On Design and Implementation of a Bioinformatics Portal in Cluster and Grid Environments Chiou-Nan Chen, Kuan-Ching Li, Chuan Yi Tang, Yaw-Lin Lin,

Presentation on theme: "On Design and Implementation of a Bioinformatics Portal in Cluster and Grid Environments Chiou-Nan Chen, Kuan-Ching Li, Chuan Yi Tang, Yaw-Lin Lin,"— Presentation transcript:

1 On Design and Implementation of a Bioinformatics Portal in Cluster and Grid Environments
Chiou-Nan Chen, Kuan-Ching Li, Chuan Yi Tang, Yaw-Lin Lin, Hsiao-Hsi Wang, Tsung-Ying Wu.

2 Outline Motivation Bioinformatics Applications Overview
The PCGrid Computing Infrastructure BioPortal: a Portal for Bioinformatics Applications in Grid Conclusions 2019/1/1 VECPAR 06

3 Motivation Biomedical researchers may need to combine many individual computation consumption works to conclude their investigation. The major goal of this project is to assist biologists to access high performance computing without additional drawbacks and to accelerate their experimental. 動機； 生醫學家的研究資料與工具通常是分散且需要浩大的運算資源的。 我們開發的系統，將主要的幾個工具結合在一起，並透過簡易的使用者界面，讓生醫學家可以輕易的運用高效能運算來增進他們的實驗與研究。 2019/1/1 VECPAR 06

4 Bioinformatics Applications Overview
reconstruct the past e.g., infer the evolution of species predict the future e.g., predict how some genes affect a certain disease Sequences Alignment Phylogenetic Tree Construction 2019/1/1 VECPAR 06

5 The PCGrid Computing Infrastructure
The Providence University Campus Grid 1. AMD Homogeneous Cluster (17 nodes) 2. Heterogeneous Cluster (9 nodes) 3. AMD 64-bit Sempron Cluster (4 nodes) 4. Intel P4 Cluster (9 nodes) 5. IBM Blade Cluster (6 computing blades) Total storage: more than 5 TB. 介紹PCGrid的架構 2019/1/1 VECPAR 06

6 PCGrid的架構圖 2019/1/1 VECPAR 06

7 The PCGrid Computing Infrastructure cont.
Graphics Interfaces: 1. Status Monitoring. Computing Node manual selection Real-time display of all computing nodes status 2. Performance Visualization. Performance data of each computing node involved in computation of PCGrid grid platform. Performance comparison of two application execution results, computing node by computing node, CPU load and memory usage. PCGrid提供圖形化的管理界面； 使用狀態，包括Node的選擇 視覺化的效能檢視 2019/1/1 VECPAR 06

8 Performance Visualization
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9 BioPortal: a Portal for Bioinformatics Applications in Grid
Web-based GUI Integrate many bioinformatics applications: sequence comparison, pairwise or multiple sequence alignment phylogeny tree construction BioPortal的特色 2019/1/1 VECPAR 06

10 BioPortal web-based GUI screenshot
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11 BioPortal workflow 2019/1/1 VECPAR 06
BLAST -> Data Transform -> ClustalW -> Phylip 2019/1/1 VECPAR 06

12 List of bioinformatics applications provided by BioPortal
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13 Contributions In this paper, we integrate several important bioinformatics applications into a user-friendly and biologist-oriented web-based portal on top of our PCGrid grid computing environment . 結論與貢獻； 我們主要的貢獻在於，建立了一個以生物學家為導向的Grid運算平台，結合了數個重要的生物資訊工具，並透過一個簡易的使用者界面來提供生物學家進行高效能的運算。 2019/1/1 VECPAR 06

14 Thank you and Welcome to visit us. http://www. pdpc. cs. pu. edu
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