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Modular Simulations and Timing Issues in Whole-Cell Models


D. Bucher

Master Thesis FS13 (10326)

Many simulation models, especially in biology, could benefit from integrating different smaller modules into a bigger system. This is partly because the complexity of the overall system is immense, so that a single monolithic block would be difficult to describe and reason about, and also because single modules might use different modeling approaches, like ordinary differential equations, boolean networks, flux balance analysis and more. Of special interest are so-called whole cell models, which try to describe and simulate everything that happens withing a biological cell. This thesis presents an analysis of existing whole cell models and a generalized framework to make integration of various modular simulations easy and fast. The work originated from the paper “A Whole- Cell Computational Model Predicts Phenotype from Genotype” by J. Karr et al. The principles of distributing variables and resources among processes are formalized, analyzed and refined. A reference implementation was developed as part of this work.


Type of Publication:

(12)Diploma/Master Thesis

H. Koeppl

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% Autogenerated BibTeX entry
@PhdThesis { Xxx:2013:IFA_4593
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