CCL Research Publications

Journal Articles

Tim Shaffer, Thanh Son Phung, Kyle Chard, and Douglas Thain, LANDLORD: Coordinating Dynamic Software Environments to Reduce Container Sprawl, IEEE Transactions on Parallel and Distributed Systems, 34(5), pages 1376-1389, May, 2023. DOI: 10.1109/TPDS.2023.3241598

Peter Ivie and Douglas Thain, Reproducibility in Scientific Computing, ACM Computing Surveys, 51(3), July, 2018. DOI: 10.1145/3186266

Benjamin Tovar, Rafael Ferreira da Silva, Gideon Juve, Ewa Deelman, William Allcock, Douglas Thain, and Miron Livny, A Job Sizing Strategy for High-Throughput Scientific Workflows, IEEE Transactions on Parallel and Distributed Systems, 29(2), pages 240-253, February, 2018. DOI: 10.1109/TPDS.2017.2762310

Nicholas Hazekamp, Nathaniel Kremer-Herman, Benjamin Tovar, Haiyan Meng, Olivia Choudhury, Scott Emrich, and Douglas Thain, Combining Static and Dynamic Storage Management for Data Intensive Scientific Workflows, IEEE Transactions on Parallel and Distributed Systems, 29(2), pages 338-350, February, 2018. DOI: 10.1109/TPDS.2017.2764897

James Sweet, David Richter, and Douglas Thain, GPU acceleration of Eulerian–Lagrangian particle-laden turbulent flow simulations, International Journal of Multiphase Flow, 99, pages 437-435, January, 2018. DOI: 10.1016/j.ijmultiphaseflow.2017.11.010

Dinesh Rajan and Douglas Thain, Designing Self-Tuning Split-Map-Merge Applications for High Cost-Efficiency in the Cloud, IEEE Transactions on Cloud Computing, 5(2), pages 303-316, April, 2017. DOI: 10.1109/TCC.2015.2415780

Haipeng Cai, Raul Santelices, and Douglas Thain, DIAPRO: Unifying Dynamic Impact Analyses for Improved and Variable Cost-Effectiveness, ACM Transactions on Software Engineering and Methodology, 25(2), May, 2016. DOI: 10.1145/2894751

Patrick Donnelly and Douglas Thain, Balancing push and pull in Confuga, an active storage cluster file system for scientific workflows, Concurrency and Computation: Practice and Experience, 29(4), May, 2016. DOI: 10.1002/cpe.3834

Jakob Blomer, Predrag Buncic, Rene Meusel, Gerardo Ganis, Igor Sfiligoi and Douglas Thain, The Evolution of Global Scale Filesystems for Scientific Software Distribution, IEEE/AIP Computing in Science and Engineering, 17(6), pages 61-71, December, 2015. DOI: 10.1109/MCSE.2015.111

Peter Sempolinski, Daniel Wei, Ahsan Kareem, and Douglas Thain, Adapting Collaborative Software Development Techniques to Structural Engineering, IEEE/AIP Computing in Science and Engineering, 17(51), pages 27-34, September, 2015. DOI: 10.1109/MCSE.2015.88

Matthew Staffelbach, Peter Sempolinski, Tracy Kijewski-Correa, Douglas Thain, Daniel Wei, Ahsan Kareem, Gregory Madey, Lessons Learned from Crowdsourcing Complex Engineering Tasks, PLOS One, 10(9), September, 2015. DOI: 10.1371/journal.pone.0134978

Haiyan Meng, Rupa Kommineni, Quan Pham, Robert Gardner, Tanu Malik and Douglas Thain, An Invariant Framework for Conducting Reproducible Computational Science, Journal of Computational Science, 9, pages 137-142, July, 2015. DOI: 10.1016/j.jocs.2015.04.012

Badi Abdul-Wahid, Haoyun Feng, Dinesh Rajan, Ronan Costaouec, Eric Darve, Douglas Thain, and Jesus A. Izaguirre, AWE-WQ: Fast-Forwarding Molecular Dynamics using the Accelerated Weighted Ensemble, Journal of Chemical Information and Modeling, 54(10), pages 3033-3043, September, 2014. DOI: 10.1021/ci500321g

Andrew Thrasher, Zachary Musgrave, Brian Kachmark, Douglas Thain, and Scott Emrich, Scaling Up Genome Annotation with MAKER and Work Queue, International Journal of Bioinformatics Research and Applications, 10(4-5), pages 447-460, June, 2014. DOI: 10.1504/IJBRA.2014.062994

Christopher Moretti, Andrew Thrasher, Li Yu, Michael Olson, Scott Emrich, and Douglas Thain, A Framework for Scalable Genome Assembly on Clusters, Clouds, and Grids, IEEE Transactions on Parallel and Distributed Systems, 23(12), December, 2012. DOI: 10.1109/TPDS.2012.80

Hoang Bui, Peter Bui, Patrick Flynn and Douglas Thain, ROARS: A Robust Object Archival System for Data Intensive Scientific Computing, Distributed and Parallel Databases, 30(5-6), Springer, August, 2012. DOI: 10.1007/s10619-012-7103-5

Rory Carmichael, Patrick Braga-Henebry, Douglas Thain, and Scott Emrich, Biocompute 2.0: An Improved Collaborative Workspace for Data Intensive Bio-Science., Concurrency and Computation: Practice and Experience, 23(17), pages 2305-2314, December, 2011. DOI: 10.1002/cpe.1782

Peter Bui, Li Yu, Andrew Thrasher, Rory Carmichael, Irena Lanc, Patrick Donnelly, Douglas Thain, Scripting distributed scientific workflows using Weaver, Concurrency and Computation: Practice and Experience, 24(15), November, 2011. DOI: 10.1002/cpe.1871

Li Yu, Christopher Moretti, Andrew Thrasher, Scott Emrich, Kenneth Judd, and Douglas Thain, Harnessing Parallelism in Multicore Clusters with the All-Pairs, Wavefront, and Makeflow Abstractions, Journal of Cluster Computing, 13(3), pages 243-256, September, 2010. DOI: 10.1007/s10586-010-0134-7

Christopher Moretti, Hoang Bui, Karen Hollingsworth, Brandon Rich, Patrick Flynn, and Douglas Thain, All-Pairs: An Abstraction for Data Intensive Computing on Campus Grids, IEEE Transactions on Parallel and Distributed Systems, 21(1), pages 33-46, January, 2010. DOI: 10.1109/TPDS.2009.49

Kyle Wheeler and Douglas Thain, Visualizing Massively Multithreaded Applications with ThreadScope, Concurrency and Computation: Practice and Experience, 22(1), pages 45-67, January, 2010. DOI: 10.1002/cpe.1469

