Logic gene network design: A CAD tool based on modularity and standardization

Logic gene network design: A CAD tool based on modularity and standardization

Van den Berg, B.A.

Bellomo, D. (mentor)
Reinders, M.J.T. (mentor)

Electrical Engineering, Mathematics and Computer Science

Mediamatics

2009-10-07

Motivation: Synthetic biology aims at building biological systems for useful purposes. Relatively simple gene networks have been engineered, but the design process is limited. Many papers advocate the use of engineering concepts like standardization and modular design to simplify the design process and enable the design of more complex systems. Currently, there are no tools available that implement both concepts in a practical way. Results: We have developed a software tool to show how standardization and modular design can be used for the design of logic gene networks. We introduce gene network templates to be able to use modular design in a practical way and use a standard model to simplify the design process and enable reuse of parameters. We have designed three logic gate templates and used them to build two logic gene networks: a demultiplexer and a D-latch. Our software tool was used to turn the templates into devices and to evaluate the performance of the devices. The results show that the devices are evaluated correctly. Furthermore, the results show that for the design of a gene network our method can be used to indicate which biological parts are preferred at what location in the network.

synthetic biology
gene network design
gene network
logic gene network
CAD tool
modularity
standardization
bioinformatics
biological systems
design process
modular design

http://resolver.tudelft.nl/uuid:fff3c287-ff65-454a-8ec1-42425d94280c

Student theses

master thesis

(c) 2009 van den Berg, B.A.