Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting. Daipayan Sarkar, Hyungro Lee, John Vant, Matteo Turilli, Josh Vermaas, Shantenu Jha, Abhishek Singharoy. Journal of Chemical Information and Modeling.
Asynchronous Execution of Heterogeneous Tasks in ML-driven HPC Workflows. Vincent R. Pascuzzi, Ozgur O. Kilic, Matteo Turilli, Shantenu Jha. Job Scheduling Strategies for Parallel Processing (JSSPP).
The Framework for Assessing Changes To Sea-level (FACTS) v1. 0-rc: A platform for characterizing parametric and structural uncertainty in future global, relative, and extreme sea-level change. Robert E. Kopp, Gregory G. Garner, Tim H. J. Hermans, Shantenu Jha, Praveen Kumar, Aimée B. A. Slangen, Matteo Turilli, Tamsin L. Edwards, Jonathan M. Gregory, George Koubbe, Anders Levermann, Andre Merzky, Sophie Nowicki, Matthew D. Palmer, and Chris Smith. The EGU interactive community platform [preprint].
PSI/J: A Portable Interface for Submitting, Monitoring, and Managing Jobs. Mihael Hategan-Marandiuc1, 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, Daniel Laney. 19th IEEE International Conference on eScience.
#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. Abigail Dommer, Lorenzo Casalino, Fiona Kearns, Mia Rosenfeld, Nicholas Wauer, Surl-Hee AhnX, John Russo, Sofia Oliveira, Clare Morris, Anthony Bogetti, Anda Trifan, Alexander Brace, Terra Sztain, Austin Clyde, Heng Ma, Chakra Chennubhotla, Hyungro Lee, Matteo Turilli, Syma Khalid, Teresa Tamayo-Mendoza, Matthew Welborn, Anders Christensen, Daniel GA Smith, Zhuoran Qiao, Sai K Sirumalla, Michael O’Connor, Frederick Manby, Anima Anandkumar, David Hardy, James Phillips, Abraham Stern, Josh Romero, David Clark, Mitchell Dorrell, Tom Maiden, Lei Huang, John McCalpin, Christopher Woods, Alan Gray, Matt Williams, Bryan Barker, Harinda Rajapaksha, Richard Pitts, Tom Gibbs, John Stone, Daniel M. Zuckerman, Adrian J. Mulholland, Thomas Miller, III, Shantenu Jha, Arvind Ramanathan, Lillian ChongX, and Rommie E Amaro. The International Journal of High Performance Computing Applications.
Workflows Community Summit 2022: A Roadmap Revolution. Rafael Ferreira da Silva, Rosa M. Badia, Venkat Bala, Debbie Bard, Peer-Timo Bremer, Ian Buckley, Silvina Caino-Lores, Kyle Chard, Carole Goble, Shantenu Jha, Daniel S. Katz, Daniel Laney, Manish Parashar, Frederic Suter, Nick Tyler, Thomas Uram, Ilkay Altintas, Stefan Andersson, William Arndt, Juan Aznar, Jonathan Bader, Bartosz Balis, Chris Blanton, Kelly Rosa Braghetto, Aharon Brodutch, Paul Brunk, Henri Casanova, Alba Cervera Lierta, Justin Chigu, Taina Coleman, Nick Collier, Iacopo Colonnelli, Frederik Coppens, Michael Crusoe, Will Cunningham, Bruno de Paula Kinoshita, Paolo Di Tommaso, Charles Doutriaux, Matthew Downton, Wael Elwasif, Bjoern Enders, Chris Erdmann, Thomas Fahringer, Ludmilla Figueiredo, Rosa Filgueira, Martin Foltin, Anne Fouilloux, Luiz Gadelha, Andy Gallo, Artur Garcia Saez, Daniel Garijo, Roman Gerlach, Ryan Grant, Samuel Grayson, Patricia Grubel, Johan Gustafsson, Valerie Hayot-Sasson, Oscar Hernandez, Marcus Hilbrich, AnnMary Justine, Ian Laflotte, Fabian Lehmann, Andre Luckow, Jakob Luettgau, Ketan Maheshwari, Motohiko Matsuda, Doriana Medic, Pete Mendygral, Marek Michalewicz, Jorji Nonaka, Maciej Pawlik, Loic Pottier, Line Pouchard, Mathias Putz, Santosh Kumar Radha, Lavanya Ramakrishnan, Sashko Ristov, Paul Romano, Daniel Rosendo, Martin Ruefenacht, Katarzyna Rycerz, Nishant Saurabh, Volodymyr Savchenko, Martin Schulz, Christine Simpson, Raul Sirvent, Tyler Skluzacek, Stian Soiland-Reyes, Renan Souza, Sreenivas Rangan Sukumar, Ziheng Sun, Alan Sussman, Douglas Thain, Mikhail Titov, Benjamin Tovar, Aalap Tripathy, Matteo Turilli, Bartosz Tuznik, Hubertus van Dam, Aurelio Vivas , Logan Ward, Patrick Widener, Sean Wilkinson, Justyna Zawalska, Mahnoor Zulfiqar. Workflows Community Summit 2022.
