@article{
 title = {Ground Deformation Data from GEER Investigations of Ridgecrest Earthquake Sequence},
 type = {article},
 year = {2020},
 month = {2},
 publisher = {Seismological Society of America (SSA)},
 day = {19},
 id = {2a45920a-f82c-30bb-b6fe-71bfa410abd5},
 created = {2020-04-21T21:03:30.152Z},
 accessed = {2020-04-21},
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 last_modified = {2020-04-21T21:03:30.223Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {Following the Ridgecrest earthquake sequence, consisting of an M 6.4 foreshock and M 7.1 mainshock along with many other events, the Geotechnical Extreme Events Reconnaissance association deployed a team to gather perishable data. The team focused their efforts on documenting ground deformations including surface fault rupture south of the Naval Air Weapons Station China Lake, and liquefaction features in Trona and Argus. The team published a report within two weeks of the M 7.1 mainshock. This article presents data products gathered by the team, which are now published and publicly accessible. The data products presented herein include ground-based observations using Global Positioning System trackers, digital cameras, and hand-measuring devices, as well as unmanned aerial vehicle-based imaging products using Structure from Motion to create point clouds and digital surface models. The article describes the data products, as well as tools available for interacting with the products.},
 bibtype = {article},
 author = {Brandenberg, Scott J. and Stewart, Jonathan P. and Wang, Pengfei and Nweke, Chukwuebuka C. and Hudson, Kenneth and Goulet, Christine A. and Meng, Xiaofeng and Davis, Craig A. and Ahdi, Sean K. and Hudson, Martin B. and Donnellan, Andrea and Lyzenga, Gregory and Pierce, Marlon and Wang, Jun and Winters, Maria A. and Delisle, Marie-Pierre and Lucey, Joseph and Kim, Yeulwoo and Gallien, Timu W. and Lyda, Andrew and Yeung, J. Sean and Issa, Omar and Buckreis, Tristan and Yi, Zhengxiang},
 doi = {10.1785/0220190291},
 journal = {Seismological Research Letters}
}

Following the Ridgecrest earthquake sequence, consisting of an M 6.4 foreshock and M 7.1 mainshock along with many other events, the Geotechnical Extreme Events Reconnaissance association deployed a team to gather perishable data. The team focused their efforts on documenting ground deformations including surface fault rupture south of the Naval Air Weapons Station China Lake, and liquefaction features in Trona and Argus. The team published a report within two weeks of the M 7.1 mainshock. This article presents data products gathered by the team, which are now published and publicly accessible. The data products presented herein include ground-based observations using Global Positioning System trackers, digital cameras, and hand-measuring devices, as well as unmanned aerial vehicle-based imaging products using Structure from Motion to create point clouds and digital surface models. The article describes the data products, as well as tools available for interacting with the products.

@inbook{
 type = {inbook},
 year = {2019},
 pages = {157-170},
 websites = {http://services.igi-global.com/resolvedoi/resolve.aspx?doi=10.4018/978-1-5225-7598-6.ch012},
 publisher = {IGI Global},
 city = {Hershey, PA, USA},
 id = {68b708e4-1b2e-35e8-a3fb-75ae09b4a0a5},
 created = {2019-08-15T19:24:16.885Z},
 file_attached = {false},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
 group_id = {0e433c5b-85c4-32aa-851c-c145aac9f80f},
 last_modified = {2019-08-27T14:14:28.997Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {CHAP},
 private_publication = {false},
 abstract = {Computers accelerate our ability to achieve scientific breakthroughs. As technology evolves and new research needs come to light, the role for cyberinfrastructure as “knowledge” infrastructure continues to expand. In essence, cyberinfrastructure can be thought of as the integration of supercomputers, data resources, visualization, and people that extends the impact and utility of information technology. This chapter discusses cyberinfrastructure, the related topics of science gateways and campus bridging, and identifies future challenges and opportunities in cyberinfrastructure.},
 bibtype = {inbook},
 author = {Stewart, Craig A and Knepper, Richard and Link, Matthew R and Pierce, Marlon and Wernert, Eric and Wilkins-Diehr, Nancy},
 editor = {Mehdi Khosrow-Pour, D B A},
 doi = {10.4018/978-1-5225-7598-6.ch012},
 chapter = {Cyberinfrastructure, Cloud Computing, Science Gateways, Visualization, and Cyberinfrastructure Ease of Use},
 title = {Advanced Methodologies and Technologies in Network Architecture, Mobile Computing, and Data Analytics}
}

Computers accelerate our ability to achieve scientific breakthroughs. As technology evolves and new research needs come to light, the role for cyberinfrastructure as “knowledge” infrastructure continues to expand. In essence, cyberinfrastructure can be thought of as the integration of supercomputers, data resources, visualization, and people that extends the impact and utility of information technology. This chapter discusses cyberinfrastructure, the related topics of science gateways and campus bridging, and identifies future challenges and opportunities in cyberinfrastructure.

@inproceedings{
 title = {The USD Science Gateway},
 type = {inproceedings},
 year = {2019},
 pages = {1-4},
 websites = {http://dl.acm.org/citation.cfm?doid=3332186.3333254},
 publisher = {ACM Press},
 city = {New York, New York, USA},
 id = {c138994c-8dc7-3c35-a93a-80a0583037a9},
 created = {2019-08-15T21:24:32.397Z},
 accessed = {2019-08-15},
 file_attached = {true},
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 group_id = {0e433c5b-85c4-32aa-851c-c145aac9f80f},
 last_modified = {2019-09-12T17:32:38.345Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {Science Gateways are virtual environments that accelerate scientific discovery by enabling scientific communities to more easily and effectively utilize distributed computing and data resources. Successful Science Gateways provide access to sophisticated and powerful resources, while shielding their users from the underlying complexities. Here we present updated work completed by the University of South Dakota (USD) Research Computing Group in conjunction with the Science Gateways Community Institute (SGCI) [1] and Science Gateways Research Center at Indiana University to set up a Science Gateway to access USD's high-performance computing resources. We also introduce improvements to the system since the previous presentation of our work. These resources are now available to both faculty and students and allow ease of access and use of USD's distributed computing and data resources. The implementation of this gateway project has been multifaceted and has included placement of federated user login, user facilitation and outreach, and integration of USD's cyberinfrastructure resources. We present this project as an example for other research computing groups so that they may learn from our successes and the challenges that we have overcome in providing this user resource. Additionally, this project serves to exemplify the importance of creating a broad user base of research computing infrastructure through the development of alternative user interfaces such as Science Gateways.},
 bibtype = {inproceedings},
 author = {Kleinsasser, Adison A. and Pamidighantam, Sudhakar and Jennewein, Douglas M. and Madison, Joseph D. and Christie, Marcus and Abeysinghe, Eroma and Marru, Suresh and Pierce, Marlon},
 doi = {10.1145/3332186.3333254},
 booktitle = {Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning) - PEARC '19}
}

Science Gateways are virtual environments that accelerate scientific discovery by enabling scientific communities to more easily and effectively utilize distributed computing and data resources. Successful Science Gateways provide access to sophisticated and powerful resources, while shielding their users from the underlying complexities. Here we present updated work completed by the University of South Dakota (USD) Research Computing Group in conjunction with the Science Gateways Community Institute (SGCI) [1] and Science Gateways Research Center at Indiana University to set up a Science Gateway to access USD's high-performance computing resources. We also introduce improvements to the system since the previous presentation of our work. These resources are now available to both faculty and students and allow ease of access and use of USD's distributed computing and data resources. The implementation of this gateway project has been multifaceted and has included placement of federated user login, user facilitation and outreach, and integration of USD's cyberinfrastructure resources. We present this project as an example for other research computing groups so that they may learn from our successes and the challenges that we have overcome in providing this user resource. Additionally, this project serves to exemplify the importance of creating a broad user base of research computing infrastructure through the development of alternative user interfaces such as Science Gateways.

@inproceedings{
 title = {InterACTWEL Science Gateway for Adaptation Planning in Food-Energy-Water Sectors of Local Communities},
 type = {inproceedings},
 year = {2019},
 pages = {1-4},
 publisher = {Association for Computing Machinery (ACM)},
 id = {ba0e9b5b-a3f7-325c-8399-1cb33bbe7104},
 created = {2019-08-19T14:44:39.569Z},
 accessed = {2019-08-19},
 file_attached = {true},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
 group_id = {0e433c5b-85c4-32aa-851c-c145aac9f80f},
 last_modified = {2019-08-27T14:14:28.803Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {Since their inception in mid 2000s, adoption of Science Gateways as interfaces and conduits for digital infrastructure needed in science and engineering research and education has significantly increased. This trend has also driven changes in the types of services and resources that are now being expected from the Science Gateways by a growing group of diverse end users. In this poster, we present a novel Science Gateway, InterACTWEL (Interactive Adaptation and Collaboration Tool for managing Water, Energy and Land), which serves as a research cyberinfrastructure as well as an applied decision support system for adaptive natural resources management in interdependent food, energy, and water sectors. End users of this gateway include not only interdisciplinary technical and social science researchers, but also public and private sectoral stakeholders. The gateway is a collaboration between Oregon State University and Science Gateways Research Center, Pervasive Technology Institute at Indiana University, and is addressing challenges and solutions related to computational services, visualization techniques, advanced software applications, collaboration capabilities, cyber security and privacy, and data repositories unique to food-energy-water sectors and their stakeholders.},
 bibtype = {inproceedings},
 author = {Babbar-Sebens, Meghna and Rivera, Samuel and Abeysinghe, Eroma and Marru, Suresh and Pierce, Marlon and Coulter, Eric and Farahani, Majid and Wannipurage, Dimuthu and Christie, Marcus},
 doi = {10.1145/3332186.3333253},
 booktitle = {Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning) - PEARC '19}
}

Since their inception in mid 2000s, adoption of Science Gateways as interfaces and conduits for digital infrastructure needed in science and engineering research and education has significantly increased. This trend has also driven changes in the types of services and resources that are now being expected from the Science Gateways by a growing group of diverse end users. In this poster, we present a novel Science Gateway, InterACTWEL (Interactive Adaptation and Collaboration Tool for managing Water, Energy and Land), which serves as a research cyberinfrastructure as well as an applied decision support system for adaptive natural resources management in interdependent food, energy, and water sectors. End users of this gateway include not only interdisciplinary technical and social science researchers, but also public and private sectoral stakeholders. The gateway is a collaboration between Oregon State University and Science Gateways Research Center, Pervasive Technology Institute at Indiana University, and is addressing challenges and solutions related to computational services, visualization techniques, advanced software applications, collaboration capabilities, cyber security and privacy, and data repositories unique to food-energy-water sectors and their stakeholders.

@inproceedings{
 title = {LSU Computational System Biology Gateway for Education},
 type = {inproceedings},
 year = {2019},
 pages = {1-4},
 websites = {http://dl.acm.org/citation.cfm?doid=3332186.3333259},
 publisher = {ACM Press},
 city = {New York, New York, USA},
 id = {11ef89c5-a63a-3627-ac30-41371d3e4431},
 created = {2019-08-19T14:45:42.294Z},
 accessed = {2019-08-19},
 file_attached = {true},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
 group_id = {0e433c5b-85c4-32aa-851c-c145aac9f80f},
 last_modified = {2019-09-12T17:32:37.962Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {Science gateways are a mechanism for delivering scientific software as a service, especially when the software requires high performance computing (HPC) resources to run effectively. The existence of a science gateway eliminates the user's need to learn to work with HPC systems and to manage software installations and updates. With well-designed user interfaces, users can more quickly become effective users of scientific applications and can manage information needed for replicating, modifying, and sharing results. All of these efficiency gains enable users to focus more on their research. In addition, science gateways are being identified as an effective educational tool, a tool to be used in classroom environments as a method to get students quickly into research on domain specific questions. In the absence of a science gateway, students are likely to need a considerable time to learn to work with HPC systems, and any time spent on such will reduce their time on the actual science. This poster presents how the Louisiana State University (LSU) gateway for the Computational System Biology Group (CSBG) - (www.brylinski.org) was updated and improved to be a classroom teaching tool. This work makes extensive use of Apache Airavata's group management capabilities.},
 bibtype = {inproceedings},
 author = {Abeysinghe, Eroma and Brylinski, Michal and Christie, Marcus and Marru, Suresh and Pierce, Marlon},
 doi = {10.1145/3332186.3333259},
 booktitle = {Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning) - PEARC '19}
}

Science gateways are a mechanism for delivering scientific software as a service, especially when the software requires high performance computing (HPC) resources to run effectively. The existence of a science gateway eliminates the user's need to learn to work with HPC systems and to manage software installations and updates. With well-designed user interfaces, users can more quickly become effective users of scientific applications and can manage information needed for replicating, modifying, and sharing results. All of these efficiency gains enable users to focus more on their research. In addition, science gateways are being identified as an effective educational tool, a tool to be used in classroom environments as a method to get students quickly into research on domain specific questions. In the absence of a science gateway, students are likely to need a considerable time to learn to work with HPC systems, and any time spent on such will reduce their time on the actual science. This poster presents how the Louisiana State University (LSU) gateway for the Computational System Biology Group (CSBG) - (www.brylinski.org) was updated and improved to be a classroom teaching tool. This work makes extensive use of Apache Airavata's group management capabilities.

@inproceedings{
 title = {The Distant Reader},
 type = {inproceedings},
 year = {2019},
 pages = {1-4},
 websites = {http://dl.acm.org/citation.cfm?doid=3332186.3333260},
 publisher = {ACM Press},
 city = {New York, New York, USA},
 id = {b60c0c89-d701-3aea-87e8-0cc135bf5119},
 created = {2019-08-19T14:46:24.989Z},
 accessed = {2019-08-19},
 file_attached = {true},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
 group_id = {0e433c5b-85c4-32aa-851c-c145aac9f80f},
 last_modified = {2019-09-12T18:48:08.623Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {The Distant Reader science gateway can be used to automatically create and analyze text corpora at a scale of thousands of user-supplied documents. These processing steps are deployed on a dynamic virtual cluster deployed on XSEDE's Jetstream academic cloud computing resource and are accessed through a Web interface. The science gateway uses Apache Airavata middleware to manage the interactions between the Web interface and the virtual clusters. The gateway leverages the Science Gateway Platform as a service (SciGaP) infrastructure at Indiana University, which provides user authentication, authorization, and identity management as well as access to the Distant Reader tools. The Distant Reader is designed to assist in the process of using & understanding corpora -- reading.},
 bibtype = {inproceedings},
 author = {Morgan, Eric Lease and Abeysinghe, Eroma and Pamidighantam, Sudhkar and Coulter, Eric and Marru, Suresh and Pierce, Marlon},
 doi = {10.1145/3332186.3333260},
 booktitle = {Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning) - PEARC '19}
}

The Distant Reader science gateway can be used to automatically create and analyze text corpora at a scale of thousands of user-supplied documents. These processing steps are deployed on a dynamic virtual cluster deployed on XSEDE's Jetstream academic cloud computing resource and are accessed through a Web interface. The science gateway uses Apache Airavata middleware to manage the interactions between the Web interface and the virtual clusters. The gateway leverages the Science Gateway Platform as a service (SciGaP) infrastructure at Indiana University, which provides user authentication, authorization, and identity management as well as access to the Distant Reader tools. The Distant Reader is designed to assist in the process of using & understanding corpora -- reading.

@inproceedings{
 title = {How the Science Gateways Community Institute Supports Those Who Are Creating Websites to Access Shared Resources},
 type = {inproceedings},
 year = {2019},
 pages = {1-4},
 websites = {http://dl.acm.org/citation.cfm?doid=3332186.3333256},
 publisher = {ACM Press},
 city = {New York, New York, USA},
 id = {5ea41de6-b05a-3a41-b8a6-6b45c1bb2744},
 created = {2019-08-19T14:51:27.240Z},
 accessed = {2019-08-19},
 file_attached = {true},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
 group_id = {0e433c5b-85c4-32aa-851c-c145aac9f80f},
 last_modified = {2019-09-12T18:48:09.005Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {The Science Gateways Community Institute (SGCI) serves the gateway community with free, NSF-funded resources, services, experts, and ideas. Our community shares expertise, technologies, and best practices for creating and sustaining gateways. Gateways offer Web-based access to shared resources, including data, software, computing services, instruments, and educational materials. Gateways are also known by other names, including portals, virtual research environments or virtual labs, eScience, and research cyberinfrastructure.},
 bibtype = {inproceedings},
 author = {Lawrence, Katherine A. and Mullinix, Nayiri and Dahan, Maytal and Hayden, Linda and Pierce, Marlon and Wilkins-Diehr, Nancy and Zentner, Michael},
 doi = {10.1145/3332186.3333256},
 booktitle = {Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning) - PEARC '19}
}

The Science Gateways Community Institute (SGCI) serves the gateway community with free, NSF-funded resources, services, experts, and ideas. Our community shares expertise, technologies, and best practices for creating and sustaining gateways. Gateways offer Web-based access to shared resources, including data, software, computing services, instruments, and educational materials. Gateways are also known by other names, including portals, virtual research environments or virtual labs, eScience, and research cyberinfrastructure.

@article{
 title = {Community Organizations: Changing the Culture in Which Research Software Is Developed and Sustained},
 type = {article},
 year = {2019},
 keywords = {research software,scientific software,software community culture,software ecosystems,software productivity,software sustainability},
 pages = {8-24},
 volume = {21},
 websites = {https://ieeexplore.ieee.org/document/8565942/},
 month = {3},
 publisher = {IEEE Computer Society},
 day = {1},
 id = {71823032-4391-33bf-ae13-ed8e7c40569f},
 created = {2019-08-19T15:22:10.293Z},
 accessed = {2019-08-19},
 file_attached = {true},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
 group_id = {0e433c5b-85c4-32aa-851c-c145aac9f80f},
 last_modified = {2019-09-12T18:48:08.636Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {Software is the key crosscutting technology that enables advances in mathematics, computer science, and domain-specific science and engineering to achieve robust simulations and analysis for science, engineering, and other research fields. However, software itself has not traditionally received focused attention from research communities; rather, software has evolved organically and inconsistently, with its development largely as by-products of other initiatives. Moreover, challenges in scientific software are expanding due to disruptive changes in computer hardware, increasing scale and complexity of data, and demands for more complex simulations involving multiphysics, multiscale modeling and outer-loop analysis. In recent years, community members have established a range of grass-roots organizations and projects to address these growing technical and social challenges in software productivity, quality, reproducibility, and sustainability. This article provides an overview of such groups and discusses opportunities to leverage their synergistic activities while nurturing work toward emerging software ecosystems.},
 bibtype = {article},
 author = {Katz, Daniel S. and McInnes, Lois Curfman and Bernholdt, David E. and Mayes, Abigail Cabunoc and Hong, Neil P. Chue and Duckles, Jonah and Gesing, Sandra and Heroux, Michael A. and Hettrick, Simon and Jimenez, Rafael C. and Pierce, Marlon and Weaver, Belinda and Wilkins-Diehr, Nancy},
 doi = {10.1109/MCSE.2018.2883051},
 journal = {Computing in Science & Engineering},
 number = {2}
}

Software is the key crosscutting technology that enables advances in mathematics, computer science, and domain-specific science and engineering to achieve robust simulations and analysis for science, engineering, and other research fields. However, software itself has not traditionally received focused attention from research communities; rather, software has evolved organically and inconsistently, with its development largely as by-products of other initiatives. Moreover, challenges in scientific software are expanding due to disruptive changes in computer hardware, increasing scale and complexity of data, and demands for more complex simulations involving multiphysics, multiscale modeling and outer-loop analysis. In recent years, community members have established a range of grass-roots organizations and projects to address these growing technical and social challenges in software productivity, quality, reproducibility, and sustainability. This article provides an overview of such groups and discusses opportunities to leverage their synergistic activities while nurturing work toward emerging software ecosystems.

@inproceedings{
 title = {Research Computing at a Business University},
 type = {inproceedings},
 year = {2019},
 pages = {1-5},
 publisher = {Association for Computing Machinery (ACM)},
 id = {17908b2c-16f9-3745-a995-1d9d03c48950},
 created = {2019-08-19T16:50:48.631Z},
 accessed = {2019-08-19},
 file_attached = {true},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
 group_id = {0e433c5b-85c4-32aa-851c-c145aac9f80f},
 last_modified = {2019-08-27T14:14:29.028Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {Research Computing demands are exploding beyond traditional disciplines due to the proliferation of data in all walks of life. At Bentley University ("Bentley"), a business university in the Boston area, this expansion has been most readily seen in our Accounting, Economics, Mathematics, and Natural Sciences departments. The result has been a small effort to build a research computing capability at this small New England university. This poster will serve as an overview of the steps taken to build such an effort at a business university, the revelations we have had along the way, and our plans for the future.},
 bibtype = {inproceedings},
 author = {Wells, Jason and Coulter, J. Eric},
 doi = {10.1145/3332186.3333161},
 booktitle = {Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning) - PEARC '19}
}

Research Computing demands are exploding beyond traditional disciplines due to the proliferation of data in all walks of life. At Bentley University ("Bentley"), a business university in the Boston area, this expansion has been most readily seen in our Accounting, Economics, Mathematics, and Natural Sciences departments. The result has been a small effort to build a research computing capability at this small New England university. This poster will serve as an overview of the steps taken to build such an effort at a business university, the revelations we have had along the way, and our plans for the future.

@inproceedings{
 title = {Beyond Campus Bridging},
 type = {inproceedings},
 year = {2019},
 pages = {1-4},
 websites = {http://dl.acm.org/citation.cfm?doid=3332186.3333151},
 publisher = {ACM Press},
 city = {New York, New York, USA},
 id = {c9b96599-b872-3426-b97d-47210e617484},
 created = {2019-08-19T16:51:48.136Z},
 accessed = {2019-08-19},
 file_attached = {true},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
 group_id = {0e433c5b-85c4-32aa-851c-c145aac9f80f},
 last_modified = {2019-09-24T19:53:51.182Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {An abstract is not available},
 bibtype = {inproceedings},
 author = {Coulter, J. Eric and Knepper, Rich and Reynolds, Resa and Sprouse, Jodie and Bird, Stephen},
 doi = {10.1145/3332186.3333151},
 booktitle = {Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning) - PEARC '19}
}

An abstract is not available

@article{
 title = {Science gateways: Sustainability via on-campus teams},
 type = {article},
 year = {2019},
 keywords = {On-campus groups,Science gateways,Science gateways community institute,Sustainability},
 pages = {97-102},
 volume = {94},
 websites = {https://linkinghub.elsevier.com/retrieve/pii/S0167739X18315395},
 month = {5},
 publisher = {Elsevier B.V.},
 day = {1},
 id = {324294eb-9887-3070-99e2-86744731308e},
 created = {2019-08-19T17:09:24.076Z},
 accessed = {2019-08-19},
 file_attached = {true},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
 group_id = {0e433c5b-85c4-32aa-851c-c145aac9f80f},
 last_modified = {2019-09-12T17:56:21.544Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {The challenges for creators of specific science gateways are manifold, and the expertise needed for well-designed science gateways is very diverse. The sustainability of science gateways is crucial to serve communities effectively, efficiently and reliably. One measure to achieve greater sustainability of science gateways is establishing on-campus teams. Researchers are served more efficiently since the support by experienced developers reduces individual project investments, and a team can bring the diversity of required expertise for a well-designed science gateway. This paper goes into detail about the challenges and the benefits of on-campus groups and of sharing resources across a campus. We provide four successful cases, describe the services of the Science Gateways Community Institute (SGCI) to support the process in building such groups, and recommend strategies for using free campus resources.},
 bibtype = {article},
 author = {Gesing, Sandra and Lawrence, Katherine and Dahan, Maytal and Pierce, Marlon E. and Wilkins-Diehr, Nancy and Zentner, Michael},
 doi = {10.1016/j.future.2018.09.067},
 journal = {Future Generation Computer Systems}
}

The challenges for creators of specific science gateways are manifold, and the expertise needed for well-designed science gateways is very diverse. The sustainability of science gateways is crucial to serve communities effectively, efficiently and reliably. One measure to achieve greater sustainability of science gateways is establishing on-campus teams. Researchers are served more efficiently since the support by experienced developers reduces individual project investments, and a team can bring the diversity of required expertise for a well-designed science gateway. This paper goes into detail about the challenges and the benefits of on-campus groups and of sharing resources across a campus. We provide four successful cases, describe the services of the Science Gateways Community Institute (SGCI) to support the process in building such groups, and recommend strategies for using free campus resources.

@inproceedings{
 title = {Towards a science gateway reference architecture},
 type = {inproceedings},
 year = {2019},
 keywords = {Cyberinfrastructure,Science gateways},
 volume = {2357},
 publisher = {CEUR-WS},
 id = {25e4bc2e-62d7-3af7-937e-d917e442a5b8},
 created = {2019-08-19T17:14:13.768Z},
 accessed = {2019-08-19},
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 last_modified = {2019-08-27T14:14:29.186Z},
 read = {false},
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 confirmed = {true},
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 abstract = {Science gateways have been developed over the last twenty years and have grown into a large community of practice, as evidenced by international workshops and conferences. Because of the diversity of approaches to creating science gateways and the always changing landscape of technologies, the community lacks a common definition for the term " science gateway " itself and common terminology for describing the common components of a gateway architecture. Instead, a wide range of definitions and understandings exist and are used in different communities; this is evident, for example, in discussions whether science gateways are the same as virtual research environments. This paper attempts to address these issues by focusing on how science gateways support scientific research and considering the consequences on cyberinfrastructure.},
 bibtype = {inproceedings},
 author = {Pierce, Marlon E. and Miller, Mark A. and Brookes, Emre H. and Wong, Mona and Afgan, Enis and Liu, Yan and Gesing, Sandra and Dahan, Maytal and Walker, Tony and Marru, Suresh},
 booktitle = {CEUR Workshop Proceedings}
}

Science gateways have been developed over the last twenty years and have grown into a large community of practice, as evidenced by international workshops and conferences. Because of the diversity of approaches to creating science gateways and the always changing landscape of technologies, the community lacks a common definition for the term " science gateway " itself and common terminology for describing the common components of a gateway architecture. Instead, a wide range of definitions and understandings exist and are used in different communities; this is evident, for example, in discussions whether science gateways are the same as virtual research environments. This paper attempts to address these issues by focusing on how science gateways support scientific research and considering the consequences on cyberinfrastructure.

@inproceedings{
 title = {Experiences from scaling scale Science Gateway operations},
 type = {inproceedings},
 year = {2019},
 pages = {1-4},
 websites = {http://dl.acm.org/citation.cfm?doid=3332186.3333159},
 publisher = {ACM Press},
 city = {New York, New York, USA},
 id = {940bfc86-7f4a-3031-8906-6400609541f0},
 created = {2019-09-12T14:52:51.712Z},
 accessed = {2019-09-12},
 file_attached = {true},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
 group_id = {0e433c5b-85c4-32aa-851c-c145aac9f80f},
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 abstract = {Science gateways are distributed computing systems that provide science-centric, end-user environments that simplify and expand the use of scientific software and data on diverse scientific software on backend resources. In this poster we describe the experiences of using a common software platform to host "Software as a Service" Science Gateways.},
 bibtype = {inproceedings},
 author = {Marru, Suresh and Piece, Marlon and Abeysinghe, Eroma and Pamidighantam, Sudhakar and Christie, Marcus and Wannipurage, Dimuthu},
 doi = {10.1145/3332186.3333159},
 booktitle = {Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning) - PEARC '19}
}

Science gateways are distributed computing systems that provide science-centric, end-user environments that simplify and expand the use of scientific software and data on diverse scientific software on backend resources. In this poster we describe the experiences of using a common software platform to host "Software as a Service" Science Gateways.

