From 2010.igem.org

Interworking: From computer science to biology and back

Schematical overview of the connection between biology and computer science. Wet laboratory provided mathematical modeling and information processing with experimental data, while mathematical modeling supported the other two with parameter evaluation. Information processing provided wet laboratory with experimental validation of the biological implementation and used the combined mathematical model as test bench.

E. lemming is a special project, because the final product has biological and computer science aspects in equal parts. For this reason, it was decided to connect the wet laboratory and the modeling subteam closely from the very beginning to make the best decisions for the whole project. This process is called interworking: multiple parts interact on each other to create a comprehensive result.

Mathematical modeling of biological pathways should never be a end in itself. Instead, mathematical models should be build to give insights into the pathway of interest which are otherwise hard to obtain, or to speed up experimental work. In the following this section we summarize the insights obtained by our modeling subgroup on the way the synthetic network should be designed (Insights for wet laboratory), which resulted in a priority list on which network alternative was implemented first in the laboratory. Furthermore, by using the model, it was possible to estimate the reaction time of the network on the red and far-red light pulses and the minimum duration of them (Insights for information processing), which are crucial parameters needed for the controller design. Finally, different controller alternatives were constructed and evaluated based on the model, the process of which we summarize in the section on Controller Design.