AI-accelerated protein-ligand docking for SARS-CoV-2 is 100-fold faster with no sig-nificant change in detection. Austin Clyde, Xuefeng Liu, Thomas Brettin, Hyunseung Yoo, Alexander Partin, Yadu Babuji, Ben Blaiszik, Jamaludin Mohd-Yusof, Andre Merzky, Matteo Turilli, Shantenu Jha, Arvind Ramanathan and Rick Stevens. Scientific Reports, Nature.
RADICAL-Pilot and PMIx/PRRTE: Executing heterogeneous workloads at large scale on partitioned HPC resources. Mikhail Titov, Matteo Turilli, Andre Merzky, Thomas Naughton, Wael Elwasif & Shantenu Jha. Workshop on Job Scheduling Strategies for Parallel Processing (JSSP).
The Ghost of Performance Reproducibility Past. Srinivasan Ramesh, Mikhail Titov, Matteo Turilli, Shantenu Jha, Allen Malony. IEEE 18th International Conference on e-Science.
Pipeline for Automating Compliance-based Elimination and Extension (PACE2): A Systematic Framework for High-throughput Biomolecular Material Simulation Workflows. Srinivas C. Mushnoori, Ethan Zang, Akash Banerjee, Mason Hooten, Andre Merzky, Matteo Turilli, Shantenu Jha, Meenakshi Dutt. arXivorg.
RAPTOR: Ravenous Throughput Computing. Andre Merzky, Matteo Turilli, and Shantenu Jha. 22nd IEEE International Symposium on Cluster, Cloud and Internet Computing (CCGrid).
A scalable solution for running ensemble simulations for photovoltaic energy. Weiming Hu, Guido Cervone, Matteo Turilli, Andre Merzky, Shantenu Jha. Recent Advancement in Geoinformatics and Data Science (book chapter).
A new hourly dataset for photovoltaic energy production for the continental USA. Weiming Hu, Guido Cervone, Andre Merzky, Matteo Turilli, Shantenu Jha. Data in Brief.
Coupling streaming AI and HPC ensembles to achieve 100–1000× faster biomolecular simulations. Alexander Brace, Igor Yakushin, Heng Ma, Anda Trifan, Todd Munson, Ian Foster, Arvind Ramanathan, Hyungro Lee, Matteo Turilli, and Shantenu Jha. IEEE International Parallel and Distributed Processing Symposium (IPDPS).
RADICAL-Pilot and Parsl: Executing Heterogeneous Workflows on HPC Platforms. Aymen Alsaadi, Logan Ward, Andre Merzky, Kyle Chard, Ian Foster, Shantenu Jha, Matteo Turilli. IEEE/ACM Workshop on Workflows in Support of Large-Scale Science (WORKS).
Large-Scale Molecular Dynamics Simulations of Cellular Compartments. Eric Wilson, John Vant, Jacob Layton, Ryan Boyd, Hyungro Lee, Matteo Turilli, Benjamín Hernández, Sean Wilkinson, Shantenu Jha, Chitrak Gupta, Daipayan Sarkar and Abhishek Singharoy. Structure and Function of Membrane Proteins.
High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor. Austin Clyde, Stephanie Galanie, Daniel W. Kneller, Heng Ma, Yadu Babuji, Ben Blaiszik, Alexander Brace, Thomas Brettin, Kyle Chard, Ryan Chard, Leighton Coates, Ian Foster, Darin Hauner, Vilmos Kertesz, Neeraj Kumar, Hyungro Lee, Zhuozhao Li, Andre Merzky, Jurgen G. Schmidt, Li Tan, Mikhail Titov, Anda Trifan, Matteo Turilli, Hubertus Van Dam, Srinivas C. Chennubhotla, Shantenu Jha, Andrey Kovalevsky, Arvind Ramanathan, Martha S. Head, and Rick Stevens*. Journal of Chemical Information and Modeling.
Pandemic drugs at pandemic speed: infrastructure for accelerating COVID-19 drug discovery with hybrid machine learning- and physics-based simulations on high-performance computers. Agastya P Bhati, Shunzhou Wan, Dario Alfè, Austin R Clyde, Mathis Bode, Li Tan, Mikhail Titov, Andre Merzky, Matteo Turilli, Shantenu Jha, Roger R Highfield, Walter Rocchia, Nicola Scafuri, Sauro Succi, Dieter Kranzlmüller, Gerald Mathias, David Wifling, Yann Donon, Alberto Di Meglio, Sofia Vallecorsa, Heng Ma, Anda Trifan, Arvind Ramanathan, Tom Brettin, Alexander Partin, Fangfang Xia, Xiaotan Duan, Rick Stevens, Peter V Coveney. Interface Focus.
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, Justin M. Wozniak. IEEE Workshop on Workflows in Support of Large-Scale Science (WORKS).
Comparing workflow application designs for high resolution satellite image analysis. Aymen Al-Saadi, Ioannis Paraskevakos, Bento Collares Gonçalves, Heather J. Lynch, Shantenu Jha, and Matteo Turilli. Future Generation Computer Systems.