Andrew Blaich, Douglas Thain, and Aaron Striegel, Reflections on the Virtues of Modularity: A Case Study in Linux Security Modules, Software: Practice and Experience, 39(15), pages 1235-1251, October, 2009. DOI: 10.1002/spe.933

Hoang Bui, Michael Kelly, Christopher Lyon, Mark Pasquier, Deborah Thomas, Patrick Flynn, and Douglas Thain, Experience with BXGrid: A Data Repository and Computing Grid for Biometrics Research, Journal of Cluster Computing, 12(4), pages 373, April, 2009. DOI: 10.1007/s10586-009-0098-7

Douglas Thain, Christopher Moretti, and Jeffrey Hemmes, Chirp: A Practical Global Filesystem for Cluster and Grid Computing, Journal of Grid Computing, 7(1), pages 51-72, March, 2009. DOI: 10.1007/s10723-008-9100-5

Paul Brenner, Justin Wozniak, Douglas Thain Aaron Striegel, Jeffrey Peng, and Jesus Izaguirre, Biomolecular Committor Probability Calculation Enabled by Processing in Network Storage, Journal of Parallel Computing, 34(11), pages 652-660, November, 2008. DOI: 10.1016/j.parco.2008.08.001

Justin Wozniak, Paul Brenner, Douglas Thain, Aaron Striegel, and Jesus Izaguirre, Making the Best of a Bad Situation: Prioritized Storage Management in GEMS, Future Generation Computing Systems, 24(1), pages 10-16, January, 2008. DOI: 10.1016/j.future.2007.04.003

Douglas Thain and Miron Livny, How to Measure a Large Open Source Distributed System, Concurrency and Computation: Practice and Experience, 18(15), pages 1989-2019, December, 2006. DOI: 10.1002/cpe.v18:15

Sander Klous, Jamie Frey, Se-Chang Son, Douglas Thain, Alain Roy, Miron Livny, and Jo van den Brand, Transparent Access to Grid Resources for User Software, Concurrency and Computation: Practice and Experience, 18(7), pages 787-801, June, 2006. DOI: 10.1002/cpe.961

Stefano Belforte, Matthew Normal, Subir Sarkar, Ifor Sfiligoi, Douglas Thain, Frank Wuerthwein, Using Condor Glide-Ins and Parrot to Move from Dedicated Resources to the Grid, Lecture Notes in Informatics, 81, pages 285-292, March, 2006.

Douglas Thain and Miron Livny, Parrot: An Application Environment for Data-Intensive Computing, Scalable Computing: Practice and Experience, 6(3), pages 9-18, September, 2005.

Douglas Thain, Todd Tannenbaum, and Miron Livny, Distributed Computing in Practice: The Condor Experience, Concurrency and Computation: Practice and Experience, 17(2-4), pages 323-356, February, 2005. DOI: 10.1002/cpe.v17:2/4

Douglas Thain and Miron Livny, Multiple Bypass: Interposition Agents for Distributed Computing, Journal of Cluster Computing, 4(1), pages 39-47, March, 2001. DOI: 10.1023/A:1011412209850

Refereed Conference Papers

Thanh Son Phung, Colin Thomas, Logan Ward, Kyle Chard, Douglas Thain, Accelerating Function-Centric Applications by Discovering, Distributing, and Retaining Reusable Context in Workflow Systems, ACM International Symposium on High-Performance Parallel and Distributed Computing (HPDC), June, 2024. DOI: 10.1145/3625549.3658663

Thanh Son Phung and Douglas Thain, Adaptive Task-Oriented Resource Allocation for Large Dynamic Workflows on Opportunistic Resources, IEEE International Parallel and Distributed Processing Symposium (IPDPS), pages 12, May, 2024.

Thanh Son Phung, Ben Clifford, Kyle Chard, Douglas Thain, Maximizing Data Utility for HPC Python Workflow Execution, SC23 Workshop: High Performance Python for Science at Scale (HPPSS), November, 2023. DOI: 10.1145/3624062.3624136

Barry Sly-Delgado, Thanh Son Phung, Colin Thomas, David Simonetti, Andrew Hennessee, Ben Tovar, Douglas Thain, TaskVine: Managing In-Cluster Storage for High-Throughput Data Intensive Workflows, 18th Workshop on Workflows in Support of Large-Scale Science, November, 2023. DOI: 10.1145/3624062.3624277

Ben Lyons and Douglas Thain, Poster: Robust Meta-Workflow Management with Mufasa, IEEE International Conference on eScience, October, 2022.

Ben Tovar, Ben Lyons, Kelci Mohrman, Barry Sly-Delgado, Kevin Lannon, and Douglas Thain, Dynamic Task Shaping for High Throughput Data Analysis Applications in High Energy Physics, IEEE International Parallel and Distributed Processing Symposium, June, 2022. DOI: 10.1109/IPDPS53621.2022.00041

Barry Sly-Delgado, Nick Locascio, David Simonetti, Brett Wiseman, Ben Tovar, Douglas Thain, PONCHO: Dynamic Package Synthesis for Distributed and Serverless Python Applications, Workshop on High Performance Serverless Computing, June, 2022. DOI: 10.1145/3526060.3535459

Kevin Lannon, Paul Brenner, Michael Hildreth, Kenya Hurtado Anampa, Alan Malta, Rodrigues, Kelci Mohrman, Douglas Thain, and Ben Tovar, Analysis Cyberinfrastructure: Challenges and Opportunities, Snowmass, pages 1-14, March, 2022.

Sanda Gesing, Ewa Deelman, Rafael Ferreira da Silva, Michael Hildreth, Mary Ann McDowell, Natalie K. Meyers, and Douglas Thain, VisDict: A Visual Dictionary in a Science Gateway, Gateways, January, 2022.

Thanh Son Phung, Logan Ward, Kyle Chard, and Douglas Thain, Not All Tasks Are Created Equal: Adaptive Resource Allocation for Heterogeneous Tasks in Dynamic Workflows, WORKS Workshop on Workflows at Supercomputing, November, 2021.

Kevin Gao, Tim Shaffer, and Kyle Chard, Regulating Traffic in Crowded Cache, Student Poster Session at Supercomputing, November, 2021.

Tim Shaffer, Kyle Chard, and Douglas Thain, An Empirical Study of Package Dependencies and Lifetimes in Binder Python Containers, IEEE International Conference on e-Science, September, 2021.

