DNA computing simulator speeds experiment design
The inventor of a program for simulating DNA computing systems hopes the benefits of computer-assisted design (CAD) will have the same impact on this field as it has in others.
Nathanaël Aubert, a computer science PhD student at the University of Tokyo, has created a program he calls DACCAD (DNA Artificial Circuits Computer Assisted Design) to help researchers design biological computing systems from a DNA toolbox – a set of DNA-and-enzyme-based modules that can be combined to carry out computational tasks.
According to Aubert, CAD has helped progress a host of fields from integrated circuits to aeronautics by allowing the automation of error-prone or repetitive tasks and easy simulation and verification of systems. He now hopes to bring these benefits to the field of computational biology.
Aubert’s inspiration came from seeing colleagues carry out real-life in vitro DNA computing experiments and struggle with the time-consuming and trial and-error nature of the work.
“I could see it took them a lot of time to simulate even simple systems because they had to input all the equations by hand,” he said. “The idea is that it’s much faster to do a simulation on a computer than doing the experiment in real life. You can detect design problems much earlier.”
The Java-based program, described in research published in the Journal of the Royal Society Interface, allows researchers to combine modules from a DNA toolbox created by Montagne et al to create chemical reaction networks.
These networks can display a variety of nonlinear behaviours that make them powerful systems for information processing, but it is hard to predict outcomes for anything but the simplest systems.
Hours of work on complex systems can yield completely unexpected results and send researchers back to the drawing board, but Aubert’s program lets them simulate systems on a computer first, using a simple graphical representation, before creating them in vitro.
“You can check if your intuition was right, and if not you can simply modify the design or use the tools provided with the software to optimise the parameters. Once it works the way you expect you can use other existing tools to design the implementation of the system,” he explained.
“Hopefully, with the help of CAD, people will be able to make much more complex and diverse DNA computing systems.”