The advent of computer-aided design in biology holds the promise of greatly increasing the efficiency of biological manipulation and experimentation while easing the process of design and optimization. The hope is that CAD will allow the design and analysis of plasmids, vectors, protocols, and synthetic pathways with a minimal need for laboratory experiments.

Classically, tools used in genetic engineering perform singular specific tasks such as codon optimization, primer design, and ribosome binding site (RBS) design to optimize DNA constructs. A more inclusive set of computational tools combines multiple DNA components’ design and optimization operations via a single toolset. One example of such a tool is ApE (http://biologylabs. utah. edu/jorgensen/wayned/ ape/). ApE is a plasmid editor that, among many things, clearly highlights the different relevant features of a plasmid (restriction sites, ORF, Dam/Dcm methyl — ation sites, etc.), shows the protein translation, creates plasmid graphics and maps, performs a virtual restriction digest, selects sites matching a given criteria, and performs primer design based on an inputted criteria. Other inclusive tools include Gene Designer 2.0 (https://www. dna20.com/resources/genedesigner), which per­forms gene, operon, vector, and primer design along with codon optimization. It also performs protein translation and restriction site modification using a graphical — based interface. A similar toolkit to Gene Designer 2.0 is Gene Design. Gene Design is, however, available via a Web interface (http://54.235.254.95/gd/). Finally, Gene Composer is yet another interesting tool worth mentioning (http:// www. genecomposer. net). Gene Composer is a CAD-based software that allows alignment generation and constructs design, gene optimization, and assembly (Medema et al. 2012; Zabawinski et al. 2001).

As for molecular and synthetic biology centric computational tools, there are already a few software suits and CAD packages that include tools to aid in biological design. One such tool is Genome Compiler (http://www. genomecompiler. com), an advanced genomic design software package. Besides facilitating, viewing, and editing DNA as constructs, protein translation, and circular views, Genome Compiler allows viewing and editing a DNA construct on a functional basis. Additionally, searching and importing DNA constructs via the NCBI database is supported.

A similar CAD toolkit to Gene Compiler is GenoCAD (http://www. genocad. org). GenoCAD, however, has the added benefit of DNA construct simulation. This allows for quick performance testing of designed constructs. Other CAD tools that are focused on DNA constructs and biological parts design include TeselaGen (https:// www. teselagen. com), Clotho (http://www. clothocad. org), and SynBioSS (http:// synbioss. sourceforge. net). Both TeselaGen and Clotho offer genetic function centric DNA editing and construction tools. They also aid in the creation of DNA constructs and parts’ databases and the utilization of existing databases. Likewise, SynBioSS allows for the design and simulation of DNA constructs and biological parts, but does that through reconstructing reaction networks from a series of genetic parts that are user defined and strung together. Another CAD toolkit that allows for DNA construct simulation, in addition to DNA design and editing, is TinkerCell (http://www. tinkercell. com). TinkerCell is built with the ambition of having optimized CAD-based biological designs feed into laboratory automation tools, and thus easing the design, experimentation, and synthesis aspects of molecular and synthetic biol­ogy. Currently, TinkerCell’s analysis capability includes a plethora of deterministic and stochastic simulation and analysis options (Medema et al. 2012).

The CAD tools discussed thus far offer powerful design capabilities, but the designer must keep in mind the limitations inherent with each tool. Biological interactions are not yet fully understood, and the models and simulations of such interactions, as provided by the CAD tools, are limited by the assumptions rooted in those tools.

9.4 Conclusion

Genetic molecular techniques have allowed for tremendous progress in the fields of biology and bioengineering. The ability to manipulate, replicate, and modify DNA, RNA, proteins, and organisms via transformation techniques, cloning, and gene­editing tools has allowed for powerful biological insights and applications devel­opment. As is already apparent, the future of molecular techniques lies in devel­oping more robust editing tools, simplifying high-throughput techniques and adopting more automatable techniques. Also, the development of multiplexing techniques, techniques that are able to perform multiple manipulations at once, will allow for great progress in discovery.

Acknowledgments Major support for this work was provided by New York University Abu Dhabi Institute grant G1205, NYU Abu Dhabi Faculty Research Funds AD060, and NYU Abu Dhabi Research Enhancement Fund AD060; K. J. was supported through NYU Abu Dhabi Global Academic Fellows program. The authors thank Khalid Sam for his help in creating the figures used in this chapter.