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1. Cancel O eS eater cert Figure 17 Enter view name dialog e The new view will be added to the list Please note that view names should be unique That is you cannot assign the same name to different views Moreover a view name should not be empty Besides when a new view is created the setting of this view will be copied from the current selected one Therefore you might not notice any changes to the steering GUI having created a new view except the name of the view In the following you will learn how to adjust the view s settings 6 2 4 Navigate to a View By default when you create a new view this view will be the current one To change the current view and select another one do the following steps e Go to the views list box in the views panel e Left click the list box a list of views will be displayed e Select one of them and hit the mouse button e The selected view setting will be loaded in the Steering GUI 6 2 5 Edit a View After you have defined a new view you can edit some properties of it e g the curve list viewer and so on In this section we focus on editing the number of curves associated with a view To edit a view do the following steps e Select the view that you want to edit as the current one e Left click the Option button 21 SOON Select curves load P1 P2 Place O Transitions TT Cancel etl Figure 18 Edit view dialog e From
2. Figure 10 Connection window 5 2 Connecting to the Server To connect to a running SSServer using Snoopy you first need to decide if you would like to use a model from those running on the SSServer if there are some or if you would like to submit a new model In the latter case you will need to open your Petri net model using Snoopy Nevertheless to open the connection window do the following steps in either of these cases 1 From the view window select Start Steering Mode see Figure 9 or just press F7 from the function keys if you prefer using short cut keys 2 The connection window will be opened see Figure 10 After you have opened the connection window you can connect to the sever using the default setting via the connect button This makes sense if you run the SSServer at the same computer as you use Snoopy or if you already configured Snoopy to connect to a certain SSServer However if you run the SSServer on another computer you must first configure the connection before pressing the connect button see Section 5 1 Another important point is that the SSServer and Snoopy should have the same version number of the communication library You cannot let Snoopy connect with an SSServer having a different version A check will be done at the beginning and you will be informed if an incompatible version is detected In this case the Snoopy and SSServer versions are displayed for your convenience
3. p and it is of string data type hence 3 8 2 Initialising the Library Before starting the actual communication between the server and the client you need to initialise the steering library This section briefly discusses how the steering library can be initialised 8 2 1 Creating a Client The SteeringClient class and its methods are mainly used to perform the communication between the SSServer and the user s client Therefore you will need to create an object of this class or to override its member functions in order to construct a client 8 2 2 Connect to the Server The first step to interact with the SSServer is to establish a connection The following routine can be used for this purpose 43 e Description tries to connect to a given computer name where the SSServer is running e Input p_sHostName the computer full name or the IP address where the SSServer is running Default is localhost p sService the service number to which the SSServer is listening Default is 3000 p_bConnectionType specifies whether the routines should block until a con nection takes place or not Default is false e Return Operation state this can be either one of the following flags SUCCESS the connection is established successfully FAILURE there is a problem doing the connection INVALIDVERSION the server version is different from the library version 8 2 3 Initialise The next
4. e The disk image will appear as another CD in your Finder with the name SSServer e Opening this disk you will find the SSServer application bundle as shown in Figure 4 e Copy the SSServer to your desired location or drag and drop it into the application folder 4 3 Install Snoopy under Windows To install Snoopy under Windows follow these steps e Obtain the windows installer package for Snoopy This should be a msi file e Double click the obtained setup package The windows installer will start as shown in Figure 5 Follow the simple instructions in this window by hitting the next button At the end of these steps Snoopy should be installed on your computer and a shortcut will be created at your desktop To start Snoopy double click the Snoopy s shortcut from your desktop 39 Snoopy o bg 7 Welcome to the Snoopy Setup Wizard 8 The installer will guide you through the steps required to instal Snoopy on your computer Cancel Baci Newt gt Figure 5 Snoopy Setup under Windows 4 4 Install SSServer under Windows Similar steps are required to install the SSServer under Windows For your convenience yi we repeat them in the following procedure e Obtain the windows installer package for SSServer This should be a msi file e Double click the obtained setup package e The windows installer will start as shown in Figure 6 e Follow the simple instructions in this window by hitting the ne
5. 1 6 5 1 6 8 D 2 2 J 3 Printing and Binding BTU Cottbus ISSN 1437 7969 schmitt tu cottbus de Headed by Prof Dr H Th Vierhaus Prof Dr H Konig Prof Dr M Heiner Prof Dr I Schmitt Prof Dr P Hofstedt Prof Dr C Lewerentz Prof Dr K Meer Prof Dr D Cunningham Prof Dr R Kraemer Prof Dr J Nolte Prof Dr G Wagner Snoopy Computational Steering Framework User Manual Version 1 0 Mostafa Herajy and Monika Heiner Data Structures and Software Dependability Institute of Computer Science Brandenburg University of Technology Cottbus Germany snoopy Q informatik tu cottbus de August 21 2013 Please sent all questions comments and suggestions how to improve this material to this address Contents 1 Introduction 2 Overview 2 1 Framework 2 2 Application Scenario 3 System Requirements 3 1 Hardware Requirements 3 2 Software Requirements 4 Installation 5 6 ia ra ith jee di Ae See ake Bd eat ge ee ee ae ar Serge eae e a ee Lt Duh a eee ee kee eee Ee eee 4 4 Install SSServer under Windows nn Getting Started 5 1 Launching Snoopy and SSServer 2 22 2 Cm on nn nn 5 2 Connecting to the Server 5 2 1 Configuring Connection Settings 2 2222 222 5 2 2 Saving Connection Settings 2 22 2m nn 5 3 Submit a New Modell 5 4 Using an Existing Model 5 5 Replacing an Existing Modell 2 222 Common S
6. 13 ADO Connect to the server Disconnected C Connect Hide Details Close Connection Properties Service 300 E Server localhost B Figure 11 Configuring connection setting 5 2 1 Configuring Connection Settings To configure the connection settings to connect to a certain SSServer do the following steps e Press the Show details button from the connection window e New fields appear as illustrated in Figure 11 e In the service text box enter the service number as discussed in Section 5 1 e In the server text box enter the server name or the IP address The default value of the service number is 3000 and the default for the server name is localhost To simplify entering these information you can also select from previous setting using a list 5 2 2 Saving Connection Settings The connection settings which you have entered in the previous step are automatically saved to the Snoopy registry Therefore you do not need to re enter them again when you later want to re connect to the same SSServer 5 3 Submit a New Model To use a new model in the steering mode do the following steps 1 Open the Petri net file in Snoopy 14 ano Steering Options 0 Send a New Model CO Use an Existing Model Model Name Running Models testllspcontped testcolor colcontped Cancel Com Figure 12 The steering options window 2 Open the connection window as discussed in Section
7. 2 D E E D e a lt 2 O a 2 lt D c pam 2 N Model N External Simulator N Steering Visualization Result output PN definition Model Views Internal Simulator Figure 1 Petri nets and computational steering framework The framework consists of four components steering server steering graphical user interface GUI steering ap plication programming interface Steering API and simulators internal and external The flow of information goes in two opposite directions from the simulator to the user monitoring and from the user to the simulator steering The data structure inside the server is organised in terms of Petri nets places transitions arcs and parameters The place data structure includes the initial marking and the transition data structure the rate functions A model can contain different result views which are defined by the users and submitted to the server for further download and manipulation Model Definition Communication l Simulation gu a e e use an existing model s eNe want Figure 2 Graphical illustration of a typical application scenario of Snoopy s steering framework The user has two options at the beginning either reading one of the models already existing in the server or submitting a new model In the latter case the Petri net model can be created using Snoopy or other Petri net editing tools b
8. 5 2 3 Make sure that you correctly configured the connection settings to connect to a running server 4 Hit the Connect button The steering option window will appear as illustrated in Figure 12 on Make sure the send a new model option is selected 6 Enter a model name and then press ok Please note that the name of the loaded file in Snoopy is used as a default name for the new model You can edit the name as you want under the condition that there is no model running on the SSServer side with the same name After pressing the Ok button the steering dialogue will open as shown in Figure 13 Please note if you use a coloured model then the unfolding window will automat ically appear after step 6 because you need to unfold the model before submitting it to the server To unfold a model press the Start button on the unfolding window as shown in Figure 14 5 4 Using an Existing Model The Snoopy steering framework gives you the chance to use existing models that are running on the SSServer without opening them in Snoopy For example let us assume that you have one model that is already running in the SSServer and you want to disconnect and return back to it later In this case you do not need to reopen the Snoopy file or even to unfold it if it is a colored model To steer an existing model follow this procedure 1 Open Snoopy and then open the connection window as described in Section 5 2
9. SSServer to your desired location or drag and drop it into the application folder 4 3 Install Snoopy under Windows To install Snoopy under Windows follow these steps e Obtain the windows installer package for Snoopy This should be a msi file e Double click the obtained setup package e The windows installer will start as shown in Figure 5 e Follow the simple instructions in this window by hitting the next button e At the end of these steps Snoopy should be installed on your computer and a shortcut will be created at your desktop e To start Snoopy double click the Snoopy s shortcut from your desktop y Snoopy pS Welcome to the Snoopy Setup Wizard E A The installer will guide you through the steps required to install Snoopy on your computer Ga es Figure 5 Snoopy Setup under Windows 4 4 Install SSServer under Windows Similar steps are required to install the SSServer under Windows For your convenience we repeat them in the following procedure e Obtain the windows installer package for SSServer This should be a msi file e Double click the obtained setup package e The windows installer will start as shown in Figure 6 e Follow the simple instructions in this window by hitting the next button e At the end of these steps SSServer should be installed on your computer and a shortcut will be created at your desktop e To start the SSServer double click the SSServer s shortcut from your deskto
