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Getting Started with Kepler guide

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1. Workflows also provide the following documentation of all aspects of an analysis visual representation of analytical steps ability to work across multiple systems reproducibility of a given project with little effort reuse of part or all of a workflow in a different project To date most scientific workflows have involved a variety of software programs and sophisticated programming languages Traditionally scientists have used STELLA or Simulink to model systems graphically and R or MATLAB to perform statistical analyses Some users perform calculations in Excel which is user friendly but offers no record of what steps have been executed Kepler combines the advantages of all of these programs permitting users to model analyze and display data in one easy to use interface l See Lud scher B I Altintas C Berkley D Higgins E Jaeger Frank M Jones E Lee J Tao Y Zhao 2005 Scientific Workflow Management and the Kepler System DOI 10 1002 cpe 994 Kepler builds upon the open source Ptolemy II visual modeling system http ptolemy eecs berkeley edu ptolemyl creating a single work environment for scientists The result is a user friendly program that allows scientists to create their own scientific workflows without having to integrate several different software programs or enlist the assistance of computer programmers A number of ready to use components come standard with Kepler including generic mathematica
2. K Variance File Tools Help 9 1666666666667 Figure 23 The Simple Statistics workflow and its output The right hand windows in Figure 23 display the mean variance and standard deviation of the data set created by the array of values in the Constant actor Change the input array of the Constant actor for example try 1 17 6 4 12 to calculate a new set of corresponding statistics 7 2 Sample Workflow 2 Linear Regression Name Simple Linear Regression workflow using R File name 05 LinearRegression xml Detailed This workflow performs a simple linear regression analysis using the Description RExpression actor The workflow creates a scatter plot of the two variables from the Datos Meteorologicos data set and adds a regression line using the Y a bX equation where X is the explanatory variable and Y is the dependent variable The slope of the line is b and a is the intercept the value of y when x 0 Assumptions A linear regression assumes linearity independence homoscedasticity and normality R must be installed on the system running the workflow R ann is included with the full Kepler installation for Windows and Macintosh Datos Meteorologicos Datos Meteorologicos RExpression Display ImageJ 36 Parameters Datos Meteorologicos Data Output Format As Column Vector SDF Director iterations l RExpression R function or script res lt 1m BARO iT ATR res plot T_ AIR BARO
3. OAN Remove Customization Suggest D Thes is a Ai based actor R requres Ine folowing imic Wgarp so widows gap di ibapsi di Semantic Type Annotation MacOGX currenty not avatatie tor the Mac 2 16 2005 Save Archive KAR Upload to Repository View iS Parameters Preview Appearance ASAF ienne Parameter Tris it the tie tame ot te The containing tne Reset data tis uousby te tpt cf a GarpAlgorine actor a fayersetPiionameParanwetes Trin is the tie name of the chd fe used to summarize the cet of mpated Gate Mex with erronmerta data tor anch pecel Outs SCWParameter This it the fie name to be used tor the output ASCE gored the OWDUEMPParaoreter Trin is the fie mame to be used ior the output BNP raster fhe Input Ports reteSatFiename Thee s the fie name of Ov fhe Cortarsng the PiseSet data iis unushy he Olgas of a GarpAigorines actor tayersetF ionene This is the the name ot tye thd Me used to summarize the set OF apatut data thes with ervtonmerts data tor esch peed a Thit it thet fy mame to be upd toe hur aipat ASCE grat fhe 4 inai peat tad eee aseti Batter Chad Barclay Dan Hager MOEA UC Corta Berbers Figure 35 Actor documentation 51
4. The Mac installer will install the Kepler application on your system Java is included as part of the Mac OS X operating system so it does not need to be installed Kepler has many actors that utilize R so installing R is recommended http www r project org Follow these steps to download and install Kepler for Macintosh systems 1 Click the following link https kepler project org users downloads and select the Mac install file 2 Save the install file to your computer 3 Double click the install icon that appears on your desktop when the extraction is complete 4 Follow the steps presented in the install wizard to complete the Kepler installation process A Kepler icon is created under Applications Kepler x y 2 4 Installing on Linux Java 1 6 or greater is required in order to run Kepler Kepler has many actors that utilize R so installing R is recommended http www r project org Follow these steps to download and install Kepler for Linux 1 Click the following link https kepler project org users downloads and select the Linux tar gz file 2 Save the tar gz file to your computer 3 Change to the directory where you want Kepler installed and untar the tar gz file 3 Starting Kepler To start Kepler follow the instructions for your platform 3 1 Windows and Macintosh Platforms To start Kepler on a PC double click the Kepler shortcut icon on the desktop Figure 2 Kepler can also be s
