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

Miller MA, Schwartz T, Pickett BE, He S, Klem EB, Scheuermann RH, Passarotti M, Kaufman S, O'Leary MA - Evol. Bioinform. Online (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA.

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.

No MeSH data available.


Related in: MedlinePlus

Screen shot showing IRD/ViPR lightbox pop up, prompting user to choose the option of running the analysis task using the CIPRES resource.
© Copyright Policy - open-access
Related In: Results  -  Collection


getmorefigures.php?uid=PMC4362911&req=5

f2-ebo-11-2015-043: Screen shot showing IRD/ViPR lightbox pop up, prompting user to choose the option of running the analysis task using the CIPRES resource.

Mentions: The IRD and ViPR are public database and analysis resources for the study of influenza viruses and Category A–C priority pathogens, respectively. Both resources provide a workbench with integrated database and computational support for virus research. The IRD and ViPR web applications natively support tree inference and other computational biology methods using several community tools. IRD and ViPR have historically provided web forms and required infrastructure to manage job submissions and results retrieval. However, with the continued growth of available data, IRD/ViPR developers sought a mechanism to support analysis tasks that exceeded the capacity of their available compute resources. Using the CRA, IRD/ViPR now facilitates direct access to the RAxML tool on XSEDE (RAXMLHPC2_TGB) through their existing phylogenetic tree analysis portal. The tree analysis input page in IRD/ViPR allows users to configure parameters for RAxML runs. On submission, when the number and size of the input sequences exceeds a prespecified threshold, a light-box appears to recommend that the user submit their job to CIPRES through the existing IRD/ViPR interface (Fig. 2). A REST client using the Jersey framework implemented in IRD/ViPR then communicates with the RESTful services at CIPRES. After jobs are successfully submitted to CIPRES, IRD and ViPR periodically poll the job status and retrieve the results once the jobs are finished. The results are then saved to the user’s private workbench area in IRD or ViPR for further use. Thus, the results obtained either from local IRD and VIPR or CIPRES resources can be accessed, visualized, and analyzed seamlessly by the user without ever leaving the IRD and ViPR web sites.


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

Miller MA, Schwartz T, Pickett BE, He S, Klem EB, Scheuermann RH, Passarotti M, Kaufman S, O'Leary MA - Evol. Bioinform. Online (2015)

Screen shot showing IRD/ViPR lightbox pop up, prompting user to choose the option of running the analysis task using the CIPRES resource.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4362911&req=5

f2-ebo-11-2015-043: Screen shot showing IRD/ViPR lightbox pop up, prompting user to choose the option of running the analysis task using the CIPRES resource.
Mentions: The IRD and ViPR are public database and analysis resources for the study of influenza viruses and Category A–C priority pathogens, respectively. Both resources provide a workbench with integrated database and computational support for virus research. The IRD and ViPR web applications natively support tree inference and other computational biology methods using several community tools. IRD and ViPR have historically provided web forms and required infrastructure to manage job submissions and results retrieval. However, with the continued growth of available data, IRD/ViPR developers sought a mechanism to support analysis tasks that exceeded the capacity of their available compute resources. Using the CRA, IRD/ViPR now facilitates direct access to the RAxML tool on XSEDE (RAXMLHPC2_TGB) through their existing phylogenetic tree analysis portal. The tree analysis input page in IRD/ViPR allows users to configure parameters for RAxML runs. On submission, when the number and size of the input sequences exceeds a prespecified threshold, a light-box appears to recommend that the user submit their job to CIPRES through the existing IRD/ViPR interface (Fig. 2). A REST client using the Jersey framework implemented in IRD/ViPR then communicates with the RESTful services at CIPRES. After jobs are successfully submitted to CIPRES, IRD and ViPR periodically poll the job status and retrieve the results once the jobs are finished. The results are then saved to the user’s private workbench area in IRD or ViPR for further use. Thus, the results obtained either from local IRD and VIPR or CIPRES resources can be accessed, visualized, and analyzed seamlessly by the user without ever leaving the IRD and ViPR web sites.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA.

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.

No MeSH data available.


Related in: MedlinePlus