Tim Shaffer, Zhuozhao Li, Ben Tovar, Yadu Babuji, TJ Dasso, Zoe Surma, Kyle Chard, Ian Foster, and Douglas Thain, Lightweight Function Monitors for Fine-Grained Management in Large Scale Python Applications, IEEE International Parallel and Distributed Processing Symposium, May, 2021. DOI: 10.1109/IPDPS49936.2021.00088

Benjamin Tovar, Brian Bockelman, Michael Hildreth, Kevin Lannon, and Douglas Thain, Harnessing HPC resources for CMS jobs using a Virtual Private Network, 25th International Conference on Computing in High Energy and Nuclear Physics (CHEP), May, 2021. DOI: 10.1051/epjconf/202125102032

R. F. da Silva et al., A Community Roadmap for Scientific Workflows Research and Development, IEEE Workshop on Workflows in Support of Large-Scale Science (WORKS), pages 81-90, January, 2021. DOI: 10.1109/WORKS54523.2021.00016

Chao Zheng, Nathaniel Kremer-Herman, Tim Shaffer, and Douglas Thain, Autoscaling High Throughput Workloads on Container Orchestrators , IEEE Conference on Cluster Computing, pages 1-10, September, 2020. DOI: 10.1109/CLUSTER49012.2020.00024

Nathaniel Kremer-Herman and Douglas Thain, Log Discovery for Troubleshooting Open Distributed Systems with TLQ, Practice and Experience of Advanced Research Computing (PEARC), July, 2020. DOI: 10.1145/3311790.3396633

Tim Shaffer, Nicholas Hazekamp, Jakob Blomer, and Douglas Thain, Solving the Container Explosion Problem for Distributed High Throughput Computing, International Parallel and Distributed Processing Symposium, May, 2020. DOI: 10.1109/IPDPS47924.2020.00048

Nick Hazekamp, Ben Tovar, and Douglas Thain, Dynamic Sizing of Continuously Divisible Jobs for Heterogeneous Resources, IEEE International Conference on e-Science, September, 2019. DOI: 10.1109/eScience.2019.00026

Tim Shaffer, Nathaniel Kremer-Herman, and Douglas Thain, Flexible Partitioning of Scientific Workflows Using the JX Workflow Language, Practice and Experience in Advanced Research Computing (PEARC), July, 2019. DOI: 10.1145/3332186.3338100

Nathaniel Kremer-Herman, Benjamin Tovar, and Douglas Thain, A Lightweight Model for Right-Sizing Master-Worker Applications, ACM/IEEE Supercomputing (SC), November, 2018. DOI: 10.1109/SC.2018.00042

Qimin Zhang, Ben Tovar, Nate Kremer-Herman, and Douglas Thain, Reduction of Workflow Resource Consumption Using a Density-based Clustering Model, WORKS Workshop at Supercomputing, November, 2018.

Nicholas Hazekamp and Douglas Thain, An Algebra for Robust Workflow Transformations, IEEE International Conference on e-Science, pages 12, October, 2018. DOI: 10.1109/eScience.2018.00031

Tim Shaffer, Kyle M.D. Sweeney, Nathaniel Kremer-Herman, and Douglas Thain, Poster: A First Look at the JX Workflow Language, IEEE International Conference on e-Science, October, 2018. DOI: 10.1109/eScience.2018.00094

Chao Zheng, Lukas Rupprecht, Vasily Tarasov, Douglas Thain, Mohamed Mohamed, Dimitrios Skourtis, Amit S. Warke and Dean Hildrebarnd, Wharf: Sharing Docker Images in a Distributed File System, ACM Symposium on Cloud Computing, pages 12, October, 2018. DOI: 10.1145/3267809.3267836

Lincoln Bryant, Jeremy Van, Benedikt Riedel, Robert Gardner, Jose Caballero, John Hover, Ben Tovar, and Douglas Thain, VC3: A Virtual Cluster Service for Community Computation, PEARC: Practice and Experience in Advanced Research Computing, pages 1-8, July, 2018. DOI: 10.1145/3219104.3219125

Kyle Sweeney and Douglas Thain, Early Experience Using Amazon Batch for Scientific Workflows, ScienceCloud Workshop at HPDC , June, 2018. DOI: 10.1145/3217880.3217885

Kyle Sweeney and Douglas Thain, Efficient Integration of Containers into Scientific Workflows, Science Cloud Workshop at HPDC, June, 2018. DOI: 10.1145/3217880.3217887

Benjamin Tovar, Nicholas Hazekamp, Nathaniel Kremer-Herman, and Douglas Thain, Automatic Dependency Management for Scientific Applications on Clusters, IEEE International Conference on Cloud Engineering (IC2E) , April, 2018. DOI: 10.1109/IC2E.2018.00026

Nicholas Hazekamp, Upendra Kumar Devisetty, Nirav Merchant, and Douglas Thain, MAKER as a Service: Moving HPC applications to Jetstream Cloud, IEEE International Conference on Cloud Engineering, pages 6, April, 2018. DOI: 10.1109/IC2E.2018.00029

Jeffrey Kinnison, Nathaniel Kremer-Herman, Douglas Thain, Walter Scheirer, SHADHO: Massively Scalable Hardware-Aware Distributed Hyperparameter Optimization, IEEE Winter Conference on Applications of Computer Vision, pages 1-10, March, 2018. DOI: 10.1109/WACV.2018.00086

Chao Zheng, Lukas Rupprecht, Vasily Tarasov, Mohamed Mohamed, Dimitrios Skourtis, Amit S. Warke, Dean Hildebrand, Douglas Thain, Poster: Wharf: Sharing Docker Images across Hosts from a Distributed Filesystem, IEEE International Conference for High Performance Computing, Networking, Storage and Analysis, November, 2017.

Tim Shaffer and Douglas Thain, Taming Metadata Storms in Parallel Filesystems with MetaFS, Workshop on Parallel Data Storage and Data Intensive Scalable Computing Systems, pages 25-30, November, 2017. DOI: 10.1145/3149393.3149401

Haiyan Meng and Douglas Thain, Facilitating the Reproducibility of Scientific Workflows with Execution Environment Specifications, The 17th International Conference on Computational Science (ICCS), June, 2017. DOI: 10.1016/j.procs.2017.05.116

Daniel (Yue) Zhang, Charles (Chao) Zheng, Dong Wang, Doug Thain, Chao Huang, Xin Mu, Greg Madey, Towards Scalable and Dynamic Social Sensing Using A Distributed Computing Framework, The 37th IEEE International Conference on Distributed Computing Systems (ICDCS 2017), June, 2017. DOI: 10.1109/ICDCS.2017.196

Charles (Chao) Zheng, Ben Tovar and Douglas Thain, Deploying High Throughput Scientific Workflows on Container Schedulers with Makeflow and Mesos, 17th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid 2017), May, 2017. DOI: 10.1109/CCGRID.2017.9

Peter Ivie and Douglas Thain, PRUNE: A Preserving Run Environment for Reproducible Computing, IEEE Conference on e-Science, October, 2016. DOI: 10.1109/eScience.2016.7870886