5. This model shows the solution to the classic Lotka Volterra predator prey dynamics model It uses the Continuous Time domain to solve two coupled differential equations one that models the predator population and one that models the prey population The results are plotted as they are calculated showing both population change and a phase diagram of the dynamics Rich Williams 2003 NCEAS var Figure 8 The Lotka Volterra workflow in the Kepler interface 6 2 Running an Existing Scientific Workflow To run any existing scientific workflow 1 Open the desired workflow 2 From the Toolbar select the Run button gt The workflow will execute and produce the specified output ww OR 1 Open the desired workflow 18 2 From the Menu bar select Workflow then Runtime Window A Run window will appear Figure 9 If the workflow has parameters they will appear here Adjust the parameters as needed and then click the Go button 4 The workflow will execute and produce the specified output During workflow execution you may select the Pause Resume or Stop buttons ww K file C kepler 1 0 0beta3 demos gett arted 02 LotkaVolterraPredatorPrey xml Joe Eile view Workflow Tools Window Help BRAE jew Gi P Ri St XYPlotter Pause Resume Stop t F Model parameters 40 r 2 35 a 0 1 b 0 1 30 d 0 1 25 Director parameters 20 timeResolution 1E
6. e g display Figure 4 Representation of a nested workflow Kepler provides a large set of actors for creating and editing scientific workflows Actors can be added to Kepler for an individual s exclusive use and or can be made available to others 4 2 Ports Each actor in a workflow can contain one or more ports used to consume or produce data and communicate with other actors in the workflow Actors are connected in a workflow via their ports The link that represents data flow between one actor port and another actor port is called a channel Ports are categorized into three types e input port for data consumed by the actor e output port for data produced by the actor and e input output port for data both consumed and produced by the actor Each port is configured to be either a singular or multiple port A single input port can be connected to only a single channel whereas a multiple input port can be connected 10 to multiple channels Single ports are designated with a dark triangle multiple ports use a hollow triangle Workflows can also use external ports and port parameters See the Ptolemy documentation for more information 4 3 Relations Relations allow users to branch a data flow Branched data can be sent to multiple places in the workflow For example a scientist might wish to direct the output of an operational actor to another operational actor for further processing an
7. 10 15 startTime 0 0 10 stopTime 1000 initStepSize 0 1 4 4 1 4 4 4 L 4 4 l minStepSize 1e 5 0 1 2 3 4 5 6 7 8 g 10 maxStepSize 1 0 TimedPlotter BRAE maxlIterations 20 T T T T T T T T T errorTolerance 1e 6 40 4 yalueResolution 1e 8 35 4 synchronizeToRealTime 30 4 ODESalver FExplicitRK4550lver Iv 35 J breakpointODESolyer PpapivativeResolver rundheadLength 0 1 20 class ptolemy domains ct kernel CTMixedSignalDirector 15 A semanticType000 urn lsid localhost onto 1 1 Director 10 5 0 i i i i i i i i i i 1 0 0 0 1 0 2 0 3 0 4 0 5 0 6 0 7 0 8 0 9 1 0 x10 Figure 9 The Runtime window displaying the Lotka Volterra workflow Click the Go button to run the workflow Director and model parameters can be edited in the Runtime window Output is displayed in the window as well 6 2 1 Example 2 Running the Lotka Volterra Workflow with Default Parameters The Lotka Volterra model uses the continuous time domain i e a CT Director in Kepler to solve two coupled differential equations one that models the predator population and one that models the prey population The results are plotted as they are calculated showing both populations change and a phase diagram For more information about the model see Section 6 2 2 To run the Lotka Volterra workflow 1 Open the workflow file named 02 LotkaVolterraPredatorPrey from the getting started directory 2 From the Menu bar select Run
