process. The axiom can only be a communication symbol, which tells by which subprocess it should start. Last section manages the rules. User can change/remove the existing rules or add the new ones.

Agent system is steered by the system of densities, which is another modeling layer described in more detail in System of Densities subsection in the paper. In thiswindow user can add or remove the type of molecule which is in environment. Every molecule has its own image preview and the density can be adjusted.

Simulation have two global parameters: time delta of the simulation, and the number of monomers of the resulting polymer. This variables are accesible from the editor window, which can be opened from LSystem or Agent system inspector.

Comparative VIsualization of Spatial Ensemble Data

Nowadays, generation and study of spatial ensemble data is becoming more and more important for the research in the central scientific fields, such as medicine, biology, physics. A comparative visualization is highly suitable for the exploration of the ensemble members, especially if the spatial aspect is of upmost importance. The usefullness of the comparative visualization highly depends on the number of compared members, and on the visibility of the important characteristics of the members.

A Fractional Cartesian Composition Model for Semi-spatial Comparative Visualization Design

Feel free to download the unity project: Prototype, which contains a prototype implementation of our model. The project can be opened by the Unity Editor. In the prototype project hierarchy there are ensmeble input data (stored in xml format), 3 scenes which covers the demonstration of project and the scripts.

Three scenes (ivy, parp, city) covers the demonstration of the model described in the paper (Wall-covering Ivy, PARP polymerization, Parametrized Cities). Every scene have predefined GameObject (*manager) for accessing user interface of the model (for ivy example see Fig. 1).

The first step of the interaction with the model is to load an ensemble (Fig. 1a)—then the characteristics for the example are shown (Fig. 1b). Here, the user adjusts the importance of the characteristics for the optimization. After pressing “Build Samples” (Fig. 1c), our prototype picks ensemble members (randomly), applies the available abstractions and computes the selected characteristics in order to approximate the cost function for the optimization. For all the examples in this paper, we used an empirically-determined sample size of 10 ensemble members. Clearly, this is only a prototype implementation of the otherwise more general framework and ample opportunities for optimization are given here.

After the initial setup, the user interacts with the model parameters, characteristics, and axes (see Fig. 1d, b, e, respectively). After each parameter change, a preview of how the ensemble members will be positioned and how much visual space is available for each member is shown. If the user is satisfied, he/she can then create the final visualization (Fig. 1g).

Publications

2017

    [PDF] [DOI] [YT] [Bibtex]
    @ARTICLE {Kolesar-2017-FCC,
    author = "Ivan Kolesar and Stefan Bruckner and Ivan Viola and Helwig Hauser",
    title = "A Fractional Cartesian Composition Model for Semi-spatial Comparative Visualization Design",
    journal = "IEEE Transactions on Visualization and Computer Graphics",
    year = "2017",
    volume = "23",
    number = "1",
    pages = "851--860",
    month = "jan",
    abstract = "The study of spatial data ensembles leads to substantial visualization
    challenges in a variety of applications. In this paper, we present
    a model for comparative visualization that supports the design of
    according ensemble visualization solutions by partial automation.
    We focus on applications, where the user is interested in preserving
    selected spatial data characteristics of the data as much as possible—even
    when many ensemble members should be jointly studied using comparative
    visualization. In our model, we separate the design challenge into
    a minimal set of user-specified parameters and an optimization component
    for the automatic configuration of the remaining design variables.
    We provide an illustrated formal description of our model and exemplify
    our approach in the context of several application examples from
    different domains in order to demonstrate its generality within the
    class of comparative visualization problems for spatial data ensembles.",
    pdf = "pdfs/Kolesar-2017-FCC.pdf",
    images = "images/Kolesar-2017-FCC.jpg",
    thumbnails = "images/Kolesar-2017-FCC.png",
    youtube = "https://www.youtube.com/watch?v=_zk67fmryok",
    doi = "10.1109/TVCG.2016.2598870",
    event = "IEEE SciVis 2016",
    keywords = "visualization models, integrating spatial and non-spatial data visualization, design methodologies",
    location = "Baltimore, USA",
    project = "physioillustration"
    }