Design and Performance Characterization of RADICAL-Pilot on Leadership-class Platforms. Andre Merzky, Matteo Turilli, Mikhail Titov, Aymen Al-Saadi, Shantenu Jha. .
AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics. Lorenzo Casalino, Abigail Dommer, Zied Gaieb, Emilia P. Barros, Terra Sztain, Surl-Hee Ahn, Anda Trifan, Alexander Brace, Anthony Bogetti, Heng Ma, Hyungro Lee, Matteo Turilli, Syma Khalid, Lillian Chong, Carlos Simmerling, David J. Hardy, Julio D. C. Maia, James C. Phillips, Thorsten Kurth, Abraham Stern, Lei Huang, John McCalpin, Mahidhar Tatineni, Tom Gibbs, John E. Stone, Shantenu Jha, Arvind Ramanathan, Rommie E. Amaro. Biorxiv.
Extensible and Scalable Adaptive Sampling on Supercomputers. Eugen Hruska, Vivekanandan Balasubramanian, Hyungro Lee, Shantenu Jha, and Cecilia Clementi. Journal of Chemical Theory and Computation, 2020.
Comparing Workflow Application Designs for High Resolution Satellite Image Analysis. Aymen Al-Saadi, Ioannis Paraskevakos, Bento Collares Gonçalves, Heather J. Lynch, Shantenu Jha and Matteo Turilli. Arxiv.
IMPECCABLE: Integrated Modeling PipelinE for COVID Cure by Assessing Better LEads. Aymen AlSaadi, Dario Alfe, Yadu Babuji, Agastya Bhati, Ben Blaiszik, Thomas Brettin, Kyle Chard, Ryan Chard, Peter Coveney, Anda Trifan, Alex Brace, Austin Clyde, Ian Foster, Tom Gibbs, Shantenu Jha, Kristopher Keipert, Thorsten Kurth, Dieter Kranzlmüller, Hyungro Lee, Zhuozhao Li, Heng Ma, Andre Merzky, Gerald Mathias, Alexander Partin, Junqi Yin, Arvind Ramanathan, Ashka Shah, Abraham Stern, Rick Stevens, Li Tan, Mikhail Titov, Aristeidis Tsaris, Matteo Turilli, Huub Van Dam, Shunzhou Wan, David Wifling. Arxiv.
Parallel Performance of Molecular Dynamics Trajectory Analysis. Mahzad Khoshlessan, Ioannis Paraskevakos, Geoffrey C. Fox, Shantenu Jha and Oliver Beckstein. Concurrency and Computation: Practise and Experience.
Workflow Design Analysis for High Resolution Satellite Image Analysis. Ioannis Paraskevakos, Matteo Turilli, Bento Collares Gonçalves, Heather J. Lynch and Shantenu Jha. 2019 15th International Conference on eScience (eScience).
DeepDriveMD: Deep-Learning Driven Adaptive Molecular Simulations for Protein Folding. Hyungro Lee, Heng Ma, Matteo Turilli, Debsindhu Bhowmik, Shantenu Jha, Arvind Ramanathan. Deep Learning on Supercomputers Workshop.
Characterizing the Performance of Executing Many-tasks on Summit. Matteo Turilli, Andre Merzky, Thomas J. Naughton, Wael Elwasif, Shantenu Jha. IPDRM 2019, Held in conjunction with the International Conference for High Performance Computing, Networking, Storage and Analysis, (SC 19), November 17-22, 2019, Denver, Colorado, USA..
Contributions to High-Performance Big Data Computing. Geoffrey Fox, Judy Qiu, David Crandall, Gregor Von Laszewski, Oliver Beckstein, John Paden, Ioannis Paraskevakos, Shantenu Jha, Fusheng Wang, Madhav Marathe, Anil Vullikanti, and Thomas Cheatham. IOSPress.
Computational reproducibility of scientific workflows at extreme scales. Line Pouchard, Sterling Baldwin, Todd Elsethaggen, Carlos Gamboa, Shantenu Jha, Bibi Raju, Eric Stephan, Li Tang and Kerstin Kleese Van Dam. The International Journal of High Performance Computing Applications.
Middleware Building Blocks for Workflow Systems. Matteo Turilli, Vivek Balasubramanian, Andre Merzky, Ioannis Paraskevakos, Shantenu Jha. Computing in Science & Engineering.
CoCo-MD: A Simple and Effective Method for the Enhanced Sampling of Conformational Space. Ardita Shkurti, Ioanna Danai Styliari, Vivek Balasubramanian, Iain Bethune, Conrado Pedebos, Shantenu Jha, and Charles A. Laughton. Journal of Chemical Theory and Computation, 2019.
High-throughput Binding Affinity Calculations at Extreme Scales. Jumana Dakka, Matteo Turilli, David W Wright, Stefan J Zasada, Vivek Balasubramanian, Shunzhou Wan, Peter V Coveney and Shantenu Jha. BMC Bioinformatics 2018 19(Suppl 18):482 and Computational Approaches for Cancer Workshop at SuperComputing (SC 2017).
