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DISTRIBUTING BIOINFORMATICS APPLICATIONS WITH PIPER

DISTRIBUTING BIOINFORMATICS APPLICATIONS WITH PIPER. J.W. Bizzaro. 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.

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DISTRIBUTING BIOINFORMATICS APPLICATIONS WITH PIPER

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  1. DISTRIBUTING BIOINFORMATICS APPLICATIONS WITH PIPER J.W. Bizzaro

  2. 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.

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

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

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

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

  7. GUI’s can be combined according to the arrangement and hierarchy of nodes in the network, which would be hidden.

  8. 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”.

  9. 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.

  10. Build-Time Subsystem (BTS) • User Interfaces Layer (UIL) • Python • CORBA • CORBA • Definitions Layer (DL) • Python • CORBA • Run-Time Subsystem (RTS) • Multi- • protocol • Brokering Layer (BL) • C++ • Include • Processing Layer (PL) • C++ STRUCTURE OF PIPER

  11. 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)

  12. 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

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