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Afgan E, Nekrutenko A, Grüning BA, Blankenberg D, Goecks J, Schatz MC, Ostrovsky AE, Mahmoud A, Lonie AJ, Syme A, Fouilloux A, Bretaudeau A, Nekrutenko A, Kumar A, Eschenlauer AC, DeSanto AD, Guerler A, Serrano-Solano B, Batut B, Grüning BA, Langhorst BW, Carr B, Raubenolt BA, Hyde CJ, Bromhead CJ, Barnett CB, Royaux C, Gallardo C, Blankenberg D, Fornika DJ, Baker D, Bouvier D, Clements D, de Lima Morais DA, Tabernero DL, Lariviere D, Nasr E, Afgan E, Zambelli F, Heyl F, Psomopoulos F, Coppens F, Price GR, Cuccuru G, Corguillé GL, Von Kuster G, Akbulut GG, Rasche H, Hotz HR, Eguinoa I, Makunin I, Ranawaka IJ, Taylor JP, Joshi J, Hillman-Jackson J, Goecks J, Chilton JM, Kamali K, Suderman K, Poterlowicz K, Yvan LB, Lopez-Delisle L, Sargent L, Bassetti ME, Tangaro MA, van den Beek M, Čech M, Bernt M, Fahrner M, Tekman M, Föll MC, Schatz MC, Crusoe MR, Roncoroni M, Kucher N, Coraor N, Stoler N, Rhodes N, Soranzo N, Pinter N, Goonasekera NA, Moreno PA, Videm P, Melanie P, Mandreoli P, Jagtap PD, Gu Q, Weber RJM, Lazarus R, Vorderman RHP, Hiltemann S, Golitsynskiy S, Garg S, Bray SA, Gladman SL, Leo S, Mehta SP, Griffin TJ, Jalili V, Yves V, Wen V, Nagampalli VK, Bacon WA, de Koning W, Maier W, Briggs PJ. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. Nucleic Acids Res 2022; 50:W345-W351. [PMID: 35446428 PMCID: PMC9252830 DOI: 10.1093/nar/gkac247] [Citation(s) in RCA: 235] [Impact Index Per Article: 117.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/17/2022] [Accepted: 03/30/2022] [Indexed: 01/19/2023] Open
Abstract
Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues to use, maintain and contribute to the project, with support from multiple national infrastructure providers that enable freely accessible analysis and training services. The Galaxy Training Network supports free, self-directed, virtual training with >230 integrated tutorials. Project engagement metrics have continued to grow over the last 2 years, including source code contributions, publications, software packages wrapped as tools, registered users and their daily analysis jobs, and new independent specialized servers. Key Galaxy technical developments include an improved user interface for launching large-scale analyses with many files, interactive tools for exploratory data analysis, and a complete suite of machine learning tools. Important scientific developments enabled by Galaxy include Vertebrate Genome Project (VGP) assembly workflows and global SARS-CoV-2 collaborations.
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Bray SA, Senapathi T, Barnett CB, Grüning BA. Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial. J Cheminform 2020; 12:54. [PMID: 33431030 PMCID: PMC7488338 DOI: 10.1186/s13321-020-00451-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 07/27/2020] [Indexed: 11/10/2022] Open
Abstract
This paper is a tutorial developed for the data analysis platform Galaxy. The purpose of Galaxy is to make high-throughput computational data analysis, such as molecular dynamics, a structured, reproducible and transparent process. In this tutorial we focus on 3 questions: How are protein-ligand systems parameterized for molecular dynamics simulation? What kind of analysis can be carried out on molecular trajectories? How can high-throughput MD be used to study multiple ligands? After finishing you will have learned about force-fields and MD parameterization, how to conduct MD simulation and analysis for a protein-ligand system, and understand how different molecular interactions contribute to the binding affinity of ligands to the Hsp90 protein.
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Affiliation(s)
- Simon A Bray
- Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, Freiburg, Germany
| | - Tharindu Senapathi
- Department of Chemistry and Scientific Computing Research Unit, University of Cape Town, 7700, Cape Town, South Africa
| | - Christopher B Barnett
- Department of Chemistry and Scientific Computing Research Unit, University of Cape Town, 7700, Cape Town, South Africa.
| | - Björn A Grüning
- Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, Freiburg, Germany.
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Bray SA, Lucas X, Kumar A, Grüning BA. The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform. J Cheminform 2020; 12:40. [PMID: 33431029 PMCID: PMC7268608 DOI: 10.1186/s13321-020-00442-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 05/16/2020] [Indexed: 01/14/2023] Open
Abstract
Here, we introduce the ChemicalToolbox, a publicly available web server for performing cheminformatics analysis. The ChemicalToolbox provides an intuitive, graphical interface for common tools for downloading, filtering, visualizing and simulating small molecules and proteins. The ChemicalToolbox is based on Galaxy, an open-source web-based platform which enables accessible and reproducible data analysis. There is already an active Galaxy cheminformatics community using and developing tools. Based on their work, we provide four example workflows which illustrate the capabilities of the ChemicalToolbox, covering assembly of a compound library, hole filling, protein-ligand docking, and construction of a quantitative structure-activity relationship (QSAR) model. These workflows may be modified and combined flexibly, together with the many other tools available, to fit the needs of a particular project. The ChemicalToolbox is hosted on the European Galaxy server and may be accessed via https://cheminformatics.usegalaxy.eu.
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Affiliation(s)
- Simon A Bray
- Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, Freiburg, Germany.
| | - Xavier Lucas
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel, Switzerland
| | - Anup Kumar
- Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, Freiburg, Germany
| | - Björn A Grüning
- Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, Freiburg, Germany
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Litzenberger R, Morgan KM, Marden SF, Jacobs-Irvine KN, Bray SA. A nursing approach to the management of type IIA hyperlipidemia: case study of a young adult. J Cardiovasc Nurs 1991; 5:58-66. [PMID: 1987335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
This case study illustrates the chronic nature of hyperlipidemia type IIa and the important contribution of the nurse in helping the client adjust life style, manage complex health regimes, and cope with the uncertainty of disease progression and its associated risks.
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Bray SA, Cummings C, Peduzzi T. A comprehensive system to enhance the staff role in patient education. J Nurs Staff Dev 1989; 5:261-4. [PMID: 2600652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
This article describes the development and implementation of a comprehensive system to support the staff nurse's role in patient education. An overview of the content and process of a two-part workshop is presented. The system used for documenting, disseminating, filing, and revising patient education programs is discussed. The ways this system have enhanced patient education and staff satisfaction are described. This system can be used to enhance the efficiency and effectiveness of patient education in any health-care setting.
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