A Collaborative Research Environment for Avian Flu

ResearchLuo Ze

Computer Network Information Center, CAS

2006-10-21

Project Context

• Project : “Avian influenza comprehensive Project : “Avian influenza comprehensive information platform and its Alarming and information platform and its Alarming and predicting System in CAS”predicting System in CAS”

• Conducted by four institutes of CAS:Conducted by four institutes of CAS:– Institute of Microbiology, CASInstitute of Microbiology, CAS– Wuhan Institute of Virology, CASWuhan Institute of Virology, CAS– Institute of Zoology, CASInstitute of Zoology, CAS– Computer Network Information Center, CASComputer Network Information Center, CAS

• This project is a demonstration program of e-Science supported by SDB project

Project Objectives

1. Development of Data standards and metadata

2. Integration of avian-flu databases3. Epidemiological and ecological

investigation4. Bioinformatics analysis Platform5. Alarming and predicting system6. Cooperative scientific research

Environment7. Information sharing system

Collaborative Research Environment

• Most of CNIC’s work focus on the cooperative scientific research environment. It plays an important role in this project which glue the resource, information and researcher from geographically distributed institutes and provide a collaborative workshop.

Goals

• Two major goals of the research environment are followed:– Construct a web-based platform which integrate

different resource including computing, data, storage, software, documents and specifications provided by distributed institutes. Offer an user-friendly Interface

– Provide a collaborative environment based on which institutes took part in this project could make cooperative scientific research

Portal

• Currently, the research environment was presented as a Web Portal

• http://birdflu.sdg.ac.cn

• The portal was developed based on Liferay portal framework. Different resources were abstracted and presented as a portlet compliant with JSR168 standards.

Data Input Portlet

• Provide data input portlet in line with data standard and metadata requirement.

• Scientist can input, query, modify and save data in the back-end database.

• It will be convenient for biologist who go to field to capture birds and can record the data they get immediately by the palmtop or other network enabled device

Data Access Service

• DAS (Data Access Service) is designed to realize uniform access to massive, distributed, heterogeneous and autonomous databases. At present, we can access, via DAS, a wide range of relation databases, such as Oracle, Microsoft SQL Server and MySQL, and file systems. Through the interface provided by DAS, client can acquire metadata of data resource and execute query. The DAS is implemented by OGSA compliant grid services.

Data Access Service

• DAS was developed by CNIC as part of Scientific Data Grid.

• We adopt DAS to encapsulate different data resource provided by geographically distributed institutes. Through DAS, the data resource present a uniform access interface

• DAS act as back-end grid service, front-end are presented as portlets and are integrated into portal.

Bioinformatic Analysis

• Integrated bioinformatic analysis system including:– GCG Package– DS Modeling– BLAST– ClustalW– Motif Searching– ……

Bioinformatic Analysis

• One of the current work is to integrate more bioinformatic analysis software including:– TMHMM. Transmembrane prediction progr

am– SignalP. Signal Prediction program– HMMER. Profile HMM creation and databas

e search tools– Many of the programs from the EMBOSS s

uite

Collaborative System

• A collaborative system is required to allow people to interact and work together as a distributed team.

• Our e-Research project is already using portlet technology. At the same time, we think JSR168 and WSRP are appropriate approaches to collaborative tools development.

• We resolved the problem of SSO between Portal and different collaborative tools.

Collaborative System

• Collaborative tools provided in portal including:– Schedule– Blog– Wiki– Instant Messaging– BBS– File sharing– MailList– Video Conference

Next Step

• Currently, our cooperative scientific research environment is still in its baby stage. What we will do next including:– Move the research environment toward a G

rid-like system. We intend to use Globus Toolkit which provides mechanisms to harness distributed resources using global identify credentials that work across a muti-institute Grid.

Next Step

– Develop new tools to extend existing collaborative toolset. Integrate seamlessly with portal and existing tools.

– JSR168 and WSRP provide an excellent mechanism to bring together the user interfaces to tools from many disparate resource into a single portal, and we need integrate seamlessly the portal and underpinning grid middleware.

Next Step

– Knowledge building tools/software which allow scientific workflows to be produced which can be used to orchestrate scientific software. This enable users to focus on the high level decisions regarding which effors will likely yield the best results run and working with the results of the jobs instead of manually executing repeated or complex series of tasks by hand.

Networked Surveilliance System

• Networked Bird Surveilliance System– In 2005, a large scale avian flu break out at

bird island, Qinghai Lake.– The Chinese Academy of Sciences and Qin

ghai Provincial Forestry Bureau have signed an agreement to join hands carrying out research on wildlife protection at the Qinghai Lake beginning April.

Networked Surveilliance System

– The cooperation will begin from the surveillance and control of possible bird flu virus at the Bird Island, an important habitat for migrant birds

– Surveillance equipment will be upgraded in April and a database and a laboratory will be set up to monitor the migrant birds and possible bird flu virus

– The cooperation will then extend to surveillance of the diseases of wild animals and the protection of wild animals

中科院青海相关研究所

青海省林业局

保护区管理局办公自动化网络

中国科技网

中科院计算机网络信息中心

中科院微生物研究所

中科院动物研究所

中科院武汉病毒研究所

CC

C

C 核心区域

蛋岛鸬鹚岛

河流入湖口

保护区网络管理中心

C

救护中心

RFID

• Used for identifying and tracking the bird.

• The Reader is ready and the tag is modeling.

• Have tested on bird island, Qinghai Lake in July, 2006

• May be deployed at the begin of next year.

Reader

Tag

Architecture

Qinghai Lake National Reserve Portal

• CNIC help Qinghai Lake national reserve to construct a portal to introduce Qinghai Lake, disseminate science, attract tourist

• http://www.qinghailake.cn

• http://www.niaodao.cn

Thanks!