Publications

Scientific Papers, Journals, Presentations, Posters, and Technical Reports

2021

  1. Brown, D., Vahi, K., Taufer, M., Welch, V., & Deelman, E. (2021). Reproducing GW150914: the first observation of gravitational waves from a binary black hole merger. Computing in Science & Engineering. https://doi.org/10.1109/MCSE.2021.3059232 (Funding Acknowledgment: NSF 1664162, NSF 1823405)
    @article{brown2021reproducing,
      title = {Reproducing GW150914: the first observation of gravitational waves from a binary black hole merger},
      author = {Brown, Duncan and Vahi, Karan and Taufer, Michela and Welch, Von and Deelman, Ewa},
      journal = {Computing in Science \& Engineering},
      year = {2021},
      publisher = {IEEE},
      doi = {10.1109/MCSE.2021.3059232},
      note = {Funding Acknowledgment: NSF 1664162, NSF 1823405}
    }
  2. Coleman, T., Casanova, H., Gwartney, T., & Ferreira da Silva, R. (2021). Evaluating energy-aware scheduling algorithms for I/O-intensive scientific workflows. International Conference on Computational Science (ICCS). (Funding Acknowledgment: NSF 1923539, NSF 2016619)
    @inproceedings{coleman2021iccs,
      author = {Coleman, Tain\=a and Casanova, Henri and Gwartney, Ty and Ferreira da Silva, Rafael},
      title = {Evaluating energy-aware scheduling algorithms for I/O-intensive scientific workflows},
      booktitle = {International Conference on Computational Science (ICCS)},
      year = {2021},
      pages = {},
      doi = {},
      note = {Funding Acknowledgment: NSF 1923539, NSF 2016619}
    }
  3. Deelman, E., Mandal, A., Murillo, A. P., Nabrzyski, J., Pascucci, V., Ricci, R., Baldin, I., Sons, S., Christopherson, L., Vardeman, C., Ferreira da Silva, R., Wyngaard, J., Petruzza, S., Rynge, M., Vahi, K., Whitcup, W. R., Drake, J., & Scott, E. (2021). Blueprint: Cyberinfrastructure Center of Excellence. Zenodo. https://doi.org/10.5281/zenodo.4587866
    @article{deelman2021blueprint,
      title = {{Blueprint: Cyberinfrastructure Center of Excellence}},
      author = {Deelman, Ewa and Mandal, Anirban and Murillo, Angela P. and Nabrzyski, Jarek and Pascucci, Valerio and Ricci, Robert and Baldin, Ilya and Sons, Susan and Christopherson, Laura and Vardeman, Charles and Ferreira da Silva, Rafael and Wyngaard, Jane and Petruzza, Steve and Rynge, Mats and Vahi, Karan and Whitcup, Wendy R. and Drake, Josh and Scott, Erik},
      journal = {Zenodo},
      year = {2021},
      doi = {10.5281/zenodo.4587866}
    }
  4. Do, T. M. A., Pottier, L., Caíno-Lores, S., Ferreira da Silva, R., Cuendet, M. A., Weinstein, H., Estrada, T., Taufer, M., & Deelman, E. (2021). A Lightweight Method for Evaluating In Situ Workflow Efficiency. Journal of Computational Science, 48, 101259. https://doi.org/10.1016/j.jocs.2020.101259 (Funding Acknowledgments: NSF 1741040, DOE DE-SC0012636)
    @article{do2020jocs,
      title = {A Lightweight Method for Evaluating In Situ Workflow Efficiency},
      author = {Do, Tu Mai Anh and Pottier, Lo\"ic and Ca\'ino-Lores, Silvina and Ferreira da Silva, Rafael and Cuendet, Michel A. and Weinstein, Harel and Estrada, Trilce and Taufer, Michela and Deelman, Ewa},
      journal = {Journal of Computational Science},
      volume = {48},
      number = {},
      pages = {101259},
      year = {2021},
      doi = {10.1016/j.jocs.2020.101259},
      note = {Funding Acknowledgments: NSF 1741040, DOE DE-SC0012636}
    }
  5. Ferreira da Silva, R., Casanova, H., Chard, K., Laney, D., Ahn, D., Jha, S., Goble, C., Ramakrishnan, L., eerson, L., Enders, B., Thain, D., Altintas, I., Babuji, Y., Badia, R., Bonazzi, V., Coleman, T., Crusoe, M., Deelman, E., Di Natale, F., … Wozniak, J. (2021). Workflows Community Summit: Bringing the Scientific Workflows Community Together. Zenodo. https://doi.org/10.5281/zenodo.4606958
    @misc{ferreiradasilva2021wcs,
      author = {Ferreira da Silva, Rafael and Casanova, Henri and Chard, Kyle and Laney, Dan and Ahn, Dong and Jha, Shantenu and Goble, Carole and Ramakrishnan, Lavanya and eerson, Luc and Enders, Bjoern and Thain, Douglas and Altintas, Ilkay and Babuji, Yadu and Badia, Rosa and Bonazzi, Vivien and Coleman, Taina and Crusoe, Michael and Deelman, Ewa and Di Natale, Frank and Di Tommaso, Paolo and Fahringer, Thomas and Filgueira, Rosa and Fursin, Grigori and Ganose, Alex and Gruning, Bjorn and Katz, Daniel S. and Kuchar, Olga and Kupresanin, Ana and Ludascher, Bertram and Maheshwari, Ketan and Mattoso, Marta and Mehta, Kshitij and Munson, Todd and Ozik, Jonathan and Peterka, Tom and Pottier, Loic and Randles, Tim and Soiland-Reyes, Stian and Tovar, Benjamin and Turilli, Matteo and Uram, Thomas and Vahi, Karan and Wilde, Michael and Wolf, Matthew and Wozniak, Justin},
      title = {{Workflows Community Summit: Bringing the Scientific Workflows Community Together}},
      month = mar,
      year = {2021},
      publisher = {Zenodo},
      doi = {10.5281/zenodo.4606958}
    }
  6. Gil, Y., Garijo, D., Khider, D., Knoblock, C. A., Ratnakar, V., Osorio, M., Vargas, H., Pham, M., Pujara, J., Shbita, B., Vu, B., Chiang, Y.-Y., Feldman, D., Lin, Y., Song, H., Kumar, V., Khandelwal, A., Steinbach, M., Tayal, K., … Shu, L. (2021). Artificial Intelligence for Modeling Complex Systems: Taming the Complexity of Expert Models to Improve Decision Making. ACM Transactions on Interactive Intelligent Systems. (Funding Acknowledgment: DARPA W911NF-18-1-0027)
    @article{gil2021tiis,
      title = {Artificial Intelligence for Modeling Complex Systems: Taming the Complexity of Expert Models to Improve Decision Making},
      author = {Gil, Yolanda and Garijo, Daniel and Khider, Deborah and Knoblock, Craig A. and Ratnakar, Varun and Osorio, Maximiliano and Vargas, Hernán and Pham, Minh and Pujara, Jay and Shbita, Basel and Vu, Binh and Chiang, Yao-Yi and Feldman, Dan and Lin, Yijun and Song, Hayley and Kumar, Vipin and Khandelwal, Ankush and Steinbach, Michael and Tayal, Kshitij and Xu, Shaoming and Pierce, Suzanne A. and Pearson, Lissa and Hardesty-Lewis, Daniel and Deelman, Ewa and Ferreira da Silva, Rafael and Mayani, Rajiv and Kemanian, Armen R. and Shi, Yuning and Leonard, Lorne and Peckham, Scott and Stoica, Maria and Cobourn, Kelly and Zhang, Zeya and Duffy, Christopher and Shu, Lele},
      journal = {ACM Transactions on Interactive Intelligent Systems},
      volume = {},
      number = {},
      pages = {},
      doi = {},
      year = {2021},
      note = {Funding Acknowledgment: DARPA W911NF-18-1-0027}
    }
  7. Hataishi, E., Dutot, P.-F., Ferreira da Silva, R., & Casanova, H. (2021). GLUME: A Strategy for Reducing Workflow Execution Times on Batch-Scheduled Platforms. Workshop on Job Scheduling Strategies for Parallel Processing (JSSPP). (Funding Acknowledgment: NSF 1923539)
    @inproceedings{hataishi2021jsspp,
      author = {Hataishi, Evan and Dutot, Pierre-Francois and Ferreira da Silva, Rafael and Casanova, Henri},
      title = {GLUME: A Strategy for Reducing Workflow Execution Times on Batch-Scheduled Platforms},
      booktitle = {Workshop on Job Scheduling Strategies for Parallel Processing (JSSPP)},
      year = {2021},
      pages = {},
      doi = {},
      note = {Funding Acknowledgment: NSF 1923539}
    }
  8. Papadimitriou, G., Wang, C., Vahi, K., Ferreira da Silva, R., Mandal, A., Zhengchun, L., Mayani, R., Rynge, M., Kiran, M., Lynch, V. E., Kettimuthu, R., Deelman, E., Vetter, J. S., & Foster, I. (2021). End-to-End Online Performance Data Capture and Analysis for Scientific Workflows. Future Generation Computer Systems, 117, 387–400. https://doi.org/10.1016/j.future.2020.11.024 (Funding Acknowledgments: DOE DE-SC0012636)
    @article{papadimitriou-fgcs-2020,
      title = {End-to-End Online Performance Data Capture and Analysis for Scientific Workflows},
      author = {Papadimitriou, George and Wang, Cong and Vahi, Karan and Ferreira da Silva, Rafael and Mandal, Anirban and Zhengchun, Liu and Mayani, Rajiv and Rynge, Mats and Kiran, Mariam and Lynch, Vickie E. and Kettimuthu, Rajkumar and Deelman, Ewa and Vetter, Jeffrey S. and Foster, Ian},
      journal = {Future Generation Computer Systems},
      year = {2021},
      volume = {117},
      number = {},
      pages = {387-400},
      doi = {10.1016/j.future.2020.11.024},
      note = {Funding Acknowledgments: DOE DE-SC0012636}
    }

