Integrative simulation framework for modeling dynamic cellular phenomena in 3D over time

This work discusses the definition and implementation of a hybrid four-dimensional (4D) Cell Simulator - 4DiCeS. Despite the great variety of software packages available for modeling, simulation, and analysis of data, there is no application that features a complete and variable integration of different simulation methods in a 3D environment. The key improvement, which 4DiCeS has over other existing systems, is the ability not to be fixed on either deterministic or stochastic modeling and simulation approaches. A system of specialized interfaces therefore was designed to allow the bonding of interchangeable algorithmic modules of various types. The internal representation of the model is designed for the easy exchangeability of data. Furthermore, the integration of cell model file format standards is permitted by exchangeable plug-ins. The implemented system includes an Application Programming Interface (API) for writing individual plug-ins to utilize different simulation algorithms. This facilitates the implementation of tailored programs and specific algorithms that can be developed for data mining as well as visualization. The resulting 4DiCeS framework presented in this work describes a concept for the integration of heterogenous data into an easy-to-use software. Applications for such a modeling and simulation tool that allows for both 3D visualization and concurrent algorithms are imperative. The applications lie in the areas of electrical excitable cells, circadian rhythm, cell cycle, cellular motility, membrane transporters, metabolic pathways, and signal transduction networks. In comparison to 2D methods, the use of a 3D geometry provides considerably more significant data. The possibility of simulating different compartments of a cell with diverse algorithms can reduce computational effort dramatically. Consequently, this allows for both improved modeling and more information output on the spatio-temporal behavior of a system. Thus it is a scientific challenge to integrate concurrently running algorithms in combination with 3D visualization.

Level thesis:degree_level

thesis.doctoral

Grantor dc:publisher

Universität Bielefeld

Year

2008

Author dc:creator

• Oleson, Björn Edwin

Repository record source_url

https://pub.uni-bielefeld.de/record/2305352

OAI identifier oai:identifier

oai:pub.uni-bielefeld.de:2305352