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Miller MA, Schwartz T, Pickett BE, et al. A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway. Evol Bioinform Online. 2015;11:43-8doi: 10.4137/EBO.S21501.
Miller, M. A., Schwartz, T., Pickett, B. E., He, S., Klem, E. B., Scheuermann, R. H., Passarotti, M., Kaufman, S., & O'Leary, M. A. (2015). A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway. Evolutionary bioinformatics online, 1143-8. https://doi.org/10.4137/EBO.S21501
Miller, Mark A, et al. "A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway." Evolutionary bioinformatics online vol. 11 (2015): 43-8. doi: https://doi.org/10.4137/EBO.S21501
Miller MA, Schwartz T, Pickett BE, He S, Klem EB, Scheuermann RH, Passarotti M, Kaufman S, O'Leary MA. A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway. Evol Bioinform Online. 2015 Mar 16;11:43-8. doi: 10.4137/EBO.S21501. eCollection 2015. PMID: 25861210; PMCID: PMC4362911.
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Evol Bioinform Online. 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.

Evolutionary bioinformatics online

Mark A Miller, Terri Schwartz, Brett E Pickett, Sherry He, Edward B Klem, Richard H Scheuermann, Maria Passarotti, Seth Kaufman, Maureen A O'Leary

Affiliations

  1. San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA.
  2. J. Craig Venter Institute, La Jolla, CA, USA.
  3. Northrop Grumman Health Solutions, Rockville, MD, USA.
  4. Whirl-i-gig, Brooklyn, NY, USA.
  5. Department of Anatomical Sciences, Stony Brook University, Stony Brook, NY, USA.

PMID: 25861210 PMCID: PMC4362911 DOI: 10.4137/EBO.S21501

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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