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\n  \n 2024\n \n \n (5)\n \n \n
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\n \n\n \n \n \n \n \n \n Reproducibility of the DaCe Framework on NPBench Benchmarks.\n \n \n \n \n\n\n \n Govind, A.; Jing, Y.; Dao, S.; Granado, M.; Handran, R.; Margarian, D.; Mikhailov, M.; Vo, D.; Gardus, M.; Vu, K.; Bouius, D.; Chin, B.; Tatineni, M.; and Thomas, M.\n\n\n \n\n\n\n IEEE Transactions on Parallel and Distributed Systems, Accepted: 1-5. 2024.\n \n\n\n\n
\n\n\n\n \n \n \"ReproducibilityPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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@article{AGovind-SCC22,\n   author = {Anish Govind and Yuchen Jing and Stefanie Dao and Michael Granado and Rachel Handran and Davit Margarian and Matthew Mikhailov and Danny Vo and Matei-Alexandru Gardus and Khai Vu and Derek Bouius and Bryan Chin and Mahidhar Tatineni and Mary Thomas},\n   doi = {10.1109/TPDS.2024.3427130},\n   issn = {1045-9219},\n   issue = {1},\n   journal = {IEEE Transactions on Parallel and Distributed Systems},\n   keywords = {Benchmark Testing,Graphics Processing Units,Hardware,Optimization,Python,Random Access Memory,Software},\n   pages = {1-5},\n   title = {Reproducibility of the DaCe Framework on NPBench Benchmarks},\n   volume = {Accepted},\n   url = {https://ieeexplore.ieee.org/document/10596928/},\n   year = {2024},\n}\n
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\n \n\n \n \n \n \n \n \n Scaling HPC Education.\n \n \n \n \n\n\n \n Mehringer, S.; Thomas, M. P; Cahill, K.; Dey, C.; Joiner, D.; Knepper, R.; Navarro, J.; and Powell, J. H\n\n\n \n\n\n\n In Best, 2024. ACM\n \n\n\n\n
\n\n\n\n \n \n \"ScalingPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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@inproceedings{Mehringer2024,\n   abstract = {Throughout the cyberinfrastructure community there are a large range of resources available to train faculty and young scholars about successful utilization of computational resources for research. The challenge that the community faces is that training materials abound, but they can be difficult to find, and often have little information about the quality or relevance of offerings. Building on existing software technology, we propose to build a way for the community to better share and find training and education materials through a federated training repository. In this scenario, organizations and authors retain physical and legal ownership of their materials by sharing only catalog information, organizations can refine local portals to use the best and most appropriate materials from both local and remote sources, and learners can take advantage of materials that are reviewed and described more clearly. In this paper, we introduce the HPC ED pilot project, a federated training repository that is designed to allow resource providers, campus portals, schools, and other institutions to both incorporate training from multiple sources into their own familiar interfaces and to publish their local training materials.},\n   author = {Susan Mehringer and Mary P Thomas and Kate Cahill and Charlie Dey and David Joiner and Richard Knepper and John-Paul Navarro and Jeaime H Powell},\n   city = {Atlanta},\n   doi = {10.22369/issn.2153-4136/x/x/x},\n   booktitle = {Best},\n   keywords = {community engagement,education,survey * Both authors contributed equally,training},\n   publisher = {ACM},\n   title = {Scaling HPC Education},\n   url = {https://doi.org/10.22369/issn.2153-4136/x/x/x},\n   year = {2024},\n}\n
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\n Throughout the cyberinfrastructure community there are a large range of resources available to train faculty and young scholars about successful utilization of computational resources for research. The challenge that the community faces is that training materials abound, but they can be difficult to find, and often have little information about the quality or relevance of offerings. Building on existing software technology, we propose to build a way for the community to better share and find training and education materials through a federated training repository. In this scenario, organizations and authors retain physical and legal ownership of their materials by sharing only catalog information, organizations can refine local portals to use the best and most appropriate materials from both local and remote sources, and learners can take advantage of materials that are reviewed and described more clearly. In this paper, we introduce the HPC ED pilot project, a federated training repository that is designed to allow resource providers, campus portals, schools, and other institutions to both incorporate training from multiple sources into their own familiar interfaces and to publish their local training materials.\n
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\n \n\n \n \n \n \n \n COMPLECS : COMPrehensive Learning for end-users to Effectively utilize CyberinfraStructure.\n \n \n \n\n\n \n Sinkovits, R. S; Wolter, N.; Kandes, M. C; Thomas, M. P; and Sweet, M.\n\n\n \n\n\n\n In Practice and Experience in Advanced Research Computing (PEARC '24), volume 1, pages 4-7, 2024. Association for Computing Machinery\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n \n \n \n \n \n \n\n\n\n
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@inproceedings{Sinkovits-COMPLECS-2024,\n   author = {Robert S Sinkovits and Nicole Wolter and Martin C Kandes and Mary P Thomas and Monica Sweet},\n   city = {Providence},\n   doi = {10.1145/3626203.3670553},\n   isbn = {9798400704192},\n   issue = {1},\n   booktitle = {Practice and Experience in Advanced Research Computing (PEARC '24)},\n   keywords = {Computing education,advanc,workforce development},\n   pages = {4-7},\n   publisher = {Association for Computing Machinery},\n   title = {COMPLECS : COMPrehensive Learning for end-users to Effectively utilize CyberinfraStructure},\n   volume = {1},\n   year = {2024},\n}\n
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\n \n\n \n \n \n \n \n \n Building a Federated Catalog for CyberTraining Materials: The HPC-ED Pilot Project.\n \n \n \n \n\n\n \n Thomas, M. P; Mehringer, S.; Cahill, K.; Dey, C.; Guilfoos, B.; Joiner, D.; Navarro, J.; Powell, J. H; and Knepper, R.\n\n\n \n\n\n\n In Practice and Experience in Advanced Research Computing 2024: Human Powered Computing, volume 1, pages 1-5, 7 2024. ACM\n \n\n\n\n
\n\n\n\n \n \n \"BuildingPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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@inproceedings{Thomas-HPC-ED-2024,\n   author = {Mary P Thomas and Susan Mehringer and Katharine Cahill and Charlie Dey and Brian Guilfoos and David Joiner and John-Paul Navarro and Jeaime H Powell and Richard Knepper},\n   city = {New York, NY, USA},\n   doi = {10.1145/3626203.3670586},\n   isbn = {9798400704192},\n   issue = {1},\n   booktitle = {Practice and Experience in Advanced Research Computing 2024: Human Powered Computing},\n   keywords = {Community engagement,Cyberinfrastructure,Education,Globus,HPC,Metadata,Training,acm reference format,community engagement,cyberinfras-,education,globus,hpc,metadata,training,tructure},\n   month = {7},\n   pages = {1-5},\n   publisher = {ACM},\n   title = {Building a Federated Catalog for CyberTraining Materials: The HPC-ED Pilot Project},\n   volume = {1},\n   url = {https://dl.acm.org/doi/10.1145/3626203.3670586},\n   year = {2024},\n}\n
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\n \n\n \n \n \n \n \n Preliminary Results of the MLPerf BERT Inference Benchmark on AMD Instinct GPUs.\n \n \n \n\n\n \n Wang, Z.; Hodak, M.; Vu, K.; Gutierrez, F.; Garcia, A.; Mehrotra, A.; Seo, G.; Smith, K.; Chin, B.; Kandes, M.; and Thomas, M.\n\n\n \n\n\n\n In Submitted: Proceedings of Practice and Experience in Advanced Research Computing (PEARC'24), volume 1, pages 1-12, 2024. Association for Computing Machinery\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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@inproceedings{Wang2024,\n   author = {Zixian Wang and Miro Hodak and Khai Vu and Francisco Gutierrez and Austin Garcia and Aarush Mehrotra and Gloria Seo and Kyle Smith and Bryan Chin and Martin Kandes and Mary Thomas},\n   doi = {https://doi.org/10.1145/3626203.3670589},\n   issue = {1},\n   booktitle = {Submitted: Proceedings of Practice and Experience in Advanced Research Computing (PEARC'24)},\n   keywords = {BERT,MIGrap,MLPerf, BERT, SCC23, PyTorch, ONNX Runtime, MIGrap,ONNX Runtime,PyTorch,SCC23},\n   pages = {1-12},\n   publisher = {Association for Computing Machinery},\n   title = {Preliminary Results of the MLPerf BERT Inference Benchmark on AMD Instinct GPUs},\n   volume = {1},\n   year = {2024},\n}\n
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\n  \n 2023\n \n \n (4)\n \n \n
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\n \n\n \n \n \n \n \n \n Report on 2023 CyberTraining PI Meeting , 26-27 September 2023.\n \n \n \n \n\n\n \n Fox, G.; Thomas, M.; San, U C; and Report, D.\n\n\n \n\n\n\n arXiv,26-27. 2023.\n \n\n\n\n
\n\n\n\n \n \n \"ReportPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{FoxCyTrPi-2023,\n   author = {Geoffrey Fox and Mary Thomas and U C San and Diego Report},\n   doi = {https://doi.org/10.48550/arXiv.2312.14199},\n   issue = {September},\n   journal = {arXiv},\n   pages = {26-27},\n   title = {Report on 2023 CyberTraining PI Meeting , 26-27 September 2023},\n   url = {https://arxiv.org/abs/2312.14199},\n   year = {2023},\n}\n
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\n \n\n \n \n \n \n \n Assessing Shared Material Usage in the High Performance Computing ( HPC ) Education and Training Community.\n \n \n \n\n\n \n Mehringer, S.; Cahill, K.; Lathrop, S.; Dey, C.; Thomas, M.; and Powell, J. H\n\n\n \n\n\n\n In Sixth Workshop on Strategies for Enhancing HPC Education and Training (SEHET23), 2023. \n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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@inproceedings{Mehringer-SEHET23,\n   author = {Susan Mehringer and Kate Cahill and Scott Lathrop and Charlie Dey and Mary Thomas and Jeaime H Powell},\n   doi = {10.22369/issn.2153-4136/14/2/4},\n   booktitle = {Sixth Workshop on Strategies for Enhancing HPC Education and Training (SEHET23)},\n   keywords = {community engagement,education,survey,training},\n   title = {Assessing Shared Material Usage in the High Performance Computing ( HPC ) Education and Training Community},\n   year = {2023},\n}\n
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\n \n\n \n \n \n \n \n \n Development of Authenticated Clients and Applications for ICICLE CI Services – Final Report for the REHS Program, June-August, 2022.\n \n \n \n \n\n\n \n Mary Thomas Sahil Samar, M. R.; James Karpinski, M. C.; Archita Sarin, C. G.; and Matthew Lange, J. S.\n\n\n \n\n\n\n arXiv. 4 2023.\n \n\n\n\n
\n\n\n\n \n \n \"DevelopmentPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{Samar2022,\n   author = {Mary Thomas Sahil Samar, Michael Ray, James Karpinski, Mia Chen, Archita Sarin, Christian Garcia, Matthew Lange, Joe Stubbs},\n   city = {La Jolla},\n   doi = {10.48550/arXiv.2304.11086},\n   institution = {University of California San Diego},\n   journal = {arXiv},\n   month = {4},\n   title = {Development of Authenticated Clients and Applications for ICICLE CI Services -- Final Report for the REHS Program, June-August, 2022},\n   url = {https://arxiv.org/abs/2304.11086},\n   year = {2023},\n}\n
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\n \n\n \n \n \n \n \n \n Developing a Best Practices Training Program in Cyberinfrastructure-Enabled Machine Learning Research.\n \n \n \n \n\n\n \n Thomas, M. P; Götz, A. W; Kandes, M. C.; Nguyen, M.; Rodriguez, P.; Rose, P. W.; and Sinkovits, R. S\n\n\n \n\n\n\n In PEARC 2023 Conference Series - Practice and Experience in Advanced Research Computing, pages 390 -394, 2023. Association for Computing Machinery\n \n\n\n\n
\n\n\n\n \n \n \"DevelopingPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n \n \n \n \n \n \n\n\n\n
