Papers & Projects

Projects

Users of our services are encouraged to cite Tapis, Abaco and Chameleon in publications that result from using TACC Cloud resources. Please use the following reference(s):

Tapis

Reference Paper: 1) Tapis: An API Platform for Reproducible, Distributed Computational Research.

Joe Stubbs, Richard Cardone, Mike Packard, Anagha Jamthe, Smruti Padhy, Steve Terry, Julia Looney, Joseph Meiring, Steve Black, Maytal Dahan, Sean Cleveland, Gwen Jacob

Advances in Intelligent Systems and Computing. 2021.

Book chapter; DOI: 10.1007/978-3-030-73100-7_61

Part of ISSN: 2194-5357

Part of ISSN: 2194-5365
Additional Papers: 2) Scalable Scientific Interactive Research Computing With Project Scinco.

J. Stubbs, A. Jamthe, N. Freeman, M. Packard, G. Curbelo and C. Hammock

Computing in Science & Engineering, vol. 25, no. 1, pp. 43-50, Jan.-Feb. 2023.

Journal article; DOI:10.1002/cpe.6103

3) A Decentralized Authorization and Security Framework for Distributed Research Workflows.

R Cardone, S Padhy, S Black, J Stubbs, S Cleveland.

2023 IEEE 47th Annual Computers, Software, and Applications Conference

Journal article; DOI: 10.1109/COMPSAC57700.2023.00102

4) An Interactive Knowledge and Learning Environment in Smart Foodsheds.

Yamei Tu, Xiaoqi Wang, Rui Qiu, Han-Wei Shen, Michelle Miller, Jinmeng Rao, Song Gao, Patrick R Huber, Allan D Hollander, Matthew Lange, Christian R Garcia, Joe Stubbs.

IEEE Computer Graphics and Applications 2023. IEEE.

Journal article; DOI: 10.1109/MCG.2023.3263960

5) Detailed Functional Overview of an API and Workflow Engine for Scientific Research Computing.

Freeman, Nathan Dean; Stubbs, Joe; Cardone, Richard; Garcia, Christian.

PEARC’23.ACM.

Journal article; DOI: 10.1145/3569951.3593609

6) Tapis Pods Service Exploration and Initial Performance Analysis.

Garcia, Christian; Stubbs, Joe; Cardone, Richard; Freeman, Nathan

Gateways 23.

Journal article; DOI:10.5281/zenodo.10034631

7) Machine Learning Hub for Tapis.

Indrakusuma, Dhanny, Freeman, Nathan, Stubbs, Joe.

Gateways 23.

Journal article; http://dx.doi.org/10.26153/tsw/48975 (poster)

8) Custom Cost, Loss, And Reward Functions to Train Regression Models for Estimating Execution Resources using HARP.

Vallabhajosyula, Manikya Swathi, Ramnath, Rajiv, Stubbs, Joe

Gateways 23.

Journal article; https://zenodo.org/records/10055657 (poster)

9) Extending Tapis Workflow Management Framework with Elastic Google Cloud Distributed System using CloudyCluster by Omnibond.

Lam, Eric; Cleveland, Sean; Cardone, Richard; Jacobs, Gwen A; Wilson, Boyd; Mcknight, Cole; Stubbs, Joe;

Practice and Experience in Advanced Research Computing, 1 page, 2022.

Journal article; https://doi.org/10.1145/3491418.3535158

10) Using Containers and Tapis to Structure Portable, Composable and Reproducible Climate Science Workflows.

Michael Dodge II, Sean Cleveland, Gwen A Jacobs

Practice and Experience in Advanced Research Computing, 2 Pages, 2022.

Journal article; https://doi.org/10.1145/3491418.3535126

11) Experience Migrating a Pipeline for the C-MĀIKI gateway from Tapis v2 to Tapis v3.

Yick Ching Wong, Sean B. Cleveland, Gwen A. Jacobs

Practice and Experience in Advanced Research Computing, 4 pages, 2022.

Journal article; https://doi.org/10.1145/3491418.3535139

12) A Design Pattern for Recoverable Job Management.

Cardone, Richard; Stubbs, Joe; Black, Steve; Garcia, Christian; Jamthe, Anagha; Packard, Michael; Padhy, Smruti

Practice and Experience in Advanced Research Computing, 4 pages, 2022.

