otherpapers.bib

@article{
	pegasus,
	title = {Pegasus: A Framework for Mapping Complex Scientific Workflows onto Distributed Systems},
	author = {Ewa Deelman and Gurmeet Singh and Mei-Hui Su and James Blythe and Yolanda Gil and Carl Kesselman and Gaurang Mehta and Karan Vahi and Bruce Berriman and John Good and Anastasia Laity and Joseph Jacob and Daniel Kat},
	journal = {Scientific Programming Journal},
	volume = {13},
	number = {3},
	year = {200}
}

@InProceedings{10.1007/978-3-540-28642-4_2,
author="Deelman, Ewa
and Blythe, James
and Gil, Yolanda
and Kesselman, Carl
and Mehta, Gaurang
and Patil, Sonal
and Su, Mei-Hui
and Vahi, Karan
and Livny, Miron",
editor="Dikaiakos, Marios D.",
title="Pegasus: Mapping Scientific Workflows onto the Grid",
booktitle="Grid Computing",
year="2004",
publisher="Springer Berlin Heidelberg",
address="Berlin, Heidelberg",
pages="11--20",
abstract="In this paper we describe the Pegasus system that can map complex workflows onto the Grid. Pegasus takes an abstract description of a workflow and finds the appropriate data and Grid resources to execute the workflow. Pegasus is being released as part of the GriPhyN Virtual Data Toolkit and has been used in a variety of applications ranging from astronomy, biology, gravitational-wave science, and high-energy physics. A deferred planning mode of Pegasus is also introduced.",
isbn="978-3-540-28642-4"
}


@article{
	cluster_dep,
	author = "Gurmeet Singh, Carl Kesselman and Ewa Deelman",
	title = "Optimizing Grid-Based Workflow Execution", 
	journal = "Journal of Grid Computing",
	volume = "3",
	number = "3-4", 
	pages = "201-219", 
	month = "December", 
	year = "2005"
}

@inproceedings{chen2013balanced,
author={Weiwei Chen and Ferreira da Silva, Rafael and Ewa Deelman and Rizos Sakellariou},
url={http://pegasus.isi.edu/publications/2013/chen-clustering-escience2013.pdf},
title={Balanced Task Clustering in Scientific Workflows},
booktitle={9th IEEE International Conference on e-Science (eScience 2013)},
year={2013},
note={Funding Acknowledgements: NSF IIS-0905032 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}
}

@article{chen-fgcs-2014,
title={Using Imbalance Metrics to Optimize Task Clustering in Scientific Workflow Executions},
author={Weiwei Chen and Ferreira da Silva, Rafael and Ewa Deelman and Rizos Sakellariou},
url={http://pegasus.isi.edu/publications/2014/2014-fgcs-chen.pdf},
journal={Future Generation Computer Systems},
volume={46},
pages={69-84},
year={2015},
note={Funding Acknowledgements: NSF IIS-0905032 and NSF FutureGrid 0910812},
doi={10.1016/j.future.2014.09.014},
}



@inproceedings{chen2011constraints,
author={Weiwei Chen and Ewa Deelman},
url={http://pegasus.isi.edu/publications/2011/WChen-Partitioning\_and\_Scheduling.pdf},
title={Partitioning and Scheduling Workflows across Multiple Sites with Storage Constraints},
booktitle={9th International Conference on Parallel Processing and Applied Mathmatics},
year={2011},
note={Funding Acknowledgements: NSF IIS-0905032},
}

@inproceedings{
	workfow_overhead,
	author = "Weiwei Chen and Ewa Deelman", 
	title = "Workflow Overhead Analysis and Optimizations", 
	journal = "6th Workshop on Workflows in Support of Large-Scale Science (WORKS 11)", 
	year = "2011"
}