2016

    [DOI] [Bibtex]
    @ARTICLE {Michael2016Visual,
    author = "Michael Krone and Barbora Kozlikova and Norbert Lindow and Marc Baaden and Daniel Baum, and Julius Parulek and Hans-Christian Hege and Ivan Viola",
    title = "Visual Analysis of Biomolecular Cavities: State of the Art",
    journal = "Computer Graphics Forum",
    year = "2016",
    abstract = "In this report we review and structure the branch of molecular visualization that is concerned with the visual analysis of cavities in macromolecular protein structures. First the necessary background, the domain terminology, and the goals of analytical reasoning are introduced. Based on a comprehensive collection of relevant research works, we present a novel classification for cavity detection approaches and structure them into four distinct classes: grid-based, Voronoi-based, surface-based, and probe-based methods. The subclasses are then formed by their combinations. We match these approaches with corresponding visualization technologies starting with direct 3D visualization, followed with non-spatial visualization techniques that for example abstract the interactions between structures into a relational graph, straighten the cavity of interest to see its profile in one view, or aggregate the time sequence into a single contour plot. We also discuss the current state of methods for the visual analysis of cavities in dynamic data such as molecular dynamics simulations. Finally, we give an overview of the most common tools that are actively developed and used in the structural biology and biochemistry research. Our report is concluded by an outlook on future challenges in the field.",
    images = "images/STARcavities2016.png",
    thumbnails = "images/STARcavities2016.png",
    publisher = "The Eurographics Association and John Wiley \& Sons Ltd.",
    issn = "1467-8659",
    doi = "10.1111/cgf.12928",
    project = "physioillustration"
    }
    [Bibtex]
    @INPROCEEDINGS {Kolesar2016VCBM,
    author = "Ivan Kolesar and Jan Byska and Julius Parulek andHelwig Hauser and Barbora Kozlikova",
    title = "Unfolding and Interactive Exploration of Protein Tunnels andtheir Dynamics",
    booktitle = "Eurographics Workshop on Visual Computing for Biology and Medicine",
    year = "2016",
    pages = "1--10",
    month = "sep",
    abstract = "The presence of tunnels in protein structures substantially influences their reactivity with other molecules. Therefore, studying their properties and changes over time has been in the scope of biochemists for decades. In this paper we introduce a novel approach for comparative visualization and exploration of ensembles of tunnels. Our goal is to overcome occlusion problems present in traditional tunnel representations while providing users a quick way to navigate through the input dataset to identify potentially interesting tunnels. First, we unfold the input tunnels to a 2D representation enabling to observe the mutual position of amino acids forming the tunnel surface and the amount of surface they influence. These 2D images are subsequently described by image moments commonly used in image processing. This way we are able to detect similarities and outliers in the dataset, which are visualized as clusters in a scatterplot graph. The same coloring scheme is used in the linked bar chart enabling to detect the position of the cluster members over time. These views provide a way to select a subset of potentially interesting tunnels that can be further explored in detail using the 2D unfolded view and also traditional 3D representation. The usability of our approach is demonstrated on case studies conducted by the domain experts.",
    images = "images/Kolesar-2016-VCBM.png",
    thumbnails = "images/Kolesar-2016-VCBM-thumbnail.jpg",
    proceedings = "Proceedings of Eurographics Workshop on Visual Computing in Biology and Medicine",
    keywords = "unfolding, storytelling, game visualization",
    location = "Bergen, Norway",
    project = "physioillustration"
    }

