Pub Date : 2018-10-01DOI: 10.1109/eScience.2018.00117
Luis Oliveira, D. Wilkinson, D. Mossé, B. Childers
n/a
{"title":"Occam: Software Environment for Creating Reproducible Research","authors":"Luis Oliveira, D. Wilkinson, D. Mossé, B. Childers","doi":"10.1109/eScience.2018.00117","DOIUrl":"https://doi.org/10.1109/eScience.2018.00117","url":null,"abstract":"n/a","PeriodicalId":6476,"journal":{"name":"2018 IEEE 14th International Conference on e-Science (e-Science)","volume":"82 3","pages":"394-395"},"PeriodicalIF":0.0,"publicationDate":"2018-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72580099","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-10-01DOI: 10.1109/eScience.2018.00133
J. Choi, Choong-Seock Chang, J. Dominski, S. Klasky, G. Merlo, E. Suchyta, M. Ainsworth, B. Allen, F. Cappello, M. Churchill, Philip E. Davis, S. Di, G. Eisenhauer, S. Ethier, Ian T Foster, Berk Geveci, Hanqi Guo, K. Huck, F. Jenko, Mark Kim, James Kress, S. Ku, Qing Liu, Jeremy S. Logan, A. Malony, Kshitij Mehta, K. Moreland, T. Munson, M. Parashar, T. Peterka, N. Podhorszki, D. Pugmire, O. Tugluk, Ruonan Wang, Ben Whitney, M. Wolf, Chad Wood
With the growing computational complexity of science and the complexity of new and emerging hardware, it is time to re-evaluate the traditional monolithic design of computational codes. One new paradigm is constructing larger scientific computational experiments from the coupling of multiple individual scientific applications, each targeting their own physics, characteristic lengths, and/or scales. We present a framework constructed by leveraging capabilities such as in-memory communications, workflow scheduling on HPC resources, and continuous performance monitoring. This code coupling capability is demonstrated by a fusion science scenario, where differences between the plasma at the edges and at the core of a device have different physical descriptions. This infrastructure not only enables the coupling of the physics components, but it also connects in situ or online analysis, compression, and visualization that accelerate the time between a run and the analysis of the science content. Results from runs on Titan and Cori are presented as a demonstration.
{"title":"Coupling Exascale Multiphysics Applications: Methods and Lessons Learned","authors":"J. Choi, Choong-Seock Chang, J. Dominski, S. Klasky, G. Merlo, E. Suchyta, M. Ainsworth, B. Allen, F. Cappello, M. Churchill, Philip E. Davis, S. Di, G. Eisenhauer, S. Ethier, Ian T Foster, Berk Geveci, Hanqi Guo, K. Huck, F. Jenko, Mark Kim, James Kress, S. Ku, Qing Liu, Jeremy S. Logan, A. Malony, Kshitij Mehta, K. Moreland, T. Munson, M. Parashar, T. Peterka, N. Podhorszki, D. Pugmire, O. Tugluk, Ruonan Wang, Ben Whitney, M. Wolf, Chad Wood","doi":"10.1109/eScience.2018.00133","DOIUrl":"https://doi.org/10.1109/eScience.2018.00133","url":null,"abstract":"With the growing computational complexity of science and the complexity of new and emerging hardware, it is time to re-evaluate the traditional monolithic design of computational codes. One new paradigm is constructing larger scientific computational experiments from the coupling of multiple individual scientific applications, each targeting their own physics, characteristic lengths, and/or scales. We present a framework constructed by leveraging capabilities such as in-memory communications, workflow scheduling on HPC resources, and continuous performance monitoring. This code coupling capability is demonstrated by a fusion science scenario, where differences between the plasma at the edges and at the core of a device have different physical descriptions. This infrastructure not only enables the coupling of the physics components, but it also connects in situ or online analysis, compression, and visualization that accelerate the time between a run and the analysis of the science content. Results from runs on Titan and Cori are presented as a demonstration.","PeriodicalId":6476,"journal":{"name":"2018 IEEE 14th International Conference on e-Science (e-Science)","volume":"80 1","pages":"442-452"},"PeriodicalIF":0.0,"publicationDate":"2018-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73029510","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-10-01DOI: 10.1109/eScience.2018.00071
Carsten Thiel, D. V. Uytvanck, T. Kálmán
Sustainable management of research software and the application of software engineering principles are one of the biggest challenges that the operation of digital Research Infrastructures face in the Social Sciences and Humanities community. We give an overview of our approach to apply state of the art industry standards for research software, and describe ongoing efforts towards a common set of guidelines and evaluation criteria for similar issues as EURISE Network.