8. 19 3 The Lotka Volterra workflow will execute with the default parameters and produce two graphs The graph labeled TimedPlotter depicts the interaction of predator and prey over time i e the cyclical changes of the predator and prey populations over time predicted by the model The graph labeled XYPlotter depicts a phase portrait of the population cycle i e the predator population against the prey population Together these graphs show how the predator and prey populations are linked as prey increases the number of predators increase Figure 10 Ki 02 LotkaVolterraPredatorPrey TimedPlotter BAX File Tools Special Help a TimedPlotter ERME T T T T T T T 35 Lo ao a fo w oF a So a oS BRAE x10 XYPlotter T T T 0 1 2 3 4 5 6 7 8 g 10 Figure 10 Graphs output by the Lotka Volterra workflow 6 2 2 Example 3 Running the Lotka Volterra Workflow with Adjusted Parameters To better illustrate the effect of parameters on a workflow we must first provide some background about the Lotka Volterra workflow Figure 11 20 CT Director TimedPlotter dn b nl nd Integrate n2 Figure 11 Graphic of Lotka Volterra workflow The Lotka Volterra model was developed independently by Lotka 1925 and Volterra 1926 and is made up of two differential equations One describes how the prey population changes dn1 dt r n1 a n1 n2 and the second equation describes how
9. Name Description Molecular Molecular Processing actors are indicated Processing by a molecule icon in the upper left corner Other External Other External Program actors are Program indicated by a purple rectangle External Program actors include R SAS and MATLAB actors The icon displayed here is an R icon String actors are indicated with the text String string String actors are used to string manipulate strings in a variety of ways Utility Utility actors are indicated with a wrench Utility actors help manage and tune a particular aspect of an application Web Services Web Services actors are indicated by a wireframe globe Actors in this family execute remote services Units Unit components define a system of units i 2 A P Table 2 The major Kepler icons 5 4 The Workflow Canvas Scientific workflows are opened created and modified on the Workflow canvas Components are dragged and dropped from the Component Data Access and Outline area to the desired canvas location Each component is represented by an icon see Section 5 3 for examples which makes identifying the components simple Connections between the components i e channels are also represented visually so that the flow of data and processing is clear Each time you open an existing workflow or create a new workflow a new application window opens Multiple windows allow you to work on several workflows sim
10. abline res The above R script tells the RExpression actor to read the Barometric Pressure and Air Temperature data and then plot the values along with a regression line Click Commit to save your changes 14 Find the text Display actor to the Workflow canvas The Display actor is located under Components gt Data Output gt Workflow Output gt Textual Output 15 Connect the lower output port of the RExpression actor to the input port of the Display actor 16 Drag and drop the JmageJ actor to the Workflow canvas The mageJ actor is located under Components gt Data Output gt Workflow Output gt Graphical Output Connect the upper output port of the RExpression actor to the input port of the ImageJ actor You are now ready to run the workflow The resulting workflow and graphic output are shown below Figure 28 40 SDF 0 Datos Meteorologicos R_linear_regression r 2 1152049686328 jpe 480x480 pixeis S Di 225K K 05 LinearRegression Display File Took Help p setwd C ct s 5 gs Kirsten P Jpeg tfile er l 23 3pg width 480 height 480 poinrsize gt T_AIR lt c 15 0 1 42 7 21 4 13 5 t gt BARO lt 959 4 953 8 954 0 954 3 954 5 954 7 954 8 954 6 954 9 95 gt res lt lm BARO T_AIR gt tes rail Je formula BARD T_AIR fCoeffacients 5 intercept T_AIR 958 3772 0 3244 b plot T_AIR BARO i gt ablineires Figure
11. abline res RExpression input ports T AIR and BARO The Simple Linear Regression workflow runs a search for data on the EarthGrid These data are used to create a workflow conducting a linear regression In this example the input data comes from two output ports the data columns on Barometric Pressure and Air Temperature of the Datos Meteorologicos actor a data set of meteorological data collected in 2001 from the La Hechicera station The Linear Regression workflow uses four actors the Datos Meteorologicos actor the RExpression actor the ImageJ actor and the Display actor and the SDF Director The RExpression actor inserts R commands and scripts into the workflow The RExpression actor makes integrating the powerful data manipulation and statistical functions of R into workflows easy To implement the RExpression actor R must be installed on the computer running the Kepler application NOTE If you have problems creating this workflow a stored version comes with Kepler in the getting started directory named 05LinearRegression xml To create the Simple Linear Regression workflow 1 Select the Data tab in the Components and Data Access area 2 Click the Sources button and limit the scope of the search by unchecking KU Query Interface and KNB Metacat Authenticated Query Interface Because Datos Meteorologicos is stored on the KNB Metacat the data source for the search can be limited to just tho
