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################################################################################
### Drafts / Under Review (note the 'review_' prefix). These need to be sorted
### into the list after publication (with a non-prefixed key!)
################################################################################
@article{fox2019understanding,
title={Understanding ML driven HPC: Applications and Infrastructure},
author={Fox, Geoffrey and Jha, Shantenu},
journal={arXiv preprint arXiv:1909.02363},
year={2019}
}
@article{turilli2019characterizing,
title={Characterizing the Performance of Executing Many-tasks on Summit},
author={Matteo Turilli and Andre Merzky and Thomas Naughton and Wael Elwasif and Shantenu Jha},
journal={arXiv preprint arXiv:1909.03057},
year={2019}
}
@article{jha2019incorporating,
title={Incorporating Scientific Workflows in Computing Research Processes},
author={Jha, Shantenu and Lathrop, Scott and Nabrzyski, Jarek and Ramakrishnan, Lavanya},
journal={Computing in Science and Engineering},
volume={21},
number={4},
pages={4--6},
year={2019},
publisher={IEEE Computer Society}
}
@article{fox2019learning,
title={Learning Everywhere: Pervasive machine learning for effective High-Performance computation},
author={Fox, Geoffrey and Glazier, James A and Kadupitiya, JCS and Jadhao, Vikram and Kim, Minje and Qiu, Judy and Sluka, James P and Somogyi, Endre and Marathe, Madhav and Adiga, Abhijin and others},
journal={arXiv preprint arXiv:1902.10810},
url = {https://arxiv.org/abs/1902.10810},
year={2019}
}
@article{hruska2019extensible,
title={Extensible and Scalable Adaptive Sampling on Supercomputers},
author={Hruska, Eugen and Balasubramanian, Vivekanandan and Ossyra, John R and Jha, Shantenu and Clementi, Cecilia},
journal={arXiv preprint arXiv:1907.06954},
year={2019}
}
@Article{balasubramanian2019radical,
author = {Vivek Balasubramanian and Shantenu Jha and Andr{\'{e}} Merzky and Matteo Turilli},
title = {RADICAL-Cybertools: Middleware Building Blocks for Scalable Science},
journal = {CoRR},
year = {2019},
volume = {abs/1904.03085},
archiveprefix = {arXiv},
bibsource = {dblp computer science bibliography, https://dblp.org},
biburl = {https://dblp.org/rec/bib/journals/corr/abs-1904-03085},
eprint = {1904.03085},
timestamp = {Wed, 24 Apr 2019 12:21:25 +0200},
url = {http://arxiv.org/abs/1904.03085},
}
@article{turilli2019middleware,
Author={Matteo Turilli and Vivek Balasubramanian and Andre Merzky and Ioannis Paraskevakos and Shantenu Jha},
Title = {Middleware Building Blocks for Workflow Systems},
journal ={Computing in Science \& Engineering (CiSE) special issue on Incorporating Scientific Workflows in Computing Research Processes},
note = {10.1109/MCSE.2019.2920048 (2019)},
url = {\newline{https://arxiv.org/abs/1903.10057}},
}
@article{huerta2019supporting,
title={Supporting High-Performance and High-Throughput Computing for Experimental Science},
author={Huerta, EA and Haas, Roland and Jha, Shantenu and Neubauer, Mark and Katz, Daniel S},
journal={Computing and Software for Big Science},
volume={3},
number={1},
pages={5},
year={2019},
publisher={Springer}
}
@article{extasy-cocomd,
author = {Shkurti, Ardita and Styliari, Ioanna Danai and Balasubramanian, Vivek and Bethune, Iain and Pedebos, Conrado and J\
ha, Shantenu and Laughton, Charles A.},
title = {CoCo-MD: A Simple and Effective Method for the Enhanced Sampling of Conformational Space},
journal = {Journal of Chemical Theory and Computation},
volume = {0},
number = {ja},
pages = {null},
year = {0},
doi = {10.1021/acs.jctc.8b00657},
URL = {https://doi.org/10.1021/acs.jctc.8b00657},
}
@article{rp-titan,
author = {Andre Merzky and Matteo Turilli and Manuel Maldonado and Shantenu Jha},
title = {Design and Performance Characterization of RADICAL-Pilot on Titan},
journal = {in preparation},
note = {\newline{\url{https://arxiv.org/abs/1801.01843}}},
year = 2018
}
@article{resource-selection,
author = {Ming Tai Ha and Matteo Turilli and Andre Merzky and Shantenu Jha},
title = {Towards General Distributed Resource Selection},
journal = {in review},
note = {\newline \url{https://arxiv.org/abs/1801.02651}},
year = 2018,
}
@misc{review_2015-hpdc,