Journal article; https://doi.org/10.1145/3491418.3535136

13) Workflow management for scientific research computing with Tapis Workflows: Architecture and Design Decisions behind Software for Research Computing Pipelines.

Freeman, Nathan Dean; Stubbs, Joe; Cardone, Richard

Practice and Experience in Advanced Research Computing, 4 pages, 2022.

Journal article; https://doi.org/10.1145/3491418.3535142

14) Round Trip: An Automated Pipeline for Experimental Design, Execution, and AnalysisClick to copy article link

Daniel Bryce, Robert P. Goldman, Matthew DeHaven, Jacob Beal, Bryan Bartley, Tramy T. Nguyen, Nicholas Walczak, Mark Weston, George Zheng, Josh Nowak, Peter Lee, Joe Stubbs, Niall Gaffney, Matthew W. Vaughn, Chris John Myers, Robert C. Moseley, Steven Haase, Anastasia Deckard, Bree Cummins, Nick Leiby

ACS Synthetic Biology Vol 11/Issue 2

Journal article; https://pubs.acs.org/doi/10.1021/acssynbio.1c00305

15) Tapis v3 Streams API: Time‐series and data‐driven event support in science gateway infrastructure.

Cleveland, Sean B; Jamthe, Anagha; Padhy, Smruti; Stubbs, Joe; Terry, Steven; Looney, Julia; Cardone, Richard; Packard, Michael; Dahan, Maytal; Jacobs, Gwen A

Concurrency and Computation: Practice and Experience. 2021-10-10.

Journal article; DOI: 10.1002/cpe.6103

Part of ISSN: 1532-0626

Part of ISSN: 1532-0634

16) Prediction of whole-cell transcriptional response with machine learning.

Eslami, Mohammed; Borujeni, Amin Espah; Eramian, Hamed; Weston, Mark; Zheng, George; Urrutia, Joshua; Corbet, Carolyn; Becker, Diveena; Maschhoff, Paul; Clowers, Katie

Bioinformatics. 2021-09-27

Journal article; DOI: 10.1093/bioinformatics/btab676

Part of ISSN: 1367-4803

Part of ISSN: 1460-2059

17) 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, and Gwen A. Jacobs

Practice and Experience in Advanced Research Computing. 2021-07-17.

Conference paper; DOI: 10.1145/3437359.3465567

18) Real-World, Self-Hosted Kubernetes Experience

Michael Packard, Joe Stubbs, Justin Drake, and Christian Garcia

Practice and Experience in Advanced Research Computing. 2021-07-17

Conference paper; DOI: 10.1145/3437359.3465603

19) Sustainability in the Tapis Framework.

J Stubbs, R Cardone, S Cleveland, G Jacobs, M Packard, A Jamthe, S Padhy, S Black, S Terry, J Looney, J Meiring, M Dahan

Proceedings of the 54th Hawaii International Conference on System Sciences. 2021

Conference paper; DOI: 10.24251/hicss.2021.874

20) Tapis API Development with Python: Best Practices In Scientific REST API Implementation.

Sean B. Cleveland, Anagha Jamthe, Smruti Padhy, Joe Stubbs, Michael Packard, Julia Looney, Steve Terry, Richard Cardone, Maytal Dahan, and Gwen A. Jacobs

Practice and Experience in Advanced Research Computing. 2020-07-26

Conference paper; DOI: 10.1145/3311790.3396647

21) Toward Interoperable Cyberinfrastructure: Common Descriptions for Computational Resources and Applications.

Joe Stubbs, Suresh Marru, Daniel Mejia, Daniel S. Katz, Kyle Chard, Maytal Dahan, Marlon Pierce, Michael Zentner

PEARC ‘20: Practice and Experience in Advanced Research Computing 2020: Catch the Wave

Conference paper; https://doi.org/10.1145/3311790.3400848

22) SSH-Backed API Performance Case Study.

Anagha J, Packard M, Stubbs J, Curbelo G, Shapi R, and Chalhoub E

Benchmarking, Measuring, and Optimizing. 2020.

Book chapter; DOI: 10.1007/978-3-030-49556-5_27

Part of ISSN: 0302-9743

Part of ISSN: 1611-3349

23) Scientific Data Annotation and Dissemination: Using the ‘Ike Wai Gateway to Manage Research Data.

Cleveland, Sean B and Geis, Jennifel Jacobs

Practice and Experience in Advanced Research Computing, 2020.

