Snoopy Tool Evaluation

nosy Tool evaluationSnoopy is a tool which is used for designing and animating vertical graphs along with others Petri crystallizes. Snoopy in appurtenance provides the facility to construct Petri nets and anyows vitality and computer sensory systeml of the resulting memento flow. This tool is used to verify technical systems specifically softw atomic number 18-based systems and instinctive systems e.g. signal transduction, biochemical ne iirks as metabolic and gene regulatory networks. Snoopy is in use for consideration of the qualitative network structure of a personal mannerl under specific kinetic aspects of the specified Petri net fellowship and investigation of Petri net representatives in several complementary conducts. Simultaneous tradition of different Petri net companyes in Snoopy is hotshot of its outstanding features. some other features arIt is extensible as its generic design acquired immune deficiency syndrome the effectuation of sore Petri net classes.It is adaptive as numerous specimens depose be used simultaneously.It is platform indep revokeent as it is execu hedge on all common operating systems e.g. linux, mac, window acids.Two particular types of bosss i.e. logical nodes and macro nodes argon meant for supporting the systematic construction, neat arrangement and design of large Petri nets. analytical nodes act as connector or multiple used statuss or alterations sharing the identical factor or function. Macro nodes allow hierarchically designing of a Petri net. Snoopy allows edition and coloring of all components in each Petri net class and manual or automatic replace of network layout too. Prevention of syntactical errors in the network structure of a Petri net is quickend by the implementation of the graphical editor.Editor Mode gravel Snoopy and go to File New or press the parvenue hardlyton in the tool bar. It results in opening of a guide dialogue that allows selection of the document template.File New/ present/ conclusion Window/Save/Save as, Print, Export/Import, Preferences (change the default visualization) and Exit.Edit relax/Redo, Select either/Copy/Copy in new net/Paste/Cut, Clear/Clear all, Hide/Unhide, Edit selected constituents/Transform Shapes, Layout (automatic layout function), shield lymph glands (by ID or name), differentiate Net (duplicate nodes, syntax, consistency) and Convert to.View Zoom one hundred%/Zoom In/Zoom Out, Net Information (number of each element used in the amaze), Toogle Graphelements/Hierachy browser/Filebar/Log window, Show Attributes ( discern for each elements which attributes to be shown in the model), Start Anim-Mode/ assumptionMode/Steering-Mode.Elements (list of all available elements) Select/ Place/passing/ Coarse Place/Coarse Transition/ Immediate Transition/ settled Transition/Scheduled Transition/Parameter/Coarse Parameter/LookupTable, butt against/ subscribe to meet/Inhibitor Edge/ readapt Edge/ qualified Edge/Modifier E dge and Comment.Hierarchy (edit and browse hierarchy) Coarse (chosen elements be shut in in a macro node)/Flatten and Go Up in Hierarchy/Go To First Child in Hierarchy/Go To Next blood relative in Hierarchy/o To Previous Sibling in Hierarchy.Search Search nodes (by ID or name).Extra Load node sets (visualize, e.g., T-, P-invariants, siphons and traps), Interaction and General Information (title, author, description, literature).Window (arrange all opened windows) come down/Tile Horizontally/Tile vertically, Arrange Icons/Next/Previous and Open Files.Help Help, About (current version), check update.The tool bar holds four shortcuts that facilitateOpen a new document.Load a document.Save a document.Select an element.All elements accessible in the current net class are displayed in panel for the graph elements. Left-click on one of the elements enables exploiter to use one of these elements. Right click on the several(prenominal)(prenominal) element allows user to edit or sele ct all elements of the same class. All trains are displayed in hierarchy browser and any hierarchical level corporation be opened in a new window by a left-click. The editor pane outhouse be considered as the groundworkvas which allows user to leave the network. A left-click on the Editor pane activates chosen element and places the selected element on the canvas. Click left onto one node, hold the left-click, drag the line to the other node and drop the left-click, to draw an arc among two nodes. To sum up butt ons to an arc push the CRTL underlying and click left on the arc which facilitates the user to drag the edge with a nonher left-click. Grid in the canvas tab can as well be used for a better orientation. User can as well as pick edge styles i.e. line or spline in the resource dialogue in the elements tab.ElementsNodesElementsGraphicsStandard convertStandard revolutionCoarse placeCoarse passageImmediate transition settled transitionScheduled transitionImmediate Transition Immediate transitions molest as presently as they are enabled. The waiting time is constitute to zero.Standard Transition (Timed Transition) A waiting time is computed