ExaWorks Software Development Kit: A robust and scalable collection of interoperable workflows technologies
Matteo Turilli, Mihael Hategan-Marandiuc, Mikhail Titov, Ketan Maheshwari, Aymen Alsaadi, Andre Merzky, Ramon Arambula, Mikhail Zakharchanka, Matt Cowan, Justin M. Wozniak, Andreas Wilke, Ozgur Ozan Kilic, Kyle Chard, Rafael Ferreira da Silva, Shantenu Jha, and Daniel Laney.
Frontiers in HPC 2, 2024.

Diaspora: Resilience-enabling services for real-time distributed workflows
Bogdan Nicolae, Justin M. Wozniak, Tekin Bicer, Hai Nguyen, Parth Patel, Haochen Pan, Amal Gueroudji, Maxime Gonthier, Valerie Hayot-Sasson, Eliu Huerta, Kyle Chard, Ryan Chard, Matthieu Dorier, Nageswara S. V. Rao, Anees Al-Najjar, Alessandra Corsi, and Ian Foster.
Workshop on Near Real-Time Data Processing for Interconnected Scientific Instruments at eScience 2024.

Cross-HPO: Optimizing neural networks for cancer drug response using hyperparameter tuning on multiple pharmacogenomic datasets
Rajeev Jain, Justin M. Wozniak, Alexander Partin, Andreas Wilke, Yitan Zhu, Priyanka Vasanthakumari, Oleksandr Narykov, Jamie Overbeek, Rylie Weaver, Chen Wang, Yuanhang Liu, Ryan Weil, Thomas Brettin, and Rick Stevens.
Proc. SC Cancer Workshop 2024.

Drug response prediction post-evaluation via statistical standardization and distribution analysis
Jake Gwinn, Justin M. Wozniak, and Thomas Brettin.
Student Poster at SC Cancer Workshop 2024.

Tools for predicting and responding to anomalies in experiment data streams
Justin M. Wozniak, Nicholas Schwarz, Michael Prince, Tong Shu, and Bogdan Nicolae.
Proc. NOBUGS 2024.

Remote collaboration via distributed HDF file access
Justin M. Wozniak and Raymond Osborn.
NOBUGS Poster 2024. (Finalist, 3rd Place of 81.)

NXRefine: An automated workflow for single crystal x-ray diffuse scattering
Raymond Osborn, Matthew Krogstad, Stephan Rosenkranz, and Justin M. Wozniak.
Proc. NOBUGS 2024.

Distributed model exploration with EMEWS
Nicholson Collier, Justin M. Wozniak, Arindam Fadikar, Abby Stevens, and Jonathan Ozik.
Winter Simulation Conference 2024.

Tools for predicting and responding to anomalies in experiment data streams
Justin M. Wozniak.
Joint Lab Workshop 2024.

Organizer: Supercomputing for the drug response prediction community
Justin M. Wozniak and Thomas Brettin.
Minisymposium at PASC 2024.

Systematic evaluation and comparison of drug response prediction models: A case study of prediction generalization across cell lines datasets
Alexander Partin, Thomas S. Brettin, Yitan Zhu, Jamie Overbeek, Oleksandr Narykov, Priyanka Vasanthakumari, Austin Clyde, Sara E. Jones, Satishkumar Ganakammal Ranganathan, Justin M. Wozniak, Andreas Wilke, Jamaludin Mohd-Yusof, Michael R. Weil, Alexander T. Pearson, and Rick Stevens.
Cancer Research 83, 2023.
[DOI]

An automation framework for comparison of cancer response models across configurations
Justin M. Wozniak, Rajeev Jain, Andreas Wilke, Rylie Weaver, Alexander Partin, Thomas Brettin, and Rick Stevens.
Proc. eScience 2023.
[PDF] Slides: [PPTX]

PSI/J: A portable interface for submitting, monitoring, and managing jobs
Mihael Hategan-Marandiuc, Andre Merzky, Nicholson Collier, Ketan Maheshwari, Jonathan Ozik, Matteo Turilli, Andreas Wilke, Justin M. Wozniak, Kyle Chard, Ian Foster, Rafael Ferreira da Silva, Shantenu Jha, and Daniel Laney.
Proc. eScience 2023.
[PDF]

Developing distributed high-performance computing capabilities of an open science platform for robust epidemic analysis
Nicholson Collier, Justin M. Wozniak, Abby Stevens, Yadu Babuji, Mickael Binois, Arindam Fadikar, Alexandra Wurth, Kyle Chard, and Jonathan Ozik.
Proc. Workshop on Parallel and Distributed Processing for Computational Social Systems (ParSocial) 2023.
[PDF]

Systematic evaluation and comparison of drug response prediction models: A case study of prediction generalization across cell lines datasets
Alexander Partin, Thomas S. Brettin, Yitan Zhu, Jamie Overbeek, Oleksandr Narykov, Priyanka Vasanthakumari, Austin Clyde, Sara E. Jones, Satishkumar Ganakammal Ranganathan, Justin M. Wozniak, Andreas Wilke, Jamaludin Mohd-Yusof, Michael R. Weil, Alexander T. Pearson, and Rick Stevens.
Cancer Research 83, 2023.
[DOI]

A cross-study analysis of drug response prediction in cancer cell lines
Fangfang Xia, Jonathan E. Allen, Prasanna Balaprakash, Thomas S. Brettin, Cristina Garcia-Cardona, Austin Clyde, Judith D. Cohn, James H. Doroshow, Xiaotian Duan, Veronika Dubinkina, Yvonne A. Evrard, Ya Ju Fan, Jason Gans, Stewart He, Pinyi Lu, Sergei Maslov, Alexander Partin, Maulik Shukla, Eric A. Stahlberg, Justin M. Wozniak, Hyunseung Yoo, George F. Zaki, Yitan Zhu, and Rick Stevens.
Briefings Bioinform. 23(1), 2022.
[PDF] [DOI]

