%% This file was generated automatically from the CCL web page:
%% http://www.nd.edu/~ccl/research/papers

@inproceedings {
casestudies-ccgrid13,
author = "Dinesh Rajan and Andrew Thrasher and Badi Abdul-Wahid and Jesus A Izaguirre and Scott Emrich and and Douglas Thain",
title = "Case Studies in Designing Elastic Applications",
booktitle = " 13th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid)",
year = 2013,
url = "http://www.nd.edu/~ccl/research/papers/casestudies-ccgrid13.pdf",
paperid = "893"
}

@techreport {
search-tr,
author = "Brenden Kokoszka and Patrick Donnelly and and Douglas Thain",
title = "Search Should be a System Call",
booktitle = "University of Notre Dame, Computer Science and Engineering Department",
number = "2013-03",
year = 2013,
url = "http://www.nd.edu/~ccl/research/papers/search-tr.pdf",
paperid = "894"
}

@article {
assembly-tpds,
author = "Christopher Moretti and Andrew Thrasher and Li Yu and Michael Olson and Scott Emrich and and Douglas Thain",
title = "A Framework for Scalable Genome Assembly on Clusters, Clouds, and Grids",
journal = "IEEE Transactions on Parallel and Distributed Systems",
volume = "23",
number = "12",
year = 2012,
url = "http://www.nd.edu/~ccl/research/papers/assembly-tpds-preprint.pdf",
paperid = "100"
}

@inproceedings {
folding-escience12,
author = "Badi Abdul-Wahid and Li Yu and Dinesh Rajan and Haoyun Feng and Eric Darve and Douglas Thain and Jesus A. Izaguirre",
title = "Folding Proteins at 500 ns/hour with Work Queue",
booktitle = "8th IEEE International Conference on eScience (eScience 2012)",
year = 2012,
url = "http://www.nd.edu/~ccl/research/papers/folding-escience12.pdf",
paperid = "891"
}

@inproceedings {
psempoli-escience12,
author = "Peter Sempolinski and Daniel Wei and Douglas Thain and Ahsan Kareem",
title = "A System for Management of Computational Fluid Dynamics Simulations for Civil Engineering",
booktitle = "8th IEEE International Conference on eScience",
year = 2012,
url = "http://www.nd.edu/~ccl/research/papers/psempoli_escience12.pdf",
paperid = "892"
}

@article {
PAPER890,
author = "Hoang Bui and Peter Bui and Patrick Flynn and Douglas Thain",
title = "ROARS: A Robust Object Archival System for Data Intensive Scientific Computing",
journal = "Distributed and Parallel Databases",
publisher = "Springer",
year = 2012,
url = "http://www.springerlink.com/openurl.asp?genre=article&id=doi:10.1007/s10619-012-7103-5",
paperid = "890"
}

@phdthesis {
pbui-dissertation.pdf,
author = "Peter Bui",
title = "A Compiler Toolchain For Data Intensive Scientific Workflows",
school = "University of Notre Dame",
type = "Ph.D. Thesis",
year = 2012,
url = "http://www.nd.edu/~ccl/research/papers/pbui-dissertation.pdf",
paperid = "889"
}

@inproceedings {
chirp-tickets-ccgrid12,
author = "Patrick Donnelly and Douglas Thain",
title = "Fine-Grained Access Control in the Chirp Distributed File System",
booktitle = "IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing",
year = 2012,
url = "http://www.nd.edu/~ccl/research/papers/chirp-tickets-ccgrid12-camera.pdf",
paperid = "101"
}

@inproceedings {
makeflow-sweet12,
author = "Michael Albrecht and Patrick Donnelly and Peter Bui and and Douglas Thain",
title = "Makeflow: A Portable Abstraction for Data Intensive Computing on Clusters, Clouds, and Grids",
booktitle = "Workshop on Scalable Workflow Enactment Engines and Technologies (SWEET) at ACM SIGMOD",
year = 2012,
url = "http://www.nd.edu/~ccl/research/papers/makeflow-sweet12-camera.pdf",
paperid = "104"
}

@phdthesis {
hbui-dissertation,
author = "Hoang Bui",
title = "A Rich Metadata Filesystem for Scientific Data",
school = "University of Notre Dame",
type = "Ph.D. Thesis",
year = 2012,
url = "http://www.nd.edu/~ccl/research/papers/hbui-dissertation.pdf",
paperid = "105"
}

@inproceedings {
maker-iccabs12,
author = "Andrew Thrasher and Zachary Musgrave and Douglas Thain and Scott Emrich",
title = "Shifting the Bioinformatics Computing Paradigm: A Case Study in  Parallelizing Genome Annotation Using Maker and Work Queue",
booktitle = "IEEE International Conference on Computational Advances in Bio and Medical Sciences",
year = 2012,
url = "http://www.nd.edu/~ccl/research/papers/maker-iccabs12.pdf",
paperid = "102"
}

@incollection {
chirp-didc-chapter,
author = "Douglas Thain and Michael Albrecht and Hoang Bui and Peter Bui and Rory Carmichael and Scott Emrich and and Patrick Flynn",
title = "Data Intensive Computing with Clustered Chirp Servers",
booktitle = "Data Intensive Distributed Computing: Challenges and Solutions for Large Scale Information Management",
pages = "140-154",
editor = "Tevfik Kosar",
publisher = "IGI",
year = 2012,
url = "http://www.igi-global.com/chapter/data-intensive-computing-clustered-chirp/62825",
paperid = "99"
}

@article {
biocompute-ccpe,
author = "Rory Carmichael and Patrick Braga-Henebry and Douglas Thain and and Scott Emrich",
title = "Biocompute 2.0: An Improved Collaborative Workspace for Data Intensive Bio-Science.",
journal = "Concurrency and Computation: Practice and Experience",
volume = "23",
number = "17",
pages = "2305-2314",
year = 2011,
url = "http://onlinelibrary.wiley.com/doi/10.1002/cpe.1782/abstract",
paperid = "96"
}

