@techreport{
 title = {Data Integrity Threat Model},
 type = {techreport},
 year = {2019},
 keywords = {Data Integrity,Non,OSCRP,Threat Model,malicious threat model},
 pages = {9},
 websites = {http://hdl.handle.net/2022/23225},
 month = {6},
 day = {27},
 city = {Bloomington, IN},
 institution = {ScholarWorks},
 id = {c8638e62-4bb9-3e6f-8f5d-5e481ea314df},
 created = {2019-08-20T15:36:00.208Z},
 accessed = {2019-08-20},
 file_attached = {false},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
 group_id = {411048e7-0d47-3d3c-90c2-fad3d2bd6235},
 last_modified = {2019-08-21T17:03:38.146Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {This document uses OSCRP as a point of reference to construct a non-malicious Data Integrity Threat Model as a part of IRIS project. The goal of the project is to detect the source of unintentional integrity errors in the scientific workflow executions on distributed cyberinfrastructure.},
 bibtype = {techreport},
 author = {Welch, Von and Abhinit, Ishan}
}

This document uses OSCRP as a point of reference to construct a non-malicious Data Integrity Threat Model as a part of IRIS project. The goal of the project is to detect the source of unintentional integrity errors in the scientific workflow executions on distributed cyberinfrastructure.

@techreport{
 title = {The Pervasive Technology Institute at 20: Two decades of success and counting},
 type = {techreport},
 year = {2019},
 websites = {http://hdl.handle.net/2022/22607},
 city = {Bloomington, IN},
 institution = {Pervasive Technology Institute},
 id = {a51a01ba-5825-389f-882f-8c4c19b3bf07},
 created = {2019-08-20T15:53:42.310Z},
 accessed = {2019-08-20},
 file_attached = {true},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
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 last_modified = {2019-10-01T17:56:37.204Z},
 read = {false},
 starred = {false},
 authored = {false},
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 bibtype = {techreport},
 author = {Stewart, Craig A.; and Welch, Von; and Doak, Thomas G.; and Miller, Therese; and Plale, Beth; and Walsh, John A.; and Link, Matthew R.; and Snapp-Childs, Winona},
 doi = {10.5967/QDF0-S837}
}

@techreport{
 title = {A Guide for Software Assurance for SWIP},
 type = {techreport},
 year = {2019},
 pages = {1-37},
 websites = {https://pegasus.isi.edu/,http://hdl.handle.net/2022/23413},
 id = {8ce363e9-0cfa-360c-b145-86c6d34b0c4a},
 created = {2019-09-04T20:41:30.988Z},
 file_attached = {true},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
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 last_modified = {2019-09-04T20:41:31.071Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
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 abstract = {The Scientific Workflow Integrity with Pegasus (SWIP) project adds data integrity checking to the Pegasus workflow management system (https://pegasus.isi.edu/). As part of SWIP, we performed software assurance (SwA) on the Pegasus software using the Software Assurance Marketplace (SWAMP, https://www.mir-swamp.org/). Initially, we planned to perform SwA only on the parts of the code base related to SWIP, i.e., only the code related to the data integrity checks. However, during the course of the SWIP project, a decision was made to perform SwA on the entire Pegasus code base. In addition, the project took on a research effort of trying to quantify differences in SwA results between Pegasus versions. We summarize our SwA process and results here. SwA results provide insight, but they are still subjective; developers of the software being assessed (Pegasus in this project) need to determine how those results need to be addressed.},
 bibtype = {techreport},
 author = {Heiland, Randy; and Rynge, Mats; and Vahi, Karan; and Deelman, Ewa; and Welch, Von}
}

The Scientific Workflow Integrity with Pegasus (SWIP) project adds data integrity checking to the Pegasus workflow management system (https://pegasus.isi.edu/). As part of SWIP, we performed software assurance (SwA) on the Pegasus software using the Software Assurance Marketplace (SWAMP, https://www.mir-swamp.org/). Initially, we planned to perform SwA only on the parts of the code base related to SWIP, i.e., only the code related to the data integrity checks. However, during the course of the SWIP project, a decision was made to perform SwA on the entire Pegasus code base. In addition, the project took on a research effort of trying to quantify differences in SwA results between Pegasus versions. We summarize our SwA process and results here. SwA results provide insight, but they are still subjective; developers of the software being assessed (Pegasus in this project) need to determine how those results need to be addressed.

@inproceedings{
 title = {Trusted CI Experiences in Cybersecurity and Service to Open Science},
 type = {inproceedings},
 year = {2019},
 pages = {1-8},
 publisher = {Association for Computing Machinery (ACM)},
 id = {06cc0289-4cb7-386e-875b-5ce2b61881d9},
 created = {2019-09-11T16:00:39.271Z},
 accessed = {2019-09-11},
 file_attached = {true},
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 read = {false},
 starred = {false},
 authored = {false},
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 hidden = {false},
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 abstract = {This article describes experiences and lessons learned from the Trusted CI project, funded by the US National Science Foundation (NSF) to serve the community as the NSF Cybersecurity Center of Excellence (CCoE). Trusted CI is an effort to address cybersecurity for the open science community through a single organization that provides leadership, training, consulting, and knowledge to that community. The article describes the experiences and lessons learned of Trusted CI regarding both cybersecurity for open science and managing the process of providing centralized services to a broad and diverse community.},
 bibtype = {inproceedings},
 author = {Adams, Andrew and Jackson, Craig and Kiser, Ryan and Krenz, Mark and Marsteller, Jim and Miller, Barton P. and Peisert, Sean and Russell, Scott and Sons, Susan and Welch, Von and Zage, John and Avila, Kay and Basney, Jim and Brunson, Dana and Cowles, Robert and Dopheide, Jeannette and Fleury, Terry and Heymann, Elisa and Hudson, Florence},
 doi = {10.1145/3332186.3340601},
 booktitle = {Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning) (PEARC '19)}
}

This article describes experiences and lessons learned from the Trusted CI project, funded by the US National Science Foundation (NSF) to serve the community as the NSF Cybersecurity Center of Excellence (CCoE). Trusted CI is an effort to address cybersecurity for the open science community through a single organization that provides leadership, training, consulting, and knowledge to that community. The article describes the experiences and lessons learned of Trusted CI regarding both cybersecurity for open science and managing the process of providing centralized services to a broad and diverse community.