@article{
	cleanup_algo,
	author = "Sudarshan Srinivasan and Gideon Juve and Rafael Ferreira da Silva and Karan Vahi and Ewa Deelman",
	title = "A Cleanup Algorithm for Implementing Storage Constraints in Scientific Workflow Executions", 
	journal = "9th Workshop on Workflows in Support of Large-Scale Science (WORKS)", 
	year = "2014"
}

@inproceedings{
	workflow_parition,
	author = "Weiwei Chen and Ewa Deelman", 
	title = "Integration of Workflow Partitioning and Resource Provisioning", 
	journal = "The 12th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid 2012)",
	year = "2012"
}

@article{
	resource_monitor,
	author = "{Gideon Juve, Benjamin Tovar, Rafael Ferreira da Silva, Dariusz Krol, Douglas Thain, Ewa Deelman, William Allcock and Miron Livny}",
	title = "Practical Resource Monitoring for Robust High Throughput Computing",
	journal = "Workshop on Monitoring and Analysis for High Performance Computing Systems Plus Applications",
	year = "2015"
}

@inproceedings{
	deelman_workflows,
	author = "Ewa Deelman and Yolanda Gil",
	title = "Managing Large-Scale Scientific Workflows in Distributed Environments: Experiences and Challenges",
	journal = "Workflows in e-Science",
	year = "2006"
}

@article{
	data_placement,
	author = "{Ann Chervenak, Ewa Deelman, Miron Livny, Mei-Hui Su, Rob Schuler, Shishir Bharathi, Gaurang Mehta and Karan Vahi}",
	title = "Data Placement for Scientific Applications in Distributed Environments",
	journal = "Proceedings of Grid Conference 2007",
	year = "2007"
}

@article{
	resource_provision,
	author = "Gideon Juve and Ewa Deelman", 
	title = "Resource Provisioning Options for Large-Scale Scientific Workflows", 
	journal = "Third International Workshop on Scientific Workflows and Business Workflow Standards in e-Science (SWBES) in conjunction with Fourth IEEE International Conference on e-Science (e-Science 2008)", 
	year = "2008"
}

@inproceedings{
	workflow_partition,
	author = "Weiwei Chen and Ewa Deelman",
	title = "Integration of Workflow Partitioning and Resource Provisioning",
	journal = "The 12th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid 2012)",
	year = "2012"
}

@article{
	cleanup_jobs,
	author = "{Arun Ramakrishnan, Gurmeet Singh, Henan Zhao, Ewa Deelman, Rizos Sakellariou, Karan Vahi, Kent Blackburn, David Meyers and Michael Samidi}",
	title = "Scheduling Data-Intensive Workflows onto Storage-Constrained Distributed Resources",
	journal = "Seventh IEEE International Symposium on Cluster Computing and the Grid (CCGrid)",
	year = "2007"
}

@inproceedings{
	optimizing_footprint,
	author = "{Gurmeet Singh and Karan Vahi and Arun Ramakrishnan and Gaurang Mehta and Ewa Deelman and Henan Zhao and Rizos Sakellariou and Kent Blackburn and Duncan Brown and Stephen Fairhurst and David Meyers and G. Bruce Berriman}",
	title = "Optimizing Workflow Data Footprint",
	journal = "Special issue of the Scientific Programming Journal dedicated to Dynamic Computational Workflows: Discovery, Optimisation and Scheduling",
	year = "2007"
}



@inproceedings{
	bsp,
	title = "Bulk synchronous parallel computing-a paradigm for transportable software",
	author = "T. Cheatham and A. Fahmy and D. Siefanescu and L. Valiani",
	booktitle = "Hawaii International Conference on Systems Sciences",
	year = "2005"
}

@inproceedings{
	swift,
	author = "Y. Zhao and J. Dobson and L. Moreau and I. Foster and M. Wilde",
	title = "A Notation and System for Expressing and Executing Cleanly Typed Workflows on Messy Scientific Data",
	booktitle = "{SIGMOD}",
	year = "2005"
}