Adaptive Ensemble Biomolecular Simulations at Scale. Vivek Balasubramanian, Travis Jensen, Matteo Turilli, Peter Kasson, Michael Shirts and Shantenu Jha. Arxiv.
Synapse: Synthetic Application Profiler and Emulator. Andre Merzky, Ming Tai Ha, Matteo Turilli and Shantenu Jha. Journal of Computational Science (JoCS), vol. 27, pp. 329–344.
Task-parallel Analysis of Molecular Dynamics Trajectories. Ioannis Paraskevakos, Andre Luckow, Mahzad Khoshlessan, George Chantzialexiou, Thomas E. Cheatham, Oliver Beckstein, Geoffrey C. Fox and Shantenu Jha. 47th International Conference on Parallel Processing (ICPP 2018).
Building Blocks for Workflow System Middleware. M. Turilli, A. Merzky, V. Balasubramanian, S. Jha. Proceedings of the 18th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid).
Concurrent and Adaptive Extreme Scale Binding Free Energy Calculations. Jumana Dakka, Kristof Farkas-Pall, Matteo Turilli, David W Wright, Peter V Coveney and Shantenu Jha. 2018 IEEE 14th International Conference on e-Science (e-Science).
Using Pilot Systems to Execute Many Task Workloads on Supercomputers. Andre Merzky, Matteo Turilli, Manuel Maldonado, Mark Santcroos and Shantenu Jha. JSSPP 2018 (in conjunction with IPDPS’18).
Harnessing the Power of Many: Extensible Toolkit for Scalable Ensemble Applications. Vivek Balasubramanian, Matteo Turilli, Weiming Hu, Matthieu Lefebvre, Wenjie Lei, Guido Cervone, Jeroen Tromp and Shantenu Jha. 32nd IEEE International Parallel and Distributed Processing Symposium.
Pilot-Streaming: A Stream Processing Framework for High-Performance Computing. Andre Luckow, George Chantzialexiou and Shantenu Jha. Arxiv.
A Comprehensive Perspective on Pilot-Jobs. Matteo Turilli, Mark Santcroos and Shantenu Jha. ACM Computing Surveys (CSUR), 51(2), 2018.
Parallel Analysis in MDAnalysis using the Dask Parallel Computing Library. Mahzad Khoshlessan, Ioannis Paraskevakos, Shantenu Jha and Oliver Beckstein. Proceedings of the 15th Python in Science Conference. (SCIPY 2017).
Introducing distributed dynamic data-intensive (D3) science: Understanding applications and infrastructure. Jha, Shantenu and Katz, Daniel S. and Luckow, Andre and Chue Hong , Neil and Rana, Omer and Simmhan, Yogesh. Concurrency and Computation: Practice and Experience.
Learning Neural Markers of Schizophrenia Disorder Using Recurrent Neural Networks. Jumana Dakka, Pouya Bashivan, Mina Gheiratmand, Irina Rish, Shantenu Jha and Russell Greiner. Machine Learning for Health Workshop at Neural Information Processing Systems (NIPS 2017), Long Beach, California, US.
Toward Common Components for Open Workflow Systems. Jay Jay Billings and Shantenu Jha. Proceedings of Open Source SuperComputing, Workshop at SC'17.
Evaluating Distributed Execution of Workloads. M. Turilli, Y. N. Babuji, A. Merzky, M. T. Ha, M. Wilde, D. S. Katz and S. Jha. 2017 IEEE 13th International Conference on e-Science (e-Science).
High-Throughput Computing on High-Performance Platforms: A Case Study. D. Oleynik, S. Panitkin, M. Turilli, A. Angius, S. Oral, K. De, A. Klimentov, J. C. Wells and S. Jha. 2017 IEEE 13th International Conference on e-Science (e-Science).
Enabling Trade-offs Between Accuracy and Computational Cost: Adaptive Algorithms to Reduce Time to Clinical Insight. Jumana Dakka, Kristof Farkas-Pall, Vivek Balasubramanian, Matteo Turilli, Shunzhou Wan, David W Wright, Stefan Zasada, Peter V Coveney and Shantenu Jha. 2018 18th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGRID).
Executing dynamic heterogeneous workloads on Blue Waters with RADICAL-Pilot. Santcroos, Mark, Castain, Ralph, Merzky, Andre, Bethune, Iain and Jha, Shantenu. Cray User Group 2016 (London).
Synapse: Synthetic Application Profiler and Emulator. Andre Merzky and Shantenu Jha. 2016 IEEE International Parallel and Distributed Processing Symposium Workshops, IPDPS Workshops 2016, Chicago, IL, USA, May 23-27, 2016.
On the Complexities of Utilizing Large-Scale Lightpath-Connected Distributed Cyberinfrastructure. Jason Maassen et al . Concurrency and Computation: Practice and Experience.
Hadoop on HPC: Integrating Hadoop and Pilot-Based Dynamic Resource Management. Andre Luckow, Ioannis Paraskevakos, George Chantzialexiou and Shantenu Jha. 2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW).
