Enhancing UCSF Chimera through web services

Integrating access to web services with desktop applications allows for an expanded set of application features, including performing computationally intensive tasks and convenient searches of databases. We describe how we have enhanced UCSF Chimera (http://www.rbvi.ucsf.edu/chimera/), a program for...

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Main Authors:	Huang, Conrad C., Meng, Elaine C., Morris, John H., Pettersen, Eric F., Ferrin, Thomas E.
Format:	Online
Language:	English
Published:	Oxford University Press 2014
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086125/

id	pubmed-4086125
recordtype	oai_dc
spelling	pubmed-40861252014-12-01 Enhancing UCSF Chimera through web services Huang, Conrad C. Meng, Elaine C. Morris, John H. Pettersen, Eric F. Ferrin, Thomas E. Article Integrating access to web services with desktop applications allows for an expanded set of application features, including performing computationally intensive tasks and convenient searches of databases. We describe how we have enhanced UCSF Chimera (http://www.rbvi.ucsf.edu/chimera/), a program for the interactive visualization and analysis of molecular structures and related data, through the addition of several web services (http://www.rbvi.ucsf.edu/chimera/docs/webservices.html). By streamlining access to web services, including the entire job submission, monitoring and retrieval process, Chimera makes it simpler for users to focus on their science projects rather than data manipulation. Chimera uses Opal, a toolkit for wrapping scientific applications as web services, to provide scalable and transparent access to several popular software packages. We illustrate Chimera's use of web services with an example workflow that interleaves use of these services with interactive manipulation of molecular sequences and structures, and we provide an example Python program to demonstrate how easily Opal-based web services can be accessed from within an application. Web server availability: http://webservices.rbvi.ucsf.edu/opal2/dashboard?command=serviceList. Oxford University Press 2014-07-01 2014-05-26 /pmc/articles/PMC4086125/ /pubmed/24861624 http://dx.doi.org/10.1093/nar/gku377 Text en © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Huang, Conrad C. Meng, Elaine C. Morris, John H. Pettersen, Eric F. Ferrin, Thomas E.
spellingShingle	Huang, Conrad C. Meng, Elaine C. Morris, John H. Pettersen, Eric F. Ferrin, Thomas E. Enhancing UCSF Chimera through web services
author_facet	Huang, Conrad C. Meng, Elaine C. Morris, John H. Pettersen, Eric F. Ferrin, Thomas E.
author_sort	Huang, Conrad C.
title	Enhancing UCSF Chimera through web services
title_short	Enhancing UCSF Chimera through web services
title_full	Enhancing UCSF Chimera through web services
title_fullStr	Enhancing UCSF Chimera through web services
title_full_unstemmed	Enhancing UCSF Chimera through web services
title_sort	enhancing ucsf chimera through web services
description	Integrating access to web services with desktop applications allows for an expanded set of application features, including performing computationally intensive tasks and convenient searches of databases. We describe how we have enhanced UCSF Chimera (http://www.rbvi.ucsf.edu/chimera/), a program for the interactive visualization and analysis of molecular structures and related data, through the addition of several web services (http://www.rbvi.ucsf.edu/chimera/docs/webservices.html). By streamlining access to web services, including the entire job submission, monitoring and retrieval process, Chimera makes it simpler for users to focus on their science projects rather than data manipulation. Chimera uses Opal, a toolkit for wrapping scientific applications as web services, to provide scalable and transparent access to several popular software packages. We illustrate Chimera's use of web services with an example workflow that interleaves use of these services with interactive manipulation of molecular sequences and structures, and we provide an example Python program to demonstrate how easily Opal-based web services can be accessed from within an application. Web server availability: http://webservices.rbvi.ucsf.edu/opal2/dashboard?command=serviceList.
publisher	Oxford University Press
publishDate	2014
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086125/
_version_	1613109763862691840

Enhancing UCSF Chimera through web services

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