2015

    [DOI] [Bibtex]
    @INPROCEEDINGS {7156384,
    author = "Le Muzic, Mathieu and Waldner, Manuela and Parulek, Julius and Viola, Ivan",
    title = "Illustrative Timelapse: A technique for illustrative visualization of particle-based simulations",
    booktitle = "Visualization Symposium (PacificVis), 2015 IEEE Pacific",
    year = "2015",
    pages = "247-254",
    month = "April",
    abstract = "Animated movies are a popular way to communicate complex phenomena in cell biology to the broadaudience. Animation artists apply sophisticated illustration techniques to communicate a story, while trying to maintain a realistic representation of a complex dynamic environment. Since suchhand-crafted animations are time-consuming and cost-intensive to create, our goal is to formalizeillustration techniques used by artists to facilitate the automatic creation of visualizations generated from mesoscale particle-based molecular simulations. Our technique Illustrative Timelapse supports visual exploration of complex biochemical processes in dynamic environments by(1) seamless temporal zooming to observe phenomena in different temporal resolutions, (2) visualabstraction of molecular trajectories to ensure that observers are able to visually follow themain actors, (3) increased visual focus on events of interest, and (4) lens effects to preserve arealistic representation of the environment in the context. Results from a first user studyindicate that visual abstraction of trajectories improves the ability to follow a story and isalso appreciated by users. Lens effects increased the perceived amount of molecular motion in theenvironment while trading off traceability of individual molecules.",
    images = "images/illustrative_timelapse.png",
    thumbnails = "images/illustrative_timelapse.png",
    proceedings = "Proceedings of IEEE Pacific Visualization",
    keywords = "Biological system modeling;Data models;Data visualization;Lenses;Trajectory;Videos;Visualization;I.3.7[COMPUTER GRAPHICS]: Three-Dimensional Graphics and Realism—Animation;I.6.3 [SIMULATION AND MODELING]: Applications—",
    doi = "10.1109/PACIFICVIS.2015.7156384",
    project = "physioillustration"
    }
    [Bibtex]
    @INPROCEEDINGS {cellVIEW_2015,
    author = "Mathieu Le Muzic and Ludovic Autin and Julius Parulek and Ivan Viola",
    title = "cellVIEW: a Tool for Illustrative and Multi-Scale Rendering of Large Biomolecular Datasets",
    booktitle = "EG Workshop on Visual Computing for Biology and Medicine",
    year = "2015",
    month = "sep",
    abstract = "In this article we introduce cellVIEW, a new system to interactively visualize large biomolecular datasets on the atomic level. Our tool is unique and has been specifically designed to match the ambitions of our domain experts to model and interactively visualize structures comprised of several billions atom. The cellVIEW system integrates acceleration techniques to allow for real-time graphics performance of 60 Hz display rate on datasets representing large viruses and bacterial organisms. Inspired by the work of scientific illustrators, we propose a level-of-detail scheme which purpose is two-fold: accelerating the rendering and reducing visual clutter. The main part of our datasets is made out of macromolecules, but it also comprises nucleic acids strands which are stored as sets of control points. For that specific case, we extend our rendering method to support the dynamic generation of DNA strands directly on the GPU. It is noteworthy that our tool has been directly implemented inside a game engine. We chose to rely on a third party engine to reduce software development work-load and to make bleeding-edge graphics techniques more accessible to the end-users. To our knowledge cellVIEW is the only suitable solution for interactive visualization of large bimolecular landscapes on the atomic level and is freely available to use and extend.",
    images = "images/cellview2015.png",
    thumbnails = "images/cellview2015.png",
    proceedings = "Proceedings of Eurographics Workshop on Visual Computing in Biology and Medicine",
    project = "physioillustration"
    }
    [DOI] [Bibtex]
    @INPROCEEDINGS {eurovisstar20151112,
    author = "Kozlikova, Barbora and Krone, Michael and Lindow, Norbert and Falk, Martin and Baaden, Marc and Baum, Daniel and Viola, Ivan and Parulek, Julius and Hege, Hans-Christian",
    title = "Visualization of Biomolecular Structures: State of the Art",
    booktitle = "Eurographics Conference on Visualization (EuroVis) - STARs",
    year = "2015",
    editor = "R. Borgo and F. Ganovelli and I. Viola",
    volume = "-",
    publisher = "The Eurographics Association",
    abstract = "Structural properties of molecules are of primary concern in many fields. This report provides a comprehensiveoverview on techniques that have been developed in the fields of molecular graphics and visualization with a focuson applications in structural biology. The field heavily relies on computerized geometric and visual representationsof three-dimensional, complex, large, and time-varying molecular structures. The report presents a taxonomy thatdemonstrates which areas of molecular visualization have already been extensively investigated and where the fieldis currently heading. It discusses visualizations for molecular structures, strategies for efficient display regardingimage quality and frame rate, covers different aspects of level of detail, and reviews visualizations illustrating thedynamic aspects of molecular simulation data. The report concludes with an outlook on promising and importantresearch topics to enable further success in advancing the knowledge about interaction of molecular structures.",
    images = "images/molvis_star.png",
    thumbnails = "images/molvis_star.png",
    proceedings = "Eurographics Conference on Visualization (EuroVis) - STARs",
    doi = "10.2312/eurovisstar.20151112",
    journal = "-",
    number = "-",
    keywords = "-",
    project = "physioillustration"
    }

