SBIR Phase I: Design and Development of a Unified Object Oriented Software Platform for Biomolecular Computations

这个小型企业创新研究（SBIR）第一阶段项目将进行设计和构建Java面向对象的软件开发平台（SDP）所需的研究，用于序列操作，关系数据库存储，分子力学计算，蛋白质和DNA的三维结构可视化。 它将捕获已建立的方法和技术包含在遗留的软件包，如琥珀和洞察II到一个现代的框架对象层次结构，并提供一个应用程序编程接口（API），这是易于使用的计算生物学家推进蛋白质组学和生物信息学的研究和开发。 由于硬件独立性和Web可用性，Java通常用于生物信息学。 它是为快速软件开发而设计的。 虽然它在计算应用程序中的性能很差，但它也提供了一种通过Java本机接口（JNI）纠正这个问题的方法。生物分子操作的计算机密集型部分将被编写为C中的本地Java方法，以恢复传统程序的性能。该项目的商业应用是在生物信息学和计算生物技术领域。 学术研究团体和制药行业的研究人员是可能的客户，他们可以使用所提出的软件开发平台快速原型化新的想法，并探索新的计算算法和方法。

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.