10. Setting There are a number of properties that can remotely be adjusted for a simulator using the steering GUI Generally speaking the number and type of these properties will depend on the selected simulation algorithm Please note that your changes of the simulation properties will not take effect until the simulator is restarted Moreover these properties are global settings i e changes related to these settings will affect all other users who are connected to this model To change the simulation settings do the following steps e Hit the setting button in front of the simulator algorithm e A new dialogue will appear as shown in Figure 25 e Change the specific item s you want and press ok e The simulator setting will be sent to the server and they will take effect next time the simulator will start 32 A Simulator Setting Number of Runs Number of Thread 1 H4 Run in a loop M Speed distance ms 200 Figure 25 Simulator setting dialogue 6 5 Steering In this section we discuss one of the distinguished features of the Snoopy steering frame work the ability to steer the simulation while it is running 6 5 1 What Could be Steered Through the Snoopy steering framework you can either change a value of a key parameter or a value of a certain place marking The simulation will not stop during such a change instead it will continue execution from the point of time where the changes have been applied
11. and any necessary re initialisation will be done 6 5 2 Selecting an Item to Steer Before you perform the steering you need to select a subset of the parameters or the places to steer their values during the simulation However you can also do this step during the execution i e you will not need to stop the simulation or to do such a step in advance To select a parameter or a place to steer its value follow this procedure e From the edit parameter place sub window hit the button Select e A new dialogue will open as shown in Figure e Select the parameters places of which you want to steer their values via the buttons in the middle of the dialogue 33 ea select parameters to edit mu lamda Se Figure 26 A dialog to select a parameter to steer e Press Ok button e The selected parameters places will appear on the edit parameter place window as illustrated in Figure 6 5 3 Change a Parameter Place Value There are two methods to change a value of a parameter or a place during the simulation you either increase or decrease the current value by a constant or you can enter a new value directly In the former method you can easily steer the simulation by just one mouse click and your changes will directly be propagated to the running simulation while in the latter one you can enter a value with the precision that you want To increase decrease the current parameter place value by a c
12. do the following steps e Go to the parameter place of which you want to change its value e Enter a new value and hit Enter 6 5 4 Reset a Parameter Place Value Sometimes it is useful to reset the simulation parameter values to the initial ones More over when you restart the simulation it will restart using the current values Therefore we added the option to reset the simulation parameter values or the current marking to the initial values To do such a step hit the reset button from the steering sub window 6 6 Local Settings Using the Steering GUI you are able to change some local settings and your changes will only affect your client during the simulation and the steering To open the local setting 35 window click the setting button from the control button panel A dialogue will appear with some options on it as illustrated in Figure In the following we pinpoint these options 6 6 1 Runtime Statistics Options This set of options control refreshing runtime statistics which include simulation state the simulation speed simulation progress etc The refresh periodically option com pletely enables or disables refreshing the runtime statistics Please note if you disable this option you will not receive any update from the server concerning the current simulation progress and the other statistics The second option is refresh where you can select a period of time after which these runtime statist
13. less powerful com puter The simulation will run at a server machine while the visualization of the results is done at a different machine serving as GUI client e Execute the same model using different simulation algorithms Sometimes it is useful to study a model in different paradigms i e stochastic con tinuous or hybrid In this framework the same model definition can be executed with different simulation algorithms e Manage concurrently different models with possibly different simulators Different models can be simultaneously executed at the server side Each model is assigned a separate simulator and is executed independently from other simulta neously running models Define different result views to explore the simulation results Result views or views for short provide a quick means to explore model results from different perspectives Each view is defined by a set of curves and their associated attributes Different views can be defined for the same model Explore on the fly your running models Using the steering graphical user interface Steering GUI you can easily navigate among different models Besides the list of running models at the server side can be refreshed if another user adds a new model to the server Steer the simulation parameters while the simulation is running The main goal of Snoopy steering framework is to enable users to interact with their models during simulations Users can chan
14. note that you will be asked to stop the server before saving the models into a file 7 4 2 Load the Models To load models from a file select load from the file menu A dialog box will appear where you can select a file to load the models from Please note that saving and loading coloured models might take a long time as the unfolded version of the model is saved to the file 7 5 Log Window The log window is used to display information about the current activity of the server In this section we list some of the operations that can be performed on the log window 7 5 1 Clear the Log You can clear the history of the log window by selecting clear from the log menu 40 spsa SteeringCommunicator spsa SteeringBase spsa SteeringVector spsa ModelView spsa SteeringControl spsa ColoredModel spsa SteeringCMD spsa SteeringClient spsa SteeringServer Figure 30 Inheritance diagram of Snoopy s steering APIs SPSA The Snoopy steering API classes can be classified into four main categories communication data structures control commands and end point components 7 5 2 Save the Log To save the information in the log window select save from the log menu 8 Steering API To keep the computational steering framework simple yet extendible an API library is of paramount importance Modern software permits users to extend existing capabilities by adding new fea
15. of which you want to change its value e pnParamValue the new value of the parameter Return e SUCCESS the change is done successfully e FAILURE there is a problem doing the change Change a Marking value To change a making value at the server side you can call the following function inputs e p_nPlacePosition The position of the place that you want to change e p_nPlaceValue the new value of the place marking Return e SUCCESS the change is done successfully e FAILURE there is a problem doing the change 46 Reset Parameter You can also reset the values of the parameters or the marking to their initial values after making a change resets the current making to the initial ones resets the parameter values to the initial one Return e SUCCESS the reset is done successfully e FAILURE there is a problem doing the reset 8 5 3 Other APIs Besides those few functions which have been discussed in this section the steering API library contains a rich set of APIs that deserve a special document 9 Further Reading Her13 Mostafa Herajy Computational Steering of Multi Scale Biochemical Reac tion Networks PhD thesis Brandenburg University of Technology Cottbus Computer Science Institute 2013 HH12al M Herajy and M Heiner Hybrid representation and simulation of stiff biochemical networks Nonlinear Analysis Hybrid Systems 6 4 942 959 2012 HH12b M Herajy and M Heiner Towar
16. or the next one respectively will be set as the current view Please note that you will not be able to delete a view if there is only one defined for a model 6 2 7 Change Curves Properties Each view contains a number of curves These curves represent places or transitions You can change the attributes associated to each curve e g colour line width and line 23 Edit curve properties Curve color O Curve width 2 req Line ste Sold MM M use default setting Figure 20 Edit curve properties style If you do not want to change these attributes individually and you would like to make a change to all of them then see Section 6 3 3 To change the attributes of a curve do e In the list of the item list box double click the curve of which you want to change lts properties e A dialog will be displayed as in Figure 20 e Change the values of some properties and press Ok e If you want to use the default settings you can check the box use default setting e The curve properties will be changed in the steering GUI 6 2 8 Export a View A view can be exported as a comma separated values CSV or as image format Export to CSV To export the view to a CSV file do the following 24 e Left click the Option button e From the pop up menu select CSV export e From the sub menu you can export either the currently selected items or all of the places transitions e A new dial
17. step is to initialise the library before you can call any of the routines except those which do not require initialisation see Section 8 3 1 You have two options to initialise the Steering API library either using a new model or using an existing one from the server see Section 2 2 Input 1pcModel a pointer to the model data structure see the next section Input p_sExistingModelName the existing model name that you want to use Return e SUCCESS the initialisation is done successfully e FAILURE there is a problem doing the initialisation Please note if you initialise the library using an existing model the library will receive a copy from the server 44 8 3 Dealing with Models The steering API library provides two data structures to facilitate the construction and manipulation of models They are spsa Model and spsa ColoredModel A model is created by creating an object of either of these two classes and fill in the object with the Petri net definition and the metadata Please note after the initialisation there will be a copy of the model inside the library which is used during the initialisation 8 3 1 Receive Model Names To get the currently running model names you can call the following function Return e p_asModelNames a vector of strings containing the model names e SUCCESS the initialisation is done successfully e FAILURE there is a problem doing the initialisation Please note that you
18. the loaded file in Snoopy is used as a default name for the new model You can edit the name as you want under the condition that there is no model running on the SSServer side with the same name After pressing the Ok button the steering dialogue will open as shown in Figure 14 Please note if you use a coloured model then the unfolding window will automat ically appear after step 6 because you need to unfold the model before submitting it to the server To unfold a model press the Start button on the unfolding window as shown in Figure 5 4 Using an Existing Model The Snoopy steering framework gives you the chance to use existing models that are running on the SSServer without opening them in Snoopy For example let us assume that you have one model that is already running in the SSServer and you want to disconnect and return back to it later In this case you do not need to reopen the Snoopy file or even to unfold it if it is a colored model To steer an existing model follow this procedure 1 Open Snoopy and then open the connection window as described in Section 5 2 14 8009 Unfolding Unfold N Write to a file Browse seme M CSP solver Thread count 16 3 hud F Start J 4 Pause Unfolding run time 0 0 sec Close Figure 13 Automatic unfolding window 2 Press the Connect button 3 A new window will appear with the models currently running on the S
19. 0 GB Space LAN adapter X X X X August 20 2013 B Quick Start The quick start material includes everything one needs to know to give the computational steering framework a try Actually its contents is a subset of the complete user manual which aims to give a comprehensive description of all features It has been compiled for the user s convenience to allow for a quick test of the framework without having to read the whole manual 50 Snoopy Computational Steering Framework Quick Start Version 1 0 Mostafa Herajy and Monika Heiner Data Structures and Software Dependability Institute of Computer Science Brandenburg University of Technology Cottbus Germany snoopy informatik tu cottbus de August 20 2013 Please sent all questions comments and suggestions how to improve this material to this address Contents 1 Introduction 2 Overview 2 1 Pramework ta A A A tee FS A ee 2 2 Application Scenanion ur nase ae e ee he 3 System Requirements 3 1 Hardware Requirements osc emsou noketa ee ee 3 2 Software Requirements ee ed i a 4 Installation 4 1 Install Snoopy under MacOSX 2 en 4 2 Install SSServer under MacOSX 2 ee 4 3 Install Snoopy under Windows 0 0000000000004 4 4 Install SSServer under Windows o e 5 Getting Started 5 1 Launching Snoopy and SSServer o o 9 2 Connecting to the Servers u die a re eh 5 2 1