Conference paper; https://doi.org/10.1145/3311790.3396661

24) Streamed Data via Cloud-Hosted Real-Time Data Services for the Geosciences as an Ingestion Interface into the Planet Texas Science Gateway and Integrated Modeling Platform.

Powell J, Stubbs J, Cleveland S, Pierce S and Daniels M

Gateways 2019.

25) Tapis-CHORDS Integration: Time-Series Data Support in Science Gateway Infrastructure.

Cleveland S, Jamthe A, Padhy S, Stubbs J, Powell H, Daniels M, Pierce S, and Jacobs G

Gateways 2019.

Journal article; http://dx.doi.org/10.26153/tsw/11286

26) Building Science Gateway Infrastructure in the Middle of the Pacific and Beyond.

Proceedings of the Practice and Experience on Advanced Research Computing. 2018-07-22

Conference paper; DOI: 10.1145/3219104.3219151

27) Virtualizing the Stampede2 Supercomputer with Applications to HPC in the Cloud.

Proceedings of the Practice and Experience on Advanced Research Computing. 2018-07-22

Conference paper; DOI: 10.1145/3219104.3219131

28) Distributed Systems of Microservices Using Docker and Serfnode.

J. Stubbs, W. Moreira and R. Dooley

7th International Workshop on Science Gateways (IWSG). 2015-06.

Conference paper; DOI: 10.1109/iwsg.2015.16

Abaco

Reference Paper: 1) Rapid development of scalable, distributed computation with Abaco.

Proceedings of the 10th International Workshop on Science Gateways (2018).

Conference paper; http://ceur-ws.org/Vol-2357/paper3.pdf
Additional Papers: 2) Designing and Proving Properties of the Abaco Autoscaler Using TLA+

S. Smruti Padhy and Joe Stubbs

In the 13th Working Conference on Verified Software: Theories, Tools, and Experiments (VSTTE 21), October 18-19, 2021. Published in Springer Lecture Notes in Computer Science (LNCS) series, vol. 13124, February 22, 2022. Springer, Cham.

Journal article; https://doi.org/10.1007/978-3-030-95561-8_6

3) Tapis v3 Streams API: Time‐series and data‐driven event support in science gateway infrastructure.

Concurrency and Computation: Practice and Experience. 2021-10-10.

Journal-article; DOI: 10.1002/cpe.6103

Part of ISSN: 1532-0626

Part of ISSN: 1532-0634

4) Prediction of whole-cell transcriptional response with machine learning.

Bioinformatics. 2021-09-27

Journal article; DOI: 10.1093/bioinformatics/btab676

Part of ISSN: 1367-4803

Part of ISSN: 1460-2059

5) The Abaco Platform: A Performance and Scalability Study on the Jetstream Cloud.

Advances in Parallel & Distributed Processing, and Applications. 2021

Conference paper; DOI: 10.1007/978-3-030-69984-0_77 <DOI: 10.1007/978-3-030-69984-0_77>_

Part of ISBN: 978-3-030-69984-0

6) Enabling Science with Functions-as-a-Service: New Features and Usage of the Abaco Platform.

J. Stubbs, C. Garcia, J. Looney, A. Jamthe, M. Packard, M. Vaughn

Gateways 20, Oct 3, 2020. https://par.nsf.gov/servlets/purl/10314665

7) GenApp, containers and Abaco.

Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning). 2019-07-28.

Conference paper; DOI: 10.1145/3332186.3332191

Chameleon

Keahey, K., Riteau, P., Stanzione, D., Cockerill, T., Mambretti, J., Rad, P., Ruth, P. Chameleon: a Scalable Production Testbed for Computer Science Research, book chapter in “Contemporary High Performance Computing: From Petascale toward Exascale, Volume 3”, Jeffrey Vetter ed., 2018

JetStream

Stewart, C.A., Cockerill, T.M., Foster, I., Hancock, D., Merchant, N., Skidmore, E., Stanzione, D., Taylor, J., Tuecke, S., Turner, G., Vaughn, M., and Gaffney, N.I., Jetstream: a self-provisioned, scalable science and engineering cloud environment. 2015, In Proceedings of the 2015 XSEDE Conference: Scientific Advancements Enabled by Enhanced Cyberinfrastructure. St. Louis, Missouri. ACM: 2792774. p. 1-8. http://dx.doi.org/10.1145/2792745.2792774

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