{"title":"Software Engineering and Digital Research Infrastructures","authors":"Carsten Thiel, D. V. Uytvanck, T. Kálmán","doi":"10.1109/eScience.2018.00071","DOIUrl":"https://doi.org/10.1109/eScience.2018.00071","url":null,"abstract":"Sustainable management of research software and the application of software engineering principles are one of the biggest challenges that the operation of digital Research Infrastructures face in the Social Sciences and Humanities community. We give an overview of our approach to apply state of the art industry standards for research software, and describe ongoing efforts towards a common set of guidelines and evaluation criteria for similar issues as EURISE Network.","PeriodicalId":6476,"journal":{"name":"2018 IEEE 14th International Conference on e-Science (e-Science)","volume":"3 1","pages":"316-317"},"PeriodicalIF":0.0,"publicationDate":"2018-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73221717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-10-01DOI: 10.1109/eScience.2018.00064
A. Kuzniar, J. Maassen, S. Verhoeven, L. Santuari, C. Shneider, W. Kloosterman, J. Ridder
n/a
{"title":"A Portable and Scalable Workflow for Detecting Structural Variants in Whole-Genome Sequencing Data","authors":"A. Kuzniar, J. Maassen, S. Verhoeven, L. Santuari, C. Shneider, W. Kloosterman, J. Ridder","doi":"10.1109/eScience.2018.00064","DOIUrl":"https://doi.org/10.1109/eScience.2018.00064","url":null,"abstract":"n/a","PeriodicalId":6476,"journal":{"name":"2018 IEEE 14th International Conference on e-Science (e-Science)","volume":"610 1","pages":"303-304"},"PeriodicalIF":0.0,"publicationDate":"2018-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77613450","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-10-01DOI: 10.1109/eScience.2018.00055
N. Baltzer, M. Nygård, K. Sundstrom, J. Dillner, J. Nygård, J. Komorowski
The cervical cancer screening programmes in Sweden and Norway have successfully reduced the frequency of cervical cancer incidence but have not implemented any form of evaluation for screening needs. This means that the screening frequency for individuals can be suboptimal, increasing either the cost of the programme or the risk of missing an early stage cancer development. We developed a framework for assessing an individual's risk of cervical cancer based on their available screening history and computing a primary risk factor called CRS from a data-driven separation model together with multiple derived attributes. The results show that this approach is highly practical, validates against multiple established trends, and can be effective in personalizing the screening needs for individuals.
{"title":"Stratifying Cervical Cancer Risk with Registry Data","authors":"N. Baltzer, M. Nygård, K. Sundstrom, J. Dillner, J. Nygård, J. Komorowski","doi":"10.1109/eScience.2018.00055","DOIUrl":"https://doi.org/10.1109/eScience.2018.00055","url":null,"abstract":"The cervical cancer screening programmes in Sweden and Norway have successfully reduced the frequency of cervical cancer incidence but have not implemented any form of evaluation for screening needs. This means that the screening frequency for individuals can be suboptimal, increasing either the cost of the programme or the risk of missing an early stage cancer development. We developed a framework for assessing an individual's risk of cervical cancer based on their available screening history and computing a primary risk factor called CRS from a data-driven separation model together with multiple derived attributes. The results show that this approach is highly practical, validates against multiple established trends, and can be effective in personalizing the screening needs for individuals.","PeriodicalId":6476,"journal":{"name":"2018 IEEE 14th International Conference on e-Science (e-Science)","volume":"210 1","pages":"288-289"},"PeriodicalIF":0.0,"publicationDate":"2018-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74837419","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-10-01DOI: 10.1109/eScience.2018.00031
Nicholas L. Hazekamp, D. Thain
Scientific workflows are often designed with a particular compute site in mind. As a user changes sites the workflow needs to adjust. These changes include moving from a cluster to a cloud, updating an operating system, or investigating failures on a new cluster. As a workflow is moved, its tasks do not fundamentally change, but the steps to configure, execute, and evaluate tasks differ. When handling these changes it may be necessary to use a script to analyze execution failure or run a container to use the correct operating system. To improve workflow portability and robustness, it is necessary to have a rigorous method that allows transformations on a workflow. These transformations do not change the tasks, only the way tasks are invoked. Using technologies such as containers, resource managers, and scripts to transform workflows allow for portability, but combining these technologies can lead to complications with execution and error handling. We define an algebra to reason about task transformations at the workflow level and express it in a declarative form using JSON. We implemented this algebra in the Makeflow workflow system and demonstrate how transformations can be used for resource monitoring, failure analysis, and software deployment across three sites.