2020

  1. Adams, J. C., Back, G., Bala, P., Bane, M. K., Cameron, K., Casanova, H., Ellis, M., Ferreira da Silva, R., Jethwani, G., Koch, W., Lee, T., & Zhu, T. (2020). Lightning Talks of EduHPC 2020. 2020 IEEE/ACM Workshop on Education for High-Performance Computing (EduHPC), 59–64. https://doi.org/10.1109/EduHPC51895.2020.00013 (Funding Acknowledgments: NSF 1923539)
    @inproceedings{adams2020eduhpc,
      author = {Adams, Joel C. and Back, Godmar and Bala, Piotr and Bane, Michael K. and Cameron, Kirk and Casanova, Henri and Ellis, Margaret and Ferreira da Silva, Rafael and Jethwani, Gautam and Koch, William and Lee, Tabitha and Zhu, Tongyu},
      title = {Lightning Talks of EduHPC 2020},
      booktitle = {2020 IEEE/ACM Workshop on Education for High-Performance Computing (EduHPC)},
      pages = {59--64},
      year = {2020},
      doi = {10.1109/EduHPC51895.2020.00013},
      note = {Funding Acknowledgments: NSF 1923539}
    }
  2. Casanova, H., Ferreira da Silva, R., Gonzalez-Escribano, A., Koch, W., Torres, Y., & Bunde, D. P. (2020). Peachy Parallel Assignments (EduHPC 2020). 2020 IEEE/ACM Workshop on Education for High-Performance Computing (EduHPC), 53–58. https://doi.org/10.1109/EduHPC51895.2020.00012 (Funding Acknowledgments: NSF 1923539)
    @inproceedings{casanova2020eduhpc,
      title = {Peachy Parallel Assignments (EduHPC 2020)},
      author = {Casanova, Henri and Ferreira da Silva, Rafael and Gonzalez-Escribano, Arturo and Koch, William and Torres, Yuri and Bunde, David P.},
      booktitle = {2020 IEEE/ACM Workshop on Education for High-Performance Computing (EduHPC)},
      pages = {53--58},
      year = {2020},
      doi = {10.1109/EduHPC51895.2020.00012},
      note = {Funding Acknowledgments: NSF 1923539}
    }
  3. Casanova, H., Ferreira da Silva, R., Tanaka, R., Pandey, S., Jethwani, G., Koch, W., Albrecht, S., Oeth, J., & Suter, F. (2020). Developing Accurate and Scalable Simulators of Production Workflow Management Systems with WRENCH. Future Generation Computer Systems, 112, 162–175. https://doi.org/10.1016/j.future.2020.05.030 (Funding Acknowledgments: NSF 1642335, NSF 1923539)
    @article{casanova2020fgcs,
      title = {Developing Accurate and Scalable Simulators of Production Workflow Management Systems with WRENCH},
      author = {Casanova, Henri and Ferreira da Silva, Rafael and Tanaka, Ryan and Pandey, Suraj and Jethwani, Gautam and Koch, William and Albrecht, Spencer and Oeth, James and Suter, Fr\'{e}d\'{e}ric},
      journal = {Future Generation Computer Systems},
      volume = {112},
      number = {},
      pages = {162--175},
      year = {2020},
      doi = {10.1016/j.future.2020.05.030},
      note = {Funding Acknowledgments: NSF 1642335, NSF 1923539}
    }
  4. Deelman, E., Ferreira da Silva, R., Vahi, K., Rynge, M., Mayani, R., Tanaka, R., Whitcup, W., & Livny, M. (2020). The Pegasus Workflow Management System: Translational Computer Science in Practice. Journal of Computational Science. https://doi.org/10.1016/j.jocs.2020.101200 (Funding Acknowledgments: NSF 1664162)
    @article{deelman2020jocs,
      title = {The Pegasus Workflow Management System: Translational Computer Science in Practice},
      author = {Deelman, Ewa and Ferreira da Silva, Rafael and Vahi, Karan and Rynge, Mats and Mayani, Rajiv and Tanaka, Ryan and Whitcup, Wendy and Livny, Miron},
      journal = {Journal of Computational Science},
      volume = {},
      number = {},
      pages = {},
      year = {2020},
      doi = {10.1016/j.jocs.2020.101200},
      note = {Funding Acknowledgments: NSF 1664162}
    }
  5. Do, T. M. A., Pottier, L., Thomas, S., Ferreira da Silva, R., Cuendet, M. A., Weinstein, H., Estrada, T., Taufer, M., & Deelman, E. (2020). A Novel Metric to Evaluate In Situ Workflows. International Conference on Computational Science (ICCS), 538–553. https://doi.org/10.1007/978-3-030-50371-0_40 (Funding Acknowledgments: NSF 1741040)
    @inproceedings{do2020iccs,
      author = {Do, Tu Mai Anh and Pottier, Loic and Thomas, Stephen and Ferreira da Silva, Rafael and Cuendet, Michel A. and Weinstein, Harel and Estrada, Trilce and Taufer, Michela and Deelman, Ewa},
      title = {A Novel Metric to Evaluate In Situ Workflows},
      booktitle = {International Conference on Computational Science (ICCS)},
      year = {2020},
      pages = {538--553},
      doi = {10.1007/978-3-030-50371-0_40},
      note = {Funding Acknowledgments: NSF 1741040}
    }
  6. Ferreira da Silva, R., Casanova, H., Orgerie, A.-C., Tanaka, R., Deelman, E., & Suter, F. (2020). Characterizing, Modeling, and Accurately Simulating Power and Energy Consumption of I/O-intensive Scientific Workflows. Journal of Computational Science, 44, 101157. https://doi.org/10.1016/j.jocs.2020.101157 (Funding Acknowledgments: NSF 1642335, NSF 1923539, NSF 1664162, DOE DE-SC0012636)
    @article{ferreiradasilva2020jocs,
      title = {Characterizing, Modeling, and Accurately Simulating Power and Energy Consumption of I/O-intensive Scientific Workflows},
      author = {Ferreira da Silva, Rafael and Casanova, Henri and Orgerie, Anne-C\'{e}cile and Tanaka, Ryan and Deelman, Ewa and Suter, Fr\'{e}d\'{e}ric},
      journal = {Journal of Computational Science},
      volume = {44},
      number = {},
      pages = {101157},
      year = {2020},
      doi = {10.1016/j.jocs.2020.101157},
      note = {Funding Acknowledgments: NSF 1642335, NSF 1923539, NSF 1664162, DOE DE-SC0012636}
    }
  7. Ferreira da Silva, R., Pottier, L., Coleman, T., Deelman, E., & Casanova, H. (2020). WorkflowHub: Community Framework for Enabling Scientific Workflow Research and Development. 2020 IEEE/ACM Workflows in Support of Large-Scale Science (WORKS), 49–56. https://doi.org/10.1109/WORKS51914.2020.00012 (Funding Acknowledgments: NSF 2016619, DOE DE-SC0012636, NSF 1664162, NSF 1923539)
    @inproceedings{ferreiradasilva2020works,
      title = {WorkflowHub: Community Framework for Enabling Scientific Workflow Research and Development},
      author = {Ferreira da Silva, Rafael and Pottier, Lo\"ic and Coleman, Tain\=a and Deelman, Ewa and Casanova, Henri},
      booktitle = {2020 IEEE/ACM Workflows in Support of Large-Scale Science (WORKS)},
      year = {2020},
      pages = {49--56},
      doi = {10.1109/WORKS51914.2020.00012},
      note = {Funding Acknowledgments: NSF 2016619, DOE DE-SC0012636, NSF 1664162, NSF 1923539}
    }
  8. Kiran, M., Wang, C., Papadimitriou, G., Mandal, A., & Deelman, E. (2020). Detecting Anomalous Packets in Network Transfers: Investigations using PCA, Autoencoder and Isolation Forest in TCP. Machine Learning. https://doi.org/10.1007/s10994-020-05870-y (Funding Acknowledgments: DOE DESC0012636)
    @article{kiran-ml-2020,
      author = {Kiran, Mariam and Wang, Cong and Papadimitriou, George and Mandal, Anirban and Deelman, Ewa},
      title = {Detecting Anomalous Packets in Network Transfers: Investigations using PCA, Autoencoder and Isolation Forest in TCP},
      journal = {Machine Learning},
      year = {2020},
      volume = {},
      number = {},
      pages = {},
      issn = {1573-0565},
      doi = {10.1007/s10994-020-05870-y},
      url = {https://doi.org/10.1007/s10994-020-05870-y},
      note = {Funding Acknowledgments: DOE DESC0012636}
    }
  9. Lyons, E., Westbrook, D., Grote, A., Papadimitriou, G., Thareja, K., Wang, C., Zink, M., Deelman, E., Mandal, A., & Ruth, P. (2020). An On-Demand Weather Avoidance System for Small Aircraft Flight Path Routing. In F. Darema, E. Blasch, S. Ravela, & A. Aved (Eds.), Dynamic Data Driven Application Systems (pp. 311–319). Springer International Publishing. https://doi.org/10.1007/978-3-030-61725-7_36 (Funding Acknowledgments: NSF 1826997, 2018074)
    @inproceedings{lyons-dddas-2020,
      author = {Lyons, Eric and Westbrook, David and Grote, Andrew and Papadimitriou, George and Thareja, Komal and Wang, Cong and Zink, Michael and Deelman, Ewa and Mandal, Anirban and Ruth, Paul},
      editor = {Darema, Frederica and Blasch, Erik and Ravela, Sai and Aved, Alex},
      title = {An On-Demand Weather Avoidance System for Small Aircraft Flight Path Routing},
      booktitle = {Dynamic Data Driven Application Systems},
      year = {2020},
      publisher = {Springer International Publishing},
      address = {Cham},
      pages = {311--319},
      isbn = {978-3-030-61725-7},
      doi = {10.1007/978-3-030-61725-7_36},
      note = {Funding Acknowledgments: NSF 1826997, 2018074}
    }
  10. Lyons, E., Zink, M., Mandal, A., Wang, C., Ruth, P., Radhakrishnan, C., Papadimitriou, G., Deelman, E., Thareja, K., & Rodero, I. (2020). DyNamo: Scalable Weather Workflow Processing in the Academic MultiCloud. 100th American Meteorological Society Annual Meeting. (Funding Acknowledgments: NSF 1826997)
    @article{lyons-ams100-2020,
      title = {DyNamo: Scalable Weather Workflow Processing in the Academic MultiCloud},
      author = {Lyons, Eric and Zink, Michael and Mandal, Anirban and Wang, Cong and Ruth, Paul and Radhakrishnan, Chandrasekar and Papadimitriou, George and Deelman, Ewa and Thareja, Komal and Rodero, Ivan},
      journal = {100th American Meteorological Society Annual Meeting},
      volume = {},
      number = {},
      pages = {},
      year = {2020},
      doi = {},
      note = {Funding Acknowledgments: NSF 1826997}
    }
  11. Papadimitriou, G., Lyons, E., Wang, C., Thareja, K., Tanaka, R., Ruth, P., Villalobos, J. J., Rodero, I., Deelman, E., Zink, M., & Mandal, A. (2020, November). Application Aware Software Defined Flows of Workflow Ensembles. 2020 IEEE/ACM Innovating the Network for Data-Intensive Science (INDIS). (Funding Acknowledgments: NSF 1826997)
    @inproceedings{papadimitriou-indis-2020,
      title = {Application Aware Software Defined Flows of Workflow Ensembles},
      author = {Papadimitriou, George and Lyons, Eric and Wang, Cong and Thareja, Komal and Tanaka, Ryan and Ruth, Paul and Villalobos, J.J. and Rodero, Ivan and Deelman, Ewa and Zink, Michael and Mandal, Anirban},
      booktitle = {2020 IEEE/ACM Innovating the Network for Data-Intensive Science (INDIS)},
      year = {2020},
      pages = {},
      doi = {},
      month = nov,
      note = {Funding Acknowledgments: NSF 1826997}
    }
  12. Papadimitriou, G., Vahi, K., Kincl, J., Anantharaj, V., Deelman, E., & Wells, J. (2020). Workflow Submit Nodes as a Service on Leadership Class Systems. Proceedings of the Practice and Experience in Advanced Research Computing. https://doi.org/10.1145/3311790.3396671 (Funding Acknowledgments: DOE DESC0012636)
    @inproceedings{papadimitriou-pearc-2020,
      author = {Papadimitriou, George and Vahi, Karan and Kincl, Jason and Anantharaj, Valentine and Deelman, Ewa and Wells, Jack},
      title = {Workflow Submit Nodes as a Service on Leadership Class Systems},
      year = {2020},
      isbn = {978-1-4503-6689-2/20/07},
      publisher = {Association for Computing Machinery},
      address = {New York, NY, USA},
      url = {http://doi.acm.org/10.1145/3311790.3396671},
      doi = {10.1145/3311790.3396671},
      booktitle = {Proceedings of the Practice and Experience in Advanced Research Computing},
      articleno = {},
      numpages = {},
      location = {Portland, OR, USA},
      series = {PEARC '20},
      note = {Funding Acknowledgments: DOE DESC0012636}
    }
  13. Pottier, L., Ferreira da Silva, R., Casanova, H., & Deelman, E. (2020). Modeling the Performance of Scientific Workflow Executions on HPC Platforms with Burst Buffers. 2020 IEEE International Conference on Cluster Computing (CLUSTER), 92–103. https://doi.org/10.1109/CLUSTER49012.2020.00019 (Funding Acknowledgments: DOE DE-SC0012636, NSF 1664162, NSF 1741040, NSF 1923539, NSF 1923621)
    @inproceedings{pottier2020cluster,
      author = {Pottier, Loic and Ferreira da Silva, Rafael and Casanova, Henri and Deelman, Ewa},
      title = {Modeling the Performance of Scientific Workflow Executions on HPC Platforms with Burst Buffers},
      booktitle = {2020 IEEE International Conference on Cluster Computing (CLUSTER)},
      year = {2020},
      pages = {92--103},
      doi = {10.1109/CLUSTER49012.2020.00019},
      note = {Funding Acknowledgments: DOE DE-SC0012636, NSF 1664162, NSF 1741040, NSF 1923539, NSF 1923621}
    }
  14. Vahi, K., Goldstein, D., Papadimitriou, G., Nugent, P., & Deelman, E. (2020). Gearing the DECam Analysis Pipeline for Multi-Messenger Astronomy using Pegasus Workflows. Astronomical Data Analysis Software and Systems (ADASS) XXIX. (Funding Acknowledgments: NSF 1664162, DOE DESC0012636)
    @article{vahi-adass-2019,
      title = {Gearing the DECam Analysis Pipeline for Multi-Messenger Astronomy using Pegasus Workflows},
      author = {Vahi, Karan and Goldstein, Danny and Papadimitriou, George and Nugent, Peter and Deelman, Ewa},
      journal = {Astronomical Data Analysis Software and Systems (ADASS) XXIX},
      volume = {},
      year = {2020},
      pages = {},
      note = {Funding Acknowledgments: NSF 1664162, DOE DESC0012636}
    }
  15. Versluis, L., Mathá, R., Talluri, S., Hegeman, T., Prodan, R., Deelman, E., & Iosup, A. (2020). The Workflow Trace Archive: Open-Access Data from Public and Private Computing Infrastructures. IEEE Transactions on Parallel and Distributed Systems, 31(9), 2170–2184. https://doi.org/10.1109/TPDS.2020.2984821 (Funding Acknowledgments: NSF 1664162)
    @article{versluis-tpds-2020,
      author = {Versluis, Laurens and Mathá, Roland and Talluri, Sacheendra and Hegeman, Tim and Prodan, Radu and Deelman, Ewa and Iosup, Alexandru},
      title = {The Workflow Trace Archive: Open-Access Data from Public and Private Computing Infrastructures},
      journal = {IEEE Transactions on Parallel and Distributed Systems},
      year = {2020},
      volume = {31},
      number = {9},
      doi = {10.1109/TPDS.2020.2984821},
      pages = {2170-2184},
      note = {Funding Acknowledgments: NSF 1664162}
    }
  16. Wang, C., Papadimitriou, G., Kiran, M., Mandal, A., & Deelman, E. (2020). Identifying Execution Anomalies for Data Intensive Workflows Using Lightweight ML Techniques. 2020 IEEE High Performance Extreme Computing Conference (HPEC). (Funding Acknowledgments: DOE DESC0012636)
    @inproceedings{wang-hpec-2020,
      title = {Identifying Execution Anomalies for Data Intensive Workflows Using Lightweight ML Techniques},
      author = {Wang, Cong and Papadimitriou, George and Kiran, Mariam and Mandal, Anirban and Deelman, Ewa},
      booktitle = {2020 IEEE High Performance extreme Computing Conference (HPEC)},
      year = {2020},
      volume = {},
      number = {},
      pages = {},
      doi = {},
      note = {Funding Acknowledgments: DOE DESC0012636}
    }