author = {Andre Luckow and Ioannis Paraskevakos and Shantenu Jha},
title = {{Pilot-Abstraction: A Valid Abstraction for Data-Intensive Application on HPC, Hadoop and Cloud Infrastructures?}},
booktitle = {The 24th International ACM Symposium on High Performance Distributed Computing},
year = {2015},
location = {Portland, Oregon, USA},
note = {\newline \url{http://arxiv.org/pdf/1501.05041v1.pdf}},
OPTnote = {Submitted, Under Review},
}
################################################################################
## Book Chapters
################################################################################
@incollection{ideas,
author = {Shantenu Jha and Daniel S. Katz and Andre Luckow and
Andre Merzky and Katerina Stamou},
title = {{Understanding Scientific Applications for Cloud
Environments}},
booktitle = {{Cloud Computing: Principles and Paradigms}},
chapter = 13,
editor = {Rajkumar Buyya and James Broberg and Andrzej M. Goscinski},
year = 2011,
month = {March},
pages = {664},
url = {http://cct.lsu.edu/~sjha/select\_publications/cloud_book_chapter.pdf},
isbn = {978-0-470-88799-8},
}
################################################################################
## Journal Publications
################################################################################
@article{synapse-jocs,
title = "Synapse: Synthetic application profiler and emulator",
journal = "Journal of Computational Science",
volume = "27",
pages = "329 - 344",
year = "2018",
issn = "1877-7503",
doi = "https://doi.org/10.1016/j.jocs.2018.06.012",
url = "http://www.sciencedirect.com/science/article/pii/S1877750318300966",
author = "Andre Merzky and Ming Tai Ha and Matteo Turilli and Shantenu Jha",
keywords = "Emulation, Profiling"
}
@article{turilli2017comprehensive,
author = {Turilli, Matteo and Santcroos, Mark and Jha, Shantenu},
title = {A Comprehensive Perspective on Pilot-Job Systems},
journal = {ACM Comput. Surv.},
issue_date = {June 2018},
volume = {51},
number = {2},
month = apr,
year = {2018},
issn = {0360-0300},
pages = {43:1--43:32},
articleno = {43},
numpages = {32},
url = {http://doi.acm.org/10.1145/3177851},
doi = {10.1145/3177851},
acmid = {3177851},
publisher = {ACM},
address = {New York, NY, USA},
keywords = {Distributed applications, Pilot-Jobs, distributed systems},
}
####################
# 2016
@article {3dpas_intro,
author = {Jha, Shantenu and Katz, Daniel S. and Luckow, Andre and Chue Hong , Neil and Rana, Omer and Simmhan, Yogesh},
title = {Introducing distributed dynamic data-intensive (D3) science: Understanding applications and infrastructure},
journal = {Concurrency and Computation: Practice and Experience},
publisher = {John Wiley & Sons, Ltd},
issn = {1532-0634},
url = {http://dx.doi.org/10.1002/cpe.4032},
doi = {10.1002/cpe.4032},
pages = {e4032--n/a},
keywords = {dynamic, distributed, data intensive, scientific applications},
year = {2017},
note = {e4032 cpe.4032},
}
@article{Zhang2016,
doi = {10.21105/joss.00017},
url = {https://doi.org/10.21105/joss.00017},
year = {2016},
month = {May},
publisher = {The Open Journal},
volume = {1},
number = {1},
author = {Zhao Zhang and Daniel S. Katz and Andre Merzky and Matteo Turilli and Shantenu Jha and Yadu Nand},
title = {Application Skeleton: Generating Synthetic Applications for Infrastructure Research},
journal = {The Journal of Open Source Software}
}
@article{ccpe-2016-error,
author = {Jason Maassen et al },
title = {On the Complexities of Utilizing Large-Scale Lightpath-Connected Distributed Cyberinfrastructure},
journal = {Concurrency and Computation: Practice and Experience},
issn = {in press},
opturl = {http://dx.doi.org/10.1002/cpe.3013},
optdoi = {10.1002/cpe.3013},
optpages = {n/a--n/a},
optkeywords = {next-generation sequencing data analytics, science gateway, BFAST, mapping, ChIP-Seq, human genome, Burkerholderia glumae, mouse genome, runtime environment, distributed computing, simple API for grid applications (SAGA), pilot-job abstraction},
year = {2016},
}
@Article{panda2016,
author="De, K.
and Jha, S.
and Klimentov, A.
and Maeno, T.
and Mashinistov, R.
and Nilsson, P.
and Novikov, A.
and Oleynik, D.
and Panitkin, S.
and Poyda, A.
and Read, K. F.
and Ryabinkin, E.
and Teslyuk, A.
and Velikhov, V.
and Wells, J. C.