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@inproceedings{Thomas-PEARC23-CIML,\n   author = {Mary P Thomas and Andreas W Götz and Martin C. Kandes and Mai Nguyen and Paul Rodriguez and Peter W. Rose and Robert S Sinkovits},\n   city = {Portland, OR, USA},\n   doi = {10.1145/3569951.3597543},\n   booktitle = {PEARC 2023 Conference Series - Practice and Experience in Advanced Research Computing},\n   keywords = {advanced cyberinfrastructure,machine learning,workforce development},\n   pages = {390 -394},\n   publisher = {Association for Computing Machinery},\n   title = {Developing a Best Practices Training Program in Cyberinfrastructure-Enabled Machine Learning Research},\n   url = {https://dl.acm.org/doi/10.1145/3569951.3597543},\n   year = {2023},\n}\n
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\n \n\n \n \n \n \n \n Approaching Exascale : Best Practices for Training a Diverse Workforce using Hackathons.\n \n \n \n\n\n \n Barker, I.; Chimeh, M. K.; Gott, K.; Papatheodore, T.; and Thomas, M. P\n\n\n \n\n\n\n In Best Practices for HPC Traning and Education (BPHTE22), 2022. \n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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@inproceedings{Barker2022,\n   author = {Izumi Barker and Mozhgan Kabiri Chimeh and Kevin Gott and Thomas Papatheodore and Mary P Thomas},\n   city = {Dallas, TX},\n   doi = {https://doi.org/10.22369/issn.2153-4136/14/1/3},\n   booktitle = {Best Practices for HPC Traning and Education (BPHTE22)},\n   keywords = {exascale,hackathons,hpc,hpc education,hpc training},\n   title = {Approaching Exascale : Best Practices for Training a Diverse Workforce using Hackathons},\n   year = {2022},\n}\n
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\n \n\n \n \n \n \n \n \n Image Classification Between Butterflies and Bees using Deep Convolutional Neural Networks; Image Classification Between Butterflies and Bees using Deep Convolutional Neural Networks.\n \n \n \n \n\n\n \n Mar, J.; and Thomas, M.\n\n\n \n\n\n\n 2021.\n \n\n\n\n
\n\n\n\n \n \n \"ImagePaper\n  \n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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@misc{Mar2021,\n   abstract = {The objective of this project was to apply a deep convolutional neural network to classify new images of winged insects, more specifically, butterflies and bees. The basic CNN was trained on the SDSC Expanse supercomputer using around 5000 images of each category, and was tasked with determining if a new image was of a butterfly or of a bee. The deep learning model was based off of Machine Learning Mastery's "How to Classify Photos of Dogs and Cats" VGG model, consisting of several convolutional layers followed by max pooling layers. In order to address the issue of overfitting of the data, dropout regularization and image data augmentation methods were applied to the VGG 3 block model. With a 95.4% accuracy rate, the model performed quite effectively with the new data sets.},\n   author = {Jenny Mar and Mary Thomas},\n   keywords = {Convolutional Neural Networks,Deep Learning,HPC,Interactive Computing,Jupyter,Jupyter Notebooks,Machine Learning},\n   title = {Image Classification Between Butterflies and Bees using Deep Convolutional Neural Networks; Image Classification Between Butterflies and Bees using Deep Convolutional Neural Networks},\n   url = {https://doi.org/12345},\n   year = {2021},\n}\n
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\n The objective of this project was to apply a deep convolutional neural network to classify new images of winged insects, more specifically, butterflies and bees. The basic CNN was trained on the SDSC Expanse supercomputer using around 5000 images of each category, and was tasked with determining if a new image was of a butterfly or of a bee. The deep learning model was based off of Machine Learning Mastery's \"How to Classify Photos of Dogs and Cats\" VGG model, consisting of several convolutional layers followed by max pooling layers. In order to address the issue of overfitting of the data, dropout regularization and image data augmentation methods were applied to the VGG 3 block model. With a 95.4% accuracy rate, the model performed quite effectively with the new data sets.\n
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\n \n\n \n \n \n \n \n start-jupyter: Developing a Client for Launching Jupyter Notebooks on HPC Systems Using the Satellite Reverse Proxy Service.\n \n \n \n\n\n \n McDougall, J.; Kandes, M.; Sakai, S.; and Thomas, M.\n\n\n \n\n\n\n In PEARC21: Practice and Experience in Advanced Research Computing, 2021. \n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@inproceedings{McDougalPEARC21,\n   author = {James McDougall and Marty Kandes and Scott Sakai and Mary Thomas},\n   booktitle = {PEARC21: Practice and Experience in Advanced Research Computing},\n   title = {start-jupyter: Developing a Client for Launching Jupyter Notebooks on HPC Systems Using the Satellite Reverse Proxy Service},\n   year = {2021},\n}\n
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\n \n\n \n \n \n \n \n Experiences in building a user portal for Expanse supercomputer.\n \n \n \n\n\n \n Sakai, S.; Irving, C.; Kandes, M.; Mishin, D.; Sivagnanam, S.; Strande, S.; Tatineni, M.; Thomas, M.; and Norman, M.\n\n\n \n\n\n\n In PEARC21: Practice and Experience in Advanced Research Computing, pages Accepted. ACM., 2021. ACM\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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@inproceedings{Sakai-ExpPort-2021,\n   author = {Scott Sakai and Christopher Irving and Martin Kandes and Dmitry Mishin and Subhashini Sivagnanam and Shawn Strande and Mahidhar Tatineni and Mary Thomas and Michael Norman},\n   doi = {10.1145/3437359.3465590},\n   booktitle = {PEARC21: Practice and Experience in Advanced Research Computing},\n   keywords = {and phrases,cyberinfrastructure,gateway,hpc,user portal},\n   pages = {Accepted. ACM.},\n   publisher = {ACM},\n   title = {Experiences in building a user portal for Expanse supercomputer},\n   year = {2021},\n}\n
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\n \n\n \n \n \n \n \n Expanse : Computing without Boundaries.\n \n \n \n\n\n \n Strande, S.; Altintas, I.; Cai, H.; Cooper, T.; Irving, C.; Kandes, M.; Majumdar, A.; Mishin, D.; Perez, I.; Pfeiffer, W.; Shantharam, M.; Sinkovits, R. S.; Sivagnanam, S.; Tatineni, M.; Thomas, M.; Wolter, N.; and Norman, M.\n\n\n \n\n\n\n In PEARC '21: Practice and Experience in Advanced Research Computing, 2021. \n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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@inproceedings{Strande-Exp-2021,\n   author = {Shawn Strande and Ilkay Altintas and Haisong Cai and Trevor Cooper and Christopher Irving and Marty Kandes and Amitava Majumdar and Dmitry Mishin and Ismael Perez and Wayne Pfeiffer and Manu Shantharam and Robert S. Sinkovits and Subhashini Sivagnanam and Mahidhar Tatineni and Mary Thomas and Nicole Wolter and Michael Norman},\n   doi = {10.1145/3437359.3465588},\n   booktitle = {PEARC '21: Practice and Experience in Advanced Research Computing},\n   keywords = {1,and expertise are evolving,diversification in,high performance computing,high throughput computing,high-performance computing system architectures,science gateways,scientific applications,software,system architecture,to support the growing,user support},\n   title = {Expanse : Computing without Boundaries},\n   year = {2021},\n}\n
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\n \n\n \n \n \n \n \n Development of the Satellite Jupyter Notebook Proxy Service.\n \n \n \n\n\n \n Thomas, M. P; Kandes, M.; McDougall, J.; Sakai, S.; and Tatineni, M.\n\n\n \n\n\n\n 2021.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@unpublished{Thomas-SRPS-2021,\n   author = {Mary P Thomas and Martin Kandes and James McDougall and Scott Sakai and Mahidhar Tatineni},\n   institution = {San Diego Supercomputer Center},\n   title = {Development of the Satellite Jupyter Notebook Proxy Service},\n   year = {2021},\n}\n
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\n \n\n \n \n \n \n \n Satellite : A Down-to-Earth Approach to Serving Jupyter Notebooks Over HTTPS.\n \n \n \n\n\n \n Thomas, M.; Kandes, M.; McDougall, J.; Mishin, D.; Sakai, S.; Sivagnanam, S.; and Tatineni, M.\n\n\n \n\n\n\n 2021.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
\n 
@unpublished{Thomas2021-Satellite,\n   author = {M. Thomas and M. Kandes and J. McDougall and D. Mishin and S. Sakai and S. Sivagnanam and M. Tatineni},\n   journal = {SDSC Technical Report, 2021},\n   keywords = {HPC,Interactive Computing,Jupyter,Jupyter Notebooks,Proxy,acm reference format,dmitry mishin,hpc,interactive computing,james mcdougall,jupyter,jupyter notebooks,martin kandes,mary p,proxy,scott,thomas},\n   publisher = {San Diego Supercomputer Center},\n   title = {Satellite : A Down-to-Earth Approach to Serving Jupyter Notebooks Over HTTPS},\n   year = {2021},\n}\n
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\n  \n 2020\n \n \n (3)\n \n \n
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\n \n\n \n \n \n \n \n Developing Interactive Jupyter Notebooks for SDSC HPC Systems.\n \n \n \n\n\n \n Kumar, D.; Gu, L.; Xie, S.; and Thomas, M.\n\n\n \n\n\n\n 2020.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@misc{Thomas-REHS-2020,\n   author = {Dhruv Kumar and Leo Gu and Sarah Xie and Mary Thomas},\n   institution = {San Diego Supercomuter Center},\n   journal = {SDSC Technical Report},\n   title = {Developing Interactive Jupyter Notebooks for SDSC HPC Systems},\n   year = {2020},\n}\n
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\n \n\n \n \n \n \n \n Developing Interactive Jupyter Notebooks for SDSC HPC Systems.\n \n \n \n\n\n \n Kumar, D.; Gu, L.; Xie, S.; and Thomas, M.\n\n\n \n\n\n\n 2020.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@misc{Kumar2020,\n   abstract = {The goal of this research project is to develop a set of Jupyter Notebooks that can be used to train users on the Comet supercomputer. These notebooks will be hosted on the San Diego Supercomputer Center (SDSC) GitHub.io training pages. The purpose of this project is to understand the basics of High Performance Computing, Jupyter Notebooks and GitHub. For this, we worked with existing projects to develop new notebooks. The research components are to contribute to the body of knowledge needed for hosting live, dynamic, interactive services that interface to HPC systems, and to learn how to develop interactive notebooks to be used for education and training of the users of these systems. As a result of our efforts, we produced several new Jupyter Notebooks that will be used for Comet/SDSC training.},\n   author = {Dhruv Kumar and Leo Gu and Sarah Xie and Mary Thomas},\n   title = {Developing Interactive Jupyter Notebooks for SDSC HPC Systems},\n   year = {2020},\n}\n
\n
\n\n\n
\n The goal of this research project is to develop a set of Jupyter Notebooks that can be used to train users on the Comet supercomputer. These notebooks will be hosted on the San Diego Supercomputer Center (SDSC) GitHub.io training pages. The purpose of this project is to understand the basics of High Performance Computing, Jupyter Notebooks and GitHub. For this, we worked with existing projects to develop new notebooks. The research components are to contribute to the body of knowledge needed for hosting live, dynamic, interactive services that interface to HPC systems, and to learn how to develop interactive notebooks to be used for education and training of the users of these systems. As a result of our efforts, we produced several new Jupyter Notebooks that will be used for Comet/SDSC training.\n
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\n \n\n \n \n \n \n \n Interactive Training Videos: Turning Static Training Webinars Into Engaging Interactive Learning Experiences.\n \n \n \n\n\n \n Sale, J.; and Thomas, M. P\n\n\n \n\n\n\n 2020.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n \n \n \n \n \n \n \n \n\n\n\n
\n 