2019

  1. Bogol, S., Brenner, P., Brinckman, A., Deelman, E., Ferreira da Silva, R., Gupta, S., Nabrzyski, J., Park, S., Perez, D., Rynge, M., Taylor, I., Vahi, K., Werf, M. V., Sarah, R., & Wyngaard, S. (2019). A Secure Gateway for Enabling ASIC Design Collaborations. 11th International Workshop on Science Gateways (IWSG 2019). (Funding Acknowledgments: DARPA HR0011-16-C-0043)
    @inproceedings{bogol-iwsg-2019,
      title = {A Secure Gateway for Enabling ASIC Design Collaborations},
      author = {Bogol, Steve and Brenner, Paul and Brinckman, Adam and Deelman, Ewa and Ferreira da Silva, Rafael and Gupta, Sandeep and Nabrzyski, Jarek and Park, Soowang and Perez, Damian and Rynge, Mats and Taylor, Ian and Vahi, Karan and Werf, Matt Vander and Sarah, Rucker and Wyngaard, Sebastian},
      booktitle = {11th International Workshop on Science Gateways (IWSG 2019)},
      year = {2019},
      pages = {},
      doi = {},
      note = {Funding Acknowledgments: DARPA HR0011-16-C-0043}
    }
  2. Brinckman, A., Deelman, E., Gupta, S., Nabrzyski, J., Park, S., Ferreira da Silva, R., Taylor, I. J., & Vahi, K. (2019). Collaborative Circuit Designs using the CRAFT Repository. Future Generation Computer Systems, 94, 841–853. https://doi.org/10.1016/j.future.2018.01.018 (Funding Acknowledgments: DARPA HR0011-16-C-0043)
    @article{brinckman-fgcs-2018,
      title = {Collaborative Circuit Designs using the CRAFT Repository},
      author = {Brinckman, Adam and Deelman, Ewa and Gupta, Sandeep and Nabrzyski, Jarek and Park, Soowang and Ferreira da Silva, Rafael and Taylor, Ian J. and Vahi, Karan},
      journal = {Future Generation Computer Systems},
      volume = {94},
      number = {},
      pages = {841--853},
      year = {2019},
      doi = {10.1016/j.future.2018.01.018},
      note = {Funding Acknowledgments: DARPA HR0011-16-C-0043}
    }
  3. Chang, P., Allen, G., Anderson, W., Bianco, F. B., Bloom, J. S., Brady, P. R., Brazier, A., Cenko, S. B., Couch, S. M., DeYoung, T., Deelman, E., Etienne, Z. B., Foley, R. J., Fox, D. B., Golkhou, V. Z., Grant, D. R., Hanna, C., Holley-Bockelmann, K., Howell, D. A., … Zhang, Z. (2019). Cyberinfrastructure Requirements to Enhance Multi-messenger Astrophysics. https://arxiv.org/abs/1903.04590
    @misc{chang-astro2020-2019,
      author = {Chang, Philip and Allen, Gabrielle and Anderson, Warren and Bianco, Federica B. and Bloom, Joshua S. and Brady, Patrick R. and Brazier, Adam and Cenko, S. Bradley and Couch, Sean M. and DeYoung, Tyce and Deelman, Ewa and Etienne, Zachariah B and Foley, Ryan J. and Fox, Derek B and Golkhou, V. Zach and Grant, Darren R and Hanna, Chad and Holley-Bockelmann, Kelly and Howell, D. Andrew and Huerta, E. A. and Johnson, Margaret W. G. and Juric, Mario and Kaplan, David L. and Katz, Daniel S. and Keivani, Azadeh and Kerzendorf, Wolfgang and Kopper, Claudio and Lam, Michael T. and Lehner, Luis and Marka, Zsuzsa and Marka, Szabolcs and Nabrzyski, Jarek and Narayan, Gautham and O'Shea, Brian W. and Petravick, Donald and Quick, Rob and Street, Rachel A. and Taboada, Ignacio and Timmes, Frank and Turk, Matthew J. and Weltman, Amanda and Zhang, Zhao},
      title = {Cyberinfrastructure Requirements to Enhance Multi-messenger Astrophysics},
      year = {2019},
      eprint = {arXiv:1903.04590},
      url = {https://arxiv.org/abs/1903.04590}
    }
  4. Chapp, D., Rorabaugh, D., Brown, D. A., Deelman, E., Vahi, K., Welch, V., & Taufer, M. (2019). Applicability Study of the PRIMAD Model to LIGO Gravitational Wave Search Workflows. Proceedings of the 2nd International Workshop on Practical Reproducible Evaluation of Computer Systems (P-RECS’19), 1–6. https://doi.org/10.1145/3322790.3330591
    @inproceedings{chap2019precs,
      author = {Chapp, Dylan and Rorabaugh, Danny and Brown, Duncan A. and Deelman, Ewa and Vahi, Karan and Welch, Von and Taufer, Michela},
      title = {Applicability Study of the PRIMAD Model to LIGO Gravitational Wave Search Workflows},
      year = {2019},
      doi = {10.1145/3322790.3330591},
      booktitle = {Proceedings of the 2nd International Workshop on Practical Reproducible Evaluation of Computer Systems (P-RECS'19)},
      pages = {1–6}
    }
  5. Deelman, E., Mandal, A., Jiang, M., & Sakellariou, R. (2019). The role of machine learning in scientific workflows. The International Journal of High Performance Computing Applications. https://doi.org/10.1177/1094342019852127 (Funding Acknowledgments: LLNL-ABS-755833 DE-AC52-07NA27344, DOE DESC0012636, NSF 1839900, LLNL-JRNL-765200)
    @article{deelman-ijhpca-2019,
      title = {The role of machine learning in scientific workflows},
      author = {Deelman, Ewa and Mandal, Anirban and Jiang, Ming and Sakellariou, Rizos},
      journal = {The International Journal of High Performance Computing Applications},
      volume = {},
      number = {},
      pages = {},
      year = {2019},
      doi = {10.1177/1094342019852127},
      note = {Funding Acknowledgments: LLNL-ABS-755833 DE-AC52-07NA27344, DOE DESC0012636, NSF 1839900, LLNL-JRNL-765200}
    }
  6. Deelman, E., Mandal, A., Pascucci, V., Sons, S., Wyngaard, J., Vardeman II, C. F., Petruzza, S., Baldin, I., Christopherson, L., Mitchell, R., Pottier, L., Rynge, M., Scott, E., Vahi, K., Kogank, M., Mann, J. A., Gulbransen, T., Allen, D., Barlow, D., … Stone, S. (2019). Cyberinfrastructure Center of Excellence Pilot: Connecting Large Facilities Cyberinfrastructure. 15th International Conference on EScience (EScience). (Funding Acknowledgments: NSF 1842042)
    @inproceedings{deelman-escience-2019,
      title = {Cyberinfrastructure Center of Excellence Pilot: Connecting Large Facilities Cyberinfrastructure},
      author = {Deelman, Ewa and Mandal, Anirban and Pascucci, Valerio and Sons, Susan and Wyngaard, Jane and Vardeman II, Charles F and Petruzza, Steve and Baldin, Ilya and Christopherson, Laura and Mitchell, Ryan and Pottier, Loic and Rynge, Mats and Scott, Erik and Vahi, Karan and Kogank, Marina and Mann, Jasmine A and Gulbransen, Tom and Allen, Daniel and Barlow, David and Bonarrigo, Santiago and Clark, Chris and Goldman, Leslie and Goulden, Tristan and Harvey, Phil and Hulsander, David and Jacob, Steve and Laney, Christine and Lobo-Padilla, Ivan and Sampson, Jeremey and Staarmann, John and Stone, Steve},
      booktitle = {15th International Conference on eScience (eScience)},
      year = {2019},
      location = {San Diego, CA, USA},
      pages = {},
      doi = {},
      note = {Funding Acknowledgments: NSF 1842042}
    }
  7. Deelman, E., Vahi, K., Rynge, M., Mayani, R., Ferreira da Silva, R., Papadimitriou, G., & Livny, M. (2019). The Evolution of the Pegasus Workflow Management Software. Computing in Science Engineering, 21(4), 22–36. https://doi.org/10.1109/MCSE.2019.2919690 (Funding Acknowledgments: NSF 1664162, NSF 1148515, DOE DESC0012636, NSF 1642053)
    @article{deelman-cise-2019,
      title = {The Evolution of the Pegasus Workflow Management Software},
      author = {Deelman, Ewa and Vahi, Karan and Rynge, Mats and Mayani, Rajiv and Ferreira da Silva, Rafael and Papadimitriou, George and Livny, Miron},
      journal = {Computing in Science Engineering},
      volume = {21},
      number = {4},
      pages = {22--36},
      year = {2019},
      doi = {10.1109/MCSE.2019.2919690},
      note = {Funding Acknowledgments: NSF 1664162, NSF 1148515, DOE DESC0012636, NSF 1642053}
    }
  8. Edwards, R., Abeysinghe, E., Pierce, M., & Rynge, M. (2019). Search SRA Gateway for Metagenomics Data. Gateways 2019.
    @inproceedings{edwards-gateways-2019,
      title = {Search SRA Gateway for Metagenomics Data},
      author = {Edwards, Robert and Abeysinghe, Eroma and Pierce, Marlon and Rynge, Mats},
      booktitle = {Gateways 2019},
      year = {2019},
      pages = {},
      doi = {}
    }
  9. Ferreira da Silva, R., Callaghan, S., Do, T. M. A., Papadimitriou, G., & Deelman, E. (2019). Measuring the Impact of Burst Buffers on Data-Intensive Scientific Workflows. Future Generation Computer Systems, 101, 208–220. https://doi.org/10.1016/j.future.2019.06.016 (Funding Acknowledgments: DOE DESC0012636, NSF 1664162, NSF 1741040)
    @article{ferreiradasilva-fgcs-bb-2019,
      title = {Measuring the Impact of Burst Buffers on Data-Intensive Scientific Workflows},
      author = {Ferreira da Silva, Rafael and Callaghan, Scott and Do, Tu Mai Anh and Papadimitriou, George and Deelman, Ewa},
      journal = {Future Generation Computer Systems},
      volume = {101},
      number = {},
      pages = {208--220},
      year = {2019},
      doi = {10.1016/j.future.2019.06.016},
      note = {Funding Acknowledgments: DOE DESC0012636, NSF 1664162, NSF 1741040}
    }
  10. Ferreira da Silva, R., Casanova, H., Tanaka, R., & Suter, F. (2019). Bridging Concepts and Practice in eScience via Simulation-driven Engineering. Workshop on Bridging from Concepts to Data and Computation for EScience (BC2DC’19), 15th International Conference on EScience (EScience), 609–614. https://doi.org/10.1109/eScience.2019.00084 (Funding Acknowledgements: NSF 1642335, NSF 1923539)
    @inproceedings{ferreiradasilva2019escience,
      title = {Bridging Concepts and Practice in eScience via Simulation-driven Engineering},
      author = {Ferreira da Silva, Rafael and Casanova, Henri and Tanaka, Ryan and Suter, Frederic},
      booktitle = {Workshop on Bridging from Concepts to Data and Computation for eScience (BC2DC'19), 15th International Conference on eScience (eScience)},
      year = {2019},
      pages = {609--614},
      doi = {10.1109/eScience.2019.00084},
      note = {Funding Acknowledgements: NSF 1642335, NSF 1923539}
    }