12. actor To connect the ports left click and hold on the output port black triangle on the right side of the Image Converter actor drag the pointer to the upper input port on the left side of the Browser Display actor and then release the mouse If the connection is made you will see a thick black line If the connection is not made the line will be thin Run the workflow From the Menu bar select File then Save or Export to save the workflow to a KAR or MoML file as desired 26 SDF Director Image Filename Image Converter Browser Display Figure 15 The Image Display workflow with the Browser Display actor substituted for the ImageJ actor NOTE Sometimes the easiest way to connect actors is to go from the output port of the source to the input port of the destination 6 4 Searching in Kepler Kepler provides searching mechanisms to locate data on the EarthGrid and analytical processing components on the local system or both the local system and a remote component repository The examples given in this section describe searching for data and components in Kepler 6 4 1 Searching for Available Data Via its search capabilities Kepler provides access to data from the EarthGrid EarthGrid resources are stored in the KNB Metacat http knb ecoinformatics org database To search for data on the EarthGrid through Kepler 1 Inthe Components Data Access and Outline area select the Data tab Figure 16 2 Type
13. save your own executable workflows The general steps in creating a workflow are as follows Create a conceptual paper or other medium model of your scientific workflow Open the Kepler application Map the data and actor components available in Kepler to your conceptual model Select a director for your workflow and drag it to the Workflow canvas For more information about choosing a director please see Chapter 5 of the Kepler User Manual 5 Drag the desired workflow components to the Workflow canvas 6 Connect the workflow components 7 Save the workflow a A The examples in this section illustrate how to begin to create your own workflows The first example is the classic Hello World workflow that demonstrates how easy it is to create a functioning workflow in Kepler The second example is more practical and shows how to use your desktop data in a workflow 6 5 1 Example 5 Creating a Hello World Workflow To create the Hello World workflow begin by thinking about the type of data used e g text or string data the type of output desired e g textual or image display and the type of director needed to execute this model e g synchronous or parallel The Hello World workflow requires a constant actor a text display actor and an SDF director The SDF director executes actors based on their order in the workflow and each actor will only execute once 1 Open Kepler A blank Workflow canvas w
14. the predator population changes dn2 dt d n2 b n1 n2 The Lotka Volterra model is based on certain assumptions the prey has unlimited resources the prey s only threat is the predator the predator is a specialist i e the predator s only food supply is the prey and the predator s growth depends on the prey it catches The Lotka Volterra model as represented in Kepler as a scientific workflow contains e six actors two plotters two equations and two integral functions e one director and Lotka Alfred J 1925 Elements of physical biology Baltimore Williams amp Williams Co gt Volterra Vito 1926 Fluctuations in the abundance of a species considered mathematically Nature 118 558 560 21 e four workflow parameters Table 3 NOTE The director of the Lotka_ Volterra model has several configurable parameters as do the two plotter actors The critical assumptions above provide the basis for the workflow parameters The workflow parameters and their defaults are as follows Parameter Default Description Value r 2 The intrinsic rate of growth of prey in the absence of predation a 0 1 Capture efficiency of a predator or death rate of prey due to predation b 0 1 Proportion of consumed prey biomass converted into predator biomass i e efficiency of turning prey into new predators d 0 1 Death rate of the predator Table 3 Description of the default parameters for the Lotka Volterra wo
15. workflow visually so that it is easy to understand how data flow from one component to another The resulting workflow emailed to colleagues and or published for sharing with colleagues worldwide Kepler users with little background in computer science can create workflows with standard components or modify existing workflows to suit their needs Quantitative analysts can use the visual interface to create and share R and other statistical analyses Users need not know how to program in R in order to take advantage of its powerful analytical features pre programmed Kepler components can simply be dragged into a visually represented workflow Even advanced users will find that Kepler offers many advantages particularly when it comes to presenting complex programs and analyses in a comprehensible and easily shared way Kepler includes distributed computing technologies that allow scientists to share their data and workflows with other scientists and to use data and analytical workflows from others around the world Kepler also provides access to a continually expanding geographically distributed set of data repositories computing resources and workflow libraries e g ecological data from field stations specimen data from museum collections data from the geosciences etc 1 2 What are Scientific Workflows Scientific workflows are a flexible tool for accessing scientific data streaming sensor data medical and satellite images simulati