@inproceedings{
 title = {Implementing a Flexible, Fault Tolerant Job Management System for Science Gateways},
 type = {inproceedings},
 year = {2019},
 pages = {1-8},
 websites = {http://dl.acm.org/citation.cfm?doid=3332186.3332233},
 publisher = {ACM Press},
 city = {New York, New York, USA},
 id = {d7960396-ea86-374e-8e21-19aff8754c14},
 created = {2019-09-12T15:02:36.044Z},
 accessed = {2019-09-12},
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 abstract = {This paper summarizes our experiences evaluating and deploying a new task execution management system within the open source Apache Airavata framework for science gateways. We base our choices on our operational requirements and experiences running Airavata software as a multi-tenanted production service for multiple gateway clients. Our considerations include integrating semi-independent components, making major upgrades to those components while retaining the system's overall functionality, and choosing between integrating third party and in-house developed components. While we focus on Apache Airavata as the platform for evaluation, our results should be of general interest. After considering the options of extensions to our previous, in-house job management system using Apache Kafka or replacing it with Kubernetes, we ultimately chose Apache Helix, primarily for its ability to execute multiple tasks coupled into directed acyclic graphs. We have integrated this approach into Apache Airavata and have tested extensively over several months with many thousands of jobs, both from our internal throughput testing and operational tests with early adopter science gateway clients. The new system has proven to be at least as reliable as the previous system with the advantages that we now have simplified maintenance, do not need to support an in-house system that required extensive developer training to modify, and can support more sophisticated job execution scenarios.},
 bibtype = {inproceedings},
 author = {Wannipurage, Dimuthu and Marru, Suresh and Piece, Marlon and Abeysinghe, Eroma and Pamidighantam, Sudhakar and Christie, Marcus and Shenoy, Gourav and Dhamnaskar, Ajinkya and Jayathilaka, Lahiru},
 doi = {10.1145/3332186.3332233},
 booktitle = {Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning) - PEARC '19}
}

This paper summarizes our experiences evaluating and deploying a new task execution management system within the open source Apache Airavata framework for science gateways. We base our choices on our operational requirements and experiences running Airavata software as a multi-tenanted production service for multiple gateway clients. Our considerations include integrating semi-independent components, making major upgrades to those components while retaining the system's overall functionality, and choosing between integrating third party and in-house developed components. While we focus on Apache Airavata as the platform for evaluation, our results should be of general interest. After considering the options of extensions to our previous, in-house job management system using Apache Kafka or replacing it with Kubernetes, we ultimately chose Apache Helix, primarily for its ability to execute multiple tasks coupled into directed acyclic graphs. We have integrated this approach into Apache Airavata and have tested extensively over several months with many thousands of jobs, both from our internal throughput testing and operational tests with early adopter science gateway clients. The new system has proven to be at least as reliable as the previous system with the advantages that we now have simplified maintenance, do not need to support an in-house system that required extensive developer training to modify, and can support more sophisticated job execution scenarios.

@inproceedings{
 title = {Towards Run Time Estimation of the Gaussian Chemistry Code for SEAGrid Science Gateway},
 type = {inproceedings},
 year = {2019},
 pages = {1-8},
 websites = {http://dl.acm.org/citation.cfm?doid=3332186.3338101},
 publisher = {ACM Press},
 city = {New York, New York, USA},
 id = {3c9ce98b-b753-3c39-a498-c48fb5d00a72},
 created = {2019-09-12T17:32:23.055Z},
 accessed = {2019-09-12},
 file_attached = {true},
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 abstract = {Accurate estimation of the run time of computational codes has a number of significant advantages for scientific computing. It is required information for optimal resource allocation, improving turnaround times and utilization of science gateways. Furthermore, it allows users to better plan and schedule their research, streamlining workflows and improving the overall productivity of cyberinfrastructure. Predicting run time is challenging, however. The inputs to scientific codes can be complex and high dimensional. Their relationship to the run time may be highly non-linear, and, in the most general case is completely arbitrary and thus unpredictable (i.e., simply a random mapping from inputs to run time). Most codes are not so arbitrary, however, and there has been significant prior research on predicting the run time of applications and workloads. Such predictions are generally application-specific, however. In this paper, we focus on the Gaussian computational chemistry code. We characterize a data set of runs from the SEAGrid science gateway with a number of different studies. We also explore a number of different potential regression methods and present promising future directions.},
 bibtype = {inproceedings},
 author = {Beltre, Angel and Zaman, Shehtab and Chiu, Kenneth and Pamidighantam, Sudhakar and Qiao, Xingye and Govindaraju, Madhusudhan},
 doi = {10.1145/3332186.3338101},
 booktitle = {Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning) - PEARC '19}
}

Accurate estimation of the run time of computational codes has a number of significant advantages for scientific computing. It is required information for optimal resource allocation, improving turnaround times and utilization of science gateways. Furthermore, it allows users to better plan and schedule their research, streamlining workflows and improving the overall productivity of cyberinfrastructure. Predicting run time is challenging, however. The inputs to scientific codes can be complex and high dimensional. Their relationship to the run time may be highly non-linear, and, in the most general case is completely arbitrary and thus unpredictable (i.e., simply a random mapping from inputs to run time). Most codes are not so arbitrary, however, and there has been significant prior research on predicting the run time of applications and workloads. Such predictions are generally application-specific, however. In this paper, we focus on the Gaussian computational chemistry code. We characterize a data set of runs from the SEAGrid science gateway with a number of different studies. We also explore a number of different potential regression methods and present promising future directions.

@inproceedings{
 title = {Virtual Clusters in the Jetstream Cloud},
 type = {inproceedings},
 year = {2019},
 pages = {1-6},
 websites = {http://dl.acm.org/citation.cfm?doid=3355738.3355752},
 publisher = {ACM Press},
 city = {New York, New York, USA},
 id = {54b66bc6-cf93-37d4-80f4-d1cf6ef1458f},
 created = {2019-09-24T19:28:18.895Z},
 accessed = {2019-09-24},
 file_attached = {true},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
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 last_modified = {2019-09-24T19:53:51.173Z},
 read = {false},
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 abstract = {We discuss our work providing resources for batch computing via the Jetstream cloud, in the form of SLURM clusters. While these are mainly used by science gateways, there have been a few used in the more traditional commandline manner. The flexible nature of these has also lent itself well to educational work, and has provided the basis for a very successful series of tutorials and workshops. This paper discusses the technical evolution of the Virtual Cluster product, and gives an overview of the science enabled. We discuss the challenges in supporting an ecosystem of these virtual clusters, and in supporting research on cloud resources in general.},
 bibtype = {inproceedings},
 author = {Coulter, J. Eric and Abeysinghe, Eroma and Pamidighantam, Sudhakar and Pierce, Marlon},
 doi = {10.1145/3355738.3355752},
 booktitle = {Proceedings of the Humans in the Loop: Enabling and Facilitating Research on Cloud Computing - HARC '19}
}

We discuss our work providing resources for batch computing via the Jetstream cloud, in the form of SLURM clusters. While these are mainly used by science gateways, there have been a few used in the more traditional commandline manner. The flexible nature of these has also lent itself well to educational work, and has provided the basis for a very successful series of tutorials and workshops. This paper discusses the technical evolution of the Virtual Cluster product, and gives an overview of the science enabled. We discuss the challenges in supporting an ecosystem of these virtual clusters, and in supporting research on cloud resources in general.

@article{
 title = {Programmable Education Infrastructure: Cloud resources as HPC Education Environments},
 type = {article},
 year = {2019},
 pages = {107-107},
 volume = {10},
 websites = {http://www.jocse.org/articles/10/1/18/},
 month = {1},
 publisher = {The Shodor Education Foundation, Inc.},
 id = {a110bf64-b3ce-3998-8535-e35d2badac31},
 created = {2019-09-24T19:55:27.980Z},
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 abstract = {Cloud computing is growing area for educating students and per- forming meaningful scientific research. The challenge for many educators and researchers is knowing how to use some of the unique aspects of computing in the cloud. One key feature is true elastic computing - resources on demand. The elasticity and programmability of cloud resources make them an excellent tool for educators who require access to a wide range of computing environments. In the field of HPC education, such environments are an absolute necessity, and getting access to them can create a large burden on the educators above and beyond designing content. While cloud resources won't replace traditional HPC environments for large research projects, they are an excellent option for providing both user and administrator education on HPC environments. The highly configurable nature of cloud environments allows educators to tailor the educational resource to the needs of their attendees, and provide a wide range of hands-on experiences. In this demo, we'll show how the Jetstream cloud environment can be used to provide training for both new HPC administrators and users, by showing a ground-up build of a simple HPC system. While this approach uses the Jetstream cloud, it is generalizable across any cloud provider. We will show how this allows an educator to tackle everything from basic command-line concepts and scheduler use to advanced cluster-management concepts such as elasticity and management of scientific software.},
 bibtype = {article},
 author = {Coulter, Eric and Knepper, Richard and Fischer, Jeremy},
 doi = {10.22369/issn.2153-4136/10/1/18},
 journal = {The Journal of Computational Science Education},
 number = {1}
}

Cloud computing is growing area for educating students and per- forming meaningful scientific research. The challenge for many educators and researchers is knowing how to use some of the unique aspects of computing in the cloud. One key feature is true elastic computing - resources on demand. The elasticity and programmability of cloud resources make them an excellent tool for educators who require access to a wide range of computing environments. In the field of HPC education, such environments are an absolute necessity, and getting access to them can create a large burden on the educators above and beyond designing content. While cloud resources won't replace traditional HPC environments for large research projects, they are an excellent option for providing both user and administrator education on HPC environments. The highly configurable nature of cloud environments allows educators to tailor the educational resource to the needs of their attendees, and provide a wide range of hands-on experiences. In this demo, we'll show how the Jetstream cloud environment can be used to provide training for both new HPC administrators and users, by showing a ground-up build of a simple HPC system. While this approach uses the Jetstream cloud, it is generalizable across any cloud provider. We will show how this allows an educator to tackle everything from basic command-line concepts and scheduler use to advanced cluster-management concepts such as elasticity and management of scientific software.

@article{
 title = {Managing authentication and authorization in distributed science gateway middleware},
 type = {article},
 year = {2019},
 websites = {https://linkinghub.elsevier.com/retrieve/pii/S0167739X18314729},
 month = {10},
 id = {b85f4a0a-e986-3c15-8415-ba33ea5e2c8a},
 created = {2019-10-15T16:21:56.516Z},
 accessed = {2019-10-15},
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 abstract = {Establishing users’ identities and determining their permissions before they access research infrastructure resources are key features of science gateways. With many science gateways now relying on general purpose gateway platform services, the challenges of managing identity-derived features have expanded to include network-based authentication and authorization scenarios that connect science gateway tenants, science gateway platform middleware, and third party identity provider services, including campus identity management systems. This paper examines both architectural and implementation considerations for integrating these services. We provide a summary case study that further shows how end-to-end authentication and authorization can be provided between gateways, campus authentication systems, science gateway middleware, and campus computing resources. We conclude with observations on lifecycle management of third party components in science gateway platform services, which is an important consideration for both selection of new technologies and transitioning from older systems.},
 bibtype = {article},
 author = {Christie, Marcus A. and Bhandar, Anuj and Nakandala, Supun and Marru, Suresh and Abeysinghe, Eroma and Pamidighantam, Sudhakar and Pierce, Marlon E.},
 doi = {10.1016/j.future.2019.07.018},
 journal = {Future Generation Computer Systems}
}

Establishing users’ identities and determining their permissions before they access research infrastructure resources are key features of science gateways. With many science gateways now relying on general purpose gateway platform services, the challenges of managing identity-derived features have expanded to include network-based authentication and authorization scenarios that connect science gateway tenants, science gateway platform middleware, and third party identity provider services, including campus identity management systems. This paper examines both architectural and implementation considerations for integrating these services. We provide a summary case study that further shows how end-to-end authentication and authorization can be provided between gateways, campus authentication systems, science gateway middleware, and campus computing resources. We conclude with observations on lifecycle management of third party components in science gateway platform services, which is an important consideration for both selection of new technologies and transitioning from older systems.

@inproceedings{
 title = {InterACTWEL Science Gateway for Adaptation Planning in Food-Energy-Water Sectors of Local Communities: Data, Methods, Lessons Learned and Future Directions},
 type = {inproceedings},
 year = {2019},
 month = {12},
 publisher = {American Geophysical Union},
 day = {11},
 id = {9c6f1444-6db4-30c6-96a5-819d8e2d71ec},
 created = {2020-04-21T21:06:41.273Z},
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 abstract = {The management of our limited natural resources has become increasingly critical due to climate change and pressures from growing populations. Unfortunately, these problems continue to be aggravated due to the lack of strategic coordination amongst the food, energy, and water (FEW) sectors. InterACTWEL (Interactive Adaptation and Collaboration Tool for managing Water, Energy and Land) is envisioned to be transformational decision support cyberinfrastructure (DSC) with state-of-the-art analytics and visualization capabilities that will empower land, water, energy managers and food producers (i.e., FEW actors) to conceptualize and co-plan towards a resilient future for their local communities. Developed as a novel Science Gateway (ScG), InterACTWEL is aimed to help communities effectively coordinate and identify robust natural resources management decisions over time, and for long-term adaptation to acute or chronic perturbations that they do not have control of (e.g., changing state laws or climatic patterns).
To enable large communities to prepare for an evolving future of changes the development of this flexible, secure and human computation-base DSC required the creation of, access to, and use of complex and multi-sectoral datasets of varying sizes, advanced simulation models, large-scale optimization algorithms, visualization techniques for rendering of complex decision and goal spaces, as well as interfaces that facilitate end-user engagement and cognitive learning. Moreover, since the end users of this gateway include not only interdisciplinary technical and social science researchers, but also public and private sectoral stakeholders (e.g., farmers, energy producers, municipalities, governmental agencies, non-governmental organizations, tribes), the DSC had to support the needs and activities of a diverse personas of end-user. Using the Hermiston region, in Oregon, as a case study, this talk will describe the user base, functionalities, and services included in InterACTWEL. Furthermore, we will share current challenges, lessons learned and future directions of DSC that are intended to improve the adaptation planning and resiliency of local communities by sustaining translational research goals and long-lasting collaboration between researchers and citizens.},
 bibtype = {inproceedings},
 author = {Rivera, Samuel J. and Giles, Nicholas Alan and Tilt, Jenna and Reimer, Jeff and Murthy, Ganti and Mukhopadhyay, Snehasis and Durresi, Arjan and Marru, Suresh and Pierce, Marlon Edwin and Babbar-Sebens, Meghna},
 booktitle = {American Geophysical Union Fall Meeting}
}

The management of our limited natural resources has become increasingly critical due to climate change and pressures from growing populations. Unfortunately, these problems continue to be aggravated due to the lack of strategic coordination amongst the food, energy, and water (FEW) sectors. InterACTWEL (Interactive Adaptation and Collaboration Tool for managing Water, Energy and Land) is envisioned to be transformational decision support cyberinfrastructure (DSC) with state-of-the-art analytics and visualization capabilities that will empower land, water, energy managers and food producers (i.e., FEW actors) to conceptualize and co-plan towards a resilient future for their local communities. Developed as a novel Science Gateway (ScG), InterACTWEL is aimed to help communities effectively coordinate and identify robust natural resources management decisions over time, and for long-term adaptation to acute or chronic perturbations that they do not have control of (e.g., changing state laws or climatic patterns). To enable large communities to prepare for an evolving future of changes the development of this flexible, secure and human computation-base DSC required the creation of, access to, and use of complex and multi-sectoral datasets of varying sizes, advanced simulation models, large-scale optimization algorithms, visualization techniques for rendering of complex decision and goal spaces, as well as interfaces that facilitate end-user engagement and cognitive learning. Moreover, since the end users of this gateway include not only interdisciplinary technical and social science researchers, but also public and private sectoral stakeholders (e.g., farmers, energy producers, municipalities, governmental agencies, non-governmental organizations, tribes), the DSC had to support the needs and activities of a diverse personas of end-user. Using the Hermiston region, in Oregon, as a case study, this talk will describe the user base, functionalities, and services included in InterACTWEL. Furthermore, we will share current challenges, lessons learned and future directions of DSC that are intended to improve the adaptation planning and resiliency of local communities by sustaining translational research goals and long-lasting collaboration between researchers and citizens.

@inproceedings{
 title = {Advancing Access to Global Flood Modeling and Alerting using the PDC DisasterAWARE Platform and Remote Sensing Technologies},
 type = {inproceedings},
 year = {2019},
 month = {12},
 publisher = {AGU},
 day = {9},
 id = {54ad34bd-0b9b-38dc-bf33-b7611b5dded6},
 created = {2020-04-21T21:25:50.160Z},
 accessed = {2020-04-21},
 file_attached = {false},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
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 abstract = {Disaster managers face significant challenges in managing essential information for preparedness, response, and recovery efforts. The development of an open access, global flood alerting system for effective classification of potential impacts and the formulation of effective emergency response measures requires incorporation of a wide variety of flood model and remote sensing (RS) data sources from multiple platforms.
We seek to rapidly classify flood severity and alerts based on the potential for impacts in a way similar to the USGS PAGER impact analysis for earthquakes. The proposed approach is to use a model of models that leverages existing capabilities and products, as well as the incorporation of RS products for ground-truthing model results and delineation of flood areas. The ground-truthing would provide continued adjustment of parameters in the model of models approach. Administrative area resilience indicators for flood affected areas will support incorporation of vulnerability and lack of capacity into rapid assessment of potential impacts.

The work will build on the current DisasterAWARE platform, operated by the Pacific Disaster Center (PDC) and currently providing global multi-hazard alerting and Situational Awareness information to the public. DisasterAWARE supports hazard monitoring and early warning needs of Disaster Managers across the globe, as well as providing the Common Operating Picture in support of US DOD’s humanitarian assistance and disaster response mission. However, the current systems lack global flood alerting or incorporation of a RS component that will allow near real-time validation of simulated flood modeling results.

The use of RS images and derivative products will enable users to validate in near real-time the results of high-resolution simulation modeling outputs to be incorporated into DisasterAWARE, and that are often imported into loss estimation software to quantify disaster impacts. The objective is to integrate and leverage publicly-available global flood modeling sources with available RS platforms (satellite and airborne) to produce a robust and comprehensive platform for flood damage assessment and alerting. This will help communities build their capacity and resilience by rapidly responding to flood impacts.},
 bibtype = {inproceedings},
 author = {Glasscoe, Margaret T and Bausch, Douglas B and Chiesa, Chris and Hampe, Greg and Tiampo, Kristy French and Eguchi, Ronald T and Huyck, Charles K and Pierce, Marlon Edwin and Wang, Jun and Chen, ZhiQiang and Kar, Bandana and Schumann, Guy},
 booktitle = {American Geophysical Union Fall Meeting}
}

Disaster managers face significant challenges in managing essential information for preparedness, response, and recovery efforts. The development of an open access, global flood alerting system for effective classification of potential impacts and the formulation of effective emergency response measures requires incorporation of a wide variety of flood model and remote sensing (RS) data sources from multiple platforms. We seek to rapidly classify flood severity and alerts based on the potential for impacts in a way similar to the USGS PAGER impact analysis for earthquakes. The proposed approach is to use a model of models that leverages existing capabilities and products, as well as the incorporation of RS products for ground-truthing model results and delineation of flood areas. The ground-truthing would provide continued adjustment of parameters in the model of models approach. Administrative area resilience indicators for flood affected areas will support incorporation of vulnerability and lack of capacity into rapid assessment of potential impacts. The work will build on the current DisasterAWARE platform, operated by the Pacific Disaster Center (PDC) and currently providing global multi-hazard alerting and Situational Awareness information to the public. DisasterAWARE supports hazard monitoring and early warning needs of Disaster Managers across the globe, as well as providing the Common Operating Picture in support of US DOD’s humanitarian assistance and disaster response mission. However, the current systems lack global flood alerting or incorporation of a RS component that will allow near real-time validation of simulated flood modeling results. The use of RS images and derivative products will enable users to validate in near real-time the results of high-resolution simulation modeling outputs to be incorporated into DisasterAWARE, and that are often imported into loss estimation software to quantify disaster impacts. The objective is to integrate and leverage publicly-available global flood modeling sources with available RS platforms (satellite and airborne) to produce a robust and comprehensive platform for flood damage assessment and alerting. This will help communities build their capacity and resilience by rapidly responding to flood impacts.

@inproceedings{
 title = {Stakeholder-Driven Adaptation Planning of Food-Energy-Water Nexus in Local Communities},
 type = {inproceedings},
 year = {2019},
 month = {12},
 publisher = {AGU},
 day = {12},
 id = {485ef04f-24b6-3e93-9e08-3a7d4d95c55b},
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 abstract = {For long it has been realized that the complexity in the interconnectedness between humans and the natural environment is an important justification for engaging stakeholders in any natural resource management problem. The same argument can be extended to the management of the food-energy-water (FEW) nexus that requires multiple considerations including the relationship of humans with water, energy, and land resources, and the economic sectors that depend on these resources. Especially, managing the nexus for an uncertain future will require better understanding of how humans respond to diverse stresses and threats, such as climate change impacts, changing political and socio-economic considerations, natural hazards, etc. This understanding can then be used to improve how stakeholder knowledge is formulated into “stakeholder-relevant” mitigation and adaptation decision problems. In this presentation, the process of discovering and formulating an adaptation planning problem for a community of large number of FEW stakeholders is examined in the regions of Umatilla and Morrow counties in Oregon. Discovery of the FEW nexus adaptation problem was accomplished via co-production of knowledge, involving researchers and community stakeholders. The iterative process of discovery was then used to formulate and validate a conceptual model of how the community’s FEW nexus would adapt to changes in water rights and availability in the region. The conceptual model was validated using stakeholder engagement, before the model was quantified using hierarchical decision approaches and integrated within a novel cyberinfrastructure, InterACTWEL (Interactive Adaptation and Collaboration Tool for managing Water, Energy and Land).},
 bibtype = {inproceedings},
 author = {Babbar-Sebens, Meghna and Rivera, Samuel J. and Giles, Nicholas Alan and Tilt, Jenna and Reimer, Jeff and Murthy, Ganti and Mukhopadhyay, Snehasis and Durresi, Arjan and Marru, Suresh and Pierce, Marlon Edwin},
 booktitle = {American Geophysical Union Fall Meeting}
}

For long it has been realized that the complexity in the interconnectedness between humans and the natural environment is an important justification for engaging stakeholders in any natural resource management problem. The same argument can be extended to the management of the food-energy-water (FEW) nexus that requires multiple considerations including the relationship of humans with water, energy, and land resources, and the economic sectors that depend on these resources. Especially, managing the nexus for an uncertain future will require better understanding of how humans respond to diverse stresses and threats, such as climate change impacts, changing political and socio-economic considerations, natural hazards, etc. This understanding can then be used to improve how stakeholder knowledge is formulated into “stakeholder-relevant” mitigation and adaptation decision problems. In this presentation, the process of discovering and formulating an adaptation planning problem for a community of large number of FEW stakeholders is examined in the regions of Umatilla and Morrow counties in Oregon. Discovery of the FEW nexus adaptation problem was accomplished via co-production of knowledge, involving researchers and community stakeholders. The iterative process of discovery was then used to formulate and validate a conceptual model of how the community’s FEW nexus would adapt to changes in water rights and availability in the region. The conceptual model was validated using stakeholder engagement, before the model was quantified using hierarchical decision approaches and integrated within a novel cyberinfrastructure, InterACTWEL (Interactive Adaptation and Collaboration Tool for managing Water, Energy and Land).

@inproceedings{
 title = {CyberWater—An open and sustainable framework for diverse data and model integration},
 type = {inproceedings},
 year = {2019},
 month = {12},
 publisher = {AGU},
 day = {9},
 id = {bc0ec2aa-3e2b-323c-bf47-e67552a9851c},
 created = {2020-04-21T22:35:26.829Z},
 accessed = {2020-04-21},
 file_attached = {false},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
 group_id = {0e433c5b-85c4-32aa-851c-c145aac9f80f},
 last_modified = {2020-04-21T22:37:08.627Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {To tackle fundamental scientific questions regarding health, resilience and sustainability of water resources which encompass hydrological, biological, environmental, atmospheric, and other geosciences that define the Earth system, researchers need to be able to easily access diverse data sources and to also effectively incorporate these data into heterogeneous models. Furthermore, models need to be easily integrated, and many models require supercomputing power to run. To address these cyberinfrastructure challenges, a new sustainable and easy-to-use Open Data and Open Modeling framework called CyberWater is currently under development, which is a collaborative NSF-funded project among University of Pittsburgh, IUPUI/IU, CUAHSI, University of Iowa, NC State University, and Ball State University. CyberWater addresses the challenges of accessing heterogeneous data sources via the Open Data architecture which adopts a common internal data model and representation to facilitate the integration of various external data sources. Data Agents are used to handle remote data access protocols, metadata standards, and source-specific implementations. The Open Modeling architecture allows different models to be easily integrated into CyberWater via Model Agents. CyberWater adopts a graphical scientific workflow system (VisTrails) and offers generic tools to help users develop model agents without coding.
At present, CyberWater can run a land surface model (LSM) of Variability Infiltration Capacity (VIC) model and a hydrological model of Distributed Hydrology Soil Vegetation Model (DHSVM), and let the user to easily couple an LSM with a routing model. Examples will be presented to illustrate the CyberWater system via the automatic flow from accessing data to model simulation results in a user-friendly workflow-controlled environment. A diverse set of new tools such as spatial and temporal transformations, GIS-related analyses, and high performance computing is under development. All of the current and future functionalities of CyberWater will not only be thoroughly tested and evaluated by the development team but also by the water community. The CyberWater is aimed for the next generation of open data and modeling framework in cyberinfrastructure for broad earth science communities.},
 bibtype = {inproceedings},
 author = {Luna, Daniel and Chen, Ranran and Yuan, Cao and Liang, Yao and Liang, Xu and Bales, Jerad and Castronova, Anthony M and Demir, Ibrahim and Hooper, Richard P and Krajewski, Witold F and Lin, Lan and Mantilla, Ricardo and Pamidighantam, Sudhakar and Song, Fengguang and Zhang, Yang},
 booktitle = {American Geophysical Union Fall Meeting}
}

To tackle fundamental scientific questions regarding health, resilience and sustainability of water resources which encompass hydrological, biological, environmental, atmospheric, and other geosciences that define the Earth system, researchers need to be able to easily access diverse data sources and to also effectively incorporate these data into heterogeneous models. Furthermore, models need to be easily integrated, and many models require supercomputing power to run. To address these cyberinfrastructure challenges, a new sustainable and easy-to-use Open Data and Open Modeling framework called CyberWater is currently under development, which is a collaborative NSF-funded project among University of Pittsburgh, IUPUI/IU, CUAHSI, University of Iowa, NC State University, and Ball State University. CyberWater addresses the challenges of accessing heterogeneous data sources via the Open Data architecture which adopts a common internal data model and representation to facilitate the integration of various external data sources. Data Agents are used to handle remote data access protocols, metadata standards, and source-specific implementations. The Open Modeling architecture allows different models to be easily integrated into CyberWater via Model Agents. CyberWater adopts a graphical scientific workflow system (VisTrails) and offers generic tools to help users develop model agents without coding. At present, CyberWater can run a land surface model (LSM) of Variability Infiltration Capacity (VIC) model and a hydrological model of Distributed Hydrology Soil Vegetation Model (DHSVM), and let the user to easily couple an LSM with a routing model. Examples will be presented to illustrate the CyberWater system via the automatic flow from accessing data to model simulation results in a user-friendly workflow-controlled environment. A diverse set of new tools such as spatial and temporal transformations, GIS-related analyses, and high performance computing is under development. All of the current and future functionalities of CyberWater will not only be thoroughly tested and evaluated by the development team but also by the water community. The CyberWater is aimed for the next generation of open data and modeling framework in cyberinfrastructure for broad earth science communities.

