1 / 12

Internet-Distributed Bioinformatics Applications with Piper: The Collaborative Paradigm

The Piper paradigm offers an innovative approach to distributing bioinformatics applications over the Internet. Nodes are linked to create data paths and procedural steps, fostering collaboration. Join the community of developers advancing open-source bioinformatics technology with Piper.

serge
Télécharger la présentation

Internet-Distributed Bioinformatics Applications with Piper: The Collaborative Paradigm

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related