Tracking dubious data: Protecting scientific workflows from invalidated experiments
Jim Pruyne, Justin M. Wozniak, and Ian Foster.
Workshop on Reproducible Workflows, Data Management, and Security (ReWoRDS) 2022.
[PDF] Slides: [PPTX]

Data object distribution for experimental science pipelines
Justin M. Wozniak, Ray Osborn, and Jacob Ruff.
ASCR Workshop on the Management and Storage of Scientific Data 2022.
[PDF]

XD/ML Pipelines: Challenges in automated experimental science data processing
Justin M. Wozniak, Ryan Chard, Kyle Chard, Bogdan Nicolae, and Ian Foster.
ASCR Workshop on the Management and Storage of Scientific Data 2022.
[PDF]

Scaling diffuse scattering workflows with hybrid HPC workflows
Justin M. Wozniak, Ray Osborn, Matthew Krogstad, Guy Jennings, and Stephan Rosenkranz.
NOBUGS 2022.
[PDF]

Supporting a community of cancer models with the CANDLE checkpoint module
Rajeev Jain, Justin M. Wozniak, and Jamaludin Mohd-Yusof.
Cancer Workshop poster @ SC 2022.
[PDF]

Building infrastructure and methods for policy-relevant epidemiological modeling
Justin M. Wozniak, Jonathan Ozik, Nicholson Collier, Charles M. Macal, and Mickaël Binois.
JointLab 2022.

WfBench: Automated generation of scientific workflow benchmarks
Taina Coleman, Henri Casanova, Ketan Maheshwari, Loic Pottier, Sean Wilkinson, Justin M. Wozniak, Frederic Suter, Mallikarjun Shankar, and Rafael Ferreira da Silva.
Proc. Workshop on Performance Modeling, Benchmarking and Simulation of High Performance Computer System @ SC 2022.
[PDF]

Measuring the performance of generated workflow benchmarks at scale
Rafael Ferreira da Silva, Taina Coleman, Ketan Maheshwari, Loic Pottier, Sean Wilkinson, Justin M. Wozniak, Mallikarjun Shankar, and Henri Casanova.
Proc. ModSim 2022.

Large scale caching and streaming of training data for online deep learning
Jie Liu, Bogdan Nicolae, Dong Li, Justin M. Wozniak, Tekin Bicer, Zhengchun Liu, and Ian Foster.
Proc. FlexScience 2022.
[PDF]

LearnPack: Capturing learning patterns for science-oriented AI infrastructure
Justin M. Wozniak.
AI@DOE Roundtable 2021.
[PDF]

Software Monsters: Quantifying, reporting, and controlling composite applications
Justin M. Wozniak.
ASCR Workshop on the Science of Scientific-Software Development and Use 2021.
[PDF]

Bootstrapping in-situ workflow auto-tuning via combining performance models of component applications
Tong Shu, Yanfei Guo, Justin M. Wozniak, Xiaoning Ding, Ian Foster, and Tahsin Kurc.
Proc. SC 2021.
[PDF]

Probing decision boundaries in cancer data using noise injection and counterfactual analysis
Rajeev Jain, Ashka Shah, Jamaludin Mohd-Yusof, Justin M. Wozniak, Thomas Brettin, Fangfang Xia, and Rick Stevens.
Computational Approaches for Cancer Workshop @ SC 2021.
[PDF]

ExaWorks: Workflows for exascale
Aymen Al-Saadi, Dong H. Ahn, Yadu Babuji, Kyle Chard, James Corbett, Mihael Hategan, Stephen Herbein, Shantenu Jha, Daniel Laney, Andre Merzky, Todd Munson, Michael Salim, Mikhail Titov, Matteo Turilli, Thomas D. Uram, and Justin M. Wozniak.
Proc. WORKS @ SC 2021.
[PDF]

Braid-DB: Toward AI-driven science with machine learning provenance
Justin M. Wozniak, Zhengchun Liu, Rafael Vescovi, Ryan Chard, Bogdan Nicolae, and Ian Foster.
Proc. Smoky Mountains Conference 2021.
[PDF]

A population data-driven workflow for COVID-19 modeling and learning
Jonathan Ozik, Justin M. Wozniak, Nicholson Collier, Charles M. Macal, and Mickaël Binois.
International Journal of High Performance Computing Applications (Finalist for Gordon Bell COVID-19 Special Prize), 2021.
[PDF] [DOI]

Online data analysis and reduction: An important Co-design motif for extreme-scale computers
Ian Foster, Mark Ainsworth, Julie Bessac, Franck Cappello, Jong Choi, Sheng Di, Zichao Di, Ali M. Gok, Hanqi Guo, Kevin A. Huck, Christopher Kelly, Scott Klasky, Kerstin Kleese van Dam, Xin Liang, Kshitij Mehta, Manish Parashar, Tom Peterka, Line Pouchard, Tong Shu, Ozan Tugluk, Hubertus van Dam, Lipeng Wan, Matthew Wolf, Justin M. Wozniak, Wei Xu, Igor Yakushin, Shinjae Yoo, and Todd Munson.
The International Journal of High Performance Computing Applications, 2021.
[PDF] [DOI]

