系统生物 第三章 建模与仿真学习资料

第三章建模与仿真3-9Thecomponentsmaybesimulationcodes,仿真analysistools,userinterfaces,databaseinterfaces,scriptlanguageinterpreters,orinfactanypieceofsoftwarethatconformstoacertainwell-definedinterface3-12TheSystemsBiologyWorkbenchisprimarilyasystemforintegratingresources.Itprovidesinfrastructurethatcanbeusedbysoftwaredeveloperstointerfacesoftwarecomponentstogetherandenablethemtocommunicatewitheachother.3-16模块是可以提供共享计算机资源的应用软件，broker是提供各个模块可以相互通信的平台模块可以用任何语言编写，只要它们能够运用一致的协议传送，接收和处理适当结构的信息，就可以与sbw平台相联结SBW的模块可以在用户或程序控制下方便的交换，添加或移出，甚至在运行的时候也可以实现，有动态可扩展性每个模块都有特定数值标识的handle(numericidentificationhandle)当一个模块要与另一个模块实现通信时，它向Broker发送信息请求，请求中包含终点模块的handle标识远程的服务可以通过信息传送（messagepassing）与其它软件实体实现信息交流3-17通过sbw交互库，编程人员将他们的模块与sbw系统实现交互，库执行必要的应用编程接口，使不同模块通过sbw框架相互通讯对模块本身来说，通信是直接的（模块到模块），在底层的。信息通过sbw的传输是不可见的3-18下面介绍一下信息传输的约定格式1.代表对其他模块中方法或函数或对broker本身的封闭的应答ReplyMessage0SendMessage1CallMessage2ErrorMessage32.代表非封闭的对其他模块中方法或函数或对broker本身的应答3.对之前信息的回应4.当传递信息格式错误或执行模块事发生异常时的error信息3-21模块与SBW初始连接当模块连接时，sbw会创建一个moduleobjectModulename是唯一的，但是可以为空，当值提供服务时。Id唯一，不变模块尝试将请求传递到sbw中，如果成功就将name以string提交到sbwbroker中的监听线程获得请求，并读出模块名监听线程为模块创建一个线程来处理模块与sbw间的通信这时候就创建了一个muduleobject，直到服务结束模块对象会添加到broker的索引中保存3-22模块线程只有两个功能，首先是决定信息是传递到下一个模块还是到达broker（即broker服务信息）如果是传递到另外的模块，就会根据信息中的终点模块标示，直接准确地传递到目的地。如何判断是传向broker的呢？Broker也有一个brokerid.作为信息接口，它的id是-1，因为线程的索引中是以0开始的，为了避免冲突就用-1来作为id。3-23模块为什么可以与broker向来连接起来呢？下面介绍一下模块的体系结构。它主要由四个类组成：ModuleComponent是应用程序与sbw连接的主要接口ThisisthemainentrypointforapplicationswishingtouseSBWfacilities.和javabean比较相似。AsimilarapproachcouldbeadoptedunderJavaintheformofaJavaBean.RecvThread负责接听来自broker的所有信息。它在一个监听线程中运行，当接收到一个信息以后，就创建了一个线程MessageThreadobject来处理信息的细节。RecvThreadrunscontinuouslyinathreadsothatlisteningforbrokermessagesdoesnotinterferewiththenormalprocessingoftheapplication.WhentheRecvThreadreceivesamessagefromthebrokeritspawnsaspecialMessageThreadobjectwhichhastheresponsibilityfordealingwiththeparticularsofthemessage.OncetheRecvThreadhasspawnedamessagethread,itreturnstoitsnormalmodeoflisteningforSBWmessages.Thus,eachtimeamessageisreceivedbyRecvThread,amessagethreadiscreated.However,toeliminatetheperformancehitwhichissufferedeachtimeathreadisspawned,intheactualimplementation,athreadpoolismaintainedandspawningamessagethreadinsteadinvolvesrequestingaexistingsuspendedthreadfromathreadpool.Whenmessagethreadsarenolongerrequiredtheyarereturnedtothethreadpoolforfutureuse.Testshaveshownthatthissimpleuseofathreadpoolimprovesmessagetransportroughlysix-foldcomparedtonothreadpooling.MessageThread对RecvThread接收到的信息进行解析，判断是什么信息call/send,replyorerrorconditionThemessagethreadisresponsiblefordecodingmessageswhichitreceivesfromRecvThread.Themessagethreadwillresponddifferentlydependingonwhetherthemessageisacall/send,replyorerrorcondition.Oncethemessagethreadhascompleteditstaskitisreturnedtothemessagethreadpool.ServiceListAlistofservicesandmethodsprovidedbythismodule3-24•Themodulemakesacallusingthesbw.call()method•Themessageissenttothebrokerandisreceivedbythemainlisteningthreadinthebroker.•ThemodulecreatesaWaitEventandaddsittothelistofwaiteventsstoredintheRecvThreadobject.•ThemodulewaitsusingtheWaitEvent.•Sometimelater,thebrokerreturnsareplytothemodule.•TheRecvThreadreceivesamessageandrecruitsamessagethreadfromthethreadpoolandpassesthecompletemessagetothemessagethread.RecvThreadthenresumesitsnormalmodeoflisteningformessagesfromthebroker.•Themessagethreadinterpretsthemessageasareply,butatthisstagedoesnotknowwhothereplyisfor.ThemessagethreadsearchestheEventListforthecorrespondingcallwhichinitiatedthisreply.Whenitlocatestheevent(anexceptionresultsifitcannotfindtheevent),itsavesthemessageandperformsaSetEventcallontheappropriatewaitingevent.Thiscausesthewaiteventtoresumeexecutionwhereisretrievesthestoredmessageandreturnsittotheoriginalcallerforprocessing.•Oncethereplyhasbeenfinallydispatched,themessagethreadisreturnedtothethreadpool.3-25TheRecvThreadinterceptsthemessagefromthebroker,recruitsamessagethread,passesthemessagetothemessagethreadandreturnstoitsnormalmodeoflisteningformessagesfromthebroker.•Themessagethreadexaminesthemessagetodetermineifthemessageisacall,asend,areplyoranerrorcondition.Ifthemessageisacall,thethreadroutesthemessagetothecallprocedure.Inthecallprocedureoneoftwothingscanhappen:1)thecallmethodwaspreviouslyregistered,inwhichcase,themessagethreadautomaticallycallstheappropriatemethodinthemodule;2)themethodwasnotregistered,inthiscasethemessagethreadfi