16. 28 Linear Regression workflow and its output The left hand window in Figure 28 displays the scatter plot of Barometric pressure to Air Temperature along with a regression line The graph shows a strong negative relationship between the two as air temperature lowers the Barometric pressure rises The right hand window displays the Barometric Pressure and Air Temperature data used in the scatter plot Additionally the intercept on the Y axis 958 38 Barometric Pressure and the slope 0 32 for the linear regression equation y mx b is displayed You can change the data type and the data set that is run through the workflow When changing the data remember to make sure that the data meets the assumptions mentioned in workflow table at the beginning of Section 7 2 7 3 Sample Workflow 3 Web Services Name WebService workflow File name 06 WebService xml Detailed This workflow demonstrates the use of the remote Description genomics data service to retrieve gene ID from its gene name Assumptions The WSWithComplexTypes actor assumes that the target 41 Web service is RPC based and uses primitive XML types and arrays Director SDF Director Data The data consists of an initial input gene accession number that is specified by the String Constant actor and an intermediate input retrieved from the remote genomics data service Actors String Constant WSWithComplexTypes Display Para
17. 7a 38c 37g ORIGIN 1 cacctggaga aa 61 caagtgattt aatttcagct gatto 121 tttggnatct ggagacagga ga S H lt SEQUENCE gt 09 XMLDataTransformation HTML Display BASE COUNT 47a 38c 37 ORIGIN 1 cacctggaga az 61 caagtgattt aatttcagct gatt 121 tttggnatct ggagacagga s I ii lt li gt lt ul gt lt body gt lt html gt x z eoo 09 XMLDataTransformation XML Entry Display BASE COUNT 47a 38c ORIGIN 37 1 cacctggaga a 61 caagtgattt aatttcagct gatti 121 tttggnatct ggagacagga g lt SEQUENCE gt lt DDBJXML gt O a execution finished NOTE To add an annotation to your workflow drag and drop the Annotation actor onto the Workflow canvas Double click the default text Double click to edit to customize the annotation 7 5 Sample Workflow 5 Figure 32 The results of the XML Data Transformation Workflow Workflow SDF Director Using Data Transformation Actors XML Entry Display Sequence Getter Using XPath Sequence Display HTML Generator Using XSLT HTML Display This workflow demonstrates the use of the data tranformation actors to process a genetic sequence The sequence is displayed in three different ways first in its native format XML second as a sequence element that has been extracted from the XML format and third as an HTML document that might be used for display on a web site Both of the latter two operations are performed using a composite actor that
18. Actor HE Customize Name Configure Ports Configure Units Open Actor BL Customize Listen to Actor Auer _ Remove Customization Suggest Semantic Type Annotation Save Archive KAR Upload to Repository View LSID Preview Appearance Figure 13 Displaying actor documentation To edit an existing scientific workflow aS Open the desired workflow Identify which workflow component is the target for substitution Select the target component data actor or processing actor by clicking it The selected component will be highlighted in a thick yellow border Press the Delete key on your keyboard The highlighted component will disappear from the Workflow canvas From the Components Data Access and Outline area drag either an appropriate data or processing actor to the Workflow canvas Connect the appropriate input and output ports Run the workflow From the Menu bar select File then Save or Export to save the workflow as desired to a KAR or MoML file as desired 6 3 1 Example 4 Editing Substituting Analytical Processes in the Image J Workflow In this example we will show how two different actors can perform the same function in a workflow We will work with the Image Display workflow 03 ImageDisplay xml found in the getting started directory and we will substitute the Browser Display actor for the ImageJ actor Both actors will display a bitmapped image representing the specie