  11. Ferreira da Silva, R., Filgueira, R., Deelman, E., Pairo-Castineira, E., Overton, I. M., & Atkinson, M. (2019). Using Simple PID-inspired Controllers for Online Resilient Resource Management of Distributed Scientific Workflows. Future Generation Computer Systems, 95, 615–628. https://doi.org/10.1016/j.future.2019.01.015 (Funding Acknowledgments: DOE DE-SC0012636)
    @article{ferreiradasilva-fgcs-2019,
      title = {Using Simple PID-inspired Controllers for Online Resilient Resource Management of Distributed Scientific Workflows},
      author = {Ferreira da Silva, Rafael and Filgueira, Rosa and Deelman, Ewa and Pairo-Castineira, Erola and Overton, Ian Michael and Atkinson, Malcolm},
      journal = {Future Generation Computer Systems},
      volume = {95},
      number = {},
      pages = {615-628},
      year = {2019},
      doi = {10.1016/j.future.2019.01.015},
      note = {Funding Acknowledgments: DOE DE-SC0012636}
    }
  12. Ferreira da Silva, R., Mayani, R., Shi, Y., Kemanian, A. R., Rynge, M., & Deelman, E. (2019). Empowering Agroecosystem Modeling with HTC Scientific Workflows: The Cycles Model Use Case. First International Workshop on Big Data Tools, Methods, and Use Cases for Innovative Scientific Discovery (BTSD), 4545–4552. https://doi.org/10.1109/BigData47090.2019.9006107 (Funding Acknowledgments: DARPA W911NF-18-1-0027, NSF 1664162)
    @inproceedings{ferreiradasilva2019btsd,
      title = {Empowering Agroecosystem Modeling with HTC Scientific Workflows: The Cycles Model Use Case},
      author = {Ferreira da Silva, Rafael and Mayani, Rajiv and Shi, Yuning and Kemanian, Armen R. and Rynge, Mats and Deelman, Ewa},
      booktitle = {First International Workshop on Big Data Tools, Methods, and Use Cases for Innovative Scientific Discovery (BTSD)},
      year = {2019},
      pages = {4545--4552},
      doi = {10.1109/BigData47090.2019.9006107},
      note = {Funding Acknowledgments: DARPA W911NF-18-1-0027, NSF 1664162}
    }
  13. Ferreira da Silva, R., Orgerie, A.-C., Casanova, H., Tanaka, R., Deelman, E., & Suter, F. (2019). Accurately Simulating Energy Consumption of I/O-intensive Scientific Workflows. Computational Science – ICCS 2019, 138–152. https://doi.org/10.1007/978-3-030-22734-0_11 (Funding Acknowledgments: NSF 1642335, NSF 1664162, DOE DE-SC0012636)
    @inproceedings{ferreiradasilva-iccs-2019,
      author = {Ferreira da Silva, Rafael and Orgerie, Anne-C\'{e}cile and Casanova, Henri and Tanaka, Ryan and Deelman, Ewa and Suter, Fr\'{e}d\'{e}ric},
      title = {Accurately Simulating Energy Consumption of I/O-intensive Scientific Workflows},
      booktitle = {Computational Science -- ICCS 2019},
      year = {2019},
      pages = {138--152},
      publisher = {Springer International Publishing},
      doi = {10.1007/978-3-030-22734-0_11},
      note = {Funding Acknowledgments: NSF 1642335, NSF 1664162, DOE DE-SC0012636}
    }
  14. Garijo, D., Khider, D., Ratnakar, V., Gil, Y., Deelman, E., Ferreira da Silva, R., Knoblock, C., Chiang, Y.-Y., Pham, M., Pujara, J., Vu, B., Feldman, D., Mayani, R., Cobourn, K., Duffy, C., Kemanian, A., Shu, L., Kumar, V., Khandelwal, A., … Pierce, S. (2019). An Intelligent Interface for Integrating Climate, Hydrology, Agriculture, and Socioeconomic Models. ACM 24th International Conference on Intelligent User Interfaces (IUI’19), 111–112. https://doi.org/10.1145/3308557.3308711 (Funding Acknowledgments: DARPA W911NF-18-1-0027)
    @inproceedings{garijo-iui-2019,
      author = {Garijo, Daniel and Khider, Deborah and Ratnakar, Varun and Gil, Yolanda and Deelman, Ewa and Ferreira da Silva, Rafael and Knoblock, Craig and Chiang, Yao-Yi and Pham, Minh and Pujara, Jay and Vu, Binh and Feldman, Dan and Mayani, Rajiv and Cobourn, Kelly and Duffy, Chris and Kemanian, Armen and Shu, Lele and Kumar, Vipin and Khandelwal, Ankush and Tayal, Kshitij and Peckham, Scott and Stoica, Maria and Dabrowski, Anna and Hardesty-Lewis, Daniel and Pierce, Suzanne},
      title = {An Intelligent Interface for Integrating Climate, Hydrology, Agriculture, and Socioeconomic Models},
      booktitle = {ACM 24th International Conference on Intelligent User Interfaces (IUI'19)},
      year = {2019},
      pages = {111--112},
      doi = {10.1145/3308557.3308711},
      note = {Funding Acknowledgments: DARPA W911NF-18-1-0027}
    }
  15. Lyons, E., Papadimitriou, G., Wang, C., Thareja, K., Ruth, P., Villalobos, J. J., Rodero, I., Deelman, E., Zink, M., & Mandal, A. (2019). Toward a Dynamic Network-centric Distributed Cloud Platform for Scientific Workflows: A Case Study for Adaptive Weather Sensing. 15th International Conference on EScience (EScience), 67–76. https://doi.org/10.1109/eScience.2019.00015 (Funding Acknowledgments: NSF 1826997)
    @inproceedings{lyons-escience-2019,
      title = {Toward a Dynamic Network-centric Distributed Cloud Platform for Scientific Workflows: A Case Study for Adaptive Weather Sensing},
      author = {Lyons, Eric and Papadimitriou, George and Wang, Cong and Thareja, Komal and Ruth, Paul and Villalobos, J.J. and Rodero, Ivan and Deelman, Ewa and Zink, Michael and Mandal, Anirban},
      booktitle = {15th International Conference on eScience (eScience)},
      year = {2019},
      location = {San Diego, CA, USA},
      pages = {67--76},
      doi = {10.1109/eScience.2019.00015},
      note = {Funding Acknowledgments: NSF 1826997}
    }
  16. Mitchell, R., Pottier, L., Jacobs, S., Ferreira da Silva, R., Rynge, M., Vahi, K., & Deelman, E. (2019). Exploration of Workflow Management Systems Emerging Features from Users Perspectives. First International Workshop on Big Data Tools, Methods, and Use Cases for Innovative Scientific Discovery (BTSD), 4537–4544. https://doi.org/10.1109/BigData47090.2019.9005494 (Funding Acknowledgments: NSF 1842042)
    @inproceedings{mitchell2019btsd,
      title = {Exploration of Workflow Management Systems Emerging Features from Users Perspectives},
      author = {Mitchell, Ryan and Pottier, Loic and Jacobs, Steve and Ferreira da Silva, Rafael and Rynge, Mats and Vahi, Karan and Deelman, Ewa},
      booktitle = {First International Workshop on Big Data Tools, Methods, and Use Cases for Innovative Scientific Discovery (BTSD)},
      year = {2019},
      pages = {4537--4544},
      doi = {10.1109/BigData47090.2019.9005494},
      note = {Funding Acknowledgments: NSF 1842042}
    }
  17. Papadimitriou, G., Kiran, M., Wang, C., Mandal, A., & Deelman, E. (2019). Training Classifiers to Identify TCP Signatures in Scientific Workflows. 2019 IEEE/ACM Innovating the Network for Data-Intensive Science (INDIS), 61–68. https://doi.org/10.1109/INDIS49552.2019.00012 (Funding Acknowledgments: DOE DESC0012636)
    @inproceedings{papadimitriou-indis-2019,
      title = {Training Classifiers to Identify TCP Signatures in Scientific Workflows},
      author = {Papadimitriou, George and Kiran, Mariam and Wang, Cong and Mandal, Anirban and Deelman, Ewa},
      booktitle = {2019 IEEE/ACM Innovating the Network for Data-Intensive Science (INDIS)},
      year = {2019},
      location = {Denver, CO, USA},
      pages = {61-68},
      doi = {10.1109/INDIS49552.2019.00012},
      month = nov,
      note = {Funding Acknowledgments: DOE DESC0012636}
    }
  18. Pendergrass, S. A., Buyske, S., Jeff, J. M., Frase, A., Dudek, S., Bradford, Y., Ambite, J. L., Avery, C. L., Buzkova, P., Deelman, E., Fesinmeyer, M. D., Haiman, C., Heiss, G., Hindorff, L. A., Hsu, C. N., Jackson, R. D., Lin, Y., Le Marchand, L., Matise, T. C., … Crawford, D. C. (2019). A phenome-wide association study (PheWAS) in the Population Architecture using Genomics and Epidemiology (PAGE) study reveals potential pleiotropy in African Americans. PLoS ONE, 14(12), e0226771. (Funding Acknowledgments: NIH U01HG004801 (Coordinating Center))
    @article{pmid31891604,
      author = {Pendergrass, S. A. and Buyske, S. and Jeff, J. M. and Frase, A. and Dudek, S. and Bradford, Y. and Ambite, J. L. and Avery, C. L. and Buzkova, P. and Deelman, E. and Fesinmeyer, M. D. and Haiman, C. and Heiss, G. and Hindorff, L. A. and Hsu, C. N. and Jackson, R. D. and Lin, Y. and Le Marchand, L. and Matise, T. C. and Monroe, K. R. and Moreland, L. and North, K. E. and Park, S. L. and Reiner, A. and Wallace, R. and Wilkens, L. R. and Kooperberg, C. and Ritchie, M. D. and Crawford, D. C.},
      title = {A phenome-wide association study (PheWAS) in the Population Architecture using Genomics and Epidemiology (PAGE) study reveals potential pleiotropy in African Americans},
      journal = {PLoS ONE},
      year = {2019},
      volume = {14},
      number = {12},
      pages = {e0226771},
      note = {Funding Acknowledgments: NIH U01HG004801 (Coordinating Center)}
    }
  19. Pendergrass, S. A., Buyske, S., Jeff, J. M., Frase, A., Dudek, S., Bradford, Y., Ambite, J.-L., Avery, C. L., Buzkova, P., Deelman, E., & others. (2019). A phenome-wide association study (PheWAS) in the Population Architecture using Genomics and Epidemiology (PAGE) study reveals potential pleiotropy in African Americans. PloS One, 14(12). https://doi.org/10.1371/journal.pone.0226771
    @article{pendergrass2019phenome,
      title = {A phenome-wide association study (PheWAS) in the Population Architecture using Genomics and Epidemiology (PAGE) study reveals potential pleiotropy in African Americans},
      author = {Pendergrass, Sarah A and Buyske, Steven and Jeff, Janina M and Frase, Alex and Dudek, Scott and Bradford, Yuki and Ambite, Jose-Luis and Avery, Christy L and Buzkova, Petra and Deelman, Ewa and others},
      journal = {PloS one},
      volume = {14},
      number = {12},
      year = {2019},
      publisher = {Public Library of Science},