High-bypass learning: Automated detection of tumor cells that significantly impact drug response
Justin M. Wozniak, Hyunseung Yoo, Jamaludin Mohd-Yusof, Bogdan Nicolae, Nicholson Collier, Jonathan Ozik, Thomas Brettin, and Rick Stevens.
Proc. Machine Learning in High Performance Computing Environments (MLHPC) @ SC 2020.
[PDF] [DOI]

Training data error impacts on deep neural networks for classifying RNA-seq expressions
Rajeev Jain, Jamaludin Mohd-Yusof, Justin M. Wozniak, Thomas Brettin, and Rick Stevens.
Cancer Workshop @ SC 2020.
[PDF]

DeepFreeze: Towards scalable asynchronous checkpointing of deep learning models
Bogdan Nicolae, Jiali Li, Justin M. Wozniak, George Bosilca, Matthieu Dorier, and Franck Cappello.
Proc. CCGrid 2020.
[PDF] [DOI]

DeepClone: Lightweight state replication of deep learning models for data parallel training
Bogdan Nicolae, Justin M. Wozniak, Matthieu Dorier, and Franck Cappello.
Proc. Cluster 2020.
[PDF]

Reciprocal space imaging of ionic correlations in intercalation compounds
Matthew Krogstad, Stephan Rosenkranz, Justin M. Wozniak, Guy Jennings, Jacob Ruff, John Vaughey, and Raymond Osborn.
Nature Materials, 2019.
[PDF] [DOI]

Managing genomic variant calling workflows with Swift/T
Azza E. Ahmed, Jacob Heldenbrand, Yan Asmann, Faisal M. Fadlelmola, Daniel S. Katz, Katherine Kendig, Matthew C. Kendzior, Tiffany Li, Yingxue Ren, Elliott Rodriguez, Matthew R. Weber, Justin M. Wozniak, Jennie Zermeno, and Liudmila S. Mainzer.
PLOS ONE 14(7), 2019.
[PDF] [DOI]

Understanding scalability and fine-grain parallelism of synchronous data parallel training
Jiali Li, Bogdan Nicolae, Justin M. Wozniak, and George Bosilca.
Proc. Machine Learning in High Performance Computing Environments (MLHPC) @ SC 2019.
[PDF]

Accelerating deep learning adoption in biomedicine with the CANDLE framework
Justin M. Wozniak, Thomas Brettin, and Rick Stevens.
Proc. CompBioMed 2019.
[PDF]

MPI jobs within MPI jobs: A practical way of enabling task-level fault-tolerance in HPC workflows
Justin M. Wozniak, Matthieu Dorier, Robert Ross, Tong Shu, Tahsin Kurc, Li Tang, Norbert Podhorszki, and Matthew Wolf.
Future Generation Computing Systems 101, 2019.
[PDF] [DOI]

Parsl: Pervasive parallel programming in Python
Yadu Babuji, Anna Woodard, Zhuozhao Li, Ben Clifford, Rohan Kumar, Lukasz Lacinski, Ryan Chard, Justin M. Wozniak, Ian Foster, Michael Wilde, Daniel S. Katz, and Kyle Chard.
Proc. HPDC 2019.
[PDF]

Performance, energy, and scalability analysis and improvement of parallel cancer deep learning CANDLE benchmarks
Xingfu Wu, Valerie Taylor, Justin M. Wozniak, Rick Stevens, Thomas Brettin, and Fangfang Xia.
Proc. ICPP 2019.
[PDF]

CANDLE/Supervisor: A workflow framework for machine learning applied to cancer research
Justin M. Wozniak, Rajeev Jain, Prasanna Balaprakash, Jonathan Ozik, Nicholson Collier, John Bauer, Fangfang Xia, Thomas Brettin, Rick Stevens, Jamaludin Mohd-Yusof, Cristina Garcia Cardona, Brian Van Essen, and Matthew Baughman.
BMC Bioinformatics 19(18), 2018.
[PDF]

Scaling deep learning for cancer with advanced workflow storage integration
Justin M. Wozniak, Philip E. Davis, Tong Shu, Jonathan Ozik, Nicholson Collier, Manish Parashar, Ian Foster, Thomas Brettin, and Rick Stevens.
Proc. Machine Learning in High Performance Computing Environments (MLHPC) @ SC 2018.
[PDF]

Methodology for the rapid development of scalable HPC data services
Matthieu Dorier, Philip Carns, Kevin Harms, Robert Latham, Robert Ross, Shane Snyder, Justin M. Wozniak, Samuel K. Gutierrez, Bob Robey, Brad Settlemyer, Galen Shipman, Jerome Soumagne, James Kowalkowski, Marc Paterno, and Saba Sehrish.
Proc. PDSW-DISCS @ SC 2018.
[PDF]

Toward understanding I/O behavior in HPC workflows
Jakob Luttgau, Shane Snyder, Philip Carns, Justin M. Wozniak, Julian Kunkel, and Thomas Ludwig.
Proc. PDSW-DISCS @ SC 2018.
[PDF]

Portable and reusable deep learning infrastructure with containers to accelerate cancer studies
George F. Zaki, Justin M. Wozniak, Jonathan Ozik, Nicholson Collier, Thomas Brettin, and Rick Stevens.
Proc. ESPM @ SC 2018.
[PDF]

Performance, power, and scalability analysis of the Horovod implementation of the CANDLE NT3 Benchmark on the Cray XC40 Theta
Xingfu Wu, Valerie Taylor, Justin M. Wozniak, Rick Stevens, Thomas Brettin, and Fangfang Xia.
Proc. PyHPC @ SC 2018.
[PDF]

HEP Software Foundation Community White Paper Working Group – Data and software preservation to enable reuse.
M. D. Hildreth, A. Boehnlein, K. Cranmer, S. Dallmeier, R. Gardner, T. Hacker, L. Heinrich, I. Jimenez, M. Kane, D. S. Katz, T. Malik, C. Maltzahn, M. Neubauer, S. Neubert, J. Pivarski, E. Sexton, J. Shiers, T. Simko, S. Smith, D. South, A. Verbytskyi, G. Watts, and J. M. Wozniak.
arXiv e-prints, page arXiv:1810.01191 2018.