@article{Kwok:1999:SSA:344588.344618,
	author = {Kwok, Yu-Kwong and Ahmad, Ishfaq},
	title = {Static Scheduling Algorithms for Allocating Directed Task Graphs to Multiprocessors},
	journal = {ACM Comput. Surv.},
	issue_date = {Dec. 1999},
	volume = {31},
	number = {4},
	month = dec,
	year = {1999},
	issn = {0360-0300},
	pages = {406--471},
	numpages = {66},
	url = {http://doi.acm.org/10.1145/344588.344618},
	doi = {10.1145/344588.344618},
	acmid = {344618},
	publisher = {ACM},
	address = {New York, NY, USA},
	keywords = {DAG, automatic parallelization, multiprocessors, parallel processing, software tools, static scheduling, task graphs},
}

@inproceedings{
	hybrid_heuristic, 
	author="Sakellariou, R. and Henan Zhao", 
	booktitle={Parallel and Distributed Processing Symposium, 2004. Proceedings. 18th International}, 
	title={A hybrid heuristic for DAG scheduling on heterogeneous systems}, 
	year={2004}, 
	pages={111-}, 
	keywords={directed graphs;scheduling;DAG scheduling;directed graph;heterogeneous system;hybrid heuristic;minimization;task scheduling;Computer science;Costs;Distributed processing;Processor scheduling}, 
	doi={10.1109/IPDPS.2004.1303065}, 
	month={April}
}

@article{Topcuouglu:2002:PLT:566137.566142,
 author = {Topcuouglu, Haluk and Hariri, Salim and Wu, Min-you},
 title = {Performance-Effective and Low-Complexity Task Scheduling for Heterogeneous Computing},
 journal = {IEEE Trans. Parallel Distrib. Syst.},
 issue_date = {March 2002},
 volume = {13},
 number = {3},
 month = mar,
 year = {2002},
 issn = {1045-9219},
 pages = {260--274},
 numpages = {15},
 url = {http://dx.doi.org/10.1109/71.993206},
 doi = {10.1109/71.993206},
 acmid = {566142},
 publisher = {IEEE Press},
 address = {Piscataway, NJ, USA},
 keywords = {DAG scheduling, task graphs, heterogeneous systems, list scheduling, mapping},
} 

@inproceedings{eshaghian1997mapping,
  title={Mapping heterogeneous task graphs onto heterogeneous system graphs},
  author={Eshaghian, Mary Mehrnoosh and Wu, Ying-Chieh},
  booktitle={Heterogeneous Computing Workshop, 1997.(HCW'97) Proceedings., Sixth},
  pages={147--160},
  year={1997},
  organization={IEEE}
}

@MISC{He04dynamiccapability-driven,
    author = {Ligang He and Stephen A. Jarvis and Daniel P. Spooner and Graham R. Nudd},
    title = {Dynamic, capability-driven scheduling of DAG-based real-time jobs in heterogeneous clusters},
    year = {2004}
}


@article{goecks2010galaxy,
  title={Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences},
  author={Goecks, Jeremy and Nekrutenko, Anton and Taylor, James and {the Galaxy Team}},
  journal={Genome Biol},
  volume={11},
  number={8},
  pages={R86},
  year={2010}
}

@article{blankenberg2010galaxy,
  title={Galaxy: A Web-Based Genome Analysis Tool for Experimentalists},
  author={Blankenberg, Daniel and Kuster, Gregory Von and Coraor, Nathaniel and Ananda, Guruprasad and Lazarus, Ross and Mangan, Mary and Nekrutenko, Anton and Taylor, James},
  journal={Current protocols in molecular biology},
  pages={19--10},
  year={2010},
  publisher={John Wiley \& Sons, Inc.}
}