Integration Of PanDA Workload Management System with Supercomputers for ATLAS and Data-Intensive Sciences. A. Klimentov, K. De, S. Jha, T. Maeno, R. Mashinistov, P. Nilsson, A. Novikov, D. Oleynik, S. Panitkin, A.Poyda, K.F.Read, E. Ryabinkin, A. Teslyuk, J.C. Wells and T. Wenaus. Journal of Physics: Conference Series, Volume 762 (2016), 012021, 17th International Workshop on Advanced Computing and Analysis Techniques in Physics Research (ACAT 2016, Valparaiso, Chile, 20160118, 20160122).
Integration of Panda Workload Management System with supercomputers. De, K., Jha, S., Klimentov, A., Maeno, T., Mashinistov, R., Nilsson, P., Novikov, A., Oleynik, D., Panitkin, S., Poyda, A., Read, K. F., Ryabinkin, E., Teslyuk, A., Velikhov, V., Wells, J. C. and Wenaus, T.. Physics of Particles and Nuclei Letters.
ExTASY: Scalable and flexible coupling of MD simulations and advanced sampling techniques. V. Balasubramanian, I. Bethune, A. Shkurti, E. Breitmoser, E. Hruska, C. Clementi, C. Laughton and S. Jha. 2016 IEEE 12th International Conference on e-Science (e-Science).
RepEx: A Flexible Framework for Scalable Replica Exchange Molecular Dynamics Simulations. A. Treikalis, A. Merzky, H. Chen, T. S. Lee, D. M. York and S. Jha. 2016 45th International Conference on Parallel Processing (ICPP).
Ensemble Toolkit: Scalable and Flexible Execution of Ensembles of Tasks. Vivekanandan Balasubramanian, Antons Treikalis, Ole Weidner, and Shantenu Jha. 45th International Conference on in Parallel Processing (ICPP), pp. 458-463. IEEE, 2016.
Application Skeleton: Generating Synthetic Applications for Infrastructure Research. Zhao Zhang and Daniel S. Katz and Andre Merzky and Matteo Turilli and Shantenu Jha and Yadu Nand. The Journal of Open Source Software.
Integrating Abstractions to Enhance the Execution of Distributed Applications. Matteo Turilli, Feng (Francis) Liu, Zhao Zhang, Andre Merzky, Michael Wilde, Jon Weissman, Daniel S. Katz and Shantenu Jha. Proceedings of 30th IEEE International Parallel and Distributed Processing Symposium (IPDPS).
Characterization of the Three-Dimensional Free Energy Manifold for the Uracil Ribonucleoside from Asynchronous Replica Exchange Simulations. Brian K. Radak, Melissa Romanus, Tai-Sung Lee, Haoyuan Chen, Ming Huang, Antons Treikalis, Vivekanandan Balasubramanian, Shantenu Jha and Darrin M. York. Journal of Chemical Theory and Computation.
{SAGA}: A Standardized Access Layer to Heterogeneous Distributed Computing Infrastructure. Andre Merzky, Ole Weidner and Shantenu Jha. Software-X.
Next Generation Workload Management System For Big Data on Heterogeneous Distributed Computing. A Klimentov, P Buncic, K De, S Jha, T Maeno, R Mount, P Nilsson, D Oleynik and S Panitkin, A Petrosyan, R J Porter, K F Read, A Vaniachine, J C Wells and T Wenaus. Journal of Physics: Conference Series.
Application skeletons: Construction and use in eScience . Daniel S. Katz, Andre Merzky, Zhao Zhang and Shantenu Jha. Future Generation Computer Systems.
Computing Clinically Relevant Binding Free Energies of HIV-1 Protease Inhibitors. David W. Wright, Benjamin A. Hall, Owain A. Kenway, Shantenu Jha and Peter V. Coveney. Chemical Theory and Computation.
Developing eThread Pipeline Using SAGA- Pilot Abstraction for Large-Scale Structural Bioinformatics. Anjani Ragothaman, Sairam Chowdary Boddu, Nayong Kim, Wei Feinstein, Michal Brylinski, Shantenu Jha and Joohyun Kim. BioMed Research International.
Numerical Experiments of Solving Moderate-velocity Flow Field Using a Hybrid Computational Fluid Dynamics Molecular Dynamics Approach. Soon-Heum Ko, Nayong Kim, Shantenu Jha, Dimitris E. Nikitopoulos, Dorel Moldovan. Mechanical Science and Technology.
A Tale of Two Data-Intensive Paradigms: Applications, Abstractions, and Architectures. Shantenu Jha, Judy Qiu, Andre Luckow, Pradeep Mantha and Geoffrey C.Fox. 2014 IEEE International Congress on Big Data (BigData Congress).
Pilot-Data: An Abstraction for Distributed Data. Andre Luckow, Mark Santcroos, Ashley Zebrowski and Shantenu Jha. Journal Parallel and Distributed Computing.
Comparative analysis of nucleotide translocation through protein nanopores using steered molecular dynamics and an adaptive biasing force. Hugh S. C. Martin and Shantenu Jha and Peter V.Coveney. Computational Chemistry.