and Wenaus, T.",
title="Integration of Panda Workload Management System with supercomputers",
journal="Physics of Particles and Nuclei Letters",
year="2016",
volume="13",
number="5",
pages="647--653",
issn="1531-8567",
doi="10.1134/S1547477116050150",
url="http://dx.doi.org/10.1134/S1547477116050150"
}
####################
# 2015
@article{skeleton-synapse15,
title = "Application skeletons: Construction and use in e{S}cience ",
journal = "Future Generation Computer Systems",
volume = "",
number = "",
OPTpages = " - ",
year = "2015",
note = "\url{http://dx.doi.org/10.1016/j.future.2015.10.001}",
issn = "0167-739X",
doi = "http://dx.doi.org/10.1016/j.future.2015.10.001",
url = "http://www.sciencedirect.com/science/article/pii/S0167739X15003143",
author = "Daniel S. Katz and Andre Merzky and Zhao Zhang and Shantenu Jha",
keywords = "Computational science",
keywords = "Data science",
keywords = "Application modeling",
keywords = "System modeling",
keywords = "Performance modeling",
keywords = "Parallel and distributed systems ",
}
@article{saga-x,
author = {Andre Merzky and Ole Weidner and Shantenu Jha},
title = {{SAGA}: A Standardized Access Layer to Heterogeneous Distributed
Computing Infrastructure},
journal = {Software-X},
year = 2015,
doi = {10.1016/j.softx.2015.03.001},
url = {http://dx.doi.org/10.1016/j.softx.2015.03.001},
note = {DOI: 10.1016/j.softx.2015.03.001},
}
@article{ct500776j,
author = {Brian K. Radak and Melissa Romanus and Tai-Sung Lee and Haoyuan Chen and Ming Huang and Antons Treikalis and Vivekanandan Balasubramanian and Shantenu Jha and Darrin M. York},
title = {Characterization of the Three-Dimensional Free Energy Manifold for the
{Uracil Ribonucleoside} from Asynchronous Replica Exchange Simulations},
journal = {Journal of Chemical Theory and Computation},
volume = {11},
number = {2},
pages = {373-377},
year = {2015},
doi = {10.1021/ct500776j},
URL = {http://dx.doi.org/10.1021/ct500776j},
eprint = {http://dx.doi.org/10.1021/ct500776j},
note = {\newline\url{http://dx.doi.org/10.1021/ct500776j}},
}
@article{titan-panda,
author={A Klimentov and P Buncic and K De and S Jha and T Maeno and R Mount
and P Nilsson and D Oleynik and S Panitkin and A Petrosyan and
R J Porter and K F Read and A Vaniachine and J C Wells and T
Wenaus},
title={Next Generation Workload Management System For Big Data on Heterogeneous Distributed Computing},
journal={Journal of Physics: Conference Series},
volume={608},
number={1},
pages={012040},
url={http://stacks.iop.org/1742-6596/608/i=1/a=012040},
year={2015},
}
####################
# 2014
@article{drmaaocci-jogc-2014,
journal = {{Journal of Grid Computing}},
month = {{March}},
year = 2014,
volume = 12,
number = 1,
pages = {111-125},
title = {{Towards Standardized Job Submission and Control in
Infrastructure Clouds}},
author = {Peter Tröger and Andre Merzky},
note = {\url{http://link.springer.com/article/10.1007%2Fs10723-013-9275-2}}
}
@article{luckow2015pilot,
title={Pilot-data: an abstraction for distributed data},
author={Luckow, Andre and Santcroos, Mark and Zebrowski, Ashley and Jha, Shantenu},
journal={Journal of Parallel and Distributed Computing},
volume={79},
pages={16--30},
year={2015},
publisher={Elsevier}
}
@article{ethread-biomed-2014,
author = {Anjani Ragothaman and Sairam Chowdary Boddu and Nayong Kim and
Wei Feinstein and Michal Brylinski and Shantenu Jha and
Joohyun Kim},
title = {{Developing eThread Pipeline Using SAGA- Pilot Abstraction for
Large-Scale Structural Bioinformatics}},
journal = {BioMed Research International},
volume = {2014},
year = 2014,
doi = {10.1155/2014/348725},
}
@article{nanopore-jcc-2014,
author = {Hugh S. C. Martin and Shantenu Jha and Peter V.Coveney},
title = {{Comparative analysis of nucleotide translocation through
protein nanopores using steered molecular dynamics and an
adaptive biasing force}},
journal = {Computational Chemistry},
volume = {35},
number = {9},
pages = {692-702},
month = {April},
year = 2014,
doi = {10.1002/jcc.23525},
note = {\url{http://onlinelibrary.wiley.com/doi/10.1002/jcc.23572/abstract}}
}
@article{bfe-jctc-2014,
author = {David W. Wright and Benjamin A. Hall