@inproceedings{
 title = {Integrity Protection for Scientific Workflow Data: Motivation and Initial Experiences},
 type = {inproceedings},
 year = {2019},
 pages = {1-8},
 publisher = {Association for Computing Machinery (ACM)},
 id = {221e2cfc-bb7e-3db8-bbfc-f23fb0058b83},
 created = {2019-09-11T16:02:21.529Z},
 accessed = {2019-09-11},
 file_attached = {true},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
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 last_modified = {2019-09-12T14:53:04.063Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
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 abstract = {With the continued rise of scientific computing and the enormous increases in the size of data being processed, scientists must consider whether the processes for transmitting and storing data sufficiently assure the integrity of the scientific data. When integrity is not preserved, computations can fail and result in increased computational cost due to reruns, or worse, results can be corrupted in a manner not apparent to the scientist and produce invalid science results. Technologies such as TCP checksums, encrypted transfers, checksum validation, RAID and erasure coding provide integrity assurances at different levels, but they may not scale to large data sizes and may not cover a workflow from end-to-end, leaving gaps in which data corruption can occur undetected. In this paper we explore an approach of assuring data integrity - considering either malicious or accidental corruption - for workflow executions orchestrated by the Pegasus Workflow Management System. To validate our approach, we introduce Chaos Jungle - a toolkit providing an environment for validating integrity verification mechanisms by allowing researchers to introduce a variety of integrity errors during data transfers and storage. In addition to controlled experiments with Chaos Jungle, we provide analysis of integrity errors that we encountered when running production workflows.},
 bibtype = {inproceedings},
 author = {Rynge, Mats and Poehlman, William L. and Feltus, F. Alex and Vahi, Karan and Deelman, Ewa and Mandal, Anirban and Baldin, Ilya and Bhide, Omkar and Heiland, Randy and Welch, Von and Hill, Raquel},
 doi = {10.1145/3332186.3332222},
 booktitle = {Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning) (PEARC '19)}
}

With the continued rise of scientific computing and the enormous increases in the size of data being processed, scientists must consider whether the processes for transmitting and storing data sufficiently assure the integrity of the scientific data. When integrity is not preserved, computations can fail and result in increased computational cost due to reruns, or worse, results can be corrupted in a manner not apparent to the scientist and produce invalid science results. Technologies such as TCP checksums, encrypted transfers, checksum validation, RAID and erasure coding provide integrity assurances at different levels, but they may not scale to large data sizes and may not cover a workflow from end-to-end, leaving gaps in which data corruption can occur undetected. In this paper we explore an approach of assuring data integrity - considering either malicious or accidental corruption - for workflow executions orchestrated by the Pegasus Workflow Management System. To validate our approach, we introduce Chaos Jungle - a toolkit providing an environment for validating integrity verification mechanisms by allowing researchers to introduce a variety of integrity errors during data transfers and storage. In addition to controlled experiments with Chaos Jungle, we provide analysis of integrity errors that we encountered when running production workflows.

@inproceedings{
 title = {Initial Thoughts on Cybersecurity And Reproducibility},
 type = {inproceedings},
 year = {2019},
 pages = {13-15},
 publisher = {Association for Computing Machinery (ACM)},
 id = {2f76dbc3-b76e-3785-b8cc-9b880f76d6d5},
 created = {2019-09-11T16:05:13.387Z},
 accessed = {2019-09-11},
 file_attached = {true},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
 group_id = {411048e7-0d47-3d3c-90c2-fad3d2bd6235},
 last_modified = {2019-09-11T16:05:13.456Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {Cybersecurity, which serves to protect computer systems and data from malicious and accidental abuse and changes, both supports and challenges the reproducibility of computational science. This position paper explores a research agenda by enumerating a set of two types of challenges that emerge at the intersection of cybersecurity and reproducibility: challenges that cybersecurity has in supporting the reproducibility of computational science, and challenges cybersecurity creates for reproducibility of computational science.},
 bibtype = {inproceedings},
 author = {Deelman, Ewa and Stodden, Victoria and Taufer, Michela and Welch, Von},
 doi = {10.1145/3322790.3330593},
 booktitle = {Proceedings of the 2nd International Workshop on Practical Reproducible Evaluation of Computer Systems (P-RECS '19)}
}

Cybersecurity, which serves to protect computer systems and data from malicious and accidental abuse and changes, both supports and challenges the reproducibility of computational science. This position paper explores a research agenda by enumerating a set of two types of challenges that emerge at the intersection of cybersecurity and reproducibility: challenges that cybersecurity has in supporting the reproducibility of computational science, and challenges cybersecurity creates for reproducibility of computational science.

@inproceedings{
 title = {Applicability Study of the PRIMAD Model to LIGO Gravitational Wave Search Workflows},
 type = {inproceedings},
 year = {2019},
 pages = {1-6},
 websites = {http://dl.acm.org/citation.cfm?doid=3322790.3330591},
 publisher = {ACM Press},
 city = {New York, New York, USA},
 id = {5c88d52d-7956-3e10-8529-d1f22d6c13f6},
 created = {2019-09-11T16:06:47.021Z},
 accessed = {2019-09-11},
 file_attached = {true},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
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 last_modified = {2019-09-12T18:48:09.360Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {The PRIMAD model with its six components (i.e., Platform, Research Objective, Implementation, Methods, Actors, and Data), provides an abstract taxonomy to represent computational experiments and enforce reproducibility by design. In this paper, we assess the model applicability to a set of Laser Interferometer Gravitational-Wave Observatory (LIGO) workflows from literature sources (i.e., published papers). Our work outlines potentials and limits of the model in terms of its abstraction levels and application process.},
 bibtype = {inproceedings},
 author = {Chapp, Dylan and Rorabaugh, Danny and Brown, Duncan A. and Deelman, Ewa and Vahi, Karan and Welch, Von and Taufer, Michela},
 doi = {10.1145/3322790.3330591},
 booktitle = {Proceedings of the 2nd International Workshop on Practical Reproducible Evaluation of Computer Systems - P-RECS '19}
}

The PRIMAD model with its six components (i.e., Platform, Research Objective, Implementation, Methods, Actors, and Data), provides an abstract taxonomy to represent computational experiments and enforce reproducibility by design. In this paper, we assess the model applicability to a set of Laser Interferometer Gravitational-Wave Observatory (LIGO) workflows from literature sources (i.e., published papers). Our work outlines potentials and limits of the model in terms of its abstraction levels and application process.