      doi = {10.1371/journal.pone.0226771}
    }
  20. Rodero, I., Qin, Y., Valls, J., Simonet, A., Villalobos, J. J., Parashar, M., Youn, C., Wang, C., Thareja, K., Ruth, P., Papadimitriou, G., Lyons, E., & Zink, M. (2019). Enabling Data Streaming-based Science Gateway through Federated Cyberinfrastructure. Gateways 2019. (Funding Acknowledgments: NSF 1835692, NSF 1745246, NSF 1826997)
    @inproceedings{rodero-gateways-2019,
      title = {Enabling Data Streaming-based Science Gateway through Federated Cyberinfrastructure},
      author = {Rodero, Ivan and Qin, Yubo and Valls, Jesus and Simonet, Anthony and Villalobos, J.J. and Parashar, Manish and Youn, Chooban and Wang, Cong and Thareja, Komal and Ruth, Paul and Papadimitriou, George and Lyons, Eric and Zink, Michael},
      booktitle = {Gateways 2019},
      year = {2019},
      location = {San Diego, CA, USA},
      pages = {},
      doi = {},
      note = {Funding Acknowledgments: NSF 1835692, NSF 1745246, NSF 1826997}
    }
  21. Rynge, M., Vahi, K., Deelman, E., Mandal, A., Baldin, I., Bhide, O., Heiland, R., Welch, V., Hill, R., Poehlman, W. L., & Feltus, F. A. (2019). Integrity Protection for Scientific Workflow Data: Motivation and Initial Experiences. Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (Learning), 17:1–17:8. https://doi.org/10.1145/3332186.3332222 (Funding Acknowledgments: NSF 1642070, NSF 1642053, NSF 1642090. Best Paper in Advanced Research Computing Software and Applications Track. The Phil Andrews Most Transformative Contribution Award.)
    @inproceedings{rynge-pearc-2019,
      author = {Rynge, Mats and Vahi, Karan and Deelman, Ewa and Mandal, Anirban and Baldin, Ilya and Bhide, Omkar and Heiland, Randy and Welch, Von and Hill, Raquel and Poehlman, William L. and Feltus, F. Alex},
      title = {Integrity Protection for Scientific Workflow Data: Motivation and Initial Experiences},
      booktitle = {Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (Learning)},
      series = {PEARC '19},
      year = {2019},
      isbn = {978-1-4503-7227-5},
      location = {Chicago, IL, USA},
      pages = {17:1--17:8},
      articleno = {17},
      numpages = {8},
      url = {http://doi.acm.org/10.1145/3332186.3332222},
      doi = {10.1145/3332186.3332222},
      acmid = {3332222},
      publisher = {ACM},
      address = {New York, NY, USA},
      note = {Funding Acknowledgments: NSF 1642070, NSF 1642053, NSF 1642090. Best Paper in Advanced Research Computing Software and Applications Track. The Phil Andrews Most Transformative Contribution Award.}
    }
  22. Tanaka, R., Casanova, H., & Ferreira da Silva, R. (2019). Teaching Parallel and Distributed Computing Concepts in Simulation with WRENCH. Workshop on Education for High-Performance Computing (EduHPC). (Funding Acknowledgements: NSF 1642335, NSF 1923539)
    @inproceedings{tanaka2019eduhpc,
      title = {Teaching Parallel and Distributed Computing Concepts in Simulation with WRENCH},
      author = {Tanaka, Ryan and Casanova, Henri and Ferreira da Silva, Rafael},
      booktitle = {Workshop on Education for High-Performance Computing (EduHPC)},
      year = {2019},
      pages = {},
      doi = {},
      note = {Funding Acknowledgements: NSF 1642335, NSF 1923539}
    }
  23. Thomas, S., Wyatt, M., Do, T. M. A., Pottier, L., Ferreira da Silva, R., Weinstein, H., Cuendet, M. A., Estrada, T., Deelman, E., & Taufer, M. (2019). Characterization of In Situ and In Transit Analytics of Molecular Dynamics Simulations for Next-generation Supercomputers. 15th International Conference on EScience (EScience), 188–198. https://doi.org/10.1109/eScience.2019.00027 (Funding Acknowledgments: NSF 1741040)
    @inproceedings{thomas-escience-2019,
      title = {Characterization of In Situ and In Transit Analytics of Molecular Dynamics Simulations for Next-generation Supercomputers},
      author = {Thomas, Stephen and Wyatt, Michael and Do, Tu Mai Anh and Pottier, Loic and Ferreira da Silva, Rafael and Weinstein, Harel and Cuendet, Michel A. and Estrada, Trilce and Deelman, Ewa and Taufer, Michela},
      booktitle = {15th International Conference on eScience (eScience)},
      year = {2019},
      pages = {188--198},
      doi = {10.1109/eScience.2019.00027},
      note = {Funding Acknowledgments: NSF 1741040}
    }
  24. Vahi, K., Rynge, M., Papadimitriou, G., Brown, D., Mayani, R., Ferreira da Silva, R., Deelman, E., Mandal, A., Lyons, E., & Zink, M. (2019). Custom Execution Environments with Containers in Pegasus-enabled Scientific Workflows. 15th International Conference on EScience (EScience), 281–290. https://doi.org/10.1109/eScience.2019.00039 (Funding Acknowledgments: NSF 1664162, NSF 1826997, NSF 1443047)
    @inproceedings{vahi-escience-2019,
      title = {Custom Execution Environments with Containers in Pegasus-enabled Scientific Workflows},
      author = {Vahi, Karan and Rynge, Mats and Papadimitriou, George and Brown, Duncan and Mayani, Rajiv and Ferreira da Silva, Rafael and Deelman, Ewa and Mandal, Anirban and Lyons, Eric and Zink, Michael},
      booktitle = {15th International Conference on eScience (eScience)},
      year = {2019},
      location = {San Diego, CA, USA},
      pages = {281--290},
      doi = {10.1109/eScience.2019.00039},
      note = {Funding Acknowledgments: NSF 1664162, NSF 1826997, NSF 1443047}
    }
  25. Vahi, K., Wang, M. H., Chang, C., Dodelson, S., Rynge, M., & Deelman, E. (2019). Workflows using Pegasus: Enabling Dark Energy Survey Pipelines. Astronomical Data Analysis Software and Systems XXVIII, 523, 689–692. (Funding Acknowledgments: NSF 1664162)
    @article{2018-vahi-adass-weak-leansing,
      title = {Workflows using Pegasus: Enabling Dark Energy Survey Pipelines},
      author = {Vahi, Karan and Wang, Michael H. and Chang, Chihway and Dodelson, Scott and Rynge, Mats and Deelman, Ewa},
      journal = {Astronomical Data Analysis Software and Systems XXVIII},
      volume = {523},
      year = {2019},
      pages = {689--692},
      note = {Funding Acknowledgments: NSF 1664162}
    }
  26. Weitzel, D., Zvada, M., Vukotic, I., Gardner, R. W., Bockelman, B., Rynge, M., Hernandez, E. F., Lin, B., & Selmeci, M. (2019). StashCache: A Distributed Caching Federation for the Open Science Grid. CoRR, abs/1905.06911. http://arxiv.org/abs/1905.06911
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      author = {Weitzel, Derek and Zvada, Mari{\'{a}}n and Vukotic, Ilija and Gardner, Robert W. and Bockelman, Brian and Rynge, Mats and Hernandez, Edgar Fajardo and Lin, Brian and Selmeci, Matyas},
      title = {StashCache: {A} Distributed Caching Federation for the Open Science
       Grid},
      journal = {CoRR},
      volume = {abs/1905.06911},
      year = {2019},
      url = {http://arxiv.org/abs/1905.06911},
      archiveprefix = {arXiv},
      eprint = {1905.06911},
      timestamp = {Tue, 28 May 2019 12:48:08 +0200},
      biburl = {https://dblp.org/rec/bib/journals/corr/abs-1905-06911},
      bibsource = {dblp computer science bibliography, https://dblp.org}
    }
  27. Wojcik, G. L., Graff, M., Nishimura, K. K., Tao, R., Haessler, J., Gignoux, C. R., Highland, H. M., Patel, Y. M., Sorokin, E. P., Avery, C. L., Belbin, G. M., Bien, S. A., Cheng, I., Cullina, S., Hodonsky, C. J., Hu, Y., Huckins, L. M., Jeff, J., Justice, A. E., … Carlson, C. S. (2019). Genetic analyses of diverse populations improves discovery for complex traits. Nature, 570, 514–518. https://doi.org/10.1038/s41586-019-1310-4
    @article{wojcik2019genetic,
      title = {Genetic analyses of diverse populations improves discovery for complex traits},
      author = {Wojcik, Genevieve L and Graff, Mariaelisa and Nishimura, Katherine K and Tao, Ran and Haessler, Jeffrey and Gignoux, Christopher R and Highland, Heather M and Patel, Yesha M and Sorokin, Elena P and Avery, Christy L and Belbin, Gillian M. and Bien, Stephanie A. and Cheng, Iona and Cullina, Sinead and Hodonsky, Chani J. and Hu, Yao and Huckins, Laura M. and Jeff, Janina and Justice, Anne E. and Kocarnik, Jonathan M. and Lim, Unhee and Lin, Bridget M. and Lu, Yingchang and Nelson, Sarah C. and Park, Sung-Shim L. and Poisner, Hannah and Preuss, Michael H. and Richard, Melissa A. and Schurmann, Claudia and Setiawan, Veronica W. and Sockell, Alexandra and Vahi, Karan and Verbanck, Marie and Vishnu, Abhishek and Walker, Ryan W. and Young, Kristin L. and Zubair, Niha and Acuña-Alonso, Victor and Ambite, Jose Luis and Barnes, Kathleen C. and Boerwinkle, Eric and Bottinger, Erwin P. and Bustamante, Carlos D. and Caberto, Christian and Canizales-Quinteros, Samuel and Conomos, Matthew P. and Deelman, Ewa and Do, Ron and Doheny, Kimberly and Fernández-Rhodes, Lindsay and Fornage, Myriam and Hailu, Benyam and Heiss, Gerardo and Henn, Brenna M. and Hindorff, Lucia A. and Jackson, Rebecca D. and Laurie, Cecelia A. and Laurie, Cathy C. and Li, Yuqing and Lin, Dan-Yu and Moreno-Estrada, Andres and Nadkarni, Girish and Norman, Paul J. and Pooler, Loreall C. and Reiner, Alexander P. and Romm, Jane and Sabatti, Chiara and Sandoval, Karla and Sheng, Xin and Stahl, Eli A. and Stram, Daniel O. and Thornton, Timothy A. and Wassel, Christina L. and Wilkens, Lynne R. and Winkler, Cheryl A. and Yoneyama, Sachi and Buyske, Steven and Haiman, Christopher A. and Kooperberg, Charles and Marchand, Loic Le and Loos, Ruth J. F. and Matise, Tara C. and North, Kari E. and Peters, Ulrike and Kenny, Eimear E. and Carlson, Christopher S.},
      journal = {Nature},
      volume = {570},
      pages = {514--518},
      year = {2019},
      publisher = {Nature Publishing Group},
      doi = {10.1038/s41586-019-1310-4}
    }