@article{giardine2005galaxy,
  title={Galaxy: a platform for interactive large-scale genome analysis},
  author={Giardine, Belinda and Riemer, Cathy and Hardison, Ross C and Burhans, Richard and Elnitski, Laura and Shah, Prachi and Zhang, Yi and Blankenberg, Daniel and Albert, Istvan and Taylor, James and Miller, Webb C and Kent, W James and Nekrutenko, Anton},
  journal={Genome research},
  volume={15},
  number={10},
  pages={1451--1455},
  year={2005},
  publisher={Cold Spring Harbor Lab}
}

@article{Wolstencroft01072013,
	author = {Wolstencroft, Katherine and Haines, Robert and Fellows, Donal and Williams, Alan and Withers, David and Owen, Stuart and Soiland-Reyes, Stian and Dunlop, Ian and Nenadic, Aleksandra and Fisher, Paul and Bhagat, Jiten and Belhajjame, Khalid and Bacall, Finn and Hardisty, Alex and Nieva de la Hidalga, Abraham and Balcazar Vargas, Maria P. and Sufi, Shoaib and Goble, Carole}, 
	title = {The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud},
	volume = {41}, 
	number = {W1}, 
	pages = {W557-W561}, 
	year = {2013}, 
	doi = {10.1093/nar/gkt328}, 
	abstract ={The Taverna workflow tool suite (http://www.taverna.org.uk) is designed to combine distributed Web Services and/or local tools into complex analysis pipelines. These pipelines can be executed on local desktop machines or through larger infrastructure (such as supercomputers, Grids or cloud environments), using the Taverna Server. In bioinformatics, Taverna workflows are typically used in the areas of high-throughput omics analyses (for example, proteomics or transcriptomics), or for evidence gathering methods involving text mining or data mining. Through Taverna, scientists have access to several thousand different tools and resources that are freely available from a large range of life science institutions. Once constructed, the workflows are reusable, executable bioinformatics protocols that can be shared, reused and repurposed. A repository of public workflows is available at http://www.myexperiment.org. This article provides an update to the Taverna tool suite, highlighting new features and developments in the workbench and the Taverna Server.}, 
	URL = {http://nar.oxfordjournals.org/content/41/W1/W557.abstract}, 
	eprint = {http://nar.oxfordjournals.org/content/41/W1/W557.full.pdf+html}, 
	journal = {Nucleic Acids Research} 
}

@inproceedings{Zaharia:2010:SCC:1863103.1863113,
	author = {Zaharia, Matei and Chowdhury, Mosharaf and Franklin, Michael J. and Shenker, Scott and Stoica, Ion},
	title = {Spark: Cluster Computing with Working Sets},
	booktitle = {Proceedings of the 2Nd USENIX Conference on Hot Topics in Cloud Computing},
	series = {HotCloud'10},
	year = {2010},
	location = {Boston, MA},
	pages = {10--10},
	numpages = {1},
	url = {http://dl.acm.org/citation.cfm?id=1863103.1863113},
	acmid = {1863113},
	publisher = {USENIX Association},
	address = {Berkeley, CA, USA},
} 

@inproceedings{Isard:2007:DDD:1272996.1273005,
	author = {Isard, Michael and Budiu, Mihai and Yu, Yuan and Birrell, Andrew and Fetterly, Dennis},
	title = {Dryad: Distributed Data-parallel Programs from Sequential Building Blocks},
	booktitle = {Proceedings of the 2Nd ACM SIGOPS/EuroSys European Conference on Computer Systems 2007},
	series = {EuroSys '07},
	year = {2007},
	isbn = {978-1-59593-636-3},
	location = {Lisbon, Portugal},
	pages = {59--72},
	numpages = {14},
	url = {http://doi.acm.org/10.1145/1272996.1273005},
	doi = {10.1145/1272996.1273005},
	acmid = {1273005},
	publisher = {ACM},
	address = {New York, NY, USA},
	keywords = {cluster computing, concurrency, dataflow, distributed programming},
} 

