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A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway

The CIPRES Science Gateway is a community web application that provides public access to a set of parallel tree inference and multiple sequence alignment codes run on large computational resources. These resources are made available at no charge to users by the NSF Extreme Science and Engineering Di...

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Autores principales: Miller, Mark A, Schwartz, Terri, Pickett, Brett E, He, Sherry, Klem, Edward B, Scheuermann, Richard H, Passarotti, Maria, Kaufman, Seth, O’Leary, Maureen A
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Libertas Academica 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4362911/
https://www.ncbi.nlm.nih.gov/pubmed/25861210
http://dx.doi.org/10.4137/EBO.S21501
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author Miller, Mark A
Schwartz, Terri
Pickett, Brett E
He, Sherry
Klem, Edward B
Scheuermann, Richard H
Passarotti, Maria
Kaufman, Seth
O’Leary, Maureen A
author_facet Miller, Mark A
Schwartz, Terri
Pickett, Brett E
He, Sherry
Klem, Edward B
Scheuermann, Richard H
Passarotti, Maria
Kaufman, Seth
O’Leary, Maureen A
author_sort Miller, Mark A
collection PubMed
description The CIPRES Science Gateway is a community web application that provides public access to a set of parallel tree inference and multiple sequence alignment codes run on large computational resources. These resources are made available at no charge to users by the NSF Extreme Science and Engineering Discovery Environment (XSEDE) project. Here we describe the CIPRES RESTful application programmer interface (CRA), a web service that provides programmatic access to all resources and services currently offered by the CIPRES Science Gateway. Software developers can use the CRA to extend their web or desktop applications to include the ability to run MrBayes, BEAST, RAxML, MAFFT, and other computationally intensive algorithms on XSEDE. The CRA also makes it possible for individuals with modest scripting skills to access the same tools from the command line using curl, or through any scripting language. This report describes the CRA and its use in three web applications (Influenza Research Database – www.fludb.org, Virus Pathogen Resource – www.viprbrc.org, and MorphoBank – www.morphobank.org). The CRA is freely accessible to registered users at https://cipresrest.sdsc.edu/cipresrest/v1; supporting documentation and registration tools are available at https://www.phylo.org/restusers.
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spelling pubmed-43629112015-04-08 A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway Miller, Mark A Schwartz, Terri Pickett, Brett E He, Sherry Klem, Edward B Scheuermann, Richard H Passarotti, Maria Kaufman, Seth O’Leary, Maureen A Evol Bioinform Online Software or Database Review The CIPRES Science Gateway is a community web application that provides public access to a set of parallel tree inference and multiple sequence alignment codes run on large computational resources. These resources are made available at no charge to users by the NSF Extreme Science and Engineering Discovery Environment (XSEDE) project. Here we describe the CIPRES RESTful application programmer interface (CRA), a web service that provides programmatic access to all resources and services currently offered by the CIPRES Science Gateway. Software developers can use the CRA to extend their web or desktop applications to include the ability to run MrBayes, BEAST, RAxML, MAFFT, and other computationally intensive algorithms on XSEDE. The CRA also makes it possible for individuals with modest scripting skills to access the same tools from the command line using curl, or through any scripting language. This report describes the CRA and its use in three web applications (Influenza Research Database – www.fludb.org, Virus Pathogen Resource – www.viprbrc.org, and MorphoBank – www.morphobank.org). The CRA is freely accessible to registered users at https://cipresrest.sdsc.edu/cipresrest/v1; supporting documentation and registration tools are available at https://www.phylo.org/restusers. Libertas Academica 2015-03-16 /pmc/articles/PMC4362911/ /pubmed/25861210 http://dx.doi.org/10.4137/EBO.S21501 Text en © 2015 the author(s), publisher and licensee Libertas Academica Ltd. This is an open-access article distributed under the terms of the Creative Commons CC-BY-NC 3.0 License.
spellingShingle Software or Database Review
Miller, Mark A
Schwartz, Terri
Pickett, Brett E
He, Sherry
Klem, Edward B
Scheuermann, Richard H
Passarotti, Maria
Kaufman, Seth
O’Leary, Maureen A
A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway
title A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway
title_full A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway
title_fullStr A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway
title_full_unstemmed A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway
title_short A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway
title_sort restful api for access to phylogenetic tools via the cipres science gateway
topic Software or Database Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4362911/
https://www.ncbi.nlm.nih.gov/pubmed/25861210
http://dx.doi.org/10.4137/EBO.S21501
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