research-article

The CIPRES workbench: a flexible framework for creating science gateways

Authors:

Mark A. Miller,

Terri Schwartz,

Kenneth Yoshimoto,

Subhashini Sivagnanam,

Amit MajumdarAuthors Info & Claims

XSEDE '15: Proceedings of the 2015 XSEDE Conference: Scientific Advancements Enabled by Enhanced Cyberinfrastructure

Article No.: 39, Pages 1 - 8

https://doi.org/10.1145/2792745.2792784

Published: 26 July 2015 Publication History

Abstract

Here we describe the CIPRES Workbench (CW), an open source software framework for creating new science gateways with minimal overhead. The CW is a web application that can be deployed on a modest server, and can be configured to submit command line instructions to any resource where the application has submission privileges. It is designed to be highly configurable/customizable, and supports GUI-based access to HPC resources through a web browser interface as well as programmatic access via a ReSTful API. Using browser access, the CW architecture creates an environment with secure user accounts where user input data, job results, and job provenance are stored. The ReSTful API allows users with a registered a client application to deliver command lines to analytical codes and retrieve results from remote compute resources. A development effort is underway to allow the CW to submit jobs via the Science Gateways as a Platform (SciGaP) services hosted at Indiana University.

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Cited By

Hosie A(2025) Phylogenetic assessment of a new species of Amigdoscalpellum Zevina, 1978 (Cirripedia: Scalpellidae) associated with caryophyllid cup corals from New Zealand, with a key to the genus Journal of Crustacean Biology10.1093/jcbiol/ruaf01045:1Online publication date: 27-Feb-2025
https://doi.org/10.1093/jcbiol/ruaf010
Iizuka RHattori SKosaka YMasaki YKawano YOhtsu IHibbett DKatayama YYoshida M(2024) Sulfur assimilation using gaseous carbonyl sulfide by the soil fungus Trichoderma harzianum Applied and Environmental Microbiology10.1128/aem.02015-23Online publication date: Feb-2024
https://doi.org/10.1128/aem.02015-23
López-Hervas KSantos JRon SBetancourth-Cundar MCannatella DTarvin R(2024)Deep divergences among inconspicuously colored clades of Epipedobates poison frogsMolecular Phylogenetics and Evolution10.1016/j.ympev.2024.108065195(108065)Online publication date: Jun-2024
https://doi.org/10.1016/j.ympev.2024.108065
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Index Terms

The CIPRES workbench: a flexible framework for creating science gateways
1. Software and its engineering
  1. Software notations and tools
    1. General programming languages
      1. Language features
        Modules / packages

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cover image ACM Other conferences

XSEDE '15: Proceedings of the 2015 XSEDE Conference: Scientific Advancements Enabled by Enhanced Cyberinfrastructure

July 2015

296 pages

ISBN:9781450337205

DOI:10.1145/2792745

General Chair:
Gregory D. Peterson
National Institute of Computational Sciences

Copyright © 2015 ACM.

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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San Diego Super Computing Ctr: San Diego Super Computing Ctr
HPCWire: HPCWire
Omnibond: Omnibond Systems, LLC
SGI
Internet2
Indiana University: Indiana University
CASC: The Coalition for Academic Scientific Computation
NICS: National Institute for Computational Sciences
Intel: Intel
DDN: DataDirect Networks, Inc
DELL
CORSA: CORSA Technology
ALLINEA: Allinea Software
Cray
RENCI: Renaissance Computing Institute

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Association for Computing Machinery

New York, NY, United States

Publication History

Published: 26 July 2015

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National Science Foundation

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XSEDE '15

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San Diego Super Computing Ctr
HPCWire
Omnibond
Indiana University
CASC
NICS
Intel
DDN
CORSA
ALLINEA
RENCI

XSEDE '15: Extreme Science Engineering Discovery Environment 2015 Conference

July 26 - 30, 2015

Missouri, St. Louis

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XSEDE '15 Paper Acceptance Rate 49 of 70 submissions, 70%;