The relation of local order to material properties in relaxor ferroelectrics
Matthew J. Krogstad, Peter M. Gehring, Stephan Rosenkranz, Raymond Osborn, Feng Ye, Yaohua Liu, Jacob P. C. Ruff, W. Chen, Justin M. Wozniak, Haosu Luo, Omar Chmaissem, Zuo-Guang Ye, and Daniel Phelan.
Nature Materials 17, 2018.
[PDF] [DOI]

Extreme-scale dynamic exploration of a distributed agent-based model with the EMEWS framework
Jonathan Ozik, Nicholson T. Collier, Justin M. Wozniak, Charles Macal, and Gary An.
IEEE Transactions on Computational Social Systems 5(3), 2018.
[PDF]

Auxetic metamaterials from disordered networks
Daniel R. Reid, Nidhi Pashine, Justin M. Wozniak, Heinrich Jaeger, Andrea Liu, Sidney Nagel, and Juan de Pablo.
Proceedings of the National Academy of Sciences, 2018.
[DOI]

Parsl: Scalable parallel scripting in Python
Yadu Babuji, Kyle Chard, Ian Foster, Daniel S. Katz, Michael Wilde, Anna Woodard, and Justin M. Wozniak.
Proc. IWSG 2018.

Parsl: Enabling scalable interactive computing in Python
Kyle Chard, Yadu Nand, Ian Foster, Daniel S. Katz, Michael Wilde, Anna Woodard, and Justin M. Wozniak.
Proc. SciPy 2018.

Interactive, scalable, reproducible data analysis with containers, Jupyter, and Parsl
Yadu Babuji, Kyle Chard, Ian Foster, Daniel S. Katz, Michael Wilde, Anna Elizabeth Woodard, and Justin M. Wozniak.
Proc. CHEP 2018.

Predictive automated combustion chemistry: Massively parallel high-accuracy thermochemistry
Murat Keceli, Sarah N. Elliott, Yi-Pei Li, Matt Johnson, Carlo Cavallotti, Justin Wozniak, Yuri Georgievskii, Ahren Jasper, William Green, and Stephen Klippenstein.
Proc. APS March Meeting 2018.

Automated computational thermochemistry for butane oxidation: A prelude to predictive automated combustion kinetics
Murat Keceli, Sarah Elliott, Yi-Pei Li, Matthew S. Johnson, Carlo Cavallotti, Yuri Georgievskii, William H. Green, Matteo Pelucchi, Justin M. Wozniak, Ahren W. Jasper, and Stephen J. Klippenstein.
Proc. Combustion Institute 2018.

ECP Workflow Survey Report
Justin M. Wozniak. Technical report ANL-24/20. 2017.

Launching MPI applications inside MPI applications
Matthieu Dorier, Justin M. Wozniak, and Robert Ross.
Proc. WORKS @ SC 2017.
[PDF]

CANDLE/Supervisor: A workflow framework for machine learning applied to cancer research
Justin M. Wozniak, Rajeev Jain, Prasanna Balaprakash, Jonathan Ozik, Nicholson Collier, John Bauer, Fangfang Xia, Thomas Brettin, Rick Stevens, Jamaludin Mohd-Yusof, Cristina Garcia Cardona, Brian Van Essen, and Matthew Baughman.
Proc. Computational Approaches for Cancer @ SC 2017.
[PDF]

High-throughput cancer hypothesis testing with an integrated PhysiCell-EMEWS workflow
Jonathan Ozik, Nicholas Collier, Justin M. Wozniak, Charles Macal, Chase Cockrell, Samuel H. Friedman, Ahmadreza Ghaffarizadeh, Randy Heiland, Gary An, and Paul Macklin.
BMC Bioinformatics 19(483), 2018.
[PDF] [DOI]

Recent developments in single crystal diffuse scattering: Imaging nanoscale disorder in reciprocal space
Stephan Rosenkranz, Matthew Krogstad, Raymond Osborn, Peter Zapol, Justin M. Wozniak, Jacob Ruff, Feng Ye, and Yaohua Liu.
Proc. Crystallography 2017.

Computing just what you need: Online data analysis and reduction at extreme scales
Ian Foster, Mark Ainsworth, Bryce Allen, Julie Bessac, Franck Cappello, Jong Youl Choi, Emil Constantinescu, Philip E. Davis, Sheng Di, Wendy Di, Hanqi Guo, Scott Klasky, Kerstin Kleese van Dam, Tahsin Kurc, Qing Liu, Abid Malik, Kshitij Mehta, Klaus Mueller, Todd Munson, George Ostrouchov, Manish Parashar, Tom Peterka, Line Pouchard, Dingwen Tao, Ozan Tugluk, Stefan Wild, Matthew Wolf, Justin M. Wozniak, Wei Xu, and Shinjae Yoo.
Proc. EuroPar 2017.
[PDF]

High performance machine learning and evolutionary computing to develop personalized therapeutics
Chase Cockrell, Jonathan Ozik, Nick Collier, Justin Wozniak, and Gary An.
University of Chicago MindBytes Posters 2017. (Best poster, scalability and performance.)
Poster: [PDF]

Streaming supercomputing needs workflow-enabled programming-in-the-large
Justin M. Wozniak, Jonathan Ozik, Daniel S. Katz, and Michael Wilde.
Workshop on a Future Online Analysis Platform 2017.