@article{
 title = {Gathering requirements for advancing simulations in HPC infrastructures via science gateways},
 type = {article},
 year = {2018},
 pages = {544-554},
 volume = {82},
 publisher = {Elsevier},
 id = {3f281b57-92d2-34e3-bd76-a786fee1e57b},
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 bibtype = {article},
 author = {Gesing, Sandra and Dooley, Rion and Pierce, Marlon and Krüger, Jens and Grunzke, Richard and Herres-Pawlis, Sonja and Hoffmann, Alexander},
 journal = {Future Generation Computer Systems}
}

@inbook{
 type = {inbook},
 year = {2018},
 pages = {101-116},
 publisher = {Springer},
 id = {52b9887d-2a6c-3c0f-b28f-4c33b6de52f7},
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 source_type = {CHAP},
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 bibtype = {inbook},
 author = {Parker, Jay and Glasscoe, Margaret and Donnellan, Andrea and Stough, Timothy and Pierce, Marlon and Wang, Jun},
 chapter = {Radar Determination of Fault Slip and Location in Partially Decorrelated Images},
 title = {Earthquakes and Multi-hazards Around the Pacific Rim, Vol. I}
}

@inproceedings{
 title = {A New Science Gateway to Provide Decision Support on Carbon Capture and Storage Technologies},
 type = {inproceedings},
 year = {2018},
 keywords = {Carbon capture,Science gateways},
 pages = {1-3},
 websites = {http://doi.acm.org/10.1145/3219104.3229244,http://dl.acm.org/citation.cfm?doid=3219104.3229244},
 publisher = {ACM Press},
 city = {New York, New York, USA},
 series = {PEARC '18},
 id = {70898097-a46c-32c2-82a2-902971b9ada9},
 created = {2018-08-09T16:38:15.107Z},
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 last_modified = {2019-09-12T17:32:38.312Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Wang:2018:NSG:3219104.3229244},
 source_type = {inproceedings},
 private_publication = {false},
 abstract = {Carbon dioxide capture and storage (CCS) is a promising technology for mitigating climate change, and its implementation is considered critical to meeting threshold targets for global warming in the 21st century. We have developed a new science gateway application for the successful modeling software known as SimCCS that is used for evaluating complex, integrated CCS infrastructure. Using the Apache Airavata middleware and high-performance computing resources made available by the Extreme Science and Engineering Discovery Environment, we built the SimCCS Gateway to expand the tool's scalability for decision support and risk assessment. Case studies developed for evaluating a proposed CCS technology at Duke Energy's Gibson Station coal-fired power plant in southwest Indiana demonstrate its improved ability in data analysis as well as risk assessment at various uncertainty levels. Further work is continuing to expand the functionality of both web and desktop clients, and to develop an active user group community in research and industry via the SimCCS Gateway interface.},
 bibtype = {inproceedings},
 author = {Wang, Yinzhi and Pamidighantam, Sudhakar and Yaw, Sean and Abeysinghe, Eroma and Marru, Suresh and Christie, Marcus and Ellett, Kevin and Pierce, Marlon and Middleton, Richard},
 doi = {10.1145/3219104.3229244},
 booktitle = {Proceedings of the Practice and Experience on Advanced Research Computing - PEARC '18}
}

Carbon dioxide capture and storage (CCS) is a promising technology for mitigating climate change, and its implementation is considered critical to meeting threshold targets for global warming in the 21st century. We have developed a new science gateway application for the successful modeling software known as SimCCS that is used for evaluating complex, integrated CCS infrastructure. Using the Apache Airavata middleware and high-performance computing resources made available by the Extreme Science and Engineering Discovery Environment, we built the SimCCS Gateway to expand the tool's scalability for decision support and risk assessment. Case studies developed for evaluating a proposed CCS technology at Duke Energy's Gibson Station coal-fired power plant in southwest Indiana demonstrate its improved ability in data analysis as well as risk assessment at various uncertainty levels. Further work is continuing to expand the functionality of both web and desktop clients, and to develop an active user group community in research and industry via the SimCCS Gateway interface.

@inproceedings{
 title = {Searching the Sequence Read Archive Using Jetstream and Wrangler},
 type = {inproceedings},
 year = {2018},
 keywords = {Apache Airavata,Bacteriophage,Credential Store,Jetstream,Metagenomics,Metagenomics Discovery Challenge,SRA,SRA Gateway,SciGaP,Search SRA,Sequence Read Archive,Wrangler},
 pages = {50:1--50:7},
 websites = {http://doi.acm.org/10.1145/3219104.3229278},
 publisher = {ACM},
 city = {New York, NY, USA},
 series = {PEARC '18},
 id = {8edab5b8-1e5d-3dcb-9511-f795a75e64ed},
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 last_modified = {2018-08-09T16:38:15.110Z},
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 starred = {false},
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 confirmed = {true},
 hidden = {false},
 citation_key = {Levi:2018:SSR:3219104.3229278},
 source_type = {inproceedings},
 private_publication = {false},
 bibtype = {inproceedings},
 author = {Levi, Kyle and Rynge, Mats and Abeysinghe, Eroma and Edwards, Robert A},
 doi = {10.1145/3219104.3229278},
 booktitle = {Proceedings of the Practice and Experience on Advanced Research Computing}
}

@inproceedings{
 title = {Building a Science Gateway For Processing and Modeling Sequencing Data Via Apache Airavata},
 type = {inproceedings},
 year = {2018},
 keywords = {Apache Airavata,Next Generation Sequencing,Science gateway,cloud computing,sequencing data,software-as-a-service},
 pages = {39:1--39:7},
 websites = {http://doi.acm.org/10.1145/3219104.3219141},
 publisher = {ACM},
 city = {New York, NY, USA},
 series = {PEARC '18},
 id = {f8592a94-44bb-3fd4-82dc-4a8c9863cbcf},
 created = {2018-08-09T16:38:15.119Z},
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 last_modified = {2019-08-19T16:28:11.744Z},
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 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Wang:2018:BSG:3219104.3219141},
 source_type = {inproceedings},
 private_publication = {false},
 abstract = {The amount of DNA sequencing data has been exponentially growing during the past decade due to advances in sequencing technology. Processing and modeling large amounts of sequencing data can be computationally intractable for desktop computing platforms. High performance computing (HPC) resources offer advantages in terms of computing power, and can be a general solution to these problems. Using HPCs directly for computational needs requires skilled users who know their way around HPCs and acquiring such skills take time. Science gateways acts as the middle layer between users and HPCs, providing users with the resources to accomplish compute-intensive tasks without requiring specialized expertise. We developed a web-based computing platform for genome biologists by customizing the PHP Gateway for Airavata (PGA) framework that accesses publicly accessible HPC resources via Apache Airavata. This web computing platform takes advantage of the Extreme Science and Engineering Discovery Environment (XSEDE) which provides the resources for gateway development, including access to CPU, GPU, and storage resources. We used this platform to develop a gateway for the dREG algorithm, an online computing tool for finding functional regions in mammalian genomes using nascent RNA sequencing data. The dREG gateway provides its users a free, powerful and user-friendly GPU computing resource based on XSEDE, circumventing the need of specialized knowledge about installation, configuration, and execution on an HPC for biologists. The dREG gateway is available at: https://dREG.dnasequence.org/.},
 bibtype = {inproceedings},
 author = {Wang, Zhong and Christie, Marcus A and Abeysinghe, Eroma and Chu, Tinyi and Marru, Suresh and Pierce, Marlon and Danko, Charles G},
 doi = {10.1145/3219104.3219141},
 booktitle = {Proceedings of the Practice and Experience on Advanced Research Computing (PEARC '18)}
}

The amount of DNA sequencing data has been exponentially growing during the past decade due to advances in sequencing technology. Processing and modeling large amounts of sequencing data can be computationally intractable for desktop computing platforms. High performance computing (HPC) resources offer advantages in terms of computing power, and can be a general solution to these problems. Using HPCs directly for computational needs requires skilled users who know their way around HPCs and acquiring such skills take time. Science gateways acts as the middle layer between users and HPCs, providing users with the resources to accomplish compute-intensive tasks without requiring specialized expertise. We developed a web-based computing platform for genome biologists by customizing the PHP Gateway for Airavata (PGA) framework that accesses publicly accessible HPC resources via Apache Airavata. This web computing platform takes advantage of the Extreme Science and Engineering Discovery Environment (XSEDE) which provides the resources for gateway development, including access to CPU, GPU, and storage resources. We used this platform to develop a gateway for the dREG algorithm, an online computing tool for finding functional regions in mammalian genomes using nascent RNA sequencing data. The dREG gateway provides its users a free, powerful and user-friendly GPU computing resource based on XSEDE, circumventing the need of specialized knowledge about installation, configuration, and execution on an HPC for biologists. The dREG gateway is available at: https://dREG.dnasequence.org/.

@inproceedings{
 title = {Simplifying Access to Campus Resources at Southern Illinois University with a Science Gateway},
 type = {inproceedings},
 year = {2018},
 keywords = {Apache Airavata,MaSuRCA,Science Gateway},
 pages = {1-4},
 websites = {http://doi.acm.org/10.1145/3219104.3229252,http://dl.acm.org/citation.cfm?doid=3219104.3229252},
 publisher = {ACM Press},
 city = {New York, New York, USA},
 series = {PEARC '18},
 id = {02e6cd41-a400-3b0e-a640-388e686f16a0},
 created = {2018-08-09T16:38:15.123Z},
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 last_modified = {2019-09-12T18:48:08.844Z},
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 confirmed = {true},
 hidden = {false},
 citation_key = {Sunkara:2018:SAC:3219104.3229252},
 source_type = {inproceedings},
 private_publication = {false},
 abstract = {Not all the researchers are comfortable in using High Performance Computing (HPC) Systems. Southern Illinois University's Office of Information Technology (OIT) Research Computing assists our researchers to get on these systems and use them for their research activities. One such potential use case at SIU involves the group of researchers from Life Sciences who were trying to use MaSuRCA [3], a genome-sequencing tool for their research. Although the leaders of this research are well versed in using BigDog [4](SIU's HPC Cluster), other fellow researchers did have issues in using the cluster for their work. It was time to look for efficient ways of enabling them to use the cluster. We examined using Science Gateways which can help our researchers to use the computational cluster without logging on to a Linux-based HPC system. OIT is currently collaborating with the Science Gateways Research Center at Indiana University (IU) on the use of Apache Airavata [1] as a Science Gateway framework for the MaSuRCA user community at SIU. The IU team members provide hosting and operations for Apache Airavata middleware as part of the SciGaP.org project. IU collaborators also provide a basic science gateway user interface, the PGA. The SIU gateway, although hosted off campus, is integrated with SIU's BigDog cluster.},
 bibtype = {inproceedings},
 author = {Sunkara, Sai Susheel and Langin, Chet and Pierce, Marlon and Abeysinghe, Eroma and Pamidighantam, Sudhakar and Marru, Suresh},
 doi = {10.1145/3219104.3229252},
 booktitle = {Proceedings of the Practice and Experience on Advanced Research Computing - PEARC '18}
}

Not all the researchers are comfortable in using High Performance Computing (HPC) Systems. Southern Illinois University's Office of Information Technology (OIT) Research Computing assists our researchers to get on these systems and use them for their research activities. One such potential use case at SIU involves the group of researchers from Life Sciences who were trying to use MaSuRCA [3], a genome-sequencing tool for their research. Although the leaders of this research are well versed in using BigDog [4](SIU's HPC Cluster), other fellow researchers did have issues in using the cluster for their work. It was time to look for efficient ways of enabling them to use the cluster. We examined using Science Gateways which can help our researchers to use the computational cluster without logging on to a Linux-based HPC system. OIT is currently collaborating with the Science Gateways Research Center at Indiana University (IU) on the use of Apache Airavata [1] as a Science Gateway framework for the MaSuRCA user community at SIU. The IU team members provide hosting and operations for Apache Airavata middleware as part of the SciGaP.org project. IU collaborators also provide a basic science gateway user interface, the PGA. The SIU gateway, although hosted off campus, is integrated with SIU's BigDog cluster.

@inproceedings{
 title = {Using a Science Gateway to Deliver SimVascular Software As a Service for Classroom Instruction},
 type = {inproceedings},
 year = {2018},
 keywords = {ACM proceedings,Apache Airavata,Science Gateway},
 pages = {102:1--102:4},
 websites = {http://doi.acm.org/10.1145/3219104.3229242},
 publisher = {ACM},
 city = {New York, NY, USA},
 series = {PEARC '18},
 id = {a775d443-7f37-34b9-81a6-d57bb92afd9e},
 created = {2018-08-09T16:38:15.298Z},
 file_attached = {false},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
 group_id = {0e433c5b-85c4-32aa-851c-c145aac9f80f},
 last_modified = {2019-09-12T15:10:39.099Z},
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 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Wilson:2018:USG:3219104.3229242},
 source_type = {inproceedings},
 private_publication = {false},
 abstract = {SimVascular (http://www.simvascular.org) is open source software enabling users to construct image-based, patient-specific anatomic models and perform realistic blood flow simulation useful in disease research, medical device design, and surgical planning. The software consists of two core executables: a front-end application and a flow solver. The front-end application enables users to create patient-specific anatomic models from imaging data, generate finite-element meshes, prescribe boundary conditions, and set up an analysis. The finite-element based blood flow solver utilizes MPI and is massively scalable. SimVascular has been successfully integrated into graduate level courses on cardiovascular modeling at multiple institutions including Stanford, UC Berkeley, Purdue, and Marquette to introduce state-of-the-art modeling to the students and provide a basis for hands-on projects. While the front-end application can be installed and run on a laptop, the flow solver requires high performance computing (HPC) for realistic problem sizes. This provides a significant challenge for instructors as many students are unfamiliar with HPC, and local resources might be limited or difficult to administer. There is also a need to provide user and group management capabilities for courses: students should authenticate using campus credentials, instructors should be able to access students' work, and students' access to computing allocations should be limited. Our poster will detail an Apache Airavata-based science gateway to address these needs. XSEDE's Comet provides the backend computing power. This approach allows the SimVascular team to provision HPC resources and install and maintain the software providing students access at institutions across the country. The science gateway interface provides access to SimVascular's flow solver, while allowing students to use SimVascular's desktop interfaces.},
 bibtype = {inproceedings},
 author = {Wilson, Nathan M and Marru, Suresh and Abeysinghe, Eroma and Christie, Marcus A and Maher, Gabriel D and Updegrove, Adam R and Pierce, Marlon and Marsden, Alison L},
 doi = {10.1145/3219104.3229242},
 booktitle = {Proceedings of the Practice and Experience on Advanced Research Computing}
}

SimVascular (http://www.simvascular.org) is open source software enabling users to construct image-based, patient-specific anatomic models and perform realistic blood flow simulation useful in disease research, medical device design, and surgical planning. The software consists of two core executables: a front-end application and a flow solver. The front-end application enables users to create patient-specific anatomic models from imaging data, generate finite-element meshes, prescribe boundary conditions, and set up an analysis. The finite-element based blood flow solver utilizes MPI and is massively scalable. SimVascular has been successfully integrated into graduate level courses on cardiovascular modeling at multiple institutions including Stanford, UC Berkeley, Purdue, and Marquette to introduce state-of-the-art modeling to the students and provide a basis for hands-on projects. While the front-end application can be installed and run on a laptop, the flow solver requires high performance computing (HPC) for realistic problem sizes. This provides a significant challenge for instructors as many students are unfamiliar with HPC, and local resources might be limited or difficult to administer. There is also a need to provide user and group management capabilities for courses: students should authenticate using campus credentials, instructors should be able to access students' work, and students' access to computing allocations should be limited. Our poster will detail an Apache Airavata-based science gateway to address these needs. XSEDE's Comet provides the backend computing power. This approach allows the SimVascular team to provision HPC resources and install and maintain the software providing students access at institutions across the country. The science gateway interface provides access to SimVascular's flow solver, while allowing students to use SimVascular's desktop interfaces.

@article{
 title = {Jetstream—Early operations performance, adoption, and impacts},
 type = {article},
 year = {2018},
 keywords = {OpenStack,cloud computing,long tail of science,science impacts,user adoption,virtual machines},
 publisher = {John Wiley and Sons Ltd},
 id = {7deb1933-c2c5-3411-8bdb-ca71043c4d1b},
 created = {2019-08-14T19:53:57.708Z},
 accessed = {2019-08-14},
 file_attached = {true},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
 group_id = {0e433c5b-85c4-32aa-851c-c145aac9f80f},
 last_modified = {2019-08-14T19:53:57.799Z},
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 bibtype = {article},
 author = {Hancock, David Y. and Stewart, Craig A. and Vaughn, Matthew and Fischer, Jeremy and Lowe, John Michael and Turner, George and Swetnam, Tyson L. and Chafin, Tyler K. and Afgan, Enis and Pierce, Marlon E. and Snapp-Childs, Winona},
 doi = {10.1002/cpe.4683},
 journal = {Concurrency Computation }
}

@inproceedings{
 title = {Django Content Management System Evaluation and Integration with Apache Airavata},
 type = {inproceedings},
 year = {2018},
 keywords = {ACM proceedings,Apache Airavata,Django Framework,Science Gateway,Text tagging,Wagtail CMS},
 pages = {1-4},
 websites = {http://dl.acm.org/citation.cfm?doid=3219104.3229272},
 month = {7},
 publisher = {ACM Press},
 day = {22},
 city = {New York, New York, USA},
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 hidden = {false},
 private_publication = {false},
 abstract = {Apache Airavata is an open-source software framework that enables scientific researchers to compose, manage, execute and monitor large-scale applications and workflows on distributed computing resources. Airavata is currently leveraged by many science gateways to perform computations on shared clusters. Currently, Gateway Administrators managing content on their websites will require the assistance of the Airavata Developer Team to make the slightest of change to their website. This paper will overcome this challenge by presenting the benefits of integrating a content management system. It will also briefly evaluate various options available for choosing a Content Management Platform which complies with the Airavata Architecture Standards. This feature will enable researchers with minimal web design knowledge to easily manage content across their gateway. It is also poised to drastically increase the productivity of the Airavata developer team and the gateway administrators. © 2018 Association for Computing Machinery.},
 bibtype = {inproceedings},
 author = {Adithela, Stephen Paul and Christie, Marcus and Marru, Suresh and Pierce, Marlon},
 doi = {10.1145/3219104.3229272},
 booktitle = {Proceedings of the Practice and Experience on Advanced Research Computing - PEARC '18}
}

Apache Airavata is an open-source software framework that enables scientific researchers to compose, manage, execute and monitor large-scale applications and workflows on distributed computing resources. Airavata is currently leveraged by many science gateways to perform computations on shared clusters. Currently, Gateway Administrators managing content on their websites will require the assistance of the Airavata Developer Team to make the slightest of change to their website. This paper will overcome this challenge by presenting the benefits of integrating a content management system. It will also briefly evaluate various options available for choosing a Content Management Platform which complies with the Airavata Architecture Standards. This feature will enable researchers with minimal web design knowledge to easily manage content across their gateway. It is also poised to drastically increase the productivity of the Airavata developer team and the gateway administrators. © 2018 Association for Computing Machinery.

@inproceedings{
 title = {The Science Gateways Community Institute at Two Years},
 type = {inproceedings},
 year = {2018},
 keywords = {Science gateways,Software institutes,Software sustainability},
 pages = {1-8},
 websites = {http://dl.acm.org/citation.cfm?doid=3219104.3219142},
 month = {7},
 publisher = {ACM Press},
 day = {22},
 city = {New York, New York, USA},
 id = {dbac391d-e052-3625-aa14-b565a7e0644e},
 created = {2019-08-19T15:57:41.245Z},
 accessed = {2019-08-19},
 file_attached = {true},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
 group_id = {0e433c5b-85c4-32aa-851c-c145aac9f80f},
 last_modified = {2019-09-12T17:32:38.171Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {The Science Gateways Community Institute was one of the first two software institutes funded by the National Science Foundation's Office of Advanced Cyberinfrastructure in August, 2016. The structure of and services offered by the institute were developed as a result of seven years of planning grants that funded focus groups, a 5000-person survey and the development of a strategic plan. Now two years in, we provide an overview of the institute's service offerings and their usage, reflect on the experiences of some early clients, review our approaches to metrics and evaluation, and describe some lessons learned. We also describe the lightweight, adaptive management approach employed by the institute. SGCI is organized into five service areas: Incubator, Extended Developer Support, Scientific Software Collaborative, Community Engagement and Exchange, and Workforce Development. This paper will highlight early successes in all five areas, from client achievements to conference experiences to our impact on students. We highlight areas where the institute has evolved - based on community feedback - from what was originally envisioned. We describe our use of the Entrepreneurial Operating System as a lightweight management approach for a highly adaptive organization. Finally, we include early plans for the execution phase of the institute. © 2018 Copyright is held by the owner/author(s). Publication rights licensed to ACM.},
 bibtype = {inproceedings},
 author = {Wilkins-Diehr, Nancy and Zentner, Michael and Pierce, Marlon and Dahan, Maytal and Lawrence, Katherine and Hayden, Linda and Mullinix, Nayiri},
 doi = {10.1145/3219104.3219142},
 booktitle = {Proceedings of the Practice and Experience on Advanced Research Computing - PEARC '18}
}

The Science Gateways Community Institute was one of the first two software institutes funded by the National Science Foundation's Office of Advanced Cyberinfrastructure in August, 2016. The structure of and services offered by the institute were developed as a result of seven years of planning grants that funded focus groups, a 5000-person survey and the development of a strategic plan. Now two years in, we provide an overview of the institute's service offerings and their usage, reflect on the experiences of some early clients, review our approaches to metrics and evaluation, and describe some lessons learned. We also describe the lightweight, adaptive management approach employed by the institute. SGCI is organized into five service areas: Incubator, Extended Developer Support, Scientific Software Collaborative, Community Engagement and Exchange, and Workforce Development. This paper will highlight early successes in all five areas, from client achievements to conference experiences to our impact on students. We highlight areas where the institute has evolved - based on community feedback - from what was originally envisioned. We describe our use of the Entrepreneurial Operating System as a lightweight management approach for a highly adaptive organization. Finally, we include early plans for the execution phase of the institute. © 2018 Copyright is held by the owner/author(s). Publication rights licensed to ACM.

@inproceedings{
 title = {Apache Airavata Resource Allocation System: A Tool for Allocating Resources in Science Gateways},
 type = {inproceedings},
 year = {2018},
 pages = {1-4},
 websites = {http://dl.acm.org/citation.cfm?doid=3219104.3229271},
 publisher = {ACM Press},
 city = {New York, New York, USA},
 id = {d3605b73-ba0e-3aa8-b7a2-3d9c24e97eaa},
 created = {2019-08-19T16:01:47.740Z},
 accessed = {2019-08-19},
 file_attached = {true},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
 group_id = {0e433c5b-85c4-32aa-851c-c145aac9f80f},
 last_modified = {2019-09-12T17:32:38.128Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {Science Gateways provide user environments and a set of supporting services that help researchers make effective and enhanced use of a diverse set of computing, storage, and related resources. In a software framework like Airavata, the distributed computing resources such as local clusters, supercomputers, computational grids, and computing clouds are shared among multiple researchers. Hence it requires an allocations process to track the demand for their resources, understand the scientific objectives of their users, and decide among competing needs when faced with user demand that is greater than the available resources can supply. We describe the design and a prototype implementation in this presentation.},
 bibtype = {inproceedings},
 author = {Phulwani, Harsha and Thapa, Madrina and Marru, Suresh and Pierce, Marlon and Pamidighantam, Sudhakar and Christie, Marcus},
 doi = {10.1145/3219104.3229271},
 booktitle = {Proceedings of the Practice and Experience on Advanced Research Computing - PEARC '18}
}

Science Gateways provide user environments and a set of supporting services that help researchers make effective and enhanced use of a diverse set of computing, storage, and related resources. In a software framework like Airavata, the distributed computing resources such as local clusters, supercomputers, computational grids, and computing clouds are shared among multiple researchers. Hence it requires an allocations process to track the demand for their resources, understand the scientific objectives of their users, and decide among competing needs when faced with user demand that is greater than the available resources can supply. We describe the design and a prototype implementation in this presentation.

@inproceedings{
 title = {Evaluating NextCloud as a File Storage for Apache Airavata},
 type = {inproceedings},
 year = {2018},
 keywords = {Apache Airavata,File Storage,File Transfer,NextCloud,WebDAV},
 pages = {1-4},
 websites = {http://dl.acm.org/citation.cfm?doid=3219104.3229270},
 month = {7},
 publisher = {ACM Press},
 day = {22},
 city = {New York, New York, USA},
 id = {afa22125-775a-322d-9c99-b494c17f1aaa},
 created = {2019-08-19T16:06:31.741Z},
 accessed = {2019-08-19},
 file_attached = {true},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
 group_id = {0e433c5b-85c4-32aa-851c-c145aac9f80f},
 last_modified = {2019-09-12T18:48:08.861Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {Science gateways enable researchers from broad communities to access advanced computing and storage resources. The researchers analyze large amounts of data using the compute resources and the generated results, usually files are saved in the storage. Consider a scenario where a researcher has large output data files of historically run experiments on an external server. If the researcher wants to move the data to the gateway storage, then the only way to do it is through data transfer. This task would be cumbersome and time consuming. The paper discusses an approach through which historic or any data existing on a different server or in a cloud storage (Google Drive) or in an object storage (Amazon S3) can be ingested into the existing gateway without actually transferring it to the server. We discuss about a software called NextCloud and how it can be used as a gateway storage by integrating it with Apache Airavata. Airavata currently uses local file storage to store user related data files. On the client side, Airavata clients use different protocols like HTTP and SFTP for file transfer. NextCloud is an open source file share and communication platform that provides a common file access layer through its universal file access to different data sources. Integrating NextCloud with Airavata could solve the problem of providing unified file transfer API across all the Airavata clients. As NextCloud supports various external storages, its integration with Airavata would also enable the data ingestion and importing large data from different storage sources to Airavata.},
 bibtype = {inproceedings},
 author = {Kariyattin, Sachin and Marru, Suresh and Pierce, Marlon},
 doi = {10.1145/3219104.3229270},
 booktitle = {Proceedings of the Practice and Experience on Advanced Research Computing - PEARC '18}
}

Science gateways enable researchers from broad communities to access advanced computing and storage resources. The researchers analyze large amounts of data using the compute resources and the generated results, usually files are saved in the storage. Consider a scenario where a researcher has large output data files of historically run experiments on an external server. If the researcher wants to move the data to the gateway storage, then the only way to do it is through data transfer. This task would be cumbersome and time consuming. The paper discusses an approach through which historic or any data existing on a different server or in a cloud storage (Google Drive) or in an object storage (Amazon S3) can be ingested into the existing gateway without actually transferring it to the server. We discuss about a software called NextCloud and how it can be used as a gateway storage by integrating it with Apache Airavata. Airavata currently uses local file storage to store user related data files. On the client side, Airavata clients use different protocols like HTTP and SFTP for file transfer. NextCloud is an open source file share and communication platform that provides a common file access layer through its universal file access to different data sources. Integrating NextCloud with Airavata could solve the problem of providing unified file transfer API across all the Airavata clients. As NextCloud supports various external storages, its integration with Airavata would also enable the data ingestion and importing large data from different storage sources to Airavata.