@misc{Sale-IntVideo-2020,\n   author = {Jeff Sale and Mary P Thomas},\n   institution = {San Diego Supercomputer Center},\n   keywords = {gui design,hpc training,interactive videos,webinar},\n   title = {Interactive Training Videos: Turning Static Training Webinars Into Engaging Interactive Learning Experiences},\n   year = {2020},\n}\n
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\n  \n 2019\n \n \n (3)\n \n \n
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\n \n \n
\n \n\n \n \n \n \n \n Mining online training log data.\n \n \n \n\n\n \n Mehringer, S.; Myers, C. R.; Houchins, J.; and Rivera, L.\n\n\n \n\n\n\n ACM International Conference Proceeding Series. 2019.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n \n \n \n \n \n \n \n \n\n\n\n
\n 
@article{Mehringer2019,\n   abstract = {Online training has been growing in popularity, and offers many advantages for both trainers and learners. Assessing the usage and impact of online material can be difficult, especially if content is made available to anyone and is not part of a course requiring formal enrollment. The Cornell Virtual Workshop (CVW) first offered online training on topics in high-performance computing and computational science in 1994, and ten years ago we began logging usage. We are now performing our first in-depth analysis of those log data to identify patterns in usage, so that we can better understand how users access the material, which types of topics and materials result in the greatest impact, how topic usage changes over time, and what types of presentation format might be preferred. While the CVW is built around a cohesive, sequential narrative for each training topic, we find that many users access our content in a more targeted fashion, suggesting that we rethink how we package our material. We anticipate that ongoing analysis using data science and machine learning methods will enable us to produce more useful training materials, and provide the educational community with valuable information about patterns in online material usage.},\n   author = {Susan Mehringer and Christopher R. Myers and Jennifer Houchins and Lorna Rivera},\n   doi = {10.1145/3332186.3332235},\n   isbn = {9781450372275},\n   journal = {ACM International Conference Proceeding Series},\n   keywords = {HPC,Training,Usage Statistics,XSEDE},\n   title = {Mining online training log data},\n   year = {2019},\n}\n
\n
\n\n\n
\n Online training has been growing in popularity, and offers many advantages for both trainers and learners. Assessing the usage and impact of online material can be difficult, especially if content is made available to anyone and is not part of a course requiring formal enrollment. The Cornell Virtual Workshop (CVW) first offered online training on topics in high-performance computing and computational science in 1994, and ten years ago we began logging usage. We are now performing our first in-depth analysis of those log data to identify patterns in usage, so that we can better understand how users access the material, which types of topics and materials result in the greatest impact, how topic usage changes over time, and what types of presentation format might be preferred. While the CVW is built around a cohesive, sequential narrative for each training topic, we find that many users access our content in a more targeted fashion, suggesting that we rethink how we package our material. We anticipate that ongoing analysis using data science and machine learning methods will enable us to produce more useful training materials, and provide the educational community with valuable information about patterns in online material usage.\n
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\n \n\n \n \n \n \n \n Creation of Jupyter Notebooks for Science Tutorials.\n \n \n \n\n\n \n Moezzi, S.; Bay, J.; Chakraborty, A.; Wei, R.; and Thomas, M.\n\n\n \n\n\n\n In Gateways 2019: Science Gateways Community Institute (SGCI) 2019, 2019. \n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@inproceedings{Thomas-Gateways-2019,\n   author = {Shayda Moezzi and Joshua Bay and Alisha Chakraborty and Ryan Wei and Mary Thomas},\n   booktitle = {Gateways 2019: Science Gateways Community Institute (SGCI) 2019},\n   title = {Creation of Jupyter Notebooks for Science Tutorials},\n   year = {2019},\n}\n
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\n \n\n \n \n \n \n \n Parallel Implementation of a PETSc-Based Framework for the General Curvilinear Coastal Ocean Model.\n \n \n \n\n\n \n Valera, M.; Thomas, M. P.; Garcia, M.; and Castillo, J. E.\n\n\n \n\n\n\n Marine Science and Engineering, 7: 2-26. 2019.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
\n 
@article{Valera2019,\n   abstract = {The General Curvilinear Coastal Ocean Model (GCCOM) is a 3D curvilinear, structured-mesh, non-hydrostatic, large-eddy simulation model that is capable of running oceanic simulations. GCCOM is an inherently computationally expensive model: it uses an elliptic solver for the dynamic pressure; meter-scale simulations requiring memory footprints on the order of 10 12 cells and terabytes of output data. As a solution for parallel optimization, the Fortran-interfaced Portable&ndash;Extensible Toolkit for Scientific Computation (PETSc) library was chosen as a framework to help reduce the complexity of managing the 3D geometry, to improve parallel algorithm design, and to provide a parallelized linear system solver and preconditioner. GCCOM discretizations are based on an Arakawa-C staggered grid, and PETSc DMDA (Data Management for Distributed Arrays) objects were used to provide communication and domain ownership management of the resultant multi-dimensional arrays, while the fully curvilinear Laplacian system for pressure is solved by the PETSc linear solver routines. In this paper, the framework design and architecture are described in detail, and results are presented that demonstrate the multiscale capabilities of the model and the parallel framework to 240 cores over domains of order 10 7 total cells per variable, and the correctness and performance of the multiphysics aspects of the model for a baseline experiment stratified seamount.},\n   author = {Manuel Valera and Mary P. Thomas and Mariangel Garcia and Jose E. Castillo},\n   doi = {https://doi.org/10.3390/jmse7060185},\n   issue = {6},\n   journal = {Marine Science and Engineering},\n   keywords = {curvilinear,gccom,high performance computing,hpc,non-hydrostatic,ocean modeling,parallel,parallelization,performance,petsc,scalability,streams},\n   pages = {2-26},\n   title = {Parallel Implementation of a PETSc-Based Framework for the General Curvilinear Coastal Ocean Model},\n   volume = {7},\n   year = {2019},\n}\n
\n
\n\n\n
\n The General Curvilinear Coastal Ocean Model (GCCOM) is a 3D curvilinear, structured-mesh, non-hydrostatic, large-eddy simulation model that is capable of running oceanic simulations. GCCOM is an inherently computationally expensive model: it uses an elliptic solver for the dynamic pressure; meter-scale simulations requiring memory footprints on the order of 10 12 cells and terabytes of output data. As a solution for parallel optimization, the Fortran-interfaced Portable–Extensible Toolkit for Scientific Computation (PETSc) library was chosen as a framework to help reduce the complexity of managing the 3D geometry, to improve parallel algorithm design, and to provide a parallelized linear system solver and preconditioner. GCCOM discretizations are based on an Arakawa-C staggered grid, and PETSc DMDA (Data Management for Distributed Arrays) objects were used to provide communication and domain ownership management of the resultant multi-dimensional arrays, while the fully curvilinear Laplacian system for pressure is solved by the PETSc linear solver routines. In this paper, the framework design and architecture are described in detail, and results are presented that demonstrate the multiscale capabilities of the model and the parallel framework to 240 cores over domains of order 10 7 total cells per variable, and the correctness and performance of the multiphysics aspects of the model for a baseline experiment stratified seamount.\n
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\n  \n 2018\n \n \n (1)\n \n \n
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\n \n\n \n \n \n \n \n Implementation of a PETSc-based Parallel General Curvilinear Coastal Ocean Model.\n \n \n \n\n\n \n Valera, M.; Garcia, M. V.; Patel, N.; Thomas, M. P.; and Castillo, J. E.\n\n\n \n\n\n\n Journal of Computational Science, Manuscript. 2018.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n \n \n\n\n\n
\n 
@article{Valera2018,\n   author = {M. Valera and M. V. Garcia and N. Patel and M. P. Thomas and J. E. Castillo},\n   journal = {Journal of Computational Science},\n   keywords = {parallel ocean models},\n   title = {Implementation of a PETSc-based Parallel General Curvilinear Coastal Ocean Model},\n   volume = {Manuscript},\n   year = {2018},\n}\n
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\n  \n 2017\n \n \n (2)\n \n \n
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\n \n\n \n \n \n \n \n \n COMP 605: Introduction to Parallel Computing.\n \n \n \n \n\n\n \n Thomas, M. P (. D. S. U.\n\n\n \n\n\n\n 2017.\n \n\n\n\n
\n\n\n\n \n \n \"COMPPaper\n  \n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@misc{ThomasLectures,\n   author = {Mary P (San Diego State University) Thomas},\n   title = {COMP 605: Introduction to Parallel Computing},\n   url = {http://edoras.sdsu.edu/~mthomas/sp17.605/},\n   year = {2017},\n}\n
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\n \n\n \n \n \n \n \n SC16 Student Cluster Competition Challenge : Investigating the Reproducibility of Results for the ParConnect Application.\n \n \n \n\n\n \n Williams, G; Behm, G; Nguyen, T; Esparza, A; Haka, V G; Ramos, A; Wright, B; Otto, J.; Paolini, C. P.; and Thomas, M. P.\n\n\n \n\n\n\n Parallel Computing, 70: 27-24. 2017.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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@article{GWilliams-ParCon2017,\n   author = {G Williams and G Behm and T Nguyen and A Esparza and V G Haka and A Ramos and B Wright and J. Otto and C. P. Paolini and M. P. Thomas},\n   journal = {Parallel Computing},\n   keywords = {MPI,message passing,parallel,performance,reproducibility},\n   pages = {27-24},\n   title = {SC16 Student Cluster Competition Challenge : Investigating the Reproducibility of Results for the ParConnect Application},\n   volume = {70},\n   year = {2017},\n}\n
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\n  \n 2016\n \n \n (5)\n \n \n
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\n \n\n \n \n \n \n \n Nesting Nonhydrostatic GCCOM within Hydrostatic ROMS for Multiscale Coastal Ocean Modeling.\n \n \n \n\n\n \n Choboter, P. F.; Garcia, M.; Cecchis, D. D.; Thomas, M.; Walter, R. K.; and Castillo, J. E.\n\n\n \n\n\n\n In OCEANS 2016 MTS/IEEE Monterey, OCE 2016 (2016), 2016. \n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n \n \n \n \n \n \n\n\n\n
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@inproceedings{Choboter2016a,\n   author = {Paul F. Choboter and Mariangel Garcia and Dany De Cecchis and Mary Thomas and Ryan K. Walter and José E. Castillo},\n   city = {Monterey},\n   doi = {10.1109/OCEANS.2016.7761488},\n   booktitle = {OCEANS 2016 MTS/IEEE Monterey, OCE 2016 (2016)},\n   keywords = {nesting,nonhydrostatic,numerical models},\n   title = {Nesting Nonhydrostatic GCCOM within Hydrostatic ROMS for Multiscale Coastal Ocean Modeling},\n   year = {2016},\n}\n
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\n \n\n \n \n \n \n \n Interfacing GCCOM within DART : A Sensitivity Analysis .\n \n \n \n\n\n \n Garcia, M.; Hoar, T.; Bailey, B.; and Thomas, M.\n\n\n \n\n\n\n In Oceans'11 MTS/IEEE, 2016. \n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@inproceedings{Garcia2016a,\n   author = {Mariangel Garcia and Timothy Hoar and Barbara Bailey and Mary Thomas},\n   city = {Monterey Bay},\n   booktitle = {Oceans'11 MTS/IEEE},\n   title = {Interfacing GCCOM within DART : A Sensitivity Analysis .},\n   year = {2016},\n}\n
