BOODLE - INTO3D

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 real-time speeds.

Tasks

This BOODLE project focusses on designing the virtual assays considering the processes of interactions of the individual cells, the substances they express, the reactions they have based on their environment etc. The biologist who wants to use BOODLE for in-silico experimentation needs to be empowered to adjust the cells’ behaviours. In order to foster the link between cells and their behaviour, this thesis work resumes preceding work on an immersive programming approach called INTO3D (interaction-oriented 3D modelling and simulation). By means of INTO3D, code can be visually programmed in 3D by arranging and nesting spherical operators and connecting their inputs and outputs. The execution of these operators implements behaviour trees that are often used when defining complex behaviours of virtual agents or non-player characters in games. By projecting programmatic operators into space, INTO3D empowers the user to dive into the different components of his model and to define and to re-wire their functionality. Based on this projection of programming code into the virtual experimentation environment, the algorithmic and biological processes will be transparently traceable by the experimenter. In this thesis, the student needs to augment an existing VR BOODLE simulation by means of INTO3D visual programming.

Prerequisites

A background in user interfaces, computer graphics, agent-based modelling and Game Engines 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