Stein, J., Lu, J., Noutsos, C., Wang, L., Barthelson, R., Wei, F., et al. (2013). Biological Computing Using the iPlant Discovery Environment. Biological Computing Using the iPlant Discovery Environment. San Diego, CA.
Hilgert, U., McKay, S., Khalfan, M., Williams, J., Ghiban, C., & Micklos, D. (2014). DNA Subway: Making Genome Analysis Egalitarian. Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment - XSEDE 14. Atlanta, GA, USA: ACM Press. http://doi.org/10.1145/2616498.2616575
Matasci, N., & McKay, S. (2013). Phylogenetic Analysis with the iPlant Discovery Environment. Current Protocols In Bioinformatics, 42, 1-6. http://doi.org/10.1002/0471250953.bi0613s42
McKay, S. (2012). How to Use the iPlant s Discovery Environment for Your Research. Plant and Animal Genome XX. San Diego, CA. Retrieved from https://pag.confex.com/pag/xx/webprogram/Paper2931.html
McKay, S., Lyons, E., Tang, H., Miller, N., Eichten, S. R., Goff, S. A., et al. (2012). The iPlant Collaborative. Plant and Animal Genome XX. San Diego, CA. Retrieved from https://pag.confex.com/pag/xx/webprogram/Paper2918.html
Goff, S. A., Vaughn, M., McKay, S., Lyons, E., Stapleton, A. E., Gessler, D., et al. (2011). The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Frontiers In Plant Science, 2. http://doi.org/10.3389/fpls.2011.00034
Lotterhos, K. E., Moore, J. H., & Stapleton, A. E. (2018). Analysis validation has been neglected in the Age of Reproducibility. Plos Biology, 16, e3000070. http://doi.org/10.1371/journal.pbio.3000070
Manching, H. C., Carlson, K., Kosowsky, S., Smitherman, T., & Stapleton, A. E. (2017). Maize Phyllosphere Microbial Community Niche Development Across Stages of Host Leaf Growth. F1000Research, 6, 1698. http://doi.org/10.12688/f1000research.12490.2
Lotterhos, K. E., Moore, J. H., & Stapleton, A. E. (2018). Analysis validation has been neglected in the Age of Reproducibility. Plos Biology, 16, e3000070. http://doi.org/10.1371/journal.pbio.3000070
Goff, S. A., Vaughn, M., McKay, S., Lyons, E., Stapleton, A. E., Gessler, D., et al. (2011). The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Frontiers In Plant Science, 2. http://doi.org/10.3389/fpls.2011.00034
Vasquez-Gross, H., Figueroa, B., Yu, J., Gessler, D., Neale, D., & Wergrzyn, J. (2013). CartograTree: Connection Forest Tree Genomes, Phenotypes, and Environment. Proceedings from Plant and Animal Gemone XXI.
Vasquez-Gross, H., Zieve, J., Gessler, D., Neale, D., & Wegrzyn, J. (2014). Case Study: Enabling Forest Tree Genomics through Association Studies with the use of SSWAP. Proceedings from Plant and Animal Gemone XXII.
Goff, S. A., Vaughn, M., McKay, S., Lyons, E., Stapleton, A. E., Gessler, D., et al. (2011). The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Frontiers In Plant Science, 2. http://doi.org/10.3389/fpls.2011.00034
Hart, D. L., Schuele, A., Soriano, E., Dahan, M., & Hanlon, M. (2014). XRAS: Allocations software as a service in XSEDE. Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment - XSEDE 14. Atlanta, GA, USA: ACM Press. http://doi.org/10.1145/2616498.2616562
Goff, S. A., Vaughn, M., McKay, S., Lyons, E., Stapleton, A. E., Gessler, D., et al. (2011). The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Frontiers In Plant Science, 2. http://doi.org/10.3389/fpls.2011.00034
Hanlon, M. R., Vaughn, M., Mock, S., Dooley, R., Moreira, W., Stubbs, J., et al. (2014). The Arabidopsis Information Portal: An Application Platform for Data Discovery. 2014 9th Gateway Computing Environments Workshop. New Orleans, LA, USA: IEEE. http://doi.org/10.1109/GCE.2014.10
Coronel, J. B., & Mock, S. (2017). DesignSafe: Using Elasticsearch to Share and Search Data on a Science Web Portal. Proceedings of the Practice and Experience in Advanced Research Computing 2017 on Sustainability, Success and Impact - PEARC17. New Orleans, LA, USA: ACM Press. http://doi.org/10.1145/3093338.3093386
