BOODLE - Immersive Assay Design

Closed Human-Computer Interaction Computer Science Games Engineering Bachelor Master Project Thesis Games Research Lab

Background

The BOODLE project (BiOlOgical DeveLopment Environment) aims at in-silico experimentation with developmental biology assays. Existing cell simulations focus on intricate models of cell states and intercellular communication. However, they typically fall short of integrating actual biological data sets and rarely consider complex biophysical dynamics. BOODLE incorporates the essential data and routines that biologists work with on a day-to-day basis and complex, interactive cell simulations. Based on large computer tomographic (CT) data sets, we harness existing structural tissue information to facilitate applying cell models that are developed in small, isolated model spaces to the organismal scale. BOODLE allows one to accessibly model and interactively simulate developmental biology assays at realtime speeds.

Tasks

This BOODLE project focusses on the design and evaluation of the user interface for immersive developmental biological assays. The experimenter needs to be able to (1) compose an assay based on predefined cell types and environmental factors, such as physical constraints (such as Petri dishes) or morphogenetic substances that are introduced into the virtual cell population. (2) He needs to be empowered to run the simulation, investigate the process of development and cellular interaction at different speeds and different perspectives. Screenshots and movies need to be taken, the simulation state needs to be saved at given keyframes. (3) The stored assays need to be loaded again. For this, an adequate visualisation and user interface need to be designed in the immersive environment. Digital “aquariums” might, for instance, provide a clean and lean way to represent individual assays and allow the user to select specific contents without much cognitive effort. (4) The experimenter needs to be supported by a visual chronology that makes the developmental processes of different assays comparable over time. (5) Finally, the generated simulation data needs to be stored in a generic format (e.g. JSON) that can be easily interpreted by generic visualisation toolkits such as R.

Prerequisites

A background in HCI, computer graphics, realtime physics, agent-based modelling and Unreal Engine is a great asset for this work.

References

[1] Jean Disset, Sylvain Cussat-Blanc, and Yves Duthen. Self-organization of Symbiotic Multicellular Structures. In Artificial Life, New York, 30/07/14-02/08/14, page (electronic medium), http://www-mitpress.mit.edu/, juillet 2014. The MIT Press.

[2] Benedikt Hallgrímsson, Julia C. Boughner, Andrei Turinsky, Trish E. Parsons, Cairine Logan, and Christoph W. Sensen. Geometric morphometrics and the study of development. Advanced Imaging in Biology and Medicine, pages 319–336, 2009.

[3] Sebastian von Mammen and Melanie Däschinger. Time series evolution for integrating developmental processes. In Proceedings of European Conference on Artificial Life. MIT press, in press 2015.

[4] Sebastian von Mammen, David Phillips, Timothy Davison, Heather Jamniczky, Benedikt Hallgrímsson, and Christian Jacob. Swarm-based Computational Development, chapter 18, pages 473–499. Understanding Complex Systems. Springer Verlag, November 2012.

Contact Persons at the University Würzburg