{"title":"An Algebra for Robust Workflow Transformations","authors":"Nicholas L. Hazekamp, D. Thain","doi":"10.1109/eScience.2018.00031","DOIUrl":"https://doi.org/10.1109/eScience.2018.00031","url":null,"abstract":"Scientific workflows are often designed with a particular compute site in mind. As a user changes sites the workflow needs to adjust. These changes include moving from a cluster to a cloud, updating an operating system, or investigating failures on a new cluster. As a workflow is moved, its tasks do not fundamentally change, but the steps to configure, execute, and evaluate tasks differ. When handling these changes it may be necessary to use a script to analyze execution failure or run a container to use the correct operating system. To improve workflow portability and robustness, it is necessary to have a rigorous method that allows transformations on a workflow. These transformations do not change the tasks, only the way tasks are invoked. Using technologies such as containers, resource managers, and scripts to transform workflows allow for portability, but combining these technologies can lead to complications with execution and error handling. We define an algebra to reason about task transformations at the workflow level and express it in a declarative form using JSON. We implemented this algebra in the Makeflow workflow system and demonstrate how transformations can be used for resource monitoring, failure analysis, and software deployment across three sites.","PeriodicalId":6476,"journal":{"name":"2018 IEEE 14th International Conference on e-Science (e-Science)","volume":"25 1","pages":"156-167"},"PeriodicalIF":0.0,"publicationDate":"2018-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89444160","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-10-01DOI: 10.1109/escience.2018.00007
{"title":"International Steering and Supervisory Committee","authors":"","doi":"10.1109/escience.2018.00007","DOIUrl":"https://doi.org/10.1109/escience.2018.00007","url":null,"abstract":"","PeriodicalId":6476,"journal":{"name":"2018 IEEE 14th International Conference on e-Science (e-Science)","volume":"184 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80553336","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-10-01DOI: 10.1109/eScience.2018.00096
D. Ceolin, J. V. Ossenbruggen, Lora Aroyo, O. Sener, Robin Sharma, L. Tkacz, J. Noordegraaf
n/a
{"title":"Assessing and Visualising Online Information Quality","authors":"D. Ceolin, J. V. Ossenbruggen, Lora Aroyo, O. Sener, Robin Sharma, L. Tkacz, J. Noordegraaf","doi":"10.1109/eScience.2018.00096","DOIUrl":"https://doi.org/10.1109/eScience.2018.00096","url":null,"abstract":"n/a","PeriodicalId":6476,"journal":{"name":"2018 IEEE 14th International Conference on e-Science (e-Science)","volume":"7 1","pages":"356-357"},"PeriodicalIF":0.0,"publicationDate":"2018-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73341891","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-10-01DOI: 10.1109/eScience.2018.00116
Timo Petteri Sipila, A. Metspalu, P. Happola, P. Palta, M. Kals, A. Palotie
Nordic Exome Variant Catalogue is a web tool to browse human genomic aggregation data from Nordic cohorts. This allows viewing, querying, comparison, filtering and sorting the data in graphical user interface. The main end users are researchers and clinicians studying genetic variance in genes of interest.
{"title":"Nordic Exome Variant Catalogue a Web Resource for Genomic Data Browsing","authors":"Timo Petteri Sipila, A. Metspalu, P. Happola, P. Palta, M. Kals, A. Palotie","doi":"10.1109/eScience.2018.00116","DOIUrl":"https://doi.org/10.1109/eScience.2018.00116","url":null,"abstract":"Nordic Exome Variant Catalogue is a web tool to browse human genomic aggregation data from Nordic cohorts. This allows viewing, querying, comparison, filtering and sorting the data in graphical user interface. The main end users are researchers and clinicians studying genetic variance in genes of interest.","PeriodicalId":6476,"journal":{"name":"2018 IEEE 14th International Conference on e-Science (e-Science)","volume":"65 1","pages":"393-393"},"PeriodicalIF":0.0,"publicationDate":"2018-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72846417","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-10-01DOI: 10.1109/ESCIENCE.2018.00030
José L. Fuertes, Luis F. González, Loïc Martínez
{"title":"Visual Programming Languages for Programmers with Dyslexia: An Experiment","authors":"José L. Fuertes, Luis F. González, Loïc Martínez","doi":"10.1109/ESCIENCE.2018.00030","DOIUrl":"https://doi.org/10.1109/ESCIENCE.2018.00030","url":null,"abstract":"","PeriodicalId":6476,"journal":{"name":"2018 IEEE 14th International Conference on e-Science (e-Science)","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73094806","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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