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\n \n\n \n \n \n \n \n Jupyter Notebooks—a publishing format for reproducible computational workflows.\n \n \n \n\n\n \n Kluyver, T.; Ragan-kelley, B.; Pérez, F.; Granger, B. E.; Bussonnier, M.; Frederic, J.; Kelley, K.; Hamrick, J.; Grout, J.; Corlay, S.; Ivanov, P.; Avila, D.; Abdalla, S.; and Willing, C.\n\n\n \n\n\n\n Positioning and Power in Academic Publishing: Players, Agents and Agendas,87-90. 2016.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n \n \n \n \n \n \n\n\n\n
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@article{Kluyver1016,\n   abstract = {It is increasingly necessary for researchers in all fields to write computer code, and in order to reproduce research results, it is important that this code is published. We present Jupyter notebooks, a document format for publishing code, results and explanations in a form that is both readable and executable. We discuss various tools and use cases for notebook documents.},\n   author = {Thomas Kluyver and Benjamin Ragan-kelley and Fernando Pérez and Brian E. Granger and Matthias Bussonnier and Jonathan Frederic and Kyle Kelley and Jessica Hamrick and Jason Grout and Sylvain Corlay and Paul Ivanov and Damián Avila and Safia Abdalla and Carol Willing},\n   doi = {10.3233/978-1-61499-649-1-87},\n   isbn = {9781614996491},\n   issn = {0015-0193},\n   journal = {Positioning and Power in Academic Publishing: Players, Agents and Agendas},\n   keywords = {notebook,reproducibility,research code},\n   pages = {87-90},\n   pmid = {23502158},\n   title = {Jupyter Notebooks—a publishing format for reproducible computational workflows},\n   year = {2016},\n}\n
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\n It is increasingly necessary for researchers in all fields to write computer code, and in order to reproduce research results, it is important that this code is published. We present Jupyter notebooks, a document format for publishing code, results and explanations in a form that is both readable and executable. We discuss various tools and use cases for notebook documents.\n
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\n \n\n \n \n \n \n \n Reducing Analysis Time for Identifying Drug Compounds and Screening Large Chemical Libraries with the Parallel evoQSAR (ParEvoQSAR) Modeling Framework.\n \n \n \n\n\n \n Su, E.; Ko, G.; Kumar, S.; Thomas, M. P.; and Garg, R.\n\n\n \n\n\n\n 2016.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@unpublished{ESu2015b,\n   author = {E. Su and Gene Ko and Sunil Kumar and Mary P. Thomas and Rajni Garg},\n   isbn = {9788578110796},\n   issn = {1098-6596},\n   journal = {Manuscript in preparation},\n   title = {Reducing Analysis Time for Identifying Drug Compounds and Screening Large Chemical Libraries with the Parallel evoQSAR (ParEvoQSAR) Modeling Framework.},\n   year = {2016},\n}\n
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\n \n\n \n \n \n \n \n Development of an Ocean Sciences Education Portal for Simulating Coastal Ocean Processes.\n \n \n \n\n\n \n Thomas, M. P.; Bucciarelli1, R.; Chao, Y.; Choboter, P.; Garcia, M.; Manjunanth, S.; and Castillo, J. E.\n\n\n \n\n\n\n In GCE2016: The 11th Gateway Computing Environments Workshop, pages Poster presentation, 2016. \n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@inproceedings{ThomasGCE2016,\n   author = {M. P. Thomas and R. Bucciarelli1 and Y. Chao and P. Choboter and M. Garcia and S. Manjunanth and J. E. Castillo},\n   city = {San Diego},\n   booktitle = {GCE2016: The 11th Gateway Computing Environments Workshop},\n   pages = {Poster presentation},\n   title = {Development of an Ocean Sciences Education Portal for Simulating Coastal Ocean Processes},\n   year = {2016},\n}\n
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\n  \n 2015\n \n \n (6)\n \n \n
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\n \n\n \n \n \n \n \n Nesting nonhydrostatic UCOAM within hydrostatic ROMS.\n \n \n \n\n\n \n Choboter, P. F.; Thomas, M. P.; and Castillo, J. E.\n\n\n \n\n\n\n In SIAM Conf. Math. Comput. Issues Geosci. (GS'15), pages presentation by paul choboter, 2015. \n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@inproceedings{Choboter2015,\n   author = {Paul F. Choboter and Mary P. Thomas and Jose E. Castillo},\n   city = {Stanford, CA},\n   booktitle = {SIAM Conf. Math. Comput. Issues Geosci. (GS'15)},\n   pages = {presentation by paul choboter},\n   title = {Nesting nonhydrostatic UCOAM within hydrostatic ROMS},\n   year = {2015},\n}\n
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\n \n\n \n \n \n \n \n Nesting nonhydrostatic UCOAM within hydrostatic ROMS.\n \n \n \n\n\n \n Choboter, P. F.; Thomas, M. P.; and Castillo, J. E.\n\n\n \n\n\n\n In 2015 SIAM Conference on Mathematical & Computational Issues in the Geosciences, 2015. \n \n\n\n\n
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@inproceedings{Choboter2015,\n   author = {Paul F. Choboter and Mary P. Thomas and Jose E. Castillo},\n   city = {Stanford, CA},\n   booktitle = {2015 SIAM Conference on Mathematical & Computational Issues in the Geosciences},\n   title = {Nesting nonhydrostatic UCOAM within hydrostatic ROMS},\n   year = {2015},\n}\n
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\n \n\n \n \n \n \n \n \n Parallellization of evoQSAR Modeling Framework and Graphical User Interface Design using PyQt for Drug Design.\n \n \n \n \n\n\n \n And Eric Su, G. M. K.; and Thomas, M.\n\n\n \n\n\n\n In Applied Computational Science and Engineering Student Support (ACSESS'15), 2015. \n \n\n\n\n
\n\n\n\n \n \n \"ParallellizationPaper\n  \n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@inproceedings{ESU2015a,\n   author = {And Eric Su, Gene M. Ko, Rajni Garg, Sunil Kumar and Mary Thomas},\n   city = {San Diego, CA},\n   booktitle = {Applied Computational Science and Engineering Student Support (ACSESS'15)},\n   title = {Parallellization of evoQSAR Modeling Framework and Graphical User Interface Design using PyQt for Drug Design},\n   url = {http://www.csrc.sdsu.edu/acsess/acsess2015/index.html},\n   year = {2015},\n}\n
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\n \n\n \n \n \n \n \n GCCOM_DART Ensemble Data Assimilation Analysis System for the 3D-Non-Hydrsotatic General Curvilinear Coastal Ocean Model (GCCOM).\n \n \n \n\n\n \n Garcia, M.; Hoar, T.; Thomas, M.; Bailey, B.; and Castillo, J. E.\n\n\n \n\n\n\n In International Council for Industrial and Applied Mathematics (ICIAM 2015), pages Poster, 2015. \n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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@inproceedings{GarciaICIAM2015,\n   author = {Mariangel Garcia and Tim Hoar and Mary Thomas and Barbara Bailey and Jose E. Castillo},\n   city = {Beijing, China},\n   booktitle = {International Council for Industrial and Applied Mathematics (ICIAM 2015)},\n   keywords = {3d,c,curvilinear coordinates,data assimila,enakf,gccom,high resolu,hydrosta,non-,on},\n   pages = {Poster},\n   title = {GCCOM_DART Ensemble Data Assimilation Analysis System for the 3D-Non-Hydrsotatic General Curvilinear Coastal Ocean Model (GCCOM)},\n   year = {2015},\n}\n
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\n \n\n \n \n \n \n \n GCCOM-DART: Ensemble Data Assimilation Analysis System for Sub-mesoscale Processes. Sensitivity Analysis of a 3D Nonhydrostatic Coastal Ocean Model.\n \n \n \n\n\n \n Garcia, M.; Hoar, T.; Bailey, B.; Thomas, M. P.; and Castillo, J. E.\n\n\n \n\n\n\n 2015.\n \n\n\n\n
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@unpublished{Garcia2015a,\n   abstract = {This paper presents the successful integration of a data assimilation framework and a nonhydrostatic coastal ocean model for the study of sub-mesoscale processes and state variables. When provided with the proper data, mesoscale phenomena have been modeled with a certain level of accuracy; however, many sub-mesoscale features are still poorly modeled, causing them to remain largely unpredictable from deterministic event and statistical property standpoints. 3D nonhydrostatic models are required to accurately capture these key dynamics. Although this implementation is essential for the successful development of physical ocean models, a major challenge posed by this approach is the high computational cost incurred by high-resolution numerical models with three-dimensional data assimilation schemes within complicated, stratified systems. However, by interfacing our General Curvilinear Coastal Ocean Model (GCCOM) with NCAR's Data Assimilation Research Testbed (DART), we were able to integrate very high-resolution observations into the system. Our research included observation system simulation experiments (OSSEs) for test cases using very steep seamounts. Our results demonstrated that the DART-GCCOM model can successfully assimilate high-resolution observations (to tenths of meters) using},\n   author = {Mariangel Garcia and Tim Hoar and Barbara Bailey and Mary P. Thomas and Jose E. Castillo},\n   isbn = {1619594226},\n   journal = {Computational Geosciences},\n   keywords = {3d curvilinear,castillo,computational science research center,dart,data assimilation,garcia,m,non-hydrostatic,san diego state university,thomas and j},\n   title = {GCCOM-DART: Ensemble Data Assimilation Analysis System for Sub-mesoscale Processes. Sensitivity Analysis of a 3D Nonhydrostatic Coastal Ocean Model.},\n   volume = {Submitted/},\n   year = {2015},\n}\n
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\n This paper presents the successful integration of a data assimilation framework and a nonhydrostatic coastal ocean model for the study of sub-mesoscale processes and state variables. When provided with the proper data, mesoscale phenomena have been modeled with a certain level of accuracy; however, many sub-mesoscale features are still poorly modeled, causing them to remain largely unpredictable from deterministic event and statistical property standpoints. 3D nonhydrostatic models are required to accurately capture these key dynamics. Although this implementation is essential for the successful development of physical ocean models, a major challenge posed by this approach is the high computational cost incurred by high-resolution numerical models with three-dimensional data assimilation schemes within complicated, stratified systems. However, by interfacing our General Curvilinear Coastal Ocean Model (GCCOM) with NCAR's Data Assimilation Research Testbed (DART), we were able to integrate very high-resolution observations into the system. Our research included observation system simulation experiments (OSSEs) for test cases using very steep seamounts. Our results demonstrated that the DART-GCCOM model can successfully assimilate high-resolution observations (to tenths of meters) using\n
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\n \n\n \n \n \n \n \n Parallelization of a 3D Curvilinear Non-hydrostatic Coastal Ocean Model.\n \n \n \n\n\n \n Thomas, M.; and Castillo, J.\n\n\n \n\n\n\n In SIAM Conference on Mathematical and Computational Issues in the Geosciences (GS’15), 2015. \n \n\n\n\n
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@inproceedings{Thomas-2015a,\n   author = {Mary Thomas and Jose Castillo},\n   city = {Stanford, CA},\n   booktitle = {SIAM Conference on Mathematical and Computational Issues in the Geosciences (GS’15)},\n   keywords = {curvilinear,cyberinfrastructure,hpc,ocean models,parallel computing},\n   title = {Parallelization of a 3D Curvilinear Non-hydrostatic Coastal Ocean Model},\n   year = {2015},\n}\n
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\n  \n 2014\n \n \n (4)\n \n \n
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\n \n\n \n \n \n \n \n Development of JSON and AJAX enabled, database driven, user interfaces for science application portals.\n \n \n \n\n\n \n Shah, H. G.; and Thomas, M.\n\n\n \n\n\n\n 2014.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@misc{Hetang2014,\n   author = {Hetang G. Shah and Mary Thomas},\n   city = {San Diego},\n   institution = {Computational Sciences Research Center},\n   title = {Development of JSON and AJAX enabled, database driven, user interfaces for science application portals},\n   year = {2014},\n}\n
