Keynote: Application of Software Development Methods for Biological and Scientific Research
Calton Pu, Professor, School of Computer Science and CERCS, Georgia Institute of Technology
Abstract
The application of software development methods for scientific and biological research tools has been considered a desirable approach. Through a number of examples, we illustrate the advantages of applying such methods in terms of software development, maintenance, and addition of new functionality. Specifically, we describe our current experience with Predictive Health Initiative, a collaboration between Emory University and Georgia Tech, to explain the application of modern software development methods for data and system integration. For example, we use domain-specific code generation to integrate data from heterogeneous and evolving data sources. In addition, we apply concepts and techniques from event processing and services computing to implement required functionality that would have been prohibitively expensive without them.
General Scope:
Integration of data sources and tools, and performing computations on them is one of the key areas of experimental biology. However, these resources are highly diverse in nature (representation, data formats, and computer systems) and are distributed across the network. Although this broad spectrum of information is accessible over the Web, each data source comes with its own concepts, semantics, data formats, and access methods. Currently, the burden falls on the scientist to manually (via programs) convert between the data formats, resolve conflicts, integrate data, and interpret results in order to make viable use of this information. Surveys have shown that, due to the burden of manual integration, more often than not scientists use and limit their search for information to a select few data sources (three to five out of a possible 500 or more). Therefore, manual composition and analysis has become impractical. Efficient and robust tools/methodologies are needed to automate the biological data and integration of tools. Such methodologies should address fundamental research issues in areas that range from data/tool representation to automation of workflow configuration and deployment.
This workshop will provide a forum to bring together researches and practitioners working to solve these problems with biological data and tools using service oriented technologies. Submissions are specially invited on the following topics, but the scope is not limited by these. We also encourage the submission of survey and case study papers.