The various contributions to the diffuse scattering from PMN-xPT
Daniel Phelan, Matthew Krogstad, Peter Gehring, Stephan Rosenkranz, Ray Osborn, Zuo-Guang Ye, Feng Ye, Yaohua Liu, Jacob Ruff, and Justin M. Wozniak.
Proc. American Crystallographic Association Annual Meeting 2017.

Experimental evaluation of a flexible I/O architecture for accelerating workflow engines in ultrascale environments
Francisco Rodrigo Duro, Javier Garcia Blas, Florin Isaila, Jesus Carretero, Justin M. Wozniak, and Robert Ross.
Parallel Computing 61, 2017.
[PDF] [DOI]

From desktop to large-scale model exploration with Swift/T
Jonathan Ozik, Nicholson Collier, and Justin M. Wozniak.
Proc. Winter Simulation Conference 2016.
[PDF]

High performance model exploration of mutation patterns in an agent-based model of colorectal cancer
Jonathan Ozik, Nicholson Collier, Justin M. Wozniak, Charles Macal, Chase Cockrell, Melinda Stack, and Gary An.
Computational Approaches for Cancer Workshop @ SC 2016. (Best paper.)
[PDF]

High performance calibration of a colorectal cancer natural history model with Incremental Mixture Importance Sampling
Jonathan Ozik, Nicholson Collier, Justin M. Wozniak, Carolyn Rutter, and Jessica Hwang.
Computational Approaches for Cancer Workshop at SC 2016.
[PDF]

On-demand infrastructure for data analytics and storage
Franck Cappello, Katrin Heitmann, Gabrielle Allen, William Gropp, Salman Habib, Ed Seidel, Brandon George, Brett Bode, Tim Boerner, Maxine D. Brown, Michelle Butler, Randal L. Butler, Kenton G. McHenry, Joe Insley, Athol J. Kemball, Rajkumar Kettimuthu, Ravi Madduri, Alex Parga, Silvio Rizzi, Roberto R. Sisneros, Corby B. Schmitz, Sean R. Stevens, Matthew J. Turk, Tom Uram, David Wheeler, Michael J. Wilde, and Justin M. Wozniak.
SC16 BOF Report 2016.

Challenges and opportunities for dataflow processing on exascale computers
Justin M. Wozniak, Michael Wilde, and Ian Foster.
Proc. Data-Flow Execution Models for Extreme-Scale Computing at PACT 2016.

Flexible data-aware scheduling for workflows over an in-memory object store
Francisco Rodrigo Duro, Javier Garcia Blas, Florin Isaila, Justin M. Wozniak, Jesus Carretero, and Robert Ross.
Proc. CCGrid 2016.

High performance workflows for experiment-in-the-loop computing
Justin M. Wozniak and Robert Ross.
S2I2 HEP/CS Workshop @ NCSA/UIUC Poster Session 2016.

Big data remote access interfaces for light source science
Justin M. Wozniak, Kyle Chard, Ben Blaiszik, Ray Osborn, Michael Wilde, and Ian Foster.
Proc. Big Data Computing 2015.
[PDF]

Modeling diffuse scattering using first-principles based methods
Anh Ngo, Justin M. Wozniak, Jonathan Morris, Stephan Rosenkranz, Raymond Osborn, and Peter Zapol.
Proc. Materials Research Society Fall Meeting 2015.
Abstract: [TXT]

Integrating big data tools for X-ray science
Justin M. Wozniak.
Talk at Joint Laboratory for Extreme-Scale Computing Workshop 2015.
Abstract: [TXT]

Many resident task computing in support of dynamic ensemble computations
Jonathan Ozik, Nicholson Collier, and Justin M. Wozniak.
Proc. MTAGS at SC 2015.
[PDF]

Lessons learned from building in situ coupling frameworks
Matthieu Dorier, Matthieu Dreher, Tom Peterka, Justin M. Wozniak, Gabriel Antoniu, and Bruno Raffin.
Proc. In Situ Infrastructures for Enabling Extreme-scale Analysis and Visualization @ SC 2015.
[PDF]

Interlanguage parallel scripting for distributed-memory scientific computing
Justin M. Wozniak, Timothy G. Armstrong, Ketan C. Maheshwari, Daniel S. Katz, Michael Wilde, and Ian T. Foster.
Proc. WORKS @ SC 2015.
[PDF]

Swift: Extreme-scale, implicitly parallel scripting
Timothy G. Armstrong, Justin M. Wozniak, Michael Wilde, and Ian T. Foster.
In: Programming Models for Parallel Computing, 2015.
[PDF]

Swift: Parallel scripting for simulation ensembles
Justin M. Wozniak.
ExMatEx all-hands meeting 2015.