20. 02 57 The server is listening to the service number 3000 In the status bar there are some useful information about the status of the SSServer The first one gives information about the current state of the server For example in Figure 7 the SSServer state is Running Other possible states are stopped and Restarted Make sure before connecting to a server that its state is Running The second information in the status bar is the number of currently running models inside the server Each time you submit a new model this number will increase The third and final information is the number of clients users that are currently connected to the server After you have started the SSServer you need to open Snoopy on your machine Figure 8 gives a screenshot of Snoopy under Mac OS X 11 10 32 5 Notice The server has been Started 10 32 53 Notice Server Name swqlab3 informatik tu cottbus de 141 43 202 57 Service 3000 Running Models 0 Clients 0 Figure 7 Snoopy Steering Server under Mac OS X Hierarchy Welcome j Figure 8 Snoopy under Mac OS X 12 snoopy File M Window Help DOO Toggle Graphelements xo if E Toggle Filebar x1 FP Toggle Hierarchy browser X2 5 Toggle Log window x3l Start Steering Mode F7 Figure 9 Open Snoopy in the steering mode here with no Petri net open A Comnecttotheserver Disconnected Connect Show Details Close
21. 15 epo Unfolding 2 Unfold Olsan Gs C Write to a file Browse M CSP solver Thread count 16 1 C Start VC Pause Unfolding run time 0 0 sec Close Figure 13 Automatic unfolding window 2 Press the Connect button 3 A new window will appear with the models currently running on the SSServer 4 Select one of these models and press ok on The steering dialogue will open with the selected model loaded Please note if there are no running models on the server side then you will be informed and the process of opening the steering GUI will terminate Besides you can do these steps while a Petri net model is opened in Snoopy However you will need to select the option Use an Existing Model After that you can select one of the running models from the list 16 Steering GUI BreabRepalrGHPN sphyond Default view 28 00 5 2520 2240 nzo aso 5 0 Type void TE Mori Stave partio TEN Serting Stopped 1 11 see HybridStaticparttoning 100 E selectdesetect all Resume Refresh Compare with Setting Close Figure 14 The steering GUI 5 5 Replacing an Existing Model When constructing a Petri model for the first time you might need to submit the same model several times with some modifications Such modifications might involve adding new places or new transitions to the model definition In this cas
22. 50 4 8 jo 0 0239483 4 oo 0 00327428 4 10 0 0 00044767 4 u jo 6 12074e 0 4 327 lo 8 36626e 0 4 B 251678 3 00 8 00926 5 16 o 1 095085 7 o 0 149726 5 u o 0 0204716 5 19 0 0 00279901 5 z o 0 0011596 5 w 431 868 6 A 508 315 5 3 1 503 101 6 24 o 68 7847 6 33 o 9 40449 6 2 1 319 084 5 Jar 523 436 4 Type Hybrid T Algorithm Statie partition 15 Setting 9 10 ee Stopped Osec Hybrid Static partitioning 100 Bselect deseiect all Start Stop Restart Pause Resume Refresh Compare with Setting Close Figure 22 Example of tabular viewer Steering GUl PhegaT7StaticPartition sphybrid it Parameter Values Untitled Output start point 0 53 00 Output end point 200 RR Output step size T 42 80 modets PhegaT7StatieP Refresh 37 70 Model Views Main plots Options 32 60 z histogram TE kit 3 E Select an tem to vow teme O struc gt O gen Gere 22 40 E cee tait Pace Values 17 30 12 20 7 10 2 00 2 60 5 98 9 36 12 74 16 12 19 50 22 88 26 26 29 54 33 02 36 40 Values Simulator Type Hybrid E Algorithm Static partition TE Getting i oo LO Select X Reset Stopped O sec Hybrid Static partitioning 100 o E Select deselect all C san Estos Restart Pause Resume Refresh Compare with Setting Close Figure 23 Example of histogram plot table with the first column representing the time and
23. 6 4 General Setting 2 aa 36 37 EMSs 2S a wend eons 38 Sie heh Rede Ge Mi we Ge Ge eee ee See oe ee 38 hve has eee a e ee Der Gef 38 7 1 3 Restart the Server e 38 SETE ws eG ee oe ee a 39 eee Mut Tas de oe ates tk ee ow Br he 39 ii 7 3 1 Service Number oaa a 40 1 3 2 listening IP 2 ses esea k 80 we ee ek re eek 40 ae Goa Atak Eh oe pe OO ae ee E 40 cee ett e bo ke BEDE ee 40 741 Save the Models 2 oraaa noa amea ee 40 7 4 2 Load the Modelsl 2 22 2 22 mon nn 40 Da a Hod eh eG aR Ba A Dane ee me ee G 40 7 5 1 Clear the Log l 2 22 CC Con nn 40 a oie eee ee Ge Ge Gees ee ee 41 8 Steering API 41 Sd Notations u a daa a en 43 8 2 Initialising the Library 222222 oo oo nn 43 8 2 1 Creating a Qlient 2 2 22 CE En 43 8 2 2 Connect to the Server 22222 aa 43 8 2 3 Initialise 222 2 oo onen 44 bof Go ade ee eek ee th ae ee ee og he 45 8 3 1 Receive Model Names 2 2 2 2 nn nn nn 45 DAA A A ee 45 8 5 Monitoring and Steering o 2 2 Cm mn nn nn 45 8 9 1 Monitoring csse 2 28 A Ei as 46 8 9 2 Steering 2 eee oe be a eee Ee 46 8 5 3 Other AP S e 47 9 Further Reading 47 48 48 50 iii 1 Introduction With the advances of computing power and the proliferation of multi core processors it becomes essential to execute long running and computationally expensive simulations at powerful and remote computers which enjoy high spee
24. Brandenburg U University of Technology Cottbus Faculty of Mathematics Natural Sciences and Computer Science Institute of Computer Science COMPUTER SCIENCE REPORTS Report 02 13 July 2013 SNOOPY COMPUTATIONAL STEERING FRAMEWORK USER MANUAL VERSION 1 0 Mostafa Herajy Monika Heiner Computer Science Reports Brandenburg University of Technology Cottbus ISSN 1437 7969 Send requests to BTU Cottbus Institut f r Informatik Postfach 10 13 44 D 03013 Cottbus Mostafa Herajy Monika Heiner snoopy informatik tu cottbus de http dssz informatik tu cottbus de Snoopy Computational Steering Framework User Manual Version 1 0 Computer Science Reports 02 13 July 2013 Brandenburg University of Technology Cottbus Faculty of Mathematics Natural Sciences and Computer Science Institute of Computer Science Computer Science Reports Brandenburg University of Technology Cottbus Institute of Computer Science Head of Institute Prof Dr Ingo Schmitt BTU Cottbus Institut fiir Informatik Postfach 10 13 44 D 03013 Cottbus Research Groups Computer Engineering Computer Network and Communication Systems Data Structures and Software Dependability Database and Information Systems Programming Languages and Compiler Construction Software and Systems Engineering Theoretical Computer Science Graphics Systems Systems Distributed Systems and Operating Systems Internet Technology CR Subject Classification 1998
25. Configuring Connection Settings o o e 5 2 2 Saving Connection Settings 2 2 o oo a 5 3 Submit a New Models ei o we u ok 2 he ee Sos eek a de 5 4 Using an Existing Modele egiie Ee ad aupa E eee 5 5 Replacing an Existing Model aaa naaa aaa 6 Further Reading 17 1 Introduction With the advances of computing power and the proliferation of multi core processors it becomes essential to execute long running and computationally expensive simulations at powerful and remote computers which enjoy high speed computational units to profit from such precious processing resources However such powerful computers do not provide a direct interactive visualisation and analysis of the resulting simulation data due to either the intrinsic patch processing approach of these computers or the m naring of their resources between different users Thus there is a need to remotely mange and analyse the simulation output traces simultaneously while the simulation is in progress Correspondingly many different techniques have been proposed to overcome these limitations Computational steering is among the elegant and promising tools that provide a tight coupling between simulation and visualisation modules of scientific models In this Quick Start manual we briefly discuss the use of Snoopy s computational steering framework to simulate and interactively steer Petri nets e g biochemical net work
26. Default V C Op o gt laa xy plot amp Remove Edit 7 504 Pl Select an item to view P2 CSV Export gt load Image Export 6 004 m m Select Reset Mr Change X axis Edit Place Values Save 4 504 Refresh ee 3 004 1 504 0 0047 T T T T 7 7 T T T T 0 00 10 00 20 00 30 00 40 00 50 00 60 00 70 00 80 00 90 00 100 00 Time Simulator Type Hybrid we Algorithm Static partition y Setting 2597 230 Running 6 27e 04 sec Hybrid Static partitioning 96 oo E Select deselect all Start Stop Restart Pause Resume Refresh Compare with Setting Close Figure 16 Creating a new view contain all the coloured places of the net as default curves If you load an existing Snoopy file then all views which are defined inside this file will be loaded by default 6 2 3 Create a New View You can create as much views as you want There is no limit for the number of views that can be created for a single model unless your computer resources do not allow that To create a new view follow these steps button next to the view list box Go to the Option e Left click the Option in Figure 16 button a pop up menu will be displayed as illustrated Select New from the menu A new dialog will open asking you to enter a name for the new view compare Figure 17 e Give a name to the view and press Ok 20 BOO Input Text Enter view name
27. SServer 4 Select one of these models and press ok 5 The steering dialogue will open with the selected model loaded Please note if there are no running models on the server side then you will be informed and the process of opening the steering GUI will terminate Besides you can do these steps while a Petri net model is opened in Snoopy However you will need to select the option Use an Existing Model After that you can select one of the running models from the list 15 ADS Steering GUI BreakRepairGHPN sphybrid Edit Parameter Values Default view Output start point 0 28 00 0 4 Output end point 100 a 25 20 Output step size 1 250 E Models BreakRepairGH IS Refresh Model Views Default v 19 Options xy plot Wa Edit Select an item to view 22 40 7000 19 60 16 80 14 00 Select Reset 11 20 Edit Place Values load E 10 0 00 10 00 20 00 30 00 40 00 50 00 60 00 70 00 80 00 90 00 100 00 Simulator Type Hybrid E Algorithm Static partitioni Setting er SEE Stopped 1 11 sec _Hybrid Static partitioning 100 E Select deselect all Start Stop Pause Restart Resume Refresh Compare with Setting Close Figure 14 The steering GUI 5 5 Replacing an Existing Model When constructing a Petri model for the first time you might need to submit the same model several times with some mo
28. a view name New views get the view name as title The title field applies to all the viewer types Legend Tab Applies for XY plot and Histogram plot e Show legend Switch on and off the legend e Horizontal position Control the vertical position of a legend Possible values are right centre and left e Vertical position Control the horizontal position of a legend Possible values are top centre and bottom e Sort curves Sort alphabetically the curve names in the legend position Possible values are ascending sort the curve names from A to Z descending sort the curve name from Z to A and not sorted use the order in which the user checks the curves 28 A Result Viewer Properties General Legend Axes Fixed Curves Ok z Cancel A oeaicasiesesmm Figure 24 Adjusting viewer properties Axes Tab Applies to the XY plot and Histogram plot e Show X axis Switch on and off showing the X axis label e X axis label Set the label of the X axis e Show Y axis Switch on and off showing the Y axis label e Y axis label Set the label of the Y axis Fixed Tab Applies to the XY plot and Histogram plot e Fixed X axis adjustment Switch on and off using a fixed interval for the X axis e Fixed Y axis adjustment Switch on and off using a fixed interval for the Y axis 29 e Min X value Set the minimum value of the X axis the default is zero e Max X value Set the maximum value of the X axis the d
