Integrating Biomolecular Analysis and Visual Programming: Flexibility and Interactivity in the Design of Bioinformatics Tools

One of the challenges in bio-computing is to enable the efficient use of a wide variety of rapidly evolving computational methods to simulate, analyze and understand complex interactions of molecular systems. Our laboratory is interested in the development of novel computational technologies and in the application of these technologies to the analysis and understanding of complex biological systems. We have been using the Python programming language as a platform to develop reusable and interoperable components dealing with different aspects of structural bioinformatics. These components are the basic building blocks from which several domain specific applications have been developed. In this paper we describe the integration of two applications developed in our laboratory: PMV and a visual-programming environment. PMV is a general purpose, command-driven molecular visualization and manipulation program built from reusable software components. The visual-programming environment enables a user to build interactively networks describing novel combinations of computational methods. We describe several applications demonstrating the synergy created by combining these two programs.