Streaming, storing, and sharing big data for light source science
Justin M. Wozniak, Kyle Chard, Ben Blaiszik, Michael Wilde, and Ian Foster.
Proc. STREAM 2015.
[PDF] Slides: [PPTX]

Accelerating the experimental feedback loop: Data streams at the APS
Ian Foster, Tekin Bicer, Raj Kettimuthu, Michael Wilde, Justin M. Wozniak, Francesco de Carlo, Ben Blaiszik, Kyle Chard, and Ray Osborn.
Proc. STREAM 2015.
[PDF]

Big data tools for light source science
Justin M. Wozniak.
Talk at Cornell High Energy Synchrotron Source 2015.
Slides: [PPTX]

Swift/T: Dataflow composition of Tcl scripts for petascale computing
Justin M. Wozniak, Timothy G. Armstrong, Michael Wilde, and Ian Foster.
Proc. Annual Tcl/Tk Conference 2015.
[PDF] Slides: [PPTX]

Porting ordinary applications to Blue Gene/Q supercomputers
Ketan Maheshwari, Justin Wozniak, Timothy Armstrong, Daniel S. Katz, T. Andrew Binkowski, Xiaoliang Zhong, Olle Heinonen, Dmitry Karpeyev, and Michael Wilde.
Proc. eScience 2015.
[PDF]

Single crystal diffuse scattering: Beyond the workflow
Ray Osborn et al.
APS Users Meeting 2015.
Slides: [PPTX]

Toward interlanguage parallel scripting for distributed-memory scientific computing
Justin M. Wozniak, Timothy G. Armstrong, Ketan C. Maheshwari, Daniel S. Katz, Michael Wilde, and Ian T. Foster.
Proc. CLUSTER 2015.
[PDF] [DOI]

Swift parallel scripting for fast, productive beamline data analysis
Hemant Sharma, Justin M. Wozniak, Jun Park, Guy Jennings, Ian Foster, Jonathan Almer, Raymond Osborn, and Michael Wilde.
APS Users Meeting 2015.

Globus data publication services and their application at the Advanced Photon Source
Ben Blaiszik, Kyle Chard, Rachana Ananthakrishnan, Jim Pruyne, Justin M. Wozniak, Michael Wilde, Raymond Osborn, Steve Tuecke, and Ian Foster.
APS Users Meeting 2015.

Implicitly parallel functional dataflow for DOE science workflows
Daniel S. Katz, Michael Wilde, and Justin M. Wozniak.
Proc. Workshop on the Future of Scientific Workflows 2015.
[PDF]

Workflows at experimental facilities: Use cases from the Advanced Photon Source
Ian Foster, Tekin Bicer, Raj Kettimuthu, Michael Wilde, Justin M. Wozniak, Francesco de Carlo, Ben Blaiszik, Kyle Chard, Francesco de Carlo, and Ray Osborn.
Proc. Workshop on the Future of Scientific Workflows 2015.
[PDF]

Big data staging with MPI-IO for interactive X-ray science
Justin M. Wozniak, Hemant Sharma, Timothy G. Armstrong, Michael Wilde, Jonathan D. Almer, and Ian Foster.
Proc. Big Data Computing 2014.
[PDF] Slides: [PDF]

Exploiting data locality in Swift/T workflows using Hercules
Francisco Rodrigo Duro, Javier Garcia Blas, Florin Isaila, Jesus Carretero, Justin M. Wozniak, and Robert Ross.
Proc. NESUS Workshop 2014.
[PDF]

Case studies in dataflow composition of scalable high performance applications
Justin M. Wozniak, Timothy G. Armstrong, Daniel S. Katz, Michael Wilde, and Ian T. Foster.
Proc. Extreme-scale Programming Tools at SC 2014.

Petascale Tcl with NAMD, VMD, and Swift/T
James C. Phillips, John E. Stone, Kirby L. Vandivort, Timothy G. Armstrong, Justin M. Wozniak, Michael Wilde, and Klaus Schulten.
Proc. High Performance Technical Computing in Dynamic Languages at SC 2014.
[PDF]

Language features for scalable distributed-memory dataflow computing
Justin M. Wozniak, Michael Wilde, and Ian T. Foster.
Proc. Data-Flow Execution Models for Extreme-Scale Computing at PACT 2014.
[PDF]

The assembly and management of scalable computational experiments
Justin M. Wozniak.
Computation Institute Fellow Nomination Talk 2014.
[PDF]

Networking materials data: Accelerating discovery at an experimental facility
Ian Foster, Rachana Ananthakrishnan, Ben Blaiszik, Kyle Chard, Ray Osborn, Steve Tuecke, Michael Wilde, and Justin M. Wozniak.
Proc. Workshop on High Performance Computing, Grids and Clouds 2014.

Compiler techniques for massively scalable implicit task parallelism
Timothy G. Armstrong, Justin M. Wozniak, Michael Wilde, and Ian T. Foster.
Proc. SC 2014.
[PDF]

Design and evaluation of the GeMTC framework for GPU-enabled many task computing
Scott J. Krieder, Justin M. Wozniak, Timothy G. Armstrong, Michael Wilde, Daniel S. Katz, Benjamin Grimmer, Ian T. Foster, and Ioan Raicu.
Proc. HPDC 2014.
[PDF]

Evaluating storage systems for scientific data in the cloud
Ketan Maheshwari, Justin M. Wozniak, Hao Yang, Daniel S. Katz, Matei Ripeanu, Victor Zavala, and Michael Wilde.
Proc. ScienceCloud 2014. (Best paper.)
[PDF]

Implicitly-parallel functional dataflow for productive cloud programming on Chameleon
Scott Krieder, Ioan Raicu, Justin M. Wozniak, and Michael Wilde.
Proc. NSFCloud Workshop on Experimental Support for Cloud Computing 2014.

Toward computational experiment management via multi-language applications
Justin M. Wozniak, Timothy G. Armstrong, Daniel S. Katz, Michael Wilde, and Ian T. Foster.
DOE Workshop on Software Productivity for eXtreme scale Science (SWP4XS) 2014.
[PDF]

Productive composition of extreme-scale applications using implicitly parallel dataflow
Michael Wilde, Justin M. Wozniak, Timothy G. Armstrong, Daniel S. Katz, and Ian T. Foster.
DOE Workshop on Software Productivity for eXtreme scale Science (SWP4XS) 2014.
[PDF]

Parallel scripting for beamline science: Connecting Big Data and HPC
Justin M. Wozniak.
At BES Facilities Computing Working Group Technical Meeting 2014.