@inproceedings {
elasticrepex-cloudcom11,
author = "Dinesh Rajan and Anthony Canino and Jesus A Izaguirre and and Douglas Thain",
title = "Converting a High Performance Application to an Elastic Cloud Application",
booktitle = "The 3rd IEEE International Conference on Cloud Computing Technology and Science (CloudCom 2011)",
year = 2011,
url = "http://www.cse.nd.edu/~ccl/research/papers/elasticreplex_cloudcom11.pdf",
paperid = "93"
}

@inproceedings {
wq-python-pyhpc2011,
author = "Peter Bui and Dinesh Rajan and Badi Abdul-Wahid and Jesus Izaguirre and Douglas Thain",
title = "Work Queue + Python: A Framework For Scalable Scientific Ensemble Applications",
booktitle = "Workshop on Python for High Performance and Scientific Computing (PyHPC) at the ACM/IEEE International Conference for High Performance Computing, Networking, Storage, and Analysis (Supercomputing) ",
year = 2011,
url = "http://www.nd.edu/~ccl/research/papers/wq-python-pyhpc2011.pdf",
paperid = "95"
}

@article {
weaver-ccpe,
author = "Peter Bui and Li Yu and Andrew Thrasher and Rory Carmichael and Irena Lanc and Patrick Donnelly and Douglas Thain",
title = "Scripting distributed scientific workflows using Weaver",
journal = "Concurrency and Computation: Practice and Experience",
year = 2011,
url = "http://onlinelibrary.wiley.com/doi/10.1002/cpe.1871/abstract",
paperid = "98"
}

@inproceedings {
adapting-ecmls11,
author = "Irena Lanc and Peter Bui and Douglas Thain and and Scott Emrich",
title = "Adapting Bioinformatics Applications for Heterogeneous Systems: A Case Study",
booktitle = "Emerging Computational Methods for the Life Sciences Workshop at ACM HPDC",
pages = "7-13",
year = 2011,
url = "http://www.nd.edu/~ccl/research/papers/adapting-ecmls11.pdf",
paperid = "94"
}

@incollection {
cloud-chapter,
author = "Peter Sempolinski and Douglas Thain",
title = "An Introductino to Open-Source IaaS Cloud Middleware",
booktitle = "Cloud Computing: Methodology, Systems, and Applications",
pages = "133-149",
editor = "Boualem Benatallah",
publisher = "CRC Press",
year = 2011,
url = "http://www.crcnetbase.com/doi/pdf/10.1201/b11149-9",
paperid = "895"
}

@inproceedings {
survey-cloudCom2010,
author = "Peter Sempolinski and Douglas Thain",
title = "A Comparison and Critique of Eucalyptus, OpenNebula and Nimbus",
booktitle = "IEEE International Conference on Cloud Computing Technology and Science",
pages = "417-426",
year = 2010,
url = "http://www.nd.edu/~ccl/research/papers/psempoli-cloudcom.pdf",
paperid = "89"
}

@inproceedings {
chirp+parrot+hdfs,
author = "Patrick Donnelly and Peter Bui and Douglas Thain",
title = "Attaching Cloud Storage to a Campus Grid Using Parrot, Chirp, and Hadoop ",
booktitle = "IEEE International Conference on Cloud Computing Technology and Science",
pages = "488-495",
year = 2010,
url = "http://www.nd.edu/~ccl/research/papers/chirp+parrot+hdfs.pdf",
paperid = "90"
}

@inproceedings {
taming-works10.pdf,
author = "Andrew Thrasher and Rory Carmichael and Peter Bui and Li Yu and Douglas Thain and and Scott Emrich",
title = "Taming Complex Bioinformatics Workflows with Weaver, Makeflow, and Starch",
booktitle = "Workshop on Workflows in Support of Large Scale Science",
pages = "1-6",
year = 2010,
url = "http://www.nd.edu/~ccl/research/papers/taming-works10.pdf",
paperid = "92"
}

@article {
abstr-jcc,
author = "Li Yu and Christopher Moretti and Andrew Thrasher and Scott Emrich and Kenneth Judd and and Douglas Thain",
title = "Harnessing Parallelism in Multicore Clusters with the All-Pairs, Wavefront, and Makeflow Abstractions",
journal = "Journal of Cluster Computing",
volume = "13",
number = "3",
pages = "243-256",
year = 2010,
url = "http://www.nd.edu/~ccl/research/papers/abstr-jcc.pdf",
paperid = "83"
}

@inproceedings {
eoc-green,
author = "Paul Brenner and Ryan Jansen and David Go and and Douglas Thain",
title = "Environmentally Opportunistic Computing: Transforming the Data Center for Economic and Environmental Sustainability",
booktitle = "IEEE Green Computing Conference",
pages = "383-388",
year = 2010,
url = "http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5598289",
paperid = "97"
}

@incollection {
abstr-cloudbook,
author = "Douglas Thain and Christopher Moretti",
title = "Abstractions for Cloud Computing with Condor",
booktitle = "Cloud Computing and Software Services: Theory and Techniques",
pages = "153-171",
editor = "Syed Ahson and Mohammad Ilyas",
publisher = "CRC Press",
year = 2010,
url = "http://www.nd.edu/~ccl/research/pubs/abstractions-cloud-chapter.pdf",
paperid = "78"
}

