Welcome to Reciprocal Net!

Reciprocal Net  a distributed crystallography network for researchers, students and the general public

Reciprocal Net is funded by the U.S. National Science Foundation as part of the National Science Digital Library project.  NSDL Logo
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Site Network

Imaginary picture of the Reciprocal Net Site Network

The Reciprocal Net Site Network is an online community that maintains a distributed database of crystallographic information. Its membership includes crystallographic service facilities (that analyze crystals submitted by research chemists) located at major universities. These labs analyze anywhere from a few dozen to several hundred molecular structures each year and post the data online for the public to access. A distributed database engine takes care of shuttling this data across the Internet so that every structure can be located by the search engine at Reciprocalnet.org.  Frequently there may be a delay of a year or more between the time a structure is first analyzed and the time it finally becomes available for the public to see. This is due to intellectual property issues - the intervening time allows the chemists who first discovered the structure to publish it in a trade journal.

The Reciprocal Net Site Network is the source of Reciprocal Net's molecular structure data. An active volunteer base ensures the viability of Reciprocal Net as an educational resource with outstanding value. This server at Reciprocalnet.org is the master server in the Site Network. Currently it's hosted by Indiana University's Molecular Structure Center because it is they who were awarded the NSF grant that jumpstarted Reciprocal Net. Efforts are underway to transition to a self-supporting, community-managed model.

Technical information

The Reciprocal Net project, so far as the National Science Digital Library (NSDL) is concerned, comprises three collections:

  • A collection of molecular structures, solved and ready to be visualized. Submissions into this collection originate from respected service crystallography facilities, generally affiliated with major universities.
  • A collection of educational modules – sequences of web pages – that instruct students on specific aspects of chemistry. Submissions into this collection originate from professional educators in primary schools, secondary schools, and universities.
  • A collection of visualization programs for rendering molecular structures. Submissions into this collection generally originate from computer programmers associated with the field of chemistry in some way.

The latter two collections are managed entirely by Reciprocalnet.org, this site; it is the first collection (of molecular structures) that draws upon the resources of the Reciprocal Net Site Network.

It will be useful to become familiar with some basic terminology.

  • A sample is the basic data entity in this collection; this is what the Reciprocal Net Site Network tracks. Crystal samples usually are grown by one particular sample provider (the lab of a research chemist) and subsequently submitted to one particular service crystallography lab for processing.
  • Structures may be contrasted with samples in that while one sample always illustrates one molecular structure, it is conceivable that two samples in Reciprocal Net would have the same underlying molecular structure. Generally, a duplicate flag is added to both samples when such a condition is discovered.
  • A lab is a participating crystallography laboratory that uses the Reciprocal Net site software for its daily operations. Most management features of the Reciprocal Net Site Network take place at the lab level. For this reason, each sample has a data field where the originating lab is recorded at the time of sample creation.
  • A site is a server (or cluster of servers) in the Reciprocal Net Site Network. More specifically, a site is a web server that runs the Reciprocal Net site software and is connected to the Internet. It is possible for a single site to host multiple labs (perhaps in an outsourced Application Service Provider model). All sites in the network communicate with one another over the Internet to keep the distributed database of publicly visible samples in a consistent and accessible state. Sites may also maintain their own collection of private samples that are not shared with other sites.
  • The site database contains metadata about samples in Reciprocal Net and is stored in a Relational Database Management System (RDBMS) like MySQL.
  • The site repository contains actual data files for samples in Reciprocal Net and is stored on the server's file system directly. These data files might include .CIF files, .SDT files, .ORT files, .CRT files, .PDB files, and so forth. The site database contains metadata, the site repository contains data.

When the recipnet package is installed on a server, the server becomes a site in the Reciprocal Net Site Network and may begin contributing to the Reciprocal Net molecular structure collection. Documentation elsewhere on this site can assist new users in getting their site up and running. In the Reciprocal Net site network there are two distinguished (i.e. unusual) sites.

  • The first is Reciprocalnet.org, the "portal". This is just another site so far as the recipnet software package is concerned, but this server runs additional software that provides a network-wide search engine for samples that have been made public. This means that the search engine on Reciprocalnet.org may link visitors to your site if their search finds a matching, publicly-visible structure on it.
  • The second is the Reciprocal Net Coordinator. This is a deliberately ephemeral and portable entity that helps all the other sites in the Reciprocal Net Site Network communicate with one another and maintain a consistent distributed database. The Reciprocal Net Coordinator is the only site that does not operate a web server. Most of the work of the Reciprocal Net Coordinator takes place behind-the-scenes; about the only interaction you'll ever have with this entity is when you first bring your site online. Currently the Coordinator function is being served by the people at the Molecular Structure Center at Indiana University, but this may change in the future.
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