Software to Facilitate DNA Cloning

DESCRIPTION (provided by applicant): DNA cloning, also known as gene splicing or recombinant DNA technology, underlies all of modern biomedical and biotechnology research. Yet DNA cloning frequently goes awry because this process involves a large number of variables, has many subtleties, and is hard to document with existing tools. DNA cloning is linked to a variety of other procedures, and researchers struggle to manage and integrate the resulting information. This situation impedes progress and forces scientists to divert attention from more creative activities. Well crafted software can solve these problems, but the currently available programs are ineffective at helping users to meet their goals. GSL Biotech is developing advanced software, provisionally named Kamino , that streamlines the design, execution, and documentation of molecular biology projects. During Phase I, we created a working alpha prototype of Kamino. During Phase II, we will develop a finished software product. Aim #1 is to refine Kamino so that it provides comprehensive functionality while retaining an intuitive user interface. The alpha version of Kamino offers a responsive interface for visualizing and annotating DNA sequences, and for simulating common DNA manipulations. The software is designed so that users can achieve their goals quickly and without distraction. Future work will optimize existing functions for speed and flexibility, and will supply important additional functions. Aim #2 is to extend Kamino with additional modules, thereby creating an integrated multi- functional software suite. Kamino currently manages double-stranded DNA sequences. In addition to this DNA module, we will introduce an Oligos module for managing single-stranded oligonucleotides, a Proteins module for managing polypeptide sequences, an Alignment module for aligning DNA or protein sequences, a Sequencing module for assembling DNA contigs, and an RNA module for managing single- and double-stranded RNA molecules. Information transfer between the modules will be uniquely easy and transparent. The resulting integrated software suite will provide efficient data management for molecular biology projects. We anticipate that Kamino will substantially accelerate research and development, thereby boosting productivity. This innovation will make biomedical research more cost-effective. Our product will revolutionize DNA cloning by making the experts more efficient, and by enabling the novices to clone like today's experts. From an educational perspective, the intuitive and visually rich Kamino interface will be ideally suited to undergraduate-level instruction in molecular biology. PUBLIC HEALTH RELEVANCE: Kamino will substantially accelerate research and development, thereby boosting productivity. This innovation will make biomedical research more cost-effective and more efficient at generating improvements in health care.