JavaScript and function call makes it more difficult
to find the email address. Since the key to encrypt
and decrypt the email address is randomly generated
each time the page is loaded, spam harvesters find
email addresses.
4.6 Future Work
Enhancements could be made to SWA that would
provide more context-sensitive help and examples.
As more data is gathered from actual users we may
need to enhance the user interface and job history to
allow users to run previous jobs again or we may
need to modify default values used by ScalaBLAST.
When more features are added to SWA which
complicated the design, we may revisit using a more
extensive development framework like Drupal. In
addition, we are expanding this approach to other
high-performance applications in bioinformatics and
computational biology, such as a high-performance
peptide identification tool called Polygraph (Cannon
et al. 2005) that will run from the same web portal
on the same cluster. Because of the extensibility of
this framework this addition will be accomplished in
a fraction of the time.
5 CONCLUSIONS
The SWA system provides secure yet public web-
based access to a high-performance sequence
alignment tool, ScalaBLAST. It was written to be
extensible and flexible while staying consistent with
BLAST applications currently in use. This project
used innovative design to integrate many pieces of
existing technology such as PHP, MySQL,
JavaScript, job launching, job monitoring, user-
notification, file management, et al. This system is
fully operational and can be found at
http://www.biopilot.org.
ACKNOWLEDGEMENTS
The research described in this paper was supported
in part by the US Department of Energy, Office of
Advanced Scientific Computing Research through
the “Data Intensive Computing for Complex
Biological Systems” project at the Pacific Northwest
National Laboratory, a multiprogram national
laboratory operated by Battelle for the US
Department of Energy under Contract DE-AC06-
76RL01830. The authors would like to thank Leigh
Williams for helping design the web page template
and working with scientists to generate most of the
public content on the web site.
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