2014

    [Bibtex]
    @MISC {Kingman14PARP1,
    author = "Pina Kingman and Anne-Kristin Stavrum and Ivan Viola and Helwig Hauser",
    title = "PARP-1 Binds Damaged DNA",
    howpublished = "Poster presented at the VizBi conference 2014",
    month = "March",
    year = "2014",
    abstract = "This image is an excerpt from the animation entitled Negative charge and poly(ADP)-ribosylation: a scientific animation. The molecules where uploaded from the Protein Data Bank using the Embedded Python Molecular Viewer plug-in for Autodesk Maya (Johnson et al. 2001; Sanner et al. 1996). The scene was rendered using Maxon Cinema 4D and composited in Adobe Photoshop. Subsurface Scattering was chosen to give the molecules a translucent appearance. Two PARP-1 molecules are shown bound to damaged DNA (Coquelle and Glover 2012). This work has been carried out within the PhysioIllustration project (funded by NFR, project #218023).",
    images = "images/Kingman13PARP1.jpg",
    thumbnails = "images/Kingman13PARP1_thumb.jpg",
    location = "Heidelberg, Germany",
    project = "physioillustration"
    }
    [Bibtex]
    @MISC {Kingman14GenomeMaking,
    author = "Pina Kingman",
    title = "Our Resilient Genome: The Making of a Science Film",
    howpublished = "Presentation in the EG VCBM workshop 2014",
    month = "September",
    year = "2014",
    abstract = "Every single human cell has to fix 10,000 to 20,000 lesions in its DNA every day. Our cells are constantly exposed to many different types of threats that damage our genome. These lesions could cause mutations in our DNA, potentially leading to cancer and other diseases. With such continuous onslaught, how can our cells possibly protect our DNA from damage and mutations? This presentation will showcase the first public screening of a short film about DNA repair, which blends computer graphics and biology to communicate exciting up-and-coming research. This film was developed in conjunction with the Department of Informatics and the Department of Molecular Biology at the University of Bergen, and the Institute of Computer Graphics and Algorithms at the Vienna University of Technology. Along with a discussion on the visualisation process, I will also talk about the intersection between film and science that helps us communicate complex information.",
    images = "images/no_thumb.png",
    thumbnails = "images/no_thumb.png",
    location = "Wien, Austria",
    project = "physioillustration"
    }
    [Bibtex]
    @MISC {Kingman14ResilientGenome,
    author = "Pina Kingman",
    title = "Our Resilient Genome",
    howpublished = "Talk in the Forshkningsdagene UNG 2014",
    month = "September",
    year = "2014",
    abstract = "Motivation: Make science research accessible to the public through film. Inspire and instil an interest in science and molecular biology. Story: The short animated film will describe the molecular pathways involved in single strand break DNA repair. Every single human cell has to repair an estimated 10,000-20,000 DNA lesion every day. DNA is constantly exposed to a variety of genotoxic events, leading to many different types of lesions. If the damage is not repaired, these lesions may lead to mutations that in turn lead to cancer and ageing. Your cells, however, have fine tuned mechanisms that maintain the integrity of our genome. This film describes one of those mechanisms. Length: About 3 minutes. Audience: We are aiming for the type of person who would attend a science film festival. We are thus assuming an interest in biology and medicine, at least a high-school degree (with the high probability of intending to continue to higher education), and a basic understanding of biology. Timeline: The film is currently in production and will be finished mid/late summer.",
    images = "images/no_thumb.png",
    thumbnails = "images/no_thumb.png",
    location = "Bergen, Norway",
    project = "physioillustration"
    }
    [PDF] [Bibtex]
    @MISC {LeMusic14Temporal,
    author = "Mathieu Le Muzic and Julius Parulek and Manuela Waldner and Ivan Viola",
    title = "Illustrative Visualization of Biochemical Processes Featuring Multiple Temporal Scales",
    howpublished = "Poster presented at the EG VCBM workshop 2014",
    month = "September",
    year = "2014",
    pdf = "pdfs/LeMusic14Temporal.pdf",
    images = "images/LeMuzic14Temporal.png",
    thumbnails = "images/LeMuzic14Temporal_thumb.png",
    location = "Wien, Austria",
    project = "physioillustration"
    }
    [Bibtex]
    @MISC {Kingman14Integrating,
    author = "Pina Kingman and Anne-Kristin Stavrum and Ivan Viola and Helwig Hauser",
    title = "Integrating 2D and 3D Animation to Comprehensively Communicate Biology",
    howpublished = "Poster presented at the VizBi conference 2014",
    month = "March",
    year = "2014",
