
 
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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