Mark A. Miller
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.
- Wilkins-Diehr, N., Gannon, D., Klimeck, G., Oster, S., and Pamidighantam, S. (2008) TeraGrid Science Gateways and Their Impact on Science. Computer 41,(11) 32--41. Google Scholar
Digital Library
- (2015) SCI-BUS Gateway Listing. http://www.sci-bus.eu/wiki/-/wiki/Public/PublicationsGoogle Scholar
- (2015) XSEDE Gateway Listing. http://www.xsede.org/web/guest/gateways-listingGoogle Scholar
- Giardine, B., Riemer, C., Hardison, R. C., et al. (2005) Galaxy: A platform for interactive large-scale genome analysis. Genome Res. 15,(10) 1451--1455.Google ScholarCross Ref
- McLennan, M. (2008) The Hub Concept for Scientific Collaboration. https://hubzero.org/resources/12Google Scholar
- Rifaieh, R., Unwin, R., Carver, J., and Miller, M. A. (2007) SWAMI: Integrating Biological Databases and Analysis Tools Within User Friendly Environment. In Data Integration in Life Sciences (DILS 07), pp. 48--58. Google ScholarDigital Library
- Chard, R., Sehrish, S., Rodriguez, A., et al. (2014) PDACS: a portal for data analysis services for cosmological simulations,. In 9th Gateway Computing Environments Workshop, pp. 30--33, IEEE Press Google ScholarDigital Library
- (2015) HubZero Powered Sites.Google Scholar
- Montella, R., Brizius, A., Elliott, J., et al. (2014) FACE-IT: a science gateway for food security research. In 9th Gateway Computing Environments Workshop, pp. 42--46, IEEE Press Google ScholarDigital Library
- Rekapalli, B., Giblock, P., and Reardon, C. (2013) PoPLAR: Portal for Petascale Lifescience Applications and Research. BMC Bioinformatics 14,(Suppl 9) S3.DOI: http://www.biomedcentral.com/1471-2105/14/S9/S3Google ScholarCross Ref
- Miller, M. A., Pfeiffer, W., and Schwartz, T. (2010) Creating the CIPRES Science Gateway for Inference of Large Phylogenetic Trees In SC10: Workshop on Gateway Computing Environments (GCE10)Google Scholar
- Dooley, R., Vaughn, M., Stanzione, D., Terry, S., and Skidmore, S. (2012) Software-as-a-Service: The iPlant Foundation API. In 5th IEEE Workshop on Many-Task Computing on Grids and Supercomputers (MTAGS).Google Scholar
- Cholia, S., Skinner, D., and Boverhof, D. (2010) NEWT: A RESTful service for building High Performance Computing web applications.. Gateway Computing Environments Workshop (GCE) 1--11.DOI:Google ScholarCross Ref
- Sivagnanam, S., Majumdar, A., Yoshimoto, K., Astakhov, V., Bandrowski, A., Martone, M., and Carnevale, N. T. (2014) Early experiences in developing and managing the neuroscience gateway. Journal of Concurrency and Computation: Practice and Experience, 27,(2) 473--488.DOI: http://dx.doi.org/10.1002/cpe.3283Google ScholarCross Ref
- Rifaieh, R., Unwin, R., Carver, J., and Miller, M. A. (2007) SWAMI: Integrating Biological Databases and Analysis Tools Within User Friendly Environment. In Data Integration in Life Sciences (DILS 07), pp. 48--58. Google ScholarDigital Library
- Miller, M. A., Pfeiffer, W., and Schwartz, T. (2011) The CIPRES Science Gateway: a community resource for phylogenetic analyses. In 2011 TeraGrid Conference: Extreme Digital Discovery, pp. 1--8 Google ScholarDigital Library
- Miller, M. A., Pfeiffer, W., and Schwartz, T. (2012) The CIPRES Science Gateway: enabling high-impact science for phylogenetics researchers with limited resources. In Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the campus and beyond, pp. 1--8, ACM Google ScholarDigital Library
- Miller, M. A., Schwartz, T., Pickett, B. E., et al. (2015) A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway. Evolutionary Bioinformatics 11,(4726-EBO-A-RESTful-API-for-Access-to-Phylogenetic-Tools-via-the-CIPRES-Science-.pdf) 43--48.DOI: 10.4137/EBO.S21501 www.la-press.com/a-restful-api-for-access-to-phylogenetic-tools-via-the-cipres-science--article-a4726.Google Scholar
- (2013) Jersey. http://jersey.java.net/Google Scholar
- Maddison, W. P. and D. R., M. (2008) Mesquite: a modular system for evolutionary analysis. Version 2.5. http://mesquiteproject.orgGoogle Scholar
