The MyProxy Gateway. - Rion Dooley; Joe Stubbs; Jim Basney (IWSG, 2014)

The arabidopsis information portal: an application platform for data discovery. - Matthew R. Hanlon; Matthew Vaughn; Stephen A. Mock; Rion Dooley; Walter Moreira; Joe Stubbs; Christopher Town 002; Jason R. Miller; Vivek Krishnakumar; Erik S. Ferlanti; Eleanor Pence (GCE@SC, 2014)

Integrating Science Gateways with XSEDE Security: A Survey of Credential Management Approaches. - Jim Basney; Jeff Gaynor; Suresh Marru; Marlon E. Pierce; Thejaka Amila Kanewala; Rion Dooley; Joe Stubbs (XSEDE, 2014)

Dynamically Provisioning Portable Gateway Infrastructure Using Docker and Agave. - Rion Dooley; Joe Stubbs (XSEDE, 2014)

Araport: an application platform for data discovery. - Matthew R. Hanlon; Matthew Vaughn; Stephen A. Mock; Rion Dooley; Walter Moreira; Joe Stubbs; Christopher Town 002; Jason R. Miller; Vivek Krishnakumar; Erik S. Ferlanti; Eleanor Pence (Concurr. Comput. Pract. Exp., 2015)

Araport: the Arabidopsis Information Portal. - 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; et al. (Nucleic Acids Res., 2015)

Endofday: A Container Workflow Engine for Scalable, Reproducible Computation. - Joe Stubbs; Stephen Talley; Walter Moreira; Rion Dooley; Ann Stapleton (IWSG, 2016)

Rapid Development of Scalable, Distributed Computation with Abaco. - Joe Stubbs; Matthew Vaughn; Julia Looney (IWSG, 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. - Sean B. Cleveland; Rion Dooley; David Perry; Joe Stubbs; John M. Fonner; Gwen A. Jacobs (PEARC, 2018)

Virtualizing the Stampede2 Supercomputer with Applications to HPC in the Cloud. - W. Cyrus Proctor; Mike Packard; Anagha Jamthe; Richard Cardone; Joseph Stubbs (PEARC, 2018)

SSH-Backed API Performance Case Study. - Anagha Jamthe; Mike Packard; Joe Stubbs; Gilbert Curbelo; Roseline Shapi; Elias Chalhoub (Bench, 2019)

GenApp, Containers and Abaco: Technical Paper. - Emre H. Brookes; Joe Stubbs (PEARC, 2019)

Lessons Learned from the Chameleon Testbed. - 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; et al. (USENIX ATC, 2020)

Tapis API Development with Python: Best Practices In Scientific REST API Implementation: Experience implementing a distributed Stream API. - Sean B. Cleveland; Anagha Jamthe; Smruti Padhy; Joe Stubbs; Michael Packard; Julia Looney; Steve Terry; Richard Cardone; Maytal Dahan; Gwen A. Jacobs (PEARC, 2020)

Tapis early adopter workshop. - 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 (PEARC Companion, 2020)

Integrating Jupyter into Research Computing Ecosystems: Challenges and Successes in Architecting JupyterHub for Collaborative Research Computing Ecosystems. - Joe Stubbs; Julia Looney; Marjo Poindexter; Elias Chalhoub; Gregory J. Zynda; Erik S. Ferlanti; Matthew Vaughn; John M. Fonner; Maytal Dahan (PEARC, 2020)

Toward Interoperable Cyberinfrastructure: Common Descriptions for Computational Resources and Applications. - Joe Stubbs; Suresh Marru; Daniel Mejia 003; Daniel S. Katz; Kyle Chard; Maytal Dahan; Marlon E. Pierce; Michael G. Zentner (PEARC, 2020)

Introduction to the Minitrack on Software Survivability: Strategies for Long-Lasting and Usable Research Software. - Maytal Dahan; Joe Stubbs; Sandra Gesing (HICSS, 2021)

Sustainability in the Tapis Framework. - 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 (HICSS, 2021)

Designing and Proving Properties of the Abaco Autoscaler Using TLA+. - Smruti Padhy; Joe Stubbs (VSTTE, 2021)

Real-World, Self-Hosted Kubernetes Experience. - Michael Packard; Joe Stubbs; Justin A. Drake; Christian Garcia (PEARC, 2021)

Building Tapis v3 Streams API Support for Real-Time Streaming Data Event-Driven Workflows. - 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 (PEARC, 2021)