Haiyan Meng, Douglas Thain, Alexander Vyushkov, Matthias Wolf, and Anna Woodard, Conducting Reproducible Research with Umbrella: Tracking, Creating, and Preserving Execution Environments, IEEE Conference on e-Science, October, 2016. DOI: 10.1109/eScience.2016.7870889

Matthias Wolf, Anna Woodard, Wenzhao Li, Kenyi Hurtado Anampa, Yannakopoulos, Benjamin Tovar, Patrick Donnelly, Paul Brenner, Kevin Lannon, Mike Hildreth, and Douglas Thain, Opportunistic Computing with Lobster: Lessons Learned from Scaling up to 25K Non-Dedicated Cores, International Conference on Computing in High Energy Physics, October, 2016. DOI: 10.1088/1742-6596/898/5/052036

Matthias Wolf and Anna Woodard and Wenzhao Li and Kenyi Hurtado Anampa and Benjamin Tovar and Paul Brenner and Kevin Lannon and Mike Hildreth and Douglas Thain, Scaling Up a CMS Tier-3 Site with Campus Resources and a 100Gb/s Network Connection: What Could Go Wrong?, International Conference on Computing in High Energy Physics, October, 2016. DOI: 10.1088/1742-6596/898/8/082041

Peter Ivie, Charles (Chao) Zheng, and Douglas Thain, An Analysis of Reproducibility and Non-Determinism in HEP Software and ROOT Data, International Conference on Computing in High Energy and Nuclear Physics, October, 2016. DOI: 10.1088/1742-6596/898/10/102007

Haipeng Cai and Douglas thain, DistIA: A Cost-Effective Dynamic Impact Analysis for Distributed Prorgams, IEEE/ACM International Conference on Automated Software Engineering, September, 2016. DOI: 10.1145/2970276.2970352

Haiyan Meng, Matthias Wolf, Peter Ivie, Anna Woodard, Michael Hildreth, Douglas Thain, A Case Study in Preserving a High Energy Physics Application with Parrot, Journal of Physics: Conference Series (CHEP 2015), December, 2015. DOI: 10.1088/1742-6596/664/3/032022

Douglas Thain, Peter Ivie, and Haiyan Meng, Techniques for Preserving Scientific Software Executions: Preserve the Mess or Encourage Cleanliness?, 12th International Conference on Digital Preservation (iPres), November, 2015. DOI: 10.7274/R0CZ353M

An Huynh, Douglas Thain, Miquel Pericas, and Kenjiro Taura, DAGViz: A DAG Visualization Tool for Analzying Task Parallel Program Traces, Workshop on Visual Performance Analysis (VPA) at ACM Supercomputing (SC), November, 2015.

Anna Woodard, Matthias Wolf, Charles Mueller, Nil Valls, Ben Tovar, Patrick Donnelly, Peter Ivie, Kenyi Hurtado Anampa, Paul Brenner, Douglas Thain, Kevin Lannon and Michael Hildreth, Scaling Data Intensive Physics Applications to 10k Cores on Non-Dedicated Clusters with Lobster, IEEE Conference on Cluster Computing, September, 2015.

Olivia Choudhury, Dinesh Rajan, Nicholas Hazekamp, Sandra Gesing, Douglas Thain, and Scott Emrich, Balancing Thread-level and Task-level Parallelism for Data-Intensive Workloads on Clusters and Clouds, IEEE Conference on Cluster Computing, September, 2015.

Gideon Juve, Benjamin Tovar, Rafael Ferreira da Silva, Dariusz Krol, Douglas Thain, Ewa Deelman, William Allcock, and Miron Livny, Practical Resource Monitoring for Robust High Throughput Computing, Workshop on Monitoring and Analysis for High Performance Computing Systems Plus Applications at IEEE Cluster Computing, September, 2015.

Nicholas Hazekamp, Joseph Sarro, Olivia Choudhury, Sandra Gesing, Scott Emrich, and Douglas Thain, Scaling Up Bioinformatics Workflows with Dynamic Job Expansion, IEEE International Conference on e-Science, August, 2015.

Charles (Chao) Zheng and Douglas Thain, Integrating Containers into Workflows: A Case Study Using Makeflow, Work Queue, and Docker, Workshop on Virtualization Technologies in Distributed Computing (VTDC), June, 2015. DOI: 10.1145/2755979.2755984

Haiyan Meng and Douglas Thain, Umbrella: A Portable Environment Creator for Reproducible Computing on Clusters, Clouds, and Grids, Workshop on Virtualization Technologies in Distributed Computing (VTDC) at HPDC, June, 2015. DOI: 10.1145/2755979.2755982

Patrick Donnelly, Nicholas Hazekamp, Douglas Thain, Confuga: Scalable Data Intensive Computing for POSIX Workflows, IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing, pages 392-401, May, 2015. DOI: 10.1109/CCGrid.2015.95

Haiyan Meng, Matthias Wolf, Anna Woodard, Peter Ivie, Michael Hildreth, and Douglas Thain, A Case Study in Preserving a High Energy Physics Application, Computing in High Energy Physics, January, 2015.

Anna Woodard, Matthias Wolf, Charles Nicholas Mueller, Ben Tovar, Patrick Donnelly, Kenyi Hurtado Anampa, Paul Brenner, Kevin Lannon, and Michael Hildreth, Exploiting Volatile Opportunistic Computing Resources with Lobster, Computing in High Energy Physics, January, 2015.

Peter Ivie, Douglas Thain, DeltaDB: A Scalable Database Design for Time-Varying Schema-Free Data, IEEE International Congress on Big Data (BigData 2014), pages 104-111, June, 2014. DOI: 10.1109/BigData.Congress.2014.24

Dillon Skeehan, Paul Brenner, Ben Tovar, Douglas Thain, Nil Valls, Anna Woodard, Matthew Wolf, Tessa Pearson, Sean Lynch, and Kevin Lannon, Opportunistic High Energy Physics Computing in User Space with Parrot, IEEE Symposium on Cluster, Cloud, and Grid Computing (CCGrid), pages 170-175, May, 2014. DOI: 10.1109/CCGrid.2014.34

Olivia Choudhury, Nicholas L. Hazekamp, Douglas Thain, Scott Emrich, Accelerating Comparative Genomics Workflows in a Distributed Environment with Optimized Data Partitioning, C4BIO Workshop at IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGRID), May, 2014.

Matthew Staffelbach, Peter Sempolinski, David Hachen, Ahsan Kareem, Tracy Kijewski-Correa, Douglas Thain, Daniel Wei and Gregory Madey, Lessons Learned from an Experiment in Crowdsourcing Complex Citizen Engineering Tasks with Amazon Mechanical Turk, Collective Intelligence, April, 2014.

