Visual orchestration and autonomous execution of distributed and heterogeneous computational biology pipelines

Xin Mou, H. Jamil, R. Rinker
{"title":"Visual orchestration and autonomous execution of distributed and heterogeneous computational biology pipelines","authors":"Xin Mou, H. Jamil, R. Rinker","doi":"10.1109/BIBM.2016.7822615","DOIUrl":null,"url":null,"abstract":"Data integration continues to baffle researchers even though substantial progress has been made. Although the emergence of technologies such as XML, web services, semantic web and cloud computing have helped, a system in which biologists are comfortable articulating new applications and developing them without technical assistance from a computing expert is yet to be realized. The distance between a friendly graphical interface that does little, and a “traditional” system though clunky yet powerful, is deemed too great more often than not. The question that remains unanswered is, if a user can state her query involving a set of complex, heterogeneous and distributed life sciences resources in an easy to use language and execute it without further help from a computer savvy programmer. In this paper, we present a declarative meta-language, called VisFlow, for requirement specification, and a translator for mapping requirements into executable queries in a variant of SQL augmented with integration artifacts.","PeriodicalId":345384,"journal":{"name":"2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","volume":"54 1","pages":"0"},"PeriodicalIF":0.0000,"publicationDate":"2016-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"4","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1109/BIBM.2016.7822615","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 4

Abstract

Data integration continues to baffle researchers even though substantial progress has been made. Although the emergence of technologies such as XML, web services, semantic web and cloud computing have helped, a system in which biologists are comfortable articulating new applications and developing them without technical assistance from a computing expert is yet to be realized. The distance between a friendly graphical interface that does little, and a “traditional” system though clunky yet powerful, is deemed too great more often than not. The question that remains unanswered is, if a user can state her query involving a set of complex, heterogeneous and distributed life sciences resources in an easy to use language and execute it without further help from a computer savvy programmer. In this paper, we present a declarative meta-language, called VisFlow, for requirement specification, and a translator for mapping requirements into executable queries in a variant of SQL augmented with integration artifacts.
查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
分布式和异构计算生物学管道的可视化编排和自主执行
尽管已经取得了实质性进展,但数据整合仍然困扰着研究人员。尽管诸如XML、web服务、语义网和云计算等技术的出现有所帮助,但生物学家在没有计算专家的技术帮助下轻松表述和开发新应用程序的系统尚未实现。一个没有什么功能的友好图形界面和一个虽然笨重但功能强大的“传统”系统之间的距离往往被认为太大了。仍未解决的问题是,用户是否可以用一种易于使用的语言陈述涉及一组复杂、异构和分布式生命科学资源的查询,并在没有精通计算机的程序员进一步帮助的情况下执行该查询。在本文中,我们提出了一种声明性元语言,称为VisFlow,用于需求规范,以及一种转换器,用于将需求映射到带有集成构件的SQL变体中的可执行查询。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 去求助
来源期刊
自引率
0.00%
发文量
0
期刊最新文献
The role of high performance, grid and cloud computing in high-throughput sequencing A novel algorithm for identifying essential proteins by integrating subcellular localization CNNsite: Prediction of DNA-binding residues in proteins using Convolutional Neural Network with sequence features Inferring Social Influence of anti-Tobacco mass media campaigns Emotion recognition from multi-channel EEG data through Convolutional Recurrent Neural Network
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1