@inproceedings{
 title = {Supporting Science Gateways Using Apache Airavata and SciGaP Services},
 type = {inproceedings},
 year = {2018},
 keywords = {Cyberinfrastructure,Science gateways,Software as a service},
 pages = {1-4},
 websites = {http://dl.acm.org/citation.cfm?doid=3219104.3229240},
 month = {7},
 publisher = {ACM Press},
 day = {22},
 city = {New York, New York, USA},
 id = {604b9bf7-802c-3984-b974-1c39d3f1e44b},
 created = {2019-08-19T16:27:56.630Z},
 accessed = {2019-08-19},
 file_attached = {true},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
 group_id = {0e433c5b-85c4-32aa-851c-c145aac9f80f},
 last_modified = {2019-09-12T17:32:38.207Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {The Science Gateways Platform as a service (SciGaP.org) project provides a rapid development and stable hosting platform for a wide range of science gateways that focus on software as a service. Based on the open source Apache Airavata project, SciGaP services include user management, workflow execution management, computational experiment archiving and access, and sharing services that allow users to share results and other digital artifacts. SciGaP services are multi-tenanted, with clients accessing services through a well-defined, programming language-independent API. SciGaP services can be integrated into web, mobile, and desktop clients. To simplify development for new clients, SciGaP includes the PGA, a generic PHP-based gateway client for SciGaP services that also acts as a reference implementation of the API. Several example gateways using these services are summarized. © 2018 Copyright held by the owner/author(s).},
 bibtype = {inproceedings},
 author = {Pierce, Marlon and Marru, Suresh and Abeysinghe, Eroma and Pamidighantam, Sudhakar and Christie, Marcus and Wannipurage, Dimuthu},
 doi = {10.1145/3219104.3229240},
 booktitle = {Proceedings of the Practice and Experience on Advanced Research Computing - PEARC '18}
}

The Science Gateways Platform as a service (SciGaP.org) project provides a rapid development and stable hosting platform for a wide range of science gateways that focus on software as a service. Based on the open source Apache Airavata project, SciGaP services include user management, workflow execution management, computational experiment archiving and access, and sharing services that allow users to share results and other digital artifacts. SciGaP services are multi-tenanted, with clients accessing services through a well-defined, programming language-independent API. SciGaP services can be integrated into web, mobile, and desktop clients. To simplify development for new clients, SciGaP includes the PGA, a generic PHP-based gateway client for SciGaP services that also acts as a reference implementation of the API. Several example gateways using these services are summarized. © 2018 Copyright held by the owner/author(s).

@inproceedings{
 title = {Science Gateway Implementation at the University of South Dakota},
 type = {inproceedings},
 year = {2018},
 keywords = {Apache Airavata,Gateway,Keycloak,SciGaP},
 pages = {1-4},
 websites = {http://dl.acm.org/citation.cfm?doid=3219104.3229265},
 month = {7},
 publisher = {ACM Press},
 day = {22},
 city = {New York, New York, USA},
 id = {5ffd051d-f501-3b43-b48a-07e799cf73c4},
 created = {2019-08-19T16:31:05.309Z},
 accessed = {2019-08-19},
 file_attached = {true},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
 group_id = {0e433c5b-85c4-32aa-851c-c145aac9f80f},
 last_modified = {2019-09-12T17:32:38.171Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {Science Gateways are virtual environments that accelerate scientific discovery by enabling scientific communities to more easily and effectively utilize distributed computing and data resources. Successful Science Gateways provide access to sophisticated and powerful resources, while shielding their users from the underlying complexities. Here we present work completed by the University of South Dakota (USD) Research Computing Group in conjunction with the Science Gateways Community Institute (SGCI) [1] and Indiana University on setting up a Science Gateway to access USD's high-performance computing resources. These resources are now available to both faculty and students and allow ease of access and use of USD's distributed computing and data resources. The implementation of this gateway project has been multifaceted and has included placement of federated user login, user facilitation and outreach, and integration of USD's cyberinfrastructure resources. We present this project as an example for other research computing groups so that they may learn from our successes and the challenges that we have overcome in providing this user resource. Additionally, this project serves to exemplify the importance of creating a broad user base of research computing infrastructure through the development of alternative user interfaces such as Science Gateways.},
 bibtype = {inproceedings},
 author = {Madison, Joseph D. and Abeysinghe, Eroma and Pamidighantam, Sudhakar and Marru, Suresh and Christie, Marcus and Jennewein, Douglas M. and Pierce, Marlon},
 doi = {10.1145/3219104.3229265},
 booktitle = {Proceedings of the Practice and Experience on Advanced Research Computing - PEARC '18}
}

Science Gateways are virtual environments that accelerate scientific discovery by enabling scientific communities to more easily and effectively utilize distributed computing and data resources. Successful Science Gateways provide access to sophisticated and powerful resources, while shielding their users from the underlying complexities. Here we present work completed by the University of South Dakota (USD) Research Computing Group in conjunction with the Science Gateways Community Institute (SGCI) [1] and Indiana University on setting up a Science Gateway to access USD's high-performance computing resources. These resources are now available to both faculty and students and allow ease of access and use of USD's distributed computing and data resources. The implementation of this gateway project has been multifaceted and has included placement of federated user login, user facilitation and outreach, and integration of USD's cyberinfrastructure resources. We present this project as an example for other research computing groups so that they may learn from our successes and the challenges that we have overcome in providing this user resource. Additionally, this project serves to exemplify the importance of creating a broad user base of research computing infrastructure through the development of alternative user interfaces such as Science Gateways.

@inproceedings{
 title = {The CSBG - LSU Gateway},
 type = {inproceedings},
 year = {2018},
 keywords = {Apache Airavata,Bioinformatics,Computational System Biology,Science Gateway},
 pages = {1-4},
 websites = {http://dl.acm.org/citation.cfm?doid=3219104.3229245},
 month = {7},
 publisher = {ACM Press},
 day = {22},
 city = {New York, New York, USA},
 id = {f2d1d333-dad2-37e5-b728-4bae03a90ee4},
 created = {2019-08-19T16:35:52.772Z},
 accessed = {2019-08-19},
 file_attached = {true},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
 group_id = {0e433c5b-85c4-32aa-851c-c145aac9f80f},
 last_modified = {2019-09-12T17:32:38.355Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {Science gateways are identified as an effective way to publish and distribute software for research communities without the burden of learning HPC (High Performance Computer) systems. In the past, researchers were expected to have in-depth knowledge about using HPC systems for computations along with their respective science field in order to do effective research. Science gateways eliminate the need to learn HPC systems and allows the research communities to focus more on their science and let the gateway handle communicating with HPCs. In this poster we are presenting the science gateway project of CSBG (Computational System Biology Group - www.brylinski.org) of Department of Biological Sciences with Center for Computation & Technology at LSU (Louisiana State University). The gateway project was initiated in order to provide CSBG software tools as a service through a science gateway.},
 bibtype = {inproceedings},
 author = {Abeysinghe, Eroma and Brylinski, Michal and Christie, Marcus and Marru, Suresh and Pierce, Marlon},
 doi = {10.1145/3219104.3229245},
 booktitle = {Proceedings of the Practice and Experience on Advanced Research Computing - PEARC '18}
}

Science gateways are identified as an effective way to publish and distribute software for research communities without the burden of learning HPC (High Performance Computer) systems. In the past, researchers were expected to have in-depth knowledge about using HPC systems for computations along with their respective science field in order to do effective research. Science gateways eliminate the need to learn HPC systems and allows the research communities to focus more on their science and let the gateway handle communicating with HPCs. In this poster we are presenting the science gateway project of CSBG (Computational System Biology Group - www.brylinski.org) of Department of Biological Sciences with Center for Computation & Technology at LSU (Louisiana State University). The gateway project was initiated in order to provide CSBG software tools as a service through a science gateway.

@article{
 title = {Fracture Advancing Step Tectonics Observed in the Yuha Desert and Ocotillo, CA, Following the 2010 M w 7.2 El Mayor-Cucapah Earthquake},
 type = {article},
 year = {2018},
 keywords = {GPS,UAVSAR,earthquake,fault,geodetic imaging,stepover},
 pages = {456-472},
 volume = {5},
 websites = {http://doi.wiley.com/10.1029/2017EA000351},
 month = {9},
 publisher = {Wiley-Blackwell Publishing Ltd},
 day = {1},
 id = {4c57442e-5ae6-3d39-889e-5706df7141eb},
 created = {2019-08-19T17:16:36.069Z},
 accessed = {2019-08-19},
 file_attached = {false},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
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 last_modified = {2019-09-12T17:56:21.623Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {©2018. The Authors. Uninhabited aerial vehicle synthetic aperture radar (UAVSAR) observations 2009–2017 of the Yuha Desert area and Global Positioning System (GPS) time series encompassing the region reveal a northward migrating pattern of deformation following the 4 April 2010 Mw7.2 El Mayor-Cucapah (EMC) earthquake. The north end of the EMC rupture exhibits an asymmetric pattern of deformation that is substantial and smooth northeast of the rupture and limited but with surface fracturing slip northwest. The earthquake triggered ~1 cm of surface coseismic slip at the Yuha fault, which continued to slip postseismically. 2.5 cm of Yuha fault slip occurred by the time of the 15 June 2010 Mw5.7 Ocotillo aftershock and 5 cm of slip occurred by 2017 following a logarithmic afterslip decay 16-day timescale. The Ocotillo aftershock triggered 1.4 cm of slip on a northwest trend extending to the Elsinore fault and by 7 years after the EMC earthquake 2.4 cm of slip had accumulated with a distribution following an afterslip function with a 16-day timescale consistent with other earthquakes and a rate strengthening upper crustal sedimentary layer. GPS data show broad coseismic uplift of the Salton Trough and delayed postseismic motion that may be indicative of fluid migration there and subsidence west of the rupture extension, which continues following the earthquake. The data indicate that the Elsinore, Laguna Salada, and EMC ruptures are part of the same fault system. The results also suggest that north-south shortening and east-west extension across the region drove fracture advancing step tectonics north of the EMC earthquake rupture.},
 bibtype = {article},
 author = {Donnellan, Andrea and Parker, Jay and Heflin, Michael and Lyzenga, Gregory and Moore, Angelyn and Ludwig, Lisa Grant and Rundle, John and Wang, Jun and Pierce, Marlon},
 doi = {10.1029/2017EA000351},
 journal = {Earth and Space Science},
 number = {9}
}

©2018. The Authors. Uninhabited aerial vehicle synthetic aperture radar (UAVSAR) observations 2009–2017 of the Yuha Desert area and Global Positioning System (GPS) time series encompassing the region reveal a northward migrating pattern of deformation following the 4 April 2010 Mw7.2 El Mayor-Cucapah (EMC) earthquake. The north end of the EMC rupture exhibits an asymmetric pattern of deformation that is substantial and smooth northeast of the rupture and limited but with surface fracturing slip northwest. The earthquake triggered ~1 cm of surface coseismic slip at the Yuha fault, which continued to slip postseismically. 2.5 cm of Yuha fault slip occurred by the time of the 15 June 2010 Mw5.7 Ocotillo aftershock and 5 cm of slip occurred by 2017 following a logarithmic afterslip decay 16-day timescale. The Ocotillo aftershock triggered 1.4 cm of slip on a northwest trend extending to the Elsinore fault and by 7 years after the EMC earthquake 2.4 cm of slip had accumulated with a distribution following an afterslip function with a 16-day timescale consistent with other earthquakes and a rate strengthening upper crustal sedimentary layer. GPS data show broad coseismic uplift of the Salton Trough and delayed postseismic motion that may be indicative of fluid migration there and subsidence west of the rupture extension, which continues following the earthquake. The data indicate that the Elsinore, Laguna Salada, and EMC ruptures are part of the same fault system. The results also suggest that north-south shortening and east-west extension across the region drove fracture advancing step tectonics north of the EMC earthquake rupture.

@inproceedings{
 title = {Scaling JupyterHub Using Kubernetes on Jetstream Cloud},
 type = {inproceedings},
 year = {2018},
 keywords = {Cloud Computing,JupyterHub,Kubernetes,Magnum,OpenStack,Unidata,Workforce Development},
 pages = {1-4},
 websites = {http://dl.acm.org/citation.cfm?doid=3219104.3229249},
 month = {7},
 publisher = {ACM Press},
 day = {22},
 city = {New York, New York, USA},
 id = {f0df3ae7-0fa6-3d95-9126-666f5649f424},
 created = {2019-08-19T19:17:43.656Z},
 accessed = {2019-08-19},
 file_attached = {true},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
 group_id = {0e433c5b-85c4-32aa-851c-c145aac9f80f},
 last_modified = {2019-09-12T18:48:08.983Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {Unidata, an NSF funded project that started in 1983, is a diverse community of education and research institutions with the common goal of sharing geoscience data and the tools to access and visualize that data. Unidata provides weather observations and other data, software tools, and support to enhance Earth-system education and research, and continuously examines ways of adapting their workflows for new technologies to maximize the reach of their education and research efforts. In support of Unidata objectives to host workshops for atmospheric data analysis using JupyterHub, we explore a cloud computing approach leveraging Kubernetes coupled with JupyterHub that when combined will provide a solution for researchers and students to pull data from Unidata and burst onto Jetstream cloud by requesting resources dynamically via easy to use JupyterHub. More specifically, on Jetstream, Kubernetes is used for automating deployment and scaling of domain specific containerized applications, and JupyterHub is used for spawning multiple hubs within the same Kubernetes cluster instance that will be used for supporting classroom settings. JupyterHub's modular kernel feature will support dynamic needs of classroom application requirements. The proposed approach will serve as an end-to-end solution for researchers to execute their workflows, with JupyterHub serving as a powerful tool for user training and next-generation workforce development in atmospheric sciences.},
 bibtype = {inproceedings},
 author = {Sarajlic, Semir and Chastang, Julien and Marru, Suresh and Fischer, Jeremy and Lowe, Mike},
 doi = {10.1145/3219104.3229249},
 booktitle = {Proceedings of the Practice and Experience on Advanced Research Computing - PEARC '18}
}

Unidata, an NSF funded project that started in 1983, is a diverse community of education and research institutions with the common goal of sharing geoscience data and the tools to access and visualize that data. Unidata provides weather observations and other data, software tools, and support to enhance Earth-system education and research, and continuously examines ways of adapting their workflows for new technologies to maximize the reach of their education and research efforts. In support of Unidata objectives to host workshops for atmospheric data analysis using JupyterHub, we explore a cloud computing approach leveraging Kubernetes coupled with JupyterHub that when combined will provide a solution for researchers and students to pull data from Unidata and burst onto Jetstream cloud by requesting resources dynamically via easy to use JupyterHub. More specifically, on Jetstream, Kubernetes is used for automating deployment and scaling of domain specific containerized applications, and JupyterHub is used for spawning multiple hubs within the same Kubernetes cluster instance that will be used for supporting classroom settings. JupyterHub's modular kernel feature will support dynamic needs of classroom application requirements. The proposed approach will serve as an end-to-end solution for researchers to execute their workflows, with JupyterHub serving as a powerful tool for user training and next-generation workforce development in atmospheric sciences.

@inproceedings{
 title = {Grid technology for supporting health education and measuring the health outcome},
 type = {inproceedings},
 year = {2018},
 keywords = {Community health,Cyberinfrastructure,Data grid,Data integration,Grid computing,Health education,IRODS,Mobile technology,Portal,Virtual,XSEDE},
 month = {7},
 publisher = {Association for Computing Machinery},
 day = {22},
 id = {cd44f519-9c9d-3208-aac4-48f822df5acc},
 created = {2019-08-26T16:31:55.075Z},
 accessed = {2019-08-26},
 file_attached = {false},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
 group_id = {0e433c5b-85c4-32aa-851c-c145aac9f80f},
 last_modified = {2019-08-26T16:31:55.075Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
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 abstract = {In this paper, we present our developed health-IT solution that address these challenges: developing the strategies not only to store such a vast amount of data but also making those available to the researchers for further analysis that can measure the outcome on the participant's health. The developed community health grid (C-Grid) solution to store, manage and share large amounts of these instruction materials and participant's health related data, where the remote management and analysis of this data grid is performed using iRODS, the Integrated Rule-Oriented Data System is discussed and presented in this paper.},
 bibtype = {inproceedings},
 author = {Sukhija, Nitin and Sevin, Sonny and Datta, Arun K. and Coulter, Eric},
 doi = {10.1145/3219104.3229247},
 booktitle = {Proceedings of the Practice and Experience on Advanced Research Computing (PEARC '18)}
}

In this paper, we present our developed health-IT solution that address these challenges: developing the strategies not only to store such a vast amount of data but also making those available to the researchers for further analysis that can measure the outcome on the participant's health. The developed community health grid (C-Grid) solution to store, manage and share large amounts of these instruction materials and participant's health related data, where the remote management and analysis of this data grid is performed using iRODS, the Integrated Rule-Oriented Data System is discussed and presented in this paper.

@inproceedings{
 title = {Searching the sequence read archive using Jetstream and Wrangler},
 type = {inproceedings},
 year = {2018},
 keywords = {Apache Airavata,Bacteriophage,Credential Store,Jetstream,Metagenomics,Metagenomics Discovery Challenge,SRA,SRA Gateway,SciGaP,Search SRA,Sequence Read Archive,Wrangler},
 month = {7},
 publisher = {Association for Computing Machinery},
 day = {22},
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 abstract = {The Sequence Read Archive (SRA), the world’s largest database of sequences, hosts approximately 10 petabases (1016 bp) of sequence data and is growing at the alarming rate of 10 TB per day. Yet this rich trove of data is inaccessible to most researchers: searching through the SRA requires large storage and computing facilities that are beyond the capacity of most laboratories. Enabling scientists to analyze existing sequence data will provide insight into ecology, medicine, and industrial applications. In this project we specifi- cally focus on metagenomic sequences (whole community data sets from different environments). We are developing a set of tools to enable biologists to mine the metagenomes in the SRA using the NSF-funded cloud computing resources, Jetstream and Wrangler. We have developed a proof-of-principle pipeline to demonstrate the feasibility of the approach. We are leveraging our existing in- frastructure to enable all scientists to access the SRA metagenomes regardless of their computational ability and are working to create a stable pipeline with a science gateway portal that is accessible to all researchers.تنيىسبت},
 bibtype = {inproceedings},
 author = {Levi, Kyle and Abeysinghe, Eroma and Rynge, Mats and Edwards, Robert A.},
 doi = {10.1145/3219104.3229278},
 booktitle = {Proceedings of the Practice and Experience on Advanced Research Computing (PEARC '18)}
}

The Sequence Read Archive (SRA), the world’s largest database of sequences, hosts approximately 10 petabases (1016 bp) of sequence data and is growing at the alarming rate of 10 TB per day. Yet this rich trove of data is inaccessible to most researchers: searching through the SRA requires large storage and computing facilities that are beyond the capacity of most laboratories. Enabling scientists to analyze existing sequence data will provide insight into ecology, medicine, and industrial applications. In this project we specifi- cally focus on metagenomic sequences (whole community data sets from different environments). We are developing a set of tools to enable biologists to mine the metagenomes in the SRA using the NSF-funded cloud computing resources, Jetstream and Wrangler. We have developed a proof-of-principle pipeline to demonstrate the feasibility of the approach. We are leveraging our existing in- frastructure to enable all scientists to access the SRA metagenomes regardless of their computational ability and are working to create a stable pipeline with a science gateway portal that is accessible to all researchers.تنيىسبت

@inproceedings{
 title = {PHASTA Science Gateway for High Performance Computational Fluid Dynamics},
 type = {inproceedings},
 year = {2018},
 keywords = {Apache Airavata,CFD,Paralllel Unstructured Mesh,Pervasive Technology Institute,Science Gateway,Science Gateways Research Center},
 pages = {1-4},
 websites = {http://dl.acm.org/citation.cfm?doid=3219104.3229243},
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 abstract = {The Parallel Hierarchic Adaptive Stabilized Transient Analysis (PHASTA) software supports modeling compressible or incompressible, laminar or turbulent, steady or unsteady flows in 3D using unstructured grids. PHASTA has been applied to industrial and academic flows on complex, as-designed geometric models with over one billion mesh elements using upwards of one million compute cores. The PHASTA Science Gateway (phasta.scigap.org) brings these increasingly critical technologies to a larger user base by providing a central hub for simulation execution, simulation data management, and documentation. Researchers and engineers using the gateway can easily define and execute simulations on the TACC Stampede2 Skylake and Knights Landing nodes without being burdened by the details of remote access, the job scheduler, and filesystem configuration. In addition to simplifying the simulation execution process, the gateway creates a searchable archive of past jobs that can be shared with other users to support reproducibility and increase productivity. Our poster presents the construction of the gateway with Apache Airavata, the simulation definition process, applications it currently supports, and our ongoing efforts to expand functionality, the user base, and the community.},
 bibtype = {inproceedings},
 author = {Smith, Cameron W. and Abeysinghe, Eroma and Marru, Suresh and Jansen, Kenneth E.},
 doi = {10.1145/3219104.3229243},
 booktitle = {Proceedings of the Practice and Experience on Advanced Research Computing - PEARC '18}
}

The Parallel Hierarchic Adaptive Stabilized Transient Analysis (PHASTA) software supports modeling compressible or incompressible, laminar or turbulent, steady or unsteady flows in 3D using unstructured grids. PHASTA has been applied to industrial and academic flows on complex, as-designed geometric models with over one billion mesh elements using upwards of one million compute cores. The PHASTA Science Gateway (phasta.scigap.org) brings these increasingly critical technologies to a larger user base by providing a central hub for simulation execution, simulation data management, and documentation. Researchers and engineers using the gateway can easily define and execute simulations on the TACC Stampede2 Skylake and Knights Landing nodes without being burdened by the details of remote access, the job scheduler, and filesystem configuration. In addition to simplifying the simulation execution process, the gateway creates a searchable archive of past jobs that can be shared with other users to support reproducibility and increase productivity. Our poster presents the construction of the gateway with Apache Airavata, the simulation definition process, applications it currently supports, and our ongoing efforts to expand functionality, the user base, and the community.

@inproceedings{
 title = {Using the Jetstream Research Cloud to Provide Science Gateway Resources},
 type = {inproceedings},
 year = {2017},
 pages = {753-757},
 websites = {http://ieeexplore.ieee.org/document/7973774/},
 month = {5},
 publisher = {IEEE},
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 bibtype = {inproceedings},
 author = {Knepper, Richard and Coulter, Eric and Pierce, Marlon and Marru, Suresh and Pamidighantam, Sudhakar},
 doi = {10.1109/CCGRID.2017.121},
 booktitle = {Proceedings of the 17th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid '17)}
}

We describe the use of the Jetstream research-cloud, a purpose-built system with the goal of supporting "long-tail" research by providing a flexible, on-demand research infrastructure, to provide scalable back-end resources for science gateways. In addition to providing cloud-like resources for on-demand science, Jetstream offers the capability to instantiate long-running clusters which support science gateways. Science gateways are web-based systems built on computational infrastructure which provide commonly-used tools to a community of users. We created a persistent cluster on the Jetstream system which is connected to the SEAGrid science gateway and provides additional compute resources for a variety of quantum chemistry calculations. We discuss the further application of toolkits provided by the Extreme Science and Engineering Discovery Environment (XSEDE) to build general-purpose clusters on the research cloud.

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@article{
 title = {Gathering requirements for advancing simulations in HPC infrastructures via science gateways},
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 journal = {Future Generation Computer Systems}
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@techreport{
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@inproceedings{
 title = {Science Gateways: Sustainability via On-Campus Teams},
 type = {inproceedings},
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 doi = {10.6084/m9.figshare.5483566.v1},
 booktitle = {Gateways 2017}
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@inproceedings{
 title = {Better Data Discoverability in Science Gateways},
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 author = {Nakandala, Supun and Pamidighantam, Sudhakar and Marru, Suresh and Pierce, Marlon},
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@techreport{
 title = {Indiana University Pervasive Technology Institute},
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@techreport{
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@article{
 title = {Radar Determination of Fault Slip and Location in Partially Decorrelated Images},
 type = {article},
 year = {2017},
 pages = {2295-2310},
 volume = {174},
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 author = {Parker, Jay and Glasscoe, Margaret and Donnellan, Andrea and Stough, Timothy and Pierce, Marlon and Wang, Jun},
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Parker, J., Glasscoe, M., Donnellan, A., Stough, T., Pierce, M., & Wang, J. (2017). Radar Determination of Fault Slip and Location in Partially Decorrelated Images. Pure and Applied Geophysics, 174(6), 2295–2310.

@inbook{
 type = {inbook},
 year = {2017},
 pages = {1063-1074},
 websites = {http://services.igi-global.com/resolvedoi/resolve.aspx?doi=10.4018/978-1-5225-2255-3.ch092},
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 author = {Stewart, Craig A and Knepper, Richard and Link, Matthew R and Pierce, Marlon and Wernert, Eric and Wilkins-Diehr, Nancy},
 editor = {Mehdi Khosrow-Pour, D B A},
 doi = {10.4018/978-1-5225-2255-3.ch092},
 chapter = {Cyberinfrastructure, Cloud Computing, Science Gateways, Visualization, and Cyberinfrastructure Ease of Use},
 title = {Encyclopedia of Information Science and Technology, Fourth Edition}
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Computers accelerate our ability to achieve scientific breakthroughs. As technology evolves and new research needs come to light, the role for cyberinfrastructure as “knowledge” infrastructure continues to expand. In essence, cyberinfrastructure can be thought of as the integration of supercomputers, data resources, visualization, and people that extends the impact and utility of information technology. This article discusses cyberinfrastructure, the related topics of science gateways and campus bridging, and identifies future challenges and opportunities in cyberinfrastructure.

@inproceedings{
 title = {Science gateways incubator: Software sustainability meets community needs},
 type = {inproceedings},
 year = {2017},
 keywords = {community,incubator,science gateways bootcamp,science gateways community institute,sustainability},
 pages = {477-485},
 month = {11},
 publisher = {Institute of Electrical and Electronics Engineers Inc.},
 day = {14},
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 abstract = {© 2017 IEEE. The main goal of the US Science Gateways Community Institute (SGCI) is to serve science gateways to achieve sustainability and growth. Science gateways allow science and engineering communities to access shared data, software, computing services, instruments, educational materials, and other resources specific to their disciplines. Thus, science gateways are a subgroup of scientific software and the means for addressing software sustainability are also suitable for science gateways and vice versa, e.g., best practices for software engineering. Since science gateways are tailored to specific communities, understanding users' requirements is critical for sustainability. SGCI consists of five service areas that closely interact with each other. The Incubator acknowledges the value of business strategy to inform well-designed science gateways and offers two main types of services: Individualized consultancy, tailored to specific challenges a gateway faces, and the Science Gateways Bootcamp. The cornerstone of the Bootcamp is a one-week onsite intensive workshop where participants create their own roadmap for a sustainable science gateway via sessions with experts, hands-on exercises, and group work. This paper offers an overview of the work of the Incubator and shares lessons learned from the inaugural session of the Bootcamp in April 2017.},
 bibtype = {inproceedings},
 author = {Gesing, Sandra and Zentner, Michael and Casavan, Juliana and Hillery, Betsy and Vorvoreanu, Mihaela and Heiland, Randy and Marru, Suresh and Pierce, Marlon and Mullinix, Nayiri and Maron, Nancy},
 doi = {10.1109/eScience.2017.77},
 booktitle = {Proceedings - 13th IEEE International Conference on eScience, eScience 2017}
}

© 2017 IEEE. The main goal of the US Science Gateways Community Institute (SGCI) is to serve science gateways to achieve sustainability and growth. Science gateways allow science and engineering communities to access shared data, software, computing services, instruments, educational materials, and other resources specific to their disciplines. Thus, science gateways are a subgroup of scientific software and the means for addressing software sustainability are also suitable for science gateways and vice versa, e.g., best practices for software engineering. Since science gateways are tailored to specific communities, understanding users' requirements is critical for sustainability. SGCI consists of five service areas that closely interact with each other. The Incubator acknowledges the value of business strategy to inform well-designed science gateways and offers two main types of services: Individualized consultancy, tailored to specific challenges a gateway faces, and the Science Gateways Bootcamp. The cornerstone of the Bootcamp is a one-week onsite intensive workshop where participants create their own roadmap for a sustainable science gateway via sessions with experts, hands-on exercises, and group work. This paper offers an overview of the work of the Incubator and shares lessons learned from the inaugural session of the Bootcamp in April 2017.

@inproceedings{
 title = {Science Gateways: The Long Road to the Birth of an Institute},
 type = {inproceedings},
 year = {2017},
 pages = {10 pages},
 websites = {http://hdl.handle.net/10125/41919},
 publisher = {Hawaii International Conference on System Sciences},
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 bibtype = {inproceedings},
 author = {Gesing, Sandra and Wilkins-Diehr, Nancy and Dahan, Maytal and Lawrence, Katherine and Zentner, Michael and Pierce, Marlon and Hayden, Linda and Marru, Suresh},
 doi = {10.24251/HICSS.2017.755},
 booktitle = {Proceedings of the 50th Hawaii International Conference on System Sciences (2017)}
}

Nowadays, research in various disciplines is enhanced via computational methods, cutting-edge technologies and diverse resources including computational infrastructures and instruments. Such infrastructures are often complex and researchers need means to conduct their research in an efficient way without getting distracted with information technology nuances. Science gateways address such demands and offer user interfaces tailored to a specific community. Creators of science gateways face a breadth of topics and manifold challenges, which necessitate close collaboration with the domain specialists but also calling in experts for diverse aspects of a science gateway such as project management, licensing, team composition, sustainability, HPC, visualization, and usability specialists. The Science Gateway Community Institute tackles the challenges around science gateways to support domain specialists and developers via connecting them to diverse experts, offering consultancy as well as providing a software collaborative, which contains ready-to-use science gateway frameworks and science gateway components.