Nicholas Hazekamp, Olivia Choudhury, Sandra Gesing, Scott Emrich, and Douglas Thain, Poster: Expanding Tasks of Logical Workflows into Independent Workflows for Improved Scalability, IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing, pages 548-549, January, 2014. DOI: 10.1109/CCGrid.2014.84

Casey Robinson and Douglas Thain, Automated Packaging of Bioinformatics Workflows for Portability and Durability Using Makeflow, Workshop on Workflows in Support of Large-Scale Science (WORKS), November, 2013. DOI: 10.1145/2534248.2534258

Patrick Donnelly and Douglas Thain, Design of an Active Storage Cluster File System for DAG Workflows, International Workshop on Data-Intensive Scalable Computing Systems, pages 37-42, November, 2013. DOI: 10.1145/2534645.2534656

Rafael Ferreira da Silva, Gideon Juve, Ewa Deelman, Tristan Glatard, Frederic Desprez, Douglas Thain, Benjamin Tovar, and Miron Livny, Toward Fine Grained Online Task Chracteristics Estimation in Scientific Workflows, Workshop on Workflows in Support of Large Scale Science (WORKS), pages 58-67, November, 2013. DOI: 10.1145/2534248.2534254

Michael Albrecht, Dinesh Rajan, Douglas Thain, Making Work Queue Cluster-Friendly for Data Intensive Scientific Applications, IEEE International Conference on Cluster Computing, September, 2013. DOI: 10.1109/CLUSTER.2013.6702628

Dinesh Rajan, Andrew Thrasher, Badi Abdul-Wahid, Jesus A Izaguirre, Scott Emrich, and Douglas Thain, Case Studies in Designing Elastic Applications, 13th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid), May, 2013. DOI: 0.1109/CCGrid.2013.46

Badi Abdul-Wahid, Li Yu, Dinesh Rajan, Haoyun Feng, Eric Darve, Douglas Thain, Jesus A. Izaguirre, Folding Proteins at 500 ns/hour with Work Queue, 8th IEEE International Conference on eScience (eScience 2012), October, 2012. DOI: 10.1109/eScience.2012.6404429

Peter Sempolinski, Daniel Wei, Douglas Thain and Ahsan Kareem, A System for Management of Computational Fluid Dynamics Simulations for Civil Engineering, 8th IEEE International Conference on eScience, pages 1-8, October, 2012. DOI: 10.1109/eScience.2012.6404433

Patrick Donnelly and Douglas Thain, Fine-Grained Access Control in the Chirp Distributed File System, IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing, May, 2012. DOI: 10.1109/CCGrid.2012.128

Michael Albrecht, Patrick Donnelly, Peter Bui, and Douglas Thain, Makeflow: A Portable Abstraction for Data Intensive Computing on Clusters, Clouds, and Grids, Workshop on Scalable Workflow Enactment Engines and Technologies (SWEET) at ACM SIGMOD, May, 2012. DOI: 10.1145/2443416.2443417

Andrew Thrasher, Zachary Musgrave, Douglas Thain, Scott Emrich, Shifting the Bioinformatics Computing Paradigm: A Case Study in Parallelizing Genome Annotation Using Maker and Work Queue, IEEE International Conference on Computational Advances in Bio and Medical Sciences, February, 2012.

Dinesh Rajan, Anthony Canino, Jesus A Izaguirre, and Douglas Thain, Converting a High Performance Application to an Elastic Cloud Application, The 3rd IEEE International Conference on Cloud Computing Technology and Science (CloudCom 2011), November, 2011.

Peter Bui, Dinesh Rajan, Badi Abdul-Wahid, Jesus Izaguirre, Douglas Thain, Work Queue + Python: A Framework For Scalable Scientific Ensemble Applications, Workshop on Python for High Performance and Scientific Computing (PyHPC) at the ACM/IEEE International Conference for High Performance Computing, Networking, Storage, and Analysis (Supercomputing) , November, 2011.

Irena Lanc, Peter Bui, Douglas Thain, and Scott Emrich, Adapting Bioinformatics Applications for Heterogeneous Systems: A Case Study, Emerging Computational Methods for the Life Sciences Workshop at ACM HPDC, pages 7-13, June, 2011. DOI: 10.1145/1996023.1996025

Peter Sempolinski and Douglas Thain, A Comparison and Critique of Eucalyptus, OpenNebula and Nimbus, IEEE International Conference on Cloud Computing Technology and Science, pages 417-426, November, 2010. DOI: 10.1109/CloudCom.2010.42

Patrick Donnelly, Peter Bui, Douglas Thain, Attaching Cloud Storage to a Campus Grid Using Parrot, Chirp, and Hadoop, IEEE International Conference on Cloud Computing Technology and Science, pages 488-495, November, 2010. DOI: 10.1109/CloudCom.2010.74

Andrew Thrasher, Rory Carmichael, Peter Bui, Li Yu, Douglas Thain, and Scott Emrich, Taming Complex Bioinformatics Workflows with Weaver, Makeflow, and Starch, Workshop on Workflows in Support of Large Scale Science, pages 1-6, November, 2010. DOI: 10.1109/WORKS.2010.5671858

Paul Brenner, Ryan Jansen, David Go, and Douglas Thain, Environmentally Opportunistic Computing: Transforming the Data Center for Economic and Environmental Sustainability, IEEE Green Computing Conference, pages 383-388, August, 2010. DOI: 10.1109/GREENCOMP.2010.5598289

Hoang Bui, Peter Bui, Patrick Flynn and Douglas Thain, ROARS: A Scalable Repository for Data Intensive Scientific Computing, The Third International Workshop on Data Intensive Distributed Computing at ACM HPDC 2010, June, 2010. DOI: 10.1145/1851476.1851587

Peter Bui, Li Yu and Douglas Thain, Weaver: Integrating Distributed Computing Abstractions into Scientific Workflows using Python, Challenges of Large Applications in Distributed Environments at ACM HPDC 2010, June, 2010. DOI: 10.1145/1851476.1851570

Hoang Bui, Diane Wright, Clarence Helm, Rachel Witty, Patrick Flynn and Douglas Thain, Towards Long Term Data Quality in a Large Scale Biometrics Experiment, Managing Data Quality for Collaborative Science at ACM HPDC 2010, June, 2010. DOI: 10.1145/1851476.1851559

Rory Carmichael, Patrick Braga-Henebry, Douglas Thain, and Scott Emrich, Biocompute: Toward a Collaborative Workspace for Data Intensive Bio-Science, Workshop on Emerging Computational Methods for Life Sciences at ACM HPDC 2010, pages 489-498, June, 2010. DOI: 10.1145/1851476.1851547

Christopher Moretti, Michael Olson, Scott Emrich, and Douglas Thain, Highly Scalable Genome Assembly on Campus Grids, Many-Task Computing on Grids and Supercomputers (MTAGS), November, 2009. DOI: 10.1145/1646468.1646480

Jeffrey Hemmes, Douglas Thain, and Christian Poellabauer, Cooperative Localization in GPS-Limited Urban Environments, ICST AdHocNets, September, 2009.