29. amples of these information are the name and type of the simulator used to execute the model simulator settings etc 17 6 1 2 Types of Model There are two main types of models when using the Snoopy steering framework e Uncoloured models Uncoloured models are the standard low level Petri nets without additional coloured information They do not require unfolding in order to use them in the steering mode e Coloured models Uncoloured models do not scale easily particularly if we need to define models with repetitive components Therefore coloured models use colours to let a user define bigger models in a concise manner Coloured models however require an automatic unfolding before they can be used in the steering mode 6 1 3 Refreshing the Model List The list of models appearing in the list box are only those which did exist when the steering GUI client was connected to the SSServer These models may change if someone else adds removes a model To refresh the models in the list box hit the refresh button next to the model list box The list of models will be updated 6 1 4 Changing the Current Model To change the current model which is used in the steering GUI and use another one from those running on the server side follow these steps e Go to the model list box on the right side of the steering GUI e Drop down the model box a list of running models will be displayed e Select a model from the list e A m
30. and to what is called TO DO list Later on when the simulator is ready to dispatch this command the command is executed and its effect is displayed to peer users i e collaborating users The steering commands can be altering model parameters altering place marking restarting pausing stopping the simulator etc The reason behind such organisation is that we can not steer the biochemical simulation at any point of execution we have to wait for a suitable time point before the change can take place Furthermore using such an approach the simulator does not need to wait for the user input and accordingly any delay is eliminated due to the incorporation of computational steering into the simulation algorithm The appropriate time point of a change depends on the simulation algorithm i e continuous stochastic or hybrid algorithm For instance appropriate time points to change in continuous simulation are between integration steps of the ordinary differential equations In case of conflicts between different users sending the same steering command to the same running model at about the same simulation time point e g two users want to change model parame ters at time 20 only the latest command will take effect and afterwards other users are informed of the decision In this section we discuss some of the options that are available at the server side 7 1 Starting and Stopping the Server In some situations you will need to stop the
31. ar viewer displays the simulation output using a table Views come along with many advantages to increase the user s experience of us ing the steering framework They provide an easy way of exploring the model results Having several views defined for a model a user can explore the results by just switch ing between these views Additionally views increase the collaboration among users Users at different computers are able to define different views independently from each other After that they can share them by submitting their views to the server Finally views can be defined on the fly while the simulation is running Users do not need to interrupt the simulator to define a new view The currently defined views can be located at the right side of the steering GUI window There you will find a list box that contains your local views i e the user copy of the result views holding any changes before committing the changes to the server 6 2 2 Default View When you run a model for the first time using the Snoopy steering framework a default view will be created This new view will obtain the name Default View and it will 19 800 Steering GUI BreakRepairGHPN sphybrid Edit Parameter Values 15 004 Output start point O i Output end point 13 504 Output step size 12 004 Models BreakRepairGH El Refresh 10 504 Model Views 9 004 f Default V C Op o gt
32. can call this function to get a list of model names before you call Initialize so that you can use one of these names as a parameter to Initialize 8 4 Sending Commands Similar to using the steering GUI to send commands to the server you can use the steering API to call functions which send commands to the SSServer The following is a list of these functions with a brief description e CMD _Start starts the simulation e CMD_Stop stops the simulation e CMD_Restart restarts the simulation e CMD_Pause pauses the simulation e CMD_Resume resumes the simulation 8 5 Monitoring and Steering The monitoring is performed by asking the server to send the result in a matrix form while the steering is performed by asking the server to change some parameter or values In the following we discuss both of them individually 45 8 5 1 Monitoring To read the current simulation results from the SSServer you can call one function which receives the result in the form of a two dimensional 2D matrix Return e p_anResultMatrix a 2D matrix where the rows represent the recorded time points and columns represent the places or transitions e SUCCESS the operation is done successfully e FAILURE there is a problem receiving the result matrix 8 5 2 Steering Change a Parameter value To change a parameter value at the server side you can call the following function inputs e p_nParamPosition The position of the parameter
33. d by the user optional component The communication 4 External simulator optional Users Steering Server Steering Model 1 Change parameters Visualization External PN definition Model Views Result output Simulator 1 Internal Simulator Steering External Visualization Simulator 2 Change parameters Steering Steering Application Programming Interface Steering Application Programming Interface External Visualization Result output Internal Simulator Figure 1 Petri nets and computational steering framework The framework consists of four components steering server steering graphical user interface GUI steering ap plication programming interface Steering API and simulators internal and external The flow of information goes in two opposite directions from the simulator to the user monitoring and from the user to the simulator steering The data structure inside the server is organised in terms of Petri nets places transitions arcs and parameters The place data structure includes the initial marking and the transition data structure the rate functions A model can contain different result views which are defined by the users and submitted to the server for further download and manipulation on Model Definition Communication Simulation use an existing model Figure 2 Graphical illustration of a typical application scenario of Snoopy s steering framewo
34. d computational units to profit from such precious processing resources However such powerful computers do not provide a direct interactive visualisation and analysis of the resulting simulation data due to either the intrinsic patch processing approach of these computers or the sharing of their resources between different users Thus there is a need to remotely manage and analyse the simulation output traces simultaneously while the simulation is still in progress Correspondingly many different techniques have been proposed to overcome these limitations Computational steering is among the elegant and promising tools that provide a tight coupling between simulation and visualisation modules for scientific computational models In this manual we discuss the use of Snoopy s computational steering framework to simulate and interactively steer stochastic continuous hybrid Petri nets e g bio chemical network models There are many important functionalities that are provided by this framework in order to facilitate the conduction of wet lab experiments If you are wondering about what these tools can add to your work flow it might be worth reading the following paragraphs Here are some aspects of what you can do using the Snoopy steering framework e Remotely run and control a simulation You can run your simulation at a remote computer This feature allows the control of high computational power machines from a local typically
35. der Cancel Figure 21 Exporting the view to an image format e Confirm the warning message Please note that this action will overwrite any changes related to this result view on the server side including those that were done by other users 6 2 10 Refresh Model Views If another user makes some changes to the result views e g creating a new view and you would like to use these settings instead of redoing them again you can use the refresh tool To refresh model views do e Left click the Option button e From the pop up menu select Refresh e Confirm the warning message 6 3 Viewers In order to visualise the simulation results you need to select one of the available viewers Viewers are associated with a view That is each view is assigned a viewer to show the simulation output Latter when you change the current view the viewer is changed too 6 3 1 Types of Viewer Currently Snoopy supports three types of viewers tabular see Figure 22 XY plot see Figure 16 and histogram plot see Figure P3 A tabular viewer shows the data in a 26 aca Steering GUI PhegaT7StaticPartition sphybrid dit Parameter Values Bee Output start point 0 temp Struct gen Output end point 200 o 1 o o m 433 820 0 Output step size T O 496 778 2 an 501266 4 Models a o 68 5338 4 Refresh lar le PhegaTzstatiep JE Refresh 6 o 128112 4 Model Views z jo 0 1751
36. difications Such modifications might involve adding new places or new transitions to the model definition In this case submitting the same model with a different name will increase the number of models running on the SSServer A better procedure is to submit the modified model with the same name as the old one In this case the modified model will replace the previous one Please note in order to replace an existing model there should be no other users connected to it If there are other users connected the server will refuse to replace this model and the client will get a notice 6 Steering GUI The ultimate goal of the Steering GUI is to provide the user with a remote control like facility to interact with the currently running models The connection between the steering GUI and the steering server is dynamically established meaning that a connection does not need to be set up in advance before the simulation starts Among the helpful features that Snoopy s steering GUI provides are viewing the models running on a remote server selecting between different simulator algorithms 16 Circadian_rhythmStatic sphybrid repressilator colhybpn Y PhegaT7StaticPartition sphybrid f Figure 15 Model list changing the simulation key parameters and the current Petri net marking providing the user with different views of the simulation results including intermediate and final outputs and remotely changing the simulator properti
37. ds a computational steering and Petri nets framework for the modelling of biochemical reaction networks In proceedings of 21th international Workshop on Concurrency Specification and Program ming CS amp P 2012 volume 21 Humboldt University of Berlin 2012 HHL 12 M Heiner M Herajy F Liu C Rohr and M Schwarick Snoopy a unifying Petri net tool In Proceedings of 33rd International Conference on Application and Theory of Petri Nets and Concurrency volume 7347 pages 398 407 Springer 2012 47 Appendices A Product Sheet The product sheet summarises the most important features of the computational steering framework and the required system resources for its application It has been compiled for the user s convenience to allow for a quick assessment of the framework s potential usability 48 Snoopy Computational Steering Framework Product Sheet http www dssz informatik tu cottbus de Overview The Snoopy steering framework consists of the Snoopy Steering Server SSServer the Steering Graphical User Interface Steering GUI the Steering Application Programming Interface APIs and the internal and external simulators In a typical application scenario a user constructs a model using a Petri net editing tool e g Snoopy Afterwards the Petri net model is submitted to one of the running servers to quantitatively simulate it Later other users can adapt their steering GUIs to connect to this model On