@inproceedings {
roars-didc10,
author = "Hoang Bui and Peter Bui and Patrick Flynn and Douglas Thain",
title = "ROARS: A Scalable Repository for Data Intensive Scientific Computing",
booktitle = "The Third International Workshop on Data Intensive Distributed Computing at ACM HPDC 2010",
year = 2010,
url = "http://www.cse.nd.edu/~ccl/research/pubs/roars-didc.pdf",
paperid = "85"
}

@inproceedings {
weaver-clade10,
author = "Peter Bui and Li Yu and Douglas Thain",
title = "Weaver: Integrating Distributed Computing Abstractions into Scientific Workflows using Python",
booktitle = "Challenges of Large Applications in Distributed Environments at ACM HPDC 2010",
year = 2010,
url = "http://www.cse.nd.edu/~ccl/research/pubs/weaver-clade2010.pdf",
paperid = "86"
}

@inproceedings {
quality-didc10,
author = "Hoang Bui and Diane Wright and Clarence Helm and Rachel Witty and Patrick Flynn and Douglas Thain",
title = "Towards Long Term Data Quality in a Large Scale Biometrics Experiment",
booktitle = "Managing Data Quality for Collaborative Science at ACM HPDC 2010",
year = 2010,
url = "http://www.nd.edu/~ccl/research/pubs/bxgrid-mdqcs10.pdf",
paperid = "87"
}

@phdthesis {
moretti-dissertation,
author = "Christopher Moretti",
title = "Abstractions for Scientific Computing on Campus Grids",
school = "University of Notre Dame",
type = "Ph.D. Thesis",
year = 2010,
url = "http://www.nd.edu/~ccl/research/papers/moretti-dissertation.pdf",
paperid = "88"
}

@inproceedings {
biocompute-ecmls,
author = "Rory Carmichael and Patrick Braga-Henebry and Douglas Thain and and Scott Emrich",
title = "Biocompute: Toward a Collaborative Workspace for Data Intensive Bio-Science",
booktitle = "Workshop on Emerging Computational Methods for Life Sciences at ACM HPDC 2010",
pages = "489-498",
year = 2010,
url = "http://www.nd.edu/~ccl/research/papers/biocompute-ecmls2010.pdf",
paperid = "91"
}

@article {
allpairs-tpds,
author = "Christopher Moretti and Hoang Bui and Karen Hollingsworth and Brandon Rich and Patrick Flynn and and Douglas Thain",
title = "All-Pairs: An Abstraction for Data Intensive Computing on Campus Grids",
journal = "IEEE Transactions on Parallel and Distributed Systems",
volume = "21",
number = "1",
pages = "33-46",
year = 2010,
url = "http://www.nd.edu/~ccl/research/papers/allpairs-tpds-preprint.pdf",
paperid = "12"
}

@article {
threadscope-ccpe09,
author = "Kyle Wheeler and Douglas Thain",
title = "Visualizing Massively Multithreaded Applications with ThreadScope",
journal = "to appear in Concurrency and Computation: Practice and Experience",
volume = "22",
number = "1",
pages = "45-67",
year = 2010,
url = "http://dx.doi.org/10.1002/cpe.1469",
paperid = "59"
}

@incollection {
raicu-manytask-chapter,
author = "Ioan Raicu and Ian Foster and Yong Zhao and Alex Szalay and Philip Little and Christopher Moretti and Amitabh Chaudhary and and Douglas Thain",
title = "Towards Data Intensive Many Task Computing",
booktitle = "Data Intensive Distributed Computing: Challenges and Solutions for Large-Scale Information Management",
editor = "Tevfik Kosar",
publisher = "IGI",
year = 2009,
paperid = "80"
}

@phdthesis {
wheeler-thesis,
author = "Kyle Wheeler",
title = "Exploiting Locality with QThreads for Portable Parallel Performance",
school = "University of Notre Dame",
type = "Ph.D. Thesis",
year = 2009,
url = "http://www.nd.edu/~ccl/research/papers/wheeler-thesis.pdf",
paperid = "81"
}

@inproceedings {
assembly-mtags09,
author = "Christopher Moretti and Michael Olson and Scott Emrich and and Douglas Thain",
title = "Highly Scalable Genome Assembly on Campus Grids",
booktitle = "Many-Task Computing on Grids and Supercomputers (MTAGS)",
year = 2009,
url = "http://www.nd.edu/~ccl/research/papers/assembly-mtags09.pdf",
paperid = "82"
}

@article {
modularity-spe,
author = "Andrew Blaich and Douglas Thain and and Aaron Striegel",
title = "Reflections on the Virtues of Modularity: A Case Study in Linux Security Modules",
journal = "Software: Practice and Experience",
volume = "39",
number = "15",
pages = "1235-1251",
year = 2009,
url = "http://dx.doi.org/10.1002/spe.933",
paperid = "11"
}

@inproceedings {
teamtrak-adhocnets,
author = "Jeffrey Hemmes and Douglas Thain and and Christian Poellabauer",
title = "Cooperative Localization in GPS-Limited Urban Environments",
booktitle = "ICST AdHocNets",
year = 2009,
url = "http://www.nd.edu/~ccl/research/pubs/teamtrak-adhocnets09.pdf",
paperid = "61"
}

@inproceedings {
multicore-grid09,
author = "Michael Lammie and Douglas Thain and and Paul Brenner",
title = "Scheduling Grid Workloads on Multicore Clusters to Minimize Energy and Maximize Performance",
booktitle = "IEEE Grid Computing",
year = 2009,
url = "http://www.nd.edu/~ccl/research/pubs/multicore-grid09.pdf",
paperid = "75"
}

@inproceedings {
qthreads-pmea09,
author = "Kyle Wheeler and Douglas Thain and Rich Murphy",
title = "Portable Performance from Workstation to Supercomputer: Distributing Data Structures with Qthreads",
booktitle = "Workshop on Programming Models for Emerging Architectures",
pages = "1-8",
year = 2009,
url = "http://www.nd.edu/~dthain/papers/qthreads-pmea09.pdf",
paperid = "76"
}