Turbine: A distributed-memory dataflow engine for high performance many-task applications
Justin M. Wozniak, Timothy G. Armstrong, Ketan Maheshwari, Ewing L. Lusk, Daniel S. Katz, Michael Wilde, and Ian T. Foster.
Fundamenta Informaticae 28(3), 2013.
[PDF]

JETS: Language and system support for many-parallel-task workflows
Justin M. Wozniak, Michael Wilde, and Daniel S. Katz.
J. Grid Computing 11(3), 2013.
[PDF] [DOI]

Extending the Galaxy portal with parallel and distributed execution capability
Ketan Maheshwari, Alex Rodriguez, David Kelly, Ravi Madduri, Justin M. Wozniak, Michael Wilde, and Ian T. Foster.
Proc. DataCloud 2013.
[PDF]

Dataflow coordination of data-parallel tasks via MPI 3.0
Justin M. Wozniak, Tom Peterka, Timothy G. Armstrong, James Dinan, Ewing L. Lusk, Michael Wilde, and Ian T. Foster.
Proc. EuroMPI 2013.
[PDF]

MTC Envelope: Defining the capability of large scale computers in the context of parallel scripting applications
Zhao Zhang, Daniel S. Katz, Justin M. Wozniak, Michael Wilde, and Ian T. Foster.
Proc. HPDC 2013.
[PDF]

Parallelizing the execution of sequential scripts
Zhao Zhang, Daniel S. Katz, Timothy G. Armstrong, Justin M. Wozniak, and Ian T. Foster.
Proc. SC 2013.
[PDF]

Reusability in science: From initial user engagement to dissemination of results
Ketan Maheshwari, David Kelly, Scott J. Krieder, Justin M. Wozniak, Daniel S. Katz, Zhi-Gang Mei, and Mainak Mookherjee.
Proc. Workshop on Sustainable Software for Science: Practice and Experiences at SC 2013.
[PDF]

Swift/T: Scalable data flow programming for distributed-memory task-parallel applications
Justin M. Wozniak, Timothy G. Armstrong, Michael Wilde, Daniel S. Katz, Ewing Lusk, and Ian T. Foster.
Proc. CCGrid 2013.
[PDF]

Evaluating cloud computing techniques for smart power grid design using parallel scripting
Ketan Maheshwari, Ken Birman, Justin M. Wozniak, and Devin Van Zandt.
Proc. CCGrid 2013.
[PDF]

A model for tracing and debugging large-scale task-parallel programs with MPE
Justin M. Wozniak, Anthony Chan, Timothy G. Armstrong, Michael Wilde, Ewing Lusk, and Ian T. Foster.
Proc. Workshop on Leveraging Abstractions and Semantics in High-performance Computing (LASH-C) at PPoPP 2013.
[PDF]

Rapid development of highly concurrent multi-scale simulators with Swift
Justin M. Wozniak.
ExMatEx all-hands meeting 2013.
Slides: [PDF]

Swift+Chirp for synchrotron beamline data analysis
Justin M. Wozniak.
At Cooperative Computing Laboratory Workshop 2013.

Swift: A scientist's gateway to clusters, clouds, grids and supercomputers
Justin M. Wozniak.
Annual Meeting of the Organization for Human Brain Mapping 2013.

Design and analysis of data management in scalable parallel scripting
Zhao Zhang, Daniel S. Katz, Justin M. Wozniak, Allan Espinosa, and Ian Foster.
Proc. SC 2012.
[PDF]

Aesop: Expressing concurrency in high-performance system software
Dries Kimpe, Philip Carns, Kevin Harms, Justin M. Wozniak, Samuel Lang, and Robert Ross.
Proc. Conference on Networking, Architecture, and Storage 2012.
[PDF]

Turbine: A distributed-memory dataflow engine for extreme-scale many-task applications
Justin M. Wozniak, Timothy G. Armstrong, Michael Wilde, Ketan Maheshwari, Daniel S. Katz, Matei Ripeanu, Ewing L. Lusk, and Ian T. Foster.
Proc. Workshop on Scalable Workflow Enactment Engines and Technologies 2012.
[PDF] Slides: [PDF]

A case for optimistic coordination in HPC storage systems
Philip Carns, Kevin Harms, Dries Kimpe, Justin M. Wozniak, Robert Ross, Lee Ward, Matthew Curry, Ruth Klundt, Geoff Danielson, Cengiz Karakoyunlu, John Chandy, Bradley Settlemyer, and William Gropp.
Proc. Petascale Data Storage Workshop (PDSW) at SC 2012.
[PDF] Slides: [PDF]

ExM: High level dataflow programming for extreme-scale systems
Timothy G. Armstrong, Justin M. Wozniak, Michael Wilde, Ketan Maheshwari, Daniel S. Katz, Matei Ripeanu, Ewing L. Lusk, and Ian T. Foster.
HotPar (poster series) 2012.
[PDF] Poster: [PDF]

Swift/T: Scalable dataflow programming for composite applications
Justin M. Wozniak.
Invited talk at LANS informal seminar 2012.

