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ORCIDJoe Stubbs
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- affiliation: University of Texas, Texas Advanced Computing Center, Austin, TX, USA
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Journal Articles
- 2023
[j6]Yamei Tu
, Xiaoqi Wang, Rui Qiu, Han-Wei Shen, Michelle Miller, Jinmeng Rao, Song Gao, Patrick R. Huber, Allan Hollander, Matthew Lange, Christian Garcia, Joe Stubbs:
An Interactive Knowledge and Learning Environment in Smart Foodsheds. IEEE Computer Graphics and Applications 43(3): 36-47 (2023)- [j5]Joe Stubbs, Anagha Jamthe, Nathan Dean Freeman, Mike Packard, Gilbert Curbelo, Cody Hammock:
Scalable Scientific Interactive Research Computing With Project Scinco. Comput. Sci. Eng. 25(1): 43-50 (2023) - 2022
- [j4]Mohammed Eslami, Amin Espah Borujeni, Hamed Eramian, Mark Weston, George Zheng, Joshua Urrutia, Carolyn Corbet, Diveena Becker, Paul Maschhoff, Katie Clowers, Alexander Cristofaro, Hamid Doost Hosseini, D. Benjamin Gordon, Yuval Dorfan, Jedediah Singer, Matthew Vaughn, Niall Gaffney, John Fonner, Joe Stubbs, Christopher A. Voigt, Enoch Yeung:
Prediction of whole-cell transcriptional response with machine learning. Bioinform. 38(2): 404-409 (2022) - 2021
- [j3]Sean B. Cleveland, Anagha Jamthe, Smruti Padhy, Joe Stubbs, Steven Terry, Julia Looney, Richard Cardone, Michael Packard, Maytal Dahan, Gwen A. Jacobs:
Tapis v3 Streams API: Time-series and data-driven event support in science gateway infrastructure. Concurr. Comput. Pract. Exp. 33(19) (2021) - 2015
- [j2]Matthew R. Hanlon, Matthew Vaughn, Stephen A. Mock, Rion Dooley, Walter Moreira, Joe Stubbs, Christopher Town, Jason R. Miller, Vivek Krishnakumar, Erik S. Ferlanti, Eleanor Pence:
Araport: an application platform for data discovery. Concurr. Comput. Pract. Exp. 27(16): 4412-4422 (2015) - [j1]Vivek Krishnakumar, Matthew R. Hanlon, Sergio Contrino, Erik S. Ferlanti, Svetlana Karamycheva, Maria Kim, Benjamin D. Rosen, Chia-Yi Cheng, Walter Moreira, Stephen A. Mock, Joseph Stubbs, Julie M. Sullivan, Konstantinos Krampis, Jason R. Miller, Gos Micklem, Matthew Vaughn, Christopher D. Town:
Araport: the Arabidopsis Information Portal. Nucleic Acids Res. 43(Database-Issue): 1003-1009 (2015)
Conference and Workshop Papers
- 2024
- [c32]Joe Stubbs, Smruti Padhy, Richard Cardone, Steve Black:
CloudSec: An Extensible Automated Reasoning Framework for Cloud Security Policies. ACR 2024: 268-279 - [c31]Maytal Dahan, Joe Stubbs, Sandra Gesing:
Introduction to the Minitrack on Software Sustainability: Research on Usability, Maintainability, and Reproducibility Minitrack. HICSS 2024: 7675-7676 - [c30]Joe Stubbs, Dhanny Indrakusuma, Christian Garcia, François Halbach, Cody Hammock, Nathan Dean Freeman, Anagha Jamthe, Michael Packard, Alexander Fields, Gilbert Curbelo:
A Comprehensive Cloud Architecture for Machine Learning-enabled Research. PEARC 2024: 26:1-26:8 - [c29]Jeanette M. Sperhac, Sandra Gesing, Michael G. Zentner, Claire Stirm, Rob Quick, Joe Stubbs:
AI and Science Gateways: A Promising Combination for Accelerating Science and Research Computing. PEARC 2024: 56:1-56:4 - 2023
- [c28]Richard Cardone, Smruti Padhy, Steve Black, Joe Stubbs, Sean B. Cleveland:
A Decentralized Authorization and Security Framework for Distributed Research Workflows. COMPSAC 2023: 741-746 - [c27]Sandra Gesing, Maytal Dahan, Joe Stubbs:
