Extend-NMR: Extending NMR for Functional and Structural Genomics
Partner 1:University of Cambridge, UK
Partner 2:European Bioinformatics Institute, Hinxton, UK
People involved:Ernest Laue, Wayne Boucher, Rasmus Fogh, John Ionides, Chris Penkett, Tim Stevens, Wim Vranken

CCPN: The Collaborative Computing Project for NMR

CCPN was started by the UK BBSRC in 1999 to promote the integration, sharing, and collaborative development of NMR software. At the time NMR software was mostly stand-alone programs with limited facilities for data flow between them, and gathering project data for final deposition was a demanding task.

The CCP data model specifies how different programs can store all their data in a common repository, from sample preparation through NMR analysis to structure determination and validation. The data model is supported by subroutine libraries in Python, Java, and C with storage in XML files or databases. All code is generated from the data model, using CCPNs automatic code generation software.

Data exchange is further supported by the CcpNmr FormatConverter that lets you import and export data from more than thirty pre-existing data formats for NMR and structural biology. The CcpNmr ECI Deposition tool allows easy deposition of final data to the BioMagResBank and PDB.

CcpNmr Analysis is an interactive graphics program for NMR visualization and analysis, built on top of the CCP data model. It has a highly developed user interface with extensive support for assignment and data extraction. The user interface components originally developed for Analysis have been used to integrate a number of third-party programs, notably to produce the graphical user interface that is used for the Extend-NMR pipeline.

The flow of information from the CCPN data model via automatic code generation to the strorage system, programming libraries, applications and documentation.
Protein backbone resonance assignment in CcpNmr Analysis

CCPN Features

  • The CCP Data Model for macromolecular NMR and related areas
  • A means to integrate existing NMR software within a unified syste
  • CcpNmr Analysis: Spectrum visualiation & data analysis
  • CcpNmr FormatConverter: Convert between 30+ NMR formats
  • CcpNmr ECI: Deposition interface to Biological Magnetic Resonance Bank
  • Meetings to determine and spread best practice in NMR

How the CcpNmr Format Converter exchanges data between NMR formats using the CCPN data model as a hub.
Selecting NMR data for database deposition using CcpNmr ECI