Crivelli, S., Dooley, R., Holmes, R., Mock, S., & Community, T. W. F. (2015). Creating a gateway that enables large-scale science coopetition: LARGE-SCALE SCIENCE COOPETITION. Concurrency And Computation: Practice And Experience, 27, 446-457. http://doi.org/10.1002/cpe.3270
Goff, S. A., Vaughn, M., McKay, S., Lyons, E., Stapleton, A. E., Gessler, D., et al. (2011). The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Frontiers In Plant Science, 2. http://doi.org/10.3389/fpls.2011.00034
Goff, S. A., Vaughn, M., McKay, S., Lyons, E., Stapleton, A. E., Gessler, D., et al. (2011). The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Frontiers In Plant Science, 2. http://doi.org/10.3389/fpls.2011.00034
Goff, S. A., Vaughn, M., McKay, S., Lyons, E., Stapleton, A. E., Gessler, D., et al. (2011). The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Frontiers In Plant Science, 2. http://doi.org/10.3389/fpls.2011.00034
Goff, S. A., Vaughn, M., McKay, S., Lyons, E., Stapleton, A. E., Gessler, D., et al. (2011). The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Frontiers In Plant Science, 2. http://doi.org/10.3389/fpls.2011.00034
Stein, J., Lu, J., Noutsos, C., Wang, L., Barthelson, R., Wei, F., et al. (2013). Biological Computing Using the iPlant Discovery Environment. Biological Computing Using the iPlant Discovery Environment. San Diego, CA.
Boyle, B., Hopkins, N., Lu, Z., Garay, J. A. R., Mozzherin, D., Rees, T., et al. (2013). The taxonomic name resolution service: an online tool for automated standardization of plant names. Bmc Bioinformatics, 14, 16. http://doi.org/10.1186/1471-2105-14-16
Goff, S. A., Vaughn, M., McKay, S., Lyons, E., Stapleton, A. E., Gessler, D., et al. (2011). The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Frontiers In Plant Science, 2. http://doi.org/10.3389/fpls.2011.00034
Goff, S. A., Vaughn, M., McKay, S., Lyons, E., Stapleton, A. E., Gessler, D., et al. (2011). The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Frontiers In Plant Science, 2. http://doi.org/10.3389/fpls.2011.00034
Merchant, N., Lyons, E., Goff, S., Vaughn, M., Ware, D., Micklos, D., & Antin, P. (2016). The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences. Plos Biology, 14, e1002342. http://doi.org/10.1371/journal.pbio.1002342
Hilgert, U., McKay, S., Khalfan, M., Williams, J., Ghiban, C., & Micklos, D. (2014). DNA Subway: Making Genome Analysis Egalitarian. Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment - XSEDE 14. Atlanta, GA, USA: ACM Press. http://doi.org/10.1145/2616498.2616575
Barone, L., Williams, J., & Micklos, D. (2017). Unmet needs for analyzing biological big data: A survey of 704 NSF principal investigators. Plos Computational Biology, 13, e1005755. http://doi.org/10.1371/journal.pcbi.1005755
Goff, S. A., Vaughn, M., McKay, S., Lyons, E., Stapleton, A. E., Gessler, D., et al. (2011). The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Frontiers In Plant Science, 2. http://doi.org/10.3389/fpls.2011.00034
Hilgert, U., McKay, S., Khalfan, M., Williams, J., Ghiban, C., & Micklos, D. (2014). DNA Subway: Making Genome Analysis Egalitarian. Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment - XSEDE 14. Atlanta, GA, USA: ACM Press. http://doi.org/10.1145/2616498.2616575
Goff, S. A., Vaughn, M., McKay, S., Lyons, E., Stapleton, A. E., Gessler, D., et al. (2011). The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Frontiers In Plant Science, 2. http://doi.org/10.3389/fpls.2011.00034
Friesner, J., Assmann, S. M., Bastow, R., Bailey-Serres, J., Beynon, J., Brendel, V., et al. (2017). The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology. Plant Physiology, 175, 1499-1509. http://doi.org/10.1104/pp.17.01490
Goff, S. A., Vaughn, M., McKay, S., Lyons, E., Stapleton, A. E., Gessler, D., et al. (2011). The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Frontiers In Plant Science, 2. http://doi.org/10.3389/fpls.2011.00034
Jordan, C., Esteva, M., Walling, D., Urban, T., & Kulasekaran, S. (2013). Responses to Data Management Requirements at the National Scale. Research Data Management, 64.