and Owain A. Kenway and Shantenu Jha
and Peter V. Coveney},
title = {{Computing Clinically Relevant Binding Free Energies
of HIV-1 Protease Inhibitors}},
journal = {Chemical Theory and Computation},
volume = {10},
number = {3},
pages = {1228-1241},
year = 2014,
doi = {10.1021/ct4007037},
}
@article{cfd-multiscale-2014,
author = {Soon-Heum Ko and Nayong Kim and Shantenu Jha
and Dimitris E. Nikitopoulos and Dorel Moldovan},
title = {{Numerical Experiments of Solving Moderate-velocity Flow
Field Using a Hybrid Computational Fluid Dynamics Molecular
Dynamics Approach}},
journal = {Mechanical Science and Technology},
volume = {1},
number = {28},
pages = {245-253},
year = 2014,
doi = {10.1007/s12206-013-0962-5},
}
####################
# 2012
@article {dpa_surveypaper,
author = {Jha, Shantenu and Cole, Murray and Katz, Daniel S. and Parashar, Manish and Rana, Omer and Weissman, Jon},
title = {Distributed computing practice for large-scale science and engineering applications},
journal = {Concurrency and Computation: Practice and Experience},
note = "\url{http://dx.doi.org/10.1002/cpe.2897}",
volume = {25},
number = {11},
issn = {1532-0634},
XXurl = {http://dx.doi.org/10.1002/cpe.2897},
XXdoi = {10.1002/cpe.2897},
pages = {1559--1585},
year = {2013},
}
@article{jogc-2012-dare,
author = {Maddineni, Sharath and Kim, Joohyun and El-Khamra, Yaakoub and Jha, Shantenu},
title = {Distributed Application Runtime Environment (DARE): A Standards-based Middleware Framework for Science-Gateways},
journal = {J. Grid Comput.},
issue_date = {December 2012},
volume = {10},
number = {4},
month = dec,
year = {2012},
issn = {1570-7873},
pages = {647--664},
numpages = {18},
url = {http://dx.doi.org/10.1007/s10723-012-9244-1},
doi = {10.1007/s10723-012-9244-1},
acmid = {2424948},
publisher = {Springer-Verlag New York, Inc.},
address = {Secaucus, NJ, USA},
keywords = {Clouds, DARE, EGI, Grids, Interoperability, Middleware, Pilot Jobs, SAGA, Science gateways, Standards, XSEDE},
}
@article{ccpe-2012-ngs,
author = {Kim, Joohyun and Maddineni, Sharath and Jha, Shantenu},
title = {Advancing next-generation sequencing data analytics with scalable distributed infrastructure},
journal = {Concurrency and Computation: Practice and Experience},
issn = {, , },
url = {http://dx.doi.org/10.1002/cpe.3013},
doi = {10.1002/cpe.3013},
pages = {n/a--n/a},
keywords = {next-generation sequencing data analytics, science gateway, BFAST, mapping, ChIP-Seq, human genome, Burkerholderia glumae, mouse genome, runtime environment, distributed computing, simple API for grid applications (SAGA), pilot-job abstraction},
year = {2013},
}
@article{biochem-2012-jha,
author = {Benjamin A. Hall and David W. Wright and Shantenu Jha
and Peter V. Coveney},
title = {{Quantized Water Access to the HIV-1 Protease Active Site as a
Proposed Mechanism for Cooperative Mutations in Drug Affinity}},
journal = {Biochemistry},
volume = {51},
number = {33},
pages = {6487-6489},
year = 2012,
doi = {10.1021/bi300432u},
}
@article{jmb-2012-jha,
author = {Wei Huang and Joohyun Kim and Shantenu Jha
and Fareed Aboul-ela},
title = {{Conformational Heterogeneity of the SAM-I Riboswitch
Transcriptional ON State: A Chaperone-Like Role for
S-Adenosyl Methionine}},
journal = {{Journal of Molecular Biology}},
year = 2012,
volume = {418},
number = {5},
pages = {331 - 349},
issn = {0022-2836},
doi = {10.1016/j.jmb.2012.02.019},
note = {\url{http://www.sciencedirect.com/science/article/pii/S0022283612001763}},
keywords = {RNA},
keywords = {riboswitch},
keywords = {secondary-structure prediction},
keywords = {dimmer switch},
keywords = {conformation ensemble},
}
####################
# 2011
@article{async_repex11,
author = {Abhinav Thota and Andre Luckow and Shantenu Jha},
title = {{Efficient large-scale Replica-Exchange Simulations on
Production Infrastructure}},
journal = {{Philosophical Transactions of the Royal Society A:
Mathematical, Physical and Engineering Sciences}},
year = 2011,
volume = {369},
number = {1949},
pages = {3318-3335},
url = {http://rsta.royalsocietypublishing.org/content/369/1949/3318.abstract},
}
@article{csc7700-iccs,
author = {Gabrielle Allen and Werner Benger and Andrei Hutanu and
