The CCPN Project

In addition to our research, we coordinate the CCPN project, a collaborative computing project for the NMR community, which aims to:

1) Develop a data model for NMR with associated tools, and based on this;

2) Develop a new software suite for NMR that allows data harvesting.

In collaboration with the Research Collaboratory for Structural Biology (RCSB), the BioMagResBank (BMRB), Michael Nilges at the Pasteur Institute, as well as major NMR software developers and instrument manufacturers, we have developed a sophisticated data model for NMR. We have also developed a software framework which, based on the data model, can automatically generate application program interfaces (APIs) in Python, Java and C as well as input/output (I/O) code for XML and SQL databases.

These lay the essential groundwork for the development of new versions of the different software packages commonly used by NMR spectroscopists that read and write data in a CCPN format. The development of such a software pipeline allows the loss-less transfer of all the data in a project from one program to another for eventual deposition.

Using this software generation framework, we have developed a new platform independent processing and analysis package (CcpNMR) that, in conjunction with other programs, will carry out data harvesting – the automated collation and generation of all the data needed for deposition at both the BMRB (NMR data) and wwPDB (structures). This software facilitates the deposition of a much richer set of data, which is particularly required for high-throughput (HTP) structural genomics and validation projects.

For more details see Fogh et al., Nat. Struct. Biol., 2002, 9, 416-18; Fogh et al., Bioinformatics, 2005, 21, 1678-84; Vranken et al., Proteins, 2005, 59, 687-96; www.ccpn.ac.uk

This work is supported by the BBSRC and the EU. We are collaborating with Bruno Guigas at Bruker, Aleks Gutmanas and Gerard Kleywegt at EBI, Michael Nilges at the Pasteur Institute, Geerten Vuister and Gert Vriend at the Radboud University of Nijmegen, John Westbrook and Guy Montelione at the Rutgers State University of New Jersey, Alexandre Bonvin at Utrecht University and Eldon Ulrich at the University of Wisconsin.

Wayne Boucher, Rasmus Fogh, John Ionides and Tim Stevens are working on these projects in the Department of Biochemistry.