Cloud-R:以R軟體與雲端技術為基礎的生物統計應用網站

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林坤賢(Kun-hsien Lin) 查詢紙本館藏

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系統生物與生物資訊研究所

論文名稱

Cloud-R:以R軟體與雲端技術為基礎的生物統計應用網站
(Cloud-R: an R biostatistical computation and graphics environment in the cloud)

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摘要(中)

R是一種開放原始碼的程式語言，在統計和圖形運算上有著非常出色的表現[1,2]，目前廣泛應用在統計與生物資訊的領域中。而Bioconductor則是專在R語言環境中所設計來分析生物晶片資料與基因組數據分析的套件包[3]。目前公開發布的R軟體提供單機版的安裝，並能在微軟的視窗系統、Linux以及MacOS X等作業系統上安裝。當基因資料越趨龐大的同時，單機版R軟體所需的電腦記憶體容量以及儲存容量也就更顯重要。雲端運算憑藉著網際網路的普及和連線速度的增快，讓軟體服務偏向透過網頁介面以減輕使用者端電腦環境的負擔，並透過遠端的資料中心提供穩定的服務[4]。Cloud-R即是一個網路服務，提供了一個線上使用R軟體所有功能的平台。對於使用Cloud-R平台的使用者最基本的要求是能夠有使用過R語言的經驗。為了讓Cloud-R平台能夠有著充足的運算資源，Cloud-R平台提供了一個快速簡單的管道讓使用者能夠貢獻閒置的電腦資源。使用者貢獻的電腦資源能夠隨心所欲的給予或是收回，依照自身的使用需求做合理的安排。貢獻者是透過在R軟體之上擴充安裝的nws套件，經由nws套件提供的函數，可以很輕易的達到電腦共同合作運算的目的[5]。Cloud-R平台可在以下網址:http://epigenomics.ncu.edu.tw/Cloud-R/登入。

摘要(英)

R is an open source programming language for statistical and graphical computation that is popular among statisticians and bioinformaticians [1,2]. In particular, an R project called Bioconductor has been dedicated to the analysis and comprehension of genomic metadata using R [3].R is available in the form of standalone software that runs on Windows, MacOS X and Linux machines. As the volume of genomic data continues to explode, a high capacity R environment is in need. Cloud computing, aided by wider Internet penetration and faster Web communication, represents a paradigm shift in computation toward deployment of applications to remote data centers [4]. We propose to let users run their R programs through web browsers. Cloud-R is such a Web server that provides R utilities over the Internet. A basic requirement of Cloud-R development is that user experience of Cloud-R be identical to that of regular R. More importantly, to the goal of virtually limitless computational resources for R, Cloud-R allows users to freely contribute their computers to Cloud-R. Users’ contributions of hardware can be made and withdrawn at anytime by themselves. Connection of a contributor’s computer is via nws, an R package for coordinate programming [5]. Cloud-R can login at this URL: http://epigenomics.ncu.edu.tw/Cloud-R/.

關鍵字(中)

★ 雲端計算
★ 統計分析
★ R軟體
★ web service

關鍵字(英)

★ cloud computing
★ statistical analysis
★ R software

論文目次

目錄
中文摘要 i
ABSTRACT ii
目錄 iii
圖目錄 v
第一章緒論 7
1-1 研究背景 7
1-1-1 自由軟體的意義 7
1-1-2 R統計軟體的發展過程 8
1-1-3 大型運算的歷史背景 10
1-1-4 網路服務的興起 12
1-1-5 雲端運算的具體意像 13
1-1-6 生物分析的需求趨勢 17
1-2 Cloud-R的研究動機 19
第二章 Cloud-R的設計與方法介紹 21
2-1 Cloud-R的基礎架構 21
2-2 使用平台、技術與系統架構設計 22
4-2 軟體規格 23
4-3 方法實作 23
4-3-1 實作輸入R命令稿 23
4-3-2 實作調用R 25
4-3-3 實作輸出R結果 27
4-3-4 實作啟動NetWorkSpaces Server、node監控 28
4-3-5 實作Cloud-R雲端運算虛擬化機制 30
第三章 Cloud-R操作步驟與數據分析 32
3-1 Cloud-R功能介紹 32
3-2 Cloud-R功能操作 34
3-3 貢獻節點者名單 41
3-4 Cloud-R效能評估 42
第四章結論及未來可能的研究方向 45
4-1 總結 45
4-2 未來可能的研究方向 48
第五章附錄 50
4-3 附錄一 50
4-4 附錄二 56
第六章參考資料 58

參考文獻

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指導教授

王孫崇(Sun-chong Wang)

審核日期

2010-7-24

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