Towards Standardized Job Submission and Control in Infrastructure Clouds. Peter Troger and Andre Merzky. Journal of Grid Computing.
Scalable Online Comparative Genomics of Mononucleosomes: A BigJob. Jack Smith, Melissa Romanus, James Solow, Pradeep Kumar Mantha, Yaakoub El Khamra, Thomas C. Bishop and Shantenu Jha. Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery.
Exploring Dynamic Enactment of Scientific Workflows using Pilot-Abstractions. Mark Santcroos, Barbera DC van Schaik, Shayan Shahand, Silvia Delgado Olabarriaga, Andre Luckow and Shantenu Jha. 13th IEEE/ACM International Conference on Cluster, Cloud and Grid Computing.
A Framework for Flexible and Scalable Replica-Exchange on Production Distributed CI. Brian K. Radak, Melissa Romanus, Emilio Gallicchio, Tai-Sung Lee, Ole Weidner, Nan-Jie Deng, Peng He, Wei Dai, Darrin M. York, Ronald M. Levy and Shantenu Jha. Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery.
Advancing next-generation sequencing data analytics with scalable distributed infrastructure. Kim, Joohyun and Maddineni, Sharath and Jha, Shantenu. Concurrency and Computation: Practice and Experience.
Distributed computing practice for large-scale science and engineering applications. Jha, Shantenu and Cole, Murray and Katz, Daniel S. and Parashar, Manish and Rana, Omer and Weissman, Jon. Concurrency and Computation: Practice and Experience.
Pilot abstractions for compute, data, and network. Mark Santcroos, Silvia Delgado Olabarriaga, Daniel S. Katz and Shantenu Jha. 2012 IEEE 8th International Conference on E-Science.
The Anatomy of Successful ECSS Projects: Lessons of supporting High-Throughput High-Performance Ensembles on XSEDE. Melissa Romanus, Pradeep Kumar Mantha, Matt McKenzie, Thomas C. Bishop, Emilio Gallichio, Andre Merzky, Yaakoub El Khamra and Shantenu Jha. Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the Campus and Beyond.
Running many Molecular Dynamics Simulations on many Supercomputers. Rajib Mukherjee, Abhinav Thota, Hideki Fujioka, Thomas C. Bishop and Shantenu Jha. Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the Campus and Beyond.
Pilot-MapReduce: an extensible and flexible MapReduce implementation for distributed data. Pradeep Kumar Mantha, Andre Luckow and Shantenu Jha. Proceedings of third international workshop on MapReduce and its Applications.
Distributed Application Runtime Environment (DARE): A Standards-based Middleware Framework for Science-Gateways. Maddineni, Sharath, Kim, Joohyun, El-Khamra, Yaakoub and Jha, Shantenu. J. Grid Comput..
P*: A model of pilot-abstractions. Andre Luckow, Mark Santcroos, Andre Merzky, Ole Weidner, Pradeep Mantha and Shantenu Jha. IEEE 8th International Conference on e-Science.
Conformational Heterogeneity of the SAM-I Riboswitch Transcriptional ON State: A Chaperone-Like Role for S-Adenosyl Methionine. Wei Huang, Joohyun Kim, Shantenu Jha and Fareed Aboul-ela. Journal of Molecular Biology.
Quantized Water Access to the HIV-1 Protease Active Site as a Proposed Mechanism for Cooperative Mutations in Drug Affinity. Benjamin A. Hall, David W. Wright, Shantenu Jha and Peter V. Coveney. Biochemistry.
Understanding MapReduce-based Next-Generation Sequencing Alignment on Distributed Cyberinfrastructure. Pradeep Mantha, Nayong Kim, Joohyun Kim, Andre Luckow and Shantenu Jha. 3rd International Workshop on Emerging Methods in Computational Life Sciences, Proceedings of the 21st International Symposium on High-Performance Parallel and Distributed Computing, HPDC'12.
Towards a common model for pilot-jobs. Andre Luckow, Mark Santcroos, Ole Weidner, Andre Merzky, Sharath Maddineni and Shantenu Jha. Proceedings of the 21st International Symposium on High-Performance Parallel and Distributed Computing, HPDC'12.
Efficient large-scale Replica-Exchange Simulations on Production Infrastructure. Abhinav Thota and Andre Luckow and Shantenu Jha. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.
Understanding Application-Level Interoperability: Scaling-Out MapReduce over High-Performance Grids and Clouds. Saurabh Sehgal, Miklos Erdelyi, Andre Merzky and Shantenu Jha. Future Generation Computer Systems.
Using the TeraGrid to teach Scientific Computing. Frank Loffler, Gabrielle Allen, Werner Benger, Andrei Hutanu, Shantenu Jha and Erik Schnetter. Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery.
Energy Landscape Analysis for Regulatory RNA Finding using Scalable Distributed Cyberinfrastructure. Joohyun Kim, Wei Huang, Sharath Maddineni, Fareed Aboul-ela and Shantenu Jha. Concurrency and Computation: Practice and Experience.
