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CCP4 Cloud for structure determination and project management in macromolecular crystallography

CCP4 Cloud for structure determination and project management in macromolecular crystallography
CCP4 Cloud for structure determination and project management in macromolecular crystallography

Nowadays, progress in the determination of three-dimensional macromolecular structures from diffraction images is achieved partly at the cost of increasing data volumes. This is due to the deployment of modern high-speed, high-resolution detectors, the increased complexity and variety of crystallographic software, the use of extensive databases and high-performance computing. This limits what can be accomplished with personal, offline, computing equipment in terms of both productivity and maintainability. There is also an issue of long-term data maintenance and availability of structure-solution projects as the links between experimental observations and the final results deposited in the PDB. In this article, CCP4 Cloud, a new front-end of the CCP4 software suite, is presented which mitigates these effects by providing an online, cloud-based environment for crystallographic computation. CCP4 Cloud was developed for the efficient delivery of computing power, database services and seamless integration with web resources. It provides a rich graphical user interface that allows project sharing and long-term storage for structure-solution projects, and can be linked to data-producing facilities. The system is distributed with the CCP4 software suite version 7.1 and higher, and an online publicly available instance of CCP4 Cloud is provided by CCP4.

CCP4, CCP4 Cloud, data management, distributed computing, macromolecular crystallography, project management
2059-7983
1079-1089
Krissinel, Eugene
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Lebedev, Andrey A
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Uski, Ville
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Ballard, Charles B
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Keegan, Ronan M
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Kovalevskiy, Oleg
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Nicholls, Robert A
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Pannu, Navraj S
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Skubák, Pavol
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Berrisford, John
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Fando, Maria
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Lohkamp, Bernhard
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Wojdyr, Marcin
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Simpkin, Adam J
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Thomas, Jens M H
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Oliver, Christopher
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Vonrhein, Clemens
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Chojnowski, Grzegorz
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Basle, Arnaud
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Purkiss, Andrew
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Isupov, Michail N
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McNicholas, Stuart
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Lowe, Edward
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Triviño, Josep
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Cowtan, Kevin
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Agirre, Jon
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Rigden, Daniel J
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Uson, Isabel
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Lamzin, Victor
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Tews, Ivo
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Bricogne, Gerard
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Leslie, Andrew G W
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Brown, David G
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Krissinel, Eugene
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Lebedev, Andrey A
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Uski, Ville
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Ballard, Charles B
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Keegan, Ronan M
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Kovalevskiy, Oleg
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Nicholls, Robert A
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Pannu, Navraj S
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Skubák, Pavol
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Berrisford, John
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Fando, Maria
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Lohkamp, Bernhard
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Wojdyr, Marcin
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Simpkin, Adam J
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Thomas, Jens M H
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Oliver, Christopher
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Vonrhein, Clemens
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Chojnowski, Grzegorz
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Basle, Arnaud
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Purkiss, Andrew
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Isupov, Michail N
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McNicholas, Stuart
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Lowe, Edward
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Triviño, Josep
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Cowtan, Kevin
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Agirre, Jon
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Rigden, Daniel J
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Uson, Isabel
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Lamzin, Victor
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Tews, Ivo
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Bricogne, Gerard
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Leslie, Andrew G W
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Brown, David G
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Krissinel, Eugene, Lebedev, Andrey A, Uski, Ville, Ballard, Charles B, Keegan, Ronan M, Kovalevskiy, Oleg, Nicholls, Robert A, Pannu, Navraj S, Skubák, Pavol, Berrisford, John, Fando, Maria, Lohkamp, Bernhard, Wojdyr, Marcin, Simpkin, Adam J, Thomas, Jens M H, Oliver, Christopher, Vonrhein, Clemens, Chojnowski, Grzegorz, Basle, Arnaud, Purkiss, Andrew, Isupov, Michail N, McNicholas, Stuart, Lowe, Edward, Triviño, Josep, Cowtan, Kevin, Agirre, Jon, Rigden, Daniel J, Uson, Isabel, Lamzin, Victor, Tews, Ivo, Bricogne, Gerard, Leslie, Andrew G W and Brown, David G (2022) CCP4 Cloud for structure determination and project management in macromolecular crystallography. Acta Crystallographica Section D: Structural Biology, 78 (Pt 9), 1079-1089. (doi:10.1107/S2059798322007987).

Record type: Article

Abstract

Nowadays, progress in the determination of three-dimensional macromolecular structures from diffraction images is achieved partly at the cost of increasing data volumes. This is due to the deployment of modern high-speed, high-resolution detectors, the increased complexity and variety of crystallographic software, the use of extensive databases and high-performance computing. This limits what can be accomplished with personal, offline, computing equipment in terms of both productivity and maintainability. There is also an issue of long-term data maintenance and availability of structure-solution projects as the links between experimental observations and the final results deposited in the PDB. In this article, CCP4 Cloud, a new front-end of the CCP4 software suite, is presented which mitigates these effects by providing an online, cloud-based environment for crystallographic computation. CCP4 Cloud was developed for the efficient delivery of computing power, database services and seamless integration with web resources. It provides a rich graphical user interface that allows project sharing and long-term storage for structure-solution projects, and can be linked to data-producing facilities. The system is distributed with the CCP4 software suite version 7.1 and higher, and an online publicly available instance of CCP4 Cloud is provided by CCP4.

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Accepted/In Press date: 8 August 2022
Published date: 1 September 2022
Additional Information: Publisher Copyright: © 2022 Eugene Krissinel et al.
Keywords: CCP4, CCP4 Cloud, data management, distributed computing, macromolecular crystallography, project management

Identifiers

Local EPrints ID: 471374
URI: http://eprints.soton.ac.uk/id/eprint/471374
ISSN: 2059-7983
PURE UUID: 8108c06e-1cc5-4504-add5-53063b151c16
ORCID for Robert A Nicholls: ORCID iD orcid.org/0000-0002-9715-1109
ORCID for Ivo Tews: ORCID iD orcid.org/0000-0002-4704-1139

Catalogue record

Date deposited: 04 Nov 2022 17:35
Last modified: 17 Mar 2024 03:21

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Contributors

Author: Eugene Krissinel
Author: Andrey A Lebedev
Author: Ville Uski
Author: Charles B Ballard
Author: Ronan M Keegan
Author: Oleg Kovalevskiy
Author: Navraj S Pannu
Author: Pavol Skubák
Author: John Berrisford
Author: Maria Fando
Author: Bernhard Lohkamp
Author: Marcin Wojdyr
Author: Adam J Simpkin
Author: Jens M H Thomas
Author: Christopher Oliver
Author: Clemens Vonrhein
Author: Grzegorz Chojnowski
Author: Arnaud Basle
Author: Andrew Purkiss
Author: Michail N Isupov
Author: Stuart McNicholas
Author: Edward Lowe
Author: Josep Triviño
Author: Kevin Cowtan
Author: Jon Agirre
Author: Daniel J Rigden
Author: Isabel Uson
Author: Victor Lamzin
Author: Ivo Tews ORCID iD
Author: Gerard Bricogne
Author: Andrew G W Leslie
Author: David G Brown

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