Shantenu Jha and Frank L{\"o}ffler and Erik Schnetter},
title = {{A Practical and Comprehensive Graduate Course preparing
Students for Research involving Scientific Computing}},
journal = {{Procedia Computer Science}},
year = 2011,
volume = {4},
number = {0},
pages = {1927 - 1936},
booktitle = {{Proceedings of the International Conference on Computational
Science, ICCS 2011}},
note = {\url{http://www.sciencedirect.com/science/article/pii/S1877050911002687}},
issn = {1877-0509},
doi = {10.1016/j.procs.2011.04.210},
keywords = {Education},
keywords = {Scientific computing},
keywords = {computation},
}
@article{ecmls10_ccpe10,
author = {Joohyun Kim and Wei Huang and Sharath Maddineni and
Fareed Aboul-ela and Shantenu Jha},
title = {{Energy Landscape Analysis for Regulatory RNA Finding using
Scalable Distributed Cyberinfrastructure}},
journal = {Concurrency and Computation: Practice and Experience},
publisher = {John Wiley \& Sons, Ltd},
year = 2011,
volume = {23},
number = {17},
pages = {2292--2304},
issn = {1532-0634},
doi = {10.1002/cpe.1796},
note = {\url{http://onlinelibrary.wiley.com/doi/10.1002/cpe.1796/abstract}},
keywords = {concurrent programming and distributed computing, Simple API
for Grid Applications (SAGA), Pilot-Job abstraction, RNA
folding energy landscape, ncRNA gene finding},
}
@article{fgcs-interop11,
author = {Saurabh Sehgal and Miklos Erdelyi and Andre Merzky and
Shantenu Jha},
title = {{Understanding Application-Level Interoperability:
Scaling-Out MapReduce over High-Performance Grids and
Clouds}},
journal = {{Future Generation Computer Systems}},
year = 2011,
volume = {27},
number = {5},
pages = {590--599},
url = {http://www.sciencedirect.com/science/article/B6V06-51KT861-2/2/0092927785fbf5e065a7788af8b65b72},
issn = {0167-739X},
doi = {10.1016/j.future.2010.11.001},
keywords = {Programming systems},
keywords = {Distributed systems},
keywords = {Scale-out},
keywords = {Interoperability},
keywords = {MapReduce},
keywords = {SAGA},
}
####################
# 2010
@article{ddia_ptrsa10,
author = {Chris Miceli and Michael Miceli and Bety Rodriguez-Milla
and Shantenu Jha},
title = {{Understanding Performance of Distributed
Data-Intensive Applications}},
journal = {{Royal Society of London Philosophical Transactions
Series A}},
year = 2010,
month = {August},
volume = {368},
pages = {4089--4102},
url = {http://www.cct.lsu.edu/~sjha/select\_publications/saga_ptrsa10.pdf},
doi = {10.1098/rsta.2010.0168},
adsurl = {http://adsabs.harvard.edu/abs/2010RSPTA.368.4089M},
adsnote = {Provided by the SAO/NASA Astrophysics Data System},
}
###################
# 2009
@article{katz2009louisiana,
author = {Daniel S. Katz and Gabrielle Allen and R. Cortez and C.
Cruz-Neira and R. Gottumukkala and Z. D. Greenwood and
L. Guice and Shantenu Jha and R. Kolluru and Tevfik Kosar and
others},
title = {{Louisiana: a model for advancing regional e-Research
through cyberinfrastructure}},
journal = {Philosophical Transactions of the Royal Society A:
Mathematical, Physical and Engineering Sciences},
volume = {367},
number = {1897},
pages = {2459},
year = 2009,
publisher = {The Royal Society},
url = {http://rsta.royalsocietypublishing.org/content/367/1897/2459.full.pdf},
}
@article{jha2009using,
author = {Shantenu Jha and Andre Merzky and Geoffrey Fox},
title = {{Using Clouds to Provide Grids with Higher Levels of
Abstraction and Explicit Support for Usage Modes}},
journal = {{Concurrency and Computation: Practice and Experience}},
publisher = {John Wiley and Sons Ltd.},
address = {Chichester, UK},
year = 2009,
volume = {21},
number = {8},
pages = {2087--1108},
url = {http://www.ogf.org/OGF_Special_Issue/cloud-grid-saga.pdf},
doi = {10.1002/cpe.v21:8},
issn = {1532-0626},
}
@article{repex_ptrsa,
author = {Andre Luckow and Shantenu Jha and Joohyun Kim and
Andre Merzky and Bettina Schnor},
journal = {Royal Society Philosophical Transactions A},
title = {{Adaptive Replica-Exchange Simulations}},
year = 2009,
month = {jun},
date = {28},
pages = {2595--2606},
url = {http://www.cct.lsu.edu/~sjha/select\_publications/adaptive_repex_ptrsa.pdf},
}
###################
# 2008
###################
# 2007
###################