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\n \n\n \n \n \n \n \n Improving the Performance of Thermochemical Computations Using Many- Task Computing Methods.\n \n \n \n\n\n \n Thomas, M. P; Cheng, C.; Bhattacharjee, S.; Edwards, R. A; and Paolini, C.\n\n\n \n\n\n\n 2014.\n \n\n\n\n
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@misc{Thomas2014-CSRC,\n   author = {Mary P Thomas and Carny Cheng and S. Bhattacharjee and Robert A Edwards and Christopher Paolini},\n   institution = {Computational Sciences Research Center, San Diego State University},\n   pages = {1-14},\n   title = {Improving the Performance of Thermochemical Computations Using Many- Task Computing Methods},\n   year = {2014},\n}\n
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\n \n\n \n \n \n \n \n \n Introduction to Scientific Computing.\n \n \n \n \n\n\n \n Thomas, M. P.\n\n\n \n\n\n\n 2014.\n \n\n\n\n
\n\n\n\n \n \n \"IntroductionPaper\n  \n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@misc{ThomasSciComp,\n   author = {Mary P. Thomas},\n   title = {Introduction to Scientific Computing},\n   url = {http://www-rohan.sdsu.edu/faculty/mthomas/courses/spring2014/cs605/index.html},\n   year = {2014},\n}\n
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\n \n\n \n \n \n \n \n \n Parallel Implementation of the Unified Curvilinear Ocean and Atmospheric (UCOAM) Model and Supporting Computational Environment.\n \n \n \n \n\n\n \n Thomas, M. P.\n\n\n \n\n\n\n ,110. 2014.\n \n\n\n\n
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@article{ThomasDissertation2014,\n   author = {Mary P. Thomas},\n   city = {San Diego},\n   institution = {Claremont Graduate University and San Diego State University},\n   pages = {110},\n   title = {Parallel Implementation of the Unified Curvilinear Ocean and Atmospheric (UCOAM) Model and Supporting Computational Environment},\n   url = {http://sdsu-dspace.calstate.edu/handle/10211.3/120387},\n   year = {2014},\n}\n
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\n \n\n \n \n \n \n \n \n Towards the Development of a Pipelined Data Movement with Globus Online.\n \n \n \n \n\n\n \n Paolini, C.; Thomas, M. P; and Kettimuthu, R.\n\n\n \n\n\n\n In XSEDE Annual Meeting, 2013. \n \n\n\n\n
\n\n\n\n \n \n \"TowardsPaper\n  \n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n \n \n\n\n\n
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@inproceedings{Paolini2013pipline,\n   author = {Christopher Paolini and Mary P Thomas and Raj Kettimuthu},\n   booktitle = {XSEDE Annual Meeting},\n   keywords = {XSEDE2013},\n   title = {Towards the Development of a Pipelined Data Movement with Globus Online},\n   url = {http://www.xsede.org},\n   year = {2013},\n}\n
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\n \n\n \n \n \n \n \n A Cyberinfrastructure-Based Computational Environment for Unified Curvilinear Ocean Atmospheric Model ( UCOAM ).\n \n \n \n\n\n \n Thomas, M.; and Castillo, J.\n\n\n \n\n\n\n In 4th International Congress on Computational Engineering and Sciences, 2013. \n \n\n\n\n
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@inproceedings{ThomasFemTec2013,\n   author = {Mary Thomas and Jose Castillo},\n   booktitle = {4th International Congress on Computational Engineering and Sciences},\n   title = {A Cyberinfrastructure-Based Computational Environment for Unified Curvilinear Ocean Atmospheric Model ( UCOAM )},\n   year = {2013},\n}\n
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\n \n\n \n \n \n \n \n Nesting ROMS and UCOAM: A Case Study in Monterey Bay.\n \n \n \n\n\n \n Thomas, M. P; Cecchis, D. D.; Choboter, P.; and Castillo, J. E.\n\n\n \n\n\n\n In Society for Industrial and Applied Mathematics Annual Meeting, 2013. Computational Sciences Research Center\n \n\n\n\n
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@inproceedings{Thomas-ACSESS-2013,\n   author = {Mary P Thomas and Dany De Cecchis and Paul Choboter and Jose E. Castillo},\n   booktitle = {Society for Industrial and Applied Mathematics Annual Meeting},\n   publisher = {Computational Sciences Research Center},\n   title = {Nesting ROMS and UCOAM: A Case Study in Monterey Bay},\n   year = {2013},\n}\n
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\n \n\n \n \n \n \n \n \n Design and architecture of visualization services for the cyberinfrastructure web application framework.\n \n \n \n \n\n\n \n More, S.; and Thomas, M.\n\n\n \n\n\n\n . 2012.\n \n\n\n\n
\n\n\n\n \n \n \"DesignPaper\n  \n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n  \n \n 3 downloads\n \n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{More2014,\n   author = {Smita More and Mary Thomas},\n   institution = {San Diego State University},\n   title = {Design and architecture of visualization services for the cyberinfrastructure web application framework},\n   url = {https://digitallibrary.sdsu.edu/islandora/object/sdsu%3A3215},\n   year = {2012},\n}\n
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\n \n\n \n \n \n \n \n Integrating HPC Resources , Services , and Cyberinfrastructure to Develop Science Applications Using Web Application Frameworks.\n \n \n \n\n\n \n Thomas, M P; Cheng, C; More, S; and Shah, H\n\n\n \n\n\n\n In International Conference on Parallel and Distributed Processing Techniques and Applications, volume 2, pages 421-427, 2012. CSREA Press\n \n\n\n\n
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@inproceedings{ThomasPDPTA2012,\n   author = {M P Thomas and C Cheng and S More and H Shah},\n   city = {Las Vegas, NV},\n   doi = {ISBN: 1-60132-227-5},\n   booktitle = {International Conference on Parallel and Distributed Processing Techniques and Applications},\n   keywords = {CyberWeb,cyberinfrastructure,portals,pylons,python,web 2.0},\n   pages = {421-427},\n   publisher = {CSREA Press},\n   title = {Integrating HPC Resources , Services , and Cyberinfrastructure to Develop Science Applications Using Web Application Frameworks},\n   volume = {2},\n   year = {2012},\n}\n
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\n \n\n \n \n \n \n \n Parallelization of the 3D Unified Curvilinear Coastal Ocean Model: Initial Results.\n \n \n \n\n\n \n Thomas, M. P; and Castillo, J. E\n\n\n \n\n\n\n In International Conference on Computational Science and Its Applications, pages 88 - 96, 2012. \n \n\n\n\n
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@inproceedings{ThomasICCSA2012a,\n   author = {Mary P Thomas and Jose E Castillo},\n   city = {Salvador de Bahia, Brazil},\n   doi = {10.1109/ICCSA.2012.24},\n   booktitle = {International Conference on Computational Science and Its Applications},\n   keywords = {3d curvilinear,computing,cyberinfrastructure,grid computing,ocean models},\n   pages = {88 - 96},\n   title = {Parallelization of the 3D Unified Curvilinear Coastal Ocean Model: Initial Results},\n   year = {2012},\n}\n
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\n \n\n \n \n \n \n \n Development of a Cyberinfrastructure-based Computational Environment for the General Curvilinear Coastal Ocean Model.\n \n \n \n\n\n \n Thomas, M. P.; Cheng, C.; and Castillo, J. E.\n\n\n \n\n\n\n In Congress on Computer Applications and Computational Science, 2010. \n \n\n\n\n
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@inproceedings{Thomas2010,\n   author = {Mary P. Thomas and Carny Cheng and Jose E. Castillo},\n   issue = {Ci},\n   booktitle = {Congress on Computer Applications and Computational Science},\n   title = {Development of a Cyberinfrastructure-based Computational Environment for the General Curvilinear Coastal Ocean Model},\n   year = {2010},\n}\n
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\n \n\n \n \n \n \n \n Improving the Performance of Thermochemical Computations Using Many - Task Computing Methods.\n \n \n \n\n\n \n Thomas, M.; Cheng, C.; Bhattacharjee, S; Edwards, R. A.; and Paolini, C. P\n\n\n \n\n\n\n 2010.\n \n\n\n\n
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@misc{ThomasCSRC,\n   author = {Mary Thomas and Carny Cheng and S Bhattacharjee and Robert A. Edwards and Christopher P Paolini},\n   institution = {Computational Sciences Research Center},\n   pages = {1-12},\n   title = {Improving the Performance of Thermochemical Computations Using Many - Task Computing Methods},\n   year = {2010},\n}\n
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\n \n\n \n \n \n \n \n Development of a Computational Environment for the General Curvilinear Ocean Model ( GCOM ).\n \n \n \n\n\n \n Thomas, M. P.; and Castillo, J. E.\n\n\n \n\n\n\n In International Congress on Computer Applications and Computational Science (CACS 2010), 2010. \n \n\n\n\n
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@inproceedings{Thomas2010CACS,\n   author = {Mary P. Thomas and Jose E. Castillo},\n   city = {Singapore},\n   booktitle = {International Congress on Computer Applications and Computational Science (CACS 2010)},\n   keywords = {computational environments,models,ocean model,of lines of,pylons,requiring thousands or millions,simulators encompassing many different,web services},\n   title = {Development of a Computational Environment for the General Curvilinear Ocean Model ( GCOM )},\n   year = {2010},\n}\n
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\n \n\n \n \n \n \n \n Open Grid Computing Environments.\n \n \n \n\n\n \n Pierce, M.; Marru, S.; Wu, W.; Kandaswami, G.; von Laszewski, G.; Dooley, R.; Dahan, M.; Wilkins-Diehr, N.; and Thomas, M.\n\n\n \n\n\n\n In Conference: Proceedings of the Fourth Annual TeraGrid Conference, 2009. \n \n\n\n\n
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@inproceedings{MPierceOGCE2009,\n   author = {Marlon Pierce and Suresh Marru and Wenjun Wu and Gopi Kandaswami and Gregor von Laszewski and Rion Dooley and Maytal Dahan and Nancy Wilkins-Diehr and Mary Thomas},\n   institution = {University of Indiana},\n   booktitle = {Conference: Proceedings of the Fourth Annual TeraGrid Conference},\n   title = {Open Grid Computing Environments},\n   year = {2009},\n}\n
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\n \n\n \n \n \n \n \n Towards a General Curvilinear Ocean Model ( GCOM ) Framework.\n \n \n \n\n\n \n Thomas, M. P.; and Castillo, J. E.\n\n\n \n\n\n\n In Poster Presented at: The Applied Computational Science and Engineering Student Support (ACSESS) Meeting, 2009. \n \n\n\n\n
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@inproceedings{Thomas2009ACSESSPoster,\n   author = {Mary P. Thomas and Jose E. Castillo},\n   booktitle = {Poster Presented at: The Applied Computational Science and Engineering Student Support (ACSESS) Meeting},\n   keywords = {GCOM,coastal ocean model,cyberinfrastructure,cyberweb,ocean model},\n   title = {Towards a General Curvilinear Ocean Model ( GCOM ) Framework},\n   year = {2009},\n}\n
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\n \n\n \n \n \n \n \n Development of a Computational Environment for the General Curvilinear Ocean Model ( GCOM ).\n \n \n \n\n\n \n Thomas, M. P.; and Castillo, J. E.\n\n\n \n\n\n\n Journal of Physics: Conference Series, 180. 2009.\n \n\n\n\n
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@article{Thomas2009,\n   author = {Mary P. Thomas and Jose E. Castillo},\n   doi = {10.1088/1742-6596/180/1/012030},\n   issn = {1742-6596},\n   issue = {1},\n   journal = {Journal of Physics: Conference Series},\n   keywords = {computational environments,models,ocean model,of lines of,pylons,requiring thousands or millions,simulators encompassing many different,web services},\n   title = {Development of a Computational Environment for the General Curvilinear Ocean Model ( GCOM )},\n   volume = {180},\n   year = {2009},\n}\n
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\n \n\n \n \n \n \n \n A Web 2 . 0 Application Framework for Social Informatics Data Grid.\n \n \n \n\n\n \n Michael E. Papka Wenjun Wu, T. U.\n\n\n \n\n\n\n In GCE '09, pages 5-8, 2009. \n \n\n\n\n