as soon as the transition is enabled. The transition flack catchers if the timer elapsed zero and the transitions is tacit enabled.Deterministic Transition Deterministic transitions give the bounce as soon as the fixed time interval elapses during the entire mannequin run time. The respective deterministic transitions must be enabled at the end of each restate interval.Scheduled Transition Scheduled transitions fire as soon as the fixed time interval elapsed during the attached time points. The respective deterministic transitions must be enabled at the end of each restate interval.EdgesElementsGraphicsDescriptionStandard edgeThe transition is enabled and may fire if both pre-places and are sufficiently attach by tokens. After fire of the transition, tokens are removed from the pre-places and n ew tokens are produced on post place.Read edgeThe transition is enabled and may fire if both pre-places A and B are sufficiently pronounced by tokens. After freeing of the transition, tokens are removed from the pre-place B but non from pre-place A, new tokens are produced on post place. The attack of the transition does not change the amount of tokens on pre-place A.Inhibitor edgeThe transition is enabled and may fire if pre-place B is sufficiently marked by tokens. The amount of tokens on pre-place A must be little than the given arc weight. After firing of the transition, tokens are removed from the pre-place B but not from pre-place A new tokens are produced on place C. The firing of the transition does not change the amount of tokens on pre-place A.Reset edgeThe transition is enabled and may fire if pre-place B is sufficiently marked by tokens. The amount of tokens on pre-place A has no effect on the ability to enable the transition and affects only the kinetics. After firi ng of the transition, tokens are removed from the pre-place B according the arc weight and all tokens on pre-places A are deleted new tokens are produced on place C.Equal edgeThe transition is enabled and may fire if number of tokens on pre-place A is equal to the corresponding arc weight and place B is sufficiently marked. After firing of the transition, tokens are removed from the pre-place B but not from preplace A new tokens are produced on place C. The firing of the transition does not change the amount of tokens on pre-place A.Modifier edgeThe transition is enabled and may fire if pre-place B is sufficiently marked with tokens. The amount of tokens on pre-place A has no effect on the ability to enable the transition and affects only the kinetics. After firing of the transition, tokens are removed from the pre-place B but not from pre-place A new tokens are produced on place C. The firing of the transition does not change the amount of tokens on pre-place A.FunctionsName marrow of functionBioMassAction(.)Stochastic law of mass action. Tokens are interpretated as sensationmolecules.BioLevelInterpretation(.)Stochastic law of mass action. Tokens are interpretated as concentration.ImmediateFiring(.)Refers to immediate transitions.TimedFiring(.)Refers to deterministic transitions.FixedTimedFiring Single(.)Refers to deterministic transitions that only res once after a given timepointFixedTimedFiring(., ., .)Refers to scheduled transitions.abs(.)Absolute valueacos(.) flicker cosine functionasin(.)Arc sine functionatan(.)Arc tangent functionceil(.)Rounding upcos(.)Cosine functionexp(.)exponential functionsin(.)Sine functionsqrt(.) straight roottan(.)Tangent functionfloor(.)Round offlog(.)Natural log with changeless e as baselog10(.)Common logarithm with constant 10 as basepow(.)ExponentParametersParameters are used for delimit individual parameters and rate or weight functions but are not able to define the number of tokens on a particular place. tierce group of macro elements are coarse parameters which facilitate encapsulating parameters. High meter of parameters are not visible on the top-level or can alike be categorized by the use of coarse parameters.Animation modeSnoopy allows user to observe the token flow in livelihood mode which starts by pressing F5 or issue to View and because start AnimationMode. It will result in opening a new window which allow user to steer the animation. This part of snoopy is precise beneficial to catch a first expression of the causality of a model and its workings as it provides information about the transitions too. In regularize to understand modeled mechanism, playing with the token flow prove to be worthwhile. The token flow can be animated manually by a single click on the transition. A message thump is displayed revealing a message This transition is not enabled when user tries to fire a transition that is not enabled. Clicking-left and clicking-right on a place aids addition of tokens and extraction of tokens respectively. Animation of the token flow can also be controlled by using the radio buttons present on the animation steering panel. Usage of radio buttons involves step-wise forward and backward or sequentially as long as one transition can be enabled, otherwise a notification Dead State There are no more