# 2006
@article{saga_cmst,
author = {Tom Goodale and Shantenu Jha and Harmut Kaiser and
Thilo Kielmann and Pascal Kleijer and Gregor von
Laszewski and Craig Lee and Andre Merzky and Hrabri
Rajic and John Shalf},
title = {{SAGA: A Simple API for Grid applications, High-Level
Application Programming on the Grid}},
journal = {{Computational Methods in Science and Technology}},
year = 2006,
number = {1},
volume = {12},
pages = {7--20},
url = {http://www.cs.vu.nl/~kielmann/papers/saga-cmst.pdf},
}
###################
# 2005
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# 2003
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# 2002
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# 2001
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# 2000
###################
# 2004
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# 2003
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# 2002
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# 2001
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# 2000
################################################################################
## Conference and Workshop Papers
@article{escience18dakka,
author = {Jumana Dakka and Kristof Pallas Vivek Balasubramanian and Matteo Turilli and David W Wright and Stefan J Zasada and Shunzhou Wan and Peter V Coveney and Shantenu Jha},
title = {Concurrent and Adaptive Extreme Scale Binding Free Energy Calculations},
journal = {14th IEEE International Conference on e-Science, e-Science 2018, Amsterdam},
pages = {189--200},
doi = {10.1109/eScience.2018.00034},
OPTnote = \url{https://arxiv.org/abs/1801.01174},
year = {2018}
}
@inproceedings{scale18dakka,
author = {Jumana Dakka and
Kristof Farkas{-}Pall and
Vivek Balasubramanian and
Matteo Turilli and
Shunzhou Wan and
David W. Wright and
Stefan J. Zasada and
Peter V. Coveney and
Shantenu Jha},
title = {Enabling Trade-offs Between Accuracy and Computational Cost: Adaptive
Algorithms to Reduce Time to Clinical Insight},
booktitle = {18th {IEEE/ACM} International Symposium on Cluster, Cloud and Grid
Computing, {CCGRID} 2018, Washington, DC, USA, May 1-4, 2018},
pages = {572--577},
year = {2018},
crossref = {DBLP:conf/ccgrid/2018},
url = {https://doi.org/10.1109/CCGRID.2018.00005},
doi = {10.1109/CCGRID.2018.00005},
timestamp = {Mon, 06 Aug 2018 15:48:22 +0200},
biburl = {https://dblp.org/rec/bib/conf/ccgrid/DakkaFBTWWZCJ18},
bibsource = {dblp computer science bibliography, https://dblp.org}
OPTnote = {IEEE/ACM SCALE Challenge Winner, CCGrid 2018},
}
@inproceedings{bb_ccgrid18,
author = {Matteo Turilli and
Andr{\'{e}} Merzky and
Vivek Balasubramanian and
Shantenu Jha},
title = {Building Blocks for Workflow System Middleware},
booktitle = {18th {IEEE/ACM} International Symposium on Cluster, Cloud and Grid
Computing, {CCGRID} 2018, Washington, DC, USA, May 1-4, 2018},
pages = {348--349},
year = {2018},
crossref = {DBLP:conf/ccgrid/2018},
url = {https://doi.org/10.1109/CCGRID.2018.00051},
doi = {10.1109/CCGRID.2018.00051},
timestamp = {Mon, 06 Aug 2018 15:48:22 +0200},
biburl = {https://dblp.org/rec/bib/conf/ccgrid/TurilliMBJ18},
bibsource = {dblp computer science bibliography, https://dblp.org}
note = {\newline \url{http://arxiv.org/abs/1609.03484}},
}
@inproceedings{merzky2018using,
title={Using pilot systems to execute many task workloads on supercomputers},
author={Merzky, Andre and Turilli, Matteo and Maldonado, Manuel and Santcroos, Mark and Jha, Shantenu},
booktitle={Workshop on Job Scheduling Strategies for Parallel Processing},
pages={61--82},
year={2018},
organization={Springer}
}
@inproceedings{balasubramanian2018harnessing,
title={Harnessing the power of many: Extensible toolkit for scalable ensemble applications},
author={Balasubramanian, Vivek and Turilli, Matteo and Hu, Weiming and Lefebvre, Matthieu and Lei, Wenjie and Modrak, Ryan and Cervone, Guido and Tromp, Jeroen and Jha, Shantenu},
booktitle={2018 IEEE International Parallel and Distributed Processing Symposium (IPDPS)},
pages={536--545},
year={2018},
organization={IEEE}
}
@article{dakka-nips17,
author = {Jumana Dakka and Pouya Bashivan and Mina Gheiratmand and Irina Rish and Shantenu Jha and Russell Greiner},
