DISTRIBUTING BIOINFORMATICS APPLICATIONS WITH PIPER

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DISTRIBUTING BIOINFORMATICS APPLICATIONS WITH
PIPER

• J.W. Bizzaro

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THE PIPER PARADIGM

• Everything is a self-contained object or node.
• Certain nodes input and/or output data flow.
• Nodes can be linked to define paths of data flow,
  procedural steps, and relationships.
• Every node has an Internet location.
• Nodes are only represented locally, if possible.

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• A database is represented as a node in the
  Pied/Piper GUI. It has an Internet location
  (Maryland) and an output.

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• A program is added. It too has a location
  (Japan), and its input is linked to the output of
  the first node.

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• Each node has a GUI defined via XML. Only the
  XML description and rudimentary widgets are local.

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• More nodes are added and linked, forming a
  network of Internet-distributed nodes.

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• GUIs can be combined according to the
  arrangement and hierarchy of nodes in the
  network, which would be hidden.

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ADDITIONAL FEATURES

• Networks can be packaged and exchanged, providing
  the appearance of a single application, but the
  components are Internet-distributed.
• Piper is general-purpose in its design, making it
  more flexible in its use as a bioinformatics
  application, plus more widely used and
  contributed to.
• The Internet-distribution of nodes allows Piper
  to be used as a bioinformatics collaboratory.

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ADDITIONAL FEATURES

• Linking of command-line programs makes Pied/Piper
  an Internet-distributed, graphical scripting
  language. Thousands of nodes are already
  available!
• Command-line options are also nodes, making the
  programs easy to port and the options easy to
  change.
• Linking of low-level objects makes Pied/Piper an
  Internet-distributed, graphical programming
  language.

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STRUCTURE OF PIPER
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PIPER DEVELOPERS

• J.W. Bizzaro (Massachusetts)
• Brad Chapman (Georgia)
• Nile Geisinger and dLoo (California)
• Dominic Letourneau (Quebec)
• Deanne Taylor (Michigan)
• Jean-Marc Valin (Quebec)
• Gary Van Domselaar (Alberta)
• Jarl Van Katwijk (Netherlands)

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BIOINFORMATICS.ORGTHE OPEN LAB

• RESEARCH Open access to bioinformatics research
• The Loci Project, a model collaboratory based
  on the Piper system
• DEVELOPMENT Open Source bioinformatics software
  development
• SourceForge project management system
• Hosted Web sites, PHP and CGI
• Shell, CVS, FTP, e-mail, MySQL, etc.
• INFORMATION Freedom of information
• Tutorials, news, featured authors, glossary, etc.
• Campaign against the proprietarization of
  biological information