    abstract = "As research in cellular and molecular biology advances, so does the need to educated both the science research community and the general public. The former must be aware of developments in associated fields, the latter must be able to take responsibility for their own well-being. In both cases, we have a willing and capable audience, ready to delve deeper into the biological sciences. To exploit this opportunity, we need to research new and advanced visual language techniques to further improve communication. We are therefore investigating novel visual communication techniques to advance knowledge translation methods, focusing on effectively communicating abstract functional aspects of biological systems. To this end, we are creating several short animations, each one exploring different design solutions. These design solutions incorporate 2D motion graphics, information visualization, 3D animation, and can be applied to any biological story. In addition to our short animations, this research will culminate in a short film describing NAD-dependent DNA Repair, intended for the general public and researchers interested in these molecular systems.",
    images = "images/Kingman13Integrating.png",
    thumbnails = "images/Kingman13Integrating_thumb.jpg",
    location = "Heidelberg, Germany",
    project = "physioillustration"
    }
    [PDF] [DOI] [Bibtex]
    @ARTICLE {Parulek-2014-CLV,
    author = "Julius Parulek and Daniel J{\"o}nsson and Timo Ropinski and Stefan Bruckner and Anders Ynnerman and Ivan Viola",
    title = "Continuous Levels-of-Detail and Visual Abstraction for Seamless Molecular Visualization",
    journal = "Computer Graphics Forum",
    year = "2014",
    volume = "33",
    number = "6",
    pages = "276--287",
    month = "sep",
    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.",
    pdf = "pdfs/Parulek-2014-CLV.pdf",
    images = "images/Parulek-2014-CLV.jpg",
    thumbnails = "images/Parulek-2014-CLV.png",
    issn = "1467-8659",
    doi = "10.1111/cgf.12349",
    keywords = "level of detail algorithms, implicit surfaces, clustering, scientific visualization",
    project = "physioillustration"
    }
    [Bibtex]
    @ARTICLE {lemuzic2014ivm,
    author = "Mathieu Le Muzic and Julius Parulek and Anne-Kristin Stavrum and Ivan Viola",
    title = "Illustrative Visualization of Molecular Reactions using Omniscient Intelligence and Passive Agents ",
    journal = "Computer Graphics Forum",
    year = "2014",
    volume = "33",
    number = "3",
    pages = "141--150",
    month = "jun",
    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.",
    images = "images/Lemuzic14Illustrative.png, images/Lemuzic14Illustrative.png",
    thumbnails = "images/Lemuzic14Illustrative0_thumb.png, images/Lemuzic14Illustrative1_thumb.png",
    event = "EuroVis",
    url = "http://www.cg.tuwien.ac.at/research/publications/2014/lemuzic-2014-ivm/",
    project = "physioillustration"
    }
    [PDF] [DOI] [YT] [Bibtex]
    @ARTICLE {Kolesar-2014-IIP,
    author = "Ivan Kolesar and Julius Parulek and Ivan Viola and Stefan Bruckner and Anne-Kristin Stavrum and Helwig Hauser",
    title = "Interactively Illustrating Polymerization using Three-level Model Fusion",
    journal = "BMC Bioinformatics",
    year = "2014",
    volume = "15",
    pages = "345",
    month = "oct",
    abstract = "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.
    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. 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.",
    pdf = "pdfs/Kolesar-2014-IIP.pdf",
    images = "images/Kolesar-2014-IIP.jpg",
    thumbnails = "images/Kolesar-2014-IIP.png",
    youtube = "https://www.youtube.com/watch?v=iMl5nDicmhg",
    doi = "10.1186/1471-2105-15-345",
    keywords = "biochemical visualization, L-system modeling, multi-agent modeling, visualization of physiology, polymerization",
    owner = "bruckner",
    project = "physioillustration",
    timestamp = "2014.12.29",
    url = "http://www.ii.uib.no/vis/projects/physioillustration/research/interactive-molecular-illustration.html"
    }
    [PDF] [VID] [Bibtex]
    @INPROCEEDINGS {Kolesar-2014-IPT,
    author = "Ivan Kolesar and Julius Parulek and Ivan Viola and Stefan Bruckner and Anne-Kristin Stavrum and Helwig Hauser",
    title = "Illustrating Polymerization using Three-level Model Fusion",
    booktitle = "Proceedings of IEEE BioVis 2014",
    year = "2014",
    month = "aug",
    abstract = "Research in cell biology is steadily contributing new knowledge about
    many different 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 different time scales. We integrate physical and
    empirical modeling, according to which approach suits the different
    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 first evaluation with
    domain experts.",
    pdf = "pdfs/Kolesar-2014-IPT.pdf",
    vid = "vids/Kolesar14Polymers.mp4",
    images = "images/Kolesar-2014-IPT.jpg",
    thumbnails = "images/Kolesar-2014-IPT.png",
    keywords = "biochemical visualization, L-system modeling, multi-agent modeling, visualization of physiology, polymerization",
    owner = "bruckner",
    project = "physioillustration",
    timestamp = "2014.12.29"
    }