@incollection {
kosar-databook,
author = "T. Kosar and A. Hutanu and J. McLaren and D. Thain",
title = "Coordination of Access to Large-scale Datasets in Distributed Environments",
booktitle = "Scientific Data Management: Challenges, Existing Technology, and Deployment",
editor = "A. Shoshani and D. Rotem",
publisher = "Chapman and Hall / CRC Press",
year = 2009,
url = "http://www.amazon.com/Scientific-Data-Management-Challenges-Computational/dp/1420069802",
paperid = "8"
}

@techreport {
assembly-tr,
author = "Christopher Moretti and Michael Olson and Scott Emrich and and Douglas Thain",
title = "Scalable Modular Genome Assembly on Campus Grids",
booktitle = "University of Notre Dame, Computer Science and Engineering Department",
number = "2009-04",
year = 2009,
url = "http://www.nd.edu/Reports/2009/TR-2009-04.pdf",
paperid = "77"
}

@phdthesis {
jhemmes-thesis,
author = "Jeffrey Hemmes",
title = "Improving Data Availability in Mobile Applications Through Enhanced Cooperative Localization",
school = "University of Notre Dame",
type = "Ph.D. Thesis",
year = 2009,
url = "http://www.nd.edu/~ccl/research/pubs/jhemmes-thesis.pdf",
paperid = "79"
}

@inproceedings {
abstr-hpdc09,
author = "Li Yu and Christopher Moretti and Scott Emrich and Kenneth Judd and and Douglas Thain",
title = "Harnessing Parallelism in Multicore Clusters with the All-Pairs and Wavefront Abstractions",
booktitle = "IEEE High Performance Distributed Computing",
pages = "1-10",
year = 2009,
url = "http://www.nd.edu/~dthain/papers/abstr-hpdc09.pdf",
paperid = "5"
}

@inproceedings {
gheat-uptime09,
author = "Paul Brenner and Douglas Thain and and Dewitt Latimer",
title = "Grid Heating Clusters: Transforming Cooling Constraints Into Thermal Benefits",
booktitle = "The Uptime Institute Green Enterprise IT Award Paper",
pages = "1-7",
year = 2009,
url = "http://www.nd.edu/~dthain/papers/gheat-uptime09.pdf",
paperid = "60"
}

@inproceedings {
parrot-chep09,
author = "Gabrielle Compostella and Simone Pagan Griso and Donatella Lucchesi and Igor Sfiligoi and and Douglas Thain",
title = "CDF Software Distribution on the Grid using Parrot",
booktitle = "Computing in High Energy Physics",
year = 2009,
url = "http://www.nd.edu/~dthain/papers/parrot-chep09.pdf",
paperid = "22"
}

@phdthesis {
pbh-thesis,
author = "Patrick Braga-Henebry",
title = "Biocompute: Harnessing Distributed Systems for Bioinformatics",
school = "University of Notre Dame",
type = "B.S. Honors Thesis",
year = 2009,
url = "http://www.nd.edu/~ccl/research/pubs/pbragahe-thesis.pdf",
paperid = "64"
}

@article {
bxgrid-jcc,
author = "Hoang Bui and Michael Kelly and Christopher Lyon and Mark Pasquier and Deborah Thomas and Patrick Flynn and and Douglas Thain",
title = "Experience with BXGrid: A Data Repository and Computing Grid for Biometrics Research",
journal = "Journal of Cluster Computing",
volume = "12",
number = "4",
pages = "373",
year = 2009,
url = "http://www.nd.edu/~dthain/papers/bxgrid-jcc-preprint.pdf",
paperid = "1"
}

@article {
chirp-jgc,
author = "Douglas Thain and Christopher Moretti and and Jeffrey Hemmes",
title = "Chirp: A Practical Global Filesystem for Cluster and Grid Computing",
journal = "Journal of Grid Computing",
volume = "7",
number = "1",
pages = "51-72",
year = 2009,
url = "http://dx.doi.org/10.1007/s10723-008-9100-5",
paperid = "14"
}

@inproceedings {
bxgrid-escience09,
author = "Hoang Bui and Deborah Thomas and Michael Kelly and Christopher Lyon and Douglas Thain and and Patrick J. Flynn",
title = "Poster: BXGrid: A Data Repository and Workflow Abstraction for Biometrics Research",
booktitle = "IEEE International Conference on e-Science",
pages = "394-395",
year = 2008,
url = "http://www.nd.edu/~ccl/research/pubs/bxgrid-poster-escience08.pdf",
paperid = "24"
}

@inproceedings {
classify-icdm08,
author = "Christopher Moretti and Karsten Steinhaeuser and Douglas Thain and and Nitesh V. Chawla",
title = "Scaling Up Classifiers to Cloud Computers",
booktitle = "IEEE International Conference on Data Mining (ICDM)",
pages = "472-481",
year = 2008,
url = "http://www.nd.edu/~ccl/research/pubs/classify-icdm08.pdf",
paperid = "25"
}

@article {
pins-jpc,
author = "Paul Brenner and Justin Wozniak and Douglas Thain Aaron Striegel and Jeffrey Peng and and Jesus Izaguirre",
title = "Biomolecular Committor Probability Calculation Enabled by Processing in Network Storage",
journal = "Journal of Parallel Computing",
volume = "34",
number = "11",
pages = "652-660",
year = 2008,
url = "http://dx.doi.org/10.1016/j.parco.2008.08.001",
paperid = "13"
}

