efficiently supports team-work by integrative data-centric knowledge-sharing platform gao, ge (...
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Efficiently supports team-work by integrative Efficiently supports team-work by integrative data-centric knowledge-sharing platformdata-centric knowledge-sharing platform
Gao, Ge (高歌 )Center for Bioinformatics, CBI
(北京大学生物信息中心 )2009-10-19
Center for Bioinformatics, Peking UniversityCenter for Bioinformatics, Peking University
• Founded in 1996 as the first bioinformatics center in China
• Administratively located within College of Life Sciences• Funded by Ministry of Science and Technology,
Natural Science Foundation, and Ministry of Education• Official national node of EMBnet in China
• 600m2 of “dry” lab and 100m2 of “wet” lab• Strong hardware and software infrastructure
Seminar/training room
121-CPU IBM cluster
Center for Bioinformatics Floor
SUN servers
CBI Graduate Students’ Office
Life Science Building(CBI is on 6th floor)
Wet lab for bench work
First and Largest Online First and Largest Online Bioinformatics Resource in ChinaBioinformatics Resource in China
Ten Millions of Hits per monthTen Millions of Hits per month
已去除来自本中心内部及搜索引擎的访问量
Users around the worldUsers around the worldThe States/Regions of most active visitors
Mainland, China United States United Kingdom India
Germany Taiwan, China Canada Spain
France Japan Sweden Netherlands
Hong Kong, China Mexico Australia Singapore
Italy Korea, Republic of
Expasy:Expasy: Chinese Official Mirror Chinese Official Mirror
Plant Transcript Factor DatabasePlant Transcript Factor Database
类别 物种 学名 转录因子数量
模式生物 拟南芥 Arabidopsis thaliana 2290
杨树 Populus trichocarpa 2576
水稻 Oryza sativa (ssp. indica) 2025
Oryza sativa (ssp. japonica) 2384
小立碗藓 Physcomitrella patens 1170
衣藻 Chlamydomonas reinhardtii 205
谷类 大麦 Hordeum vulgare 618
玉米 Zea may 764
高粱 Sorghum bicolor 397
甘蔗 Saccharum officinarum 1177
小麦 Triticum aestivum 1127
水果 苹果 Malus domestica 1025
葡萄 Vitis vinifera 867
甜橙 Citrus sinensis 599
裸子植物 火炬松 Pinus taeda 950
云杉 Picea glauca 440
经济作物 棉花 Gossypium hirsutum 1567
马铃薯 Solanum tuberosum 1340
大豆 Glycine max 1891
向日葵 Helianthus annuus 513
番茄 Lycopersicon esculentum 998
百脉根 Lotus japonicus 457
苜蓿 Medicago truncatula 1022
Mainland, China United States Germany Japan
France India Taiwan, China United Kingdom
Korea, Republic of Canada Australia Netherlands
Weblab: your Lab on the WebWeblab: your Lab on the Web
270+ Widely-used Bioinformatics Tools270+ Widely-used Bioinformatics Tools
Unified application Unified application interface for both local interface for both local and remote applicationsand remote applications
• Being compatible with SOAP-based Web service and Globus-based Grid services
DBMS(MySQL)
WebLab Architecture
Web Interface Layer Index File
Business Logical Layer
Workflow Engine Ontology Manager
Job Schedule Engine
Workflow Definition
XML
Web ServiceGrid Service Legacy Service
Program Utility
Macro Protocol
Data Literature
Tool BoxMeta
Package
Service User SpaceProgram Definition
XML
Internet
Operators-based workflow engineOperators-based workflow engine];)];:;:([;;[ fconsensefneighborfprotdistfalsefdnadisttrueisDNACfseqbootemmaP
Seamless integrating Seamless integrating various resourcesvarious resources
• Web-service based protocol• BioMart-compatible interface
Context-sensitive data workspaces Context-sensitive data workspaces
Tag
Comment
Effectively literature managementEffectively literature management
Team-work: Virtual Research GroupTeam-work: Virtual Research Group
Sharing documents among collaboratorsSharing documents among collaborators
Shared data
数据与文献的统一管理数据与文献的统一管理用户定制标签（ ta
g）
用户批注(comment)
用户间数据共享
基于文本挖掘的自动关联
WebLab as a Grid portalWebLab as a Grid portal
Rnet系统
Rnet系统
Rnet系统
Rnet系统
Rnet系统
Rnet系统
Rnet系统
• 目前，网格门户已有来自世界各地的四千余个注册用户 , 完成了近九万项分析任务。
• 相关论文发表在 Nucle. Acid Research– 瑞典 Uppsala University及中国农业科学院安装了WebLab系统的分发版本用于教学及科研
Thanks for your attention!Thanks for your attention!
BackupBackup
Some more Research-Driven Online Services@CBISome more Research-Driven Online Services@CBI
Interactive UI for defining new workflowInteractive UI for defining new workflow
基于基于 Web-serviceWeb-service 定义标准化数据接口定义标准化数据接口以整合远程数据源以整合远程数据源
DBMS(MySQL)
WebLab Architecture
Web Interface Layer Index File
Business Logical Layer
Workflow Engine Ontology Manager
Job Schedule Engine
Workflow Definition
XML
Web ServiceGrid Service Legacy Service
Program Utility
Macro Protocol
Data Literature
Tool BoxMeta
Package
Service User SpaceProgram Definition
XML
Internet
WeblabWeblab 为用户为用户提供了基于浏览提供了基于浏览器的生物信息学器的生物信息学网络整合计算环网络整合计算环境。通过支持基境。通过支持基于以用户数据为于以用户数据为中心的工作模型，中心的工作模型，用户无需关心底用户无需关心底层实现细节，即层实现细节，即可提交包含多个可提交包含多个计算任务的工作计算任务的工作流请求，完成复流请求，完成复杂的分析任务流杂的分析任务流程。程。