2018

  1. Bhide, O., Hill, R., Vahi, K., Rynge, M., & Velch, V. (2018). Combating Workflow Failures with Integrity-based Checkpoints and Blockchain. 6th International Workshop on Distributed Storage and Blockchain Technologies for Big Data. (Funding Acknowledgments: NSF 1642070, 1642053, and 1642090)
    @inproceedings{2108-bhide-workflows-blockchain,
      title = {Combating Workflow Failures with Integrity-based Checkpoints and Blockchain},
      author = {Bhide, Omkar and Hill, Raquel and Vahi, Karan and Rynge, Mats and Velch, Von},
      booktitle = {6th International Workshop on Distributed Storage and Blockchain Technologies for Big Data},
      year = {2018},
      note = {Funding Acknowledgments: NSF 1642070, 1642053, and 1642090}
    }
  2. Casanova, H., Pandey, S., Oeth, J., Tanaka, R., Suter, F., & Ferreira da Silva, R. (2018). WRENCH: A Framework for Simulating Workflow Management Systems. 13th Workshop on Workflows in Support of Large-Scale Science (WORKS’18), 74–85. https://doi.org/10.1109/WORKS.2018.00013 (Funding Acknowledgments: NSF 1642335)
    @inproceedings{casanova-works-2018,
      title = {WRENCH: A Framework for Simulating Workflow Management Systems},
      author = {Casanova, Henri and Pandey, Suraj and Oeth, James and Tanaka, Ryan and Suter, Frederic and Ferreira da Silva, Rafael},
      booktitle = {13th Workshop on Workflows in Support of Large-Scale Science (WORKS'18)},
      year = {2018},
      pages = {74--85},
      doi = {10.1109/WORKS.2018.00013},
      note = {Funding Acknowledgments: NSF 1642335}
    }
  3. Deelman, E., Peterka, T., Altintas, I., Carothers, C. D., van Dam, K. K., Moreland, K., Parashar, M., Ramakrishnan, L., Taufer, M., & Vetter, J. (2018). The future of scientific workflows. The International Journal of High Performance Computing Applications, 32(1), 159–175. https://doi.org/10.1177/1094342017704893
    @article{deelman-ijhpca-2017,
      author = {Deelman, Ewa and Peterka, Tom and Altintas, Ilkay and Carothers, Christopher D and van Dam, Kerstin Kleese and Moreland, Kenneth and Parashar, Manish and Ramakrishnan, Lavanya and Taufer, Michela and Vetter, Jeffrey},
      title = {The future of scientific workflows},
      journal = {The International Journal of High Performance Computing Applications},
      volume = {32},
      number = {1},
      pages = {159--175},
      year = {2018},
      doi = {10.1177/1094342017704893}
    }
  4. Do, T. M. A., Jiang, M., Gallagher, B., Chu, A., Harrison, C., Vahi, K., & Deelman, E. (2018). Enabling Data Analytics Workflows using Node-Local Storage. The International Conference for High Performance Computing, Networking, Storage, and Analysis (SC18), Poster. (Funding Acknowledgments: LLNL-ABS-755833 DE-AC52-07NA27344, NSF 1741040)
    @inproceedings{do-sc-18,
      title = {Enabling Data Analytics Workflows using Node-Local Storage},
      author = {Do, Tu Mai Anh and Jiang, Ming and Gallagher, Brian and Chu, Albert and Harrison, Cyrus and Vahi, Karan and Deelman, Ewa},
      booktitle = {The International Conference for High Performance Computing, Networking, Storage, and Analysis (SC18), Poster},
      year = {2018},
      note = {Funding Acknowledgments: LLNL-ABS-755833 DE-AC52-07NA27344, NSF 1741040}
    }
  5. Estrada, T., Benson, J., Carrillo-Cabada, H., Razavi, A., Cuendet, M., Weinstein, H., Deelman, E., & Taufer, M. (2018). Graphic Encoding of Macromolecules for Efficient High-Throughput Analysis. 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, 315–324. https://doi.org/10.1145/3233547.3233607 (Funding Acknowledgments: NSF 1741040)
    @inproceedings{estrada-graphic-2018,
      author = {Estrada, Trilce and Benson, Jeremy and Carrillo-Cabada, Hector and Razavi, Asghar and Cuendet, Michel and Weinstein, Harel and Deelman, Ewa and Taufer, Michela},
      year = {2018},
      month = aug,
      pages = {315-324},
      title = {Graphic Encoding of Macromolecules for Efficient High-Throughput Analysis},
      booktitle = {2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics},
      doi = {10.1145/3233547.3233607},
      note = {Funding Acknowledgments: NSF 1741040}
    }
  6. Ferreira da Silva, R., Garijo, D., Peckham, S., Gil, Y., Deelman, E., & Ratnakar, V. (2018). Towards Model Integration via Abductive Workflow Composition and Multi-Method Scalable Model Execution. 9th International Congress on Environmental Modelling and Software. (Funding Acknowledgments: DARPA W911NF-18-1-0027)
    @inproceedings{ferreiradasilva-iemss-2018,
      title = {Towards Model Integration via Abductive Workflow Composition and Multi-Method Scalable Model Execution},
      author = {Ferreira da Silva, Rafael and Garijo, Daniel and Peckham, Scott and Gil, Yolanda and Deelman, Ewa and Ratnakar, Varun},
      booktitle = {9th International Congress on Environmental Modelling and Software},
      year = {2018},
      pages = {},
      doi = {},
      note = {Funding Acknowledgments: DARPA W911NF-18-1-0027}
    }
  7. Filgueira, R., Ferreira da Silva, R., Deelman, E., Christodoulou, V., & Krause, A. (2018). IoT-Hub: New IoT data-platform for Virtual Research Environments. 10th International Workshop on Science Gateways (IWSG 2018). (Funding Acknowledgments: DOE DE-SC0012636)
    @inproceedings{filgueira-iwsg-2018,
      title = {IoT-Hub: New IoT data-platform for Virtual Research Environments},
      author = {Filgueira, Rosa and Ferreira da Silva, Rafael and Deelman, Ewa and Christodoulou, Vyron and Krause, Amrey},
      booktitle = {10th International Workshop on Science Gateways (IWSG 2018)},
      year = {2018},
      pages = {},
      doi = {},
      note = {Funding Acknowledgments: DOE DE-SC0012636}
    }
  8. Gil, Y., Cobourn, K., Deelman, E., Duffy, C., Ferreira da Silva, R., Kemanian, A., Knoblock, C., Kumar, V., Peckham, S., Carvalho, L., Chiang, Y.-Y., Garijo, D., Khider, D., Khandelwal, A., Pahm, M., Pujara, J., Ratnakar, V., Stoica, M., & Vu, B. (2018). MINT: Model Integration Through Knowledge-Powered Data and Process Composition. 9th International Congress on Environmental Modelling and Software. (Funding Acknowledgments: DARPA W911NF-18-1-0027)
    @inproceedings{gil-iemss-2018,
      title = {MINT: Model Integration Through Knowledge-Powered Data and Process Composition},
      author = {Gil, Yolanda and Cobourn, Kelly and Deelman, Ewa and Duffy, Chris and Ferreira da Silva, Rafael and Kemanian, Armen and Knoblock, Craig and Kumar, Vipin and Peckham, Scott and Carvalho, Lucas and Chiang, Yao-Yi and Garijo, Daniel and Khider, Deborah and Khandelwal, Ankush and Pahm, Minh and Pujara, Jay and Ratnakar, Varun and Stoica, Maria and Vu, Binh},
      booktitle = {9th International Congress on Environmental Modelling and Software},
      year = {2018},
      pages = {},
      doi = {},
      note = {Funding Acknowledgments: DARPA W911NF-18-1-0027}
    }
  9. Jordan, T. H., Callaghan, S., Graves, R. W., Wang, F., Milner, K. R., Goulet, C. A., Maechling, P. J., Olsen, K. B., Cui, Y., Juve, G., Vahi, K., Yu, J., Deelman, E., & Gill, D. (2018). CyberShake Models of Seismic Hazards in Southern and Central California. Seismological Research Letters, 89(2B), 875–876.
    @article{jordan-srl-2018,
      title = {CyberShake Models of Seismic Hazards in Southern and Central California},
      author = {Jordan, T. H. and Callaghan, S. and Graves, R. W. and Wang, F. and Milner, K. R. and Goulet, C. A. and Maechling, P. J. and Olsen, K. B. and Cui, Y. and Juve, G. and Vahi, K. and Yu, J. and Deelman, E. and Gill, D.},
      journal = {Seismological Research Letters},
      volume = {89},
      number = {2B},
      pages = {875--876},
      year = {2018},
      doi = {}
    }
  10. Jordan, T. H., Callaghan, S., Graves, R. W., Wang, F., Milner, K. R., Goulet, C. A., Maechling, P. J., Olsen, K. B., Cui, Y., Juve, G., Vahi, K., Yu, J., Deelman, E., & Gill, D. (2018). CyberShake Models of Seismic Hazards in Southern and Central California. 11th National Conference in Earthquake Engineering.
    @inproceedings{jordan-11ncee-2018,
      title = {CyberShake Models of Seismic Hazards in Southern and Central California},
      author = {Jordan, T. H. and Callaghan, S. and Graves, R. W. and Wang, F. and Milner, K. R. and Goulet, C. A. and Maechling, P. J. and Olsen, K. B. and Cui, Y. and Juve, G. and Vahi, K. and Yu, J. and Deelman, E. and Gill, D.},
      booktitle = {11th National Conference in Earthquake Engineering},
      year = {2018},
      pages = {},
      doi = {}
    }
  11. Levi, K., Rynge, M., Abeysinghe, E., & Edwards, R. A. (2018). Searching the Sequence Read Archive Using Jetstream and Wrangler. Proceedings of the Practice and Experience on Advanced Research Computing, 50:1–50:7. https://doi.org/10.1145/3219104.3229278
    @inproceedings{levi-pearc18-2018,
      author = {Levi, Kyle and Rynge, Mats and Abeysinghe, Eroma and Edwards, Robert A.},
      title = {Searching the Sequence Read Archive Using Jetstream and Wrangler},
      booktitle = {Proceedings of the Practice and Experience on Advanced Research Computing},
      series = {PEARC '18},
      year = {2018},
      isbn = {978-1-4503-6446-1},
      location = {Pittsburgh, PA, USA},
      pages = {50:1--50:7},
      articleno = {50},
      numpages = {7},
      url = {http://doi.acm.org/10.1145/3219104.3229278},
      doi = {10.1145/3219104.3229278},
      acmid = {3229278},
      publisher = {ACM},
      keywords = {Apache Airavata, Bacteriophage, Credential Store, Jetstream, Metagenomics, Metagenomics Discovery Challenge, SRA, SRA Gateway, SciGaP, Search SRA, Sequence Read Archive, Wrangler}
    }
  12. Pandey, S., Vahi, K., Ferreira da Silva, R., Deelman, E., Jian, M., Harrison, C., Chu, A., & Casanova, H. (2018). Event-Based Triggering and Management of Scientific Workflow Ensembles. http://sighpc.ipsj.or.jp/HPCAsia2018/poster/post102s2-file1.pdf (Poster presented at the HPC Asia 2018: Tokyo, Japan)
    @misc{suraj-hpc-asia18-event-triggers,
      author = {Pandey, Suraj and Vahi, Karan and Ferreira da Silva, Rafael and Deelman, Ewa and Jian, Ming and Harrison, Cyrus and Chu, Al and Casanova, Henri},
      title = {Event-Based Triggering and Management of Scientific Workflow Ensembles},
      year = {2018},
      url = {http://sighpc.ipsj.or.jp/HPCAsia2018/poster/post102s2-file1.pdf},
      note = {Poster presented at the HPC Asia 2018: Tokyo, Japan}
    }
  13. Thapa, S., Gardner, R. W., Herner, K., Hufnagel, D., Lesny, D., & Rynge, M. (2018). Homogenizing OSG and XSEDE: Providing Access to XSEDE Allocations Through OSG Infrastructure. Proceedings of the Practice and Experience on Advanced Research Computing, 15:1–15:7. https://doi.org/10.1145/3219104.3219157
    @inproceedings{thapa-pearc18-2018,
      author = {Thapa, Suchandra and Gardner, Robert W. and Herner, Kenneth and Hufnagel, Dirk and Lesny, David and Rynge, Mats},
      title = {Homogenizing OSG and XSEDE: Providing Access to XSEDE Allocations Through OSG Infrastructure},
      booktitle = {Proceedings of the Practice and Experience on Advanced Research Computing},
      series = {PEARC '18},
      year = {2018},
      isbn = {978-1-4503-6446-1},
      location = {Pittsburgh, PA, USA},
      pages = {15:1--15:7},
      articleno = {15},
      numpages = {7},
      url = {http://doi.acm.org/10.1145/3219104.3219157},
      doi = {10.1145/3219104.3219157},
      acmid = {3219157},
      publisher = {ACM},
      keywords = {ATLAS, Bridges, CMS, CVMFS, OSG, PSC, Stampede2, TACC, XSEDE, distributed data access}
    }
  14. Tovar, B., Ferreira da Silva, R., Juve, G., Deelman, E., Allcock, W., Thain, D., & Livny, M. (2018). A Job Sizing Strategy for High-Throughput Scientific Workflows. IEEE Transactions on Parallel and Distributed Systems, 29(2), 240–253. https://doi.org/10.1109/TPDS.2017.2762310 (Funding Acknowledgments: DOE ER26110)
    @article{tovar-tpds-2017,
      title = {A Job Sizing Strategy for High-Throughput Scientific Workflows},
      author = {Tovar, Benjamin and Ferreira da Silva, Rafael and Juve, Gideon and Deelman, Ewa and Allcock, William and Thain, Douglas and Livny, Miron},
      journal = {IEEE Transactions on Parallel and Distributed Systems},
      volume = {29},
      number = {2},
      pages = {240--253},
      year = {2018},
      doi = {10.1109/TPDS.2017.2762310},
      note = {Funding Acknowledgments: DOE ER26110}
    }