@techreport{
 title = {Trusted CI Annual Report for 2018},
 type = {techreport},
 year = {2018},
 websites = {hp://hdl.handle.net/2022/22597},
 id = {ca32dbd5-e330-3511-9ac2-c98a171b7c11},
 created = {2019-09-04T20:48:17.611Z},
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 read = {false},
 starred = {false},
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 bibtype = {techreport},
 author = {Adams, Andrew and Avila, Kay and Atkins, Joel and Basney, Jim and Bohland, Leslee and Borecky, Diana and Cowles, Robert and Dopheide, Jeannee and Fleury, Terry and Harbour, Grayson and Heymann, Elisa and Hudson, Florence and Jackson, Craig and Kiser, Ryan and Krenz, Mark and Marsteller, Jim and Miller, Barton and Raquel, Warren and Ruff, Preston and Russell, Scoo and Shah, Zalak and Shankar, Anurag and Sons, Susan and Welch, Von and Zage, John}
}

@techreport{
 title = {The Report of the 2018 NSF Cybersecurity Summit for Large Facilities and Cyberinfrastructure},
 type = {techreport},
 year = {2018},
 websites = {http://hdl.handle.net/2022/22588.},
 id = {03d3ae36-087f-3de4-91c9-7a17808f8edd},
 created = {2019-09-10T15:24:00.435Z},
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 last_modified = {2019-09-10T15:24:00.435Z},
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 bibtype = {techreport},
 author = {Andrew Adams, Jeannette Dopheide, Mark Krenz, James Marsteller, Von Welch and and John Zage, undefined}
}

@article{
 title = {The Rise of Cybersecurity and Its Impact on Data Protection},
 type = {article},
 year = {2017},
 pages = {73-75},
 volume = {7},
 id = {7f32ce95-c147-390d-98f6-7801fba0b9e4},
 created = {2018-02-27T18:07:36.673Z},
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 last_modified = {2018-02-27T18:07:36.673Z},
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 starred = {false},
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 hidden = {false},
 source_type = {JOUR},
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 bibtype = {article},
 author = {Cate, Fred H and Kuner, Christopher and Svantesson, Dan Jerker B and Lynskey, Orla and Millard, Christopher},
 doi = {https://doi.org/10.1093/idpl/ipw022},
 journal = {International Data Privacy Law},
 number = {2}
}

@techreport{
 title = {Pervasive Technology Institute Annual Report: Research Innovations and Advanced Cyberinfrastructure Services in Support of IU Strategic Goals During FY 2017},
 type = {techreport},
 year = {2017},
 websites = {http://hdl.handle.net/2022/21809},
 id = {26883fb6-be7d-39f2-ba49-db71de80bdb9},
 created = {2018-02-27T18:07:36.723Z},
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 last_modified = {2020-09-10T00:01:47.048Z},
 read = {false},
 starred = {false},
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 confirmed = {true},
 hidden = {false},
 source_type = {RPRT},
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 bibtype = {techreport},
 author = {Stewart, Craig and Plale, Beth and Welch, Von and Pierce, Marlon and Fox, Geoffrey Charles and Doak, Thomas G and Hancock, David Y and Henschel, Robert and Link, Matthew R and Miller, Therese}
}

@article{
 title = {The medical science DMZ: a network design pattern for data-intensive medical science},
 type = {article},
 year = {2017},
 id = {8aa4b240-261f-31ef-af4f-6e2820fa95dd},
 created = {2018-02-27T18:07:36.936Z},
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 last_modified = {2018-02-27T18:07:36.936Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {JOUR},
 private_publication = {false},
 bibtype = {article},
 author = {Peisert, Sean and Dart, Eli and Barnett, William and Balas, Edward and Cuff, James and Grossman, Robert L and Berman, Ari and Shankar, Anurag and Tierney, Brian},
 journal = {Journal of the American Medical Informatics Association}
}

@book{
 title = {Bulk Collection: Systematic Government Access to Private-Sector Data},
 type = {book},
 year = {2017},
 publisher = {Oxford University Press},
 id = {56f8a9a2-65d7-3077-856f-d8ef0328babe},
 created = {2018-02-27T18:07:36.942Z},
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 hidden = {false},
 source_type = {BOOK},
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 bibtype = {book},
 author = {Cate, Fred H and Dempsey, James X}
}

@article{
 title = {The Open Science Cyber Risk Profile: The Rosetta Stone for Open Science and Cybersecurity},
 type = {article},
 year = {2017},
 keywords = {Cyber security; Cyber-attacks; OSCRP; Risk profil,Natural sciences computing; Security of data,Security systems},
 pages = {94-95},
 volume = {15},
 websites = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85031689244&doi=10.1109%2FMSP.2017.3681058&partnerID=40&md5=c8539146c103a7d978d47ba1947849a6},
 publisher = {Institute of Electrical and Electronics Engineers Inc.},
 id = {878e88ba-12a0-3beb-b90f-6115f81c7538},
 created = {2018-02-27T18:07:37.619Z},
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 last_modified = {2018-02-27T18:07:37.619Z},
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 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Peisert201794},
 source_type = {article},
 notes = {cited By 0},
 private_publication = {false},
 abstract = {The Open Science Cyber Risk Profile (OSCRP) working group has created a document that motivates scientists by demonstrating how improving their security posture reduces the risks to their science. This effort aims to bridge the communication gap between scientists and IT security professionals and allows for the effective management of risks to open science caused by IT security threats. © 2003-2012 IEEE.},
 bibtype = {article},
 author = {Peisert, S and Welch, V},
 doi = {10.1109/MSP.2017.3681058},
 journal = {IEEE Security and Privacy},
 number = {5}
}

The Open Science Cyber Risk Profile (OSCRP) working group has created a document that motivates scientists by demonstrating how improving their security posture reduces the risks to their science. This effort aims to bridge the communication gap between scientists and IT security professionals and allows for the effective management of risks to open science caused by IT security threats. © 2003-2012 IEEE.

