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Nucleic Acids Res. 2014 Jul;42(Web Server issue):W478-84. doi: 10.1093/nar/gku377. Epub 2014 May 26.

Enhancing UCSF Chimera through web services.

Author information

1
Resource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94143, USA.
2
Resource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94143, USA tef@cgl.ucsf.edu.

Abstract

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.

PMID:
24861624
PMCID:
PMC4086125
DOI:
10.1093/nar/gku377
[Indexed for MEDLINE]
Free PMC Article

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