@inproceedings{
 title = {The PHASTA Science Gateway},
 type = {inproceedings},
 year = {2017},
 keywords = {ACM proceedings,Apache Airavata,LATEX,Science Gateway,Text tagging},
 pages = {1-4},
 volume = {Part F1287},
 websites = {http://dl.acm.org/citation.cfm?doid=3093338.3104151},
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 abstract = {The Parallel Hierarchic Adaptive Stabilized Transient Analysis (PHASTA) software supports modeling compressible or incompressible, laminar or turbulent, steady or unsteady flows in 3D using unstructured grids. PHASTA, coupled with the Parallel Unstructured Mesh Infrastructure (PUMI), supports parallel, automated, adaptive simulation workflows. Researchers can easily execute these workflows on the TACC Stampede Xeon and Knights Landing nodes without being burdened by the details of each system using the PHASTA science gateway (created with Apache Airavata). In addition to abstracting away job execution and filesystem details, the gateway creates a searchable archive of past jobs to support reproducibility. Our poster presents the construction of the PHASTA gateway, the workflows it currently supports, and our ongoing efforts to expand functionality and the user base.},
 bibtype = {inproceedings},
 author = {Smith, Cameron W. and Abeysinghe, Eroma},
 doi = {10.1145/3093338.3104151},
 booktitle = {Proceedings of the Practice and Experience in Advanced Research Computing 2017 on Sustainability, Success and Impact - PEARC17}
}

The Parallel Hierarchic Adaptive Stabilized Transient Analysis (PHASTA) software supports modeling compressible or incompressible, laminar or turbulent, steady or unsteady flows in 3D using unstructured grids. PHASTA, coupled with the Parallel Unstructured Mesh Infrastructure (PUMI), supports parallel, automated, adaptive simulation workflows. Researchers can easily execute these workflows on the TACC Stampede Xeon and Knights Landing nodes without being burdened by the details of each system using the PHASTA science gateway (created with Apache Airavata). In addition to abstracting away job execution and filesystem details, the gateway creates a searchable archive of past jobs to support reproducibility. Our poster presents the construction of the PHASTA gateway, the workflows it currently supports, and our ongoing efforts to expand functionality and the user base.

@inproceedings{
 title = {Apache airavata sharing service: A tool for enabling user collaboration in science gateways},
 type = {inproceedings},
 year = {2017},
 keywords = {Apache Airavata,CIPRES,Collab-oration,Groups,NSG,SEAGrid,SciGaP,Science Gateways,Sharing},
 volume = {Part F128771},
 month = {7},
 publisher = {Association for Computing Machinery},
 day = {9},
 id = {6b254ba4-ea09-33d1-a927-ad3adaad7517},
 created = {2019-09-12T17:37:01.594Z},
 accessed = {2019-09-12},
 file_attached = {true},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
 group_id = {0e433c5b-85c4-32aa-851c-c145aac9f80f},
 last_modified = {2019-09-12T17:37:01.683Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {Science Gateways provide user environments and a set of supporting services that help researchers make effective and enhanced use of a diverse set of computing, storage, and related resources. Gateways provide the services and tools users require to enable their scientific exploration, which in-cludes tasks such as running computer simulations or per-forming data analysis. Historically gateways have been con-structed to support the workflow of individual users, but collaboration between users has become an increasingly im-portant part of the discovery process. This trend has created a driving need for gateways to support data sharing between users. For example, a chemistry research group may want to run simulations collaboratively, analyze experimental data or tune parameter studies based on simulation output gen-erated by peers, whether as a default capability, or through explicit creation of sharing privileges. As another example, students in a classroom setting may be required to share their simulation output or data analysis results with the in-structor. However most existing gateways (including the pop-ularly used XSEDE gateways SEAGrid, Ultrascan, CIPRES, and NSG), do not support direct data sharing, so users have to handle these collaborations outside the gateway environ-ment. Given the importance of collaboration in current scien-tific practice, user collaboration should be a prime consider-ation in building science gateways. In this work, we present design considerations and implementation of a generic model that can be used to describe and handle a diverse set of user collaboration use cases that arise in gateways, based on gen-eral requirements gathered from the SEAGrid, CIPRES, and NSG gateways. We then describe the integration of this shar-ing service into these gateways. Though the model and the system were tested and used in the context of Science Gate-ways, the concepts are universally applicable to any domain, and the service can support data sharing in a wide varietyof use cases. © 2017 ACM.},
 bibtype = {inproceedings},
 author = {Nakandala, Supun and Marru, Suresh and Piece, Marlon and Pamidighantam, Sudhakar and Yoshimoto, Kenneth and Schwartz, Terri and Sivagnanam, Subhashini and Majumdar, Amit and Miller, Mark A.},
 doi = {10.1145/3093338.3093359},
 booktitle = {Proceedings of the Practice and Experience in Advanced Research Computing 2017 on Sustainability, Success and Impact (PEARC17)}
}

Science Gateways provide user environments and a set of supporting services that help researchers make effective and enhanced use of a diverse set of computing, storage, and related resources. Gateways provide the services and tools users require to enable their scientific exploration, which in-cludes tasks such as running computer simulations or per-forming data analysis. Historically gateways have been con-structed to support the workflow of individual users, but collaboration between users has become an increasingly im-portant part of the discovery process. This trend has created a driving need for gateways to support data sharing between users. For example, a chemistry research group may want to run simulations collaboratively, analyze experimental data or tune parameter studies based on simulation output gen-erated by peers, whether as a default capability, or through explicit creation of sharing privileges. As another example, students in a classroom setting may be required to share their simulation output or data analysis results with the in-structor. However most existing gateways (including the pop-ularly used XSEDE gateways SEAGrid, Ultrascan, CIPRES, and NSG), do not support direct data sharing, so users have to handle these collaborations outside the gateway environ-ment. Given the importance of collaboration in current scien-tific practice, user collaboration should be a prime consider-ation in building science gateways. In this work, we present design considerations and implementation of a generic model that can be used to describe and handle a diverse set of user collaboration use cases that arise in gateways, based on gen-eral requirements gathered from the SEAGrid, CIPRES, and NSG gateways. We then describe the integration of this shar-ing service into these gateways. Though the model and the system were tested and used in the context of Science Gate-ways, the concepts are universally applicable to any domain, and the service can support data sharing in a wide varietyof use cases. © 2017 ACM.

@article{
 title = {A Non-Natural Wurtzite Polymorph of HgSe: A Potential 3D Topological Insulator},
 type = {article},
 year = {2017},
 pages = {6356-6366},
 volume = {29},
 websites = {https://pubs.acs.org/doi/10.1021/acs.chemmater.7b01674},
 month = {8},
 publisher = {American Chemical Society},
 day = {8},
 id = {af4fb6b2-4833-3bb3-9773-7440f9048f25},
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 abstract = {This article demonstrates the power of topotactic synthesis coupled with density functional theory (DFT) for accessing and exploring new phases of matter. Naturally occurring HgSe is a semimetal with a zero gap. Unlike this natural zincblende form of HgSe, our DFT investigations predict that wurtzite HgSe has both an inverted band structure and a band gap, making it a 3D topological insulator (TI). Calculated band structures of HgxCd1–xSe alloys containing strongly relativistic Hg and weakly relativistic Cd show that band gap opening is a consequence of symmetry breaking resulting from a combination of crystal anisotropy and the scalar relativistic effect of Hg electrons. The relativistic contribution of Hg is significant enough in alloys with x ≥ 0.33 for achieving 3D TI behavior at room temperature. We experimentally realize the non-natural wurtzite form by topotactic ion exchange of wurtzite CdSe nanocrystals (NCs), which yields alloy NCs in the range x = 0–0.54 whose measured band gaps follow the pred...},
 bibtype = {article},
 author = {Dumett Torres, Daniel and Banerjee, Progna and Pamidighantam, Sudhakar and Jain, Prashant K.},
 doi = {10.1021/acs.chemmater.7b01674},
 journal = {Chemistry of Materials},
 number = {15}
}

This article demonstrates the power of topotactic synthesis coupled with density functional theory (DFT) for accessing and exploring new phases of matter. Naturally occurring HgSe is a semimetal with a zero gap. Unlike this natural zincblende form of HgSe, our DFT investigations predict that wurtzite HgSe has both an inverted band structure and a band gap, making it a 3D topological insulator (TI). Calculated band structures of HgxCd1–xSe alloys containing strongly relativistic Hg and weakly relativistic Cd show that band gap opening is a consequence of symmetry breaking resulting from a combination of crystal anisotropy and the scalar relativistic effect of Hg electrons. The relativistic contribution of Hg is significant enough in alloys with x ≥ 0.33 for achieving 3D TI behavior at room temperature. We experimentally realize the non-natural wurtzite form by topotactic ion exchange of wurtzite CdSe nanocrystals (NCs), which yields alloy NCs in the range x = 0–0.54 whose measured band gaps follow the pred...

@article{
 title = {GSoC 2015 student contributions to GenApp and Airavata},
 type = {article},
 year = {2016},
 pages = {1960-1970},
 volume = {28},
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 starred = {false},
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 confirmed = {true},
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 citation_key = {brookes2016gsoc},
 source_type = {article},
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 bibtype = {article},
 author = {Brookes, Emre H and Kapoor, Abhishek and Patra, Priyanshu and Marru, Suresh and Singh, Raminder and Pierce, Marlon},
 journal = {Concurrency and Computation: Practice and Experience},
 number = {7}
}

@inproceedings{
 title = {Apache Airavata security manager: Authentication and authorization implementations for a multi-tenant escience framework},
 type = {inproceedings},
 year = {2016},
 pages = {287-292},
 institution = {IEEE},
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 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {nakandala2016apache},
 source_type = {inproceedings},
 private_publication = {false},
 bibtype = {inproceedings},
 author = {Nakandala, Supun and Gunasinghe, Hasini and Marru, Suresh and Pierce, Marlon},
 booktitle = {e-Science (e-Science), 2016 IEEE 12th International Conference on}
}

@inproceedings{
 title = {Anatomy of the SEAGrid Science Gateway},
 type = {inproceedings},
 year = {2016},
 pages = {1-8},
 websites = {http://dl.acm.org/citation.cfm?doid=2949550.2949591},
 publisher = {ACM Press},
 city = {New York, New York, USA},
 institution = {ACM},
 id = {ec0fd7ce-2114-37e8-9dfe-1f72a9a8a7c3},
 created = {2018-02-27T18:07:54.623Z},
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 last_modified = {2019-09-12T17:52:49.982Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {nakandala2016anatomy},
 source_type = {inproceedings},
 private_publication = {false},
 abstract = {The SEAGrid science gateway provides scientists and educators with user interfaces and tools for conducting computational chemistry, material science, and engineering experiments online using XSEDE and campus computing resources. This paper describes the architecture of the recently completed technology refresh for the gateway, replacing its desktop user interface, adding a web browser user interface, using Apache Airavata middleware for job management, and providing enhanced data search and feature extraction capabilities. These introduce several challenges, particularly in providing unified authentication and authorization mechanisms to middleware services for the desktop and web clients, and in extending Apache Airavata middleware with new components. Access, authentication, and authorization problems were solved by using standard-based approaches (OAuth2, XACML) that were implemented by incorporating WSO2's Identity Server into both SEAGrid and Apache Airavata. SEAGrid-specific data extraction capabilities were added to Airavata middleware using a message-based component approach. This approach is generalizable to other advanced and gateway-specific capabilities and enables Airavata to add additional data analysis components without modifying its core functionality.},
 bibtype = {inproceedings},
 author = {Nakandala, Supun and Pamidighantam, Sudhakar and Yodage, Shameera and Doshi, Nipurn and Abeysinghe, Eroma and Kankanamalage, Chathuri Peli and Marru, Suresh and Pierce, Marlon},
 doi = {10.1145/2949550.2949591},
 booktitle = {Proceedings of the XSEDE16 on Diversity, Big Data, and Science at Scale - XSEDE16}
}

The SEAGrid science gateway provides scientists and educators with user interfaces and tools for conducting computational chemistry, material science, and engineering experiments online using XSEDE and campus computing resources. This paper describes the architecture of the recently completed technology refresh for the gateway, replacing its desktop user interface, adding a web browser user interface, using Apache Airavata middleware for job management, and providing enhanced data search and feature extraction capabilities. These introduce several challenges, particularly in providing unified authentication and authorization mechanisms to middleware services for the desktop and web clients, and in extending Apache Airavata middleware with new components. Access, authentication, and authorization problems were solved by using standard-based approaches (OAuth2, XACML) that were implemented by incorporating WSO2's Identity Server into both SEAGrid and Apache Airavata. SEAGrid-specific data extraction capabilities were added to Airavata middleware using a message-based component approach. This approach is generalizable to other advanced and gateway-specific capabilities and enables Airavata to add additional data analysis components without modifying its core functionality.

@article{
 title = {Integrating Apache Airavata with Docker, Marathon, and Mesos},
 type = {article},
 year = {2016},
 pages = {1952-1959},
 volume = {28},
 id = {c8d0b66e-575f-3bb7-8b0c-16f46fdf8e1e},
 created = {2018-02-27T18:07:56.052Z},
 file_attached = {false},
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 last_modified = {2018-02-27T18:07:56.052Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {saha2016integrating},
 source_type = {article},
 private_publication = {false},
 bibtype = {article},
 author = {Saha, Pankaj and Govindaraju, Madhusudhan and Marru, Suresh and Pierce, Marlon},
 journal = {Concurrency and Computation: Practice and Experience},
 number = {7}
}

@article{
 title = {Community Science Exemplars in SEAGrid Science Gateway: Apache Airavata Based Implementation of Advanced Infrastructure},
 type = {article},
 year = {2016},
 pages = {1927-1939},
 volume = {80},
 websites = {https://linkinghub.elsevier.com/retrieve/pii/S1877050916310262},
 publisher = {Elsevier},
 id = {150b240a-4759-3161-aab8-0acbc8b5882d},
 created = {2018-02-27T18:07:56.701Z},
 file_attached = {false},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
 group_id = {0e433c5b-85c4-32aa-851c-c145aac9f80f},
 last_modified = {2019-09-12T17:52:49.797Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {pamidighantam2016community},
 source_type = {article},
 private_publication = {false},
 abstract = {We describe the science discovered by some of the community of researchers using the SEAGrid Science gateway. Specific science projects to be discussed include calcium carbonate and bicarbonate hydrochemistry, mechanistic studies of redox proteins and diffraction modeling of metal and metal-oxide structures and interfaces. The modeling studies involve a variety of ab initio and molecular dynamics computational techniques and coupled execution of a workflows using specific set of applications enabled in the SEAGrid Science Gateway. The integration of applications and resources that enable workflows that couple empirical, semi-empirical, ab initio DFT, and Moller-Plesset perturbative models and combine computational and visualization modules through a single point of access is now possible through the SEAGrid gateway. Integration with the Apache Airavata infrastructure to gain a sustainable and more easily maintainable set of services is described. As part of this integration we also provide a web browser based SEAGrid Portal in addition to the SEAGrid rich client based on the previous GridChem client. We will elaborate the services and their enhancements in this process to exemplify how the new implementation will enhance the maintainability and sustainability. We will also provide exemplar science workflows and contrast how they are supported in the new deployment to showcase the adoptability and user support for services and resources.},
 bibtype = {article},
 author = {Pamidighantam, Sudhakar and Nakandala, Supun and Abeysinghe, Eroma and Wimalasena, Chathuri and Yodage, Shameera Rathnayaka and Marru, Suresh and Pierce, Marlon},
 doi = {10.1016/j.procs.2016.05.535},
 journal = {Procedia Computer Science},
 number = {C}
}

We describe the science discovered by some of the community of researchers using the SEAGrid Science gateway. Specific science projects to be discussed include calcium carbonate and bicarbonate hydrochemistry, mechanistic studies of redox proteins and diffraction modeling of metal and metal-oxide structures and interfaces. The modeling studies involve a variety of ab initio and molecular dynamics computational techniques and coupled execution of a workflows using specific set of applications enabled in the SEAGrid Science Gateway. The integration of applications and resources that enable workflows that couple empirical, semi-empirical, ab initio DFT, and Moller-Plesset perturbative models and combine computational and visualization modules through a single point of access is now possible through the SEAGrid gateway. Integration with the Apache Airavata infrastructure to gain a sustainable and more easily maintainable set of services is described. As part of this integration we also provide a web browser based SEAGrid Portal in addition to the SEAGrid rich client based on the previous GridChem client. We will elaborate the services and their enhancements in this process to exemplify how the new implementation will enhance the maintainability and sustainability. We will also provide exemplar science workflows and contrast how they are supported in the new deployment to showcase the adoptability and user support for services and resources.

@article{
 title = {Gathering requirements for advancing simulations in HPC infrastructures via science gateways},
 type = {article},
 year = {2016},
 keywords = {Computation theory; Large scale systems; Web crawl,Computational science; Computational simulation;,Distributed computer systems},
 websites = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85015395737&doi=10.1016%2Fj.future.2017.02.042&partnerID=40&md5=083c74b7a31e9af48390ff775de4f7cf},
 publisher = {Elsevier B.V.},
 id = {9c89222f-efbf-3e64-9f83-df8779fa68d9},
 created = {2018-02-27T18:07:56.874Z},
 file_attached = {false},
 profile_id = {42d295c0-0737-38d6-8b43-508cab6ea85d},
 group_id = {0e433c5b-85c4-32aa-851c-c145aac9f80f},
 last_modified = {2018-02-27T18:07:56.874Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Gesing2016},
 source_type = {article},
 notes = {cited By 0; Article in Press},
 private_publication = {false},
 abstract = {Compute-intensive simulations are often based on complex scientific theories and necessitate high-performance computing (HPC) infrastructures to deliver results in reasonable time. While domain researchers are experts in their field and apply sophisticated theoretical models in computational simulations, they are not necessarily also HPC experts or IT specialists in general. Thus, they appreciate easy-to-use solutions tailored to their research, which hide the complex underlying computing and data infrastructures. Science gateways form such end-to-end solutions and their development for compute-intensive simulations necessitates expertise to connect HPC research infrastructures including grid and cloud infrastructures to support with the efficient access to such resources. HPC experts and IT specialists fulfilling this task may have only rudimentary knowledge about the research domain of a simulation. Thus, it is crucial that they gather the requirements of a research use case, which they aim to support efficiently via a science gateway.In the last 10 years quite a few web development frameworks, science gateway frameworks and APIs with different foci and strengths have evolved to support the developers of science gateways in implementing an intuitive solution for a target research domain. The selection of a suitable technology for a specific use case is essential and helps reducing the effort in implementing the science gateway by re-using existing software or frameworks. Thus, a solution for a user community can be provided more efficiently. This paper introduces the general architecture of science gateways, goes into detail for criteria to design science gateways efficiently and gives examples of mature science gateways and science gateway frameworks. © 2017 Elsevier B.V.},
 bibtype = {article},
 author = {Gesing, S and Dooley, R and Pierce, M and Krüger, J and Grunzke, R and Herres-Pawlis, S and Hoffmann, A},
 doi = {10.1016/j.future.2017.02.042},
 journal = {Future Generation Computer Systems}
}

Compute-intensive simulations are often based on complex scientific theories and necessitate high-performance computing (HPC) infrastructures to deliver results in reasonable time. While domain researchers are experts in their field and apply sophisticated theoretical models in computational simulations, they are not necessarily also HPC experts or IT specialists in general. Thus, they appreciate easy-to-use solutions tailored to their research, which hide the complex underlying computing and data infrastructures. Science gateways form such end-to-end solutions and their development for compute-intensive simulations necessitates expertise to connect HPC research infrastructures including grid and cloud infrastructures to support with the efficient access to such resources. HPC experts and IT specialists fulfilling this task may have only rudimentary knowledge about the research domain of a simulation. Thus, it is crucial that they gather the requirements of a research use case, which they aim to support efficiently via a science gateway.In the last 10 years quite a few web development frameworks, science gateway frameworks and APIs with different foci and strengths have evolved to support the developers of science gateways in implementing an intuitive solution for a target research domain. The selection of a suitable technology for a specific use case is essential and helps reducing the effort in implementing the science gateway by re-using existing software or frameworks. Thus, a solution for a user community can be provided more efficiently. This paper introduces the general architecture of science gateways, goes into detail for criteria to design science gateways efficiently and gives examples of mature science gateways and science gateway frameworks. © 2017 Elsevier B.V.

@inproceedings{
 title = {GeoGateway: A system for analysis of UAVSAR data products},
 type = {inproceedings},
 year = {2016},
 pages = {210-213},
 institution = {IEEE},
 id = {db9f7503-9f80-3697-97ce-2d54c0f94b0c},
 created = {2018-02-27T18:07:57.270Z},
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 hidden = {false},
 citation_key = {donnellan2016geogateway},
 source_type = {inproceedings},
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 bibtype = {inproceedings},
 author = {Donnellan, Andrea and Parker, Jay and Glasscoe, Margaret and Granat, Robert and Pierce, Marlon and Wang, Jun and Ma, Yu and Ludwig, Lisa Grant and Rundle, John},
 booktitle = {Geoscience and Remote Sensing Symposium (IGARSS), 2016 IEEE International}
}

@inproceedings{
 title = {Cyberinfrastructure as a platform to facilitate effective collaboration between institutions and support collaboratories},
 type = {inproceedings},
 year = {2016},
 volume = {06-09-Nove},
 id = {4f801353-3d52-3c81-a448-cdeff4475a6d},
 created = {2018-02-27T18:08:03.154Z},
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 last_modified = {2019-08-26T16:31:58.363Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {Researchers, scientists, engineers, granting agencies, and increasingly complex research problems have given rise to the scientific "collaboratory"-large organizations that span many institutions, with individual members working together to explore a particular phenomenon. These organizations require computational resources in order to support analyses and to provide platforms where the collaborators can interact. The XSEDE Community Infrastructure (XCI) group assists campuses in using their own resources and promotes the sharing of those resources in order to create collaboratories improving use of the nation's collective cyberinfrastructure. Currently XCI provides toolkits and training, and collaborates with organizations such as ACI-REF, XSEDE Campus Champions, and the Open Science Grid to identify tools and best practices that support the community. This paper discusses the progress in and barriers to developing a robust collaborative environment where computational resources can be shared.},
 bibtype = {inproceedings},
 author = {Coulter, E. and Knepper, R. and Pierce, M. and Fischer, J. and Lifka, D. and Stewart, C. and Hallock, B. and Navarro, J.P.},
 doi = {10.1145/2974927.2974962},
 booktitle = {Proceedings ACM SIGUCCS User Services Conference}
}

Researchers, scientists, engineers, granting agencies, and increasingly complex research problems have given rise to the scientific "collaboratory"-large organizations that span many institutions, with individual members working together to explore a particular phenomenon. These organizations require computational resources in order to support analyses and to provide platforms where the collaborators can interact. The XSEDE Community Infrastructure (XCI) group assists campuses in using their own resources and promotes the sharing of those resources in order to create collaboratories improving use of the nation's collective cyberinfrastructure. Currently XCI provides toolkits and training, and collaborates with organizations such as ACI-REF, XSEDE Campus Champions, and the Open Science Grid to identify tools and best practices that support the community. This paper discusses the progress in and barriers to developing a robust collaborative environment where computational resources can be shared.

@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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 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 = {Apache Airavata as a Laboratory: Architecture and Case Study for Component-Based Gateway Middleware},
 type = {inproceedings},
 year = {2015},
 pages = {19-26},
 websites = {http://dl.acm.org/citation.cfm?doid=2753524.2753529},
 publisher = {ACM Press},
 city = {New York, New York, USA},
 institution = {ACM},
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 abstract = {Science gateways are more than user interfaces to computational grids and clouds. Gateways are middleware in their own right, providing flexible, lightweight federations of heterogenous collections of computing resources (such as campus clusters, supercomputers, computational clouds), all of which remain challenges for many alternative middleware approaches. Gateways also are notable for providing science application-centric interfaces to computing resources rather than resource-centric views. An important challenge for science gateway research is to generalize specific science gateway strategies, defining a reference architecture that emcompasses major gateway capabilities while enabling implementation flexibility. Such a reference architecture should also enable "platform as a service" approaches that provide hosted versions of common gateway capabilities. In this paper, we summarize the Apache Airavata software system as a candidate reference architecture for science gateways. We propose the use of a component-based architecture to encompass major gateway capabilities (such as metadata management, meta-scheduling, execution management, and messaging). We examine the messaging system component in this abstract architecture in detail and describe its re-implementation and validation using third party messaging system software to replace a custom-built messaging system. Besides the operational validation of this specific component, we infer a preliminary validation of the overall architecture. The flexibility of component implementations within an overall architecture is essential as it allows gateway middleware to be the subject of distributed computing research for its own sake while also ensuring that we don't get locked into less than optimal implementations for gateway operations.},
 bibtype = {inproceedings},
 author = {Marru, Suresh and Pierce, Marlon and Pamidighantam, Sudhakar and Wimalasena, Chathuri},
 doi = {10.1145/2753524.2753529},
 booktitle = {Proceedings of the 1st Workshop on The Science of Cyberinfrastructure Research, Experience, Applications and Models - SCREAM '15}
}

Science gateways are more than user interfaces to computational grids and clouds. Gateways are middleware in their own right, providing flexible, lightweight federations of heterogenous collections of computing resources (such as campus clusters, supercomputers, computational clouds), all of which remain challenges for many alternative middleware approaches. Gateways also are notable for providing science application-centric interfaces to computing resources rather than resource-centric views. An important challenge for science gateway research is to generalize specific science gateway strategies, defining a reference architecture that emcompasses major gateway capabilities while enabling implementation flexibility. Such a reference architecture should also enable "platform as a service" approaches that provide hosted versions of common gateway capabilities. In this paper, we summarize the Apache Airavata software system as a candidate reference architecture for science gateways. We propose the use of a component-based architecture to encompass major gateway capabilities (such as metadata management, meta-scheduling, execution management, and messaging). We examine the messaging system component in this abstract architecture in detail and describe its re-implementation and validation using third party messaging system software to replace a custom-built messaging system. Besides the operational validation of this specific component, we infer a preliminary validation of the overall architecture. The flexibility of component implementations within an overall architecture is essential as it allows gateway middleware to be the subject of distributed computing research for its own sake while also ensuring that we don't get locked into less than optimal implementations for gateway operations.

