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Construction and Application of Technology of Biological Information Workflow

Author: FengHongLing
Tutor: LiDongFang; ZhangLePing
School: Second Military Medical University
Course: Applied Computer Technology
Keywords: bioinformatics workflow IOC/AOP web service SOAP message JDM
CLC: TP311.52
Type: Master's thesis
Year: 2013
Downloads: 15
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Abstract


As workflow used in bioinformatics experiments, Bioinformatics workflow has beenpaid more and more attention. Bioinformatics workflow is process expression which candescribe the process of biological experiment and complete data analysis automaticallyfrom different data sets and applications.So it can improve the efficiency of experimentssignificantly.The implementations of bioinformatics workflow system focus on the combination ofweb-services and the integration of application-oriented. In this paper, Bioinformaticsworkflow platform combines the advantages of both in implementation. The former usesthe Web Service technology to get the various Web services distributed in the network.These web services can constitute bioinformatics workflow according to context andrules.The latter encapsulates a variety of applications and algorithms into the systemcomponents by JDM tool. These system components can build up bioinformatics workflowwhich can settle specific biological issues In accordance with rules. The combination ofweb services and system components which were got by the IoC/AOP in Springframework can solve the problem of Inversion of Control and loose coupled. This papermainly describes server supporting technologies as followed: The technology of IoC/AOP;Web service; SOAP; JDM.The IoC/AOP in Spring framework can implement the combination of web servicesand system components in bioinformatics workflow. It may change the parameter or theresult returned when services or components call others directly in bioinformaticsworkflow. That may effect the operation of workflow or workflow system needs to take ahigh price to maintain. This problem can solve by IoC/AOP in Spring framework. IoC is apattern of interface driven design. Each service or component has its own interface. If oneis needed, its interface is called not itself. So services and components do not be affectedby this operation. It exists the edge logical problem such as log file, thread management，SOAP message in the bioinformatics workflow. When system sends advice, Springframework receives advice from system and weave the aspect to bioinformatics workflow.Bioinformatics workflow in this paper bases on Service Oriented Architecture.Services can realize its deployment, combination and use by SOA. The SOAP message which be packaging automatic plays the key role in calling the Web service. Local dataanalysis produces can be encapsulated into components using JDM tool. Thebioinformatics workflow generates through the combination of web services andcomponents mentioned above according the context and rules. At last,we carry out somesimple bioinformatics tasks to test for the platform.The innovation points followed: It can implement the bioinformatics platform and canloose coupled between modules by IoC/AOP in Spring framework while system edge logicproblem can resolve by AOP in workflow. Besides, Data and compute-resource in WebServices and data analysis produces in JDM package are integrated and deployed inbioinformatics workflow. Therefore Life sciences workers who lack of programmingknowledge of life scientists can use it efficiently.Finally, It can build a biological WebServices resource management of client and automatically implement assembly of SOAPmessage base on analyzing Web Services dynamical.So it can settle the problem that howto define complex type object when it creates web service dynamically.

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