38. e submitting the same model with a different name will increase the number of models running on the SSServer A better procedure is to submit the modified model with the same name as the old one In this case the modified model will replace the previous one Please note in order to replace an existing model there should be no other users connected to it If there are other users connected the server will refuse to replace this model and the client will get a notice 6 Further Reading HH12a M Herajy and M Heiner Hybrid representation and simulation of stiff biochemical networks Nonlinear Analysis Hybrid Systems 6 4 942 959 2012 17 HH12b HH13 HHL 12 M Herajy and M Heiner Towards a computational steering and Petri nets ramework for the modelling of biochemical reaction networks In proceedings of 21th international Workshop on Concurrency Specification and Program ming CSBP 2012 volume 21 Humboldt University of Berlin 2012 M Herajy and M Heiner Snoopy Computational Steering Framework User manual in preparation Brandenburg University of Technology at Cottbus Data Structures and Software Dependability Cottbus Germany 2013 M Heiner M Herajy F Liu Rohr and M Schwarick Snoopy a unifying Petri net tool In proceedings of 33rd International Conference on Application and Theory of Petri Nets and Concurrency volume 7347 pages 398 407 Springer 2012 18
39. e of the connected users initialises the simulation while others could stop pause or restart it When the simulator initially starts it uses the current model settings to run the simulation Later other users can remotely join the running simulation and change on the fly parameters and the current marking Features e Remotely run and control a simulation mn sg aca e Execute the same model using different simulation algorithms e Manage concurrently different models with possibly different simulators e Define different views to explore the simulation results e Explore on the fly your running models e Steer simulation parameters while the simulation is running e Control the simulation speed o MI e Connect to your simulation at any time from whatever place e Collaborate with other people while executing model dynamics mo wm me cs mm 5 Baesa Cun Ge Gan Fause Resume Rarash Compare with Sening Clase e Platform independent implementation Technical Specifications e Client server architecture e Use of colored continuous stochastic and hybrid Petri nets to construct and manipulate models e Comes with full fedged built in simulators System Requirements Snoopy SSServer Requirements Minimal Optimal Minimal Optimal Processor 1 GHz 2 GHz 2 GHz 2 5 GHz or higher RAM 256 M 1GB 512 M gt 8 GB Free Hard Disk 500 M 2 GB 500 M 1
40. ecture is the steering server It is the central manager of the model data and communication traffic between the different framework components It is a multi user multi model multi simulator and multi threaded server Inside the server data is organised in terms of individual models which are defined by means of Petri nets ne steering graphical user interface is the user s entry point to the overall archi tecture Through it the user can monitor and steer the simulation output and the corresponding key parameters respectively Users can flexibly connect and disconnect from their local machines to the available steering servers and view the currently running models Model dynamics are produced using either an internal or an external simulator Internal simulators are implemented inside the server which currently supports deter ministic stochastic and hybrid algorithms while external simulators are defined by the user and dynamically linked to the running server The steering application programming interfaces APIs are used to incorporate ex ternal simulators into the steering server Additional responsibility of the API library is to facilitate the connections between the different framework components More specif ically it is used to carry out the communication between the steering GUI and the steering server Finally this framework permits the simulation to be remotely executed using an external simulator develope
41. efault is one e Min Y value Set the minimum value of the Y axis the default is zero e Max Y value Set the maximum value of the Y axis the default is one Curves Tab Applies to the XY plot e Show lines Switch on off drawing the curves as lines e Show symbols Switch on off drawing the curves as symbols e Line width Set the width of the line curve e Line style Set the style of the line curve Bar Tab Applies to the Histogram plot e Bar width Set the width of each bar e Interval width set the discretisation interval e Frequency Select the type of the histogram Possible values are count or percent age 6 4 Simulators The different properties of the remotely running simulation can also be adjusted from the steering GUI In this section we discuss some common tasks that can be done using the steering GUI 6 4 1 Select a Simulator After loading a model in the steering GUI you might need to select a simulator to execute it The currently running simulator if there is any is displayed at the runtime statistics panel In the steering mode a simulator has a type and a specific algorithm Available simulation types are continuous stochastic and hybrid They represent the broad simulator categories The available algorithms will depend on the selected simulator type For instance the hybrid simulation type has two different algorithms static and dynamic To select a simulator to execute a model do the following ste
42. er X X X X 3 System Requirements In this section we outline the hardware and software requirements to run Snoopy and the Snoopy steering Server SSServer on your computer 3 1 Hardware Requirements The hardware requirements depend on your specific needs For instance if you plan to run big models 100 000 to 1000 000 variables then higher requirements are needed than to run relatively small ones At the time of writing this manual a 64Bit machine preferably running native Linux is recommended for computational expensive models Table 1 outlines the minimum and the optimal hardware required to run the Snoopy steering framework 3 2 Software Requirements The Snoopy steering framework implementation is platform independent Therefore you can use it on your favourite operating system In more specific terms you will need one of the following operating systems running on your computer e Window XP or higher e Mac OS X 10 5 or higher e Linux e g Ubuntu This table is both for 32 and 64 Bit machines 800 0 _ Snoopy ry x 2 items 56 1 MB available lt Oo s rs snoopy Applications Figure 3 Snoopy Setup Next you will need a copy of Snoopy suitable for your operating system which can be downloaded from http www dssz informatik tu cottbus de DSSZ Software Finally a copy of the SSServer is required to run this framework Please note at the time of writing th
43. es Figure 14 provides a screenshot of the steering GUI 6 1 Models Through the steering GUI you can explore the currently running models A model refers to the Petri net definition supplemented by a set of metadata associated with it see the next subsection for a more precise description To view the models currently running on the server side you will find a list box in the right panel of the steering GUI Drop down this box a list of models will be displayed as illustrated in Figure 15 6 1 1 Model Skeleton A model in the Snoopy steering framework is mainly defined in terms of Petri nets More precisely a model can be defined by specifying the following items e Model Definition This includes the Petri net used to define the problem under consideration which in turn is defined by a finite non empty set of places a finite non empty set of transitions and the connections between the places transitions rate functions and initial marking We assume here that the reader is familiar with the use of Petri nets For more information about using Petri nets see e g HH12a from the reading list e Model Views Each model is associated with a set of data structures called result views Views are an elegant and quick means to explore the model s result from different perspectives For more information about defining and using views see Section e Metadata Models contain additional information about how it can be executed A few ex
44. essage box will be displayed asking you if you would like to save your local changes to the server e The model information will be downloaded to your client This might take some time depending on the model size Please note saving your local changes to the server side will overwrite the model settings there and thus they will be available for other users For instance if you 18 defined some result views see next section using your local client and then you opt to save your changes to the server a user B which connects to this model will be able to use your views 6 2 Result Views In this section we discuss a model component called result view or view for short 6 2 1 What Are Views Models could contain multiple views to provide more elaborated ways of understanding the simulation results Result views are defined by the user via the steering GUI They are saved on the server side and can further be downloaded whenever a user opens a model A view is defined by selecting a subset of the model s places or transitions to monitor their values during the simulation Each selected place transition gets assigned a curve inside the view A curve is defined by a set of attributes e g colour style width and so on In Snoopy when a model is executed for the first time a default view is created Besides each view is associated with a viewer The viewer determines how the view s data is displayed For instance a tabul
45. fined for the same model Explore on the fly your running models Using the steering graphical user interface Steering GUI you can easily navigate among different models Besides the list of running models at the server side can be refreshed if another user adds a new model to the server Steer the simulation parameters while the simulation is running The main goal of Snoopy steering framework is to enable users to interact with their models during simulations Users can change model parameters as well as current marking and immediately monitor the system s response for such changes This is an useful tool since a user is allowed to ask what if questions Control the simulation speed The simulation speed can be set to an appropriate level to facilitate the interac tion with a running model during its execution This feature is important if the simulation parameters are allowed to be changed while the simulation is running Connect to your simulation at any time from whatever place The overall organization of this framework is flexible to let users connect disconnect to from running models without affecting their execution Moreover you can con nect to your models from different places for example from your office or from your home Collaborate with other people while executing model dynamics More than one user are permitted to connect to the same models Users can collab orate in executing and steering a r
46. ge model parameters as well as the current marking and immediately monitor the system s response to such changes This is an useful tool since a user is allowed to ask what if questions Control the simulation speed The simulation speed can be set to an appropriate level to facilitate the interac tion with a running model during its execution This feature is important if the simulation parameters are allowed to be changed while the simulation is running Connect to your simulation at any time from whatever place The overall organization of this framework is flexible to let users connect disconnect to from running models without affecting their execution Moreover you can con nect to your models from different places for example from your office or from your home Collaborate with other people while executing model dynamics More than one user is permitted to connect to the same models Users can collab orate in executing and steering a running simulation This feature might promote the sharing of knowledge between different users with different backgrounds Platform independent implementation The core communication library is written in standard C and therefore it can run on different platforms among them are windows Mac OS X and Linux Moreover clients and servers do not need to run under the same platform 2 Overview In this section we give a general overview of the Snoopy steering framework to help