title = {Learning Neural Markers of Schizophrenia Disorder Using Recurrent Neural Networks},
journal = {31st Conference on Neural Information Processing Systems (NIPS 2017), Long Beach, California, US},
note = {\newline \url{https://arxiv.org/abs/1712.00512}}
}
@article{line-sc17,
author = {Line Pouchard and Sterling Baldwin and Todd Elsethaggen and Carlos Gamboa and Shantenu Jha and Bibi Raju and Eric Stephan and Li Tang and Kerstin Kleese Van Dam},
title = {Computational reproducibility for scientific workflows in large-scale environments},
journal = {Proceedings of Computational Reproducibility at Exascale 2017 (in press) \& Special Issue of IJHPCA, Workshop at ACM/IEEE SC'17 (CRE2017)},
year = 2017
}
@INPROCEEDINGS{htchpc2017converging,
author={D. Oleynik and S. Panitkin and M. Turilli and A. Angius and S. Oral and K. De and A. Klimentov and J. C. Wells and S. Jha},
booktitle={2017 IEEE 13th International Conference on e-Science (e-Science)},
title={High-Throughput Computing on High-Performance Platforms: A Case Study},
year={2017},
volume={},
number={},
pages={295-304},
doi={10.1109/eScience.2017.43},
ISSN={},
month={Oct},
}
@INPROCEEDINGS{turilli2016analysis,
author={M. Turilli and Y. N. Babuji and A. Merzky and M. T. Ha and M. Wilde and D. S. Katz and S. Jha},
booktitle={2017 IEEE 13th International Conference on e-Science (e-Science)},
title={Evaluating Distributed Execution of Workloads},
year={2017},
volume={},
number={},
pages={276-285},
doi={10.1109/eScience.2017.41},
ISSN={},
month={Oct},
OPTnote={\newline \url{https://arxiv.org/pdf/1605.09513.pdf}}
}
@article{dakka2017htbac,
title = {High-throughput Binding Affinity Calculations at Extreme Scales},
author = {Jumana Dakka and et al},
journal = {accepted Computational Approaches for Cancer Workshop, SC'17},
year = {2017},
note = {\newline\url{http://arxiv.org/abs/1712.09168}}}
OPTnote = {\newline{http://www.scworkshops.net/cancer2017/}}
}
@article{mahzad2017scipy,
title = {Parallel Analysis in MDAnalysis using the Dask Parallel Computing Library},
author = {Mahzad Khoshlessan and Ioannis Paraskevakos and Shantenu Jha and Oliver Beckstein},
journal = {Proceedings of the 15th Python in Science Conference. (SCIPY 2017)},
doi = {10.25080/shinma-7f4c6e7-00a},
note = {\newline \url{http://conference.scipy.org/proceedings/scipy2017/pdfs/mahzad_khoslessan.pdf}},
year = {2017},
}
@article{jay2017open,
title = {Toward Common Components for Open Workflow Systems},
author = {Jay Jay Billings and Shantenu Jha},
journal = {Proceedings of Open Source SuperComputing, Workshop at SC'17},
year = {2017},
note = {\newline \url{https://arxiv.org/abs/1710.06774}}
}
###################
# 2016
@inproceedings{extasy,
author={V. Balasubramanian and I. Bethune and A. Shkurti and E. Breitmoser and E. Hruska and C. Clementi and C. Laughton and S. Jha},
booktitle={2016 IEEE 12th International Conference on e-Science (e-Science)},
title={ExTASY: Scalable and flexible coupling of MD simulations and advanced sampling techniques},
year={2016},
volume={},
number={},
pages={361-370},
doi={10.1109/eScience.2016.7870921},
ISSN={},
month={Oct},
OPTnote = {\url{https://arxiv.org/abs/1606.00093}},
}
@inproceedings{entk2016bala,
author = {V. Balasubramanian and A. Treikalis and O. Weidner and S. Jha},
booktitle = {2016 45th International Conference on Parallel Processing (ICPP)},
title = {Ensemble Toolkit: Scalable and Flexible Execution of Ensembles of Tasks},
year = {2016},
volume = {00},
number = {},
pages = {458-463},
doi = {10.1109/ICPP.2016.59},
url = {doi.ieeecomputersociety.org/10.1109/ICPP.2016.59},
ISSN = {2332-5690},
month={Aug.},
OPTnote = {\newline \url{http://arxiv.org/abs/1602.00678}}
}
@inproceedings{repex2016,
author={A. Treikalis and A. Merzky and H. Chen and T. S. Lee and D. M. York and S. Jha},
booktitle={2016 45th International Conference on Parallel Processing (ICPP)},
title={RepEx: A Flexible Framework for Scalable Replica Exchange Molecular Dynamics Simulations},
year={2016},
volume={},
number={},
pages={628-637},
doi={10.1109/ICPP.2016.78},
ISSN={},
month={Aug},
OPTnote= {\newline \url{ http://arxiv.org/abs/1601.05439}},