@techreport{
 title = {Indiana University Pervasive Technology Institute},
 type = {techreport},
 year = {2017},
 city = {Bloomington, IN},
 id = {98c63812-3b4e-302d-8d1a-024af71234b6},
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 author = {Stewart, C A and Welch, V and Plale, B and Fox, Geoffrey Charles and Pierce, M and Sterling, T},
 doi = {10.5072/FK2154N14D}
}

@article{
 title = {Machine Learning with Personal Data: Is Data Protection Law Smart Enough to Meet the Challenge?},
 type = {article},
 year = {2017},
 pages = {1-2},
 volume = {7},
 id = {9b20e05f-5d31-31f4-a8fd-7c5f3d8fb7bc},
 created = {2018-02-27T18:07:40.176Z},
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 author = {Cate, Fred H and Kuner, Christopher and Svantesson, Dan Jerker B and Lynskey, Orla and Millard, Christopher},
 doi = {10.1093/idpl/ipx003},
 journal = {International Data Privacy Law},
 number = {1}
}

@inproceedings{
 title = {Modeling the Past and Future of Identity Management for Scientific Collaborations},
 type = {inproceedings},
 year = {2016},
 id = {546d26d6-48e4-3555-9d58-09254fc564f7},
 created = {2018-02-27T18:07:37.213Z},
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 hidden = {false},
 source_type = {CONF},
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 bibtype = {inproceedings},
 author = {Cowles, Robert and Jackson, Craig and Welch, Von},
 booktitle = {Proceedings of the International Symposium on Grids and Clouds (ISGC) 2016. 13-18 March 2016. Academia Sinica, Taipei, Taiwan. Online at http://pos. sissa. it/cgi-bin/reader/conf. cgi? confid= 270, id. 14}
}

@article{
 title = {A Time of Turmoil},
 type = {article},
 year = {2016},
 pages = {1-3},
 volume = {6},
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@techreport{
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@techreport{
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@article{
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@article{
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@article{
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@inproceedings{
 title = {Authentication and Authorization Considerations for a Multi-tenant Service},
 type = {inproceedings},
 year = {2015},
 pages = {29-35},
 websites = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84962377238&doi=10.1145%2F2753524.2753534&partnerID=40&md5=06c617703f402a57e3922f8a290ed55d,http://dl.acm.org/citation.cfm?doid=2753524.2753534},
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 private_publication = {false},
 abstract = {Distributed cyberinfrastructure requires users (and machines) to perform some sort of authentication and authorization (together simply known as auth). In the early days of computing, authentication was performed with just a username and password combination, and this is still prevalent today. But during the past several years, we have seen an evolution of approaches and protocols for auth: Kerberos, SSH keys, X.509, OpenID, API keys, OAuth, and more. Not surprisingly, there are trade-offs, both technical and social, for each approach. The NSF Science Gateway communities have had to deal with a variety of auth issues. However, most of the early gateways were rather restrictive in their model of access and development. The practice of using community credentials (certificates), a well-intentioned idea to alleviate restrictive access, still posed a barrier to researchers and challenges for security and auditing. And while the web portal-based gateway clients offered users easy access from a browser, both the interface and the back-end functionality were constrained in the flexibility and extensibility they could provide. Designing a well-defined application programming interface (API) to fine-grained, generic gateway services (on secure, hosted cyberinfrastructure), together with an auth approach that has a lower barrier to entry, will hopefully present a more welcoming environment for both users and developers. This paper provides a review and some thoughts on these topics, with a focus on the role of auth between a Science Gateway and a service provider.},
 bibtype = {inproceedings},
 author = {Heiland, Randy and Koranda, Scott and Marru, Suresh and Pierce, Marlon and Welch, Von},
 doi = {10.1145/2753524.2753534},
 booktitle = {Proceedings of the 1st Workshop on The Science of Cyberinfrastructure Research, Experience, Applications and Models - SCREAM '15}
}

Distributed cyberinfrastructure requires users (and machines) to perform some sort of authentication and authorization (together simply known as auth). In the early days of computing, authentication was performed with just a username and password combination, and this is still prevalent today. But during the past several years, we have seen an evolution of approaches and protocols for auth: Kerberos, SSH keys, X.509, OpenID, API keys, OAuth, and more. Not surprisingly, there are trade-offs, both technical and social, for each approach. The NSF Science Gateway communities have had to deal with a variety of auth issues. However, most of the early gateways were rather restrictive in their model of access and development. The practice of using community credentials (certificates), a well-intentioned idea to alleviate restrictive access, still posed a barrier to researchers and challenges for security and auditing. And while the web portal-based gateway clients offered users easy access from a browser, both the interface and the back-end functionality were constrained in the flexibility and extensibility they could provide. Designing a well-defined application programming interface (API) to fine-grained, generic gateway services (on secure, hosted cyberinfrastructure), together with an auth approach that has a lower barrier to entry, will hopefully present a more welcoming environment for both users and developers. This paper provides a review and some thoughts on these topics, with a focus on the role of auth between a Science Gateway and a service provider.

@inproceedings{
 title = {Facilitating Scientific Collaborations by Delegating Identity Management},
 type = {inproceedings},
 year = {2015},
 keywords = {Access control,Cyber security,Delegation,Identity,Identity ma,Risk management},
 pages = {15-19},
 websites = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84979747691&doi=10.1145%2F2752499.2752501&partnerID=40&md5=83a416d313602ca3c75ba6528f549833,http://dl.acm.org/citation.cfm?doid=2752499.2752501},
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 abstract = {DOE Labs are often presented with conflicting requirements for providing services to scientific collaboratories. An identity management model involving transitive trust is increasingly common. We show how existing policies allow for increased delegation of identity management within an acceptable risk management framework. Specific topics addressed include deemed exports, DOE orders, Inertia and Risk, Traceability, and Technology Limitations. Real life examples of an incremental approach to implementing transitive trust are presented.},
 bibtype = {inproceedings},
 author = {Cowles, Robert and Jackson, Craig and Welch, Von},
 doi = {10.1145/2752499.2752501},
 booktitle = {Proceedings of the 2015 Workshop on Changing Landscapes in HPC Security - CLHS '15}
}

DOE Labs are often presented with conflicting requirements for providing services to scientific collaboratories. An identity management model involving transitive trust is increasingly common. We show how existing policies allow for increased delegation of identity management within an acceptable risk management framework. Specific topics addressed include deemed exports, DOE orders, Inertia and Risk, Traceability, and Technology Limitations. Real life examples of an incremental approach to implementing transitive trust are presented.

