ARS | Publication request: Implementing bioinformatic workflows within the BioExtract Server

Submitted to: International Journal of Computational Biology and Drug Design
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 6, 2008
Publication Date: November 26, 2008
Citation: Lushbough, C.M., Bergman, M.K., Lawrence, C.J., Jennewein, D., Brendel, V. 2008. Implementing bioinformatic workflows within the BioExtract Server. International Journal of Computational Biology and Drug Design. 1(3):302-312.

Interpretive Summary: Researchers often use the same process to analyze many datasets. It is helpful if processes that will be carried out multiple times are automated. The BioExtract Server is a biological sequence analysis tool that enables researchers to create and document data analysis pipelines that can be re-used, enabling researchers to spend less time performing repetitive tasks at a computer and more time formulating and testing the hypotheses that underlie scientific discoveries in the agricultural sciences and beyond.

Technical Abstract: Computational workflows in bioinformatics are becoming increasingly important in the achievement of scientific advances. These workflows typically require the integrated use of multiple, distributed data sources and analytic tools. The BioExtract Server (http://bioextract.org) is a distributed service designed to provide researchers with the web ability to query multiple data sources, save results as searchable data sets, and execute analytic tools. As the researcher works with the system, their tasks are saved in the background. At any time these steps can be saved as a workflow that can then be executed again and/or modified later.