GeneJax: A Prototype CAD tool in support of Genome Refactoring

Abstract

Refactoring is a technique used by computer scientists for improving program design. The Endy Laboratory has adapted this process to make the genomes of biological organisms more amenable to human understanding and design goals. To assist in this endeavor, we implemented GeneJax, a prototype JavaScript web application for the dissection and visualization stages of the genome refactoring process. This paper reviews key genome refactoring concepts and then discusses the features, development history, user-interface, and underlying implementation issues faced during the making of GeneJax. In addition, we provide recommendations for future GeneJax development. This paper may be of interest to engineers of CAD tools for synthetic biology.