}
@inproceedings{cug-2016,
title={{Executing dynamic heterogeneous workloads on Blue Waters with RADICAL-Pilot}},
author={Santcroos, Mark and Castain, Ralph and Merzky, Andre and
Bethune, Iain and Jha, Shantenu},
note = {10.5281/zenodo.3373741},
booktitle = {{CRAY User Group}},
OPTurl = {http://dx.doi.org/10.5281/zenodo.3373741},
OPTbooktitle = {{CRAY User Group (http://dx.doi.org/10.5281/zenodo.3373741)}},
year={2016}
}
@inproceedings{ipdps-2016,
author = {Matteo Turilli and Feng (Francis) Liu and Zhao Zhang and Andre
Merzky and Michael Wilde and Jon Weissman and Daniel S. Katz
and Shantenu Jha},
title = {Integrating Abstractions to Enhance the Execution of
Distributed Applications},
booktitle = {Proceedings of 30th IEEE International Parallel and Distributed Processing Symposium (IPDPS)},
location = {Chicago, USA},
note = {\url{http://arxiv.org/abs/1504.04720}},
year = {2016},
pages={953-962},
doi={10.1109/IPDPS.2016.64},
ISSN={1530-2075},
month={May},
}
@article{hadoop-on-hpc,
author = {Andre Luckow and Ioannis Paraskevakos and George Chantzialexiou and
Shantenu Jha},
title = {Hadoop on HPC: Integrating Hadoop and Pilot-Based Dynamic Resource
Management},
journal = {2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)},
OPTvolume = {00},
OPTnumber = {undefined},
issn = {},
year = {2016},
pages = {1607-1616},
doi = {doi.ieeecomputersociety.org/10.1109/IPDPSW.2016.166},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
@inproceedings{merzky2015synapse,
author = {Andr{\'{e}} Merzky and
Shantenu Jha},
title = {Synapse: Synthetic Application Profiler and Emulator},
booktitle = {2016 {IEEE} International Parallel and Distributed Processing Symposium
Workshops, {IPDPS} Workshops 2016, Chicago, IL, USA, May 23-27, 2016},
pages = {1259--1268},
year = {2016},
OPTcrossref = {DBLP:conf/ipps/2016w},
url = {http://dx.doi.org/10.1109/IPDPSW.2016.168},
doi = {10.1109/IPDPSW.2016.168},
timestamp = {Fri, 05 Aug 2016 15:08:45 +0200},
biburl = {http://dblp.uni-trier.de/rec/bib/conf/ipps/MerzkyJ16},
bibsource = {dblp computer science bibliography, http://dblp.org}
}
@inproceedings{panda-acat16,
author = {A. Klimentov and K. De and S. Jha and T. Maeno and R. Mashinistov and P. Nilsson and A. Novikov and D. Oleynik and S. Panitkin and A.Poyda and K.F.Read and E. Ryabinkin and A. Teslyuk and J.C. Wells and T. Wenaus},
title = {Integration Of PanDA Workload Management System with Supercomputers
for ATLAS and Data-Intensive Sciences},
booktitle = {Journal of Physics: Conference Series, Volume 762 (2016), 012021, 17th International Workshop on Advanced Computing and Analysis Techniques in Physics Research (ACAT 2016, Valparaiso, Chile, 20160118, 20160122)},
doi = {\url{http://dx.doi.org/10.1088/1742-6596/762/1/012021}},
year = {2016},
url = {\url{http://iopscience.iop.org/article/10.1088/1742-6596/762/1/012021/pdf}},
}
###################
# 2014
@inproceedings{tale-of-two-ieee-2014,
author = {Shantenu Jha and Judy Qiu and Andre Luckow and Pradeep Mantha
and Geoffrey C.Fox},
title = {{A Tale of Two Data-Intensive Paradigms: Applications,
Abstractions, and Architectures}},
booktitle = {Big Data (BigData Congress), 2014 IEEE International Congress on},
series = {},
isbn = {978-1-4799-5056-0},
year = {2014},
location = {Anchorage, Alaska, USA},
pages = {645 - 652},
numpages = {7},
doi = {10.1109/BigData.Congress.2014.137},
url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6906840},
OPTnote = {\url{https://raw.github.com/saga-project/radical.wp/master/publications/pdf/tale-of-two-ieee-2014.pdf}},
}
###################
# 2013
@inproceedings{2013-xsede-cdi,
author = {Brian K. Radak and Melissa Romanus and Emilio Gallicchio
and Tai-Sung Lee and Ole Weidner and Nan-Jie Deng and
Peng He and Wei Dai and Darrin M. York and Ronald M. Levy
and Shantenu Jha},
title = {{A Framework for Flexible and Scalable Replica-Exchange on
Production Distributed CI}},
booktitle = {Proceedings of the Conference on Extreme Science and
Engineering Discovery Environment: Gateway to Discovery},
series = {XSEDE '13},
isbn = {978-1-4503-2170-9},
year = {2013},
location = {San Diego, California, USA},
pages = {26:1--26:8},