@article{Isard:2007:DDD:1272998.1273005,
	author = {Isard, Michael and Budiu, Mihai and Yu, Yuan and Birrell, Andrew and Fetterly, Dennis},
	title = {Dryad: Distributed Data-parallel Programs from Sequential Building Blocks},
	journal = {SIGOPS Oper. Syst. Rev.},
	issue_date = {June 2007},
	volume = {41},
	number = {3},
	month = mar,
	year = {2007},
	issn = {0163-5980},
	pages = {59--72},
	numpages = {14},
	url = {http://doi.acm.org/10.1145/1272998.1273005},
	doi = {10.1145/1272998.1273005},
	acmid = {1273005},
	publisher = {ACM},
	address = {New York, NY, USA},
	keywords = {cluster computing, concurrency, dataflow, distributed programming},
} 

@article{KORF198597,
	title = {Depth-first iterative-deepening"},
	journal = {Artificial Intelligence},
	volume = {27},
	number = {1},
	pages = {97--109},
	year = {1985},
	issn = {0004-3702},
	doi = {http://dx.doi.org/10.1016/0004-3702(85)90084-0},
	url = {http://www.sciencedirect.com/science/article/pii/0004370285900840},
	author = {Richard E. Korf},
}


@inproceedings{Welch:2008:SPP:1364813.1364815,
	author = {Welch, Brent and Unangst, Marc and Abbasi, Zainul and Gibson, Garth and Mueller, Brian and Small, Jason and Zelenka, Jim and Zhou, Bin},
	title = {Scalable Performance of the Panasas Parallel File System},
	booktitle = {Proceedings of the 6th USENIX Conference on File and Storage Technologies},
	series = {FAST'08},
	year = {2008},
	location = {San Jose, California},
	pages = {2:1--2:17},
	articleno = {2},
	numpages = {17},
	url = {http://dl.acm.org/citation.cfm?id=1364813.1364815},
	acmid = {1364815},
	publisher = {USENIX Association},
	address = {Berkeley, CA, USA},
} 


@inproceedings{Weil:2006:CSH:1298455.1298485,
	author = {Weil, Sage A. and Brandt, Scott A. and Miller, Ethan L. and Long, Darrell D. E. and Maltzahn, Carlos},
	title = {Ceph: A Scalable, High-performance Distributed File System},
	booktitle = {Proceedings of the 7th Symposium on Operating Systems Design and Implementation},
	series = {OSDI '06},
	year = {2006},
	isbn = {1-931971-47-1},
	location = {Seattle, Washington},
	pages = {307--320},
	numpages = {14},
	url = {http://dl.acm.org/citation.cfm?id=1298455.1298485},
	acmid = {1298485},
	publisher = {USENIX Association},
	address = {Berkeley, CA, USA},
} 

@techreport{lustre-whitepaper,
	title = {Lustre: A Scalable, High-Performance File System},
	institution = {Cluster File Systems, Inc.},
	year = {2002},
	month = {Novemeber},
	url = {http://www.cse.buffalo.edu/faculty/tkosar/cse710/papers/lustre-whitepaper.pdf},
}

@article{Jacob:2009:MGP:1568665.1568666,
 author = {Jacob, Joseph C. and Katz, Daniel S. and Berriman, G. Bruce and Good, John C. and Laity, Anastasia C. and Deelman, Ewa and Kesselman, Carl and Singh, Gurmeet and Su, Mei\&\#45;Hui and Prince, Thomas A. and Williams, Roy},
 title = {Montage\&\#58; a Grid Portal and Software Toolkit for Science\&\#45;Grade Astronomical Image Mosaicking},
 journal = {Int. J. Comput. Sci. Eng.},
 issue_date = {July 2009},
 volume = {4},
 number = {2},
 month = jul,
 year = {2009},
 issn = {1742-7185},
 pages = {73--87},
 numpages = {15},
 url = {http://dx.doi.org/10.1504/IJCSE.2009.026999},
 doi = {10.1504/IJCSE.2009.026999},
 acmid = {1568666},
 publisher = {Inderscience Publishers},
 address = {Inderscience Publishers, Geneva, SWITZERLAND},
 keywords = {TeraGrid, astronomical datasets, astronomy, grid computing, grid portals, image mosaics, software toolkit, virtual observatory},
} 

