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Review
. 2015 Mar 16:11:43-8.
doi: 10.4137/EBO.S21501. eCollection 2015.

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

Mark A Miller  1 , Terri Schwartz  1 , Brett E Pickett  2 , Sherry He  3 , Edward B Klem  3 , Richard H Scheuermann  2 , Maria Passarotti  4 , Seth Kaufman  4 , Maureen A O'Leary  5
Affiliations
Review

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

Mark A Miller et al. Evol Bioinform Online. .

Abstract

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.

Keywords: BEAST; CIPRES; MAFFT; MrBayes; RAxML; RESTful API; Science Gateway; computational biology; jMODELTEST2; phylogenetics; web portal.

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Figures

Figure 1
Figure 1
Screen shot showing web form for access to PAUPRat in MorphoBank.
Figure 2
Figure 2
Screen shot showing IRD/ViPR lightbox pop up, prompting user to choose the option of running the analysis task using the CIPRES resource.
See this image and copyright information in PMC

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References

    1. Burleigh JG, Alphonse K, Alverson AJ, et al. Next-generation phenomics for the tree of life. PLoS Curr. 2013;5:1–6. - PMC - PubMed
    1. de Queiroz A, Gatesy J. The supermatrix approach to systematics. Trends Ecol Evol. 2007;22(1):34–41. - PubMed
    1. O’Leary MA, Bloch JI, Flynn JJ. The placental mammal ancestor and the post–K-Pg radiation of placentals. Science. 2013;339(6120):662–7. - PubMed
    1. Miller MA, Pfeiffer W, Schwartz T. Creating the CIPRES Science Gateway for Inference of Large Phylogenetic Trees; SC10 Workshop on Gateway Computing Environments (GCE10); 2010.
    1. Silvestro D, Michalak I. raxmlGUI: a graphical front-end for RAxML. Org Divers Evol. 2011;12(4):335–7.

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