Characterizing deep sequencing analytics using BFAST: towards a scalable distributed architecture for next-generation sequencing data. Joohyun Kim and Sharath Maddineni and Shantenu Jha. Proceedings of the second international workshop on Emerging computational methods for the life sciences.
Building Gateways for Life-Science Applications using the Dynamic Application Runtime Environment (DARE) Framework. Joohyun Kim, Sharath Maddineni and Shantenu Jha. Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery.
Towards high-throughput, high-performance computational estimation of binding affinities for patient specific HIV-1 protease sequences. Owain Kenway, David W. Wright, Helmut Heller, Andre Merzky, Gavin Pringle, Jules Wolfrat, Peter Coveney and Shantenu Jha. Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery.
A Practical and Comprehensive Graduate Course preparing Students for Research involving Scientific Computing. Gabrielle Allen, Werner Benger, Andrei Hutanu, Shantenu Jha, Frank Loffler and Erik Schnetter. Procedia Computer Science.
Understanding Scientific Applications for Cloud Environments. Shantenu Jha and Daniel S. Katz and Andre Luckow and Andre Merzky and Katerina Stamou. Cloud Computing: Principles and Paradigms.
SAGA BigJob: An Extensible and Interoperable Pilot-Job Abstraction for Distributed Applications and Systems. Andre Luckow, Lukas Lacinski and Shantenu Jha. The 10th IEEE/ACM International Symposium on Cluster,Cloud and Grid Computing.
Abstractions for Loosely-Coupled and Ensemble-Based Simulations on Azure. Andre Luckow and Shantenu Jha. International IEEE Conference on Cloud Computing Technology and Science.
Efficient Runtime Environment for Coupled Multi-physics Simulations: Dynamic Resource Allocation and Load-Balancing. Soon-Heum Ko, Nayong Kim, Joohyun Kim, Abhinav Thota and Shantenu Jha. Proceedings of the 2010 10th IEEE/ACM International Conference on Cluster, Cloud and Grid Computing.
Exploring the {RNA} folding energy landscape using scalable distributed cyberinfrastructure. Joohyun Kim, Wei Huang, Sharath Maddineni, Fareed Aboul-Ela and Shantenu Jha. Emerging Computational Methods in the Life Sciences, Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing.
Modelling data-driven CO2 sequestration using distributed HPC cyberinfrastructure. Yaakoub El-Khamra, Shantenu Jha and Christopher D. White. {Proceedings of the 2010 TeraGrid Conference}.
What Is the Price of Simplicity? -- A Cross-Platform Evaluation of the SAGA API. Mathijs Den Burger, Ceriel Jacobs, Thilo Kielmann, Andre Merzky, Ole Weidner and Hartmut Kaiser. Proceedings of the 16th international Euro-Par conference on Parallel processing: Part I.
Understanding Performance of Distributed Data-Intensive Applications. Chris Miceli, Michael Miceli, Bety Rodriguez-Milla and Shantenu Jha. Royal Society of London Philosophical Transactions Series A.
A Fresh Perspective on Developing and Executing DAG-Based Distributed Applications: A Case-Study of SAGA-Based Montage. Andre Merzky, Katerina Stamou, Shantenu Jha and Daniel S. Katz. Proceedings of the 2009 Fifth IEEE International Conference on e-Science.
Application Level Interoperability between Clouds and Grids. Andre Merzky, Katerina Stamou and Shantenu Jha. Proceedings of the IEEE Grid and Pervasive Computing Conference '09.
Adaptive Distributed Replica--Exchange Simulations. Andre Luckow, Shantenu Jha, Joohyun Kim, Andre Merzky and Bettina Schnor. Theme Issue of the Philosophical Transactions of the Royal Society A: Crossing Boundaries: Computational Science, E-Science and Global E-Infrastructure Proceedings of the UK e-Science All Hands Meeting.
Louisiana: a model for advancing regional e-Research through cyberinfrastructure. Daniel S. Katz, Gabrielle Allen, R. Cortez, C. Cruz-Neira, R. Gottumukkala, Z. D. Greenwood, L. Guice, Shantenu Jha, R. Kolluru, Tevfik Kosar and others. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.
Using Clouds to Provide Grids with Higher Levels of Abstraction and Explicit Support for Usage Modes. Shantenu Jha, Andre Merzky and Geoffrey Fox. Concurrency and Computation: Practice and Experience.
Developing Scientific Applications with Loosely-Coupled Sub-tasks. Shantenu Jha and Yaakoub El-Khamra and Joohyun Kim. Proceedings of the 9th International Conference on Computational Science: Part I.
Critical Perspectives on Large-Scale Distributed Applications and Production Grids. Shantenu Jha, Daniel S. Katz, Manish Parashar, Omer Rana and Jon B. Weissman. The 10th IEEE/ACM Conference on Grid Computing 2009, (Best Paper Award).
Modelling Data-Driven CO_2 Sequestration Using Distributed HPC CyberInfrastructure. Yaakoub El-Khamra and Shantenu Jha. Microsoft Research eScience Workshop, Pittsburgh.