47. ics should be refreshed The default value is to make a refresh each one second 6 6 2 Results Options Similar to the runtime statistics options there are a set of options that control refreshing the results The refresh periodically check box enables or disables refreshing the simulation results Please note that if you disable this option you will not receive an automatic update of the intermediate results You can also control the refresh period of the simulation results by selecting an appropriate value for it Please note this value should be big enough that it does not block the GUI This situation could happen when there is a larger model where the steering GUI spends most of the time doing a refresh Please see the next subsections to learn how you can let the steering GUI automatically control this refreshing time 6 6 3 Timeout The communication between Snoopy and the steering GUI is a synchronous one That is when a user issues a command the GUI will block until the server responses or a certain time period is elapsed The timeout option allows you to control this period of time that the GUI should wait until it unblocks if the server does not response 6 6 4 General Setting Under this category you find some general options to control the execution of the steering GUI One option for instance permits you to let the steering GUI determine the time 36 ANO Setting Runtime statistics M Refresh periodicall
48. ing Snoopy Nevertheless to open the connection window do the following steps in either of these cases 1 From the view window select Start Steering Mode see Figure 9 or just press F7 from the function keys if you prefer using short cut keys 2 The connection window will be opened see Figure 10 After you have opened the connection window you can connect to the sever using the default setting via the connect button This makes sense if you run the SSServer at the same computer as you use Snoopy or if you already configured Snoopy to connect to a certain SSServer However if you run the SSServer on another computer you must first configure the connection before pressing the connect button see Section 5 1 Another important point is that the SSServer and Snoopy should have the same version number of the communication library You cannot let Snoopy connect with an SSServer having a different version A check will be done at the beginning and you will be informed if an incompatible version is detected In this case the Snoopy and SSServer versions are displayed for your convenience 12 BOO Connect to the server Disconnected Connect Hide Details Close Connection Properties Service 3000 E Server localhost E Figure 11 Configuring connection setting 5 2 1 Configuring Connection Settings To configure the connection settings to connect to a certain SSServer do the follo
49. is manual the SSServer is not available at Snoopy s website However it can be requested from the authors by email 4 Installation The specific installation procedure depend on your operating system version Below we give two examples using Windows and Mac OS X 4 1 Install Snoopy under Mac OS X To install Snoopy under Mac OS X first acquire a Snoopy version The Snoopy setup file under Mac OS is in a disk image format dmg All the necessary data are provided in a single file To install this file on your computer do the following steps e Mount the disk image on your computer by double clicking the dmg file e The disk image will appear as another CD in your Finder with the name Snoopy e Opening this disk you will find the Snoopy application bundle as shown in Fig ure B e Copy Snoopy to your desired location or drag and drop it into the application folder AOO L SSServer A 2 items 98 9 MB available 0 P amp Applications SSServer Figure 4 SSServer Setup 4 2 Install SSServer under Mac OS X To install the SSServer to your Mac OSX similar steps as for installing Snoopy are required We repeat them again for your convenience e Mount the disk image on your computer by double clicking the dmg file e The disk image will appear as another CD in your Finder with the name SSServer e Opening this disk you will find the SSServer application bundle as shown in Figure 4 e Copy the
50. le in Figure 7 the SSServer state is Running Other possible states are stopped and Restarted Make sure before connecting to a server that its state is Running The second information in the status bar is the number of currently running models inside the server Each time you submit a new model this number will increase The third and final information is the number of clients users that are currently connected to the server After you have started the SSServer you need to open Snoopy on your machine Figure 8 gives a screenshot of Snoopy under Mac OS X 10 10 32 53 Notice The server has been Started 10 32 53 Notice Server Name swalab3 informatik tu cottbus de 141 43 202 57 Figure 8 Snoopy under Mac OS X 11 snoopy File Window Hel 3 E Toggle Graphelements xo y re Toggle Filebar xi f DAA Toggle Hierarchy browser X2 p Toggle Log window Ad y Start Steering Mode Fr r Figure 9 Open Snoopy in the steering mode here with no Petri net open HOYO Connect to the server Disconnected Connect Show Details C Close Figure 10 Connection window 5 2 Connecting to the Server To connect to a running SSServer using Snoopy you first need to decide if you would like to use a model from those running on the SSServer if there are some or if you would like to submit a new model In the latter case you will need to open your Petri net model us
51. models There are a lot of important functionalities that are provided by this framework in order to facilitate the conduction of wet lab experiments If you are wondering about what these tools can add to your work flow it might be worth reading the following paragraphs The following are some aspects of what you can do using the Snoopy steering frame work e Remotely run and control a simulation You can run your simulation at a remote computer This feature allows the adapta tion of high computational power machines from a local computer The simulation will run at a server machine while the visualization of the results is done at a different machine serving as a GUI client e Execute the same model using different simulation algorithms Sometimes it is useful to study a model in different paradigms i e stochastic con tinuous or hybrid In this framework the same model definition can be executed with different simulation algorithms e Manage concurrently different models with possibly different simulators Different models can be simultaneously executed at the server side Each model is assigned a separate simulator and can be executed independently from other running models Define different views to explore the simulation results Views provide a quick means to explore model results from different perspectives Each view is defined by a set of curves and their associated attributes Different views can be de
52. ogue will open From this dialogue you select a file name and the separators e Click export Depending on your purpose of using the CSV file you can select a suitable separator The separator can be a tabular comma semicolon or colon Export to an image format You can export the current view to a number of image formats e g bmp gif To export the current view to an image file do the following e Left click the Option button From the pop up menu select Image export e A dialogue will open as illustrated in Figure 21 e Select a name for the image file as well as the path e Next to Format select the image format e Hit save Please note exporting a view to a postscript format is currently not available 6 2 9 Save Model Views Having made modifications to the views that are associated to a model you can submit such changes to the server side where other users can further download them or you can use them when you reconnect to the server Saving result views involves saving all the local changes related to them To save views do the following steps e Left click the Option button e From the pop up menu select Save 25 Ters Export file name Save As proteins E Ea e pum Gdemo_pn E Q ntped DEVICES A BFFZ Ly grieg s readm SHARED i dvorak PLACES F Desktop A Applicati jj Documents Format Bitmap bmp IZ New Fol
53. ons we discuss how the API library can be used to interact with the server The routines discussed here can be used to write a GUI client that is compatible with the SSServer or to interact with the SSServer via other clients Please note it is not viable to provide a full documentation for all classes and routines of the steering API library in this manual Therefore we just outline some important functionalities here The full documentation will be provided in a separate file 42 8 1 Notations We adapt the following few coding standards for the use of the steering API library e Namespace the spsa namespace is used to hide the library routines and data types from your program For instance to refer to some constant e g SUCCESS you might need to use it as spsa SUCCESS unless you include this namespace in your file which is not preferred Hereafter we sometimes discard the namespace but this should be clear for you e We redefine data types to facilitate making changes in one place For example spsa Int is the standard int data type e Type long has a known portability problem therefore we define spsa Long to be long long and spsa Ulong to be unsigned long long That is we use a 64 bit long data type on all platforms e We add a prefix to the used name to increase readability This prefix denotes the role of the name and its data type For example p_sHostName means that this name will be used as a parameter hence
54. onstant follow these steps e Go to the parameter place of which you want to change its value e In front of the text box you will find a small spin button e Click on the up down button to increase decrease the value by a constant value 34 ADP Steering GUI BreakRepairGHPN sphybrid lt lt 2800 Output start point 0 ma A Output end point 100 25 20 lamda Output step size 1 22 40 Models BreakRepairGH IP Refresh 19 60 Model Views 16 80 Default v EJ Options xyplot MX Edit 14 00 Select an item to view load Y load 11 20 B m Select Reset Dr Edit Place Values W WK 5 60 0 00 0 00 10 00 20 00 30 00 40 00 50 00 60 00 70 00 80 00 90 00 100 00 Time Simulator Type Hybrid 1 Algorithm Static partitioni la Setting 1 10 10 A Se Stopped 0 312 sec Hybrid Static partitioning 100 Gb E Select deselect all Start Stop Restart Pause Resume Refresh Compare with Setting Close Figure 27 The steering GUI dialogue after selecting some parameters to steer their values e The new value will directly be sent to the steering server without any further actions Please note that the default value for the increase decrease constant is 0 1 however you can change this value from the local setting button To completely enter a new value of a parameter or a place
55. p 5 Getting Started 5 1 Launching Snoopy and SSServer The first step to use Snoopy in the steering mode is to open the Snoopy Steering Server SSServer on your local computer or on another remote machine where you want to run the simulation Second you need to open Snoopy on your machine The exact procedure y Snoopy Steering Server T Welcome to the Snoopy Steering Server Setup Wizard a The installer will guide you through the steps required to install Snoopy Steering Server on your computer Figure 6 SSServer Setup under Windows depends on the operating system you use We assume that you have basic knowledge to run software on your operating system After starting the server it will look as shown in Figure 7Junder the Mac OS X Other platforms might have slightly different but similar interfaces There are two important information you need to notice after starting the SSServer the running server name IP and the listening service number They are written in the log window after the SSServer started successfully You will need these information when connecting to a server using Snoopy For instance in Figure 7 the server name is swqlab3 informatik tu cottbus de and the IP is 141 43 202 57 The server is listening to the service number 3000 In the status bar there are some useful information about the status of the SSServer The first one gives information about the current state of the server For examp
56. ponding key parameters respectively Users can flexibly connect and disconnect from their local machines to the available steering servers and view the currently running models Model dynamics are produced using either an internal or an external simulator Internal simulators are implemented inside the server which currently supports deter ministic stochastic and hybrid algorithms while external simulators are defined by the user and dynamically linked to the running server The steering application programming interfaces APIs are used to incorporate ex ternal simulators into the steering server Additional responsibility of the API library is to facilitate the connections between the different framework components More specif ically it is used to carry out the communication between the steering GUI and the steering server Finally this framework permits the simulation to be remotely executed using an external simulator developed by the user optional component The communication External simulator optional Users Steering Server Steering Model 1 Change parameters External Visualization sigs PN definition Model Views Result output Simulator 1 Internal Simulator Steering Change parameters Model 2 External Simulator 2 Visualizati Isualization Result output PN definition Model Views Internal Simulator Change parameters Steering Application Programming Interface Q E
