The elaboration of the sequences of the human genome and those of many cellular and viral parasites has given us an unprecedented opportunity to address the causes and treatment of every major human disease. It has also resulted in the formation of an entirely new field, bioinformatics, which promises to manage and analyze the vast amount of data being generated. Bioinformatics needs to supply tools for data analysis and tools for experimental design. Most of the scientific and corporate resources being expended in bioinformatics are being spent on data analysis tools. While these are essential, we should not neglect the opportunity to accelerate the progress of actual experimental biology. Essentially every experiment in biology now begins with cloning one or more pieces of DNA. Commercial software that facilitates virtual DNA cloning does exist, but it lacks any automation features and depends on primitive and/or fragmentary gene and vector databases. It is inadequate in planning the hundreds or thousands of clones necessary to address questions posed by the proteomics initiatives, because the lack of knowledge integration. In Phase I of this SBIR grant, we have built and tested a virtual cloning expert system, along with a very useful gene database and a uniquely annotated vector database that serve as a knowledge base for automated DNA manipulations. A collection of automated cloning modules and databases is now functional. In Phase II we will complete the virtual cloning expert system and develop a flexible platform for automated experimental design, data management and analysis. We will also construct a user database, improve the user interface and establish security protocols. The results will be a complete program suite as a stable and marketable product.