19. Bob Note that the surrounding quotation marks around the entire value are required to indicate that it is a string Click the Commit button Search for Parameter in the Component library and then drag and drop a workflow Parameter to the Workflow canvas Right click the parameter and select Customize Name from the drop down menu Name the parameter WorkingDir and click Commit Double click the parameter to set its value to the parameter to 48 property outreach workflowdir demos getting started 1 e the location of the working directory 5 Drag and drop an ExternalExecution actor onto the Workflow canvas Double click the icon and set the value of the directory parameter to SWorkingDir i e the value of the WorkingDir parameter set on the Workflow canvas Figure 33 Edit parameters for External Execution 2 finau NONE command j directory WorkingDir Browse environment name m value i prependPlatformDependentShellCommand go throwExceptionOnNonZeroReturn waitForProcess class ptolemy actor lib Exec semanticTypedd urn sid localhostonto 1 1 ExternalExecutionEnvironmentActor semanticlypel1 urnilsid localhost anta 2 1 UnieCommand Figure 33 Set the directory parameter of the ExternalExecution actor for use with this workflow 6 Connect the output port of the CommandLine actor to the command input port of the ExternalExecution actor 7 Drag and drop a
20. Display actor onto the Workflow canvas and connect its input port to the ExternalExecution actor s output port 8 You are now ready to run the workflow The workflow and its default output are displayed in Figure 34 49 ADO 07 CommandLine_1 Display Hello Kepler_User SDF Director e WorkingDir property outreach workflowdir demos getting started CommandLine tb java cp HelloWorld Kepler_User External Execution Display Figure 34 The Command Line workflow and its default output 8 Appendix 8 1 Ptolemy II The Foundation of Kepler Ptolemy II is a software framework for heterogeneous concurrent modeling and design with a Java based component assembly framework using a graphical interface called Vergil The Ptolemy II software is a product of the Ptolemy project at the University of California at Berkeley a project whose goal is the use of well defined models of computation that govern the interactions between components As explained at the project s website Ptolemy II includes a number of domains each of which realizes a model of computation It also includes a component library and a number of support packages such as graphing mathematics plot and data packages For more information about Ptolemy II see http ptolemy eecs berkeley edu index html Although not originally intended for scientific workflows Ptolemy II provides support for dataflow oriented models which is a very im
21. Ke lers pes Getting Started with Kepler The Getting Started with Kepler guide is a tutorial style manual for scientists who want to create and execute scientific workflows Table of Contents le AGE OGM CTION i 5 ccausihesawaapaceniaianesundasestiiauxs anidasas A E E AAE 2 tl What is Kepler reesei vaste Peaststeadencqnsa bee eriw in ec ce rain nto abnmetnceneGetne 2 1 2 What are Scientific Workflows ess ccsssseagisnesisnctieddsnacuexdeaceuedinnbenteianncesdinmecuseevasevies 4 2 Downloading and Installing Kepler cece ccccceseceeeceeecessceceneceseeeeeeeeaeecsaecneeeeeeenaaes 5 2 1 System Requirements asec co nacetes dv teciecue esas ecntancnnwansausuaseasueewetncernanneconameracanesstacens 5 2 2 T stalling on W MAG WS shocccsieentecaivatentouaiadaceudinestian nese ehianesniacenaeaxneeNeaneiaceies 6 2 3 Installing on Macintosh ccccasssacasdesvcceadivnccanszsosespissducssdadsecunsisdccanssion qusticdesisteeuubias 6 24 Installing on LINUX pers esers cts Ssvsaniceus aden enpasnues asie a EEE A a iah 7 3 Starting CP Si sssecnsere aaien n R TERTE T 3 1 Windows and Macintosh Platforms 0 ccccccccsscccesssssececsessececsesseeeceesssseeeessaaes 7 32 Linux Platform esien EEE EER E E REENE EAEE E 7 A Basic Components in Ke Qler ioisasssccanssancasnacatccandinaceiiabasavsananieace biadeciusstadiossndessintecandss 8 4 1 Director and AGIOS sancassancsceviucsacenssscatasinseacesdaventensndsaianteatacancniearesaaneeesscucaveisa
22. Time 300 ool initStepSize 0 1 a A 4 4 4 4 4 l i minStepSize les 0 5 1 0 1 5 2 0 2 6 3 0 3 5 40 4 6 mexsproee 1 0 Pi TimedPlotter BERAE maxlterations 20 T T T T errorTolerance te 6 4 0 yalueResolution 1e 8 ZS synchronizeToRealTime 30t ODESolver ExplicitRk455olver lv ost J breakpointODESolver DerivativeResolver rundheadLength 0 1 2 07 i class ptolemy domains ct kernel CTMixedSignalDirector 5r 7 semanticType000 urn lsid localhost onto 1 1 Director 1 0 4 EJE 00L L 4 4 4 0 0 0 5 1 0 15 2 0 25 3 0 x0 execution finished o o Figure 12 Graphs output by the Lotka Volterra model with adjusted parameters 6 3 Editing an Existing Scientific Workflow There are two ways to edit an existing scientific workflow e Substitute a different data set for the current data set or e Substitute one or more analytical processes in the workflow with other analytical processes e g substitute a neural network model actor for a probabilistic model actor Before substituting data or processes you must understand the required inputs and outputs of the actors involved NOTE To see a high level description of an actor right click that actor to display a menu select Documentation then Display Figure 13 A dialog box containing a description of the main function of the actor and its required inputs and output appears When finished with this dialog close the window 24 ReadTable Configure