2013

    [DOI] [Bibtex]
    @ARTICLE {Parulek13Visual,
    author = "Julius Parulek and Cagatay Turkay and Nathalie Reuter and Ivan Viola",
    title = "Visual cavity analysis in molecular simulations",
    journal = "BMC Bioinformatics",
    year = "2013",
    volume = "14",
    number = "Suppl 19",
    pages = "S4",
    month = "Nov.",
    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.",
    images = "images/Parulek13Visual01.png, images/Parulek13Visual02.png",
    thumbnails = "images/Parulek13Visual01_thumb.png, images/Parulek13Visual02_thumb.png",
    url = "http://www.biomedcentral.com/1471-2105/14/S19/S4",
    doi = "10.1186/1471-2105-14-S19-S4",
    issn = "1471-2105",
    project = "physioillustration"
    }
    [PDF] [Bibtex]
    @MISC {Parulek13Importance,
    author = "Julius Parulek and Timo Ropinski and Ivan Viola",
    title = "Importance Driven Visualization of Molecular Surfaces",
    howpublished = "Poster presented at the BioVis conference 2013",
    month = "October",
    year = "2013",
    pdf = "pdfs/Parulek13Importance.pdf",
    images = "images/Parulek13Importance.png",
    thumbnails = "images/Parulek13Importance.png",
    location = "Atlanta (GA)",
    project = "physioillustration"
    }
    [Bibtex]
    @MISC {Parulek13Analysis,
    author = "Julius Parulek",
    title = "Interactive Visual Exploration and Analysis of High-Dimensional, Temporal, and Heterogeneous Biological Data",
    howpublished = "Presentation in the VisBio 2013",
    month = "September",
    year = "2013",
    abstract = "High-dimensional data (hundreds of dimensions, or more) and temporal data (thousands of time frames) pose substantial challenges for both computational and interactive analysis. To reveal relevant intrinsic relations between items or dimensions, the utilization of only computational methods or standard visualization techniques is not enough. In this talk, we introduce the concept of interactive visual analysis (IVA) that enables us to combine computational methods with the user knowledge through a system of multiple linked views on the data and advanced interaction mechanisms. Our approach allows us to interact with the data on the level of individual items and also on the level of dimensions, exploiting a number of useful statistical methods in addition. To improve the understanding of temporal data, we utilize clustering methods, where the user is provided means to understand the internal cluster structure. Moreover, we also showcase how IVA can be beneficial when analyzing molecular dynamics.",
    images = "images/no_thumb.png",
    thumbnails = "images/no_thumb.png",
    location = "Bergen, Norway",
    project = "physioillustration"
    }
    [PDF] [Bibtex]
    @INPROCEEDINGS {Parulek13Seamless,
    author = "Julius Parulek and Timo Ropinski and Ivan Viola",
    title = "Seamless Abstraction of Molecular Surfaces",
    booktitle = "Proceedings of the 29th Spring Conference on Computer Graphics",
    year = "2013",
    series = "SCCG '13",
    pages = "120--127",
    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. ",
    pdf = "pdfs/Parulek13Seamless.pdf",
    images = "images/Parulek13Seamless01.png, images/Parulek13Seamless02.png",
    thumbnails = "images/Parulek13Seamless01_thumb.png, images/Parulek13Seamless02.png",
    proceedings = "Proceedings of the 29th Spring Conference on Computer Graphics",
    isbn = "978-80-223-3377-1",
    location = "Smolenice, Slovak Republic",