57. ps 30 e Select a simulator type from the simulator type drop box e Select an algorithm from the list of available algorithms Please note the simulation will not start automatically after selecting a simulator You will need to click the start button see below 6 4 2 Change Simulator Intervals Before starting the simulation you will need to enter the simulation interval The simulation interval tells the simulator from where to start and stop the simulation There are three items which you might need to change about the simulation interval e Output start point This is the point where the simulator should start to record the simulation output The simulation will always start the simulation from time zero However the user might not be interested in the simulation output before a certain time point Therefore you can tell the simulation about your preference The default value for this item is zero e Output end point This is where the simulator will stop recording the output and this also where it will stop the simulation The default value is 100 e Output step size It tells the simulator how often it should record the results 6 4 3 Start the Simulation Now you can start the remote simulation In the lower panel you will find the start button Hit start to begin simulating your model 6 4 4 Refresh the Simulation Result The simulation results as well as the runtime statistics are automatically refreshed du
58. ptimal Hardware Requirements E Snoopy SSServer Requirements Minimal Optimal Minimal Optimal Processor 1 GHz 2 GHz 2 GHz 2 5 GHz or higher RAM 256 M 1GB 512M gt 8GB Free Hard Disk 500 M 2GB 500 M 10 GB Space LAN adapter X X x X 3 System Requirements In this section we outline the hardware and software requirements to run Snoopy and the Snoopy steering Server SSServer on your computer 3 1 Hardware Requirements The hardware requirements depend on your specific needs For instance if you plan to run big models 100 000 to 1000 000 variables then higher requirements are needed than to run relatively small ones At the time of writing this manual a 64Bit machine preferably running native Linux is recommended for computational expensive models Table 1 outlines the minimum and the optimal hardware required to run the Snoopy steering framework 3 2 Software Requirements The Snoopy steering framework implementation is platform independent Therefore you can use it on your favourite operating system In more specific terms you will need one of the following operating systems running on your computer e Window XP or higher e Mac OS X 10 5 or higher e Linux e g Ubuntu This table is both for 32 and 64 Bit machines AOO i Snoopy A 2 items 56 1 MB available Q snoopy Applications Figure 3 Snoopy Setup Next you will need a copy of Snoopy suitable for your operating system
59. ransitions associated with that model while the third one lists the pre places and post places that are associated with the selected transition Hovering the mouse over any of these items will provide you with additional infor mation about it For instance hovering the mouse over the currently selected model will display the number of transitions and the number of places of this model using a tool tip control 7 3 View Server Information There are some information of the running server which can be viewed In this section we list some of them 39 7 3 1 Service Number To view the listening service number port of the server select from the view menu listening port A message box will appear with this information 7 3 2 Listening IP To view the current IP address of the server s machine select from the view menu view IP The IP address will be displayed in a message box 7 3 3 System Information For diagnosis purposes you can view the system information i e the current represen tation of the different data types To do this select system information from the view menu 7 4 Saving and Loading Running Models 7 4 1 Save the Models You can also save the currently running models to an XML file so that you can load them later To save the running models select from the file menu save A dialogue box will appear where you can specify the file name and the path The file extension is sss Please
60. ring the simulation see below However you can trigger a manual refresh when ever you want To manually refresh the simulation results and the runtime statistics hit the refresh button 6 4 5 Other Useful Buttons There are some other buttons which you can use during the simulation They are e Stop stops the simulation 31 e Restart stops the simulation and starts it again e Pause pauses the simulation e Resume resumes the simulation after the user paused it e Setting opens the local setting dialogue e Close closes the steering GUI however the remote simulation will remain running 6 4 6 Adjusting the Simulation Speed During the steering mode you might need to slow down the simulation so that you have the chance to make changes to the running simulator For this purpose you will find a slider bar in front of the simulation algorithm where you will be able to control the running simulation algorithm Many different speed levels are available however you will be able to define the speed interval between two successive speed levels see Changing simulator setting section To change the simulator speed scroll the slider bar to the left or the right The speed of one is the lowest speed level while the speed of ten is the highest speed level Please note that the value that you will change here will affect other users who connect to this model since only one simulator is created for each model 6 4 7 Change the Simulator
61. rk The user has two options at the beginning either reading one of the models already existing in the server or submitting a new model In the latter case the Petri net model can be created using Snoopy or other Petri net editing tools by use of our API library Afterwards Snoopy s steering GUI can be used to perform the monitoring and steering between these external simulation modules and the other architecture components takes place through the steering APIs This means that with modest effort users can include their own favourite simulators and perform the monitoring and steering tasks by help of the other framework components 2 2 Application Scenario In a typical application scenario a user constructs the biochemical reaction network using a Petri net editing tool e g Snoopy Afterwards the stochastic continuous hybrid Petri net model is submitted to one of the running servers to quantitatively simulate it Later other users can connect to this model by their steering GUIs One of the connected users initialises the simulation while other users could stop pause or restart it When the simulator initially starts it uses the current model settings to run the simulation Later other users can remotely join the simulation and change model parameters or the current marking Figure 2 illustrates graphically a typical application scenario of Snoopy s computational steering framework Table 1 Minimal and O
62. server and start it again 7 1 1 Stopping the Server To stop the server i e to release the currently allocated IP and service select from the server menu shutdown The server state will be changed from running to stopped Please note this will not remove the running models or stop the simulation It only closes the listening socket and it will not accept any further connections from the steering GUI clients Besides other connected clients will be disconnected too After this step you can use the IP and the service number by other servers 7 1 2 Starting the Server To start it again select from the server menu start 7 1 3 Restart the Server To make a stop immediately followed by a start select restart from the server menu 38 RAN Running Models Models Transitions Pre places BreakRepairGHPN sphybrig IE repressilator colhybpn repair PhegaT7StaticPartition sph incoming_work outgoing_work Post places Refresh X Close Figure 29 Model explorer window 7 2 Exploring the Running Models At certain situations you might need to view the models currently running inside the server To explore the running models follow these steps e From the view menu select Models explorer e A new dialogue will open as it is illustrated in Figure The new window has three columns The first from left to right column lists the currently running models the second column lists the t
63. teering GUI 6 1 Modelsl 6 2 6 1 1 Model Skeleton 6 1 2 Types of Model 6 1 3 Refreshing the Model List 0 000 6 1 4 Changing the Current Model 2 0004 Result Views 6 2 1 What Are Views 6 2 4 Navigate to a View 12 13 13 13 14 16 6 2 5 Edita View 2 oo oo on 21 sagt cosh Sta a 23 E E ae a 23 be ed tek th ak et ee ee Oe ee 24 6 2 9 Save Model Views o 25 6 2 10 Refresh Model Views 2 oaoa aa o 26 G23 VAG WETS 5 0 04 200 eth eh a eee Mee de de Free 26 6 3 1 Types of Viewer 2 2 02 ee 26 6 3 2 Associate a Viewer toa View 2 2 2 2 2 onen 28 oak be aa a u Ba eB 28 6 4 Simulator 30 6 4 1 Select a Simulator 2 22 22 Comm 30 Dou GA a re ee 31 by ae Garin ee a a ae Ee 31 6 4 4 Refresh the Simulation Result 0 31 6 4 5 Other Useful Buttons 2 0 ee ee 31 6 4 6 Adjusting the Simulation Speedl 2 2 2222 2 22 nn 32 6 4 7 Change the Simulator Setting 2 2 2 2 nn nn nn 32 6 5 Steering sa 2 45 6 oe eee ee Ha ar he as 33 6 5 1 What Could be Steered o o nn 33 ahh E ee ee 33 6 5 3 Change a Parameter Place Value 2222000 34 6 5 4 Reset a Parameter Place Value 35 bgp dacs a e ba do a eo 35 o a a a aS 36 bed e de a ee See le it ale Be ce Ale eh 36 6 6 3 Timeouth si 28 u oe ge Beek ale awe eR ee ee A ee a A 36 6
64. th other framework components In terms of functionality Snoopy s steering API can be grouped into four components communication data structures control commands and end point components The communication part provides an easy to use and portable tool to send and receive data between two connected entities The provided APIs send and receive simple data types e g integer double or character or compound types e g 1D vector or 2D vectors Moreover the API library provides two special data structures to help organising the simulation code inside clients and servers models and model views The former ones are used to encapsulate the Petri net models including all the necessary information about places transitions and arcs rate functions initial marking while the latter data structure facilitates the organisation of result views inside individual models Models can contain multiple views to provide more elaborated ways of understanding the simulation results Please notice that models can be extended to include coloured information as illustrated in Figure 30 Moreover the API library contains a number of control commands The control commands enable the user to start restart stop and pause the simulation They provide a way to manage the remotely running simulation Additionally changing parameter values or asking to refresh the current simulation output is also considered as a steering command In the following subsecti
65. the other columns representing the values of the selected nodes A X Y plot plots the data such that the values of one variable will be in the X axis and the other selected node values will be on the Y axis The X axis represents by default the time However it can be adjusted to represent a place or a transition of the Petri net The final type is the histogram viewer and it shows the simulation results as a histogram where the frequencies of node values are plotted 27 6 3 2 Associate a Viewer to a View The default viewer of a view is the XY plot However you can change it by selecting the one you prefer from the viewers list box Your changes will locally be saved when you navigate to another view 6 3 3 Edit Viewer s Properties When a viewer is selected it loads its properties from the current view These properties can be customised individually for each view The number and type of these properties depend on the viewer type i e tabular XY plot or Histogram To edit the properties of a viewer do the following steps e Next to the viewer list box click edit e A multi tab dialogue will open as illustrated in Figure e The number of tabs and properties will be different from one viewer to another e Adjust the properties and click Ok In the following we list some of these properties and their meanings Title used to give a title to the view This title is rendered on the viewer window A view title can be set differently from
