Abstract
CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy reconstruction, facilitating the processing of non-uniformly sampled time domain data. As will be shown in the paper, the unique features of WB provide it with novel abilities to enhance the quality, accuracy, and fidelity of the spectral reconstruction process. WB also provides features which promote collaboration, education, parameterization, and non-uniform data sets along with processing integrated with the Rowland NMR Toolkit (RNMRTK) and NMRPipe software packages. WB is available free of charge in perpetuity, dual-licensed under the MIT and GPL open source licenses.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
ACD/NMR Processor Academic Edition Web. http://www.acdlabs.com/resources/freeware/nmr_proc/ 17 Sept 2014
Altintas I, Berkley C, Jaeger E, Jones M, Ludascher B, Mock S (2004) Kepler: an extensible system for design and execution of scientific workflows. In: 16th International Conference on Scientific and Statistical Database Management, 2004 IEEE pp 423–424
Azara home page Web. http://www2.ccpn.ac.uk/azara/ 17 Sept 2014
Bernstein FC, Koetzle TF, Williams GJ, Meyer EF, Brice MD, Rodgers JR, Tasumi M (1977) The protein data bank. Eur J Biochem 80(2):319–324
Bowers S, Ludäscher B (2005) Actor-oriented design of scientific workflows. In: Delcambre LML, Kop C, Mayr HC, Mylopoulos J, Pastor O (eds) Conceptual modeling–ER 2005. LNCS, vol. 3716. Springer, Heidelberg, pp 369–384
Clore GM, Gronenborn AM (1994) Multidimensional heteronuclear nuclear magnetic resonance of proteins. Methods Enzymol 239:349–363
Cormen TH, Leiserson CE, Rivest RL Stein C (2001) Introduction to algorithms, Vol 2. MIT press, Cambridge, pp 531–549
Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6:277–293
Delta NMR Data Processing Software Web. http://www.jeolusa.com/tabid/380/Default.aspx 17 Sept 2014
Ernst RR, Anderson WA (1966) Application of Fourier transform spectroscopy to magnetic resonance. Rev Sci Instrum 37(1):93–102
Ernst RR, Bodenhausen G, Wokaun A (1991) Principles of nuclear magnetic resonance in one and two dimensions (No. LRMB-BOOK-1991–001)
Gryk MR, Vyas J, Maciejewski MW (2010) Biomolecular NMR data analysis. Prog Nucl Magn Reson Spectrosc 56(4):329
Güntert P, Dötsch V, Wider G, Wüthrich K (1992) Processing of multi-dimensional NMR data with the new software PROSA. J Biomol NMR 2:619–629
Hoch JC, Stern A (1985) The Rowland NMR toolkit. Rowland Institute for Science Technical Memorandum, 18t
Hoch JC, Stern AS (1996) NMR data processing. Wiley, New York
Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Wang J (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19(4):524–531
iNMR Web. http://www.inmr.net/ 17 Sept 2014
Jeener J (1971) Oral presentation in Ampere International Summer School II, Basko Polje, Yugoslavia (1971). (b) Aue WP, Bartholdi E, Ernst J Chem Phys 64:2229
Kazimierczuk K, Kozminski W, Zhukov I (2006a) Two-dimensional Fourier transform of arbitrarily sampled NMR data sets. J Magn Reson 179:323–328
Kazimierczuk K, Misiak M, Stanek J, Zawadzka-Kazimierczuk A, Kozminski W (2012) Generalized Fourier transform for non-uniform sampled data. Top Curr Chem 316:79–124
Kazimierczuk K, Zawadzka A, Kozminski W, Zhukov I (2006b) Random sampling of evolution time space and Fourier transform processing. J Biomol NMR 36:157–168
Maciejewski MW, Qui HZ, Rujan I, Mobli M, Hoch JC (2009) Nonuniform sampling and spectral aliasing. J Magn Reson 199:88–93
Mobli M, Maciejewski MW, Gryk MR, Hoch JC (2007a) An automated tool for maximum entropy reconstruction of biomolecular NMR spectra. Nat Methods 4:3–4
Mobli M, Maciejewski MW, Gryk MR, Hoch JC (2007b) Automatic maximum entropy spectral reconstruction in NMR. J Biomol NMR 39:133–139
Mnova NMR Lite Web. http://mestrelab.com/software/mnova/nmr-lite/ 17 Sept 2014
Nowling RJ, Vyas J, Weatherby G, Fenwick MW, Ellis HJ, Gryk MR (2011) CONNJUR spectrum translator: an open source application for reformatting NMR spectral data. J Biomol NMR 50(1):83–89
Nyquist H (1928) Certain topics in telegraph transmission theory. Am Inst Electr Eng Trans 47(2):617–644
Oschkinat H, Griesinger C, Kraulis PJ, Sørensen OW, Ernst RR, Gronenborn AM, Clore GM (1988) Three-dimensional NMR spectroscopy of a protein in solution. Nature 332(6162):374–376
PERCH Solutions Web. http://new.perchsolutions.com/index.php?id=36 17 Sept 2014
Schmieder P, Stern AS, Wagner G, Hoch JC (1993) Application of nonlinear sampling schemes to COSY-type spectra. J Biomol NMR 3:569–576
Shimba N, Stern AS, Craik CS, Hoch JC, Dötsch V (2003) Elimination of 13Cα splitting in protein NMR spectra by deconvolution with maximum entropy reconstruction. J Am Chem Soc 125:2382–2383
SpinWorks Web. http://www.columbia.edu/cu/chemistry/groups/nmr/SpinWorks.html 17 Sept 2014
Stern AS, Li K-, Hoch JC (2002) Modern spectrum analysis in multidimensional NMR spectroscopy: comparison of linear-prediction extrapolation and maximum-entropy reconstruction. J Am Chem Soc 124:1982–1993
Stoven V, Annereau JP, Delsuc MA, Lallemand JY (1997) A new N-channel maximum entropy method in NMR for automatic reconstruction of decoupled spectra and J-coupling determination. J Chem Inf Comput Sci 37:265–272
SwaN-MR Web. http://www.inmr.net/swan/ 17 Sept 2014
TopSpin Web. http://www.bruker.com/products/mr/nmr/nmr-software/software/topspin/overview.html 17 Sept 2014
Verdi KK, Ellis HJ, Gryk MR (2007) Conceptual-level workflow modeling of scientific experiments using NMR as a case study. BMC Bioinformatics 8:31
VnmrJ Web. http://www.chem.agilent.com/en-US/products-services/Software-Informatics/VnmrJ/Pages/default.aspx 17 Sept 2014
Vranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinas M, Laue ED (2005) The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins: Struct Funct Bioinform 59(4):687–696
Acknowledgments
This research was funded by United States National Institutes of Health grant GM-083072. The authors wish to thank Drs. Frank Delaglio, Jeffrey Hoch, Mark W. Maciejewski and Alan Stern for useful conversations and assistance with the operation of NMRPipe and the Rowland NMR Toolkit. The authors would also like to thank Dr. Eldon Ulrich for assistance with the NMR-STAR format and data dictionary.
Conflict of interest
The authors declare that they have no conflict of interest.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Fenwick, M., Weatherby, G., Vyas, J. et al. CONNJUR Workflow Builder: a software integration environment for spectral reconstruction. J Biomol NMR 62, 313–326 (2015). https://doi.org/10.1007/s10858-015-9946-3
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10858-015-9946-3