2017

  1. Abbott, B. P., Abbott, R., Abbott, T. D., Acernese, F., Ackley, K., Adams, C., Adams, T., Addesso, P., Adhikari, R. X., Adya, V. B., & others. (2017). Upper limits on gravitational waves from Scorpius X-1 from a model-based cross-correlation search in Advanced LIGO data. The Astrophysical Journal, 847(1), 47.
    @article{abbott2017upper,
      title = {Upper limits on gravitational waves from Scorpius X-1 from a model-based cross-correlation search in Advanced LIGO data},
      author = {Abbott, BP and Abbott, R and Abbott, TD and Acernese, F and Ackley, K and Adams, C and Adams, T and Addesso, P and Adhikari, RX and Adya, VB and others},
      journal = {The Astrophysical Journal},
      volume = {847},
      number = {1},
      pages = {47},
      year = {2017},
      publisher = {IOP Publishing}
    }
  2. Abbott, B. P., Abbott, R., Abbott, T. D., Acernese, F., Ackley, K., Adams, C., Adams, T., Addesso, P., Adhikari, R. X., Adya, V. B., & others. (2017). First low-frequency Einstein@ Home all-sky search for continuous gravitational waves in Advanced LIGO data. Physical Review D, 96(12), 122004.
    @article{abbott2017first,
      title = {First low-frequency Einstein@ Home all-sky search for continuous gravitational waves in Advanced LIGO data},
      author = {Abbott, Benjamin P and Abbott, R and Abbott, TD and Acernese, F and Ackley, K and Adams, C and Adams, T and Addesso, P and Adhikari, RX and Adya, VB and others},
      journal = {Physical Review D},
      volume = {96},
      number = {12},
      pages = {122004},
      year = {2017},
      publisher = {American Physical Society}
    }
  3. Abbott, B. P., Abbott, R., Abbott, T. D., Acernese, F., Ackley, K., Adams, C., Adams, T., Addesso, P., Adhikari, R. X., Adya, V. B., & others. (2017). Search for intermediate mass black hole binaries in the first observing run of Advanced LIGO. Physical Review D, 96(2), 022001.
    @article{abbott2017searci,
      title = {Search for intermediate mass black hole binaries in the first observing run of Advanced LIGO},
      author = {Abbott, Benjamin P and Abbott, R and Abbott, TD and Acernese, F and Ackley, K and Adams, C and Adams, T and Addesso, P and Adhikari, RX and Adya, VB and others},
      journal = {Physical Review D},
      volume = {96},
      number = {2},
      pages = {022001},
      year = {2017},
      publisher = {American Physical Society}
    }
  4. Abbott, B. P., Abbott, R., Abbott, T. D., Acernese, F., Ackley, K., Adams, C., Adams, T., Addesso, P., Adhikari, R. X., Adya, V. B., & others. (2017). Search for gravitational waves from Scorpius X-1 in the first Advanced LIGO observing run with a hidden Markov model. Physical Review D, 95(12), 122003.
    @article{abbott2017search,
      title = {Search for gravitational waves from Scorpius X-1 in the first Advanced LIGO observing run with a hidden Markov model},
      author = {Abbott, Benjamin P and Abbott, R and Abbott, TD and Acernese, F and Ackley, K and Adams, C and Adams, T and Addesso, P and Adhikari, RX and Adya, VB and others},
      journal = {Physical Review D},
      volume = {95},
      number = {12},
      pages = {122003},
      year = {2017},
      publisher = {American Physical Society}
    }
  5. Abbott, B. P., Abbott, R., Abbott, T. D., Acernese, F., Ackley, K., Adams, C., Adams, T., Addesso, P., Adhikari, R. X., Adya, V. B., & others. (2017). All-sky search for periodic gravitational waves in the O1 LIGO data. Physical Review D, 96(6), 062002.
    @article{abbott2017all,
      title = {All-sky search for periodic gravitational waves in the O1 LIGO data},
      author = {Abbott, Benjamin P and Abbott, Rich and Abbott, TD and Acernese, Fausto and Ackley, Kendall and Adams, Carl and Adams, Thomas and Addesso, Paolo and Adhikari, RX and Adya, VB and others},
      journal = {Physical Review D},
      volume = {96},
      number = {6},
      pages = {062002},
      year = {2017},
      publisher = {American Physical Society}
    }
  6. Callaghan, S., Juve, G., Vahi, K., Maechling, P. J., Jordan, T. H., & Deelman, E. (2017). rvGAHP - Push-based Job Submission using Reverse SSH Connections. 12th Workshop on Workflows in Support of Large-Scale Science (WORKS’17). (Funding Acknowledgments: NSF 1664162 and 1443047)
    @inproceedings{callaghan-works-2017,
      title = {{rvGAHP} - Push-based Job Submission using Reverse SSH Connections},
      author = {Callaghan, Scott and Juve, Gideon and Vahi, Karan and Maechling, Philip J. and Jordan, Thomas H. and Deelman, Ewa},
      booktitle = {12th Workshop on Workflows in Support of Large-Scale Science (WORKS'17)},
      year = {2017},
      pages = {},
      doi = {},
      note = {Funding Acknowledgments: NSF 1664162 and 1443047}
    }
  7. Deelman, E., Carothers, C., Mandal, A., Tierney, B., Vetter, J. S., Baldin, I., Castillo, C., Juve, G., Krol, D., Lynch, V., Mayer, B., Meredith, J., Proffen, T., Ruth, P., & Ferreira da Silva, R. (2017). PANORAMA: An Approach to Performance Modeling and Diagnosis of Extreme Scale Workflows. International Journal of High Performance Computing Applications, 31(1), 4–18. https://doi.org/10.1177/1094342015594515 (Funding Acknowledgements: DOE DE-SC0012636)
    @article{deelman-hpc-2015,
      title = {{PANORAMA}: An Approach to Performance Modeling and Diagnosis of Extreme Scale Workflows},
      journal = {International Journal of High Performance Computing Applications},
      volume = {31},
      number = {1},
      pages = {4--18},
      year = {2017},
      author = {Deelman, Ewa and Carothers, Christopher and Mandal, Anirban and Tierney, Brian and Vetter, Jeffrey S. and Baldin, Ilya and Castillo, Claris and Juve, Gideon and Krol, Dariusz and Lynch, Vickie and Mayer, Ben and Meredith, Jeremy and Proffen, Thomas and Ruth, Paul and Ferreira da Silva, Rafael},
      note = {Funding Acknowledgements: DOE DE-SC0012636},
      doi = {10.1177/1094342015594515},
      url = {http://dx.doi.org/10.1177/1094342015594515}
    }
  8. Ferreira da Silva, R., Callaghan, S., & Deelman, E. (2017). On the Use of Burst Buffers for Accelerating Data-Intensive Scientific Workflows. 12th Workshop on Workflows in Support of Large-Scale Science (WORKS’17). https://doi.org/10.1145/3150994.3151000 (Funding Acknowledgments: DOE DE-SC0012636, NSF 1664162)
    @inproceedings{ferreiradasilva-works-2017,
      title = {On the Use of Burst Buffers for Accelerating Data-Intensive Scientific Workflows},
      author = {Ferreira da Silva, Rafael and Callaghan, Scott and Deelman, Ewa},
      booktitle = {12th Workshop on Workflows in Support of Large-Scale Science (WORKS'17)},
      year = {2017},
      pages = {},
      doi = {10.1145/3150994.3151000},
      note = {Funding Acknowledgments: DOE DE-SC0012636, NSF 1664162}
    }
  9. Ferreira da Silva, R., Filgueira, R., Pietri, I., Jiang, M., Sakellariou, R., & Deelman, E. (2017). A Characterization of Workflow Management Systems for Extreme-Scale Applications. Future Generation Computer Systems, 75, 228–238. https://doi.org/10.1016/j.future.2017.02.026 (Funding Acknowledgments: DOE DE-SC0012636, DE-AC52-07NA27344)
    @article{ferreiradasilva-fgcs-2017,
      title = {A Characterization of Workflow Management Systems for Extreme-Scale Applications},
      author = {Ferreira da Silva, Rafael and Filgueira, Rosa and Pietri, Ilia and Jiang, Ming and Sakellariou, Rizos and Deelman, Ewa},
      journal = {Future Generation Computer Systems},
      volume = {75},
      number = {},
      pages = {228--238},
      year = {2017},
      doi = {10.1016/j.future.2017.02.026},
      note = {Funding Acknowledgments: DOE DE-SC0012636, DE-AC52-07NA27344}
    }
  10. Gil, Y., Garijo, D., Ratnakar, V., Mayani, R., Adusumilli, R., Boyce, H., Srivastava, A., & Mallick, P. (2017). Towards Continuous Scientific Data Analysis and Hypothesis Evolution. Thirty-First AAAI Conference on Artificial Intelligence, 4406–4414. ()
    @inproceedings{gil-aaai-2017,
      title = {Towards Continuous Scientific Data Analysis and Hypothesis Evolution},
      author = {Gil, Yolanda and Garijo, Daniel and Ratnakar, Varun and Mayani, Rajiv and Adusumilli, Ravali and Boyce, Hunter and Srivastava, Arunima and Mallick, Parag},
      booktitle = {Thirty-First AAAI Conference on Artificial Intelligence},
      year = {2017},
      pages = {4406--4414},
      doi = {},
      note = {}
    }
  11. Jayatilaka, B., Levshina, T., Sehgal, C., Gardner, R., Rynge, M., & Wurthwein, F. (2017). The OSG Open Facility: an on-ramp for opportunistic scientific computing. Journal of Physics: Conference Series, 898(8), 082048. http://stacks.iop.org/1742-6596/898/i=8/a=082048
    @article{jayatilaka-physics-2017,
      author = {Jayatilaka, B and Levshina, T and Sehgal, C and Gardner, R and Rynge, M and Wurthwein, F},
      title = {The OSG Open Facility: an on-ramp for opportunistic scientific computing},
      journal = {Journal of Physics: Conference Series},
      volume = {898},
      number = {8},
      pages = {082048},
      url = {http://stacks.iop.org/1742-6596/898/i=8/a=082048},
      year = {2017}
    }
  12. Lynch, V., Calvo, J. B., Deelman, E., Ferreira da Silva, R., Goswami, M., Hui, Y., Lingerfelt, E., & Vetter, J. (2017). Distributed Workflows for Modeling Experimental Data. 2017 IEEE High Performance Extreme Computing Conference (HPEC’17). https://doi.org/10.1109/HPEC.2017.8091071 (Funding Acknowledgments: DOE DE-SC0012636)
    @inproceedings{lynch-hpec-2017,
      title = {Distributed Workflows for Modeling Experimental Data},
      author = {Lynch, Vickie and Calvo, Jose Borreguero and Deelman, Ewa and Ferreira da Silva, Rafael and Goswami, Monojoy and Hui, Yawei and Lingerfelt, Eric and Vetter, Jeffrey},
      booktitle = {2017 IEEE High Performance Extreme Computing Conference (HPEC'17)},
      year = {2017},
      pages = {},
      doi = {10.1109/HPEC.2017.8091071},
      note = {Funding Acknowledgments: DOE DE-SC0012636}
    }
  13. Mandal, A., Ruth, P., Baldin, I., Ferreira da Silva, R., & Deelman, E. (2017). Toward Prioritization of Data Flows for Scientific Workflows Using Virtual Software Defined Exchanges. First International Workshop on Workflow Science (WoWS 2017), 566–575. https://doi.org/10.1109/eScience.2017.92 (Funding Acknowledgments: DOE DE-SC0012636)
    @inproceedings{mandal-wows-2017,
      title = {Toward Prioritization of Data Flows for Scientific Workflows Using Virtual Software Defined Exchanges},
      author = {Mandal, Anirban and Ruth, Paul and Baldin, Ilya and Ferreira da Silva, Rafael and Deelman, Ewa},
      booktitle = {First International Workshop on Workflow Science (WoWS 2017)},
      year = {2017},
      pages = {566--575},
      doi = {10.1109/eScience.2017.92},
      note = {Funding Acknowledgments: DOE DE-SC0012636}
    }
  14. Poehlman, W. L., Rynge, M., Balamurugan, D., Mills, N., & Feltus, F. A. (2017). OSG-KINC: High-throughput gene co-expression network construction using the open science grid. 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 1827–1831. https://doi.org/10.1109/BIBM.2017.8217938
    @inproceedings{poehlman-ieee-bibm-2017,
      author = {Poehlman, W. L. and Rynge, M. and Balamurugan, D. and Mills, N. and Feltus, F. A.},
      booktitle = {2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)},
      title = {OSG-KINC: High-throughput gene co-expression network construction using the open science grid},
      year = {2017},
      volume = {},
      number = {},
      pages = {1827-1831},
      keywords = {Biological information theory;Correlation;Gene expression;Genomics;RNA;Software},
      doi = {10.1109/BIBM.2017.8217938},
      issn = {},
      month = nov
    }
  15. Santana-Perez, I., Ferreira da Silva, R., Rynge, M., Deelman, E., Perez-Hernandez, M. S., & Corcho, O. (2017). Reproducibility of Execution Environments in Computational Science Using Semantics and Clouds. Future Generation Computer Systems, 67, 354–367. https://doi.org/10.1016/j.future.2015.12.017 (Funding Acknowledgements: NSF ACI SI2-SSI 1148515, NSF FutureGrid 0910812)
    @article{santanaperez-fgcs-2016,
      title = {Reproducibility of Execution Environments in Computational Science Using Semantics and Clouds},
      author = {Santana-Perez, Idafen and Ferreira da Silva, Rafael and Rynge, Mats and Deelman, Ewa and Perez-Hernandez, Maria S. and Corcho, Oscar},
      journal = {Future Generation Computer Systems},
      volume = {67},
      pages = {354--367},
      year = {2017},
      doi = {10.1016/j.future.2015.12.017},
      note = {Funding Acknowledgements: NSF ACI SI2-SSI 1148515, NSF FutureGrid 0910812},
      url = {http://dx.doi.org/10.1016/j.future.2015.12.017}
    }
  16. Scientific, L. I. G. O., Abbott, B. P., Abbott, R., Abbott, T. D., Acernese, F., Ackley, K., Adams, C., Adams, T., Addesso, P., Adhikari, R. X., & others. (2017). GW170104: observation of a 50-solar-mass binary black hole coalescence at redshift 0.2. Physical Review Letters, 118(22), 221101.
    @article{scientific2017gw170104,
      title = {GW170104: observation of a 50-solar-mass binary black hole coalescence at redshift 0.2},
      author = {Scientific, LIGO and Abbott, BP and Abbott, R and Abbott, TD and Acernese, F and Ackley, K and Adams, C and Adams, T and Addesso, P and Adhikari, RX and others},
      journal = {Physical Review Letters},
      volume = {118},
      number = {22},
      pages = {221101},
      year = {2017},
      publisher = {American Physical Society}
    }
  17. Taylor, I. J., Brinckman, A., Deelman, E., Ferreira da Silva, R., Gupta, S., Nabrzyski, J., Park, S., & Vahi, K. (2017). Accelerating Circuit Realization via a Collaborative Gateway of Innovations. 9th International Workshop on Science Gateways (IWSG 2017). (Funding Acknowledgments: DARPA HR0011-16-C-0043)
    @inproceedings{taylor-iwsg-2017,
      title = {Accelerating Circuit Realization via a Collaborative Gateway of Innovations},
      author = {Taylor, Ian J. and Brinckman, Adam and Deelman, Ewa and Ferreira da Silva, Rafael and Gupta, Sandeep and Nabrzyski, Jarek and Park, Soowang and Vahi, Karan},
      booktitle = {9th International Workshop on Science Gateways (IWSG 2017)},
      year = {2017},
      pages = {},
      doi = {},
      note = {Funding Acknowledgments: DARPA HR0011-16-C-0043}
    }