@inproceedings {
enavis-lisa08,
author = "Qi Liao and Andrew Blaich and Aaron Striegel and and Douglas Thain",
title = "ENAVis: Enterprise Network Activities Visualization",
booktitle = "USENIX Large Installation System Administration (LISA)",
pages = "59-74",
year = 2008,
url = "http://www.nd.edu/~dthain/papers/enavis-lisa08.pdf",
paperid = "23"
}

@inproceedings {
debug-grid08,
author = "David Cieslak and Nitesh Chawla and and Douglas Thain",
title = "Troubleshooting Thousands of Jobs on Production Grids Using Data Mining Techniques",
booktitle = "IEEE Grid Computing",
pages = "217-224",
year = 2008,
url = "http://www.nd.edu/~ccl/research/pubs/debug-grid08.pdf",
paperid = "26"
}

@inproceedings {
datalab-hpdc08,
author = "Brandon Rich and Douglas Thain",
title = "Poster: DataLab: Transactional Data Parallel Computing on an Active Storage Cloud",
booktitle = "IEEE/ACM High Performance Distributed Computing",
pages = "233-234",
year = 2008,
url = "http://www.nd.edu/~dthain/papers/datalab-hpdc08.pdf",
paperid = "27"
}

@inproceedings {
allpairs-ipdps08,
author = "Christopher Moretti and Jared Bulosan and Douglas Thain and and Patrick Flynn",
title = "All-Pairs: An Abstraction for Data Intensive Cloud Computing",
booktitle = "IEEE International Parallel and Distributed Processing Symposium (IPDPS)",
pages = "1-11",
year = 2008,
url = "http://www.nd.edu/~dthain/papers/allpairs-ipdps08.pdf",
paperid = "28"
}

@inproceedings {
qthreads-mtaap08,
author = "Kyle Wheeler and Richard Murphy and and Douglas thain",
title = "QThreads: An API for Programming with Millions of Lightweight Threads",
booktitle = "Workshop on Multithreaded Architectures and Applications at IEEE IPDPS",
pages = "1-8",
year = 2008,
url = "http://www.nd.edu/~dthain/papers/qthreads-ipdps08",
paperid = "29"
}

@techreport {
bxgrid-tr,
author = "Douglas Thain and Patrick Flynn",
title = "Towards a Data Analysis Grid for Biometrics Research",
booktitle = "University of Notre Dame, Computer Science and Engineering Department",
number = "2008-05",
year = 2008,
url = "http://www.nd.edu/~ccl/research/pubs/bxgrid-tr.pdf",
paperid = "62"
}

@article {
priority-fgcs,
author = "Justin Wozniak and Paul Brenner and Douglas Thain and Aaron Striegel and and Jesus Izaguirre",
title = "Making the Best of a Bad Situation: Prioritized Storage Management in GEMS",
journal = "Future Generation Computing Systems",
volume = "24",
number = "1",
pages = "10-16",
year = 2008,
url = "http://www.nd.edu/~dthain/papers/priority-fgcs07.pdf",
paperid = "15"
}

@techreport {
gheat-tr,
author = "Paul Brenner and Douglas Thain and and Dewitt Latimer",
title = "Grid Heating: Transforming Cooling Constraints Into Thermal Benefits",
booktitle = "University of Notre Dame, Computer Science and Engineering Department",
number = "2008-09",
year = 2008,
url = "http://www.nd.edu/~dthain/papers/gheat-uptime09.pdf",
paperid = "7"
}

@inproceedings {
teamtrak-milcom07,
author = "Jeffrey Hemmes and Christian Poellabauer and and Douglas Thain",
title = "On Demand Transient Storage and Backup in Mobile Systems",
booktitle = "IEEE Military Communications Conference",
pages = "1-7",
year = 2007,
url = "http://www.nd.edu/~dthain/papers/transient-milcom07.pdf",
paperid = "30"
}

@inproceedings {
teamtrak-wasa07,
author = "Jeffrey Hemmes and Douglas Thain and Christian Poellabauer and Christopher Moretti and Phil Snowberger and and Brendan McNutt",
title = "Lessons Learned Building TeamTrak: An Urban/Outdoor Mobile Testbed",
booktitle = "International Conference on Wireless Architectures Systems and Applications",
pages = "219-224",
year = 2007,
url = "http://www.nd.edu/~dthain/papers/tt-wasa07.pdf",
paperid = "33"
}

@inproceedings {
teamtrak-fie07,
author = "Jeffrey Hemmes and Douglas Thain and and Christian Poellabauer",
title = "Work in Progress: Integrating Undergraduate Research and Education via the TeamTrak Mobile Computing Framework",
booktitle = "IEEE Frontiers in Education",
pages = "1-2",
year = 2007,
url = "http://www.nd.edu/~dthain/papers/tt-fie07.pdf",
paperid = "35"
}

@inproceedings {
small-grid07,
author = "Douglas Thain and Christopher Moretti",
title = "Efficient Access to Many Small Files in a Filesystem for Grid Computing",
booktitle = "IEEE Grid Computing",
pages = "243-250",
year = 2007,
url = "http://www.nd.edu/~dthain/papers/small-grid07.pdf",
paperid = "31"
}

@inproceedings {
lockdown-security07,
author = "Andrew Blaich and Qi Liao and Greg Allan and Aaron Striegel and and Douglas Thain",
title = "Poster: Lockdown: Distributed Policy Analysis and Enforcement within the Enterprise Network",
booktitle = "USENIX Security Symposium",
year = 2007,
url = "http://www.nd.edu/~dthain/papers/lockdown-usenix07.pdf",
paperid = "32"
}

@inproceedings {
allpairs-grid07,
author = "Christopher Moretti and Jared Bulosan and Douglas Thain and and Patrick J. Flynn",
title = "Poster: All-Pairs: An Abstraction for Data Intensive Computing",
booktitle = "IEEE/ACM Grid Computing",
year = 2007,
url = "http://www.nd.edu/~ccl/research/papers/allpairs-grid07.pdf",
paperid = "63"
}

