The Gaggle: An open-source software system for integrating bioinformatics software and data sources

Background: Systems biologists work with many kinds of data, from many different sources, using a variety of software tools. Each of these tools typically excels at one type of analysis, such as of microarrays, of metabolic networks and of predicted protein structure. A crucial challenge is to combine the capabilities of these (and other forthcoming) data resources and tools to create a data exploration and analysis environment that does justice to the variety and complexity of systems biology data sets. A solution to this problem should recognize that data types, formats and software in this high throughput age of biology are constantly changing. Results: In this paper we describe the Gaggle -a simple, open-source Java software environment that helps to solve the problem of software and database integration. Guided by the classic software engineering strategy of separation of concerns and a policy of semantic flexibility, it integrates existing popular programs and web resources into...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Paul T. Shannon, David J. Reiss, Richard Bonneau, Nitin S. Baliga
• Keywords: BMCBI 2006, Data Exploration, Data Types, Software