Toward the commoditization of translational genomic research: Design and implementation features of the Galaxy genomic workbench

Summit Transl Bioinform. 2008 Mar 1;2008:56-60.


Although there is now plenty of genomic data and no shortage of analysis methods for translational genomic research, many biologists do not have efficient and transparent access to the computational resources they need. No single data resource or analysis application is ever likely to efficiently address all aspects of any individual researcher's needs, so most researchers are forced to manually integrate data and outputs from multiple resources. The inevitable heterogeneity of data formats and of command syntax between data resources and software applications presents a major obstacle, particularly to those biologists lacking practical informatics skills. We describe some design and implementation features of an open-source application that supports the integration of the best available third-party genomics software applications, data and annotation resources into a coherent framework, substantially overcoming many practical challenges associated with actually doing translational genomic research.