Introduction to the Minitrack on Software Sustainability: Strategies for Long-Lasting and Usable Software. HICSS 2023: 6954-6955 - [c26]Nathan Dean Freeman, Joe Stubbs, Richard Cardone, Christian Garcia:
Detailed Functional Overview of an API and Workflow Engine for Scientific Research Computing. PEARC 2023: 10-17 - 2022
- [c25]Maytal Dahan, Sandra Gesing, Joe Stubbs:
Introduction to the Minitrack on Software Sustainability: Strategies for Long-Lasting and Usable Research Software. HICSS 2022: 1-2 - [c24]Richard Cardone, Joe Stubbs, Steve Black, Christian Garcia, Anagha Jamthe, Mike Packard, Smruti Padhy:
A Design Pattern for Recoverable Job Management. PEARC 2022: 29:1-29:4 - [c23]Nathan Dean Freeman, Joe Stubbs, Richard Cardone:
Workflow management for scientific research computing with Tapis Workflows: Architecture and Design Decisions behind Software for Research Computing Pipelines. PEARC 2022: 32:1-32:4 - [c22]Eric Lam, Sean B. Cleveland, Richard Cardone, Gwen A. Jacobs, Boyd Wilson, Cole McKnight, Joe Stubbs:
Extending Tapis Workflow Management Framework with Elastic Google Cloud Distributed System using CloudyCluster by Omnibond. PEARC 2022: 79:1 - 2021
- [c21]Maytal Dahan, Joe Stubbs, Sandra Gesing:
Introduction to the Minitrack on Software Survivability: Strategies for Long-Lasting and Usable Research Software. HICSS 2021: 1-2 - [c20]Joe Stubbs, Richard Cardone, Sean B. Cleveland, Gwen A. Jacobs, Michael Packard, Anagha Jamthe, Smruti Padhy, Steve Black, Steve Terry, Julia Looney, Joseph Meiring, Maytal Dahan:
Sustainability in the Tapis Framework. HICSS 2021: 1-10 - [c19]Smruti Padhy, Joe Stubbs:
Designing and Proving Properties of the Abaco Autoscaler Using TLA+. VSTTE 2021: 86-103 - [c18]Michael Packard, Joe Stubbs, Justin A. Drake, Christian Garcia:
Real-World, Self-Hosted Kubernetes Experience. PEARC 2021: 16:1-16:5 - [c17]Smruti Padhy, Anagha Jamthe, Sean B. Cleveland, Jack A. Smith, Joe Stubbs, Christian Garcia, Michael Packard, Steve Terry, Julia Looney, Richard Cardone, Maytal Dahan, Gwen A. Jacobs:
Building Tapis v3 Streams API Support for Real-Time Streaming Data Event-Driven Workflows. PEARC 2021: 17:1-17:8 - [c16]Joe Stubbs, Suresh Marru, Daniel Mejia, John-Paul Navarro, Eric Franz, Steve Black, Dimuthu Wannipurage, Sudhakar Pamidighantam, Claire Stirm, Maytal Dahan, Marlon E. Pierce, Michael G. Zentner:
Common Resource Descriptions for Interoperable Gateway Cyberinfrastructure. PEARC 2021: 20:1-20:9 - 2020
- [c15]Kate Keahey, Jason Anderson, Zhuo Zhen, Pierre Riteau, Paul Ruth, Dan Stanzione, Mert Cevik, Jacob Colleran, Haryadi S. Gunawi, Cody Hammock, Joe Mambretti, Alexander Barnes, François Halbach, Alex Rocha, Joe Stubbs:
Lessons Learned from the Chameleon Testbed. USENIX ATC 2020: 219-233 - [c14]Joe Stubbs, Gwen A. Jacobs, Maytal Dahan, Sean B. Cleveland, Anagha Jamthe, Steve Black, Richard Cardone, Smruti Padhy, Julia Looney, Joseph Meiring, Mike Packard, Steve Terry:
Tapis early adopter workshop. PEARC Companion 2020: 14:1 - [c13]Joe Stubbs, Julia Looney, Marjo Poindexter, Elias Chalhoub, Gregory J. Zynda, Erik S. Ferlanti, Matthew Vaughn, John M. Fonner, Maytal Dahan:
Integrating Jupyter into Research Computing Ecosystems: Challenges and Successes in Architecting JupyterHub for Collaborative Research Computing Ecosystems. PEARC 2020: 91-98 - [c12]Sean B. Cleveland, Anagha Jamthe, Smruti Padhy, Joe Stubbs, Michael Packard, Julia Looney, Steve Terry, Richard Cardone, Maytal Dahan, Gwen A. Jacobs:
