Bio-STEER

Bio-STEER is an application of Task Computing Technology in a bioinformatics domain, leveraging several bioinformatics web services, grid services, and web-based applications. The same concept however can be applied to various other domains.

As life science research becomes evermore computationally intensive, Grid computing has been explored as means for providing needed computational resources. There are however several barriers that prevent the widespread use of Grid computing in life sciences. Life science research often involves connecting multiple bioinformatics applications together to form a workflow. This process of constructing a workflow is quite complex. When combined with the difficulty of using Grid services, composing meaningful workflows from bioinformatics tools available on the Grid can present daunting challenges to life scientists.  Bio-STEER attempts to reduce the difficulty of using grid services by life scientists.

Bio-STEER maps bioinformatics Grid services to Semantic Web services. These services are described in OWL-S and further related by OWL ontologies that describe bioinformatics application concepts, terms and variables. Our graphical user interface helps users to construct a scientific workflow by showing a list of services that are semantically relevant; that is, the output of one service is semantically compatible with the input of the connected service.

The benefits of Bio-STEER include:

• A user-friendly computing environment, in which various levels of users of varying expertise can easily achieve their end goals
• Suggestions about semantic-based service compositions help to easily create complex, yet sound scientific workflows

• Transparent integration of heterogeneous, distributed computing resources as composed semantic services

The prototype system is built in collaboration with Professor Cummings of University of Maryland, Institute for Advanced Computer Studies. The Lattice Project is developing a community-based Grid system that integrates Grid middleware technologies and widely used life science applications. In addition to Grid services available through the Lattice Project, our prototype system also uses web-based bioinformatics tools available from National Center for Biotechnology Information. Web Services technology enables us to transparently integrate various, dispersed sources of bioinformatics applications. We are also working with domain experts to enhance the features and ease of use of our Bio-STEER tool.

Bio-STEER and related articles:

• Bio-STEER video: This short video features our latest implementation of the prototype system. It first shows a workflow construction process. After a user selects an initial application from the list of available services, Bio-STEER assists him/her by suggesting semantically compatible services to be connected to construct a desired workflow. The execution can be completely automated, or user can insert a break point to inspect and/or modify the intermediate results. The execution progress can be easily tracked on our graphical user interface. Bio-STEER provides an option to save a workflow as a task. Such a task can be later executed or further modified as needed. In some cases, sharing of such workflows would be beneficial in collaborating with other scientists. When saved with complete descriptions of services, the saved workflow can be easily shared with collaborators from different organizations.




• Sung Lee, Taowei David Wang, Nada Hashmi, and Michael Cummings, "Bio-STEER: A Semantic Web Workflow Tool for Grid Computing in the Life Sciences," submitted to Future Generation Computing Systems, December 2005.

• Sung Lee, Nada Hashmi, Jim Hendler, and Bijan Parsia, "Bio-STEER: an Application of Task Computing - the Semantic Web meets Grid Computing," Technical Memorandum FLA-PCR-TM-3, Fujitsu Laboratories of America, Inc, College Park, MD, March 2004.

• Nada Hashmi, Sung Lee, and Michael Cummings, "Abstracting Workflows: Unifying Bioinformatics Task Conceptualization and Specification Through Semantic Web Services," W3C Workshop on Semantic Web for Life Sciences, October 2004, Cambrid ge, MA.

• Michal Galdzicki and Sung Lee, "Bio-Central - Semantic Knowledgebase of Biomolecular Interaction Data," W3C Workshop on Semantic Web for Life Sciences, October 2004, Cambrid ge, MA.

• Sung Lee, Michal Galdzicki, Ryusuke Masuoka, Yannis Labrou, and Jon Agre, "MED-STEER: Enabling Composition and Execution of Semantically Described Medical Informatics Services for Mobile Caregivers," BECON/BISTIC 2004 Symposium , June 2004, Bethesda, MD.