@article{zaharia2010spark,
  title={Spark: Cluster computing with working sets.},
  author={Zaharia, Matei and Chowdhury, Mosharaf and Franklin, Michael J and Shenker, Scott and Stoica, Ion},
  journal={HotCloud},
  volume={10},
  number={10-10},
  pages={95},
  year={2010}
}

@inproceedings{zaharia2012resilient,
  title={Resilient distributed datasets: A fault-tolerant abstraction for in-memory cluster computing},
  author={Zaharia, Matei and Chowdhury, Mosharaf and Das, Tathagata and Dave, Ankur and Ma, Justin and McCauley, Murphy and Franklin, Michael J and Shenker, Scott and Stoica, Ion},
  booktitle={Proceedings of the 9th USENIX conference on Networked Systems Design and Implementation},
  pages={2--2},
  year={2012},
  organization={USENIX Association}
}

@inproceedings{CharmppOOPSLA93,
  author        = "{Kal\'{e}}, L.V. and Krishnan, S.",
  title         = "{CHARM++: A Portable Concurrent Object Oriented System
                   Based on C++}",
  editor        = "Paepcke, A.",
  fulleditor    = "Paepcke, Andreas",
  pages         = "91--108",
  Month         = "September",
  Year          = "1993",
  booktitle     = "{Proceedings of OOPSLA'93}",
  publisher     = "{ACM Press}",
}

@inproceedings{Bauer:2012:LEL:2388996.2389086,
 author = {Bauer, Michael and Treichler, Sean and Slaughter, Elliott and Aiken, Alex},
 title = {Legion: Expressing Locality and Independence with Logical Regions},
 booktitle = {Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis},
 series = {SC '12},
 year = {2012},
 isbn = {978-1-4673-0804-5},
 location = {Salt Lake City, Utah},
 pages = {66:1--66:11},
 articleno = {66},
 numpages = {11},
 url = {http://dl.acm.org/citation.cfm?id=2388996.2389086},
 acmid = {2389086},
 publisher = {IEEE Computer Society Press},
 address = {Los Alamitos, CA, USA},
} 

@INPROCEEDINGS{868632, 
author={J. Davison de St. Germain and J. McCorquodale and S. G. Parker and C. R. Johnson}, 
booktitle={Proceedings the Ninth International Symposium on High-Performance Distributed Computing}, 
title={Uintah: a massively parallel problem solving environment}, 
year={2000}, 
pages={33-41}, 
keywords={data visualisation;digital simulation;natural sciences computing;parallel programming;problem solving;programming environments;subroutines;visual programming;Common Component Architecture;SCIRun;Uintah;component-based visual problem-solving environment;component-level software reusability;debugging;massively parallel computation;parallel execution complexities;scientific application lifecycle;scientific programming;simulation results visualization;tera-scale computing platforms;Application software;Component architectures;Computational modeling;Concurrent computing;Problem-solving;Programming profession;Runtime;Scientific computing;Software reusability;Visualization}, 
doi={10.1109/HPDC.2000.868632}, 
ISSN={1082-8907}, 
month={},}

