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

By Mark A. Miller, Terri Schwartz, B. Pickett, Sherry He, E. Klem, Richard H. Scheuermann, Maria Passarotti, Seth Kaufman, Maureen A. OLeary. Evolutionary bioinformatics online, 2015

461 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/05b275a2366e8447316f3003f19d87654aa3816b

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In Molecular Biology

1. Richard H. Scheuermann
2. Christian M. Zmasek
3. Yun Zhang
4. Peer Bork
5. Ivica Letunic
6. Gernot G. Presting

Citations in the corpus

• Influenza Research Database: An integrated bioinformatics resource for influenza virus research (2016, methodology): “If the user chooses this option, the sequences needed to generate a tree are sent to CIPRES through an application programming interface (8).”