- O'Leary, M. A. and Kaufman, S. (2011) MorphoBank: phylophenomics in the "cloud". Cladistics 27,(5) 529--537.DOI: 10.1111/j.1096-0031.2011.00355.x http://dx.doi.org/10.1111/j.1096-0031.2011.00355.xGoogle ScholarCross Ref
- Pickett, B. E., Sadat, E. L., Zhang, Y., et al. (2012) ViPR: an open bioinformatics database and analysis resource for virology research. Nucleic Acids Res. 40D593--598.Google Scholar
- Squires, R. B., Noronha, J., Hunt, V., García-Sastre, A., Macken, C., Baumgarth, N., Suarez, D., Pickett, B. E., Zhang, Y., Larsen, C. N., Ramsey, A., Zhou, L., Zaremba, S., Kumar, S., Deitrich, J., Klem, E., and Scheuermann, R. H. (2012) Influenza Research Database: an integrated bioinformatics resource for influenza research and surveillance. Influenza and Other Respiratory Viruses 6, 404--416.Google ScholarCross Ref
- Mishra, B., and Thines, M. (2014) siMBa---a simple graphical user interface for the Bayesian phylogenetic inference program MrBayes. Mycol Progress, 1--4Google Scholar
- Silvestro, D., and Michalak, I. (2011) raxmlGUI: a graphical front-end for RAxML. Organisms Diversity and Evolution. 12, 335--337.Google ScholarCross Ref
- Maddison, W. P., and D. R., M. (2008) Mesquite: a modular system for evolutionary analysis. Version 2.5Google Scholar
- Letondal, C. (2007) PISE (*), a tool to generate Web interfaces for Molecular Biology programs. http://www.pasteur.fr/recherche/unites/sis/Pise/Google Scholar
- Marru, S., Gunathilake, L., Herath, C., et al. (2011) Apache airavata: a framework for distributed applications and computational workflows. In 2011 ACM workshop on Gateway computing environments., pp. 21--28, ACM Press Google ScholarDigital Library
- (2015) Expression Engine https://ellislab.com/expressionengineGoogle Scholar
- (2015) Bootstrap CMS. https://github.com/BootstrapCMS/CMSGoogle Scholar
- Davison, A., Morse, T., Migliore, M., Shepherd, G., and Hines, M. (2004) Semi-automated population of an online database of neuronal models (ModelDB) with citation information, using PubMed for validation. Neuroinform 2,(3) 327--332.DOI: 10.1385/NI:2:3:327 http://dx.doi.org/10.1385/NI%3A2%3A3%3A327Google ScholarCross Ref
- Hines, M. L. and Carnevale, N. T. (2003) The NEURON simulation environment. In: The Handbook of Brain Theory and Neural Networks. MIT Press, pp.Google Scholar
- Afgan, E., Baker, D., Coraor, N., Chapman, B., Nekrutenko, A., and Taylor, J. (2010) Galaxy CloudMan: delivering cloud compute clusters. BMC Bioinformatics 11,(Suppl 12) S4.DOI: http://www.biomedcentral.com/1471-2105/11/S12/S4Google ScholarCross Ref
Index Terms
- The CIPRES workbench: a flexible framework for creating science gateways
Recommendations
Apache Airavata Sharing Service: A Tool for Enabling User Collaboration in Science Gateways
PEARC '17: Proceedings of the Practice and Experience in Advanced Research Computing 2017 on Sustainability, Success and ImpactScience Gateways provide user environments and a set of supporting services that help researchers make effective and enhanced use of a diverse set of computing, storage, and related resources. Gateways provide the services and tools users require to ...
The CIPRES science gateway: a community resource for phylogenetic analyses
TG '11: Proceedings of the 2011 TeraGrid Conference: Extreme Digital DiscoveryThe CIPRES Science Gateway (CSG) provides researchers and educators with browser-based access to community codes for inference of phylogenetic relationships from DNA and protein sequence data. The CSG allows users to deploy jobs on the high-performance ...
The CIPRES science gateway: enabling high-impact science for phylogenetics researchers with limited resources
XSEDE '12: Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the campus and beyondThe CIPRES Science Gateway (CSG) provides browser-based access to computationally demanding phylogenetic codes run on large HPC resources. Since its release in December 2009, there has been a sustained, near-linear growth in the rate of CSG use, both in ...
Comments