@InProceedings{10.1007/978-3-540-24669-5_107,
author="Deelman, Ewa
and Blythe, James
and Gil, Yolanda
and Kesselman, Carl
and Koranda, Scott
and Lazzarini, Albert
and Mehta, Gaurang
and Papa, Maria Alessandra
and Vahi, Karan",
editor="Wyrzykowski, Roman
and Dongarra, Jack
and Paprzycki, Marcin
and Wa{\'{s}}niewski, Jerzy",
title="Pegasus and the Pulsar Search: From Metadata to Execution on the Grid",
booktitle="Parallel Processing and Applied Mathematics",
year="2004",
publisher="Springer Berlin Heidelberg",
address="Berlin, Heidelberg",
pages="821--830",
abstract="This paper describes the Pegasus workflow mapping and planning system that can map complex workflows onto the Grid. In particular, Pegasus can be configured to generate an executable workflow based on application-specific attributes. In that configuration, Pegasus uses and AI-based planner to perform the mapping from high-level metadata descriptions to a workflow that can be executed on the Grid. This configuration of Pegasus was used in the context of the Laser Interferometer Gravitational Wave Observatory (LIGO) pulsar search. We conducted a successful demonstration of the system at SC 2002 during which time we ran approximately 200 pulsar searches.",
isbn="978-3-540-24669-5"
}

@article{Merkel:2014:DLL:2600239.2600241,
 author = {Merkel, Dirk},
 title = {Docker: Lightweight Linux Containers for Consistent Development and Deployment},
 journal = {Linux J.},
 issue_date = {March 2014},
 volume = {2014},
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 year = {2014},
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 articleno = {2},
 url = {http://dl.acm.org/citation.cfm?id=2600239.2600241},
 acmid = {2600241},
 publisher = {Belltown Media},
 address = {Houston, TX},
}

@article{Singularity,
 author = {Kurtzer GM, Sochat V, Bauer MW},
 title = {Singularity: Scientific containers for mobility of compute},
 journal = {PLoS ONE},
 issue_date = {May 11, 2017},
 month = may,
 year = {2017},
 url = {https://doi.org/10.1371/journal.pone.0177459},
}

@article{doi:10.1002-cpe.94,
 author = {Ludäscher Bertram and Altintas Ilkay and Berkley Chad and Higgins Dan and Jaeger Efrat and Jones Matthew and Lee Edward A. and Tao Jing and Zhao Yang},
 title = {Scientific workflow management and the Kepler system},
 journal = {Concurrency and Computation: Practice and Experience},
 volume = {18},
 number = {10},
 pages = {1039-1065},
 keywords = {scientific workflows, Grid workflows, scientific data management, problem‐solving environments, dataflow networks},
 doi = {10.1002/cpe.994},
 url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/cpe.994},
 eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/cpe.994},
}

@Article{pmid20080505,
   Author="Li, H.  and Durbin, R. ",
   Title="{{F}ast and accurate long-read alignment with {B}urrows-{W}heeler transform}",
   Journal="Bioinformatics",
   Year="2010",
   Volume="26",
   Number="5",
   Pages="589--595",
   Month="Mar",
}

@Article{pmid2231712,
   Author="Altschul, S. F.  and Gish, W.  and Miller, W.  and Myers, E. W.  and Lipman, D. J. ",
   Title="{{B}asic local alignment search tool}",
   Journal="J. Mol. Biol.",
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   Pages="403--410",
   Month="Oct"
}


@misc{makeflow-examples,
 author={Nick Hazekamp and Douglas Thain},
 title={Makeflow Examples Repository}, url={http://github.com/cooperative-computing-lab/makeflow-examples, 2017.},
}

@ARTICLE{4404805,
author={Y. Gil and E. Deelman and M. Ellisman and T. Fahringer and G. Fox and D. Gannon and C. Goble and M. Livny and L. Moreau and J. Myers},
journal={Computer},
title={Examining the Challenges of Scientific Workflows},
year={2007},
volume={40},
number={12},
pages={24-32},
keywords={data analysis;distributed processing;natural sciences computing;workflow management software;National Science Foundation;complex distributed computation;data analysis;scientific workflow;Acceleration;Application software;Collaborative work;Concurrent computing;Distributed computing;Earthquakes;collaboratories;computing practices;scientific workflows},
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@inproceedings{Priedhorsky:2017:CUC:3126908.3126925,
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 title = {Charliecloud: Unprivileged Containers for User-defined Software Stacks in HPC},
 booktitle = {Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis},
 series = {SC '17},
 year = {2017},
 isbn = {978-1-4503-5114-0},
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 url = {http://doi.acm.org/10.1145/3126908.3126925},
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 keywords = {containers, least privilege, user environments},
} 