    numpages = "8",
    project = "physioillustration"
    }
    [Bibtex]
    @MISC {Kolesar13HumanPhysiology,
    author = "Ivan Kolesar",
    title = "Approaches for Visualizing Human Physiology",
    howpublished = "Presentation in the VisBio 2013",
    month = "September",
    year = "2013",
    abstract = "Physiology is scientific study of function in living systems. All in all, we presents several visual abstractions used to communicate physiological processes through different functional human systems in different scales from molecules to whole human body. However there are still several challenges for visualizing multi-scale physiological processes.",
    images = "images/no_thumb.png",
    thumbnails = "images/Kolesar13HumanPhysiology.jpg",
    location = "Bergen, Norway",
    project = "physioillustration"
    }
    [PDF] [Bibtex]
    @ARTICLE {Parulek13Fast,
    author = "Julius Parulek and Andrea Brambilla",
    title = "Fast Blending Scheme for Molecular Surface Representation",
    journal = "Visualization and Computer Graphics, IEEE Transactions on",
    year = "2013",
    pages = "2653--2662",
    month = "Dec.",
    abstract = "Representation of molecular surfaces is a well established way to study the interaction of molecules. The state-of-theart molecular representation is the SES model, which provides a detailed surface visualization. Nevertheless, it is computationally expensive, so the less accurate Gaussian model is traditionally preferred. We introduce a novel surface representation that resembles the SES and approaches the rendering performance of the Gaussian model. Our technique is based on the iterative blending of implicit functions and avoids any pre-computation. Additionally, we propose a GPU-based ray-casting algorithm that efficiently visualize our molecular representation. A qualitative and quantitative comparison of our model with respect to the Gaussian and SES models is presented. As showcased in the paper, our technique is a valid and appealing alternative to the Gaussian representation. This is especially relevant in all the applications where the cost of the SES is prohibitive.",
    pdf = "pdfs/Parulek13Fast.pdf",
    images = "images/Parulek13Fast01.png, images/Parulek13Fast02.png",
    thumbnails = "images/Parulek13Fast01_thumb.png, images/Parulek13Fast02_thumb.png",
    event = "Vis2013",
    project = "physioillustration",
    extra = "extra/Parulek13Fast_code.pdf"
    }
    [Bibtex]
    @MISC {Kingman13ScienceFilm,
    author = "Pina Kingman",
    title = "Animating Biology: The making of a science film",
    howpublished = "Presentation in the VisBio 2013",
    month = "September",
    year = "2013",
    abstract = "Biology is complicated. Understanding cellular and molecular biology is particularly difficult. Amongst the many effective communication tools at our disposal, animated film is at the forefront. Animation brings biological stories to life, and thus aids in our understanding of biological structure and function. Whether used to inform patients, to teach undergraduate biology, or to disseminate advances in research, animated film is a tool worth employing. But what goes into an animation? I will explain the step-by-step process of creating animations and show a lot of inspiring examples.",
    images = "images/no_thumb.png",
    thumbnails = "images/no_thumb.png",
    location = "Bergen, Norway",
    project = "physioillustration"
    }