@article{
 title = {Internet Balkanization Gathers Pace: Is Privacy the Real Driver?},
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 year = {2015},
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 number = {1}
}

@article{
 title = {Risk Management in Data Protection},
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 number = {2}
}

@techreport{
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@article{
 title = {The Data Protection Credibility Crisis},
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@techreport{
 title = {XSIM Final Report: Modelling the Past and Future of Identity Management for Scientific Collaborations},
 type = {techreport},
 year = {2015},
 websites = {http://hdl.handle.net/2022/20399},
 month = {9},
 city = {Bloomington, IN},
 institution = {Indiana University},
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@inproceedings{
 title = {Sustained software for cyberinfrastructure - Analyses of successful efforts with a focus on NSF-funded software},
 type = {inproceedings},
 year = {2015},
 id = {2ef3fe8c-9dd6-3aed-8dbe-49ae96ec88fd},
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 abstract = {Reliable software that provides needed functionality is clearly essential for an effective distributed cyberinfrastructure (CI) that supports comprehensive, balanced, and flexible distributed CI. Effective distributed cyberinfrastructure, in turn, supports science and engineering applications. The purpose of this study was to understand what factors lead to software projects being well sustained over the long run, focusing on software created with funding from the US National Science Foundation (NSF) and/or used by researchers funded by the NSF. We surveyed NSF-funded researchers and performed in-depth studies of software projects that have been sustained over many years. Successful projects generally used open-source software licenses and employed good software engineering practices and test practices. However, many projects that have not been well sustained over time also met these criteria. The features that stood out about successful projects included deeply committed leadership and some sort of user forum or conference at least annually. In some cases, software project leaders have employed multiple financial strategies over the course of a decades-old software project. Such well-sustained software is used in major distributed CI projects that support thousands of users, and this software is critical to the operation of major distributed CI facilities in the US. The findings of our study identify some characteristics of software that is relevant to the NSF-supported research community, and that has been sustained over many years.},
 bibtype = {inproceedings},
 author = {Stewart, C.A. and Barnett, W.K. and Wernert, E.A. and Wernert, J.A. and Welch, V. and Knepper, R.},
 doi = {10.1145/2753524.2753533},
 booktitle = {SCREAM 2015 - Proceedings of the 2015 Workshop on the Science of Cyberinfrastructure: Research, Experience, Applications and Models, Part of HPDC 2015}
}

Reliable software that provides needed functionality is clearly essential for an effective distributed cyberinfrastructure (CI) that supports comprehensive, balanced, and flexible distributed CI. Effective distributed cyberinfrastructure, in turn, supports science and engineering applications. The purpose of this study was to understand what factors lead to software projects being well sustained over the long run, focusing on software created with funding from the US National Science Foundation (NSF) and/or used by researchers funded by the NSF. We surveyed NSF-funded researchers and performed in-depth studies of software projects that have been sustained over many years. Successful projects generally used open-source software licenses and employed good software engineering practices and test practices. However, many projects that have not been well sustained over time also met these criteria. The features that stood out about successful projects included deeply committed leadership and some sort of user forum or conference at least annually. In some cases, software project leaders have employed multiple financial strategies over the course of a decades-old software project. Such well-sustained software is used in major distributed CI projects that support thousands of users, and this software is critical to the operation of major distributed CI facilities in the US. The findings of our study identify some characteristics of software that is relevant to the NSF-supported research community, and that has been sustained over many years.

@inproceedings{
 title = {Cyberinfrastructure resources enabling creation of the loblolly pine reference transcriptome},
 type = {inproceedings},
 year = {2015},
 pages = {1-6},
 volume = {2015-July},
 websites = {http://hdl.handle.net/2022/20488,http://dl.acm.org/citation.cfm?doid=2792745.2792748},
 month = {7},
 publisher = {ACM Press},
 city = {New York, New York, USA},
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 citation_key = {Wu2015},
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 abstract = {Today's genomics technologies generate more sequence data than ever before possible, and at substantially lower costs, serving researchers across biological disciplines in transformative ways. Building transcriptome assemblies from RNA sequencing reads is one application of next-generation sequencing (NGS) that has held a central role in biological discovery in both model and non-model organisms, with and without whole genome sequence references. A major limitation in effective building of transcriptome references is no longer the sequencing data generation itself, but the computing infrastructure and expertise needed to assemble, analyze and manage the data. Here we describe a currently available resource dedicated to achieving such goals, and its use for extensive RNA assembly of up to 1.3 billion reads representing the massive transcriptome of loblolly pine, using four major assembly software installations. The Mason cluster, an XSEDE second tier resource at Indiana University, provides the necessary fast CPU cycles, large memory, and high I/O throughput for conducting large-scale genomics research. The National Center for Genome Analysis Support, or NCGAS, provides technical support in using HPC systems, bioinformatic support for determining the appropriate method to analyze a given dataset, and practical assistance in running computations. We demonstrate that a sufficient supercomputing resource and good workflow design are elements that are essential to large eukaryotic genomics and transcriptomics projects such as the complex transcriptome of loblolly pine, gene expression data that inform annotation and functional interpretation of the largest genome sequence reference to date.},
 bibtype = {inproceedings},
 author = {Wu, Le-Shin and Ganote, Carrie L. and Doak, Thomas G and Barnett, William and Mockaitis, Keithanne and Stewart, Craig A},
 doi = {10.1145/2792745.2792748},
 booktitle = {Proceedings of the 2015 XSEDE Conference on Scientific Advancements Enabled by Enhanced Cyberinfrastructure - XSEDE '15}
}

