SBIR-STTR Award

DMA cloning, also known as gene splicing or recombinant DMA technology, is crucial for all aspects of biomedical and biotechnology research. For example, DMA cloning has been of central importance for sequencing the human genome, generating safer vaccines, identifying genes involved in cancer and many other diseases, and producing therapeutic drugs such as insulin, growth hormones, blood clotting factors, and novel antibiotics. Tens of thousands of laboratories regularly perform DMA cloning. Yet the design and execution of DMA cloning projects is often remarkably inefficient. This situation impedes progress and forces scientists to divert attention from more creative activities. Well crafted software could solve these problems, but available programs do a poor job of facilitating DMA cloning. We plan to overcome this limitation by developing commercial software that will streamline the design and documentation of DMA cloning projects. This proposal has three Specific Aims. Aim #1: To develop software so versatile and easy to use that every step of DMA cloning will be simplified. An intuitive visual interface will simulate an entire cloning project. The software will enable users to achieve their goals quickly and without distraction. Aim #2: To provide complete, accessible documentation of the history of a DNA construct. The software will automatically record the procedure that was used to generate a DNA construct, together with the multi- generation histories of the precursor constructs. Aim #3: To prevent common errors in DNA cloning while educating users about efficient cloning methods. The software will be uniquely designed to prevent cloning errors. An uncluttered but information- rich interface will help users to visualize the steps of their cloning projects, while text messages and optional explanatory notes will teach beginners how to clone effectively. RELEVANCE By making the everyday procedure of DNA cloning faster and more reliable, this software will enhance many aspects of biomedical research and development, thereby improving public health

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.

Public Health Relevance Statement:
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.

Project Terms:
Amino Acid Sequence; Amino Acid Sequence Analysis; Attention; Biomedical Research; Biotechnology; Biotechnology, Genetic Engineering; Care, Health; Cloning; Computer Programs; Computer software; DNA; DNA Molecular Biology; DNA Recombination; DNA Sequence; DNA recombination (naturally occurring); Data; Deoxyribonucleic Acid; Development and Research; Distraction; Documentation; Double-Stranded DNA; Double-Stranded RNA; Environment; Finding of distraction; Flexibility; Future; Gel; Gene Products, RNA; Gene Splicing; Genetic Engineering; Genetic Recombination; Genetics-Mutagenesis; Goals; Health Care Research; Health Services Evaluation; Health Services Research; Healthcare; Healthcare Research; Industry; Instruction; Investigators; Jobs; Libraries; Link; Marketing; Medical; Medical Care Research; Molecular Biology; Molecular Biology, Genetic Engineering; Molecular Biology, Mutagenesis; Molecular Biology, Protein Sequencing; Mutagenesis; Names; Occupations; Oligo; Oligonucleotides; Peptide Sequence Analysis; Peptide Sequence Determination; Phase; Pliability; Problem Solving; Procedures; Process; Productivity; Professional Postions; Programs (PT); Programs [Publication Type]; Protein Sequence Analysis; Protein Sequencing; Protein Structure, Primary; Proteins; Psyche structure; R & D; R&D; RNA; RNA, Double-Stranded; RNA, Non-Polyadenylated; Recombinant DNA Technology; Recombination; Recombination, Genetic; Research; Research Personnel; Researchers; Ribonucleic Acid; Scientist; Sequence Alignment; Sequence Analyses, Amino Acid; Sequence Analyses, Peptide; Sequence Analyses, Protein; Sequence Analysis, Protein; Sequence Determinations, Amino Acid; Sequence Determinations, Protein; Simulate; Software; Speed; Speed (motion); Spliced Genes; Testing; Work; Writing; base; computer program/software; cost; data management; design; designing; distraction; ds-DNA; dsRNA; experience; gene product; improved; innovate; innovation; innovative; meetings; mental; polypeptide; prevent; preventing; programs; protein sequence; prototype; public health relevance; research and development; services research; tool; virtual