@inproceedings {
challenges-pcgrid07,
author = "Christopher Moretti and Timothy Faltemier and Douglas Thain and and Patrick J. Flynn",
title = "Challenges in Executing Data Intensive Biometric Workloads on a Desktop Grid",
booktitle = "Workshop on Large Scale and Volatile Desktop Grids at IEEE IPDPS",
pages = "481-489",
year = 2007,
url = "http://www.nd.edu/~dthain/papers/challenges-pcgrid07.pdf",
paperid = "34"
}

@inproceedings {
pins-bio07,
author = "Paul Brenner and Justin Wozniak and Douglas Thain and Aaron Striegel and Jeffrey Peng and and Jesus Izaguirre",
title = "Biomolecular Path Sampling Enabled by Processing in Network Storage",
booktitle = "Workshop on High Performance Computational Biology at IEEE IPDPS",
pages = "1-6",
year = 2007,
url = "http://www.nd.edu/~dthain/papers/bio-pins.pdf",
paperid = "36"
}

@phdthesis {
moretti-ms-thesis,
author = "Christopher Moretti",
title = "Flexible Object Based Filesystems for Scientific Computing",
school = "University of Notre Dame",
type = "M.S. Thesis",
year = 2007,
url = "http://www.nd.edu/~ccl/research/pubs/moretti-thesis.pdf",
paperid = "65"
}

@phdthesis {
snowberger-ms-thesis,
author = "Philip Snowberger",
title = "Sub-Identities: A Hierarchical Identity Model for Practical Containment",
school = "University of Notre Dame",
type = "M.S. Thesis",
year = 2007,
url = "http://www.nd.edu/~ccl/research/pubs/snowberger-thesis.pdf",
paperid = "66"
}

@article {
measure-ccpe,
author = "Douglas Thain and Miron Livny",
title = "How to Measure a Large Open Source Distributed System",
journal = "Concurrency and Computation: Practice and Experience",
volume = "18",
number = "15",
pages = "1989-2019",
year = 2006,
url = "http://www.nd.edu/~dthain/papers/measure-ccpe.pdf",
paperid = "16"
}

@inproceedings {
gems-sss06,
author = "Justin Wozniak and Paul Brenner and Douglas Thain and Aaron Striegel and Jesus Izaguirre",
title = "Access Control for a Replica Management Database",
booktitle = "ACM Workshop on Storage Security and Survivability at ACM CCS",
pages = "41-46",
year = 2006,
url = "http://www.nd.edu/~dthain/papers/access-storagess06.pdf",
paperid = "40"
}

@inproceedings {
bio-grid06,
author = "Christophe Blanchet and Remi Mollon and Douglas Thain and and Gilbert Deleage",
title = "Grid Deployment of Legacy Bioinformatics Applications with Transparent Data Access",
booktitle = "IEEE Grid Computing",
pages = "120-127",
year = 2006,
url = "http://www.nd.edu/~dthain/papers/bio-grid06.pdf",
paperid = "37"
}

@inproceedings {
alloc-grid06,
author = "Douglas Thain",
title = "Operating System Support for Space Allocation in Grid Storage Systems",
booktitle = "IEEE Grid Computing",
pages = "104-111",
year = 2006,
url = "http://www.nd.edu/~dthain/papers/alloc-grid06.pdf",
paperid = "41"
}

@inproceedings {
groups-grid06,
author = "Jeffrey Hemmes and Douglas Thain",
title = "Cacheable Decentralized Groups for Grid Resource Access Control",
booktitle = "IEEE Grid Computing",
pages = "192-199",
year = 2006,
url = "http://www.nd.edu/~dthain/papers/groups-grid06.pdf",
paperid = "42"
}

@inproceedings {
caches-hyperio06,
author = "Sudharshan Vazhkudai and Douglas Thain and Xiaosong Ma and and Vincent Freeh",
title = "Positioning Dynamic Storage Caches for Transient Data",
booktitle = "Workshop on High-Performance I/O Techniques and Deployment of Very Large Scale I/O Systems at IEEE Cluster Computing",
pages = "1-9",
year = 2006,
url = "http://www.nd.edu/~dthain/papers/caches-hyperio06.pdf",
paperid = "43"
}

@inproceedings {
subid-sec06,
author = "Phil Snowberger and Douglas Thain",
title = "Poster: Sub-Identities: Security for Mere Mortals",
booktitle = "USENIX Security",
year = 2006,
url = "http://www.nd.edu/~dthain/papers/subid-usesec06.pdf",
paperid = "45"
}

@inproceedings {
literate-fie06,
author = "Douglas Thain and Christian Poellabauer",
title = "Experience with a Literate Approach to Computer Science",
booktitle = "IEEE Frontiers in Education",
pages = "8-13",
year = 2006,
url = "http://www.nd.edu/~dthain/papers/literate-fie2006.pdf",
paperid = "44"
}

@inproceedings {
idibs-icpads06,
author = "Faruck Morcos and Thidapat Chantem and Philip Little and Tiago Gasiba and and Douglas Thain",
title = "iDIBS: An Improved Distributed Internet Backup System",
booktitle = "IEEE International Conference on Parallel and Distributed Systems (ICPADS)",
pages = "58-67",
year = 2006,
url = "http://www.nd.edu/~dthain/papers/idibs-icpads06.pdf",
paperid = "46"
}

@article {
transparent-ccpe,
author = "Sander Klous and Jamie Frey and Se-Chang Son and Douglas Thain and Alain Roy and Miron Livny and and Jo van den Brand",
title = "Transparent Access to Grid Resources for User Software",
journal = "Concurrency and Computation: Practice and Experience",
volume = "18",
number = "7",
pages = "787-801",
year = 2006,
url = "http://www.nd.edu/~dthain/papers/transparent-ccpe.pdf",
paperid = "17"
}