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@inproceedings{WenjunWu2009,\n   author = {Michael E. Papka Wenjun Wu, Thomas Uram},\n   booktitle = {GCE '09},\n   pages = {5-8},\n   title = {A Web 2 . 0 Application Framework for Social Informatics Data Grid},\n   year = {2009},\n}\n
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\n  \n 2008\n \n \n (2)\n \n \n
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\n \n\n \n \n \n \n \n Using the Pylons Web Framework for Science Gateways.\n \n \n \n\n\n \n Thomas, M. P.\n\n\n \n\n\n\n In Grid Computing Environments Workshop (GCE08), pages 1-9, 2008. \n \n\n\n\n
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@inproceedings{Thomas2008,\n   author = {Mary P. Thomas},\n   city = {Austin, TX},\n   doi = {10.1109/GCE.2008.4738447},\n   booktitle = {Grid Computing Environments Workshop (GCE08)},\n   pages = {1-9},\n   title = {Using the Pylons Web Framework for Science Gateways},\n   year = {2008},\n}\n
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\n \n\n \n \n \n \n \n Towards a General Curvilinear Ocean Model (GCOM) Framework.\n \n \n \n\n\n \n Thomas, M.; and Castillo, J.\n\n\n \n\n\n\n In Applied Computational Science and Engineering Student Support Workshop, volume I, 2008. \n \n\n\n\n
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@inproceedings{Thomas2008a,\n   author = {Mary Thomas and Jose Castillo},\n   issue = {block 2},\n   booktitle = {Applied Computational Science and Engineering Student Support Workshop},\n   title = {Towards a General Curvilinear Ocean Model (GCOM) Framework},\n   volume = {I},\n   year = {2008},\n}\n
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\n  \n 2007\n \n \n (2)\n \n \n
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\n \n\n \n \n \n \n \n The Open Grid Computing Environments collaboration: Portlets and services for science gateways.\n \n \n \n\n\n \n Alameda, J.; Christie, M.; Fox, G.; Futrelle, J.; Gannon, D.; Hategan, M.; Kandaswamy, G.; Laszewski, G. V.; Nacar, M. A.; Pierce, M.; Roberts, E.; Severance, C.; and Thomas, M.\n\n\n \n\n\n\n Concurrency and Computation: Practice and Experience, 19: 921-942. 2007.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n \n \n \n \n \n \n\n\n\n
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@article{Alameda2007,\n   abstract = {We review the efforts of the Open Grid Computing Environments collaboration. By adopting a general three-tiered architecture based on common standards for portlets and Grid Web services, we can deliver numerous capabilities to science gateways from our diverse constituent efforts. In this paper, we discuss our support for standards-based Grid portlets using the Velocity development environment. Our Grid portlets are based on abstraction layers provided by the Java CoG kit, which hide the differences of different Grid toolkits. Sophisticated services are decoupled from the portal container using Web service strategies. We describe advance information, semantic data, collaboration, and science application services developed by our consortium. Copyright © 2006 John Wiley & Sons, Ltd.},\n   author = {Jay Alameda and Marcus Christie and Geoffrey Fox and Joe Futrelle and Dennis Gannon and Mihael Hategan and Gopi Kandaswamy and Gregor Von Laszewski and Mehmet A. Nacar and Marlon Pierce and Eric Roberts and Charles Severance and Mary Thomas},\n   doi = {10.1002/cpe.1078},\n   issn = {15320634},\n   issue = {6},\n   journal = {Concurrency and Computation: Practice and Experience},\n   keywords = {Collaboration,Grid services,Portlets},\n   pages = {921-942},\n   title = {The Open Grid Computing Environments collaboration: Portlets and services for science gateways},\n   volume = {19},\n   year = {2007},\n}\n
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\n We review the efforts of the Open Grid Computing Environments collaboration. By adopting a general three-tiered architecture based on common standards for portlets and Grid Web services, we can deliver numerous capabilities to science gateways from our diverse constituent efforts. In this paper, we discuss our support for standards-based Grid portlets using the Velocity development environment. Our Grid portlets are based on abstraction layers provided by the Java CoG kit, which hide the differences of different Grid toolkits. Sophisticated services are decoupled from the portal container using Web service strategies. We describe advance information, semantic data, collaboration, and science application services developed by our consortium. Copyright © 2006 John Wiley & Sons, Ltd.\n
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\n \n\n \n \n \n \n \n Editorial: Special Issue: Workshop on Grid Computing Portals (GCE 2005).\n \n \n \n\n\n \n Thomas, M. P\n\n\n \n\n\n\n In Concurency and Computation: Practice and Experience, pages 1563-1570, 2007. \n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@inproceedings{ThomasGCE2005,\n   author = {Mary P Thomas},\n   booktitle = {Concurency and Computation: Practice and Experience},\n   pages = {1563-1570},\n   title = {Editorial: Special Issue: Workshop on Grid Computing Portals (GCE 2005)},\n   year = {2007},\n}\n
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\n \n\n \n \n \n \n \n Investigations into the Parallelization of the General Curvilinear Ocean Model ( GCOM ) and its Operation Across Cyberinfrastructure Environments.\n \n \n \n\n\n \n Thomas, M. P.\n\n\n \n\n\n\n ,1-17. 2006.\n \n\n\n\n
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@article{Thomas2006,\n   author = {Mary P. Thomas},\n   pages = {1-17},\n   title = {Investigations into the Parallelization of the General Curvilinear Ocean Model ( GCOM ) and its Operation Across Cyberinfrastructure Environments},\n   year = {2006},\n}\n
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\n \n\n \n \n \n \n \n SRB Portlet Development for the Grid Portals.\n \n \n \n\n\n \n Thomas, M. P; Bansal, T.; Gupta, T.; Seth, A.; and Thomas, D.\n\n\n \n\n\n\n In Storage Resource Broker Workshop, 2006. \n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@inproceedings{Thomas2006SRB,\n   author = {Mary P Thomas and Tarun Bansal and Tushar Gupta and Akhil Seth and Dave Thomas},\n   city = {La Jolla},\n   booktitle = {Storage Resource Broker Workshop},\n   title = {SRB Portlet Development for the Grid Portals},\n   year = {2006},\n}\n
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\n  \n 2005\n \n \n (1)\n \n \n
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\n \n\n \n \n \n \n \n \n Grid portal architectures for scientific applications.\n \n \n \n \n\n\n \n Thomas, M P; Burruss, J; Cinquini, L; Fox, G; Gannon, D; Gilbert, L; Laszewski, G V.; Jackson, K; Middleton, D; Moore, R; Pierce, M; Plale, B; Rajasekar, A; Regno, R; Roberts, E; Schissel, D; Seth, A; and Schroeder, W\n\n\n \n\n\n\n In Journal of Physics: Conference Series, volume 16, pages 596-600, 1 2005. \n \n\n\n\n
\n\n\n\n \n \n \"GridPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n  \n \n 2 downloads\n \n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@inproceedings{Thomas2005,\n   author = {M P Thomas and J Burruss and L Cinquini and G Fox and D Gannon and L Gilbert and G Von Laszewski and K Jackson and D Middleton and R Moore and M Pierce and B Plale and A Rajasekar and R Regno and E Roberts and D Schissel and A Seth and W Schroeder},\n   doi = {10.1088/1742-6596/16/1/083},\n   issn = {1742-6588},\n   booktitle = {Journal of Physics: Conference Series},\n   month = {1},\n   pages = {596-600},\n   title = {Grid portal architectures for scientific applications},\n   volume = {16},\n   url = {http://stacks.iop.org/1742-6596/16/i=1/a=083?key=crossref.729da3cd99f04421d1a9090b74d0a3f0},\n   year = {2005},\n}\n
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\n  \n 2004\n \n \n (1)\n \n \n
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\n \n\n \n \n \n \n \n Grid Portal Toolkit 3 . 0 ( GridPort ).\n \n \n \n\n\n \n Dahan, M.; Thomas, M.; Roberts, E.; Seth, A.; Urban, T.; Walling, D.; and Boisseau, J. R\n\n\n \n\n\n\n In The 13th IEEE International Symposium on High Performance Distributed Computing (HPDC’04), volume 0, pages 272-273, 2004. \n \n\n\n\n
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@inproceedings{MDahan2004,\n   author = {Maytal Dahan and Mary Thomas and Eric Roberts and Akhil Seth and Tomislav Urban and David Walling and John R Boisseau},\n   booktitle = {The 13th IEEE International Symposium on High Performance Distributed Computing (HPDC’04)},\n   pages = {272-273},\n   title = {Grid Portal Toolkit 3 . 0 ( GridPort )},\n   volume = {0},\n   year = {2004},\n}\n
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\n \n\n \n \n \n \n \n \n Grid Portals: A Scientist's Access Point for Grid Services (DRAFT 1) GGF DOCUMENT SUBMISSION CHECKLIST (include as front page of submission) COMPLETED (X)-Date Grid Portals: A Scientist's Access Point for Grid Services (DRAFT 1).\n \n \n \n \n\n\n \n Gannon, D.; Hardin, J.; Alameda, J.; Thomas, M.; Boisseau, J.; Pierce, M.; Plale, B.; Fox, G.; Laszewski, G. V.; and Severance, C.\n\n\n \n\n\n\n 9 2003.\n \n\n\n\n
\n\n\n\n \n \n \"GridPaper\n  \n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@misc{gannon2003grid,\n   abstract = {This document describes an architecture for web portals designed to support access to Grid Services. It draws upon best practices derived from the collective experience of many projects, a GGF Workshop on Grid Portals, commercial standards, and the proposed Open Grid Service Architecture. This draft is presented for discussion and revision at the GGF9 GCE-RG session.},\n   author = {Dennis Gannon and Joseph Hardin and Jay Alameda and Mary Thomas and Jay Boisseau and Marlon Pierce and Beth Plale and Geoffrey Fox and Gregor Von Laszewski and Charles Severance},\n   institution = {University of Indiana},\n   month = {9},\n   title = {Grid Portals: A Scientist's Access Point for Grid Services (DRAFT 1) GGF DOCUMENT SUBMISSION CHECKLIST (include as front page of submission) COMPLETED (X)-Date Grid Portals: A Scientist's Access Point for Grid Services (DRAFT 1)},\n   url = {https://citeseerx.ist.psu.edu/document?repid=rep1&type=pdf&doi=08c516436ff2313a7ca6c6783a6d14477de667f6},\n   year = {2003},\n}\n
\n
\n\n\n
\n This document describes an architecture for web portals designed to support access to Grid Services. It draws upon best practices derived from the collective experience of many projects, a GGF Workshop on Grid Portals, commercial standards, and the proposed Open Grid Service Architecture. This draft is presented for discussion and revision at the GGF9 GCE-RG session.\n
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\n \n\n \n \n \n \n \n Development of NPACI Grid Application Portals and Portal Web Services.\n \n \n \n\n\n \n Thomas, M; Boisseau, J; Dahan, M; Mills, C; Mock, S; and Mueller, K\n\n\n \n\n\n\n Cluster Computing, 6: 177-188. 2003.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{Thomas2003a,\n   author = {M Thomas and J Boisseau and M Dahan and C Mills and S Mock and K Mueller},\n   journal = {Cluster Computing},\n   pages = {177-188},\n   title = {Development of NPACI Grid Application Portals and Portal Web Services},\n   volume = {6},\n   year = {2003},\n}\n
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\n \n\n \n \n \n \n \n .\n \n \n \n\n\n \n Thomas, M P; and Boisseau, J R\n\n\n \n\n\n\n Building Grid Computing Portals : The NPACI Grid Portal Toolkit, pages 675 - 700. 2003.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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@inbook{Thomas2003,\n   author = {M P Thomas and J R Boisseau},\n   journal = {Grid Computing: Making the Global Infrastructure a Reality},\n   keywords = {grid computing,ogsa,portals,portlets,toolkits,web services},\n   pages = {675 - 700},\n   title = {Building Grid Computing Portals : The NPACI Grid Portal Toolkit},\n   year = {2003},\n}\n
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\n  \n 2002\n \n \n (3)\n \n \n
