John M. Fonner

According to our database, John M. Fonner authored at least 19 papers between 2014 and 2025.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2025

Ten simple rules for building and maintaining sustainable high-performance computing infrastructure for research in resource-limited settings.

Ronald Galiwango, Christopher J. Whalen, Grace Kebirungi, Mugume T. Atwine, Rodgers Kimera, Alfred Ssekagiri, Timothy W. Kimbowa, Edward Lukyamuzi, Mike Nsubuga, Lloyd Ssentongo, Henry Mutegeki, John M. Fonner, Frank Wuerthwein, Ari Berman, Laura B. Okalebo, Meghan Coakley McCarthy, Victor S. Kramer, Mariam Quiñones, Phillip Cruz, Darrell E. Hurt, Maria Y. Giovanni, Nicola J. Mulder, Michael Tartakovsky, Jonathan K. Kayondo, Daudi Jjingo

PLoS Comput. Biol., 2025

A Model for Teaching Machine Learning, Deep Learning, and Research Computing to Domain Scientists on HPC Resources.

William J. Allen, Kelsey M. Beavers, Erik S. Ferlanti, Lorenzo Concia, Joshua Urrutia, Ernesto A. B. F. Lima, John M. Fonner, Felix Zuo, H. E. Duplechin Seymour, Ari B. Kahn, Joe Stubbs, Anagha Jamthe, Stephanie N. Baker, Tabish Khan, James P. Carson

Proceedings of the SC '25 Workshops of the International Conference for High Performance Computing, 2025

2024

CyVerse: Cyberinfrastructure for open science.

Tyson L. Swetnam, Parker B. Antin, Ryan Bartelme, Alexander Bucksch, David Camhy, Greg Chism, Illyoung Choi, Amanda M. Cooksey, Michele Cosi, Cindy Cowen, Michael Culshaw-Maurer, Robert Davey, Sean Davey, Upendra Devisetty, Tony Edgin, Andy Edmonds, Dmitry V. Fedorov, Jeremy Frady, John M. Fonner, Jeffrey K. Gillan, Iqbal Hossain, Blake Joyce, Konrad Lang, Tina Lee, Shelley Littin, Ian McEwen, Nirav C. Merchant, David Micklos, Andrew Nelson, Ashley Ramsey, Sarah Roberts, Paul Sarando, Edwin Skidmore, Jawon Song, Mary Margaret Sprinkle, Sriram Srinivasan, Dan Stanzione, Jonathan D. Strootman, Sarah Stryeck, Reetu Tuteja, Matthew Vaughn, Mojib Wali, Mariah Wall, Ramona Walls, Liya Wang, Todd Wickizer, Jason Williams, John Wregglesworth, Eric Lyons

PLoS Comput. Biol., February, 2024

Human-powered AI Gym: Lessons Learned as the Test and Evaluation Team for the DARPA SHADE Program: Human-powered AI Gym.

Justin Drake, Niall Gaffney, Nathan Dean Freeman, Erik S. Ferlanti, John M. Fonner

Proceedings of the Practice and Experience in Advanced Research Computing 2024: Human Powered Computing, 2024

2023

Scalable and Reproducible Virtual Screening through an API-Integrated Workflow.

Tiffany Huff, Austin Darrow, Joshua Medina, Erik S. Ferlanti, James D. Carson, John M. Fonner, Sal Tijerina, Stanley J. Watowich, William J. Allen

Proceedings of the Practice and Experience in Advanced Research Computing, 2023

Perspectives and Experiences Supporting Containers for Research Computing at the Texas Advanced Computing Center.

Erik S. Ferlanti, William J. Allen, Ernesto A. B. F. Lima, Yinzhi Wang, John M. Fonner

Proceedings of the SC '23 Workshops of The International Conference on High Performance Computing, 2023

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, D. Benjamin Gordon, Yuval Dorfan, Jedediah Singer, Matthew Vaughn, Niall Gaffney, John M. Fonner, Joe Stubbs, Christopher A. Voigt, Enoch Yeung

Bioinform., 2022

2021

Characterizing Containerized HPC Applications Performance at Petascale on CPU and GPU Architectures.

Amit Ruhela, Stephen Lien Harrell, Richard Todd Evans, Gregory J. Zynda, John M. Fonner, Matt Vaughn, Tommy Minyard, John Cazes

Proceedings of the High Performance Computing - 36th International Conference, 2021

RollingGantryCrane: Automation for unpacking containers into HPC environments.

Gregory J. Zynda, Shweta Gopaulakrishnan, John M. Fonner

Proceedings of the 3rd International Workshop on Containers and New Orchestration Paradigms for Isolated Environments in HPC, 2021

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

Proceedings of the PEARC '20: Practice and Experience in Advanced Research Computing, 2020

2018

The Agave Platform: An Open, Science-as-a-Service Platform for Digital Science.

Rion Dooley, Steven R. Brandt, John M. Fonner

Proceedings of the Practice and Experience on Advanced Research Computing, 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

Proceedings of the Practice and Experience on Advanced Research Computing, 2018

2017

Launcher: A simple tool for executing high throughput computing workloads.

Lucas A. Wilson, John M. Fonner, Jason Allison, Oscar Esteban, Harry Kenya, Marshall Lerner

J. Open Source Softw., 2017

VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data.

Scott Christley, Mikhail K. Levin, Inimary T. Toby, John M. Fonner, Nancy Monson, William Rounds, Florian Rubelt, Walter Scarborough, Richard H. Scheuermann, Lindsay G. Cowell

BMC Bioinform., 2017

2016

VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements.

Inimary T. Toby, Mikhail K. Levin, Edward Salinas, Scott Christley, Sanchita Bhattacharya, Felix Breden, Adam Buntzman, Brian Corrie, John M. Fonner, Namita T. Gupta, Uri Hershberg, Nishanth Marthandan, Aaron M. Rosenfeld, William Rounds, Florian Rubelt, Walter Scarborough, Jamie K. Scott, Mohamed Uduman, Jason A. Vander Heiden, Richard H. Scheuermann, Nancy Monson, Steven H. Kleinstein, Lindsay G. Cowell

BMC Bioinform., 2016

2014

Identification of a Novel Inhibitor of Dengue Virus Protease through Use of a Virtual Screening Drug Discovery Web Portal.

Usha Viswanathan, Suzanne M. Tomlinson, John M. Fonner, Stephen A. Mock, Stanley J. Watowich

J. Chem. Inf. Model., 2014

Leveraging the national cyberinfrastructure for biomedical research.

Richard D. LeDuc, Matthew Vaughn, John M. Fonner, Michael Sullivan, James G. Williams, Philip D. Blood, James Taylor, William K. Barnett

J. Am. Medical Informatics Assoc., 2014

Launcher: A Shell-based Framework for Rapid Development of Parallel Parametric Studies.

Lucas A. Wilson, John M. Fonner

Proceedings of the Annual Conference of the Extreme Science and Engineering Discovery Environment, 2014

The Texas Advanced Computing Center: A complete scientific discovery environment for biomedical informatics and health science research.

Matthew C. Cowperthwaite, James D. Carson, John M. Fonner, Oscar Jiao, Jawon Song, Matthew W. Vaughn

Proceedings of the AMIA 2014, 2014