Journal of Biomolecular NMR

, Volume 6, Issue 3, pp 277–293

NMRPipe: A multidimensional spectral processing system based on UNIX pipes

  • Frank Delaglio
  • Stephan Grzesiek
  • Geerten W. Vuister
  • Guang Zhu
  • John Pfeifer
  • Ad Bax
Research Paper

Summary

The NMRPipe system is a UNIX software environment of processing, graphics, and analysis tools designed to meet current routine and research-oriented multidimensional processing requirements, and to anticipate and accommodate future demands and developments. The system is based on UNIX pipes, which allow programs running simultaneously to exchange streams of data under user control. In an NMRPipe processing scheme, a stream of spectral data flows through a pipeline of processing programs, each of which performs one component of the overall scheme, such as Fourier transformation or linear prediction. Complete multidimensional processing schemes are constructed as simple UNIX shell scripts. The processing modules themselves maintain and exploit accurate records of data sizes, detection modes, and calibration information in all dimensions, so that schemes can be constructed without the need to explicitly define or anticipate data sizes or storage details of real and imaginary channels during processing. The asynchronous pipeline scheme provides other substantial advantages, including high flexibility, favorable processing speeds, choice of both all-in-memory and disk-bound processing, easy adaptation to different data formats, simpler software development and maintenance, and the ability to distribute processing tasks on multi-CPU computers and computer networks.

Key words

Multidimensional NMR Data processing Fourier transformation Linear prediction Maximum entropy UNIX 

Abbreviations

1D, 2D, 3D

one-, two-, three-dimensional

nD

multidimensional

CPU

central processing unit

FID

free induction decay

I/O

input/output

LP

linear prediction

MEM

maximum entropy method

Mb

megabyte

NOE

nuclear Overhauser effect

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Copyright information

© ESCOM Science Publishers B.V. 1995

Authors and Affiliations

  • Frank Delaglio
    • 1
  • Stephan Grzesiek
    • 1
  • Geerten W. Vuister
    • 2
  • Guang Zhu
    • 3
  • John Pfeifer
    • 4
  • Ad Bax
    • 1
  1. 1.Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney DiseasesNational Institutes of HealthBethesdaUSA
  2. 2.Bijvoet Center for Biomolecular ResearchUtrecht UniversityUtrechtThe Netherlands
  3. 3.Department of BiochemistryThe Hong Kong University of Science and TechnologyKowloonHong Kong
  4. 4.Division of Computer Research and TechnologyNational Institutes of HealthBethesdaUSA
  5. 5.National Institutes of Health, Laboratory of Chemical PhysicsNIDDKBethesdaUSA

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