2016

  1. Chen, W., Ferreira da Silva, R., Deelman, E., & Fahringer, T. (2016). Dynamic and Fault-Tolerant Clustering for Scientific Workflows. IEEE Transactions on Cloud Computing, 4(1), 49–62. https://doi.org/10.1109/TCC.2015.2427200 (Funding Acknowledgements: NSF IIS-0905032, NSF ACI SI2-SSI 1148515, and NSF FutureGrid 0910812)
    @article{chen-tcc-2015,
      title = {Dynamic and Fault-Tolerant Clustering for Scientific Workflows},
      journal = {{IEEE} Transactions on Cloud Computing},
      volume = {4},
      number = {1},
      pages = {49--62},
      year = {2016},
      author = {Chen, Weiwei and Ferreira da Silva, Rafael and Deelman, Ewa and Fahringer, Thomas},
      note = {Funding Acknowledgements: NSF IIS-0905032, NSF ACI SI2-SSI 1148515, and NSF FutureGrid 0910812},
      doi = {10.1109/TCC.2015.2427200},
      url = {http://pegasus.isi.edu/publications/2015/chen-tcc-2015.pdf}
    }
  2. Deelman, E., Vahi, K., Rynge, M., Juve, G., Mayani, R., & Ferreira da Silva, R. (2016). Pegasus in the Cloud: Science Automation through Workflow Technologies. IEEE Internet Computing, 20(1), 70–76. https://doi.org/10.1109/MIC.2016.15 (Funding Acknowledgements: NSF ACI SI2-SSI 1148515, NSF ACI 1245926, NSF FutureGrid 0910812, NHGRI 1U01 HG006531-01)
    @article{deelman-ic-2016,
      title = {Pegasus in the Cloud: Science Automation through Workflow Technologies},
      author = {Deelman, Ewa and Vahi, Karan and Rynge, Mats and Juve, Gideon and Mayani, Rajiv and Ferreira da Silva, Rafael},
      journal = {IEEE Internet Computing},
      volume = {20},
      number = {1},
      pages = {70--76},
      year = {2016},
      note = {Funding Acknowledgements: NSF ACI SI2-SSI 1148515, NSF ACI 1245926, NSF FutureGrid 0910812, NHGRI 1U01 HG006531-01},
      url = {http://dx.doi.org/10.1109/MIC.2016.15},
      doi = {10.1109/MIC.2016.15}
    }
  3. Ferreira da Silva, R., Deelman, E., Filgueira, R., Vahi, K., Rynge, M., Mayani, R., & Mayer, B. (2016). Automating Environmental Computing Applications with Scientific Workflows. Environmental Computing Workshop (ECW’16), IEEE 12th International Conference on e-Science, 400–406. https://doi.org/10.1109/eScience.2016.7870926 (Funding Acknowledgments: DOE DESC0012636, NSF ACI SI2-SSI 1148515)
    @inproceedings{ferreiradasilva-ecw-2016,
      author = {Ferreira da Silva, Rafael and Deelman, Ewa and Filgueira, Rosa and Vahi, Karan and Rynge, Mats and Mayani, Rajiv and Mayer, Benjamin},
      title = {Automating Environmental Computing Applications with Scientific Workflows},
      year = {2016},
      note = {Funding Acknowledgments: DOE DESC0012636, NSF ACI SI2-SSI 1148515},
      booktitle = {Environmental Computing Workshop (ECW'16), IEEE 12th International Conference on e-Science},
      doi = {10.1109/eScience.2016.7870926},
      pages = {400--406}
    }
  4. Ferreira da Silva, R., Filgueira, R., Deelman, E., Pairo-Castineira, E., Overton, I. M., & Atkinson, M. (2016). Using Simple PID Controllers to Prevent and Mitigate Faults in Scientific Workflows. 11th Workflows in Support of Large-Scale Science (WORKS’16), 15–24. (Funding Acknowledgments: DOE DE-SC0012636)
    @inproceedings{ferreiradasilva-works-2016,
      author = {Ferreira da Silva, Rafael and Filgueira, Rosa and Deelman, Ewa and Pairo-Castineira, Erola and Overton, Ian Michael and Atkinson, Malcolm},
      title = {Using Simple PID Controllers to Prevent and Mitigate Faults in Scientific Workflows},
      booktitle = {11th Workflows in Support of Large-Scale Science (WORKS'16)},
      year = {2016},
      pages = {15--24},
      note = {Funding Acknowledgments: DOE DE-SC0012636}
    }
  5. Filgueira, R., Ferreira da Silva, R., Krause, A., Deelman, E., & Atkinson, M. (2016). Asterism: Pegasus and dispel4py hybrid workflows for data-intensive science. 7th International Workshop on Data-Intensive Computing in the Clouds (DataCloud’16), 1–8. https://doi.org/10.1109/DataCloud.2016.004 (Funding Acknowledgments: NSF ACI SI2-SSI 1148515)
    @inproceedings{filgueira-datacloud-2016,
      author = {Filgueira, Rosa and Ferreira da Silva, Rafael and Krause, Amrey and Deelman, Ewa and Atkinson, Malcolm},
      title = {Asterism: Pegasus and dispel4py hybrid workflows for data-intensive science},
      booktitle = {7th International Workshop on Data-Intensive Computing in the Clouds (DataCloud'16)},
      year = {2016},
      doi = {10.1109/DataCloud.2016.004},
      pages = {1--8},
      note = {Funding Acknowledgments: NSF ACI SI2-SSI 1148515}
    }
  6. Gaikwad, P., Mandal, A., Ruth, P., Juve, G., Krol, D., & Deelman, E. (2016). Anomaly Detection for Scientific Workflow Applications on Networked Clouds. IEEE 2016 International Conference on High Performance Computing & Simulation (HPCS 2016). https://doi.org/10.1109/HPCSim.2016.7568396 (Funding Acknowledgement: DOE DE-SC0012636)
    @inproceedings{gaikwad-intercloud-2016,
      author = {Gaikwad, Prathamesh and Mandal, Anirban and Ruth, Paul and Juve, Gideon and Krol, Dariusz and Deelman, Ewa},
      title = {Anomaly Detection for Scientific Workflow Applications on Networked Clouds},
      booktitle = {IEEE 2016 International Conference on High Performance Computing & Simulation (HPCS 2016)},
      year = {2016},
      note = {Funding Acknowledgement: DOE DE-SC0012636},
      doi = {10.1109/HPCSim.2016.7568396}
    }
  7. Krol, D., Ferreira da Silva, R., Deelman, E., & Lynch, V. E. (2016). Workflow Performance Profiles: Development and Analysis. In Euro-Par 2016: Parallel Processing Workshops (pp. 108–120). https://doi.org/10.1007/978-3-319-58943-5_9 (Funding Acknowledgments: DOE DE-SC0012636)
    @incollection{krol-heteropar-2016,
      author = {Krol, Dariusz and Ferreira da Silva, Rafael and Deelman, Ewa and Lynch, Vickie E.},
      title = {Workflow Performance Profiles: Development and Analysis},
      year = {2016},
      note = {Funding Acknowledgments: DOE DE-SC0012636},
      booktitle = {Euro-Par 2016: Parallel Processing Workshops},
      doi = {10.1007/978-3-319-58943-5_9},
      pages = {108--120}
    }
  8. Krol, D., Kitowski, J., Ferreira da Silva, R., Juve, G., Vahi, K., Rynge, M., & Deelman, E. (2016). Science Automation in Practice: Performance Data Farming in Workflows. 21st IEEE International Conference on Emerging Technologies and Factory Automation (ETFA). https://doi.org/10.1109/ETFA.2016.7733677 (Funding Acknowledgments: DOE DE-SC0012636)
    @inproceedings{krol-etfa-2016,
      author = {Krol, Dariusz and Kitowski, Jacek and Ferreira da Silva, Rafael and Juve, Gideon and Vahi, Karan and Rynge, Mats and Deelman, Ewa},
      title = {Science Automation in Practice: Performance Data Farming in Workflows},
      booktitle = {21st IEEE International Conference on Emerging Technologies and Factory Automation (ETFA)},
      year = {2016},
      note = {Funding Acknowledgments: DOE DE-SC0012636},
      doi = {10.1109/ETFA.2016.7733677}
    }
  9. Liu, Y., Khan, S. M., Wang, J., Rynge, M., Zhang, Y., Zeng, S., Chen, S., Maldonado dos Santos, J. V., Valliyodan, B., Calyam, P. P., Merchant, N., Nguyen, H. T., Xu, D., & Joshi, T. (2016). PGen: large-scale genomic variations analysis workflow and browser in SoyKB. BMC Bioinformatics, 17(13), 337. https://doi.org/10.1186/s12859-016-1227-y
    @article{Liu2016,
      author = {Liu, Yang and Khan, Saad M. and Wang, Juexin and Rynge, Mats and Zhang, Yuanxun and Zeng, Shuai and Chen, Shiyuan and Maldonado dos Santos, Joao V. and Valliyodan, Babu and Calyam, Prasad P. and Merchant, Nirav and Nguyen, Henry T. and Xu, Dong and Joshi, Trupti},
      title = {PGen: large-scale genomic variations analysis workflow and browser in SoyKB},
      journal = {BMC Bioinformatics},
      year = {2016},
      volume = {17},
      number = {13},
      pages = {337},
      issn = {1471-2105},
      doi = {10.1186/s12859-016-1227-y},
      url = {http://dx.doi.org/10.1186/s12859-016-1227-y}
    }
  10. Mandal, A., Ruth, P., Baldin, I., Krol, D., Juve, G., Mayani, R., Ferreira da Silva, R., Deelman, E., Meredith, J., Vetter, J., Lynch, V., Mayer, B., Wynne III, J., Blanco, M., Carothers, C., LaPre, J., & Tierney, B. (2016). Toward an End-to-end Framework for Modeling, Monitoring, and Anomaly Detection for Scientific Workflows. Workshop on Large-Scale Parallel Processing (LSPP 2016), 1370–1379. https://doi.org/10.1109/IPDPSW.2016.202 (Funding Acknowledgments: DOE DE-SC0012636)
    @inproceedings{mandal-lspp-2016,
      author = {Mandal, Anirban and Ruth, Paul and Baldin, Ilya and Krol, Dariusz and Juve, Gideon and Mayani, Rajiv and Ferreira da Silva, Rafael and Deelman, Ewa and Meredith, Jeremy and Vetter, Jeffrey and Lynch, Vickie and Mayer, Ben and Wynne III, James and Blanco, Mark and Carothers, Chris and LaPre, Justin and Tierney, Brian},
      title = {Toward an End-to-end Framework for Modeling, Monitoring, and Anomaly Detection for Scientific Workflows},
      booktitle = {{Workshop on Large-Scale Parallel Processing (LSPP 2016)}},
      year = {2016},
      note = {Funding Acknowledgments: DOE DE-SC0012636},
      url = {http://pegasus.isi.edu/publications/2016/mandal-lspp-2016.pdf},
      doi = {10.1109/IPDPSW.2016.202},
      pages = {1370--1379}
    }
  11. Nawaz, H., Juve, G., Ferreira da Silva, R., & Deelman, E. (2016). Performance Analysis of an I/O-Intensive Workflow executing on Google Cloud and Amazon Web Services. 18th Workshop on Advances in Parallel and Distributed Computational Models (APDCM), 535–544. https://doi.org/10.1109/IPDPSW.2016.90 (Funding Acknowledgements: DOE DE-SC0012636)
    @inproceedings{nawaz-apdcm-2016,
      author = {Nawaz, Hassan and Juve, Gideon and Ferreira da Silva, Rafael and Deelman, Ewa},
      title = {Performance Analysis of an I/O-Intensive Workflow executing on Google Cloud and Amazon Web Services},
      booktitle = {{18th Workshop on Advances in Parallel and Distributed Computational Models (APDCM)}},
      year = {2016},
      note = {Funding Acknowledgements: DOE DE-SC0012636},
      url = {http://pegasus.isi.edu/publications/2016/nawaz-apdcm-2016.pdf},
      doi = {10.1109/IPDPSW.2016.90},
      pages = {535--544}
    }
  12. Poehlman, W. L., Rynge, M., Branton, C., Balamurugan, D., & Feltus, F. A. (2016). OSG-GEM: Gene Expression Matrix Construction Using the Open Science Grid. Bioinformatics and Biology Insights, 10, 133–141. https://doi.org/10.4137/BBI.S38193
    @article{10.4137/BBI.S38193,
      author = {Poehlman, William L. and Rynge, Mats and Branton, Chris and Balamurugan, D. and Feltus, Frank A.},
      journal = {Bioinformatics and Biology Insights},
      publisher = {Libertas Academica},
      title = {OSG-GEM: Gene Expression Matrix Construction Using the Open Science Grid},
      year = {2016},
      month = aug,
      volume = {10},
      url = {http://www.la-press.com/osg-gem-gene-expression-matrix-construction-using-the-open-science-gri-article-a5814},
      pages = {133--141},
      doi = {10.4137/BBI.S38193}
    }
  13. Schlagkamp, S., Ferreira da Silva, R., Allcock, W., Deelman, E., & Schwiegelshohn, U. (2016). Consecutive Job Submission Behavior at Mira Supercomputer. 25th ACM International Symposium on High-Performance Parallel and Distributed Computing (HPDC). https://doi.org/10.1145/2907294.2907314 (Funding Acknowledgements: DOE ER26110, DOE DE-SC0012636)
    @inproceedings{schlagkamp-hpdc-2016,
      author = {Schlagkamp, Stephan and Ferreira da Silva, Rafael and Allcock, William and Deelman, Ewa and Schwiegelshohn, Uwe},
      title = {Consecutive Job Submission Behavior at Mira Supercomputer},
      booktitle = {{25th ACM International Symposium on High-Performance Parallel and Distributed Computing (HPDC)}},
      year = {2016},
      note = {Funding Acknowledgements: DOE ER26110, DOE DE-SC0012636},
      url = {http://pegasus.isi.edu/publications/2016/schlagkamp-hpdc-2016.pdf},
      doi = {10.1145/2907294.2907314}
    }
  14. Schlagkamp, S., Ferreira da Silva, R., Deelman, E., & Schwiegelshohn, U. (2016). Understanding User Behavior: from HPC to HTC. International Conference on Computational Science (ICCS). https://doi.org/10.1016/j.procs.2016.05.397 (Funding Acknowledgements: DOE ER26110, DOE DE-SC0012636)
    @inproceedings{schlagkamp-iccs-2016,
      author = {Schlagkamp, Stephan and Ferreira da Silva, Rafael and Deelman, Ewa and Schwiegelshohn, Uwe},
      title = {Understanding User Behavior: from HPC to HTC},
      booktitle = {{International Conference on Computational Science (ICCS)}},
      year = {2016},
      note = {Funding Acknowledgements: DOE ER26110, DOE DE-SC0012636},
      url = {http://pegasus.isi.edu/publications/2016/schlagkamp-iccs-2016.pdf},
      doi = {10.1016/j.procs.2016.05.397}
    }
  15. Stodden, V., McNutt, M., Balley, D. H., Deelman, E., Gil, Y., Hanson, B., Heroux, M. A., Ioannidis, J. P. A., & Taufer. (2016). Enhancing reproducibility for computational methods. Science, 354(6317), 1240–1241. https://doi.org/10.1126/science.aah6168
    @article{stodden-science-2016,
      author = {Stodden, Victoria and McNutt, Marcia and Balley, David H. and Deelman, Ewa and Gil, Yolanda and Hanson, Brooks and Heroux, Michael A. and Ioannidis, John P.A. and Taufer},
      title = {Enhancing reproducibility for computational methods},
      journal = {Science},
      year = {2016},
      volume = {354},
      number = {6317},
      pages = {1240--1241},
      doi = {10.1126/science.aah6168},
      url = {http://science.sciencemag.org/content/354/6317/1240.full},
      publisher = {American Association for the Advancement of Science},
      issn = {0036-8075}
    }
  16. Swetnam, T. L., Pelletier, J. D., Rasmussen, C., Callahan, N. R., Merchant, N., Lyons, E., Rynge, M., Liu, Y., Nandigam, V., & Crosby, C. (2016). Scaling GIS Analysis Tasks from the Desktop to the Cloud Utilizing Contemporary Distributed Computing and Data Management Approaches: A Case Study of Project-based Learning and Cyberinfrastructure Concepts. XSEDE16 Conference on Diversity, Big Data, and Science at Scale, 21:1–21:6. https://doi.org/10.1145/2949550.2949573
    @inproceedings{Swetnam:2016:SGA:2949550.2949573,
      author = {Swetnam, T. L. and Pelletier, J. D. and Rasmussen, C. and Callahan, N. R. and Merchant, N. and Lyons, E. and Rynge, M. and Liu, Y. and Nandigam, V. and Crosby, C.},
      title = {Scaling GIS Analysis Tasks from the Desktop to the Cloud Utilizing Contemporary Distributed Computing and Data Management Approaches: A Case Study of Project-based Learning and Cyberinfrastructure Concepts},
      booktitle = {XSEDE16 Conference on Diversity, Big Data, and Science at Scale},
      series = {XSEDE16},
      year = {2016},
      isbn = {978-1-4503-4755-6},
      location = {Miami, USA},
      pages = {21:1--21:6},
      articleno = {21},
      numpages = {6},
      url = {http://doi.acm.org/10.1145/2949550.2949573},
      doi = {10.1145/2949550.2949573},
      acmid = {2949573},
      publisher = {ACM},
      keywords = {CyberGIS, GDAL, GRASS, Makeflow, Work Queue}
    }

2015

  1. Bryk, P., Malawski, M., Juve, G., & Deelman, E. (2015). Storage-aware Algorithms for Scheduling of Workflow Ensembles in Clouds. Journal of Grid Computing, 14(2), 359–378. https://doi.org/10.1007/s10723-015-9355-6 (Funding Acknowledgements: DOE ER26110)
    @article{bryk-jgc-2015,
      author = {Bryk, Piotr and Malawski, Maciej and Juve, Gideon and Deelman, Ewa},
      title = {Storage-aware Algorithms for Scheduling of Workflow Ensembles in Clouds},
      journal = {Journal of Grid Computing},
      volume = {14},
      number = {2},
      pages = {359--378},
      year = {2015},
      note = {Funding Acknowledgements: DOE ER26110},
      doi = {10.1007/s10723-015-9355-6},
      url = {http://link.springer.com/article/10.1007%2Fs10723-015-9355-6}
    }