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\n \n\n \n \n \n \n \n \n A batch script generator Web service for computational portals.\n \n \n \n \n\n\n \n Mock, S.; Mueller, K.; Pierce, M.; Fox, G.; and Thomas, M.\n\n\n \n\n\n\n In Proceedings 11th IEEE International Symposium on High Performance Distributed Computing, pages 421, 2002. IEEE Comput. Soc\n \n\n\n\n
\n\n\n\n \n \n \"APaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n  \n \n 2 downloads\n \n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@inproceedings{Mock200Batch,\n   author = {S. Mock and K. Mueller and M. Pierce and G. Fox and M. Thomas},\n   doi = {10.1109/HPDC.2002.1029951},\n   isbn = {0-7695-1686-6},\n   booktitle = {Proceedings 11th IEEE International Symposium on High Performance Distributed Computing},\n   pages = {421},\n   publisher = {IEEE Comput. Soc},\n   title = {A batch script generator Web service for computational portals},\n   url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=1029951},\n   year = {2002},\n}\n
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\n \n\n \n \n \n \n \n The Perl Commodity Grid Toolkit.\n \n \n \n\n\n \n Mock, S.; Thomas, M.; and Lazewski, G. V.\n\n\n \n\n\n\n Concurrency and computation: practice and experience,, 14: 1085-1095. 2002.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{Mock2002Perl,\n   author = {Stephen Mock and Mary Thomas and Gregor Von Lazewski},\n   issue = {13-15},\n   journal = {Concurrency and computation: practice and experience,},\n   pages = {1085-1095},\n   title = {The Perl Commodity Grid Toolkit},\n   volume = {14},\n   year = {2002},\n}\n
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\n \n\n \n \n \n \n \n Application portals: Practice and experience.\n \n \n \n\n\n \n Thomas, M.; Dahan, M.; Mueller, K.; Mock, S.; Mills, C.; and Regno, R.\n\n\n \n\n\n\n Concurrency and Computation: Practice and Experience, 14: 1427-1443. 2002.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n  \n \n 2 downloads\n \n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{Thomas2002,\n   abstract = {The implementation of multiple Grid computing portals has led us to develop a methodology for Grid portal development that facilitates rapid prototyping and building of portals. Based on the National Partnership for Advanced Computational Infrastructure (NPACI) Grid Portal Toolkit (GridPort) and the NPACI HotPage, all portals inherit interactive Grid services, share a single account and login environment, and share the infrastructure required to support and provide services used by each portal. We have demonstrated that the GridPort software can be used in production application portal environments, that the software can be configured to extend multiple sites. In this paper, we describe our experiences gained in building Grid portals and developing software for the Grid. We describe the architecture and design of the portal system, Grid services and systems employed, as well as the unique features of the system. We present descriptions of several application portals and the driving design choices. Finally, we discuss the new and emerging architecture system that being studied based on the Web services architecture.},\n   author = {Mary Thomas and Maytal Dahan and Kurt Mueller and Steve Mock and Cathie Mills and Ray Regno},\n   doi = {10.1002/cpe.694},\n   issn = {15320626},\n   issue = {13-15},\n   journal = {Concurrency and Computation: Practice and Experience},\n   pages = {1427-1443},\n   title = {Application portals: Practice and experience},\n   volume = {14},\n   year = {2002},\n}\n
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\n The implementation of multiple Grid computing portals has led us to develop a methodology for Grid portal development that facilitates rapid prototyping and building of portals. Based on the National Partnership for Advanced Computational Infrastructure (NPACI) Grid Portal Toolkit (GridPort) and the NPACI HotPage, all portals inherit interactive Grid services, share a single account and login environment, and share the infrastructure required to support and provide services used by each portal. We have demonstrated that the GridPort software can be used in production application portal environments, that the software can be configured to extend multiple sites. In this paper, we describe our experiences gained in building Grid portals and developing software for the Grid. We describe the architecture and design of the portal system, Grid services and systems employed, as well as the unique features of the system. We present descriptions of several application portals and the driving design choices. Finally, we discuss the new and emerging architecture system that being studied based on the Web services architecture.\n
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\n  \n 2001\n \n \n (3)\n \n \n
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\n \n\n \n \n \n \n \n Population Pharmaccokinetic/Dynamic (PK/PD) Modeling via the World Wide Web.\n \n \n \n\n\n \n Botnen, A; Wang, X; Jelliffe, R; Thomas, M; and Hoem, N\n\n\n \n\n\n\n In Proceedings of the Fourteenth IEEE Symposium on Computer-Based Medical Systems, 2001. IEEE Comput. Soc\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@inproceedings{Botnen2001,\n   author = {A Botnen and X Wang and R Jelliffe and M Thomas and N Hoem},\n   city = {Washington, DC},\n   booktitle = {Proceedings of the Fourteenth IEEE Symposium on Computer-Based Medical Systems},\n   publisher = {IEEE Comput. Soc},\n   title = {Population Pharmaccokinetic/Dynamic (PK/PD) Modeling via the World Wide Web},\n   year = {2001},\n}\n
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\n \n\n \n \n \n \n \n Message-passing computing with Java: performance evaluation and comparisons.\n \n \n \n\n\n \n Getov, V.; Lu, Q.; Thomas, M.; and Williams, M.\n\n\n \n\n\n\n In Parallel and Distributed Processing, 2001. Proceedings. Ninth Euromicro Workshop on, 2001. \n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@inproceedings{Getov2001,\n   abstract = {The development of Java has seen increasing attention as the most popular platform for distributed computing. However, despite Java's advantages in the area of portability and rapid prototyping, its efficiency is unavoidably compromised through its commitment to portability. In this paper we present performance analysis and comparisons of evaluation results for both Java and C/Fortran on three different message-passing parallel platforms-a shared memory multi-processor (Sun E4000), a Linux cluster, and a distributed memory computer (IBM SP-2). The NAS Embarrassingly Parallel and Integer Sort benchmarks were selected for this evaluation. Both the original Fortran/C codes and Java versions of these two kernels were used for obtaining the performance measurements as part of our project. The evaluation results demonstrate the feasibility of message-passing computing with Java on a wide range of computer platforms. Depending on the system and the software components installed, significant impact on the message-passing performance will have the efficiency of the native MPI library and the version of the Java platform.},\n   author = {V. Getov and Q. Lu and M. Thomas and M. Williams},\n   booktitle = {Parallel and Distributed Processing, 2001. Proceedings. Ninth Euromicro Workshop on},\n   title = {Message-passing computing with Java: performance evaluation and comparisons},\n   year = {2001},\n}\n
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\n The development of Java has seen increasing attention as the most popular platform for distributed computing. However, despite Java's advantages in the area of portability and rapid prototyping, its efficiency is unavoidably compromised through its commitment to portability. In this paper we present performance analysis and comparisons of evaluation results for both Java and C/Fortran on three different message-passing parallel platforms-a shared memory multi-processor (Sun E4000), a Linux cluster, and a distributed memory computer (IBM SP-2). The NAS Embarrassingly Parallel and Integer Sort benchmarks were selected for this evaluation. Both the original Fortran/C codes and Java versions of these two kernels were used for obtaining the performance measurements as part of our project. The evaluation results demonstrate the feasibility of message-passing computing with Java on a wide range of computer platforms. Depending on the system and the software components installed, significant impact on the message-passing performance will have the efficiency of the native MPI library and the version of the Java platform.\n
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\n \n\n \n \n \n \n \n \n The GridPort toolkit: a system for building Grid portals.\n \n \n \n \n\n\n \n Thomas, M.; Mock, S.; Dahan, M.; Mueller, K.; Sutton, D.; and Boisseau, J.\n\n\n \n\n\n\n In Proceedings 10th IEEE International Symposium on High Performance Distributed Computing, pages 216-227, 2001. IEEE Comput. Soc\n \n\n\n\n
\n\n\n\n \n \n \"ThePaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n  \n \n 2 downloads\n \n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@inproceedings{Thomas2001b,\n   author = {M. Thomas and S. Mock and M. Dahan and K. Mueller and D. Sutton and J.R. Boisseau},\n   doi = {10.1109/HPDC.2001.945191},\n   isbn = {0-7695-1296-8},\n   booktitle = {Proceedings 10th IEEE International Symposium on High Performance Distributed Computing},\n   pages = {216-227},\n   publisher = {IEEE Comput. Soc},\n   title = {The GridPort toolkit: a system for building Grid portals},\n   url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=945191},\n   year = {2001},\n}\n
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\n \n\n \n \n \n \n \n Development of Web toolkits for computational science portals: The NPACI HotPage.\n \n \n \n\n\n \n Thomas, M.; Mock, S.; and Boisseau, J.\n\n\n \n\n\n\n In Proceedings of the Ninth IEEE International Symposium on High Performance Distributed Computing, volume 2000-Janua, pages 308-309, 2000. \n \n\n\n\n
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@inproceedings{Thomas2000IEEENinth,\n   author = {M. Thomas and S. Mock and J. Boisseau},\n   doi = {10.1109/HPDC.2000.868671},\n   isbn = {0769507832},\n   issn = {10828907},\n   booktitle = {Proceedings of the Ninth IEEE International Symposium on High Performance Distributed Computing},\n   keywords = {Application software,Computer architecture,Computer interfaces,Cryptography,Distributed computing,Grid computing,High performance computing,Portals,Service oriented architecture,Web pages},\n   pages = {308-309},\n   title = {Development of Web toolkits for computational science portals: The NPACI HotPage},\n   volume = {2000-Janua},\n   year = {2000},\n}\n
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\n \n\n \n \n \n \n \n Benchmarking Java on the IBM SP-2.\n \n \n \n\n\n \n Thomas, M.; Getov, V.; Williams, M.; and Whitney, R.\n\n\n \n\n\n\n In ICS 2000 HPC Java Workshop, 2000. \n \n\n\n\n
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@inproceedings{Thomas2000-ICS00-HPJava,\n   author = {Mary Thomas and Vladimir Getov and Matthew Williams and Roger Whitney},\n   city = {Santa Fe},\n   booktitle = {ICS 2000 HPC Java Workshop},\n   title = {Benchmarking Java on the IBM SP-2},\n   year = {2000},\n}\n
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\n  \n 1999\n \n \n (2)\n \n \n
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\n \n\n \n \n \n \n \n The NPACI HotPage: A Framework for Transparent Supercomputing.\n \n \n \n\n\n \n Thomas, M.; Mock, S.; and Boisseau, J.\n\n\n \n\n\n\n In Computing Portals Workshop, 1999. \n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@inproceedings{Thomas2000Portals,\n   abstract = {The NPACI HotPage framework provides users and developers with a set of simple, modular services and tools that facilitate seamless access to the NPACI grid (including high performance computers, high-speed file archival systems, and metacomputing systems such as Globus). For the end- user, a web-browser interface has been implemented that allows these resources to be viewed as an integrated system or as individual machines. When using the secure, encrypted login features, users can access their accounts directly. For the applications programmer, these simple Perl/CGI modules can be used to process HTTP requests and access resources on the grid. This paper discusses the design, architecture, and unique approach used to solve the task of providing a simple, secure, and transparent interface to users of the computational grid.},\n   author = {Mary Thomas and Steve Mock and Jay Boisseau},\n   city = {San Francisco, CA},\n   booktitle = {Computing Portals Workshop},\n   title = {The NPACI HotPage: A Framework for Transparent Supercomputing},\n   year = {1999},\n}\n