Today's genomics technologies generate more sequence data than ever before possible, and at substantially lower costs, serving researchers across biological disciplines in transformative ways. Building transcriptome assemblies from RNA sequencing reads is one application of next-generation sequencing (NGS) that has held a central role in biological discovery in both model and non-model organisms, with and without whole genome sequence references. A major limitation in effective building of transcriptome references is no longer the sequencing data generation itself, but the computing infrastructure and expertise needed to assemble, analyze and manage the data. Here we describe a currently available resource dedicated to achieving such goals, and its use for extensive RNA assembly of up to 1.3 billion reads representing the massive transcriptome of loblolly pine, using four major assembly software installations. The Mason cluster, an XSEDE second tier resource at Indiana University, provides the necessary fast CPU cycles, large memory, and high I/O throughput for conducting large-scale genomics research. The National Center for Genome Analysis Support, or NCGAS, provides technical support in using HPC systems, bioinformatic support for determining the appropriate method to analyze a given dataset, and practical assistance in running computations. We demonstrate that a sufficient supercomputing resource and good workflow design are elements that are essential to large eukaryotic genomics and transcriptomics projects such as the complex transcriptome of loblolly pine, gene expression data that inform annotation and functional interpretation of the largest genome sequence reference to date.

@techreport{
 title = {Pervasive Technology Institute annual report: Research innovations and advanced cyberinfrastructure services in support of IU strategic goals during FY 2015},
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 journal = {International Data Privacy Law},
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 booktitle = {Proceedings of the International Conference on Software Engineering Research and Practice (SERP)}
}

@techreport{
 title = {Report of the 2014 NSF Cybersecurity Summit for Large Facilities and Cyberinfrastructure Large Facility Cybersecurity Challenges and Responses August 26‐August 28},
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@techreport{
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@article{
 title = {When Two Worlds Collide: The Interface Between Competition Law and Data Protection},
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@article{
 title = {The role of the collaboratory in enabling large-scale identity management for HEP},
 type = {article},
 year = {2014},
 keywords = {Collaboratories; Identity management; Motivation,Computation theory; High energy physics,Nuclear physics},
 volume = {513},
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 abstract = {The authors are defining a model that describes and guides existing and future scientific collaboratory identity management implementations. Our ultimate goal is to provide guidance to virtual organizations and resource providers in designing an identity management implementation. Our model is captured in previously published work. Here, we substantially extend our analysis in terms of six motivation factors (user isolation, persistence of user data, complexity of virtual organization roles, cultural and historical inertia, scaling, and incentive for collaboration), observed in interviews with community members involved in identity management, that impact implementation decisions. This analysis is a significant step towards our ultimate goal of providing guidance to virtual organizations.},
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 author = {Cowles, R and Jackson, C and Welch, V},
 doi = {10.1088/1742-6596/513/3/032022},
 journal = {Journal of Physics: Conference Series},
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}

The authors are defining a model that describes and guides existing and future scientific collaboratory identity management implementations. Our ultimate goal is to provide guidance to virtual organizations and resource providers in designing an identity management implementation. Our model is captured in previously published work. Here, we substantially extend our analysis in terms of six motivation factors (user isolation, persistence of user data, complexity of virtual organization roles, cultural and historical inertia, scaling, and incentive for collaboration), observed in interviews with community members involved in identity management, that impact implementation decisions. This analysis is a significant step towards our ultimate goal of providing guidance to virtual organizations.

@inproceedings{
 title = {A model for identity management in future scientific collaboratories},
 type = {inproceedings},
 year = {2014},
 keywords = {Collaboratories; e-Science; Extreme scale; Identit},
 volume = {23-28-Marc},
 websites = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84976254441&partnerID=40&md5=6e634aeaa09b2745f880e182e1cf237e},
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 abstract = {Over the past two decades, the virtual organization (VO) has allowed for increasingly large and complex scientific projects spanning multiple organizations and countries. The eXtreme Scale Identity Management (XSIM) project has surveyed a number of these VOs and the resource providers (RPs) that serve them, and built a model expressing the identity management (IdM) implementations supporting these large scientific VOs. The initial model was presented at eScience 2013. This work refines that initial VO-IdM model with XSIM efforts since the original eScience 2013 paper, capturing results from additional interviews and initial applications of the model, and begins to extend the model to include federated IdM environments, portal-based VOs and cloud and exascale RPs. © Copyright owned by the author(s) under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike Licence.},
 bibtype = {inproceedings},
 author = {Cowles, R and Jackson, C and Welch, V and Cholia, S},
 booktitle = {Proceedings of Science}
}

Over the past two decades, the virtual organization (VO) has allowed for increasingly large and complex scientific projects spanning multiple organizations and countries. The eXtreme Scale Identity Management (XSIM) project has surveyed a number of these VOs and the resource providers (RPs) that serve them, and built a model expressing the identity management (IdM) implementations supporting these large scientific VOs. The initial model was presented at eScience 2013. This work refines that initial VO-IdM model with XSIM efforts since the original eScience 2013 paper, capturing results from additional interviews and initial applications of the model, and begins to extend the model to include federated IdM environments, portal-based VOs and cloud and exascale RPs. © Copyright owned by the author(s) under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike Licence.