@inproceedings{
 title = {Disaster Response Tools for Decision Support and Data Discovery-E-DECIDER and GeoGateway},
 type = {inproceedings},
 year = {2015},
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 author = {Glasscoe, M T and Donnellan, A and Parker, J W and Granat, R A and Lyzenga, G A and Pierce, M E and Wang, J and Grant Ludwig, L and Eguchi, R T and Huyck, C K and others, undefined},
 booktitle = {AGU Fall Meeting Abstracts}
}

@article{
 title = {The GenApp framework integrated with Airavata for managed compute resource submissions},
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 year = {2015},
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 journal = {Concurrency and Computation: Practice and Experience},
 number = {16}
}

@article{
 title = {Science gateways today and tomorrow: Positive perspectives of nearly 5000 members of the research community},
 type = {article},
 year = {2015},
 keywords = {Web interfaces,cyberinfrastructure,portals,science/engineering gateways,software development,survey},
 pages = {4252-4268},
 volume = {27},
 websites = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84944911705&doi=10.1002%2Fcpe.3526&partnerID=40&md5=4dc5238c285d05e8713efa05ff42d452},
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 abstract = {Science gateways are digital interfaces to advanced technologies that\nsupport science/engineering research/education. Frequently implemented\nas Web and mobile applications, they provide access to community\nresources such as software, data, collaboration tools, instrumentation,\nand high-performance computing. We anticipate opportunities for growth\nwithin a fragmented community. Through a large-scale survey, we measured\nthe extent and characteristics of the gateway community (reliance on\ngateways and nature of existing resources) to understand useful services\nand support for builders and users. We administered an online survey to\nnearly 29,000 principal investigators, senior administrators, and people\nwith gateway affiliations. Nearly 5000 respondents represented diverse\nexpertise and geography. The majority of researchers/educators indicated\nthat specialized online resources were important to their work. They\nchoose technologies by asking colleagues and looking for documentation,\ndemonstrated reliability, and technical support; adaptability via\ncustomizing or open-source standards was another priority. Research\ngroups commonly provide their own resources, but public/academic\ninstitutions and commercial services also provide substantial offerings.\nApplication creators and administrators welcome external services\nproviding guidance such as technology selection, sustainability\nplanning, evaluation, and specialized expertise (e.g., quality assurance\nand design). Technologies are diverse, so flexibility and ongoing\ncommunity input are essential, as is offering specific, easy-to-access\ntraining, community support, and professional development. Copyright (c)\n2015 John Wiley & Sons, Ltd.},
 bibtype = {article},
 author = {Lawrence, Katherine A. and Zentner, Michael and Wilkins-Diehr, Nancy and Wernert, Julie A. and Pierce, Marlon and Marru, Suresh and Michael, Scott},
 doi = {10.1002/cpe.3526},
 journal = {Concurrency Computation },
 number = {16}
}

Science gateways are digital interfaces to advanced technologies that\nsupport science/engineering research/education. Frequently implemented\nas Web and mobile applications, they provide access to community\nresources such as software, data, collaboration tools, instrumentation,\nand high-performance computing. We anticipate opportunities for growth\nwithin a fragmented community. Through a large-scale survey, we measured\nthe extent and characteristics of the gateway community (reliance on\ngateways and nature of existing resources) to understand useful services\nand support for builders and users. We administered an online survey to\nnearly 29,000 principal investigators, senior administrators, and people\nwith gateway affiliations. Nearly 5000 respondents represented diverse\nexpertise and geography. The majority of researchers/educators indicated\nthat specialized online resources were important to their work. They\nchoose technologies by asking colleagues and looking for documentation,\ndemonstrated reliability, and technical support; adaptability via\ncustomizing or open-source standards was another priority. Research\ngroups commonly provide their own resources, but public/academic\ninstitutions and commercial services also provide substantial offerings.\nApplication creators and administrators welcome external services\nproviding guidance such as technology selection, sustainability\nplanning, evaluation, and specialized expertise (e.g., quality assurance\nand design). Technologies are diverse, so flexibility and ongoing\ncommunity input are essential, as is offering specific, easy-to-access\ntraining, community support, and professional development. Copyright (c)\n2015 John Wiley & Sons, Ltd.

@article{
 title = {Potential for a large earthquake near Los Angeles inferred from the 2014 La Habra earthquake},
 type = {article},
 year = {2015},
 pages = {378-385},
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 author = {Donnellan, Andrea and Grant Ludwig, Lisa and Parker, Jay W and Rundle, John B and Wang, Jun and Pierce, Marlon and Blewitt, Geoffrey and Hensley, Scott},
 journal = {Earth and Space Science},
 number = {9}
}

@article{
 title = {Multihazard simulation and cyberinfrastructure},
 type = {article},
 year = {2015},
 pages = {2083-2085},
 volume = {172},
 publisher = {Springer Basel},
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 author = {Donnellan, Andrea and Williams, Charles and Pierce, Marlon},
 journal = {Pure and Applied Geophysics},
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}

@article{
 title = {E-decider: Using earth science data and modeling tools to develop decision support for earthquake disaster response},
 type = {article},
 year = {2015},
 pages = {2305-2324},
 volume = {172},
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 author = {Glasscoe, Margaret T and Wang, Jun and Pierce, Marlon E and Yoder, Mark R and Parker, Jay W and Burl, Michael C and Stough, Timothy M and Granat, Robert A and Donnellan, Andrea and Rundle, John B and others, undefined},
 journal = {Pure and Applied Geophysics},
 number = {8}
}

@article{
 title = {Advantages to Geoscience and disaster response from QuakeSim implementation of interferometric radar maps in a GIS database system},
 type = {article},
 year = {2015},
 pages = {2295-2304},
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 author = {Parker, Jay and Donnellan, Andrea and Glasscoe, Margaret and Fox, Geoffrey and Wang, Jun and Pierce, Marlon and Ma, Yu and Wang, Jun and Ma, Yu},
 journal = {Pure and Applied Geophysics},
 number = {8}
}

@article{
 title = {Web Services for Dynamic Coloring of UAVSAR Images},
 type = {article},
 year = {2015},
 pages = {2325-2332},
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 journal = {Pure and Applied Geophysics},
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@inproceedings{
 title = {An Overview of the XSEDE Extended Collaborative Support Program},
 type = {inproceedings},
 year = {2015},
 keywords = {Collaborative support,Computer science,Computers,Cyber infrastructures,Sci,Supercomputers},
 pages = {3-13},
 volume = {595},
 websites = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84964076487&doi=10.1007%2F978-3-319-32243-8_1&partnerID=40&md5=4c26cab3d25ddd6fb9bd0205e1f593e6},
 publisher = {Springer Verlag},
 institution = {Springer International Publishing},
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 citation_key = {Wilkins-Diehr20163},
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 notes = {<b>From Duplicate 2 (<i>An overview of the XSEDE extended collaborative support program</i> - Wilkins-Diehr, N; Sanielevici, S; Alameda, J; Cazes, J; Crosby, L; Pierce, M; Roskies, R)<br/></b><br/>cited By 4; Conference of 6th International Conference on High Performance Computer Applications, ISUM 2015 ; Conference Date: 9 March 2015 Through 13 March 2015; Conference Code:173549},
 private_publication = {false},
 abstract = {The Extreme Science and Engineering Discovery Environment (XSEDE) is a flagship cyberinfrastructure project funded by the US National Science Foundation (NSF). XSEDE’s Extended Collaborative Support Services (ECSS) program is a significant component of the XSEDE effort, dedicated to extended engagements with our user community which transform their research. We describe the organization, operation and some highlights of the program in this submission. © Springer International Publishing Switzerland 2016.},
 bibtype = {inproceedings},
 author = {Wilkins-Diehr, Nancy and Sanielevici, Sergiu and Alameda, Jay and Cazes, John and Crosby, Lonnie and Pierce, Marlon and Roskies, Ralph},
 editor = {Gitler I., Klapp J},
 doi = {10.1007/978-3-319-32243-8_1},
 booktitle = {International Conference on Supercomputing}
}

The Extreme Science and Engineering Discovery Environment (XSEDE) is a flagship cyberinfrastructure project funded by the US National Science Foundation (NSF). XSEDE’s Extended Collaborative Support Services (ECSS) program is a significant component of the XSEDE effort, dedicated to extended engagements with our user community which transform their research. We describe the organization, operation and some highlights of the program in this submission. © Springer International Publishing Switzerland 2016.

@inproceedings{
 title = {Science gateways-leveraging modeling and simulations in HPC infrastructures via increased usability},
 type = {inproceedings},
 year = {2015},
 pages = {19-26},
 institution = {IEEE},
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 author = {Gesing, Sandra and Dooley, Rion and Pierce, Marlon and Krüger, Jens and Grunzke, Richard and Herres-Pawlis, Sonja and Hoffmann, Alexander},
 booktitle = {High Performance Computing & Simulation (HPCS), 2015 International Conference on}
}

@inproceedings{
 title = {GenApp module execution and airavata integration},
 type = {inproceedings},
 year = {2015},
 keywords = {Compute resources; Direct execution; Execution mo,Computer aided software engineering; Middleware; R,Computer circuits},
 pages = {9-12},
 websites = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84963550688&doi=10.1109%2FGCE.2014.12&partnerID=40&md5=4b4ed50208af0ca2e7fe08841ae71ba7},
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 citation_key = {Brookes20159},
 source_type = {conference},
 notes = {cited By 0; Conference of 9th Gateway Computing Environments Workshop, GCE 2014 ; Conference Date: 21 November 2014; Conference Code:118652},
 private_publication = {false},
 abstract = {A new framework (GenApp) for rapid generation of scientific applications running on a variety of systems including science gateways has recently been developed. This framework builds a user interface for a variety of target environments on a collection of executable modules. The method for execution of the modules is unrestricted by the framework. Initial implementation supports direct execution, and not queue managed submission, on a user's workstation, a web server, or a compute resource accessible from the web server. After a successful workshop, it was discovered that long running jobs would sometimes fail, due to the loss of a TCP connection. This precipitated an improvement to the execution method with the bonus of easily allowing multiple web clients to attach to the running job. Finally, to support a diversity of queue managed compute resources, a Google Summer of Code project was completed to integrate the Apache Airavata middleware as an additional execution model within the GenApp framework. © 2014 IEEE.},
 bibtype = {inproceedings},
 author = {Brookes, E H and Anjum, N and Curtis, J E and Marru, S and Singh, R and Pierce, M},
 doi = {10.1109/GCE.2014.12},
 booktitle = {Proceedings of GCE 2014: 9th Gateway Computing Environments Workshop, held in conjunction with SC 2014: The International Conference for High Performance Computing, Networking, Storage and Analysis}
}

A new framework (GenApp) for rapid generation of scientific applications running on a variety of systems including science gateways has recently been developed. This framework builds a user interface for a variety of target environments on a collection of executable modules. The method for execution of the modules is unrestricted by the framework. Initial implementation supports direct execution, and not queue managed submission, on a user's workstation, a web server, or a compute resource accessible from the web server. After a successful workshop, it was discovered that long running jobs would sometimes fail, due to the loss of a TCP connection. This precipitated an improvement to the execution method with the bonus of easily allowing multiple web clients to attach to the running job. Finally, to support a diversity of queue managed compute resources, a Google Summer of Code project was completed to integrate the Apache Airavata middleware as an additional execution model within the GenApp framework. © 2014 IEEE.

@inproceedings{
 title = {Sustained software for cyberinfrastructure: Analyses of successful efforts with a focus on NSF-funded software},
 type = {inproceedings},
 year = {2015},
 pages = {63-72},
 websites = {http://dl.acm.org/citation.cfm?doid=2753524.2753533},
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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, Craig A. and Barnett, William K. and Wernert, Eric A. and Wernert, Julie A. and Welch, Von and Knepper, Richard},
 doi = {10.1145/2753524.2753533},
 booktitle = {Proceedings of the 1st Workshop on The Science of Cyberinfrastructure Research, Experience, Applications and Models - SCREAM '15}
}

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 = {Publishing and consuming GLUE v2.0 resource information in XSEDE},
 type = {inproceedings},
 year = {2015},
 pages = {1-8},
 volume = {2015-July},
 websites = {http://dl.acm.org/citation.cfm?doid=2792745.2792770},
 month = {7},
 publisher = {ACM Press},
 day = {26},
 city = {New York, New York, USA},
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 bibtype = {inproceedings},
 author = {Smith, Warren and Pamidighantam, Sudhakar and Navarro, John-Paul},
 doi = {10.1145/2792745.2792770},
 booktitle = {Proceedings of the 2015 XSEDE Conference on Scientific Advancements Enabled by Enhanced Cyberinfrastructure - XSEDE '15}
}

XSEDE users, science gateways, and services need a variety of accurate information about XSEDE resources so that they can use those resources effectively. They need information to decide which resources to use, to track their usage of resources, and to provide services to their users. To support this, XSEDE is deploying a new system to gather and publish static and dynamic resource information. This paper gives an overview of the resource information available with this new system, describes the design and performance of the software and services that make up this system, and finally provides examples of how to use this new resource information.

@article{
 title = {Ab Initio Studies of Calcium Carbonate Hydration},
 type = {article},
 year = {2015},
 keywords = {CaCO3,bidentate,cluster,hydration,monodentate},
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 abstract = {Ab initio simulations of large hydrated calcium carbonate clusters are challenging due to the existence of multiple local energy minima. Extensive conformational searches around hydrated calcium carbonate clusters (CaCO3·nH2O for n = 1-18) were performed to find low-energy hydration structures using an efficient combination of Monte Carlo searches, density-functional tight binding (DFTB+) method, and density-functional theory (DFT) at the B3LYP level, or Møller-Plesset perturbation theory at the MP2 level. This multilevel optimization yields several low-energy structures for hydrated calcium carbonate. Structural and energetics analysis of the hydration of these clusters revealed a first hydration shell composed of 12 water molecules. Bond-length and charge densities were also determined for different cluster sizes. The solvation of calcium carbonate in bulk water was investigated by placing the explicitly solvated CaCO3·nH2O clusters in a polarizable continuum model (PCM). The findings of this study provide new insights into the energetics and structure of hydrated calcium carbonate and contribute to the understanding of mechanisms where calcium carbonate formation or dissolution is of relevance. © 2015 American Chemical Society.},
 bibtype = {article},
 author = {Lopez-Berganza, Josue A. and Diao, Yijue and Pamidighantam, Sudhakar and Espinosa-Marzal, Rosa M.},
 doi = {10.1021/acs.jpca.5b09006},
 journal = {The Journal of Physical Chemistry A},
 number = {47}
}

Ab initio simulations of large hydrated calcium carbonate clusters are challenging due to the existence of multiple local energy minima. Extensive conformational searches around hydrated calcium carbonate clusters (CaCO3·nH2O for n = 1-18) were performed to find low-energy hydration structures using an efficient combination of Monte Carlo searches, density-functional tight binding (DFTB+) method, and density-functional theory (DFT) at the B3LYP level, or Møller-Plesset perturbation theory at the MP2 level. This multilevel optimization yields several low-energy structures for hydrated calcium carbonate. Structural and energetics analysis of the hydration of these clusters revealed a first hydration shell composed of 12 water molecules. Bond-length and charge densities were also determined for different cluster sizes. The solvation of calcium carbonate in bulk water was investigated by placing the explicitly solvated CaCO3·nH2O clusters in a polarizable continuum model (PCM). The findings of this study provide new insights into the energetics and structure of hydrated calcium carbonate and contribute to the understanding of mechanisms where calcium carbonate formation or dissolution is of relevance. © 2015 American Chemical Society.

@article{
 title = {Apache Airavata: design and directions of a science gateway framework},
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 keywords = {cyberinfrastructure,distributed computing infrastructure,science gateways},
 pages = {4282-4291},
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 bibtype = {article},
 author = {Pierce, Marlon E. and Marru, Suresh and Gunathilake, Lahiru and Wijeratne, Don Kushan and Singh, Raminder and Wimalasena, Chathuri and Ratnayaka, Shameera and Pamidighantam, Sudhakar},
 doi = {10.1002/cpe.3534},
 journal = {Concurrency and Computation: Practice and Experience},
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}

This paper provides an overview of the Apache Airavata software system for science gateways. Gateways use Airavata to manage application and workflow executions on a range of backend resources (grids, computing clouds, and local clusters). Airavata's design goal is to provide component abstractions for major tasks required to provide gateway application management. Components are not directly accessed but are instead exposed through a client Application Programming Interface. This design allows gateway developers to take full advantage of Airavata's capabilities, and Airavata developers (including those interested in middleware research) to modify Airavata's implementations and behavior. This is particularly important as Airavata evolves to become a scalable, elastic "platform as a service" for science gateways. We illustrate the capabilities of Airavata through the discussion of usage vignettes. As an Apache Software Foundation project, Airavata's open community governance model is as important as its software base. We discuss how this works within Airavata and how it may be applicable to other distributed computing infrastructure and cyber infrastructure efforts. © 2014 IEEE.

@techreport{
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@techreport{
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@inproceedings{
 title = {The apache airavata application programming interface: Overview and evaluation with the Ultrascan Science Gateway},
 type = {inproceedings},
 year = {2014},
 keywords = {Application programming interfaces (API),Cloud computing,Computer circuits,Cyber infrastructures,Execution management,Gate,Open source so},
 pages = {25-29},
 websites = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84963569382&doi=10.1109%2FGCE.2014.15&partnerID=40&md5=9baf83939a077ba2598086ca44d020c3},
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 abstract = {We present an overview of the Apache Airavata Application Programming Interface (API), describe the design choices and implementation details, and describe how API methods map to the UltraScan Science Gateway use case. The Airavata API is designed to standardize access to Airavata services that provide gateways with scientific application metadata and execution management. The API also represents an important milestone in the development of Science Gateway Platform as a Service (SciGaP), a hosted, multi-tenanted gateway service based on open source Airavata software. The UltraScan gateway is a production XSEDE gateway that has been using Airavata services for over three years through customized interfaces and represents a stringent test of the API design and implementation. © 2014 IEEE.},
 bibtype = {inproceedings},
 author = {Pierce, M and Marru, S and Demeler, B and Singh, R and Gorbet, G},
 doi = {10.1109/GCE.2014.15},
 booktitle = {Proceedings of the 9th Gateway Computing Environments Workshop (GCE '14)}
}

We present an overview of the Apache Airavata Application Programming Interface (API), describe the design choices and implementation details, and describe how API methods map to the UltraScan Science Gateway use case. The Airavata API is designed to standardize access to Airavata services that provide gateways with scientific application metadata and execution management. The API also represents an important milestone in the development of Science Gateway Platform as a Service (SciGaP), a hosted, multi-tenanted gateway service based on open source Airavata software. The UltraScan gateway is a production XSEDE gateway that has been using Airavata services for over three years through customized interfaces and represents a stringent test of the API design and implementation. © 2014 IEEE.

@inproceedings{
 title = {Apache Airavata: Design and Directions of a Science Gateway Framework},
 type = {inproceedings},
 year = {2014},
 keywords = {Apache software foundations,Application manageme,Application programming interfaces (API),Design,Distributed computer systems},
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 abstract = {This paper provides an overview of the Apache Airavata software system for science gateways. Gateways use Airavata to manage application and workflow executions on a range of backend resources (grids, computing clouds, and local clusters). Airavata's design goal is to provide component abstractions for major tasks required to provide gateway application management. Components are not directly accessed but are instead exposed through a client Application Programming Interface. This design allows gateway developers to take full advantage of Airavata's capabilities, and Airavata developers (including those interested in middleware research) to modify Airavata's implementations and behavior. This is particularly important as Airavata evolves to become a scalable, elastic "platform as a service" for science gateways. We illustrate the capabilities of Airavata through the discussion of usage vignettes. As an Apache Software Foundation project, Airavata's open community governance model is as important as its software base. We discuss how this works within Airavata and how it may be applicable to other distributed computing infrastructure and cyber infrastructure efforts. © 2014 IEEE.},
 bibtype = {inproceedings},
 author = {Pierce, Marlon and Marru, Suresh and Gunathilake, Lahiru and Kanewala, Thejaka Amila and Singh, Raminder and Wijeratne, Saminda and Wimalasena, Chathuri and Herath, Chathura and Chinthaka, Eran and Mattmann, Chris and Slominski, Aleksander and Tangchaisin, Patanachai},
 doi = {10.1109/IWSG.2014.15},
 booktitle = {2014 6th International Workshop on Science Gateways}
}

This paper provides an overview of the Apache Airavata software system for science gateways. Gateways use Airavata to manage application and workflow executions on a range of backend resources (grids, computing clouds, and local clusters). Airavata's design goal is to provide component abstractions for major tasks required to provide gateway application management. Components are not directly accessed but are instead exposed through a client Application Programming Interface. This design allows gateway developers to take full advantage of Airavata's capabilities, and Airavata developers (including those interested in middleware research) to modify Airavata's implementations and behavior. This is particularly important as Airavata evolves to become a scalable, elastic "platform as a service" for science gateways. We illustrate the capabilities of Airavata through the discussion of usage vignettes. As an Apache Software Foundation project, Airavata's open community governance model is as important as its software base. We discuss how this works within Airavata and how it may be applicable to other distributed computing infrastructure and cyber infrastructure efforts. © 2014 IEEE.

@inproceedings{
 title = {E-DECIDER Rapid Response to the M 6.0 South Napa Earthquake},
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@techreport{
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@inproceedings{
 title = {E-DECIDER Disaster Response and Decision Support Cyberinfrastructure: Technology and Challenges},
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@inproceedings{
 title = {Integrating science gateways with xsede security: A survey of credential management approaches},
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@article{
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@article{
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@inproceedings{
 title = {Cloud computing for geodetic imaging data processing, analysis, and modeling},
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 pages = {1-9},
 institution = {IEEE},
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 author = {Donnellan, Andrea and Parker, Jay W and Wang, Jun and Ma, Yu and Pierce, Marlon},
 booktitle = {Aerospace Conference, 2014 IEEE}
}

@inproceedings{
 title = {Science Gateways, Scientific Workflows and Open Community Software},
 type = {inproceedings},
 year = {2014},
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 bibtype = {inproceedings},
 author = {Pierce, M E and Marru, S},
 booktitle = {AGU Fall Meeting Abstracts}
}

@inproceedings{
 title = {A credential store for multi-tenant science gateways},
 type = {inproceedings},
 year = {2014},
 pages = {445-454},
 institution = {IEEE},
 id = {6c105b9d-2e86-3a84-b270-6cdd70e5154a},
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 citation_key = {kanewala2014credential},
 source_type = {inproceedings},
 private_publication = {false},
 bibtype = {inproceedings},
 author = {Kanewala, Thejaka Amila and Marru, Suresh and Basney, Jim and Pierce, Marlon},
 booktitle = {Cluster, Cloud and Grid Computing (CCGrid), 2014 14th IEEE/ACM International Symposium on}
}

@inproceedings{
 title = {Combined UAVSAR and GPS Estimates of Fault Slip for the M 6.0 South Napa Earthquake},
 type = {inproceedings},
 year = {2014},
 id = {bdb7d726-e5f8-3658-81dd-59bd24b6cfdf},
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 citation_key = {donnellan2014combined},
 source_type = {inproceedings},
 private_publication = {false},
 bibtype = {inproceedings},
 author = {Donnellan, A and Parker, J W and Hawkins, B and Hensley, S and Jones, C E and Owen, S E and Moore, A W and Wang, J and Pierce, M E and Rundle, J B},
 booktitle = {AGU Fall Meeting Abstracts}
}

@book{
 title = {Applications of E-DECIDER Decision Support Tools for Disaster Response and Recovery},
 type = {book},
 year = {2014},
 id = {41d16fe6-8d69-30a1-af4b-43694651f734},
 created = {2018-02-27T18:08:00.610Z},
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 author = {Glasscoe, Margaret T and Parker, Jay W and Wang, Jun and Pierce, Marlon E and Yoder, Mark R and Eguchi, Ronald T and Huyck, Charles K and Hu, ZhengHui and Bevington, John and Ghosh, Shubharoop and others, undefined}
}

@inproceedings{
 title = {GenApp module execution and airavata integration},
 type = {inproceedings},
 year = {2014},
 pages = {9-12},
 institution = {IEEE Press},
 id = {6a66678e-f395-3f0b-9b4f-c75ac3aaba03},
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 citation_key = {brookes2014genapp},
 source_type = {inproceedings},
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 bibtype = {inproceedings},
 author = {Brookes, Emre H and Anjum, Nadeem and Curtis, Joseph E and Marru, Suresh and Singh, Raminder and Pierce, Marlon},
 booktitle = {Proceedings of the 9th Gateway Computing Environments Workshop}
}

@inbook{
 type = {inbook},
 year = {2014},
 pages = {6562-6572},
 websites = {http://services.igi-global.com/resolvedoi/resolve.aspx?doi=10.4018/978-1-4666-5888-2.ch645,http://hdl.handle.net/2022/18608},
 publisher = {IGI Global},
 city = {Hershey, PA, USA},
 id = {4c18f066-2686-3cbf-b58f-90cfeb7186c0},
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 source_type = {CHAP},
 private_publication = {false},
 abstract = {Computers accelerate our ability to achieve scientific breakthroughs. As technology evolves and new research needs come to light, the role for cyberinfrastructure as “knowledge” infrastructure continues to expand. This article defines and discusses cyberinfrastructure and the related topics of science gateways and campus bridging; identifies future challenges in cyberinfrastructure; and discusses challenges and opportunities related to the evolution of cyberinfrastructure, “big data” (datacentric, data-enabled, and data-intensive research and data analytics), and cloud computing.},
 bibtype = {inbook},
 author = {Stewart, Craig A and Knepper, Richard and Link, Matthew R and Pierce, Marlon and Wernert, Eric and Wilkins-Diehr, Nancy},
 editor = {Mehdi Khosrow-Pour, D B A},
 doi = {10.4018/978-1-4666-5888-2.ch645},
 chapter = {Cyberinfrastructure, Science Gateways, Campus Bridging, and Cloud Computing},
 title = {Encyclopedia of Information Science and Technology, Third Edition}
}

Computers accelerate our ability to achieve scientific breakthroughs. As technology evolves and new research needs come to light, the role for cyberinfrastructure as “knowledge” infrastructure continues to expand. This article defines and discusses cyberinfrastructure and the related topics of science gateways and campus bridging; identifies future challenges in cyberinfrastructure; and discusses challenges and opportunities related to the evolution of cyberinfrastructure, “big data” (datacentric, data-enabled, and data-intensive research and data analytics), and cloud computing.

@inproceedings{
 title = {Who Cares about Science Gateways? A Large-Scale Survey of Community Use and Needs},
 type = {inproceedings},
 year = {2014},
 keywords = {Cyberinfrastructure,High-performance computing,Science/engineering gateways/portals,Software development,Web interfaces},
 pages = {1-4},
 websites = {http://ieeexplore.ieee.org/document/7021839/},
 month = {11},
 publisher = {IEEE},
 day = {23},
 id = {8098444f-e925-3591-9bf5-77f0b9de2eb1},
 created = {2019-09-18T17:42:04.077Z},
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 authored = {false},
 confirmed = {true},
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 bibtype = {inproceedings},
 author = {Lawrence, Katherine A. and Wilkins-Diehr, Nancy and Wernert, Julie A. and Pierce, Marlon and Zentner, Michael and Marru, Suresh},
 doi = {10.1109/GCE.2014.11},
 booktitle = {2014 9th Gateway Computing Environments Workshop}
}

With the rise of science gateway use in recent years, we anticipate there are additional opportunities for growth, but the field is currently fragmented. We describe our efforts to measure the extent and characteristics of the gateway community through a large-scale survey. Our goal was to understand what type of support services might be provided to the gateway community.

