VisBio 2014 meeting - The Role of Visual Computing in Biology
VisBio 2014 is an expert forum related to the WWTF Vienna Research Groups project “Visual Computing: Illustrative Visualization”, jointly organized with our colleagues from the University of Bergen, Norway, within the research project Physioillustration supported by the Norwegian Research Council. For further questions, please contact Ivan Viola.
The target audience covers, analogously to the spirit of the event, a wide spectrum of disciplines. This includes researchers from visualization, bioinformatics, and biology, as well as illustrators and others interested in automated techniques for meaningful knowledge discovery in and communication of complex biological data and processes.
Time and Location
The meeting will take place on the 3rd of September from 8:45 to 12:40. The meeting's venue, Hörsaal D is located at Altes AKH (short for “Altes Allgemeines Krankenhaus”, the former general hospital of Vienna) within the campus of the University of Vienna.
Opening: 8:45 - 9:00
Session 1: 9:00 - 10:30
Wolfgang Busch, Gregor Mendel Institut, Vienna BioCenter
Systems Genetics of Root Growth
Plants have colonized almost the entire land surface of our planet without significant motility or a nervous system. Key to this success is that plants have evolved genetically encoded programs that allow them to adjust their growth to their environment. This tuning of form and function of plants is ultimately controlled by instructions for cellular programs that are encoded in genes and mainly executed by proteins. These programs include the sensing of environmental information, information processing and the regulation of spatial and temporal patterns of cell divisions and cellular growth. Together, these processes eventually determine form and function of a plant. We try to unravel the molecular mechanisms that are underlying these processes at a systems level. We use the plant root, an organ that is highly responsive to environmental cues, as a model. There we mainly measure the differences in root growth (phenotypes) of genetically distinct plant strains and correlate the variation of root growth between the strains to the genetic variation between the strains using a method called genome wide association (GWA) mapping. Candidates for genes and gene networks underlying this variation are refined using independent information such as gene expression or protein interaction data. Using this approach, we have been able to identify genes and gene networks that determine variation of root growth. Our broad aim is to use such information to determine by which molecular mechanisms root growth phenotypes are quantitatively determined by the genotype (the genetic configuration of an organism) and, using this knowledge in conjunction with independent information such as gene expression or protein interaction data, to develop mathematical models with predictive power that accurately capture how the genotype determines root growth in given environments. To test predictions of hypotheses and mathematical models that that can be derived from our approaches, visualization technology promises to be of great utility. In particular, it might help experimentalists to evaluate complex predictions of dynamic phenotypes such as root growth.
Ivan Kolesar, University of Bergen
Illustrating Polymerization using Three-level Model Fusion
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 ?rst evaluation with domain experts.
Pina Kingman, University of Bergen
Our Resilient Genome: The Making of a Science Film
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.
Coffee Break: 10:30 - 10:50
Session 2: 10:50 - 11:40
Mathieu Le Muzic, Vienna University of Technology
Towards Interactive Storytelling From Computational Biology Data
Scientific illustrators are commonly utilising structural descriptions of molecular compounds when depicting cellular biology. However, computational biology also provides procedural models describing the function of biological processes and which are not currently used in the production pipeline. Instead, animators use scientific knowledge to manually animate molecular structures and mimic their functioning. We are exploring the use of such models in order to accomplish the very same task, but in an automated manner. The output data we obtain via scientific simulations features quantitative information only in the case of kinetic models and also spatial information in the case of particle-base models. In this presentation we explain how we manage to exploit both type of data in order to automatically generate animated visuals that depict the machinery of life.
Manuela Waldner, Vienna University of Technology
Visual Attention Guidance in Molecular Visualizations
Dynamic visualizations of physiological processes can be interactively explored by the user, but at the same time they tell a story. To guide the user through such a narrative visualization, different focus+context techniques have been introduced, giving strong visual prominence to elements of interest while the context is suppressed. However, finding visual features to make focus elements pop out from their context, while leading to minimal visual deformation and subjective disturbance, is challenging. We compared different visual guidance techniques for complex dynamic visualizations on large displays and found that flicker is a strong visual attractor in the entire visual field, without distorting, suppressing, or adding any scene elements. To make flicker acceptable for continuous visual guidance, we developed a new two-stage attention guidance model, consisting of a strong initial attention guidance stimulus and a subsequent minimally disturbing visual support to keep track of focus elements. We showcase the resulting two-stage flicker attractor in a study of molecular interactions, where users could easily follow the narrative of the visualization on a large display, while it was easy to ignore when observing the context.
Panel Discussion: 11:40 - 12:40
The VisBio 2014 panel addresses the visualization of biology in the context of the currently emerging field of data science (compare to the discussion of data-oriented scientific discovery as the fourth paradigm in science, as discussed by Jim Gray and Microsoft Research in 2007 and 2009, respectively). In line with the 2011-prediction of MIT that the convergence of medicine, natural sciences, and technology will constitute the third biomedical revolution (after molecular and cellular biology and genomics), we attempt to discuss the particular challenges which emerge from the meeting of modern biology and visualization technology.