系統(tǒng)生物 第三章 建模與仿真學(xué)習(xí)資料

第三章建模與仿真3-9Thecomponentsmaybesimulationcodes,仿真analysistools,userinterfaces,databaseinterfaces,scriptlanguageinterpreters,orinfactanypieceofsoftwarethatconformstoacertainwell-definedinterface3-12TheSystemsBiologyWorkbenchisprimarilyasystemforintegratingresources.Itprovidesinfrastructurethatcanbeusedbysoftwaredeveloperstointerfacesoftwarecomponentstogetherandenablethemtocommunicatewitheachother.3-16模塊是可以提供共享計(jì)算機(jī)資源的應(yīng)用軟件，broker是提供各個(gè)模塊可以相互通信的平臺(tái)模塊可以用任何語(yǔ)言編寫，只要它們能夠運(yùn)用一致的協(xié)議傳送，接收和處理適當(dāng)結(jié)構(gòu)的信息，就可以與sbw平臺(tái)相聯(lián)結(jié)SBW的模塊可以在用戶或程序控制下方便的交換，添加或移出，甚至在運(yùn)行的時(shí)候也可以實(shí)現(xiàn)，有動(dòng)態(tài)可擴(kuò)展性每個(gè)模塊都有特定數(shù)值標(biāo)識(shí)的handle(numericidentificationhandle)當(dāng)一個(gè)模塊要與另一個(gè)模塊實(shí)現(xiàn)通信時(shí)，它向Broker發(fā)送信息請(qǐng)求，請(qǐng)求中包含終點(diǎn)模塊的handle標(biāo)識(shí)遠(yuǎn)程的服務(wù)可以通過(guò)信息傳送（messagepassing）與其它軟件實(shí)體實(shí)現(xiàn)信息交流3-17通過(guò)sbw交互庫(kù)，編程人員將他們的模塊與sbw系統(tǒng)實(shí)現(xiàn)交互，庫(kù)執(zhí)行必要的應(yīng)用編程接口，使不同模塊通過(guò)sbw框架相互通訊對(duì)模塊本身來(lái)說(shuō)，通信是直接的（模塊到模塊），在底層的。信息通過(guò)sbw的傳輸是不可見(jiàn)的3-18下面介紹一下信息傳輸?shù)募s定格式1.代表對(duì)其他模塊中方法或函數(shù)或?qū)roker本身的封閉的應(yīng)答ReplyMessage0SendMessage1CallMessage2ErrorMessage32.代表非封閉的對(duì)其他模塊中方法或函數(shù)或?qū)roker本身的應(yīng)答3.對(duì)之前信息的回應(yīng)4.當(dāng)傳遞信息格式錯(cuò)誤或執(zhí)行模塊事發(fā)生異常時(shí)的error信息3-21模塊與SBW初始連接當(dāng)模塊連接時(shí)，sbw會(huì)創(chuàng)建一個(gè)moduleobjectModulename是唯一的，但是可以為空，當(dāng)值提供服務(wù)時(shí)。Id唯一，不變模塊嘗試將請(qǐng)求傳遞到sbw中，如果成功就將name以string提交到sbwbroker中的監(jiān)聽(tīng)線程獲得請(qǐng)求，并讀出模塊名監(jiān)聽(tīng)線程為模塊創(chuàng)建一個(gè)線程來(lái)處理模塊與sbw間的通信這時(shí)候就創(chuàng)建了一個(gè)muduleobject，直到服務(wù)結(jié)束模塊對(duì)象會(huì)添加到broker的索引中保存3-22模塊線程只有兩個(gè)功能，首先是決定信息是傳遞到下一個(gè)模塊還是到達(dá)broker（即broker服務(wù)信息）如果是傳遞到另外的模塊，就會(huì)根據(jù)信息中的終點(diǎn)模塊標(biāo)示，直接準(zhǔn)確地傳遞到目的地。如何判斷是傳向broker的呢？Broker也有一個(gè)brokerid.作為信息接口，它的id是-1，因?yàn)榫€程的索引中是以0開(kāi)始的，為了避免沖突就用-1來(lái)作為id。3-23模塊為什么可以與broker向來(lái)連接起來(lái)呢？下面介紹一下模塊的體系結(jié)構(gòu)。它主要由四個(gè)類組成：ModuleComponent是應(yīng)用程序與sbw連接的主要接口ThisisthemainentrypointforapplicationswishingtouseSBWfacilities.和javabean比較相似。AsimilarapproachcouldbeadoptedunderJavaintheformofaJavaBean.RecvThread負(fù)責(zé)接聽(tīng)來(lái)自broker的所有信息。它在一個(gè)監(jiān)聽(tīng)線程中運(yùn)行，當(dāng)接收到一個(gè)信息以后，就創(chuàng)建了一個(gè)線程MessageThreadobject來(lái)處理信息的細(xì)節(jié)。RecvThreadrunscontinuouslyinathreadsothatlisteningforbrokermessagesdoesnotinterferewiththenormalprocessingoftheapplication.WhentheRecvThreadreceivesamessagefromthebrokeritspawnsaspecialMessageThreadobjectwhichhastheresponsibilityfordealingwiththeparticularsofthemessage.OncetheRecvThreadhasspawnedamessagethread,itreturnstoitsnormalmodeoflisteningforSBWmessages.Thus,eachtimeamessageisreceivedbyRecvThread,amessagethreadiscreated.However,toeliminatetheperformancehitwhichissufferedeachtimeathreadisspawned,intheactualimplementation,athreadpoolismaintainedandspawningamessagethreadinsteadinvolvesrequestingaexistingsuspendedthreadfromathreadpool.Whenmessagethreadsarenolongerrequiredtheyarereturnedtothethreadpoolforfutureuse.Testshaveshownthatthissimpleuseofathreadpoolimprovesmessagetransportroughlysix-foldcomparedtonothreadpooling.MessageThread對(duì)RecvThread接收到的信息進(jìn)行解析，判斷是什么信息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