CADMAD aims at a foundational breakthrough in the way computers and computer-aided design and manufacturing is employed in DNA-based research and development, introducing a radically new use of information technologies in biology and biotechnology. Biology and biotechnology research and development involves “DNA programming”, which is akin to computer programming. Researchers modify and combine DNA of interest in a programmatic way to uncover its function, improve its function, or to create new functions. Whereas the composition and editing of computer programs is as easy as using a word processor, the design, construction and editing of DNA in a programmatic fashion is still a slow, expensive, labor-intensive wet-lab process.
CADMAD will replace the labor-intensive DNA processing carried out today by tens of thousands of skilled wet-lab workers around the world by high-throughput computer-aided DNA design and manufacturing, which would be fundamentally more efficient than plain de novo DNA synthesis by effectively reusing existing DNA.
Computed-aided design and manufacturing of semiconductor chips has enabled the computer revolution, the Internet revolution, and the mobile phone revolution. Computer-aided design and manufacturing of DNA may similarly enable a revolution in biology and biotechnology, in which high-throughput computer-aided and robotically executed experiments replace manual wet-lab work, resulting in accelerated progress in key areas of research and development.
We believe that bringing the intellectual and technological power of computer science concepts, tools and methods to biology can greatly advance biological and biomedical research and development. A DNA molecule can be justifiably viewed as a biological program, analogous to a computer program. In the same vein, we use “DNA processing” analogously to word processing, referring to the act of willfully modifying the text of one or more DNA molecules, and “DNA programming” as the overall process of modifying DNA in a programmatic way to understand, change, or improve its function, analogously to computer programming. Thinking and operating in these terms will enable us to usher a biotechnology revolution comparable in magnitude to the computer and software engineering revolution of the past three decades.
The computer-aided DNA processing technology and platform of CADMAD will serve as a key supportive tool for addressing the broad DNA programming needs of systems biology and synthetic biology in understanding and building complex biological systems, while boosting current and future emerging DNA-based applications as illustrated below. The key requirement for effective programming is short program development cycle. CADMAD will support rapid DNA programming by providing an efficient DNA processing platform that can take existing (natural or synthetic) DNA as input and produce the desired variations, combinations and extensions of this DNA as output quickly and efficiently. One cannot imagine computer programming without the use of a word processor to modify programs as needed. Similarly, in the future one would not be able to imagine DNA programming without the support of a CADMAD-like computer-aided system for efficient DNA processing.
Figure 1: The DNA program development cycle is analogous to the computer program development cycle. Both go through an iterative process of changing the (computer or DNA) program, testing it, and analyzing the results, until the desired program behavior is achieved. Changing computer programs is trivial while changing DNA programs is hard and expensive. CADMAD aims to eliminate this key hurdle to rapid DNA programming.