BioExtract

The BioExtract Server is a web-based system for querying biomolecular sequence data, executing analytic tools on the resulting extracts, and constructing workflows composed of such queries and tools.[1]

It offers a central distribution point for uniformly formatted data from a variety of resources including EMBL, SwissProt, and PlantGDB.

It also gives researchers access to a variety of analytic tools, including BLAST, Clustal, and T-Coffee, and the BioMOBY and EBI Soaplab Web services.

Researchers create workflows implicitly by working with the system. Tasks such as saving a data extract, executing an analytic tool, and querying a data source are automatically saved each time they are performed during a session. At any time, a workflow can be created by saving these recorded tasks, and once saved, the workflow can be edited.[2][3][4]

The BioExtract Server was created in The Brendel Group[5] at Iowa State University in collaboration with Visual Metrics Corporation funded by NSF grant 0090732.[6] Continuing development by the Lushbough Bioinformatics Group at The University of South Dakota is supported by NSF grant 0321600.[7]

External links

References

  1. ↑ Lushbough, C., Lawrence, C.J., Bergman, M., Jennewein, D., and Brendel, V., (2008) BioExtract Server – An Integrated System to Access and Analyze Heterogeneous, Distributed Biomolecular Data, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 11 Sept 2008. IEEE Computer Society Digital Library. IEEE Computer Society, 8 January 2009.
  2. ↑ Lushbough, C., Lawrence, C.J., Bergman, M., Jennewein, D., and Brendel, V., (2008) Implementing Bioinformatic Workflows within the BioExtract Server, International Journal of Computational Biology and Drug Design 2008 - Vol. 1, No.3 pp. 302 – 312.
  3. ↑ Lushbough, C., Lawrence, C.J., Bergman, M., Jennewein, D., and Brendel, V., (2008) An Overview of the BioExtract Server – a Distributed, Web Based Application for Bioinformatics Analysis, Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology, WorldComp’08, Las Vegas, Nevada, USA July 14–17, 2008.
  4. ↑ Lushbough, C., Lawrence, C.J., Bergman, M., Jennewein, D., and Brendel, V., (2007) Creating Bioinformatic Workflows with the BioExtract Server, Proceedings of the 2007 International Conference on Bioinformatics and Computational Biology, WorldComp’07, Las Vegas, Nevada, USA June 25–28, 2007.
  5. ↑ http://brendelgroup.org
  6. ↑ Award Abstract #0090732 Efficient Web-based Serving of Consolidated Multi-Source Biological Sequence Data Extracts
  7. ↑ Award Abstract #0321600 PlantGDB - Plant Genome Database and Analysis Tools
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