GEMS: User control for cooperative scientific repositories
Justin M. Wozniak, Paul Brenner, Santanu Chatterjee, Douglas Thain, Aaron Striegel, and Jesus A. Izaguirre.
In: Computational and Data Grids: Principles, Designs, and Applications, 2011.
[PDF]

Swift: A language for distributed parallel scripting
Michael Wilde, Mihael Hategan, Justin M. Wozniak, Ben Clifford, Daniel S. Katz, and Ian Foster.
Parallel Computing 37(9), 2011.
[PDF] [DOI]

Coasters: Uniform resource provisioning and access for scientific computing on clouds and grids
Mihael Hategan, Justin M. Wozniak, and Ketan Maheshwari.
Proc. Utility and Cloud Computing 2011.
[PDF] Slides: [PDF]

Accelerating climate data analysis and visualization with parallel scripting
Sheri Mickelson, Robert Jacob, Michael Wilde, Justin M. Wozniak, and John Dennis.
Proc. American Geophysical Union Fall Meeting 2011.

JETS: Language and system support for many parallel task computing
Justin M. Wozniak and Michael Wilde.
Proc. Workshop on Parallel Programming Models and Systems Software for High-End Computing (P2S2) at ICPP 2011.
[PDF] Slides: [PDF]

Flexible cloud computing through Swift coasters
Ketan Maheshwari, Justin M. Wozniak, Allan Espinosa, Daniel Katz, and Michael Wilde.
Proc. Cloud Computing and its Applications 2011.

Enabling scripted high-performance computing
Justin M. Wozniak.
At Computation Institute Data Lunch 2011.

Distributed object storage rebuild analysis via simulation with GOBS
Justin M. Wozniak, Seung Woo Son, and Ross, Robert.
Proc. Workshop on Fault Tolerance in Extreme Scale Systems 2010.
[PDF] Slides: [PDF] Slides: [PPTX]

Many task computing and Blue Waters
Daniel S. Katz, Timothy G. Armstrong, Zhao Zhang, Michael Wilde, and Justin M. Wozniak.
2010.

C-MPI: A DHT implementation for Grid and HPC environments
Justin M. Wozniak, Bryan Jacobs, Robert Latham, Samuel Lang, Seung Woo Son, and Robert Ross. Technical report ANL/MCS-P1746-0410. 2010.
[PDF]

Future directions in large-scale storage systems
Justin M. Wozniak.
At CUCIS, Northwestern University 2010.

Investigating deadline-driven metascheduling policy via simulation with East
Justin M. Wozniak and Aaron Striegel.
In: Quantitative Quality of Service for Grid Computing: Applications for Heterogeneity, Large-Scale Distribution and Dynamic Environments, 2009.
[PDF]

Case studies in storage access by loosely coupled petascale applications
Justin M. Wozniak and Michael Wilde.
Proc. Petascale Data Storage Workshop at SC 2009.
[PDF] Slides: [PDF] Slides: [PPTX]

Biomolecular committor probability calculation enabled by processing in network storage
Paul Brenner, Justin M. Wozniak, Douglas Thain, Aaron Striegel, Jeff W. Peng, and Jesus A. Izaguirre.
Parallel Computing 34(11), 2008.
[PDF] [DOI]

Making the best of a bad situation: Prioritized storage management in GEMS
Justin M. Wozniak, Paul Brenner, Douglas Thain, Aaron Striegel, and Jesus A. Izaguirre.
Future Generation Computer Systems 24(1), 2008.
[PDF] [DOI]

Pathways into large parameter search spaces: Experiences with molecular hyperdynamics
Justin M. Wozniak, Santanu Chatterjee, Paul Brenner, Douglas Thain, Aaron Striegel, Jeff Peng, and Jesus A. Izaguirre.
Proc. UK e-Science All Hands Meeting 2008.
[PDF] Slides: [PDF]

Overdrive controllers for distributed scientific computation
Justin M. Wozniak. Ph.D. dissertation, University of Notre Dame. 2008.
[PDF]

Overdrive controllers for distributed scientific computation
Justin M. Wozniak.
Proc. TCSC Doctoral Symposium 2007.
[PDF] Slides: [PDF]

Effects of low-quality computation time estimates in policed schedulers
Justin M. Wozniak, Yingxin Jiang, and Aaron Striegel.
Proc. Annual Simulation Symposium 2007.
[PDF] Slides: [PDF]

Biomolecular path sampling enabled by processing in network storage
Paul Brenner, Justin M. Wozniak, Douglas Thain, Aaron Striegel, Jeff W. Peng, and Jesus A. Izaguirre.
Proc. Workshop on High Performance Computational Biology 2007.
[PDF]

Access control for a replica management database
Justin M. Wozniak, Paul Brenner, Douglas Thain, Aaron Striegel, and Jesus A. Izaguirre.
Proc. Workshop on Storage Security and Survivability 2006.
[PDF] Slides: [PDF]

Applying feedback control to a replica management system
Justin M. Wozniak, Paul Brenner, Douglas Thain, Aaron Striegel, and Jesus A. Izaguirre.
Proc. Southeastern Symposium on System Theory 2006.
[PDF]

Separating abstractions from resources in a tactical storage system
Douglas Thain, Sander Klous, Justin Wozniak, Paul Brenner, Aaron Striegel, and Jesus Izaguirre.
Proc. Supercomputing 2005.
[PDF]

Generosity and gluttony in GEMS: Grid-Enabled Molecular Simulation
Justin M. Wozniak, Paul Brenner, Douglas Thain, Aaron Striegel, and Jesus A. Izaguirre.
Proc. High Performance Distributed Computing 2005.
[PDF]

GIPSE: Streamlining the management of simulation on the grid
Justin M. Wozniak, Aaron Striegel, David Salyers, and Jesus A. Izaguirre.
Proc. Annual Simulation Symposium 2005.
[PDF]

Message passing in Maple
Justin M. Wozniak. Technical report CS-2004-02. 2004.
[PDF]

Control system theory in Maple
Justin M. Wozniak. Masters thesis, University of Waterloo. 2003.
[PDF]