Literature DB >> 26066803

CONNJUR Workflow Builder: a software integration environment for spectral reconstruction.

Matthew Fenwick1, Gerard Weatherby, Jay Vyas, Colbert Sesanker, Timothy O Martyn, Heidi J C Ellis, Michael R Gryk.   

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.

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Year:  2015        PMID: 26066803      PMCID: PMC4864993          DOI: 10.1007/s10858-015-9946-3

Source DB:  PubMed          Journal:  J Biomol NMR        ISSN: 0925-2738            Impact factor:   2.835


  18 in total

1.  Modern spectrum analysis in multidimensional NMR spectroscopy: comparison of linear-prediction extrapolation and maximum-entropy reconstruction.

Authors:  Alan S Stern; Kuo-Bin Li; Jeffrey C Hoch
Journal:  J Am Chem Soc       Date:  2002-03-06       Impact factor: 15.419

2.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

Authors:  M Hucka; A Finney; H M Sauro; H Bolouri; J C Doyle; H Kitano; A P Arkin; B J Bornstein; D Bray; A Cornish-Bowden; A A Cuellar; S Dronov; E D Gilles; M Ginkel; V Gor; I I Goryanin; W J Hedley; T C Hodgman; J-H Hofmeyr; P J Hunter; N S Juty; J L Kasberger; A Kremling; U Kummer; N Le Novère; L M Loew; D Lucio; P Mendes; E Minch; E D Mjolsness; Y Nakayama; M R Nelson; P F Nielsen; T Sakurada; J C Schaff; B E Shapiro; T S Shimizu; H D Spence; J Stelling; K Takahashi; M Tomita; J Wagner; J Wang
Journal:  Bioinformatics       Date:  2003-03-01       Impact factor: 6.937

3.  Elimination of 13Calpha splitting in protein NMR spectra by deconvolution with maximum entropy reconstruction.

Authors:  Nobuhisa Shimba; Alan S Stern; Charles S Craik; Jeffrey C Hoch; Volker Dötsch
Journal:  J Am Chem Soc       Date:  2003-03-05       Impact factor: 15.419

4.  Two-dimensional Fourier transform of arbitrarily sampled NMR data sets.

Authors:  Krzysztof Kazimierczuk; Wiktor Koźmiński; Igor Zhukov
Journal:  J Magn Reson       Date:  2006-02-20       Impact factor: 2.229

5.  The Protein Data Bank. A computer-based archival file for macromolecular structures.

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6.  Three-dimensional NMR spectroscopy of a protein in solution.

Authors:  H Oschkinat; C Griesinger; P J Kraulis; O W Sørensen; R R Ernst; A M Gronenborn; G M Clore
Journal:  Nature       Date:  1988-03-24       Impact factor: 49.962

7.  Application of nonlinear sampling schemes to COSY-type spectra.

Authors:  P Schmieder; A S Stern; G Wagner; J C Hoch
Journal:  J Biomol NMR       Date:  1993-09       Impact factor: 2.835

8.  NMRPipe: a multidimensional spectral processing system based on UNIX pipes.

Authors:  F Delaglio; S Grzesiek; G W Vuister; G Zhu; J Pfeifer; A Bax
Journal:  J Biomol NMR       Date:  1995-11       Impact factor: 2.835

Review 9.  Multidimensional heteronuclear nuclear magnetic resonance of proteins.

Authors:  G M Clore; A M Gronenborn
Journal:  Methods Enzymol       Date:  1994       Impact factor: 1.600

10.  The CCPN data model for NMR spectroscopy: development of a software pipeline.

Authors:  Wim F Vranken; Wayne Boucher; Tim J Stevens; Rasmus H Fogh; Anne Pajon; Miguel Llinas; Eldon L Ulrich; John L Markley; John Ionides; Ernest D Laue
Journal:  Proteins       Date:  2005-06-01
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  4 in total

1.  NMRbox: A Resource for Biomolecular NMR Computation.

Authors:  Mark W Maciejewski; Adam D Schuyler; Michael R Gryk; Ion I Moraru; Pedro R Romero; Eldon L Ulrich; Hamid R Eghbalnia; Miron Livny; Frank Delaglio; Jeffrey C Hoch
Journal:  Biophys J       Date:  2017-04-25       Impact factor: 4.033

2.  Semantic Mediation to Improve Reproducibility for Biomolecular NMR Analysis.

Authors:  Michael R Gryk; Bertram Ludäscher
Journal:  Transform Digit Worlds (2018)       Date:  2018-03-15

3.  Workflows and Provenance: Toward Information Science Solutions for the Natural Sciences.

Authors:  Michael R Gryk; Bertram Ludäscher
Journal:  Libr Trends       Date:  2017

4.  Curating Scientific Workflows for Biomolecular Nuclear Magnetic Resonance Spectroscopy.

Authors:  Douglas Heintz; Michael R Gryk
Journal:  Int J Digit Curation       Date:  2019-04-19
  4 in total

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