A modelling framework for Synthetic Biology

Jakob Jakobsen Boysen, Sune Mølgaard Laursen

AbstractSynthetic biology is the field of engineering new biological functions through composition and regulation of genes. The current trend of an exponential decrease in the cost of the enabling technologies indicates that sophisticated CAD tools will soon be of significant importance which will require the involvement of computer scientists and software engineers.
The overall goal of this thesis is to establish a foundation for the construction of these kinds of CAD tools in order to enable computer scientists and software engineers to more easily get engaged in the field of synthetic biology.
This thesis examines and explains how to model and simulate these gene compositions and how parallels to electronic design automation can be drawn by treating the simulated behaviour as logical lows and highs. By doing that new compositions of genes fulfilling some behavioural specifications can be proposed automatically.
The modelling framework DTU-SB employs many of the classical approaches to simulation as well as modelling and contributes with a novel way of performing genetic technology mapping oriented towards the practical issues that may arise in large gene compositions.
TypeMaster's thesis [Academic thesis]
Year2014
PublisherTechnical University of Denmark, Department of Applied Mathematics and Computer Science
AddressRichard Petersens Plads, Building 324, DK-2800 Kgs. Lyngby, Denmark, compute@compute.dtu.dk
SeriesDTU Compute M.Sc.-2014
NoteDTU supervisor: Jan Madsen, jama@dtu.dk, DTU Compute
Electronic version(s)[pdf]
Publication linkhttp://www.compute.dtu.dk/English.aspx
BibTeX data [bibtex]
IMM Group(s)Computer Science & Engineering


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