@article{
 title = {Advancements of the UltraScan scientific gateway for open standards-based cyberinfrastructures},
 type = {article},
 year = {2014},
 keywords = {Analytical ultracentrifugation,Apache Airavata,Standards,Web browsers},
 pages = {2280-2291},
 volume = {26},
 websites = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84905090240&doi=10.1002%2Fcpe.3251&partnerID=40&md5=c614403ec2443d03021feae3ea751c39,http://doi.wiley.com/10.1002/cpe.3251},
 month = {9},
 publisher = {John Wiley and Sons Ltd},
 day = {10},
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 last_modified = {2019-09-18T20:53:22.133Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Memon20142280},
 source_type = {article},
 notes = {cited By 4},
 private_publication = {false},
 abstract = {The UltraScan data analysis application is a software package that is able to take advantage of computational resources in order to support the interpretation of analytical ultracentrifugation experiments. Since 2006, the UltraScan scientific gateway has been used with Web browsers in TeraGrid by scientists studying the solution properties of biological and synthetic molecules. UltraScan supports its users with a scientific gateway in order to leverage the power of supercomputing. In this contribution, we will focus on several advancements of the UltraScan scientific gateway architecture with a standardized job management while retaining its lightweight design and end user interaction experience. This paper also presents insights into a production deployment of UltraScan in Europe. The approach is based on open standards with respect to job management and submissions to the Extreme Science and Engineering Discovery Environment in the USA and to similar infrastructures in Europe such as the European Grid Infrastructure or the Partnership for Advanced Computing in Europe (PRACE). Our implementation takes advantage of the Apache Airavata framework for scientific gateways that lays the foundation for easy integration into several other scientific gateways. Copyright © 2014 John Wiley & Sons, Ltd.},
 bibtype = {article},
 author = {Memon, Shahbaz and Riedel, Morris and Janetzko, Florian and Demeler, Borries and Gorbet, Gary and Marru, Suresh and Grimshaw, Andrew and Gunathilake, Lahiru and Singh, Raminder and Attig, Norbert and Lippert, Thomas},
 doi = {10.1002/cpe.3251},
 journal = {Concurrency and Computation: Practice and Experience},
 number = {13}
}

The UltraScan data analysis application is a software package that is able to take advantage of computational resources in order to support the interpretation of analytical ultracentrifugation experiments. Since 2006, the UltraScan scientific gateway has been used with Web browsers in TeraGrid by scientists studying the solution properties of biological and synthetic molecules. UltraScan supports its users with a scientific gateway in order to leverage the power of supercomputing. In this contribution, we will focus on several advancements of the UltraScan scientific gateway architecture with a standardized job management while retaining its lightweight design and end user interaction experience. This paper also presents insights into a production deployment of UltraScan in Europe. The approach is based on open standards with respect to job management and submissions to the Extreme Science and Engineering Discovery Environment in the USA and to similar infrastructures in Europe such as the European Grid Infrastructure or the Partnership for Advanced Computing in Europe (PRACE). Our implementation takes advantage of the Apache Airavata framework for scientific gateways that lays the foundation for easy integration into several other scientific gateways. Copyright © 2014 John Wiley & Sons, Ltd.

@inproceedings{
 title = {Performance improvement and workflow development of virtual diffraction calculations},
 type = {inproceedings},
 year = {2014},
 keywords = {Diffraction,Materials Science,Visualization,Workflow},
 publisher = {Association for Computing Machinery},
 id = {af12bedf-e635-3739-b5d6-99e616319508},
 created = {2019-09-19T15:01:23.410Z},
 accessed = {2019-09-19},
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 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
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 abstract = {Electron and x-ray diffraction are well-established experimental methods used to explore the atomic scale structure of materials. In this work, a computational algorithm is presented to produce electron and x-ray diffraction patterns directly from atomistic simulation data. This algorithm advances beyond previous virtual diffraction methods by utilizing an ultra high-resolution mesh of reciprocal space which eliminates the need for a priori knowledge of the material structure. This paper focuses on (1) algorithmic advances necessary to improve performance, memory efficiency and scalability of the virtual diffraction calculation, and (2) the integration of the diffraction algorithm into a workflow across heterogeneous computing hardware for the purposes of integrating simulations, virtual diffraction calculations and visualization of electron and x-ray diffraction patterns. Copyright 2014 ACM.},
 bibtype = {inproceedings},
 author = {Coleman, Shawn P. and Pamidighantam, Sudhakar and Koesterke, Lars and Van Moer, Mark and Spearot, Douglas E. and Wang, Yang},
 doi = {10.1145/2616498.2616552},
 booktitle = {Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment (XSEDE '14)}
}

Electron and x-ray diffraction are well-established experimental methods used to explore the atomic scale structure of materials. In this work, a computational algorithm is presented to produce electron and x-ray diffraction patterns directly from atomistic simulation data. This algorithm advances beyond previous virtual diffraction methods by utilizing an ultra high-resolution mesh of reciprocal space which eliminates the need for a priori knowledge of the material structure. This paper focuses on (1) algorithmic advances necessary to improve performance, memory efficiency and scalability of the virtual diffraction calculation, and (2) the integration of the diffraction algorithm into a workflow across heterogeneous computing hardware for the purposes of integrating simulations, virtual diffraction calculations and visualization of electron and x-ray diffraction patterns. Copyright 2014 ACM.

@article{
 title = {E-science infrastructures for molecular modeling and parametrization},
 type = {article},
 year = {2014},
 keywords = {Computational chemistry,Cyberinfrastructure,E-science,GridChem,Molecular modeling,Science and engineering simulation and design,Science gateways,Scientific workflows,Virtual organizations,XSEDE},
 pages = {576-589},
 volume = {5},
 websites = {https://linkinghub.elsevier.com/retrieve/pii/S1877750314000064},
 month = {7},
 publisher = {Elsevier},
 id = {2c3d0e82-1e36-3fbb-b20f-015e0a806e86},
 created = {2019-09-19T15:07:13.091Z},
 accessed = {2019-09-19},
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 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
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 abstract = {E-science infrastructures are becoming the essential tools for computational scientific research. In this paper, we describe two e-science infrastructures: Science and Engineering Applications Grid (SEAGrid) and molecular modeling and parametrization (ParamChem). The SEAGrid is a virtual organization with a diverse set of hardware and software resources and provides services to access such resources in a routine and transparent manner. These essential services include allocations of computational resources, client-side application interfaces, computational job and data management tools, and consulting activities. ParamChem is another e-science project dedicated for molecular force-field parametrization based on both ab-initio and molecular mechanics calculations on high performance computers (HPCs) driven by scientific workflow middleware services. Both the projects share a similar three-tier computational infrastructure that consists of a front-end client, a middleware web services layer, and a remote HPC computational layer. The client is a Java Swing desktop application with components for pre- and post-data processing, communications with middleware server and local data management. The middleware service is based on Axis2 web service and MySQL relational database, which provides functionalities for user authentication and session control, HPC resource information collections, discovery and matching, job information logging and notification. It can also be integrated with scientific workflow to manage computations on HPC resources. The grid credentials for accessing HPCs are delegated through MyProxy infrastructure. Currently SEAGrid has integrated several popular application software suites such as Gaussian for quantum chemistry, NAMD for molecular dynamics and engineering software such as Abacus for mechanical engineering. ParamChem has integrated CGenFF (CHARMM General Force-Field) for molecular force-field parametrization of drug-like molecules. Long-term storage of user data is handled by tertiary data archival mechanisms. SEAGrid science gateway serves more than 500 users while more than 1000 users use ParamChem services such as atom typing and initial force-field parameter guess at present. © 2014 Elsevier B.V.},
 bibtype = {article},
 author = {Shen, Ning and Fan, Ye and Pamidighantam, Sudhakar},
 doi = {10.1016/j.jocs.2014.01.005},
 journal = {Journal of Computational Science},
 number = {4}
}

E-science infrastructures are becoming the essential tools for computational scientific research. In this paper, we describe two e-science infrastructures: Science and Engineering Applications Grid (SEAGrid) and molecular modeling and parametrization (ParamChem). The SEAGrid is a virtual organization with a diverse set of hardware and software resources and provides services to access such resources in a routine and transparent manner. These essential services include allocations of computational resources, client-side application interfaces, computational job and data management tools, and consulting activities. ParamChem is another e-science project dedicated for molecular force-field parametrization based on both ab-initio and molecular mechanics calculations on high performance computers (HPCs) driven by scientific workflow middleware services. Both the projects share a similar three-tier computational infrastructure that consists of a front-end client, a middleware web services layer, and a remote HPC computational layer. The client is a Java Swing desktop application with components for pre- and post-data processing, communications with middleware server and local data management. The middleware service is based on Axis2 web service and MySQL relational database, which provides functionalities for user authentication and session control, HPC resource information collections, discovery and matching, job information logging and notification. It can also be integrated with scientific workflow to manage computations on HPC resources. The grid credentials for accessing HPCs are delegated through MyProxy infrastructure. Currently SEAGrid has integrated several popular application software suites such as Gaussian for quantum chemistry, NAMD for molecular dynamics and engineering software such as Abacus for mechanical engineering. ParamChem has integrated CGenFF (CHARMM General Force-Field) for molecular force-field parametrization of drug-like molecules. Long-term storage of user data is handled by tertiary data archival mechanisms. SEAGrid science gateway serves more than 500 users while more than 1000 users use ParamChem services such as atom typing and initial force-field parameter guess at present. © 2014 Elsevier B.V.

@inproceedings{
 title = {Who Cares about Science Gateways? A Large-Scale Survey of Community Use and Needs},
 type = {inproceedings},
 year = {2014},
 keywords = {Cyberinfrastructure,High-performance computing,Science/engineering gateways/portals,Software development,Web interfaces},
 pages = {1-4},
 websites = {http://ieeexplore.ieee.org/document/7021839/},
 month = {11},
 publisher = {IEEE},
 day = {23},
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 created = {2020-07-08T15:09:36.901Z},
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 bibtype = {inproceedings},
 author = {Lawrence, Katherine A. and Wilkins-Diehr, Nancy and Wernert, Julie A. and Pierce, Marlon and Zentner, Michael and Marru, Suresh},
 doi = {10.1109/GCE.2014.11},
 booktitle = {2014 9th Gateway Computing Environments Workshop}
}

With the rise of science gateway use in recent years, we anticipate there are additional opportunities for growth, but the field is currently fragmented. We describe our efforts to measure the extent and characteristics of the gateway community through a large-scale survey. Our goal was to understand what type of support services might be provided to the gateway community.

@inproceedings{
 title = {Authoring a Science Gateway Cookbook},
 type = {inproceedings},
 year = {2013},
 pages = {1-3},
 institution = {IEEE},
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 citation_key = {marru2013authoring},
 source_type = {inproceedings},
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 bibtype = {inproceedings},
 author = {Marru, Suresh and Dooley, Rion and Wilkins-Diehr, Nancy and Pierce, Marlon and Miller, Mark and Pamidighantam, Sudhakar and Wernert, Julie},
 booktitle = {Cluster Computing (CLUSTER), 2013 IEEE International Conference on}
}

@inproceedings{
 title = {US-SOMO Cluster Methods: Year One Perspective},
 type = {inproceedings},
 year = {2013},
 keywords = {2013,pti},
 websites = {http://dl.acm.org/citation.cfm?id=2484815},
 publisher = {ACM},
 city = {San Diego, CA},
 id = {16f267f5-1fd7-362a-99fb-4e7b9fce2d35},
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 hidden = {false},
 source_type = {inproceedings},
 private_publication = {false},
 bibtype = {inproceedings},
 author = {Brookes, Emre and Singh, Raminder and Pierce, Marlon and Marru, Suresh and Demeler, Borries and Rocco, Mattia},
 booktitle = {XSEDE '13 Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery}
}

@article{
 title = {Science gateways and the importance of sustainability},
 type = {article},
 year = {2013},
 pages = {790764},
 id = {7ff12462-82c1-3fe9-8954-b0ce855e695e},
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 citation_key = {wilkins2013science},
 source_type = {article},
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 bibtype = {article},
 author = {Wilkins-Diehr, Nancy and Lawrence, Katherine and Hayden, Linda and Pierce, Marlon and Marru, Suresh and McLennan, Michael and Zentner, Michael and Dooley, Rion and Stanzione, Dan},
 journal = {figshare}
}

@techreport{
 title = {Science Gateway Operational Sustainability: Adopting a Platform-as-a Service Approach},
 type = {techreport},
 year = {2013},
 id = {7cf6cb9b-1a66-3b4b-9db5-03910862dfc8},
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 author = {Pierce, Marlon and Marru, Suresh and Miller, Mark A and Majumdar, Amit and Demeler, Borries}
}

@misc{
 title = {Science Gateways},
 type = {misc},
 year = {2013},
 source = {Open Science Grid All Hands Meeting},
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@inproceedings{
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@inproceedings{
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@inproceedings{
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@techreport{
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@inproceedings{
 title = {Enabling Dark Energy Survey science analysis with simulations on XSEDE resources},
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 booktitle = {XSEDE '13 Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery}
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@inproceedings{
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@inproceedings{
 title = {Improvements of the ultrascan scientific gateway to enable computational jobs on large-scale and open-standards based cyberinfrastructures},
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 abstract = {The UltraScan data analysis application is a software package that is able to take advantage of computational resources in order to support the interpretation of analytical ultracentrifugation (AUC) experiments. Since 2006, the UltraScan scientific gateway has been used with ordinary Web browsers in TeraGrid by scientists studying the solution properties of biological and synthetic molecules. Unlike other applications, UltraScan is implemented on a gateway architecture and leverages the power of supercomputing to extract very high resolution information from the experimental data. In this contribution, we will focus on several improvements of the UltraScan scientific gateway that enable a standardized job submission and management to computational resources while retaining its lightweight design in order to not disturb the established workflows of its end-users. This paper further presents a walkthrough of the architectural design including one real installation deployment of UltraScan in Europe. The aim is to provide evidence for the added value of open standards and resulting interoperability enabling not only UltraScan application submissions to resources offered in the US cyber infrastructure Extreme Science and Engineering Discovery Environment (XSEDE), but also submissions to similar infrastructures in Europe and around the world. The use of the Apache Airavata framework for scientific gateways within our approach bears the potential to have an impact on several other scientific gateways too. © 2013 by the Association for Computing Machinery, Inc.},
 bibtype = {inproceedings},
 author = {Memon, S and Attig, N and Gorbet, G and Gunathilake, L and Riedel, M and Lippert, T and Marru, S and Grimshaw, A and Janetzko, F and Demeler, B and Singh, R},
 doi = {10.1145/2484762.2484800},
 booktitle = {Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery (XSEDE '13)}
}

The UltraScan data analysis application is a software package that is able to take advantage of computational resources in order to support the interpretation of analytical ultracentrifugation (AUC) experiments. Since 2006, the UltraScan scientific gateway has been used with ordinary Web browsers in TeraGrid by scientists studying the solution properties of biological and synthetic molecules. Unlike other applications, UltraScan is implemented on a gateway architecture and leverages the power of supercomputing to extract very high resolution information from the experimental data. In this contribution, we will focus on several improvements of the UltraScan scientific gateway that enable a standardized job submission and management to computational resources while retaining its lightweight design in order to not disturb the established workflows of its end-users. This paper further presents a walkthrough of the architectural design including one real installation deployment of UltraScan in Europe. The aim is to provide evidence for the added value of open standards and resulting interoperability enabling not only UltraScan application submissions to resources offered in the US cyber infrastructure Extreme Science and Engineering Discovery Environment (XSEDE), but also submissions to similar infrastructures in Europe and around the world. The use of the Apache Airavata framework for scientific gateways within our approach bears the potential to have an impact on several other scientific gateways too. © 2013 by the Association for Computing Machinery, Inc.

@inproceedings{
 title = {A high throughput workflow environment for cosmological simulations},
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 bibtype = {inproceedings},
 author = {Brandon, Erickson and Evrard, August E and Singh, Raminderjeet and Marru, Suresh and Pierce, Marlon and Becker, Matthew R and Kravtsov, Andrey V and Busha, Michael T and Wechsler, Risa H and Ricker, P M},
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The Simulation Working Group (SimWG) of the Dark Energy Survey (DES) is collaborating with an XSEDE science gateway team to develop a distributed workflow management layer for the production of wide-area synthetic galaxy catalogs from large N-body simulations. We use the suite of tools in Airavata, an Apache Incubator project, to generate and archive multiple 10^10-particle N-body simulations of nested volumes on XSEDE supercomputers. Lightcone outputs are moved via Globus Online to SLAC, where they are transformed into multi-band, catalog-level descriptions of gravitationally lensed galaxies covering 10,000 sq deg to high redshift. We outline the method and discuss efficiency and provenance improvements brought about in N-body production. Plans to automate data movement and post-processing within the workflow are sketched, as are risks associated with working in an environment of constantly evolving services.

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@inproceedings{
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@inproceedings{
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@inproceedings{
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@inproceedings{
 title = {Web service andworkflow abstractions to large scale nuclear physics calculations},
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@inproceedings{
 title = {Using UAVSAR to Estimate Creep Along the Superstition Hills Fault, Southern California},
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@techreport{
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@inproceedings{
 title = {Web service and workflow abstractions to large scale nuclear physics calculations},
 type = {inproceedings},
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 author = {Herath, C and Liu, F and Marru, S and Gunathilake, L and Sosonkina, M and Vary, J P and Maris, P and Pierce, M},
 doi = {10.1109/SCC.2012.112},
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This paper discusses the web service and scientificworkflow abstractions to next generation ab initio computationalnuclear physics resources as part of the Leadership ClassConfiguration Interaction (LCCI) Environment. These abstractionswill rapidly and efficiently involve new collaboratorsand graduate students in productive research. The workflowinfrastructure democratizes the access to the nuclear physicssimulations executing on remote supercomputing resources.The paper focuses on employing an open community basedworkflow system in developing and deploying LCCI infrastructures.The paper also emphasizes on the enhancementsmade to infrastructure to add advanced workflow capabilitiesproviding greater flexibility in handling parametric sweeps andprovenance aware workflows. The paper discusses on how theprovenance integration will not only capture execution tracebut dynamically modify the workflow graph at run time tore-use retrospective execution results. © 2012 IEEE.

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@article{
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@techreport{
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Annual report on IU's XSEDE activitiesThis document is a summary of the activities of the Research Technologies division of UITS, a Service & Cyberinfrastructure Center affiliated with the Indiana University Pervasive Technology Institute, as part of the eXtreme Science and Engineering Discovery Environment (XSEDE) during XSEDE Program Year 1 (1 July 2011 – 30 June 2012). This document consists of three parts: - Section 2 of this document describes IU’s activities as an XSEDE Service Provider, using the format prescribed by XSEDE for reporting such activities. - Section 3 of this document describes IU’s activities as part of XSEDE management, operations, and support activities funded under a subcontract from the National Center for Supercomputer Applications (NCSA), the lead organization for XSEDE. This section is organized by the XSEDE Work Breakdown Structure (WBS) plan. - Appendix 1 is a summary table of IU’s education, outreach, and training events funded and supported in whole or in part by IU’s subcontract from NCSA as part of XSEDE.

@inproceedings{
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}

The next generation of wide-area sky surveys offer the power to place extremely precise constraints on cosmological parameters and to test the source of cosmic acceleration. These observational programs will employ multiple techniques based on a variety of statistical signatures of galaxies and large-scale structure. These techniques have sources of systematic error that need to be understood at the percent-level in order to fully leverage the power of next-generation catalogs. Simulations of large-scale structure provide the means to characterize these uncertainties. We are using XSEDE resources to produce multiple synthetic sky surveys of galaxies and large-scale structure in support of science analysis for the Dark Energy Survey. In order to scale up our production to the level of fifty 1010-particle simulations, we are working to embed production control within the Apache Airavata workflow environment. We explain our methods and report how the workflow has reduced production time by 40% compared to manual management.

@inproceedings{
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@inproceedings{
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@inproceedings{
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@inproceedings{
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@inproceedings{
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@inproceedings{
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@inproceedings{
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@inproceedings{
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@inproceedings{
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@inproceedings{
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 abstract = {Parameter optimization for chemical systems requires generation of initial guesses. These parameters should be generated using systematic sampling of parameter space, minimizing differences between output data and the corresponding reference data. In this paper we discuss the ParamChem project, which is creating reusable and extensible infrastructure for the computational chemistry community that will reduce unnecessary and eliminate redundancies in parametrized computations using modern software engineering tools. The paper particularly focuses on constructing and executing coupled molecular chemistry models as complicated workflow graphs. These workflow management capabilities have been integrated with the GridChem Science Gateway infrastructure through the TeraGrid advanced user support program. Further, we describe how the project is enabling a sustainable growth for science gateway infrastructure by building upon tools provided by the Open Gateway Computing Environments. The paper also discusses plans for integrating TeraGrid information, monitoring and prediction services to provide automated job scheduling with resource maintenance and fault aware services.},
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 author = {Ghosh, Jayeeta and Marru, Suresh and Singh, Nikhil and Vanomesslaeghe, Kenno and Fan, Ye and Pamidighantam, Sudhakar},
 doi = {10.1145/2016741.2016779},
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Parameter optimization for chemical systems requires generation of initial guesses. These parameters should be generated using systematic sampling of parameter space, minimizing differences between output data and the corresponding reference data. In this paper we discuss the ParamChem project, which is creating reusable and extensible infrastructure for the computational chemistry community that will reduce unnecessary and eliminate redundancies in parametrized computations using modern software engineering tools. The paper particularly focuses on constructing and executing coupled molecular chemistry models as complicated workflow graphs. These workflow management capabilities have been integrated with the GridChem Science Gateway infrastructure through the TeraGrid advanced user support program. Further, we describe how the project is enabling a sustainable growth for science gateway infrastructure by building upon tools provided by the Open Gateway Computing Environments. The paper also discusses plans for integrating TeraGrid information, monitoring and prediction services to provide automated job scheduling with resource maintenance and fault aware services.

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@article{
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@article{
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 abstract = {We propose a novel approach to managing information in grids. The proposed approach is an add-on information system that provides unification and federation of grid information services. The system interacts with local information services and assembles their metadata instances under one hybrid architecture to provide a common query/publish interface to different kinds of metadata. The system also supports interoperability of major grid information services by providing federated information management. We present the semantics and architectural design for this system. We introduce a prototype implementation and present its evaluation. As the results indicate, the proposed system achieves unification and federation of custom implementations of grid information services with negligible processing overheads. Copyright © 2010, IGI Global.},
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We propose a novel approach to managing information in grids. The proposed approach is an add-on information system that provides unification and federation of grid information services. The system interacts with local information services and assembles their metadata instances under one hybrid architecture to provide a common query/publish interface to different kinds of metadata. The system also supports interoperability of major grid information services by providing federated information management. We present the semantics and architectural design for this system. We introduce a prototype implementation and present its evaluation. As the results indicate, the proposed system achieves unification and federation of custom implementations of grid information services with negligible processing overheads. Copyright © 2010, IGI Global.

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@article{
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@article{
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 abstract = {This paper describes Indiana University's implementation, performance testing, and use of a large high performance computing system. IU'S Big Red, a 20.48 TFLOPS IBM e1350 BladeCenter cluster, appeared in the 27th Top500 list as the 23rd fastest supercomputer in the world in June 2006. In spring 2007, this computer was upgraded to 30.72 TFLOPS. The e1350 BladeCenter architecture, including two internal networks accessible to users and user applications and two networks used exclusively for system management, has enabled the system to provide good scalability on many important applications while being well manageable. Implementing a system based on the JS21 Blade and PowerPC 970MP processor within the US TeraGrid presented certain challenges, given that Intel-compatible processors dominate the TeraGrid. However, the particular characteristics of the PowerPC have enabled it to be highly popular among certain application communities, particularly users of molecular dynamics and weather forecasting codes. A critical aspect of Big Red's implementation has been a focus on Science Gateways, which provide graphical interfaces to systems supporting end-to-end scientific workflows. Several Science Gateways have been implemented that access Big Red as a computational resource-some via the TeraGrid, some not affiliated with the TeraGrid. In summary, Big Red has been successfully integrated with the TeraGrid, and is used by many researchers locally at IU via grids and Science Gateways. It has been a success in terms of enabling scientific discoveries at IU and, via the TeraGrid, across the US. Copyright © 2009 John Wiley & Sons, Ltd.},
 bibtype = {article},
 author = {Stewart, Craig A. and Link, Matthew and McCaulay, D. Scott and Rodgers, Greg and Turner, George and Hancock, David and Wang, Peng and Saied, Faisal and Pierce, Marlon and Aiken, Ross and Mueller, Matthias S. and Jurenz, Matthias and Lieber, Matthias and Tillotson, Jenett and Plale, Beth A.},
 doi = {10.1002/cpe.1539},
 journal = {Concurrency and Computation: Practice and Experience},
 number = {2}
}

This paper describes Indiana University's implementation, performance testing, and use of a large high performance computing system. IU'S Big Red, a 20.48 TFLOPS IBM e1350 BladeCenter cluster, appeared in the 27th Top500 list as the 23rd fastest supercomputer in the world in June 2006. In spring 2007, this computer was upgraded to 30.72 TFLOPS. The e1350 BladeCenter architecture, including two internal networks accessible to users and user applications and two networks used exclusively for system management, has enabled the system to provide good scalability on many important applications while being well manageable. Implementing a system based on the JS21 Blade and PowerPC 970MP processor within the US TeraGrid presented certain challenges, given that Intel-compatible processors dominate the TeraGrid. However, the particular characteristics of the PowerPC have enabled it to be highly popular among certain application communities, particularly users of molecular dynamics and weather forecasting codes. A critical aspect of Big Red's implementation has been a focus on Science Gateways, which provide graphical interfaces to systems supporting end-to-end scientific workflows. Several Science Gateways have been implemented that access Big Red as a computational resource-some via the TeraGrid, some not affiliated with the TeraGrid. In summary, Big Red has been successfully integrated with the TeraGrid, and is used by many researchers locally at IU via grids and Science Gateways. It has been a success in terms of enabling scientific discoveries at IU and, via the TeraGrid, across the US. Copyright © 2009 John Wiley & Sons, Ltd.

@inproceedings{
 title = {Gateway Hosting at Indiana University},
 type = {inproceedings},
 year = {2009},
 websites = {http://hdl.handle.net/2022/13944},
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 author = {Lowe, John Michael and Shields, Corey and Hancock, David Y and Link, Matthew R and Stewart, Craig A and Pierce, Marlon},
 booktitle = {Proceedings of the TeraGrid 2009 Conference}
}

The gateway hosting service at Indiana University provides science gateways and portals with hosting resources to facilitate the use of computation resources and storage within the TeraGrid. This service is designed with high availability in mind and is deployed across the Indianapolis and Bloomington campuses with redundant network, power, and storage. The service uses OpenVZ to give each gateway or portal its own virtual environment while making the most efficient use of the hardware and administrative resources. OpenVZ’s user beancounter quota system and fair-share scheduling for processes and I/O allows fair distribution of resource between virtual machines while allowing full utilization of the hardware. The ability to do live migration allows kernel updates without service interruption. Indiana University’s research network provides multiple low latency high bandwidth connections between campuses, other TeraGrid resource providers, and the Internet at large. The service is in use by a variety of projects such as FlyBase and TeraGrid Information Services and, since the service was put into production in August 2008, there have been 5.37 hours of down time.