@article{
 title = {Systematic Government Access to Private-Sector Data Redux},
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@inproceedings{
 title = {OSG PKI transition: Experiences and lessons learned},
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 year = {2014},
 keywords = {Authentication; Distributed computer systems; Proj,Certificate Services; Federated identity; Identit,Public key cryptography},
 volume = {23-28-Marc},
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 abstract = {Over the course of 2012-13 the Open Science Grid (OSG) transitioned the identity management system for its science user community from the DOE Grids public key infrastructure (PKI) to a new OSG PKI. This transition was significant in its scope, touching on nearly all aspects of the OSG infrastructure and community. The transition also entailed the adoption of a commercial certificate service as a key component of OSG's PKI. This transition offers a rare opportunity to better understand identity management and how to prepare for and implement changes in an identity management system. In this paper, we describe OSG's transition and lessons learned from it. We discuss the overall project management approach, including a division of the project into planning, piloting, design, development, implementation and transition phases. We discuss the considered alternatives, both for implementations of the OSG PKI as well as alternatives to a PKI such as federated identity, as well as the criteria we used to make our decision. We conclude with a set of lessons learned from both implementation and in retrospect, and a set of recommendations for other identity systems. © Copyright owned by the author(s) under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike Licence.},
 bibtype = {inproceedings},
 author = {Welch, V and Deximo, A and Hayashi, S and Khadke, V D and Mathure, R and Quick, R and Altunay, M and Sehgal, C S and Tiradani, A and Basney, J},
 booktitle = {Proceedings of Science}
}

Over the course of 2012-13 the Open Science Grid (OSG) transitioned the identity management system for its science user community from the DOE Grids public key infrastructure (PKI) to a new OSG PKI. This transition was significant in its scope, touching on nearly all aspects of the OSG infrastructure and community. The transition also entailed the adoption of a commercial certificate service as a key component of OSG's PKI. This transition offers a rare opportunity to better understand identity management and how to prepare for and implement changes in an identity management system. In this paper, we describe OSG's transition and lessons learned from it. We discuss the overall project management approach, including a division of the project into planning, piloting, design, development, implementation and transition phases. We discuss the considered alternatives, both for implementations of the OSG PKI as well as alternatives to a PKI such as federated identity, as well as the criteria we used to make our decision. We conclude with a set of lessons learned from both implementation and in retrospect, and a set of recommendations for other identity systems. © Copyright owned by the author(s) under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike Licence.

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@article{
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@article{
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@article{
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@book{
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@inproceedings{
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@article{
 title = {Face-to-Data--Another Developing Privacy Threat?},
 type = {article},
 year = {2013},
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 journal = {International Data Privacy Law}
}

@inproceedings{
 title = {Science gateway security recommendations},
 type = {inproceedings},
 year = {2013},
 keywords = {Cluster computing,Research,Research communities; Research data; Research resu},
 websites = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84893618339&doi=10.1109%2FCLUSTER.2013.6702697&partnerID=40&md5=2e80780339d239a3e2703947890900ea},
 city = {Indianapolis, IN},
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 notes = {cited By 0; Conference of 15th IEEE International Conference on Cluster Computing, CLUSTER 2013 ; Conference Date: 23 September 2013 Through 27 September 2013; Conference Code:102435},
 private_publication = {false},
 abstract = {A science gateway is a web portal that provides a convenient interface to data and applications in support of a research community. Standard security concerns apply to science gateways, including confidentiality of pre-publication research data, integrity of research results, and availability of services provided to researchers. In this paper we identify existing science gateway security recommendations and provide our own perspective. © 2013 IEEE.},
 bibtype = {inproceedings},
 author = {Basney, J and Welch, V},
 doi = {10.1109/CLUSTER.2013.6702697},
 booktitle = {Proceedings - IEEE International Conference on Cluster Computing, ICCC}
}

A science gateway is a web portal that provides a convenient interface to data and applications in support of a research community. Standard security concerns apply to science gateways, including confidentiality of pre-publication research data, integrity of research results, and availability of services provided to researchers. In this paper we identify existing science gateway security recommendations and provide our own perspective. © 2013 IEEE.

@techreport{
 title = {Status, Strategies and Future Plans-OSG PKI Transition},
 type = {techreport},
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@techreport{
 title = {Year 1 Report: Center for Trustworthy Scientific Cyberinfrastructure},
 type = {techreport},
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 bibtype = {techreport},
 author = {Welch, Von}
}

This report covers CTSC project year three, from October 2014 through September 2015, during which time CTSC engaged with nine NSF CI projects, organized and hosted the 2015 NSF Cybersecurity Summits for Large Facilities and Cyberinfrastructure, developed and provided training in developing cybersecurity programs, secure coding, and incident response, provided the community guidance with dealing with vulnerabilities, and authored and submitted to NSF a section on cybersecurity for the NSF Large Facilities Manual.

@article{
 title = {The Extraterritoriality of Data Privacy Laws--An Explosive Issue Yet to Detonate},
 type = {article},
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 pages = {147-148},
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 number = {3}
}

@techreport{
 title = {HIPAA and Advanced Scientific Computing},
 type = {techreport},
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@article{
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@inproceedings{
 title = {Identity Management for Virtual Organizations: An Experience-Based Model},
 type = {inproceedings},
 year = {2013},
 keywords = {Collaboration,Computation theory,Identity management,Risks,Security,Tru},
 pages = {278-284},
 websites = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84893499173&doi=10.1109%2FeScience.2013.47&partnerID=40&md5=5f290ab32369f2caa599bf22f6c9aa1c,http://ieeexplore.ieee.org/document/6683918/},
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 notes = {cited By 0; Conference of 9th IEEE International Conference on e-Science, e-Science 2013 ; Conference Date: 22 October 2013 Through 25 October 2013; Conference Code:102409},
 private_publication = {false},
 abstract = {In this paper we present our Virtual Organization (VO) Identity Management (IdM) Model, an overview of 14 interviews that informed it, and preliminary analysis of the factors that guide VOs and Resource Providers (RPs) to choose a particular IdM implementation. This model will serve both existing and future VOs and RPs to more effectively understand and implement their IdM relationships. The Virtual Organization has emerged as a fundamental way of structuring modern scientific collaborations and has shaped the computing infrastructure that supports those collaborations. One key aspect of this infrastructure is identity management, and the emergence of VOs introduces challenges regarding how much of the IdM process should be delegated from the RP to the VO. Many different implementation choices have been made; we conducted semi-structured interviews with 14 different VOs or RPs regarding their IdM choices and the bases behind those decisions. We analyzed the interview results to extract common parameters and values, which we used to inform our VO IdM Model. Copyright © 2013 by The Institute of Electrical and Electronics Engineers, Inc.},
 bibtype = {inproceedings},
 author = {Cowles, Robert and Jackson, Craig and Welch, Von},
 doi = {10.1109/eScience.2013.47},
 booktitle = {2013 IEEE 9th International Conference on e-Science}
}