Overall Acceptance Rate 129 of 190 submissions, 68%

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Cited By

Hosie A(2025) Phylogenetic assessment of a new species of Amigdoscalpellum Zevina, 1978 (Cirripedia: Scalpellidae) associated with caryophyllid cup corals from New Zealand, with a key to the genus Journal of Crustacean Biology10.1093/jcbiol/ruaf01045:1Online publication date: 27-Feb-2025
https://doi.org/10.1093/jcbiol/ruaf010
Iizuka RHattori SKosaka YMasaki YKawano YOhtsu IHibbett DKatayama YYoshida M(2024) Sulfur assimilation using gaseous carbonyl sulfide by the soil fungus Trichoderma harzianum Applied and Environmental Microbiology10.1128/aem.02015-23Online publication date: Feb-2024
https://doi.org/10.1128/aem.02015-23
López-Hervas KSantos JRon SBetancourth-Cundar MCannatella DTarvin R(2024)Deep divergences among inconspicuously colored clades of Epipedobates poison frogsMolecular Phylogenetics and Evolution10.1016/j.ympev.2024.108065195(108065)Online publication date: Jun-2024
https://doi.org/10.1016/j.ympev.2024.108065
Lang DCitino SDonnelly KEmerson JGarner MStacy NWalden HMyers ESchumann AChildress AWellehan J(2022)IDENTIFICATION AND RETROSPECTIVE EVALUATION OF A FILARIOID NEMATODE SPECIES IN MANAGED GRASSHOPPER SPARROWS (AMMODRAMUS SAVANNARUM)Journal of Zoo and Wildlife Medicine10.1638/2021-014153:4Online publication date: 1-Dec-2022
https://doi.org/10.1638/2021-0141
Coleman JCannatella D(2022)How Phylogenetics Can Elucidate the Chemical Ecology of Poison Frogs and Their Arthropod PreyJournal of Chemical Ecology10.1007/s10886-022-01352-848:4(384-400)Online publication date: 14-Mar-2022
https://doi.org/10.1007/s10886-022-01352-8
Hosie AFromont JMunyard KJones D(2021)New Species and New Records of Sponge-Inhabiting Barnacles (Cirripedia, Balanidae, Acastinae) from AustraliaDiversity10.3390/d1307029013:7(290)Online publication date: 27-Jun-2021
https://doi.org/10.3390/d13070290
Gunn BMurphy DWalsh NConran JPires JMacfarlane TBirch J(2020)Evolution of Lomandroideae: Multiple origins of polyploidy and biome occupancy in AustraliaMolecular Phylogenetics and Evolution10.1016/j.ympev.2020.106836149(106836)Online publication date: Aug-2020
https://doi.org/10.1016/j.ympev.2020.106836
Yoshimoto KCarnevale NSivagnanam SMajumdar AMiller MFurlani T(2019)Web of Trust Tool for Gateway User VettingPractice and Experience in Advanced Research Computing 2019: Rise of the Machines (learning)10.1145/3332186.3332221(1-5)Online publication date: 28-Jul-2019
https://dl.acm.org/doi/10.1145/3332186.3332221
Rivero de Aguilar JCastillo FMoreno APeñafiel NBrowne LWalter SKarubian JBonaccorso E(2018)Patterns of avian haemosporidian infections vary with time, but not habitat, in a fragmented Neotropical landscapePLOS ONE10.1371/journal.pone.020649313:10(e0206493)Online publication date: 31-Oct-2018
https://doi.org/10.1371/journal.pone.0206493
Bentley JVerboom GBergh N(2017) Species‐level phylogenetic analysis in the Relhania clade of “everlastings” and a new generic treatment of species previously assigned to Macowania and Arrowsmithia (Asteraceae: Gnaphalieae) TAXON10.12705/666.966:6(1421-1438)Online publication date: Dec-2017
https://doi.org/10.12705/666.9
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