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@inproceedings{
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@inproceedings{
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@article{
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@misc{
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@inproceedings{
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@inproceedings{
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@inproceedings{
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 author = {Nacar, Mehmet A and Pierce, Marlon E and Fox, Geoffrey C},
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}

@article{
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 author = {Da Silva, Cesar R S and da Silveira, Pedro R C and Karki, Bijaya and Wentzcovitch, Renata M and Jensen, Paul A and Bollig, Evan F and Pierce, Marlon and Erlebacher, Gordon and Yuen, David A},
 journal = {Physics of the Earth and Planetary Interiors},
 number = {1}
}

@article{
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 author = {Zhuge, H and Shen, J and Grossmann, G and Yang, Y and Stumptner, M and Schrefl, M and Reiter, T and Dimkovski, M and Deeb, K and Kim, K H and others, undefined},
 journal = {Future Generation Computer Systems},
 number = {3}
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@article{
 title = {Building a grid portal for TeraGrid's Big Red},
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 journal = {Proceedings of TeraGrid}
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@inproceedings{
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@inproceedings{
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@article{
 title = {The Open Grid Computing Environments collaboration: portlets and services for science gateways},
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 journal = {Concurrency and Computation: Practice and Experience},
 number = {6}
}

@inproceedings{
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 author = {Granat, Robert and Pierce, Marlon and Gao, Xiaoming and Bock, Y},
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@inproceedings{
 title = {JavaScript Grid Abstractions},
 type = {inproceedings},
 year = {2007},
 pages = {11-12},
 institution = {Grid Computing Environments (GCE)},
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 booktitle = {Proceedings of the Gr id Comput ing Environme nts (GCE) workshop}
}

@article{
 title = {Grids meet too much computing, too much data and never too much simplicity},
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 journal = {White Paper}
}

@inproceedings{
 title = {QuakeSim: Enabli model interactions in solid earth science sensor webs},
 type = {inproceedings},
 year = {2007},
 keywords = {Computing resources; Earthquake forecasts; Multi,Earth sciences; Earthquake effects; Global positio,Sensor networks},
 websites = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-34548734693&doi=10.1109%2FAERO.2007.353087&partnerID=40&md5=1f4ea0ab2ef6a85bd08a10c71ff03268},
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 source_type = {conference},
 notes = {cited By 5; Conference of 2007 IEEE Aerospace Conference ; Conference Date: 3 March 2007 Through 10 March 2007; Conference Code:70231},
 private_publication = {false},
 abstract = {QuakeSim is problem-solving environment for understanding earthquake processes through the integration of multiscale models and data. The goal of QuakeSim is to substantially improve earthquake forecasts, which will ultimately lead to mitigation of damage from this natural hazard. Improved earthquake forecasting is dependent on measurement of surface deformation as well as analysis of geological and seismological data. Space-borne technologies, in the form of continuous GPS networks and InSAR satellites, are the key contributors to measuring surface deformation. We are expanding our QuakeSim Web Services environment to integrate, via Ontolody-based Federation, both real-time and archival sensor data with high-performance computing applications for data mining and assimilation. We are federating sensor data sources, with a focus on InSAR and GPS data, for an improved modeling environment for forecasting earthquakes. These disparate measurements form a complex sensor web in which data must be integrated into comprehensive multi-scale models. In order to account for the complexity of modeled fault systems, investigations must be carried out on high-performance computers. We are building upon our "Grid of Grids" approach, which included the development of extensive Geographical Information System-based "Data Grid" services. We are extending our earlier approach to integrate the Data Grid components with improved "Execution Grid" services that are suitable for interacting with high-end computing resources. These services are being deployed on the Columbia computer at NASA Ames and the Cosmos computer cluster at JPL. © 2007 IEEE.},
 bibtype = {inproceedings},
 author = {Donnellan, A and Parker, J and Norton, C and Lyzenga, G and Glasscoe, M and Fox, G and Pierce, M and Rundle, J and McLeod, D and Grant, L and Brooks, W and Tullis, T},
 doi = {10.1109/AERO.2007.353087},
 booktitle = {IEEE Aerospace Conference Proceedings}
}

QuakeSim is problem-solving environment for understanding earthquake processes through the integration of multiscale models and data. The goal of QuakeSim is to substantially improve earthquake forecasts, which will ultimately lead to mitigation of damage from this natural hazard. Improved earthquake forecasting is dependent on measurement of surface deformation as well as analysis of geological and seismological data. Space-borne technologies, in the form of continuous GPS networks and InSAR satellites, are the key contributors to measuring surface deformation. We are expanding our QuakeSim Web Services environment to integrate, via Ontolody-based Federation, both real-time and archival sensor data with high-performance computing applications for data mining and assimilation. We are federating sensor data sources, with a focus on InSAR and GPS data, for an improved modeling environment for forecasting earthquakes. These disparate measurements form a complex sensor web in which data must be integrated into comprehensive multi-scale models. In order to account for the complexity of modeled fault systems, investigations must be carried out on high-performance computers. We are building upon our "Grid of Grids" approach, which included the development of extensive Geographical Information System-based "Data Grid" services. We are extending our earlier approach to integrate the Data Grid components with improved "Execution Grid" services that are suitable for interacting with high-end computing resources. These services are being deployed on the Columbia computer at NASA Ames and the Cosmos computer cluster at JPL. © 2007 IEEE.

@inproceedings{
 title = {Building a sensor grid for real time global positioning system data},
 type = {inproceedings},
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 author = {Aydin, Galip and Qi, Zhigang and Pierce, Marlon E and Bock, Yehuda and Fox, Geoffrey C},
 booktitle = {Proc. Workshop on Principles of Pervasive Information Systems Design Sunday}
}

@inproceedings{
 title = {Analysis of streaming GPS measurements of surface displacement through a web services environment},
 type = {inproceedings},
 year = {2007},
 pages = {750-757},
 institution = {IEEE},
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 author = {Granat, Robert and Aydin, Galip and Pierce, Marlon and Qi, Zhigang and Bock, Yehuda},
 booktitle = {Computational Intelligence and Data Mining, 2007. CIDM 2007. IEEE Symposium on}
}

@inproceedings{
 title = {Matchmaking scientific workflows in grid environments},
 type = {inproceedings},
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 author = {Gong, Yili and Pierce, Marlon E and Fox, Geoffrey C},
 booktitle = {20th IASTED International Conference on Parallel and Distributed Computing and Systems (PDCS 2007), Cambridge, MA (November 2007)}
}

@article{
 title = {VLab: collaborative Grid services and portals to support computational material science},
 type = {article},
 year = {2007},
 pages = {1717-1728},
 volume = {19},
 publisher = {John Wiley & Sons, Ltd.},
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 author = {Nacar, Mehmet A and Aktas, Mehmet S and Pierce, Marlon and Lu, Zhenyu and Erlebacher, Gordon and Kigelman, Dan and Bollig, Evan F and da Silva, Cesar R S and Sowell, Benny and Yuen, David A},
 journal = {Concurrency and Computation: Practice and Experience},
 number = {12}
}

@inproceedings{
 title = {Scalable, fault-tolerant management in a service oriented architecture},
 type = {inproceedings},
 year = {2007},
 pages = {235-236},
 institution = {ACM},
 id = {b49799d3-3399-32c3-a3cc-0a8d09f7e766},
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 bibtype = {inproceedings},
 author = {Gadgil, Harshawardhan and Fox, Geoffrey and Pallickara, Shrideep and Pierce, Marlon},
 booktitle = {Proceedings of the 16th international symposium on High performance distributed computing}
}

@article{
 title = {Web service infrastructure for chemoinformatics},
 type = {article},
 year = {2007},
 keywords = {Chemical engineering,Chemoinformatics,Computational methods,Computational techniques,Computer aided software en,Computer aided software engineering,Database Management Systems,Human engineering,Informatics,Information analysis,Interne,Internet,Programming Languages,Web se,Web service infrastructure,Web services,article,computer language,data base,informatio,information science},
 pages = {1303-1307},
 volume = {47},
 websites = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-34547668730&doi=10.1021%2Fci6004349&partnerID=40&md5=d7404a909b7ed432e4d31bc6ff115ae9},
 publisher = {ACS Publications},
 id = {8c46735a-c025-3a2e-97ec-d9120295fbe8},
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 starred = {false},
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 confirmed = {true},
 hidden = {false},
 citation_key = {Xiao20071303},
 source_type = {JOUR},
 notes = {<b>From Duplicate 2 (<i>Web service infrastructure for chemoinformatics</i> - Xiao, D; Gilbert, Kevin E; Guha, Rajarshi; Heiland, Randy; Jungkee, K; Pierce, Marlon E; Fox, Geoffrey C; Wild, David J; Dong, Xiao; Gilbert, Kevin E; Guha, Rajarshi; Heiland, Randy; Kim, Jungkee; Pierce, Marlon E; Fox, Geoffrey C; Wild, David J)<br/></b><br/><b>From Duplicate 2 (<i>Web service infrastructure for chemoinformatics</i> - Xiao, D; Gilbert, K E; Guha, R; Heiland, R; Jungkee, K; Pierce, M E; Fox, G C; Wild, D J)<br/></b><br/>cited By 38<br/><br/><b>From Duplicate 3 (<i>Web service infrastructure for chemoinformatics</i> - Xiao, D; Gilbert, K E; Guha, R; Heiland, R; Jungkee, K; Pierce, M E; Fox, G C; Wild, D J)<br/></b><br/>cited By 38},
 private_publication = {false},
 abstract = {The vast increase of pertinent information available to drag discovery scientists means that there is a strong demand for tools and techniques for organizing and intelligently mining this information for manageable human consumption. At Indiana University, we have developed an infrastructure of chemoinformatics Web services that simplifies the access to this information and the computational techniques that can be applied to it. In this paper, we describe this infrastructure, give some examples of its use, and then discuss our plans to use it as a platform for chemoinformatics application development in the future. © 2007 American Chemical Society.},
 bibtype = {article},
 author = {Xiao, D and Gilbert, Kevin E and Guha, Rajarshi and Heiland, Randy and Jungkee, K and Pierce, Marlon E and Fox, Geoffrey C and Wild, David J and Dong, Xiao and Gilbert, Kevin E and Guha, Rajarshi and Heiland, Randy and Kim, Jungkee and Pierce, Marlon E and Fox, Geoffrey C and Wild, David J},
 doi = {10.1021/ci6004349},
 journal = {Journal of chemical information and modeling},
 number = {4}
}

The vast increase of pertinent information available to drag discovery scientists means that there is a strong demand for tools and techniques for organizing and intelligently mining this information for manageable human consumption. At Indiana University, we have developed an infrastructure of chemoinformatics Web services that simplifies the access to this information and the computational techniques that can be applied to it. In this paper, we describe this infrastructure, give some examples of its use, and then discuss our plans to use it as a platform for chemoinformatics application development in the future. © 2007 American Chemical Society.

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 journal = {Physics of the Earth and Planetary Interiors},
 number = {1}
}

@inproceedings{
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@inproceedings{
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@techreport{
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 institution = {The University of Texas, Texas Advanced Computing Center; Austin, TX; General Atomics, San Diego, CA; Indiana University, Bloomington, IN; San Diego State University, San Diego, CA},
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@inproceedings{
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@article{
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@inproceedings{
 title = {Building sensor filter grids: Information architecture for the data deluge},
 type = {inproceedings},
 year = {2006},
 keywords = {Data processing; Geographic information systems;,Distributed messaging; Online sensors; Real time d,Grid computing},
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 abstract = {We discuss a general architectural approach to knowledge and information management and delivery in distributed systems. Our approach is based on the recognition that time-stamped, streaming information message units form the core of seemingly disparate systems that range from online sensors and scientific instruments to Web information retrieval. Globally distributable Grid services manage these information streams. Geographical Information System services provide exemplary realizations of this picture and may be used as a model for other scientific domains. With this unified architecture in place, we may begin to consider the problems of information integration as equivalent to sensor federation. © 2006 IEEE.},
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We discuss a general architectural approach to knowledge and information management and delivery in distributed systems. Our approach is based on the recognition that time-stamped, streaming information message units form the core of seemingly disparate systems that range from online sensors and scientific instruments to Web information retrieval. Globally distributable Grid services manage these information streams. Geographical Information System services provide exemplary realizations of this picture and may be used as a model for other scientific domains. With this unified architecture in place, we may begin to consider the problems of information integration as equivalent to sensor federation. © 2006 IEEE.

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 chapter = {A grid framework for visualization services in the Earth sciences},
 title = {Computational Earthquake Physics: Simulations, Analysis and Infrastructure, Part II}
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@inproceedings{
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@inproceedings{
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@inproceedings{
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We review several aspects of building real-time streaming data Grid applications. Building on general purpose messaging system software (NaradaBrokering) and generalized collaboration services (GlobalMMCS), we are developing a diverse set of interoperable capabilities. These include dynamic information systems for managing short-lived collaborative service collections ("gaggles"), stream filters to support the integration of Geographical Information Systems services with data analysis applications, streaming video to support collaborative geospatial maps with time-dependent data, and video stream playback and annotation services to enable scientific collaboration.

@inproceedings{
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@inproceedings{
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@book{
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In this chapter, we present a discussion on our experiences with the development of Web service specifications. Web services, and the service oriented architecture model engendered therein, have gained significant traction in recent years with deployments in ever increasing domains. In this chapter, we describe our experiences with several Web service specifications. In general lessons learned, and design decisions made, during these implementations would be applicable to several other specifications. The authors hope that their insights and experiences with the development of Web service specifications would be beneficial to other researchers in this area in formulating a strategy for the development of systems based on Web services. © 2008, IGI Global.

@inproceedings{
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@inproceedings{
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@article{
 title = {Grids for real time data applications},
 type = {article},
 year = {2006},
 keywords = {Annotatable shared maps; Broker management; Grids;,Conformal mapping; Data processing; Geographic in,Real time systems},
 pages = {320-332},
 volume = {3911 LNCS},
 websites = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-33745795982&doi=10.1007%2F11752578_39&partnerID=40&md5=e511855d2b13ba9d1b08192cff1cab2c},
 city = {Poznan},
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 notes = {cited By 2; Conference of 6th International Conference on Parallel Processing and Applied Mathematics, PPAM 2005 ; Conference Date: 11 September 2005 Through 14 September 2005; Conference Code:67709},
 private_publication = {false},
 abstract = {We describe our work in building support for streaming data services for Geographical Information System Grid services. We examine how streaming approaches may be used to increase data service performance for transporting XML messages. Similarly, streaming versions of traditional static map services may be combined with general audio/video session management capabilities to build collaborative, annotatable shared maps. Distributed services linked through messaging substrates require information and broker management capabilities, and we describe our research here. Finally, we discuss efficient XML representation techniques that can be used to increase performance of Web Services and support Web enabled devices. © Springer-Verlag Berlin Heidelberg 2006.},
 bibtype = {article},
 author = {Fox, G C and Aktas, M S and Aydin, G and Bulut, H and Gadgil, H and Oh, S and Pallickara, S and Pierce, M E and Sayar, A and Zhai, G},
 doi = {10.1007/11752578_39},
 journal = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)}
}

We describe our work in building support for streaming data services for Geographical Information System Grid services. We examine how streaming approaches may be used to increase data service performance for transporting XML messages. Similarly, streaming versions of traditional static map services may be combined with general audio/video session management capabilities to build collaborative, annotatable shared maps. Distributed services linked through messaging substrates require information and broker management capabilities, and we describe our research here. Finally, we discuss efficient XML representation techniques that can be used to increase performance of Web Services and support Web enabled devices. © Springer-Verlag Berlin Heidelberg 2006.

@inproceedings{
 title = {GPS Sensor Web Time Series Analysis Using SensorGrid Technology},
 type = {inproceedings},
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 author = {Granat, Robert and Pierce, M and Aydin, G and Qi, Z},
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@inproceedings{
 title = {The Solid Earth Research Virtual Observatory: Web Services for Managing Geophysical Data and Applications},
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 author = {Pierce, Marlon E and Fox, Geoffrey C and Aktas, Mehmet S and Aydin, Galip and Gadgil, Harshawardhan and Qi, Zhigang and Sayar, Ahmet},
 booktitle = {PAGEOPH Special Issue for 5th ACES International Workshop.}
}

@inproceedings{
 title = {Cyberinfrastructure and Web 2.0.},
 type = {inproceedings},
 year = {2006},
 pages = {265-287},
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 bibtype = {inproceedings},
 author = {Pierce, Marlon E and Fox, Geoffrey C and Yuan, Huapeng and Deng, Yu},
 booktitle = {High Performance Computing Workshop}
}

@inproceedings{
 title = {Earth Science Community IT Resources through a Unified Data and Analysis Portal},
 type = {inproceedings},
 year = {2006},
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 author = {Bock, Y and Webb, F H and Kedar, S and Pierce, M and Scharber, M and Argus, D F and Aydin, G and Chang, R and Dong, D and Fang, P and others, undefined},
 booktitle = {AGU Fall Meeting Abstracts}
}

@inproceedings{
 title = {Grid portal system based on GPIR},
 type = {inproceedings},
 year = {2006},
 keywords = {(I,Computer networks,Grid portals,Grid resource,Information systems,Information theory,J) conditions,Multiple choice,Neodymium,Paper,Por,Portal technology,Portlet,Portlets,Semantics,Technology,grid resources,inter,international conferences},
 pages = {83},
 websites = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-44949143295&doi=10.1109%2FSKG.2006.52&partnerID=40&md5=6fe28b22a378c6a504ddd05029645a41},
 city = {Guilin Guangxi},
 institution = {IEEE},
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 citation_key = {juan2006grid},
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 notes = {<b>From Duplicate 2 (<i>Grid portal system based on GPIR</i> - Fang, J; Fox, Geoffrey; Pierce, Marlon; Juan, Fang Juan Fang; Fox, Geoffrey; Pierce, Marlon)<br/></b><br/><b>From Duplicate 2 (<i>Grid portal system based on GPIR</i> - Fang, J; Fox, G; Pierce, M)<br/></b><br/>cited By 2; Conference of 2006 2nd International Conference on Semantics Knowledge and Grid, SKG ; Conference Date: 1 November 2006 Through 3 November 2006; Conference Code:72224<br/><br/><b>From Duplicate 3 (<i>Grid portal system based on GPIR</i> - Fang, J; Fox, G; Pierce, M)<br/></b><br/>cited By 2; Conference of 2006 2nd International Conference on Semantics Knowledge and Grid, SKG ; Conference Date: 1 November 2006 Through 3 November 2006; Conference Code:72224},
 private_publication = {false},
 abstract = {Grid portal is the bridge between Grid and user. In this paper a Grid portal system is set up based on GPIR of GridPort. The Grid portal system provides an efficient means to user for utilizing grid resources, and provides advantaged condition for achieving effective information of database. The user can customize the application by portlet framework. In this paper we also review multiple choices for portal technology and explain why we choose GPIR. © 2006 IEEE.},
 bibtype = {inproceedings},
 author = {Fang, J and Fox, Geoffrey and Pierce, Marlon and Juan, Fang Juan Fang and Fox, Geoffrey and Pierce, Marlon},
 doi = {10.1109/SKG.2006.52},
 booktitle = {Semantics, Knowledge and Grid, 2006. SKG'06. Second International Conference on}
}

Grid portal is the bridge between Grid and user. In this paper a Grid portal system is set up based on GPIR of GridPort. The Grid portal system provides an efficient means to user for utilizing grid resources, and provides advantaged condition for achieving effective information of database. The user can customize the application by portlet framework. In this paper we also review multiple choices for portal technology and explain why we choose GPIR. © 2006 IEEE.

@inproceedings{
 title = {XML Metadata Services},
 type = {inproceedings},
 year = {2006},
 keywords = {Applied (CO); Code execution; international confer,Architectural design; Computer networks; Informat,Metadata,and integration (UDDI); XML metadata; Capability,and integrations; WS-Context,discovery},
 websites = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-44949168873&doi=10.1109%2FSKG.2006.113&partnerID=40&md5=edaa0fc3280daf19e64904cd812fa679},
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 notes = {cited By 2; Conference of 2006 2nd International Conference on Semantics Knowledge and Grid, SKG ; Conference Date: 1 November 2006 Through 3 November 2006; Conference Code:72224},
 private_publication = {false},
 abstract = {As the Service Oriented Architecture (SOA) principles have gained importance, an emerging need has appeared for methodologies to locate desired services that provide access to their capability descriptions. These services must typically be assembled Into short-term service collections that, together with code execution services, are combined into a meta-application to perform a particular task. To address metadata requirements of these problems, we introduce XML Metadata Services to manage both stateless and stateful (transient) metadata. We leverage the two widely used web service standards: Universal Description, Discovery, and Integration (UDDI) and Web Services Context (WS-Context) in our design. We describe our approach and experiences when designing "semantics" for XML Metadata Services. We report results from a prototype of the system that is applied to mobile environment for optimizing Web Service communications. © 2006 IEEE.},
 bibtype = {inproceedings},
 author = {Aktas, M S and Oh, S and Fox, G C and Pierce, M E},
 doi = {10.1109/SKG.2006.113},
 booktitle = {2006 2nd International Conference on Semantics Knowledge and Grid, SKG}
}

As the Service Oriented Architecture (SOA) principles have gained importance, an emerging need has appeared for methodologies to locate desired services that provide access to their capability descriptions. These services must typically be assembled Into short-term service collections that, together with code execution services, are combined into a meta-application to perform a particular task. To address metadata requirements of these problems, we introduce XML Metadata Services to manage both stateless and stateful (transient) metadata. We leverage the two widely used web service standards: Universal Description, Discovery, and Integration (UDDI) and Web Services Context (WS-Context) in our design. We describe our approach and experiences when designing "semantics" for XML Metadata Services. We report results from a prototype of the system that is applied to mobile environment for optimizing Web Service communications. © 2006 IEEE.

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 chapter = {Implementing ISERVO Using Grid and GIS Services},
 title = {Computational Earthquake Physics: Simulations, Analysis and ..., Part 2}
}

@inproceedings{
 title = {CINF 10-Advanced HTS data mining using web service workflows},
 type = {inproceedings},
 year = {2006},
 volume = {232},
 institution = {AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
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}

@inproceedings{
 title = {Designing Grid Tag Libraries and Grid Beans},
 type = {inproceedings},
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 author = {Nacar, Mehmet A and Pierce, Marlon E and Erlebacher, Gordon and Fox, Geoffrey C and Nacar, Mehmet A and Pierce, Marlon E},
 booktitle = {Second International Workshop on Grid Computing Environments GCE06 at SC06}
}

@inproceedings{
 title = {A framework for secure end-to-end delivery of messages in publish/subscribe systems},
 type = {inproceedings},
 year = {2006},
 pages = {215-222},
 institution = {IEEE Computer Society},
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 author = {Pallickara, Shrideep and Pierce, Marlon and Gadgil, Harshawardhan and Fox, Geoffrey and Yan, Yan and Huang, Yi},
 booktitle = {Proceedings of the 7th IEEE/ACM International Conference on Grid Computing}
}

@inproceedings{
 title = {Information services for dynamically assembled semantic grids},
 type = {inproceedings},
 year = {2006},
 keywords = {Codes (standards); Data reduction; Information se,Grid computing,Semantic grids; Semantic information; Static servi},
 websites = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-42749107932&doi=10.1109%2FSKG.2005.83&partnerID=40&md5=8cf61b579af398da95919fa9736016a0},
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 notes = {cited By 3; Conference of 1st International Conference on Semantics, Knowledge and Grid, SKG 2005 ; Conference Date: 27 November 2005 Through 29 November 2005; Conference Code:69776},
 private_publication = {false},
 abstract = {Many large semantic systems can be described as Semantic Grids of Semantic Grids with large amounts of relatively static services and associated semantic information combined with multiple dynamic regions (sessions or subgrids) where the semantic information is changing rapidly. We design a hybrid Information Service supporting both the scalability of large amounts of relatively slowly varying data and a high performance rapidly updated Information Service for dynamic regions. We use the two web service standards UDDI and WS-Context in our system. © 2006 IEEE.},
 bibtype = {inproceedings},
 author = {Aktas, M S and Fox, G C and Pierce, M},
 doi = {10.1109/SKG.2005.83},
 booktitle = {Proceedings - First International Conference on Semantics, Knowledge and Grid, SKG 2005}
}

Many large semantic systems can be described as Semantic Grids of Semantic Grids with large amounts of relatively static services and associated semantic information combined with multiple dynamic regions (sessions or subgrids) where the semantic information is changing rapidly. We design a hybrid Information Service supporting both the scalability of large amounts of relatively slowly varying data and a high performance rapidly updated Information Service for dynamic regions. We use the two web service standards UDDI and WS-Context in our system. © 2006 IEEE.

@inproceedings{
 title = {Collaboration entities on deterministic finite automata},
 type = {inproceedings},
 year = {2006},
 pages = {26-37},
 institution = {IEEE},
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 author = {Wang, Minjun and Fox, Geoffrey and Pierce, Marlon},
 booktitle = {Collaborative Technologies and Systems, 2006. CTS 2006. International Symposium on}
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@inbook{
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 chapter = {iSERVO: Implementing the international solid earth research virtual observatory by integrating computational grid and geographical information web services},
 title = {Computational Earthquake Physics: Simulations, Analysis and Infrastructure, Part II}
}

@article{
 title = {INTEGRATING AJAX MODELS WITH GIS VISUALIZATION WEB SERVICES},
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 journal = {Telecommunications, 2006. AICT-ICIW'06. International Conference on Internet and Web Applications and Services/Advanced International Conference on}
}

@inbook{
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 chapter = {Quakesim and the solid earth research virtual observatory},
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@article{
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@article{
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In this paper, we discuss reliable and secure file transfer middleware called NaradaBrokering. It is our goal to show that reliability features can be decoupled from the implementation of the service and protocol, and instead placed into the messaging substrate. This will allow us to provide file transfer quality of service comparable to GridFTP in other file transfer tools (such as normal FTP, SCP, HTTP uploads, and similar mechanisms).

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@inproceedings{
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@inproceedings{
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@inproceedings{
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@inproceedings{
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 abstract = {We describe the Gateway computational web portal, which follows a traditional three-tiered approach to portal design. Gateway provides a simplified, ubiquitously available user interface to high performance computing and related resources. This approach, while successful for straightforward applications, has limitations that make it difficult to support loosely federated, interoperable web portal systems. We examine the emerging standards in the so-called web services approach to business-to-business electronic commerce for possible solutions to these shortcomings and outline topics of research in the emerging area of computational grid web services.},
 bibtype = {article},
 author = {Pierce, Marlon E and Youn, Choonhan and Fox, Geoffrey C},
 journal = {International Conference on Computational Science}
}

We describe the Gateway computational web portal, which follows a traditional three-tiered approach to portal design. Gateway provides a simplified, ubiquitously available user interface to high performance computing and related resources. This approach, while successful for straightforward applications, has limitations that make it difficult to support loosely federated, interoperable web portal systems. We examine the emerging standards in the so-called web services approach to business-to-business electronic commerce for possible solutions to these shortcomings and outline topics of research in the emerging area of computational grid web services.

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 title = {Path-integral Monte Carlo studies of helium on graphite},
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@article{
 title = {Targeted High-Resolution Structure from Motion Observations over the M w 6.4 and 7.1 Ruptures of the Ridgecrest Earthquake Sequence},
 type = {article},
 pages = {1-9},
 websites = {https://pubs.geoscienceworld.org/ssa/srl/article-pdf/doi/10.1785/0220190274/4967856/srl-2019274.1.pdf},
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 abstract = {Cite this article as Donnellan, A., G. Lyzenga, A. Ansar, C. Goulet, J. Wang, and M. Pierce (2020). Targeted High-Resolution Structure from Motion Observations over the M w 6.4 and 7.1 We carried out six targeted structure from motion surveys using small uninhabited aerial systems over the M w 6.4 and 7.1 ruptures of the Ridgecrest earthquake sequence in the first three months after the events. The surveys cover approximately 500 × 500 m areas just south of Highway 178 with an average ground sample distance of 1.5 cm. The first survey took place five days after the M w 6.4 foreshock on 9 July 2019. The final survey took place on 27 September 2019. The time between surveys increased over time, with the first five surveys taking place in the first month after the earthquake. Comparison of imagery from before and after the M w 7.1 earthquake shows variation in slip on the main rupture and a small amount of distributed slip across the scene. Cracks can be observed and mapped in the high-resolution imagery, which show en echelon cracking, fault splays, and a northeast-striking conjugate fault at the M w 7.1 rupture south of Highway 178 and near the dirt road. Initial postseismic results show little fault afterslip, but possible subsidence in the first 7-10 days after the earthquake, followed by uplift.},
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 author = {Donnellan, Andrea and Lyzenga, Gregory and Ansar, Adnan and Goulet, Christine and Wang, Jun and Pierce, Marlon},
 doi = {10.1785/0220190274},
 journal = {Seismological Research Letters}
}

Cite this article as Donnellan, A., G. Lyzenga, A. Ansar, C. Goulet, J. Wang, and M. Pierce (2020). Targeted High-Resolution Structure from Motion Observations over the M w 6.4 and 7.1 We carried out six targeted structure from motion surveys using small uninhabited aerial systems over the M w 6.4 and 7.1 ruptures of the Ridgecrest earthquake sequence in the first three months after the events. The surveys cover approximately 500 × 500 m areas just south of Highway 178 with an average ground sample distance of 1.5 cm. The first survey took place five days after the M w 6.4 foreshock on 9 July 2019. The final survey took place on 27 September 2019. The time between surveys increased over time, with the first five surveys taking place in the first month after the earthquake. Comparison of imagery from before and after the M w 7.1 earthquake shows variation in slip on the main rupture and a small amount of distributed slip across the scene. Cracks can be observed and mapped in the high-resolution imagery, which show en echelon cracking, fault splays, and a northeast-striking conjugate fault at the M w 7.1 rupture south of Highway 178 and near the dirt road. Initial postseismic results show little fault afterslip, but possible subsidence in the first 7-10 days after the earthquake, followed by uplift.