In this paper we present our Virtual Organization (VO) Identity Management (IdM) Model, an overview of 14 interviews that informed it, and preliminary analysis of the factors that guide VOs and Resource Providers (RPs) to choose a particular IdM implementation. This model will serve both existing and future VOs and RPs to more effectively understand and implement their IdM relationships. The Virtual Organization has emerged as a fundamental way of structuring modern scientific collaborations and has shaped the computing infrastructure that supports those collaborations. One key aspect of this infrastructure is identity management, and the emergence of VOs introduces challenges regarding how much of the IdM process should be delegated from the RP to the VO. Many different implementation choices have been made; we conducted semi-structured interviews with 14 different VOs or RPs regarding their IdM choices and the bases behind those decisions. We analyzed the interview results to extract common parameters and values, which we used to inform our VO IdM Model. Copyright © 2013 by The Institute of Electrical and Electronics Engineers, Inc.

@techreport{
 title = {Globus Online Security Review},
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@techreport{
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@article{
 title = {PRIVACY, CONSUMER CREDIT, AND THE},
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@article{
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@article{
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@techreport{
 title = {Security at the Cyber Border: Exploring Cybersecurity for International Research Network Connections},
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@article{
 title = {The End of the Beginning},
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 doi = {https://doi.org/10.1093/idpl/ips012},
 journal = {International Data Privacy Law},
 number = {3}
}

@article{
 title = {The Intricacies of Independence},
 type = {article},
 year = {2012},
 pages = {1-2},
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 doi = {https://doi.org/10.1093/idpl/ipr021},
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@techreport{
 title = {OSG DigiCert Pilot Report},
 type = {techreport},
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@techreport{
 title = {A roadmap for using NSF cyberinfrastructure with InCommon},
 type = {techreport},
 year = {2011},
 websites = {http://hdl.handle.net/2022/13024},
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@inproceedings{
 title = {Cyberinfrastructure Usage Modalities on the TeraGrid},
 type = {inproceedings},
 year = {2011},
 keywords = {Component,Cyber infrastructures,Distributed parameter networks,Production grid},
 pages = {932-939},
 websites = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-83455229513&doi=10.1109%2FIPDPS.2011.239&partnerID=40&md5=1e102f58325dedaab0719725dcafbc9a,http://ieeexplore.ieee.org/document/6008940/},
 month = {5},
 publisher = {IEEE},
 city = {Anchorage, AK},
 id = {30b2e756-97ff-378d-8183-50baec2c7fdf},
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 citation_key = {Katz2011932},
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 notes = {cited By 7; Conference of 25th IEEE International Parallel and Distributed Processing Symposium, Workshops and Phd Forum, IPDPSW 2011 ; Conference Date: 16 May 2011 Through 20 May 2011; Conference Code:87731},
 private_publication = {false},
 abstract = {This paper is intended to explain how the TeraGrid would like to be able to measure "usage modalities." We would like to (and are beginning to) measure these modalities to understand what objectives our users are pursuing, how they go about achieving them, and why, so that we can make changes in the TeraGrid to better support them. © 2011 IEEE.},
 bibtype = {inproceedings},
 author = {Katz, Daniel S and Hart, David and Jordan, Chris and Majumdar, Amit and Navarro, J.P. and Smith, Warren and Towns, John and Welch, Von and Wilkins-Diehr, Nancy},
 doi = {10.1109/IPDPS.2011.239},
 booktitle = {Proceedings of the 2011 IEEE International Symposium on Parallel and Distributed Processing Workshops and PhD Forum (IPDPSW '11)}
}

This paper is intended to explain how the TeraGrid would like to be able to measure "usage modalities." We would like to (and are beginning to) measure these modalities to understand what objectives our users are pursuing, how they go about achieving them, and why, so that we can make changes in the TeraGrid to better support them. © 2011 IEEE.

@techreport{
 title = {Indiana University's Advanced Cyberinfrastructure},
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@article{
 title = {Let's Not Kill All the Privacy Laws (and Lawyers)},
 type = {article},
 year = {2011},
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@article{
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@inproceedings{
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The "Roadmap for Using NSF Cyberinfrastructure with InCommon" provides an in-depth discussion of benefits, challenges and practices for using the InCommon identity federation with National Science Foundation (NSF) cyberinfrastructure. In this abstract, we provide a summary of the Roadmap, the complete version of which can be found online [1]. © 2011 Authors.

@article{
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@article{
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@inproceedings{
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Running simulations for multi-cell tissue models can involve numerous parameters and consume considerable computing resources. This paper presents an overview and use case of two open source projects - CompuCell3D, a multi-cell modeling framework, and VisTrails, a workflow system for parameter exploration and data management.

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TeraGrid is a national-scale computational science facility supported through a partnership among thirteen institutions, with funding from the US National Science Foundation [1]. Initially created through a Major Research Equipment Facilities Construction (MREFC [2] ) award in 2001, the TeraGrid facility began providing production computing, storage, visualization, and data collections services to the national science, engineering, and education community in January 2004. In August 2005 NSF funded a five-year program to operate, enhance, and expand the capacity and capabilities of the TeraGrid facility to meet the growing needs of the science and engineering community through 2010. This paper describes TeraGrid in terms of the structures, architecture, technologies, and services that are used to provide national-scale, open cyberinfrastructure. The focus of the paper is specifically on the technology approach and use of middleware for the purposes of discussing the impact of such approaches on scientific use of computational infrastructure. While there are many individual science success stories, we do not focus on these in this paper. Similarly, there are many software tools and systems deployed in TeraGrid but our coverage is of the basic system middleware and is not meant to be exhaustive of all technology efforts within TeraGrid. We look in particular at growth and events during 2006 as the user population expanded dramatically and reached an initial 'tipping point' with respect to adoption of new 'grid' capabilities and usage modalities. © 2008 The authors and IOS Press.

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@techreport{
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 author = {Peebles, Christopher S and Stewart, Craig A and Bernbom, Gerry and McMullen, Donald F and Shankar, Anurag and Samuel, John and Daniels, John and Papakhian, Mary and Hart, David and Walsh, John}
}