enabled transitions is displayed on screen.Simulation ModePressing F6, going to view/Start Simulation or using the random show button on the animation control panel, are three shipway to perform stochastic simulations with the current model in the active window. Facilities of this mode include simulation of the time-dependent dynamic expression of the model indicated by the token flow or the firing frequency of the transitions. The fluctuating concentration levels or the discrete number of the components over time is indicated by the token flow. This provides an touch of the time-dependent changes in model under consideration which is divine servicef ul in apprehension the wet-lab system. More than a few simulation studies can be performed with considered model by manipulating the structure and perturbing the initial state and kinetics. All results can be manually and automatically exported in the standard *.csv-format and can be analyzed in other mathematical programs.Simulation ControlThe simulation control allows selection of main settings and individualities for the simulation. It splits further into four panelsConfiguration Sets adaption of configuration sets is carried out by edition of single entries or addition of new sets and picking the configuration sets that is suitable for the simulation run.Simulation Properties It includes setting interval start i.e. time point where simulation starts, interval end i.e. time points where simulation ends and output step count i.e. number of time-points that should be displayed in the given interval.Export Properties Various automatic export settings are accessible to the *.csv- format.Start Simulation It will initiate simulation with the selected settings and properties. age of simulation is indicated by the bar and the required time is displayed below.Viewer/Node ChoiceIt facilitates user by providing choices in displaying simulation results. It is divided into two panelsViewer Choice It provides user an option to select one between data tables and data darns. Provided buttons in panel allow user to edit, add and delete the data tables and data plots. Token flow (places) or the firing frequency (transitions) can be displayed in a data table or data plot.Place Choice User can choose those nodes which should be displayed in the data table or data plot. discloseThis panel allows displaying the simulation results as data table or data plot. If data table is selected, the token flow for the selected places is presented in a table. or so options which are used for model checking are present at the poop of the window. If data plot is chosen, the x-axis disp lays the time-interval and the y-axis indicates the average number of tokens. View of the plot can be altered via the buttons located below i.e. reduce/stretch x-axis, compress/stretch y-axis, zoom in/out and centre view. A csv export button allows user to export the simulation results of the selected places manually. Image of the current plot can be saved by using print button. moulding Checking ModeSnoopy is enabled to perform model checking of linear-time properties based on the stochastic simulation. A subset of probabilistic linear-time temporal logic (PLTL) is employed to formulate and certify properties. Various features of snoopy also include checking several features at the same time. In order to perform model checking in Snoopy, user ineluctably to open the simulation window and select the table view. To perform model checking on all simulation traces, user have to enter or institutionalize a property that is checked by simulating the time-dependent dynamic behavior. S imulation window allows following optionsEnter State Property User can specify a property in the dialogue box and no model checking is performed if it is empty.Load state property User can load a property which is defined in a text file.Check state property It refers to model checking which is performed on the basis of average behavior of the previous simulation.Simulation run count is of assistance to state a number of simulation traces to which model checking can be applied. It splits into two types negligence value 1 run User is only able to issue forth the information if the defined property holds true or is not false. imperative number of runs The number of simulation runs supports defining probability of the defined properties as high accuracy calls for high number of simulation runs.User can set the time interval where model checking should be applied with the help of interval start and interval end.A log window displays model checking results that includes following element sFormula displays the formula checked during simulation.Runs indicate the number of simulation runs performed.Runtime shows the number of wander used for simulation.Threads display the number of threads used for simulation.Prop indicate the computed probability for the formula.S 2 displays the partitioning of the probability.Confidence Interval indicates the size of the confidence interval.a,b reveals the interval of the probability that is calculate from the confidence interval