Anne-Kristin Stavrum

Researcher

Publications

2014

    [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] [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"
}
    [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"
}
    [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"
}