Michael Lammie, Douglas Thain, and Paul Brenner, Scheduling Grid Workloads on Multicore Clusters to Minimize Energy and Maximize Performance, IEEE Grid Computing, September, 2009.

Kyle Wheeler, Douglas Thain, Rich Murphy, Portable Performance from Workstation to Supercomputer: Distributing Data Structures with Qthreads, Workshop on Programming Models for Emerging Architectures, pages 1-8, September, 2009.

Li Yu, Christopher Moretti, Scott Emrich, Kenneth Judd, and Douglas Thain, Harnessing Parallelism in Multicore Clusters with the All-Pairs and Wavefront Abstractions, IEEE High Performance Distributed Computing, pages 1-10, June, 2009. DOI: 10.1145/1551609.1551613

Paul Brenner, Douglas Thain, and Dewitt Latimer, Grid Heating Clusters: Transforming Cooling Constraints Into Thermal Benefits, The Uptime Institute Green Enterprise IT Award Paper, pages 1-7, June, 2009.

Gabrielle Compostella, Simone Pagan Griso, Donatella Lucchesi, Igor Sfiligoi, and Douglas Thain, CDF Software Distribution on the Grid using Parrot, Computing in High Energy Physics, May, 2009. DOI: 10.1088/1742-6596/219/6/062009

Christopher Moretti, Karsten Steinhaeuser, Douglas Thain, and Nitesh V. Chawla, Scaling Up Classifiers to Cloud Computers, IEEE International Conference on Data Mining (ICDM), pages 472-481, December, 2008. DOI: 10.1109/ICDM.2008.99

Qi Liao, Andrew Blaich, Aaron Striegel, and Douglas Thain, ENAVis: Enterprise Network Activities Visualization, USENIX Large Installation System Administration (LISA), pages 59-74, November, 2008.

David Cieslak, Nitesh Chawla, and Douglas Thain, Troubleshooting Thousands of Jobs on Production Grids Using Data Mining Techniques, IEEE Grid Computing, pages 217-224, August, 2008. DOI: 10.1109/GRID.2008.4662802

Christopher Moretti, Jared Bulosan, Douglas Thain, and Patrick Flynn, All-Pairs: An Abstraction for Data Intensive Cloud Computing, IEEE International Parallel and Distributed Processing Symposium (IPDPS), pages 1-11, April, 2008. DOI: 10.1109/IPDPS.2008.4536311

Kyle Wheeler, Richard Murphy, and Douglas thain, QThreads: An API for Programming with Millions of Lightweight Threads, Workshop on Multithreaded Architectures and Applications at IEEE IPDPS, pages 1-8, April, 2008. DOI: 10.1109/IPDPS.2008.4536359

Jeffrey Hemmes, Christian Poellabauer, and Douglas Thain, On Demand Transient Storage and Backup in Mobile Systems, IEEE Military Communications Conference, pages 1-7, October, 2007. DOI: 10.1109/MILCOM.2007.4454917

Jeffrey Hemmes, Douglas Thain, Christian Poellabauer, Christopher Moretti, Phil Snowberger, and Brendan McNutt, Lessons Learned Building TeamTrak: An Urban/Outdoor Mobile Testbed, International Conference on Wireless Architectures Systems and Applications, pages 219-224, October, 2007. DOI: 10.1109/WASA.2007.35

Jeffrey Hemmes, Douglas Thain, and Christian Poellabauer, Work in Progress: Integrating Undergraduate Research and Education via the TeamTrak Mobile Computing Framework, IEEE Frontiers in Education, pages 1-2, October, 2007. DOI: 10.1109/FIE.2007.4418007

Douglas Thain and Christopher Moretti, Efficient Access to Many Small Files in a Filesystem for Grid Computing, IEEE Grid Computing, pages 243-250, September, 2007. DOI: 10.1109/GRID.2007.4354139

Christopher Moretti, Timothy Faltemier, Douglas Thain, and Patrick J. Flynn, Challenges in Executing Data Intensive Biometric Workloads on a Desktop Grid, Workshop on Large Scale and Volatile Desktop Grids at IEEE IPDPS, pages 481-489, April, 2007. DOI: 10.1109/IPDPS.2007.370671

Paul Brenner, Justin Wozniak, Douglas Thain, Aaron Striegel, Jeffrey Peng, and Jesus Izaguirre, Biomolecular Path Sampling Enabled by Processing in Network Storage, Workshop on High Performance Computational Biology at IEEE IPDPS, pages 1-6, April, 2007. DOI: 10.1109/IPDPS.2007.370446

Justin Wozniak, Paul Brenner, Douglas Thain, Aaron Striegel, Jesus Izaguirre, Access Control for a Replica Management Database, ACM Workshop on Storage Security and Survivability at ACM CCS, pages 41-46, October, 2006. DOI: 10.1145/1179559.1179567

Christophe Blanchet, Remi Mollon, Douglas Thain, and Gilbert Deleage, Grid Deployment of Legacy Bioinformatics Applications with Transparent Data Access, IEEE Grid Computing, pages 120-127, September, 2006. DOI: 10.1109/ICGRID.2006.311006

Douglas Thain, Operating System Support for Space Allocation in Grid Storage Systems, IEEE Grid Computing, pages 104-111, September, 2006. DOI: 10.1109/ICGRID.2006.311004

Jeffrey Hemmes and Douglas Thain, Cacheable Decentralized Groups for Grid Resource Access Control, IEEE Grid Computing, pages 192-199, September, 2006. DOI: 10.1109/ICGRID.2006.311015

Sudharshan Vazhkudai, Douglas Thain, Xiaosong Ma, and Vincent Freeh, Positioning Dynamic Storage Caches for Transient Data, Workshop on High-Performance I/O Techniques and Deployment of Very Large Scale I/O Systems at IEEE Cluster Computing, pages 1-9, September, 2006. DOI: 10.1109/CLUSTR.2006.311900

Douglas Thain and Christian Poellabauer, Experience with a Literate Approach to Computer Science, IEEE Frontiers in Education, pages 8-13, August, 2006. DOI: 10.1109/FIE.2006.322405

Faruck Morcos, Thidapat Chantem, Philip Little, Tiago Gasiba, and Douglas Thain, iDIBS: An Improved Distributed Internet Backup System, IEEE International Conference on Parallel and Distributed Systems (ICPADS), pages 58-67, July, 2006. DOI: 10.1109/ICPADS.2006.52

David Cieslak, Douglas Thain, Nitesh Chawla, Short Paper: Troubleshooting Distributed Systems via Data Mining, IEEE Symposium on High Performance Distributed Computing (HPDC), pages 309-312, June, 2006.