Developing Autonomic Distributed Scientific Applications: A Case Study From History Matching Using Ensemble Kalman-Filters. Yaakoub El-Khamra and Shantenu Jha. GMAC '09: Proceedings of the 6th International Conference Industry Session on Grids meets Autonomic Computing.
Adaptive Replica-Exchange Simulations. Andre Luckow, Shantenu Jha, Joohyun Kim, Andre Merzky and Bettina Schnor. Royal Society Philosophical Transactions A.
Programming Abstractions for Data Intensive Computing on Clouds and Grids. Chris Miceli and Michael Miceli and Shantenu Jha and Hartmut Kaiser and Andre Merzky. 9th IEEE/ACM International Symposium on Cluster Computing and the Grid, 2009..
Distributed Replica-Exchange Simulations on Production Environments Using SAGA and Migol. Andre Luckow, Shantenu Jha, Joohyun Kim, Andre Merzky and Bettina Schnor. Proceedings of the 2008 Fourth IEEE International Conference on eScience.
Developing Large-Scale Adaptive Scientific Applications with Hard to Predict Runtime Resource Requirements. Shantenu Jha, Yaakoub El-Khamra, Hartmut Kaiser, Ole Weidner and Andre Merzky. Proceedings of TeraGrid08.
Grid Interoperability at the Application Level Using SAGA. Shantenu Jha, Hartmut Kaiser, Andre Merzky and Ole Weidner. E-SCIENCE '07: Proceedings of the Third IEEE International Conference on e-Science and Grid Computing (e-Science 2007).
Design and Implementation of Network Performance Aware Applications Using SAGA and Cactus. Shantenu Jha, Hartmut Kaiser, Yaakoub El-Khamra and Ole Weidner. Proceedings of the Third IEEE International Conference on e-Science and Grid Computing.
SAGA: A Simple API for Grid applications, High-Level Application Programming on the Grid. Tom Goodale, Shantenu Jha, Harmut Kaiser, Thilo Kielmann, Pascal Kleijer, Gregor von Laszewski, Craig Lee, Andre Merzky, Hrabri Rajic and John Shalf. Computational Methods in Science and Technology.
GRID SuperScalar and SAGA: forming a high-level and platform-independent Grid Programming Environment. Raoul Sirvent, Andre Merzky, Rosa M. Badia and Thilo Kielmann. CoreGRID Integration WorkShop.
Towards Scalable Execution Across Multiple XSEDE Resources. Shantenu Jha.
High-level software frameworks to surmount the challenge of 100x scaling for biomolecular simulation science. Shantenu Jha and Peter M. Kasson.
Workshop on Streaming Systems, Draft Report v0.1 (08 Jan 2016). Geoffrey Fox and Shantenu Jha and Lavanya Ramakrishnan.
Scalable HPC Workflow Infrastructure for Steering Scientific Instruments and Streaming Applications. Geoffrey Fox, Shantenu Jha and Lavanya Ramakrishnan.
Implications of the HPC-ABDS High Performance Computing Enhanced Apache Big Data Stack for Workflows. Geoffrey Fox and Shantenu Jha.
From Abstractions to MOD-ELS: MOdels for Distributed and Extremely Large-scale Science. Shantenu Jha, Daniel S. Katz, Matteo Turilli and Jon Weissman. White Paper Submitted to Advanced Scientific Computing and Research, DOE Office of Science.
Modeling Distributed Extreme-Scale Applications and Systems. Shantenu Jha, Andre Merzky and Matteo Turilli. Workshop on Modeling & Simulation of Exascale Systems & Applications.
Distributed Exascale Computing: An AIMES Perspective. Shantenu Jha, Andre Merzky, Matteo Turilli, Daniel S. Katz and Jon Weissman. Workshop on Modeling & Simulation of Exascale Systems & Applications.
FutureGrid 2012 Project Challenge: Project 45: Building Scalable, Dynamic and Distributed Applications Using SAGA. Pradeep Kumar Mantha, Sivakarthik Natesan, Melissa Romanus, Sai Saripalli and Ashley Zebrowski.
SAGA Extension: Information Service Navigator API. Steve Fisher and Antony Wilson.
SAGA Extension: Message API. Andre Merzky.
SAGA Extension: Advert API. Andre Merzky.
Survey and Analysis of Production Distributed Computing Infrastructures (CI-TR-7-0811). Daniel S. Katz, Shantenu Jha, Manish Parashar, Omer F. Rana and Jon Weissman.
SAGA Extension: Checkpoint and Recovery API (CPR). Andre Merzky, Andre Luckow and Derek Simmel.
A Simple API for Grid Applications (SAGA). Tom Goodale, Shantenu Jha, Hartmut Kaiser, Thilo Kielmann, Pascal Kleijer, Andre Merzky, John Shalf and Christopher Smith.
A Collection of Use Cases for a Simple API for Grid Applications. Andre Merzky and Shantenu Jha.
A Requirements Analysis for a Simple API for Grid Applications. Shantenu Jha and Andre Merzky.