1 / 26

The Reciprocal Net- a Distributed Molecular Database

The Reciprocal Net- a Distributed Molecular Database. John C. Huffman Director, Molecular Structure Center Director, Informatics Research Institute. Outline…. Background History Research Goals Laboratory Information Management System Collaboration Tool Distributed Research Database

dwight
Download Presentation

The Reciprocal Net- a Distributed Molecular Database

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. The Reciprocal Net-a Distributed Molecular Database John C. Huffman Director, Molecular Structure Center Director, Informatics Research Institute

  2. Outline…. • Background • History • Research Goals • Laboratory Information Management System • Collaboration Tool • Distributed Research Database • Education Goals • Digital Library Goals

  3. Background • X-ray Crystallography • Expensive • Very dependent on many aspects of IT • Results of study are “compact” • Well established standards

  4. N S Undulator Mirrors CCD Detector Double Crystal Monochromator Crystal Collection of Data

  5. Collection of Data • Typical data set 3,600 frames * 2 MBytes/frame = 7.2 GBytes data

  6. Results Typically a table of “atomic coordinates” with identifying labels.

  7. Results

  8. Results • Amazing data compression! 7,200,000,000 / 6,400 = 106:1

  9. History • Evolved from a need to distribute information and data to colleagues • Paper reports • Microfiche • Dial-in BBS systems • ftp servers

  10. History • 1995 “Proficient use of the World-Wide- Web” • 1995 New Computing Initiatives Program • 2001 Funded by NSF DUE as part of NSDL

  11. Research Goals • Laboratory Information Management System (LIMS) • Allows samples to be tracked from submission to publication • Provides for billing and other local lab information • Provides convenient tools for finding information on samples

  12. Research Goals • Collaboration technologies • Allow simple web browsers for users to locate and examine structural data • Provide all necessary tabular data needed for reports, publications, etc. • Provide a simple interface to utility programs that allow collaborators to visualize and understand data. • Provide mechanism for publication quality graphics

  13. Research Goals LIMS interface-Data input

  14. Research Goals LIMS interface-Structure lookup

  15. Research Goals Collaboration toolsUser interface:

  16. Research Goals Visualization of the data is an important criteria of the interface.

  17. Participating sites On-line • Indiana University • Main Portal (Common Molecules) • Princeton University • University of Minnesota • University of Cincinnati • Youngstown State University • Northwestern University • Purdue • University of Calf-San Diego • University of Iowa • University of Kansas In Preparation • Los Alamos National Laboratory • Great Britain National Crystallographic Facility • Argonne National Laboratory • University of Sydney (Australia) • University of Pennsylvania • University of Wisconsin • Ohio State University • Harvard

  18. Architecture All software is “public domain” so that there are no continuing expenses at the individual sites.

  19. Architecture • Data access is rigidly controlled by the local administrator at each site. • Local administrator can provide levels of access to research groups, individuals, etc. • All data, files, and other activities are permanently stored and never removed. Complete history is available for each entry. • All sites are notified whenever an entry is released to the public.

  20. Education goals • Specific modules being designed that use the item-level content. • “Common Molecules” collection provides 500+ entries specifically provided for educational use. • Specialized interface for common molecules section.

  21. Education

  22. Education

  23. Education

  24. Digital Library Integration The Reciprocal Net site software supports integration with the NSDL by providing a repository interface compliant with version 2.0 of the Open Archives Initiative Protocol for Metadata Harvesting (OAI-PMH). The site software provides metadata in Dublin Core format, as well as in a richer XML format developed for the project. The project-specific metadata format expresses all item-level metadata, including many for which there is no sensible mapping onto Dublin Core; representatives of the NSDL Core Integration team have assured us that they are interested in harvesting such metadata. Although every site in the site network can service OAIPMH requests, the site software instance operated by the Reciprocal Net portal site serves as a single designated repository from which the NSDL metadata harvester can harvest all available Reciprocal Net metadata.

  25. Credits • Senior Personnel • Dr. John C. Bollinger • Dr. Gary Wiggins • Prof. William Harwood • Prof. Randall Bramley • Mr. Jon Dunn • Dr. Maren Pink • Mr. Eric Koperda • Mr. Michael Durbin • a special thanks to Gerry Bernbom

  26. Further Information http://www.reciprocalnet.org http://www.iumsc.indiana.edu

More Related