2012

    [PDF] [Bibtex]
    @INPROCEEDINGS {Parulek12Implicit,
    author = "Julius Parulek and Cagatay Turkay and Natalie Reuter and Ivan Viola",
    title = "Implicit Surfaces for Interactive Graph Based Cavity Analysis of Molecular Simulations",
    booktitle = "2nd IEEE Symposium on Biological Data Visualization",
    year = "2012",
    series = "BioVis 2012",
    abstract = "Molecular surfaces provide a suitable way to analyze and to study the evolution and interaction of molecules. The analysis is often concerned with visual identification of binding sites of ligands to a host macromolecule. We present a novel technique that is based on implicit representation, which extracts all potential binding sites and allows an advanced 3D visualization of these sites in the con- text of the molecule. We utilize implicit function sampling strategy to obtain potential cavity samples and graph algorithms to extract arbitrary cavity components defined by simple graphs. Moreover, we propose how to interactively visualize these graphs in the con- text of the molecular surface. We also introduce a system of linked views depicting various graph parameters that are used to perform a more elaborative study on created graphs.",
    pdf = "pdfs/Parulek12Implicit.pdf",
    images = "images/Parulek12Implicit01.png, images/Parulek12Implicit02.png",
    thumbnails = "images/Parulek12Implicit01_thumb.png, images/Parulek12Implicit02_thumb.png",
    location = "Seattle (WA), US",
    project = "physioillustration"
    }
    [Bibtex]
    @MISC {Viola12Physiological,
    author = "Ivan Viola",
    title = "Illustrative Visualization of Physiological Models and Imaging",
    howpublished = "Talk in the MedViz Conference 2012",
    month = "January",
    year = "2012",
    abstract = "Physiological processes are of multi-scale and multi-system nature. In general they are very difficult to comprehend. This talk discusses challenges of an upcoming research project that aims at proposing an entirely novel research agenda within the data visualization research field to enable understanding, communication, and evaluation of physiology through interactive and easy-to-understand visualization. The visualization metaphors investigated are inspired by textbook illustrations and handcrafted animated illustrations. The primary focus is on development of novel graphics data representations, visual representations, occlusion handling, visual guidance and storytelling, zooming, interaction and integration of physiological models and medical imaging. The visualization technology will be developed and evaluated on multiple scale levels, from molecular machines, up to the organ level. The physiological context for the technological development and evaluation will be primarily the muscular system. The outcome of the discussed project is new visualization technology in form of algorithms, concepts, and proof of concept implementations. The utilization of the outcome can lead to advances in the field of physiology by providing intuitive visual representation, which the user can observe and interact with.",
    images = "images/no_thumb.png",
    thumbnails = "images/no_thumb.png",
    location = "Bergen, Norway",
    project = "physioillustration, medviz"
    }
    [PDF] [Bibtex]
    @INPROCEEDINGS {Parulek12ImplicitRepresentation,
    author = "Julius Parulek and Ivan Viola",
    title = "Implicit Representation of Molecular Surfaces",
    booktitle = "Proceedings of the IEEE Pacific Visualization Symposium (PacificVis 2012)",
    year = "2012",
    pages = "217--224",
    month = "March",
    abstract = "Molecular surfaces are an established tool to analyze and to study the evolution and interaction of molecules. One of the most advanced representations of molecular surfaces is called the solvent excluded surface. We present a novel and a simple method for representing the solvent excluded surfaces (SES). Our method requires no precomputation and therefore allows us to vary SES parameters outright. We utilize the theory of implicit surfaces and their CSG operations to compose the implicit function representing the molecular surface locally. This function returns a minimal distance to the SES representation. Additionally, negative values of the implicit function determine that the point lies outside SES whereas positive ones that the point lies inside. We describe how to build this implicit function composed of three types of patches constituting the SES representation. Finally, we propose a method to visualize the iso-surface of the implicit function by means of ray-casting and the set of rendering parameters affecting the overall performance.",
    pdf = "pdfs/Parulek12ImplicitRepresentation.pdf",
    images = "images/Parulek12ImplicitRepresentation.png",
    thumbnails = "images/Parulek12ImplicitRepresentation_thumb.png",
    location = "Songdo, Korea",
    project = "physioillustration"
    }