This Small Business Innovation Research (SBIR) Phase I project will perform the research needed to design and construct an object-oriented software development platform (SDP) in Java for sequence manipulations, storage in relational databases, molecular mechanics computations, three dimensional structure visualizations of proteins and DNAs. It will capture established methodologies and techniques contained in legacy packages such as AMBER and Insight II into a modern framework of object hierarchy and provide an Application Programming Interface (API) that is easy to use by computational biologists for advancing proteomics and bioinformatics research and development. Java is commonly used in bioinformatics due to hardware independence and web availability. It is designed for rapid software development. Although it suffers from poor performance for computational applications, it also provides a means of rectifying this problem through Java Native Interface (JNI). The computer-intensive portions of biomolecular manipulations will be written as native Java methods in C to regain the performance of legacy programs.
The commercial application of this project is in the area of bioinformatics and computational biotechnology. Academic research groups and researchers in pharmaceutical industry are the likely customers, who could use the proposed software development platform to prototype new ideas rapidly and to explore new computational algorithms and methodologies.