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\n The NPACI HotPage framework provides users and developers with a set of simple, modular services and tools that facilitate seamless access to the NPACI grid (including high performance computers, high-speed file archival systems, and metacomputing systems such as Globus). For the end- user, a web-browser interface has been implemented that allows these resources to be viewed as an integrated system or as individual machines. When using the secure, encrypted login features, users can access their accounts directly. For the applications programmer, these simple Perl/CGI modules can be used to process HTTP requests and access resources on the grid. This paper discusses the design, architecture, and unique approach used to solve the task of providing a simple, secure, and transparent interface to users of the computational grid.\n
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\n \n\n \n \n \n \n \n Investigation of Java as a High Performance Computing Language (MSc thesis).\n \n \n \n\n\n \n Thomas, M. P. (.\n\n\n \n\n\n\n ,179. 1999.\n \n\n\n\n
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@article{Thomas1999ThesisJava,\n   author = {Mary P. (SDSU) Thomas},\n   institution = {San Diego State University},\n   pages = {179},\n   title = {Investigation of Java as a High Performance Computing Language (MSc thesis)},\n   year = {1999},\n}\n
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\n  \n 1992\n \n \n (1)\n \n \n
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\n \n\n \n \n \n \n \n DESIGNAND OPERATION OF THE MULTIPULSETHOMSON SCATTERING DIAGNOSTIC ON DIII-D.\n \n \n \n\n\n \n CARLSTROM, T.; CAMPBELL, G.; DeBOO, J.; EVANKO, R.; McKEE, E.; EVANS, J.; GREENFIELD, C M; HASKOVEC, J; HSIEH, C L.; SNIDER, R.; STOCKDALE, R.; TROST, P.; and THOMAS, M.\n\n\n \n\n\n\n 1992.\n \n\n\n\n
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@misc{TCarlstrom1992,\n   author = {T.N. CARLSTROM and G.L. CAMPBELL and J.C. DeBOO and R. EVANKO and E. McKEE and J. EVANS and C M GREENFIELD and J HASKOVEC and C L. HSIEH and R.T. SNIDER and R. STOCKDALE and P.K. TROST and M.P. THOMAS},\n   city = {San Diego},\n   institution = {General Atomics},\n   title = {DESIGNAND OPERATION OF THE MULTIPULSETHOMSON SCATTERING DIAGNOSTIC ON DIII-D},\n   year = {1992},\n}\n
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\n  \n 1990\n \n \n (3)\n \n \n
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\n \n\n \n \n \n \n \n Safety factor on the axis of a tokamak during Ohmically heated sawtoothing discharges from a localized measurement of circular polarization of the Lii 6708 Å line.\n \n \n \n\n\n \n Huang, L. K.; Finkenthal, M.; Wróblewski, D.; Moos, H. W.; West, W. P.; Thomas, D. M.; Thomas, M. P.; Yang, X. Z.; Phillips, P. E.; Wootton, A. J.; Bengtson, R. D.; Boedo, . A.; Bravenec, R. V.; Chen, J. Y.; Cima, G.; Gentle, K. W.; McCool, S. C.; Richards, B. U.; Rowan, W. L.; Sing, D. C.; and Wenzel, K. W.\n\n\n \n\n\n\n Physics of Fluids B: Plasma Physics, 2. 1990.\n \n\n\n\n
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@article{Huang1990,\n   author = {L. K. Huang and M. Finkenthal and D. Wróblewski and H. W. Moos and W. P. West and D. M. Thomas and M. P. Thomas and X. Z. Yang and P. E. Phillips and A. J. Wootton and Roger D. Bengtson and . A. Boedo and R. V. Bravenec and J. Y. Chen and G. Cima and K. W. Gentle and S. C. McCool and B. U. Richards and W. L. Rowan and D. C. Sing and K. W. Wenzel},\n   doi = {https://doi.org/10.1063/1.859317},\n   issue = {4},\n   journal = {Physics of Fluids B: Plasma Physics},\n   title = {Safety factor on the axis of a tokamak during Ohmically heated sawtoothing discharges from a localized measurement of circular polarization of the Lii 6708 Å line},\n   volume = {2},\n   year = {1990},\n}\n
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\n \n\n \n \n \n \n \n Safety factor on the axis of a tokamak during Ohmically heated sawtoothing discharges from a localized measurement of circular polarization of the Li I 6708 Å line.\n \n \n \n\n\n \n Huang, L. K.; Finkenthal, M.; Wróblewski, D.; Moos, H. W.; West, W. P.; Thomas, D. M.; Thomas, M. P.; Yang, X. Z.; Phillips, P. E.; Wootton, A. J.; Bengtson, R. D.; Boedo, J. A.; Bravenec, R. V.; Chen, J. Y.; Cima, G.; Gentle, K. W.; McCool, S. C.; Richards, B. U.; Rowan, W. L.; Sing, D. C.; and Wenzel, K. W.\n\n\n \n\n\n\n Physics of Fluids B, 2: 809-814. 1990.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{Huang,\n   abstract = {Analysis of the circular polarization of the Li I 6708 Å line emitted from a monoenergetic lithium beam provides a spatially resolved measurement of the poloidal magnetic field on the Texas experimental tokamak [Nucl. Technol. Fusion 1, 479 (1981)]. Determined from the measured magnetic field, the safety factor on the magnetic axis during Ohmically heated sawtoothing discharges is near unity. © 1990 American Institute of Physics.},\n   author = {L. K. Huang and M. Finkenthal and D. Wróblewski and H. W. Moos and W. P. West and D. M. Thomas and M. P. Thomas and X. Z. Yang and P. E. Phillips and A. J. Wootton and Roger D. Bengtson and J. A. Boedo and R. V. Bravenec and J. Y. Chen and G. Cima and K. W. Gentle and S. C. McCool and B. U. Richards and W. L. Rowan and D. C. Sing and K. W. Wenzel},\n   doi = {10.1063/1.859317},\n   issn = {08998221},\n   issue = {4},\n   journal = {Physics of Fluids B},\n   pages = {809-814},\n   title = {Safety factor on the axis of a tokamak during Ohmically heated sawtoothing discharges from a localized measurement of circular polarization of the Li I 6708 Å line},\n   volume = {2},\n   year = {1990},\n}\n
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\n Analysis of the circular polarization of the Li I 6708 Å line emitted from a monoenergetic lithium beam provides a spatially resolved measurement of the poloidal magnetic field on the Texas experimental tokamak [Nucl. Technol. Fusion 1, 479 (1981)]. Determined from the measured magnetic field, the safety factor on the magnetic axis during Ohmically heated sawtoothing discharges is near unity. © 1990 American Institute of Physics.\n
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\n \n\n \n \n \n \n \n Edge density fluctuation diagnostic for DIII-D using lithium beams.\n \n \n \n\n\n \n Thomas, D M; Hyatt, A W; and Thomas, M P\n\n\n \n\n\n\n Rev. Sci. Instrum, 61: 3040-3042. 1990.\n \n\n\n\n
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@article{MThomas1990,\n   author = {D M Thomas and A W Hyatt and M P Thomas},\n   issue = {10},\n   institution = {General Atomics},\n   journal = {Rev. Sci. Instrum},\n   pages = {3040-3042},\n   title = {Edge density fluctuation diagnostic for DIII-D using lithium beams},\n   volume = {61},\n   year = {1990},\n}\n
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\n  \n 1988\n \n \n (1)\n \n \n
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\n \n\n \n \n \n \n \n Poloidal field measurements using laser-enhanced attenuation of an energetic lithium beam.\n \n \n \n\n\n \n West, W.; Thomas, D.; and Thomas, M.\n\n\n \n\n\n\n Rev. Sci. Instrum, 58: 1617-1619. 1988.\n \n\n\n\n
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@article{West1988,\n   author = {W.P. West and D.M. Thomas and M.P. Thomas},\n   issue = {8},\n   journal = {Rev. Sci. Instrum},\n   pages = {1617-1619},\n   title = {Poloidal field measurements using laser-enhanced attenuation of an energetic lithium beam},\n   volume = {58},\n   year = {1988},\n}\n
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\n  \n 1986\n \n \n (1)\n \n \n
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\n \n\n \n \n \n \n \n Application Of Fourier Optical Signal Processing To Detect Surface Flaws In Transmissive And Reflective Materials.\n \n \n \n\n\n \n Thomas, M. P.; Day, T.; and Kubo, T.\n\n\n \n\n\n\n In SPIE 30th Annual Technical Symposium: Surface Characterization and Testing, volume 0680, pages 167, 1986. SPIE\n \n\n\n\n
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@inproceedings{Thomas-1987-SPIE,\n   author = {Mary P. Thomas and Timothy Day and Tracy Kubo},\n   city = {San Diego, CA},\n   doi = {10.1117/12.939607},\n   issue = {March 1987},\n   booktitle = {SPIE 30th Annual Technical Symposium: Surface Characterization and Testing},\n   pages = {167},\n   publisher = {SPIE},\n   title = {Application Of Fourier Optical Signal Processing To Detect Surface Flaws In Transmissive And Reflective Materials},\n   volume = {0680},\n   year = {1986},\n}\n
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\n \n\n \n \n \n \n \n \n Photochromic Materials Study (AD-A163 140 DTIC).\n \n \n \n \n\n\n \n Davis, J. A; and Thomas, M.\n\n\n \n\n\n\n 9 1985.\n \n\n\n\n
\n\n\n\n \n \n \"PhotochromicPaper\n  \n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@misc{Davis-Thomas-1985,\n   abstract = {This report describes a study conducted to determine the feasibility of using the photochromic material mercury dithizonate as a programmable spatial filter for optical processing.  This material has exhibited faster sriting speed and finer resolution than conventional spatial filtering techniques. Photochromics are erasable and therefore reusable. Variations in material performance were discovered and are attributed to the presence of two photo- chromic species in the material. A follow-on effort will investigate the effects of varying the composition of the photochromic material upon its optical properties.},\n   author = {Jeffrey A Davis and Mary Thomas},\n   city = {San Diego},\n   institution = {San Diego State University},\n   month = {9},\n   title = {Photochromic Materials Study (AD-A163 140 DTIC)},\n   url = {https://www.researchgate.net/profile/Mary-Thomas-29/publication/235022753_Photochromic_Materials_Study/links/0c96053a9c7c9923e1000000/Photochromic-Materials-Study.pdf},\n   year = {1985},\n}\n
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\n This report describes a study conducted to determine the feasibility of using the photochromic material mercury dithizonate as a programmable spatial filter for optical processing. This material has exhibited faster sriting speed and finer resolution than conventional spatial filtering techniques. Photochromics are erasable and therefore reusable. Variations in material performance were discovered and are attributed to the presence of two photo- chromic species in the material. A follow-on effort will investigate the effects of varying the composition of the photochromic material upon its optical properties.\n
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\n \n\n \n \n \n \n \n \n Characterization of Photochromic Materials as Optical Storage Media (MSc thesis).\n \n \n \n \n\n\n \n Thomas, M. P.\n\n\n \n\n\n\n San Diego State University, 1985.\n \n\n\n\n
\n\n\n\n \n \n \"CharacterizationPaper\n  \n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n \n \n \n \n \n \n\n\n\n
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@book{thomas1985characterization,\n   author = {Mary P. Thomas},\n   institution = {San Diego State University},\n   keywords = {laser,optical,photochromic},\n   publisher = {San Diego State University},\n   title = {Characterization of Photochromic Materials as Optical Storage Media (MSc thesis)},\n   url = {http://books.google.com/books?id=_3DYNwAACAAJ},\n   year = {1985},\n}\n
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