TY - JOUR
AU1 - Shannon, Paul
AU2 - Reiss, David
AU3 - Bonneau, Richard
AU4 - Baliga, Nitin
AB - 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 a user-friendly, easily-extended environment. We demonstrate that four simple data types (names, matrices, networks, and associative arrays) are sufficient to bring together diverse databases and software. We highlight some capabilities of the Gaggle with an exploration of Helicobacter pylori pathogenesis genes, in which we identify 
TI - The Gaggle: An open-source software system for integrating bioinformatics software and data sources
JF - BMC Bioinformatics
DO - 10.1186/1471-2105-7-176
DA - 2006-03-28
UR - https://www.deepdyve.com/lp/springer-journals/the-gaggle-an-open-source-software-system-for-integrating-L0WRPqdzjm
SP - 1
EP - 13
VL - 7
IS - 1
DP - DeepDyve
ER -