Justin Wozniak, Paul Brenner, Douglas Thain, Aaron Striegel, and Jesus Izaguirre, Applying Feedback Control to a Replica Management System, IEEE Southeastern Symposium on System Theory, pages 472-476, March, 2006. DOI: 10.1109/SSST.2006.1619125

Douglas Thain, Christopher Moretti, and Igor Sfiligoi, Transparently Distributing CDF Software with Parrot, Computing in High Energy Physics, pages 1-4, February, 2006.

Douglas Thain, Christopher Moretti, Paul Madrid, Phil Snowberger, and Jeff Hemmes, The Consequences of Decentralized Security in a Cooperative Storage System, Workshop on Security in Storage at IEEE FAST, pages 82-94, December, 2005. DOI: 10.1109/SISW.2005.11

Douglas Thain, Sander Klous, Justin Wozniak, Paul Brenner, Aaron Striegel, and Jesus Izaguirre, Separating Abstractions from Resources in a Tactical Storage System, IEEE/ACM Supercomputing, pages 55-67, November, 2005. DOI: 10.1109/SC.2005.64

Douglas Thain, Identity Boxing: A New Technique for Consistent Global Identity, IEEE/ACM Supercomputing, pages 51-61, November, 2005. DOI: 10.1109/SC.2005.34

Douglas Thain and Christian Poellabauer, Work in Progress: A Literate Approach to Graduate Computer Science Education, IEEE Frontiers in Education, pages 1-2, October, 2005. DOI: 10.1109/FIE.2005.1612087

Justin Wozniak, Paul Brenner, Douglas Thain, Aaron Striegel, and Jesus Izaguirre, Generosity and Gluttony in GEMS: Grid Enabled Molecular Simulations, IEEE Symposium on High Performance Distributed Computing, pages 191-200, June, 2005. DOI: 10.1109/HPDC.2005.1520959

Timothy Schoenharl, Scott Christley, and Douglas Thain, Patisserie: Support for Parameter Sweeps in a Fault-Tolerant, Massively Parallel, Peer-to-Peer Simulation Environment, Workshop on Agent Directed Simulation (ADS), pages 1-8, April, 2005.

John Bent, Douglas Thain, Andrea Arpaci-Dusseau, Remzi Arpaci-Dusseau, and Miron Livny, Explicit Control in a Batch Aware Distributed File System, USENIX Networked Systems Design and Implementation (NSDI), pages 365-378, April, 2004.

Douglas Thain, John Bent, Andrea Arpaci-Dusseau, Remzi Arpaci-Dusseau and Miron Livny, Pipeline and Batch Sharing in Grid Workloads, IEEE High Performance Distributed Computing, pages 152-161, June, 2003. DOI: 10.1109/HPDC.2003.1210025

Douglas Thain and Miron Livny, The Ethernet Approach to Grid Computing, IEEE High Performance Distributed Computing, pages 138-, June, 2003. DOI: 10.1109/HPDC.2003.1210024

Douglas Thain and Miron Livny, Parrot: Transparent User-Level Middleware for Data Intensive Computing, Workshop on Adaptive Grid Middleware at PACT, January, 2003.

Oleg Lodygensky, Gilles Fedak, Vincent Neri, Franck Cappello, Miron Livny, and Douglas Thain, XtremWeb and Condor: Sharing Resources Between Internet Connected Condor Pools, Workshop on Global and Peer-to-Peer Computing on Large Scale Distributed Systems at CCGRID, pages 382-390, 2003. DOI: 10.1109/CCGRID.2003.1199391

Douglas Thain and Miron Livny, Error Scope on a Computational Grid, IEEE High Performance Distributed Computing, pages 199-208, July, 2002. DOI: 10.1109/HPDC.2002.1029919

Douglas Thain, John Bent, Andrea Arpaci-Dusseau, Remzi Arpaci-Dusseau and Miron Livny, Gathering at the Well: Creating Communities for Grid I/O, IEEE/ACM Supercomputing, pages 21-31, November, 2001. DOI: 10.1109/SC.2001.10023

Douglas Thain, Jim Basney, Se-Chang Son, and Miron Livny, The Kangaroo Approach to Data Movement on the Grid, IEEE High Performance Distributed Computing, pages 325-333, August, 2001. DOI: 10.1109/HPDC.2001.945200

Douglas Thain and Miron Livny, Bypass: A Tool for Building Split Execution Systems, IEEE High Performance Distributed Computing, pages 79-85, August, 2000. DOI: 10.1109/HPDC.2000.868637

Poster Presentations

Barry Sly-Delgado and Douglas Thain, Poster: Minimizing Data Movement Using Distant Futures, ACM/IEEE Supercomputing, November, 2023.

Douglas Thain, Poster: TaskVine: A User-Level Framework for Data Intensive Scientific Applications, CSSI PI Meeting, September, 2023. DOI: 10.6084/m9.figshare.24238828.v1

David Simonetti, Ben Tovar, and Douglas Thain, Poster: Mixed Modality Workflows in TaskVine, ACM High Performance Distributed Computing, pages 331-332, August, 2023. DOI: 10.1145/3588195.3595953

Hoang Bui, Deborah Thomas, Michael Kelly, Christopher Lyon, Douglas Thain, and Patrick J. Flynn, Poster: BXGrid: A Data Repository and Workflow Abstraction for Biometrics Research, IEEE International Conference on e-Science, pages 394-395, December, 2008. DOI: 10.1109/eScience.2008.135

Brandon Rich and Douglas Thain, Poster: DataLab: Transactional Data Parallel Computing on an Active Storage Cloud, IEEE/ACM High Performance Distributed Computing, pages 233-234, June, 2008. DOI: 10.1145/1383422.1383461

Andrew Blaich, Qi Liao, Greg Allan, Aaron Striegel, and Douglas Thain, Poster: Lockdown: Distributed Policy Analysis and Enforcement within the Enterprise Network, USENIX Security Symposium, September, 2007.

Christopher Moretti, Jared Bulosan, Douglas Thain, and Patrick J. Flynn, Poster: All-Pairs: An Abstraction for Data Intensive Computing, IEEE/ACM Grid Computing, September, 2007.

Phil Snowberger and Douglas Thain, Poster: Sub-Identities: Security for Mere Mortals, USENIX Security, September, 2006.

