WeNMR: Structural Biology on the Grid

  • Authors:

  • Tsjerk A. Wassenaar;Marc Dijk;Nuno Loureiro-Ferreira;Gijs Schot;Sjoerd J. Vries;Christophe Schmitz;Johan Zwan;Rolf Boelens;Andrea Giachetti;Lucio Ferella;Antonio Rosato;Ivano Bertini;Torsten Herrmann;Hendrik R. Jonker;Anurag Bagaria;Victor Jaravine;Peter Güntert;Harald Schwalbe;Wim F. Vranken;Jurgen F. Doreleijers;Gert Vriend;Geerten W. Vuister;Daniel Franke;Alexey Kikhney;Dmitri I. Svergun;Rasmus H. Fogh;John Ionides;Ernest D. Laue;Chris Spronk;Simonas Jurkša;Marco Verlato;Simone Badoer;Stefano Dal Pra;Mirco Mazzucato;Eric Frizziero;Alexandre M. Bonvin

  • Affiliations:

  • Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, The Netherlands 3584 CH and Biocomputing Group, Department of Biological Sciences, University of Calgary, ...;Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, The Netherlands 3584 CH;Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, The Netherlands 3584 CH and European Grid Infrastructure (EGI), Amsterdam, The Netherlands 1098 XG;Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, The Netherlands 3584 CH;Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, The Netherlands 3584 CH;Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, The Netherlands 3584 CH;Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, The Netherlands 3584 CH;Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, The Netherlands 3584 CH;Magnetic Resonance Center, University of Florence, Sesto Fiorentino, Italy 50019;Magnetic Resonance Center, University of Florence, Sesto Fiorentino, Italy 50019;Magnetic Resonance Center, University of Florence, Sesto Fiorentino, Italy 50019;Magnetic Resonance Center, University of Florence, Sesto Fiorentino, Italy 50019;Centre de RMN à très Hauts Champs, Institut des Sciences Analytiques, Université de Lyon, Villeurbanne, France 69100;Institute of Organic Chemistry and Chemical Biology and Biomolecular Magnetic Resonance Center, Goethe University Frankfurt, Frankfurt am Main, Germany 60438;Institute of Biophysical Chemistry and Biomolecular Magnetic Resonance Center, Goethe University Frankfurt, Frankfurt am Main, Germany 60438;Institute of Biophysical Chemistry and Biomolecular Magnetic Resonance Center, Goethe University Frankfurt, Frankfurt am Main, Germany 60438;Institute of Biophysical Chemistry and Biomolecular Magnetic Resonance Center, Goethe University Frankfurt, Frankfurt am Main, Germany 60438;Institute of Organic Chemistry and Chemical Biology and Biomolecular Magnetic Resonance Center, Goethe University Frankfurt, Frankfurt am Main, Germany 60438;European Bioinformatics Institute, Cambridge, UK CB10 1SD and Department of Structural Biology, VIB, and Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium 1050;Protein Biophysics/IMM, Radboud University Nijmegen, Nijmegen, The Netherlands;CMBI, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands;Department of Biochemistry, School of Biological Sciences, Henry Wellcome Building, University of Leicester, Leicester, UK LE1 9HN;European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany D22603;European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany D22603;European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany D22603;Department of Biochemistry, University of Cambridge, Cambridge, UK CB2 1GA;Department of Biochemistry, University of Cambridge, Cambridge, UK CB2 1GA;Department of Biochemistry, University of Cambridge, Cambridge, UK CB2 1GA;UAB "Spronk NMR Consultancy", Vilnius, Lithuania 01402;UAB "Spronk NMR Consultancy", Vilnius, Lithuania 01402;Istituto Nazionale di Fisica Nucleare, Padova, Italy 35131;Istituto Nazionale di Fisica Nucleare, Padova, Italy 35131;Istituto Nazionale di Fisica Nucleare, Padova, Italy 35131 and Istituto Nazionale di Fisica Nucleare, CNAF, Bologna, Italy 40127;Istituto Nazionale di Fisica Nucleare, Padova, Italy 35131;Istituto Nazionale di Fisica Nucleare, Padova, Italy 35131;Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, The Netherlands 3584 CH

  • Venue:
  • Journal of Grid Computing
  • Year:
  • 2012

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Abstract

The WeNMR ( http://www.wenmr.eu ) project is a European Union funded international effort to streamline and automate analysis of Nuclear Magnetic Resonance (NMR) and Small Angle X-Ray scattering (SAXS) imaging data for atomic and near-atomic resolution molecular structures. Conventional calculation of structure requires the use of various software packages, considerable user expertise and ample computational resources. To facilitate the use of NMR spectroscopy and SAXS in life sciences the WeNMR consortium has established standard computational workflows and services through easy-to-use web interfaces, while still retaining sufficient flexibility to handle more specific requests. Thus far, a number of programs often used in structural biology have been made available through application portals. The implementation of these services, in particular the distribution of calculations to a Grid computing infrastructure, involves a novel mechanism for submission and handling of jobs that is independent of the type of job being run. With over 450 registered users (September 2012), WeNMR is currently the largest Virtual Organization (VO) in life sciences. With its large and worldwide user community, WeNMR has become the first Virtual Research Community officially recognized by the European Grid Infrastructure (EGI).