Tapis API Development with Python: Best Practices In Scientific REST API Implementation: Experience implementing a distributed Stream API. PEARC 2020: 181-187 - [c11]Joe Stubbs, Suresh Marru, Daniel Mejia, Daniel S. Katz, Kyle Chard, Maytal Dahan, Marlon E. Pierce, Michael G. Zentner:
Toward Interoperable Cyberinfrastructure: Common Descriptions for Computational Resources and Applications. PEARC 2020: 522-525 - 2019
- [c10]Anagha Jamthe, Mike Packard, Joe Stubbs, Gilbert Curbelo, Roseline Shapi, Elias Chalhoub:
SSH-Backed API Performance Case Study. Bench 2019: 295-305 - [c9]Emre H. Brookes, Joe Stubbs:
GenApp, Containers and Abaco: Technical Paper. PEARC 2019: 12:1-12:8 - 2018
- [c8]Joe Stubbs, Matthew Vaughn, Julia Looney:
Rapid Development of Scalable, Distributed Computation with Abaco. IWSG 2018 - [c7]Sean B. Cleveland, Rion Dooley, David Perry, Joe Stubbs, John M. Fonner, Gwen A. Jacobs:
Building Science Gateway Infrastructure in the Middle of the Pacific and Beyond: Experiences using the Agave Deployer and Agave Platform to Build Science Gateways. PEARC 2018: 4:1-4:8 - [c6]W. Cyrus Proctor, Mike Packard, Anagha Jamthe, Richard Cardone, Joseph Stubbs:
Virtualizing the Stampede2 Supercomputer with Applications to HPC in the Cloud. PEARC 2018: 31:1-31:6 - 2016
- [c5]Joe Stubbs, Stephen Talley, Walter Moreira, Rion Dooley, Ann Stapleton:
Endofday: A Container Workflow Engine for Scalable, Reproducible Computation. IWSG 2016 - 2014
- [c4]Rion Dooley, Joe Stubbs, Jim Basney:
The MyProxy Gateway. IWSG 2014: 6-11 - [c3]Matthew R. Hanlon, Matthew Vaughn, Stephen A. Mock, Rion Dooley, Walter Moreira, Joe Stubbs, Christopher Town, Jason R. Miller, Vivek Krishnakumar, Erik S. Ferlanti, Eleanor Pence:
The arabidopsis information portal: an application platform for data discovery. GCE@SC 2014: 38-41 - [c2]Rion Dooley, Joe Stubbs:
Dynamically Provisioning Portable Gateway Infrastructure Using Docker and Agave. XSEDE 2014: 55:1-55:2 - [c1]Jim Basney, Jeff Gaynor, Suresh Marru, Marlon E. Pierce, Thejaka Amila Kanewala, Rion Dooley, Joe Stubbs:
Integrating Science Gateways with XSEDE Security: A Survey of Credential Management Approaches. XSEDE 2014: 58:1-58:2
Informal and Other Publications
- 2024
- [i6]Joe Stubbs, Smruti Padhy, Richard Cardone:
Toward Smart Scheduling in Tapis. CoRR abs/2408.03349 (2024) - 2023
- [i5]Richard Cardone, Smruti Padhy, Steve Black, Sean B. Cleveland, Joe Stubbs:
A Decentralized Authorization and Security Framework for Distributed Research Workflows. CoRR abs/2304.08557 (2023) - [i4]Sahil Samar, Mia Chen, Jack Karpinski, Michael Ray, Archita Sarin, Christian Garcia, Matthew Lange, Joe Stubbs, Mary P. Thomas:
Development of Authenticated Clients and Applications for ICICLE CI Services - Final Report for the REHS Program, June-August, 2022. CoRR abs/2304.11086 (2023) - [i3]Joe Stubbs, Smruti Padhy, Richard Cardone, Steve Black:
CloudSec: An Extensible Automated Reasoning Framework for Cloud Security Policies. CoRR abs/2307.05745 (2023) - 2021
- [i2]Joe Stubbs, Suresh Marru, Daniel Mejia, Daniel S. Katz, Kyle Chard, Maytal Dahan, Marlon E. Pierce, Michael G. Zentner:
Toward Interoperable Cyberinfrastructure: Common Descriptions for Computational Resources and Applications. CoRR abs/2107.00417 (2021) - 2018
- [i1]W. Cyrus Proctor, Mike Packard, Anagha Jamthe, Richard Cardone, Joseph Stubbs:
Virtualizing the Stampede2 Supercomputer with Applications to HPC in the Cloud. CoRR abs/1807.04616 (2018)
Coauthor Index
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