Douglas Thain, Poster: Identity Boxing: Secure User-Level Containment for the Grid, IEEE Symposium on High Performance Distributed Computing, pages 299-300, June, 2005. DOI: 10.1109/HPDC.2005.1520984

Book Chapters

Douglas Thain, Michael Albrecht, Hoang Bui, Peter Bui, Rory Carmichael, Scott Emrich, and Patrick Flynn, Data Intensive Computing with Clustered Chirp Servers, Tevfik Kosar, Data Intensive Distributed Computing: Challenges and Solutions for Large Scale Information Management, pages 140-154, IGI, January, 2012. ISBN: 9781615209712

Peter Sempolinski and Douglas Thain, An Introduction to Open-Source IaaS Cloud Middleware, Boualem Benatallah, Cloud Computing: Methodology, Systems, and Applications, pages 133-149, CRC Press, January, 2011. ISBN: 978-1-4398-5641-3

Douglas Thain and Christopher Moretti, Abstractions for Cloud Computing with Condor, Syed Ahson and Mohammad Ilyas, Cloud Computing and Software Services: Theory and Techniques, pages 153-171, CRC Press, July, 2010. ISBN: 9781439803158

Ioan Raicu, Ian Foster, Yong Zhao, Alex Szalay, Philip Little, Christopher Moretti, Amitabh Chaudhary, and Douglas Thain, Towards Data Intensive Many Task Computing, Tevfik Kosar, Data Intensive Distributed Computing: Challenges and Solutions for Large-Scale Information Management, IGI, 2009.

T. Kosar, A. Hutanu, J. McLaren and D. Thain, Coordination of Access to Large-scale Datasets in Distributed Environments, A. Shoshani and D. Rotem, Scientific Data Management: Challenges, Existing Technology, and Deployment, Chapman and Hall / CRC Press, August, 2009. ISBN: 978-1420069808

Douglas Thain and Miron Livny, Building Reliable Clients and Servers, Ian Foster and Carl Kesselman, Grid: Blueprint for a New Computing Infrastructure, Morgan Kaufmann, 2004. ISBN: 1-55860-933-4

Douglas Thain, Todd Tannenbaum, and Miron Livny, Condor and the Grid, Fran Berman and Anthony Hey and Geoffrey Fox, Grid Computing: Making the Global Infrastructure a Reality, John Wiley, 2003. ISBN: 0-470-85319-0

Dissertations

Nathaniel Kremer-Herman, Log Discovery, Log Custody, and the Web Inspired Approach for Open Distributed Systems Troubleshooting, Ph.D. Thesis, University of Notre Dame, April, 2021.

Nicholas Hazekamp, Methods Enabling Portability of Scientific Workflows, Ph.D. Thesis, University of Notre Dame, December, 2019.

Chao Zheng, The Challenges of Scaling Up High-Throughput Workflow with Container Technologies, Ph.D. Thesis, University of Notre Dame, October, 2019.

Peter Ivie, A Workflow Management System to Facilitate Reproducibility of Scientific Computing Applications, Ph.D. Thesis, University of Notre Dame, April, 2018.

James Sweet, Enabling Implementation and Optimization of Scientific Algorithms via Graphics Processing Units, Ph.D. Thesis, University of Notre Dame, July, 2017.

Haiyan Meng, Improving the Reproducibility of Scientific Applications with Execution Environment Specifications, Ph.D. Thesis, University of Notre Dame, May, 2017.

Patrick Donnelly, Data Locality Techniques in an Active Cluster Filesystem for Scientific Workflows, Ph.D. Thesis, University of Notre Dame, April, 2016.

Dinesh Rajan, Principles for the Design and Operation of Elastic Scientific Applications on Distributed Systems, Ph.D. Thesis, University of Notre Dame, April, 2015.

Li Yu, Right-sizing Resource Allocations for Scientific Applications in Clusters, Grids, and Clouds, Ph.D. Thesis, University of Notre Dame, July, 2013.

Peter Bui, A Compiler Toolchain For Data Intensive Scientific Workflows, Ph.D. Thesis, University of Notre Dame, June, 2012.

Hoang Bui, A Rich Metadata Filesystem for Scientific Data, Ph.D. Thesis, University of Notre Dame, May, 2012.

Christopher Moretti, Abstractions for Scientific Computing on Campus Grids, Ph.D. Thesis, University of Notre Dame, June, 2010.

Kyle Wheeler, Exploiting Locality with QThreads for Portable Parallel Performance, Ph.D. Thesis, University of Notre Dame, November, 2009.

Jeffrey Hemmes, Improving Data Availability in Mobile Applications Through Enhanced Cooperative Localization, Ph.D. Thesis, University of Notre Dame, July, 2009.

Patrick Braga-Henebry, Biocompute: Harnessing Distributed Systems for Bioinformatics, B.S. Honors Thesis, University of Notre Dame, May, 2009.

Christopher Moretti, Flexible Object Based Filesystems for Scientific Computing, M.S. Thesis, University of Notre Dame, April, 2007.

Philip Snowberger, Sub-Identities: A Hierarchical Identity Model for Practical Containment, M.S. Thesis, University of Notre Dame, April, 2007.

Douglas Thain, Coordinating Access to Computation and Data in Distributed Systems, Ph.D. Thesis, University of Wisconsin, August, 2004.

Technical Reports

Peter Ivie, Charles (Chao) Zheng, and Douglas Thain, A First Look at Reproducibility and Non-Determinism in CMS Codes and ROOT Data, University of Notre Dame, Computer Science and Engineering Department, Technical Report 2016-01, October, 2016.

Beth Plale, Matt Jones, and Douglas Thain, Software in Science: a Report of Outcomes of the 2014 National Science Foundation Software Infrastructure for Sustained Innovation (SI2) Meeting, Technical Report March, 2015.

Brenden Kokoszka, Patrick Donnelly, and Douglas Thain, Search Should be a System Call, University of Notre Dame, Computer Science and Engineering Department, Technical Report 2013-03, April, 2013.

Christopher Moretti, Michael Olson, Scott Emrich, and Douglas Thain, Scalable Modular Genome Assembly on Campus Grids, University of Notre Dame, Computer Science and Engineering Department, Technical Report 2009-04, July, 2009.

Douglas Thain and Patrick Flynn, Towards a Data Analysis Grid for Biometrics Research, University of Notre Dame, Computer Science and Engineering Department, Technical Report 2008-05, April, 2008.

Paul Brenner, Douglas Thain, and Dewitt Latimer, Grid Heating: Transforming Cooling Constraints Into Thermal Benefits, University of Notre Dame, Computer Science and Engineering Department, Technical Report 2008-09, 2008.

Philip Snowberger and Douglas thain, Sub-Identities: Towards Operating System Support for Distributed System Security, University of Notre Dame, Computer Science and Engineering Department, Technical Report 2005-18, October, 2005.

Datasets

Tim Shaffer, Kyle Chard, Douglas Thain, Binder Software Environments, June, 2021. DOI: 10.5281/zenodo.4891790