BOODLE - Tissue Formation

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 retracing certain developmental biology experiments. This serves two goals: (1) We demonstrate the simulative power of the BOODLE framework. (2) We can hone the behavioural and physical parameters of the underlying interaction primitives. To this end, the student first needs to study several existing standard assays in developmental biology (under co-supervision by experts in the field). Next, he has to build the corresponding assays in-silico, run comprehensive experiments to (a) compare the results with those from literature and (b) adjust the model parameters to better fit the empirical data.

Prerequisites

A background in 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