@inproceedings {
debug-hpdc15,
author = "David Cieslak and Douglas Thain and Nitesh Chawla",
title = "Short Paper: Troubleshooting Distributed Systems via Data Mining",
booktitle = "IEEE Symposium on High Performance Distributed Computing (HPDC)",
pages = "309-312",
year = 2006,
url = "http://www.nd.edu/~dthain/papers/debug-hpdc15.pdf",
paperid = "47"
}

@inproceedings {
gems-ssst06,
author = "Justin Wozniak and Paul Brenner and Douglas Thain and Aaron Striegel and and Jesus Izaguirre",
title = "Applying Feedback Control to a Replica Management System",
booktitle = "IEEE Southeastern Symposium on System Theory",
pages = "472-476",
year = 2006,
url = "http://www.nd.edu/~dthain/papers/feedback-ssst06.pdf",
paperid = "48"
}

@article {
parrot-lni06,
author = "Stefano Belforte and Matthew Normal and Subir Sarkar and Ifor Sfiligoi and Douglas Thain and Frank Wuerthwein",
title = "Using Condor Glide-Ins and Parrot to Move from Dedicated Resources to the Grid",
journal = "Lecture Notes in Informatics",
volume = "81",
pages = "285-292",
year = 2006,
url = "http://subs.emis.de/LNI/Proceedings/Proceedings81/GI-Proceedings-81-30.pdf",
paperid = "49"
}

@inproceedings {
parrot-chep06,
author = "Douglas Thain and Christopher Moretti and and Igor Sfiligoi",
title = "Transparently Distributing CDF Software with Parrot",
booktitle = "Computing in High Energy Physics",
pages = "1-4",
year = 2006,
url = "http://www.nd.edu/~dthain/papers/cdf-parrot-chep06.pdf",
paperid = "50"
}

@inproceedings {
cons-sisw05,
author = "Douglas Thain and Christopher Moretti and Paul Madrid and Phil Snowberger and and Jeff Hemmes",
title = "The Consequences of Decentralized Security in a Cooperative Storage System",
booktitle = "Workshop on Security in Storage at IEEE FAST",
pages = "82-94",
year = 2005,
url = "http://www.nd.edu/~dthain/papers/cons-sisw05.pdf",
paperid = "51"
}

@inproceedings {
tactical-sc05,
author = "Douglas Thain and Sander Klous and Justin Wozniak and Paul Brenner and Aaron Striegel and and Jesus Izaguirre",
title = "Separating Abstractions from Resources in a Tactical Storage System  ",
booktitle = "IEEE/ACM Supercomputing",
pages = "55-67",
year = 2005,
url = "http://www.nd.edu/~dthain/papers/tss-sc05.pdf",
paperid = "52"
}

@inproceedings {
ibox-sc05,
author = "Douglas Thain",
title = "Identity Boxing: A New Technique for Consistent Global Identity",
booktitle = "IEEE/ACM Supercomputing",
pages = "51-61",
year = 2005,
url = "http://www.nd.edu/~dthain/papers/ibox-sc05.pdf",
paperid = "53"
}

@inproceedings {
literate-fie05,
author = "Douglas Thain and Christian Poellabauer",
title = "Work in Progress: A Literate Approach to Graduate Computer Science Education",
booktitle = "IEEE Frontiers in Education",
pages = "1-2",
year = 2005,
url = "http://www.nd.edu/~dthain/papers/literate-fie2005.pdf",
paperid = "54"
}

@techreport {
subid-tr,
author = "Philip Snowberger and Douglas thain",
title = "Towards Operating System Support for Distributed System Security",
booktitle = "University of Notre Dame, Computer Science and Engineering Department",
number = "2005-18",
year = 2005,
url = "http://www.nd.edu/Reports/2005/TR-2005-18.pdf",
paperid = "84"
}

@article {
parrot-scpe05,
author = "Douglas Thain and Miron Livny",
title = "Parrot: An Application Environment for Data-Intensive Computing",
journal = "Scalable Computing: Practice and Experience",
volume = "6",
number = "3",
pages = "9-18",
year = 2005,
url = "http://www.nd.edu/~dthain/papers/parrot-scpe.pdf",
paperid = "18"
}

@inproceedings {
ibox-hpdc05,
author = "Douglas Thain",
title = "Poster: Identity Boxing: Secure User-Level Containment for the Grid",
booktitle = "IEEE Symposium on High Performance Distributed Computing",
pages = "299-300",
year = 2005,
url = "http://www.nd.edu/~dthain/papers/ibox-hpdc14.pdf",
paperid = "55"
}

@inproceedings {
gems-hpdc05,
author = "Justin Wozniak and Paul Brenner and Douglas Thain and Aaron Striegel and and Jesus Izaguirre",
title = "Generosity and Gluttony in GEMS: Grid Enabled Molecular Simulations",
booktitle = "IEEE Symposium on High Performance Distributed Computing",
pages = "191-200",
year = 2005,
url = "http://www.nd.edu/~dthain/papers/gems-hpdc14.pdf",
paperid = "56"
}

@inproceedings {
patisserie-ads05,
author = "Timothy Schoenharl and Scott Christley and and Douglas Thain",
title = "Patisserie: Support for Parameter Sweeps in a Fault-Tolerant, Massively Parallel, Peer-to-Peer Simulation Environment",
booktitle = "Workshop on Agent Directed Simulation (ADS)",
pages = "1-8",
year = 2005,
url = "http://www.nd.edu/~dthain/papers/patisserie-ads05.pdf",
paperid = "57"
}