Common Resource Descriptions for Interoperable Gateway Cyberinfrastructure. - Joe Stubbs; Suresh Marru; Daniel Mejia 003; John-Paul Navarro; Eric Franz; Steve Black; Dimuthu Wannipurage; Sudhakar Pamidighantam; Claire Stirm; Maytal Dahan; Marlon E. Pierce; Michael G. Zentner (PEARC, 2021)

Tapis v3 Streams API: Time-series and data-driven event support in science gateway infrastructure. - Sean B. Cleveland; Anagha Jamthe; Smruti Padhy; Joe Stubbs; Steven Terry; Julia Looney; Richard Cardone; Michael Packard; Maytal Dahan; Gwen A. Jacobs (Concurr. Comput. Pract. Exp., 2021)

Introduction to the Minitrack on Software Sustainability: Strategies for Long-Lasting and Usable Research Software. - Maytal Dahan; Sandra Gesing; Joe Stubbs (HICSS, 2022)

A Design Pattern for Recoverable Job Management. - Richard Cardone; Joe Stubbs; Steve Black; Christian Garcia; Anagha Jamthe; Mike Packard; Smruti Padhy (PEARC, 2022)

Workflow management for scientific research computing with Tapis Workflows: Architecture and Design Decisions behind Software for Research Computing Pipelines. - Nathan Dean Freeman; Joe Stubbs; Richard Cardone (PEARC, 2022)

Extending Tapis Workflow Management Framework with Elastic Google Cloud Distributed System using CloudyCluster by Omnibond. - Eric Lam; Sean B. Cleveland; Richard Cardone; Gwen A. Jacobs; Boyd Wilson; Cole McKnight; Joe Stubbs (PEARC, 2022)

Prediction of whole-cell transcriptional response with machine learning. - 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; et al. (Bioinform., 2022)

A Decentralized Authorization and Security Framework for Distributed Research Workflows. - Richard Cardone; Smruti Padhy; Steve Black; Joe Stubbs; Sean B. Cleveland (COMPSAC, 2023)

Introduction to the Minitrack on Software Sustainability: Strategies for Long-Lasting and Usable Software. - Sandra Gesing; Maytal Dahan; Joe Stubbs (HICSS, 2023)

Detailed Functional Overview of an API and Workflow Engine for Scientific Research Computing. - Nathan Dean Freeman; Joe Stubbs; Richard Cardone; Christian Garcia (PEARC, 2023)

An Interactive Knowledge and Learning Environment in Smart Foodsheds. - Yamei Tu; Xiaoqi Wang; Rui Qiu; Han-Wei Shen; Michelle Miller 006; Jinmeng Rao; Song Gao 001; Patrick R. Huber; Allan Hollander; Matthew Lange; Christian Garcia; Joe Stubbs (IEEE Computer Graphics and Applications, 2023)

Development of Authenticated Clients and Applications for ICICLE CI Services - Final Report for the REHS Program, June-August, 2022. - Sahil Samar; Mia Chen; Jack Karpinski; Michael Ray; Archita Sarin; Christian Garcia; Matthew Lange; Joe Stubbs; Mary P. Thomas (CoRR, 2023)

Scalable Scientific Interactive Research Computing With Project Scinco. - Joe Stubbs; Anagha Jamthe; Nathan Dean Freeman; Mike Packard; Gilbert Curbelo; Cody Hammock (Comput. Sci. Eng., 2023)

CloudSec: An Extensible Automated Reasoning Framework for Cloud Security Policies. - Joe Stubbs; Smruti Padhy; Richard Cardone; Steve Black (ACR, 2024)

Toward Smart Scheduling in Tapis. - Joe Stubbs; Smruti Padhy; Richard Cardone (IEEE Big Data, 2024)

Introduction to the Minitrack on Software Sustainability: Research on Usability, Maintainability, and Reproducibility Minitrack. - Maytal Dahan; Joe Stubbs; Sandra Gesing (HICSS, 2024)

AI and Science Gateways: A Promising Combination for Accelerating Science and Research Computing. - Jeanette M. Sperhac; Sandra Gesing; Michael G. Zentner; Claire Stirm; Rob Quick; Joe Stubbs (PEARC, 2024)

A Comprehensive Cloud Architecture for Machine Learning-enabled Research. - Joe Stubbs; Dhanny Indrakusuma; Christian Garcia; François Halbach; Cody Hammock; Nathan Dean Freeman; Anagha Jamthe; Michael Packard; Alexander Fields; Gilbert Curbelo (PEARC, 2024)