66. the pop up menu select Edit e The select curves dialogue will open as illustrated in Figure e Select the node type place or transition the corresponding list of nodes will be displayed on the left list box available nodes e You can use the buttons on the middle dialogue panel to move nodes from the available list to the selected one e Having selected some nodes hit the Ok button e The selected nodes will be displayed on the item list panel Please note when you change the node type i e place to transition or vice versa the list of selected nodes will be cleared This means that you cannot mix places and transitions Moreover the dialogue in Figure 18 will adapt itself based on the Petri net type coloured uncoloured Therefore if you open the dialogue while a coloured Petri net is loaded then the dialogue will look as in Figure 19 where you will have the option to select either coloured or uncoloured nodes 22 BOO Select curves M Uncolored Nodes p2 4 Place O Transitions ar GED Figure 19 Edit a view of a coloured model 6 2 6 Delete a View To delete a view from the currently defined views do the following e Navigate to the view that you want to delete and select it as the current view e Left click the Option button e Select Remove from the pop up menu e Confirm the warning message e The current view will be deleted and the previous
67. tures or improving existing ones Such extensions could be deployed using e g plug in or API calls For our purpose we adapt the concept of APIs to provide involved functionalities for advanced users The main roles of the API library in our framework are extension of the introduced framework to include additional simulators communication between different framework components and user ability to design a new user interface as well as visualisation modules that are compatible to communicate with other components Figure 30 illustrates the different classes of our implementation of the steering API library While our framework comes with a set of full fledged simulators it is possible for 41 users to have their own simulation code included in the Snoopy framework Snoopy s steering API library renders it possible to convert such batch simulation code into an interactive one Furthermore the API library makes the entire design of the framework easy to be implemented and simultaneously promotes the reuse of existing code For instance the steering server and the steering GUI use the same API library to communicate with each other Additionally users are not confined to use the same user interface which is illustrated in Figure 14 Instead they could implement their own dialogues and use their favourite visualisation libraries The availability of such an API library ensures that the newly designed GUI is compatible to communicate wi
68. understanding the high level organization before going into details 2 1 Framework Figure 1 presents the general architecture of the Snoopy steering framework Its main components are the steering server the steering graphical user interface the steering application programming interface APIs and the internal and external simulators These interdependent ingredients enable users not only to run their biochemical net work models and obtain results but also to share distribute and interactively steer them Additionally users do not need to wait until the simulation ends in order to discover potentially incorrect results Instead using this framework errors could be discovered early and be immediately corrected during the simulation and if necessary the simulation could be restarted using the current setting Subsequently the overall time required to carry out dry lab experiments will substantially decrease The main component of the architecture is the steering server It is the central manager of the model data and communication traffic between the different framework components It is a multi user multi model multi simulator and multi threaded server Inside the server data is organised in terms of individual models which are defined by means of Petri nets The steering graphical user interface is the user s entry point to the overall archi tecture Through it the user can monitor and steer the simulation output and the corres
69. unning simulation This feature might promote the sharing of knowledge between different users with different backgrounds Platform independent implementation The core communication library is written in standard C and therefore it can run on different platforms among them are windows Mac OS X and Linux More over the client and server does not need to run under the same platform 2 Overview In this section we give a general overview of the Snoopy steering framework to help understanding the high level organization before going into details 2 1 Framework Figure 1 presents the general architecture of the Snoopy steering framework Its main components are the steering server the steering graphical user interface the steering application programming interface APIs and the internal and external simulators These interdependent ingredients enable users not only to run their biochemical net work models and obtain results but also to share distribute and interactively steer them Additionally users do not need to wait until the simulation ends in order to discover potentially incorrect results Instead using this framework errors could be discovered early and be immediately corrected during the simulation and if necessary the simulation could be restarted using the current setting Subsequently the overall time required to carry out dry lab experiments will substantially decrease The main component of the archit
70. which can be downloaded from http www dssz informatik tu cottbus de DSSZ Software Snoopy Finally a copy of the SSServer is required to run this framework Please note at the time of writing this manual the SSServer is not available at Snoopy s website However it can be requested from the authors by email 4 Installation The specific installation procedure depend on your operating system version Below we give two examples using Windows and Mac OS X 4 1 Install Snoopy under Mac OS X To install Snoopy under Mac OS X first acquire a Snoopy version The Snoopy setup file under Mac OS is in a disk image format dmg All the necessary data are provided in a single file To install this file on your computer do the following steps e Mount the disk image on your computer by double clicking the dmg file e The disk image will appear as another CD in your Finder with the name Snoopy e Opening this disk you will find the Snoopy application bundle as shown in Fig ure 3 e Copy Snoopy to your desired location or drag and drop it into the application folder Kol Li SsServer x 2 items 98 9 MB available Applications SSServer Figure 4 SSServer Setup 4 2 Install SSServer under Mac OS X To install the SSServer to your Mac OSX similar steps as for installing Snoopy are required We repeat them again for your convenience e Mount the disk image on your computer by double clicking the dmg file
71. wing steps e Press the Show details button from the connection window e New fields appear as illustrated in Figure 11 e In the service text box enter the service number as discussed in Section 5 1 e In the server text box enter the server name or the IP address The default value of the service number is 3000 and the default for the server name is localhost To simplify entering these information you can also select from previous setting using a list 5 2 2 Saving Connection Settings The connection settings which you have entered in the previous step are automatically saved to the Snoopy registry Therefore you do not need to re enter them again when you later want to re connect to the same SSServer 5 3 Submit a New Model To use a new model in the steering mode do the following steps 1 Open the Petri net file in Snoopy 13 SONO Steering Options Send a New Model O Use an Existing Model Model Name Running Models testllspcontped testcolor colcontped Figure 12 The steering options window 2 Open the connection window as discussed in Section 5 2 3 Make sure that you correctly configured the connection settings to connect to a running server 4 Hit the Connect button The steering option window will appear as illustrated in Figure 5 Make sure the send a new model option is selected 6 Enter a model name and then press ok Please note that the name of
72. xt button e At the end of these steps SSServer should be installed on your computer and a shortcut will be created at your desktop e To start the SSServer double click the SSServer s shortcut from your desktop 5 Getting Started 5 1 Launching Snoopy and SSServer The first step to use Snoopy in the steering mode is to open the Snoopy Steering Server SSServer on your local computer or on another remote machine where you want to run the simulation Second you need to open Snoopy on your machine The exact procedure 10 J Snoopy Steering Server Welcome to the Snoopy Steering Server Setup a Wizard la The installer will guide you through the steps required to instal Snoopy Steering Server on your computer Figure 6 SSServer Setup under Windows depends on the operating system you use We assume that you have basic knowledge to run software on your operating system After starting the server it will look as shown in Figure 7 under the Mac OS X Other platforms might have slightly different but similar interfaces There are two important information you need to notice after starting the SSServer the running server name IP and the listening service number They are written in the log window after the SSServer started successfully You will need these information when connecting to a server using Snoopy For instance in Figure 7 the server name is swqlab3 informatik tu cottbus de and the IP is 141 43 2
73. y Refresh qm 1 1 500 Results M Refresh periodically Refresh PH 1 1 500 Timeout Operation Timeout s gm 5 10 500 General Auto adjust the result s refresh time Figure 28 Local setting window needed to refresh the intermediate results 7 Steering Server At the core of the architecture is the steering server To support true collaboration between different users the steering server is designed to be multi user multi threaded multi model and multi simulator The server internally records information about users model specification as well as Petri net definition Moreover the server is shipped with a default set of simulators to permit the simulation of complex biological pathways without any additional components The mlti user feature allows for more than one user to simultaneously share the same model and collaboratively steer the running simulation to get deeper insights of the problem under study Furthermore the multi model and multi threaded features coupled by multi simulator capabilities of Snoopy render the concurrent execution of multiple models and flexible switching between different intermediate results The steering process takes place through an internal scheduler of the steering server Each model has its own scheduler that coordinates the operation of the associated simu lator When a user submits a remote command from the GUI client the current model 37 scheduler adds this comm
74. y use of our API library Afterwards Snoopy s steering GUI can be used to perform the monitoring and steering between these external simulation modules and the other architecture components takes place through the steering APIs This means that with modest effort users can include their own favourite simulators and perform the monitoring and steering tasks by help of the other framework components 2 2 Application Scenario In a typical application scenario a user constructs the biochemical reaction network using a Petri net editing tool e g Snoopy Afterwards the stochastic continuous hybrid Petri net model is submitted to one of the running servers to quantitatively simulate it Later other users can connect to this model by their steering GUIs One of the connected users initialises the simulation while other users could stop pause or restart it When the simulator initially starts it uses the current model settings to run the simulation Later other users can remotely join the simulation and change model parameters or the current marking Figure 2 illustrates graphically a typical application scenario of Snoopy s computational steering framework Table 1 Minimal and Optimal Hardware Requirements Snoopy SSServer Requirements Minimal Optimal Minimal Optimal Processor 1 GHz 2 GHz 2 GHz 2 5 GHz or higher RAM 256 M 1 GB 512 M gt 8 GB Free Hard Disk 500 M 2 GB 500 M 10 GB Space LAN adapt

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