Dooley, R., Brandt, S. R., & Fonner, J. (2018). The Agave Platform: An Open, Science-as-a-Service Platform for Digital Science. Proceedings of the Practice and Experience on Advanced Research Computing - PEARC 18. Pittsburgh, PA, USA: ACM Press. http://doi.org/10.1145/3219104.3219129
Dooley, R., & Stubbs, J. (2014). Dynamically Provisioning Portable Gateway Infrastructure Using Docker and Agave. Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment - XSEDE 14. Atlanta, GA, USA: ACM Press. http://doi.org/10.1145/2616498.2616561
Cleveland, S. B., Dooley, R., Perry, D., Stubbs, J., Fonner, J. M., & Jacobs, G. A. (2018). Building Science Gateway Infrastructure in the Middle of the Pacific and Beyond: Experiences using the Agave Deployer and Agave Platform to Build Science Gateways. Proceedings of the Practice and Experience on Advanced Research Computing - PEARC 18. Pittsburgh, PA, USA: ACM Press. http://doi.org/10.1145/3219104.3219151
Fonner, J., & Dooley, R. (2017). Containerizing Conda. Proceedings from 9th International Workshop on Science Gateways (IWSG 2017), 19-21 June 2017.
Lushbough, C. M., Gnimpieba, E. Z., & Dooley, R. (2015). Life science data analysis workflow development using the bioextract server leveraging the iPlant collaborative cyberinfrastructure: BIOEXTRACT SERVER WORKFLOWS LEVERAGING IPLANT COLLABORATIVE. Concurrency And Computation: Practice And Experience, 27, 408-419. http://doi.org/10.1002/cpe.3237
Goff, S. A., Vaughn, M., McKay, S., Lyons, E., Stapleton, A. E., Gessler, D., et al. (2011). The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Frontiers In Plant Science, 2. http://doi.org/10.3389/fpls.2011.00034
Cheng, C. -Y., Ferlanti, E., Krishnakumar, V., Kim, M., Karamycheva, S., Rosen, B. D., et al. (2015). Data Integration for the Plant Research Community: The Arabidopsis Information Portal. Proceedings of Plant and Animal Genome XXIII. Retrieved from https://pag.confex.com/pag/xxiii/webprogram/Paper16112.html
Crivelli, S., Dooley, R., Holmes, R., Mock, S., & Community, T. W. F. (2015). Creating a gateway that enables large-scale science coopetition: LARGE-SCALE SCIENCE COOPETITION. Concurrency And Computation: Practice And Experience, 27, 446-457. http://doi.org/10.1002/cpe.3270
Dooley, R., & Hanlon, M. R. (2015). Recipes 2.0: building for today and tomorrow: RECIPES 2.0: BUILDING FOR TODAY AND TOMORROW. Concurrency And Computation: Practice And Experience, 27, 258-270. http://doi.org/10.1002/cpe.3285
Hanlon, M. R., Vaughn, M., Mock, S., Dooley, R., Moreira, W., Stubbs, J., et al. (2014). The Arabidopsis Information Portal: An Application Platform for Data Discovery. 2014 9th Gateway Computing Environments Workshop. New Orleans, LA, USA: IEEE. http://doi.org/10.1109/GCE.2014.10
Gesing, S., Dooley, R., Pierce, M., Krüger, J., Grunzke, R., Herres-Pawlis, S., & Hoffmann, A. (2018). Gathering requirements for advancing simulations in HPC infrastructures via science gateways. Future Generation Computer Systems, 82, 544-554. http://doi.org/10.1016/j.future.2017.02.042
Goff, S. A., Vaughn, M., McKay, S., Lyons, E., Stapleton, A. E., Gessler, D., et al. (2011). The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Frontiers In Plant Science, 2. http://doi.org/10.3389/fpls.2011.00034
Izquierdo-Carrasco, F., Cazes, J., Smith, S. A., & Stamatakis, A. (2014). PUmPER: phylogenies updated perpetually. Bioinformatics, 30, 1476-1477.
Goff, S. A., Vaughn, M., McKay, S., Lyons, E., Stapleton, A. E., Gessler, D., et al. (2011). The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Frontiers In Plant Science, 2. http://doi.org/10.3389/fpls.2011.00034
McLay, R., Stanzione, D., Mckay, S. J., & Wheeler, T. (2011). A scalable parallel implementation of the neighbor joining algorithm for phylogenetic trees. ICCABS Conference.