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@inproceedings{Microsystems:2001:SGE:560889.792378,
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@inproceedings{Dolstra:2004:NSP:1052676.1052686,
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 title = {Nix: A Safe and Policy-Free System for Software Deployment},
 booktitle = {Proceedings of the 18th USENIX Conference on System Administration},
 series = {LISA '04},
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@inproceedings{Gamblin:2015:SPM:2807591.2807623,
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 title = {The Spack Package Manager: Bringing Order to HPC Software Chaos},
 booktitle = {Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis},
 series = {SC '15},
 year = {2015},
 isbn = {978-1-4503-3723-6},
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@INPROCEEDINGS{7092947,
author={W. Gerlach and W. Tang and A. Wilke and D. Olson and F. Meyer},
booktitle={2015 IEEE International Conference on Cloud Engineering},
title={Container Orchestration for Scientific Workflows},
year={2015},
volume={},
number={},
pages={377-378},
keywords={Linux;data analysis;workflow management software;AWE/Shock;Docker container technology;Linux container technology;container orchestration;data intensive scientific workflows;portability;scalable data analysis platform;scientific workflow platforms;worker machines;Conferences;Containers;Electric shock;Linux;Servers;Software;Virtual machining},
doi={10.1109/IC2E.2015.87},
ISSN={},
month={March},}


@inproceedings{Armstrong:2014:CTM:2683593.2683627,
 author = {Armstrong, Timothy G. and Wozniak, Justin M. and Wilde, Michael and Foster, Ian T.},
 title = {Compiler Techniques for Massively Scalable Implicit Task Parallelism},
 booktitle = {Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis},
 series = {SC '14},
 year = {2014},
 isbn = {978-1-4799-5500-8},
 location = {New Orleans, Louisana},
 pages = {299--310},
 numpages = {12},
 url = {https://doi.org/10.1109/SC.2014.30},
 doi = {10.1109/SC.2014.30},
 acmid = {2683627},
 publisher = {IEEE Press},
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} 

@inproceedings {194430,
author = {Tyler Harter and Brandon Salmon and Rose Liu and Andrea C. Arpaci-Dusseau and Remzi H. Arpaci-Dusseau},
title = {Slacker: Fast Distribution with Lazy Docker Containers},
booktitle = {14th {USENIX} Conference on File and Storage Technologies ({FAST} 16)},
year = {2016},
isbn = {978-1-931971-28-7},
address = {Santa Clara, CA},
pages = {181--195},
url = {https://www.usenix.org/conference/fast16/technical-sessions/presentation/harter},
publisher = {{USENIX} Association},
}


@INPROCEEDINGS{7600178,
author={K. Liu and K. Aida and S. Yokoyama and Y. Masatani},
booktitle={2016 International Conference on Cloud Computing Research and Innovations (ICCCRI)},
title={Flexible Container-Based Computing Platform on Cloud for Scientific Workflows},
year={2016},
volume={},
number={},
pages={56-63},
keywords={biology computing;cloud computing;pattern clustering;resource allocation;scientific information systems;Docker in Docker tool;Galaxy;Sibling Docker tool;biology workflow system;cloud computing;container cluster systems;data intensive scientific workflows;flexible container-based computing platform;performance overhead;reproducibility;resource utilization improvement;scientific computing;tool installation problem;Bioinformatics;Cloud computing;Computer architecture;Containers;Engines;Pipelines;Resource management;container technology;docker;galaxy;scientific workflow},
doi={10.1109/ICCCRI.2016.17},
ISSN={},
month={May},}