Proceedings ... IEEE International Conference on eScience. IEEE International Conference on eScience最新文献

ERMrest: A Collaborative Data Catalog with Fine Grain Access Control. ERMrest:具有细粒度访问控制的协作数据目录。

Proceedings ... IEEE International Conference on eScience. IEEE International Conference on eScience Pub Date : 2017-10-01 Epub Date: 2017-11-16 DOI: 10.1109/eScience.2017.83

Karl Czajkowski, Carl Kesselman, Robert Schuler

{"title":"ERMrest: A Collaborative Data Catalog with Fine Grain Access Control.","authors":"Karl Czajkowski, Carl Kesselman, Robert Schuler","doi":"10.1109/eScience.2017.83","DOIUrl":"https://doi.org/10.1109/eScience.2017.83","url":null,"abstract":"Creating and maintaining an accurate description of data assets and the relationships between assets is a critical aspect of making data findable, accessible, interoperable, and reusable (FAIR). Typically, such metadata are created and maintained in a data catalog by a curator as part of data publication. However, allowing metadata to be created and maintained by data producers as the data is generated rather then waiting for publication can have significant advantages in terms of productivity and repeatability. The responsibilities for metadata management need not fall on any one individual, but rather may be delegated to appropriate members of a collaboration, enabling participants to edit or maintain specific attributes, to describe relationships between data elements, or to correct errors. To support such collaborative data editing, we have created ERMrest, a relational data service for the Web that enables the creation, evolution and navigation of complex models used to describe and structure diverse file or relational data objects. A key capability of ERMrest is its ability to control operations down to the level of individual data elements, i.e. fine-grained access control, so that many different modes of data-oriented collaboration can be supported. In this paper we introduce ERMrest and describe its fine-grained access control capabilities that support collaborative editing. ERMrest is in daily use in many data driven collaborations and we describe a sample policy that is based on a common biocuration pattern.","PeriodicalId":90293,"journal":{"name":"Proceedings ... IEEE International Conference on eScience. IEEE International Conference on eScience","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/eScience.2017.83","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36094989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Experiences with Deriva: An Asset Management Platform for Accelerating eScience. 衍生品的经验:加速eScience的资产管理平台。

Proceedings ... IEEE International Conference on eScience. IEEE International Conference on eScience Pub Date : 2017-10-01 Epub Date: 2017-11-16 DOI: 10.1109/eScience.2017.20

Alejandro Bugacov, Karl Czajkowski, Carl Kesselman, Anoop Kumar, Robert E Schuler, Hongsuda Tangmunarunkit

引用次数: 20

Using Hidden Markov Models to Determine Changes in Subject Data over Time, Studying the Immunoregulatory effect of Mesenchymal Stem Cells. 利用隐马尔可夫模型确定受试者数据随时间的变化，研究间充质干细胞的免疫调节作用。

Proceedings ... IEEE International Conference on eScience. IEEE International Conference on eScience Pub Date : 2014-10-01 DOI: 10.1109/eScience.2014.29

Edgar F Black, Luigi Marini, Ashwini Vaidya, Dora Berman, Melissa Willman, Dan Salomon, Amelia Bartholomew, Norma Kenyon, Kenton McHenry

{"title":"Using Hidden Markov Models to Determine Changes in Subject Data over Time, Studying the Immunoregulatory effect of Mesenchymal Stem Cells.","authors":"Edgar F Black, Luigi Marini, Ashwini Vaidya, Dora Berman, Melissa Willman, Dan Salomon, Amelia Bartholomew, Norma Kenyon, Kenton McHenry","doi":"10.1109/eScience.2014.29","DOIUrl":"https://doi.org/10.1109/eScience.2014.29","url":null,"abstract":"A novel application of Hidden Markov Models is used to help research intended to test the immunuregulatory effects of mesenchymal stem cells in a cynomolgus monkey model of islet transplantation. The Hidden Markov Model, an unsupervised learning data mining technique, is used to automatically determine the postoperative day (POD) corresponding to a decrease of graft function, a possible sign of transplant rejection, on nonhuman primates after isolated islet cell transplant. Currently, decrease of graft function is being determined solely on experts' judgment. Further, information gathered from the evaluation of construted Hidden Markov Models is used as part of a clustering method to aggregate the nonhuman subjects into groups or clusters with the objective of finding similarities that could potentially help predict the health outcome of subjects undergoing postoperative care. Results on expert labeled data show the HMM to be accurate 60% of the time. Clusters based on the HMMs further suggest a possible correspondence between donor haplotypes matching and loss of function outcomes.","PeriodicalId":90293,"journal":{"name":"Proceedings ... IEEE International Conference on eScience. IEEE International Conference on eScience","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/eScience.2014.29","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33388827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Folding Proteins at 500 ns/hour with Work Queue. 用工作队列以500纳秒/小时的速度折叠蛋白质。

Proceedings ... IEEE International Conference on eScience. IEEE International Conference on eScience Pub Date : 2012-10-01 DOI: 10.1109/eScience.2012.6404429

Badi' Abdul-Wahid, Li Yu, Dinesh Rajan, Haoyun Feng, Eric Darve, Douglas Thain, Jesús A Izaguirre

{"title":"Folding Proteins at 500 ns/hour with Work Queue.","authors":"Badi' Abdul-Wahid, Li Yu, Dinesh Rajan, Haoyun Feng, Eric Darve, Douglas Thain, Jesús A Izaguirre","doi":"10.1109/eScience.2012.6404429","DOIUrl":"https://doi.org/10.1109/eScience.2012.6404429","url":null,"abstract":"Molecular modeling is a field that traditionally has large computational costs. Until recently, most simulation techniques relied on long trajectories, which inherently have poor scalability. A new class of methods is proposed that requires only a large number of short calculations, and for which minimal communication between computer nodes is required. We considered one of the more accurate variants called Accelerated Weighted Ensemble Dynamics (AWE) and for which distributed computing can be made efficient. We implemented AWE using the Work Queue framework for task management and applied it to an all atom protein model (Fip35 WW domain). We can run with excellent scalability by simultaneously utilizing heterogeneous resources from multiple computing platforms such as clouds (Amazon EC2, Microsoft Azure), dedicated clusters, grids, on multiple architectures (CPU/GPU, 32/64bit), and in a dynamic environment in which processes are regularly added or removed from the pool. This has allowed us to achieve an aggregate sampling rate of over 500 ns/hour. As a comparison, a single process typically achieves 0.1 ns/hour.","PeriodicalId":90293,"journal":{"name":"Proceedings ... IEEE International Conference on eScience. IEEE International Conference on eScience","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/eScience.2012.6404429","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32935576","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 13

rCAD: A Novel Database Schema for the Comparative Analysis of RNA. rCAD:一种用于RNA比较分析的新型数据库模式。

Proceedings ... IEEE International Conference on eScience. IEEE International Conference on eScience Pub Date : 2011-12-31 DOI: 10.1109/eScience.2011.11

Stuart Ozer, Kishore J Doshi, Weijia Xu, Robin R Gutell

引用次数: 8