@article {
condor-ccpe,
author = "Douglas Thain and Todd Tannenbaum and and Miron Livny",
title = "Distributed Computing in Practice: The Condor Experience",
journal = "Concurrency and Computation: Practice and Experience",
volume = "17",
number = "2-4",
pages = "323-356",
year = 2005,
url = "http://www.nd.edu/~dthain/papers/condor-practice.pdf",
paperid = "19"
}

@incollection {
condor-reliable,
author = "Douglas Thain and Miron Livny",
title = "Building Reliable Clients and Servers",
booktitle = "Grid: Blueprint for a New Computing Infrastructure",
editor = "Ian Foster and Carl Kesselman",
publisher = "Morgan Kaufmann",
year = 2004,
url = "http://www.nd.edu/~dthain/papers/grid2-ch19.pdf",
paperid = "10"
}

@phdthesis {
thain-dissertation,
author = "Douglas Thain",
title = "Coordinating Access to Computation and Data in Distributed Systems",
school = "University of Wisconsin",
type = "Ph.D. Thesis",
year = 2004,
url = "http://www.nd.edu/~dthain/papers/thain-dissertation.pdf",
paperid = "4"
}

@inproceedings {
badfs-nsdi-04,
author = "John Bent and Douglas Thain and Andrea Arpaci-Dusseau and Remzi Arpaci-Dusseau and and Miron Livny",
title = "Explicit Control in a Batch Aware Distributed File System",
booktitle = "USENIX Networked Systems Design and Implementation (NSDI)",
pages = "365-378",
year = 2004,
url = "http://www.usenix.org/events/nsdi04/tech/full_papers/bent/bent.pdf",
paperid = "58"
}

@incollection {
condor-grid,
author = "Douglas Thain and Todd Tannenbaum and and Miron Livny",
title = "Condor and the Grid",
booktitle = "Grid Computing: Making the Global Infrastructure a Reality",
editor = "Fran Berman and Anthony Hey and Geoffrey Fox",
publisher = "John Wiley",
year = 2003,
url = "http://media.wiley.com/product_data/excerpt/90/04708531/0470853190.pdf",
paperid = "9"
}

@inproceedings {
workload-hpdc12,
author = "Douglas Thain and John Bent and Andrea Arpaci-Dusseau and Remzi Arpaci-Dusseau and Miron Livny",
title = "Pipeline and Batch Sharing in Grid Workloads",
booktitle = "IEEE High Performance Distributed Computing",
pages = "152-161",
year = 2003,
url = "http://www.nd.edu/~dthain/papers/workload-hpdc12.pdf",
paperid = "68"
}

@inproceedings {
ethernet-hpdc12,
author = "Douglas Thain and Miron Livny",
title = "The Ethernet Approach to Grid Computing",
booktitle = "IEEE High Performance Distributed Computing",
pages = "138-",
year = 2003,
url = "http://www.nd.edu/~dthain/papers/ethernet-hpdc12.pdf",
paperid = "69"
}

@inproceedings {
parrot-agm2003,
author = "Douglas Thain and Miron Livny",
title = "Parrot: Transparent User-Level Middleware for Data Intensive Computing",
booktitle = "Workshop on Adaptive Grid Middleware at PACT",
year = 2003,
url = "http://www.nd.edu/~dthain/papers/parrot-agm2003.pdf",
paperid = "67"
}

@inproceedings {
xw-condor,
author = "Oleg Lodygensky and Gilles Fedak and Vincent Neri and Franck Cappello and Miron Livny and and Douglas Thain",
title = "XtremWeb and Condor: Sharing Resources Between Internet Connected Condor Pools",
booktitle = "Workshop on Global and Peer-to-Peer Computing on Large Scale Distributed Systems at CCGRID",
pages = "382-390",
year = 2003,
url = "http://www.nd.edu/~dthain/papers/xw-condor.pdf",
paperid = "70"
}

@inproceedings {
error-scope,
author = "Douglas Thain and Miron Livny",
title = "Error Scope on a Computational Grid",
booktitle = "IEEE High Performance Distributed Computing",
pages = "199-208",
year = 2002,
url = "http://www.nd.edu/~dthain/papers/error-scope.pdf",
paperid = "71"
}

@inproceedings {
gridio-sc01,
author = "Douglas Thain and John Bent and Andrea Arpaci-Dusseau and Remzi Arpaci-Dusseau and Miron Livny",
title = "Gathering at the Well: Creating Communities for Grid I/O",
booktitle = "IEEE/ACM Supercomputing",
pages = "21-31",
year = 2001,
url = "http://www.nd.edu/~dthain/papers/community-sc2001.pdf",
paperid = "72"
}

@inproceedings {
kangaroo-hpdc01,
author = "Douglas Thain and Jim Basney and Se-Chang Son and and Miron Livny",
title = "The Kangaroo Approach to Data Movement on the Grid",
booktitle = "IEEE High Performance Distributed Computing",
pages = "325-333",
year = 2001,
url = "http://www.nd.edu/~dthain/papers/kangaroo-hpdc10.pdf",
paperid = "73"
}

@article {
bypass-jcc,
author = "Douglas Thain and Miron Livny",
title = "Multiple Bypass: Interposition Agents for Distributed Computing",
journal = "Journal of Cluster Computing",
volume = "4",
number = "1",
pages = "39-47",
year = 2001,
url = "http://www.nd.edu/~dthain/papers/bypass-jcc-preprint.pdf",
paperid = "20"
}

@inproceedings {
bypass-hpdc00,
author = "Douglas Thain and Miron Livny",
title = "Bypass: A Tool for Building Split Execution Systems",
booktitle = "IEEE High Performance Distributed Computing",
pages = "79-85",
year = 2000,
url = "http://www.nd.edu/~dthain/papers/bypass-hpdc9.pdf",
paperid = "74"
}