23. Transformation xm Thursday May 22 2008 3 02 PM amp 07 CommandLine_1 xmi Thursday May 22 2008 3 02 PM pi lt 08 Commandline_2 xml Thursday April 17 2008 11 39 AM i HelloWorld class Tuesday January 22 2008 12 05 PM HelloWorld jar Monday January 28 2008 2 58 PM J HelloWorld java Tuesday January 22 2008 12 05 PM mollusc abundance txt Friday 21 2006 9 58 AM gt readingdata xml Tuesday February 23 2010 4 15 PM species distribution jpg Friday May 19 2006 4 53 PM File Format All Files Cancel Figure 20 Configuring the File Reader actor to use data from your local machine 32 8 Click the Commit button at the bottom of the Edit Parameters for File Reader dialog box The actor is now configured to read the specified file 9 In the Components tab search for Display Select the Display actor and drag it onto the Workflow canvas to the right of the File Reader actor 10 Connect the output port of the File Reader actor to the input port of the Display actor 11 From the displaying 12 From the Toolbar select the Run button A pop up window will appear the contents of the data file in tabular format Figure 2 Menu bar select File then Save When prompted name the newly created workflow readingdata SDE Director C File Reader IK 03 ImageDisplay Display BAX File Tools Help 28 10 Display NNN NRF RF FF Figur
24. able Processing Components Kepler comes standard with over 500 workflow components and the ability to modify and create your own You can create an innumerable number of workflows with a variety of analytic functions The default set of Kepler processing components is displayed under the Components tab Components are organized by function e g Director or Filter Actor To search for components 1 In the Components and Data Access area to the left of the Workflow canvas select the Components tab 2 Type in the desired search string e g File Copy 3 Click the Search button or hit Enter When the search is complete the search results are displayed in the Components and Data Access area The search results replace the default list of components You may notice multiple instances of the same component because components are arranged by category the same component may appear in multiple places in the search results 4 To use one or more processing components in a workflow simply drag the desired components to the Workflow canvas 29 5 To clear the search results and re display the list of default components click the Cancel button NOTE If you know which component you want to use and its location in the Component library you can navigate to it directly and then drag it to the Workflow canvas 6 5 Creating a Basic Scientific Workflow One of the strengths of Kepler is the ability to design create and
25. ation represented by a dark diamond icon will appear near the center of the Workflow canvas You can also add a relation with the keyboard shortcut Ctrl click or Command click on Mac 11 Position the Relation icon between the File Reader actor and the Sequence Getter using XPath actor 12 Connect the input port of the XML Entry Display Display actor to the Relation To make the connection start from the input port of the Display actor and drag the cursor to the center of the Relation icon 13 Connect the HTML Generator Using XSLT actor and the Sequence Getter Using XPath actor to the Relation icon as well 14 Rename the second Display actor Sequence Display and position it to the right of the Sequence Getter using XPath actor 15 Connect the input of the Sequence Display actor to the output of the Sequence Getter using XPath actor 16 Rename the third Display actor HTML Display and position it to the right of the HTML Generator Using XSLT actor 17 Connect the input of the HTML Display actor to the output of the HTML Generator Using XSLT actor You are now ready to run the workflow The resulting output from the Display actors will be displayed Figure 32 46 file Users derik KeplerData workflow g started O9 XMLDataTransformation xm alakar Me m s gt r5 c gt Components lt Data Outline 09 XMLDataTransformation Sequence Display BASE COUNT 4
26. d to a display actor to display the data at that specific reference point By placing a Relation in the output data channel the user can direct the information to both places simultaneously 4 4 Parameters Parameters are configurable values that can be attached to a workflow or to individual directors or actors For example the Integrator actor has a parameter called InitialState that should be set to the initial value of the function being integrated The parameters of simulation model actors can be configured to control certain aspects of the simulation such as initial values Director parameters control the number of workflow iterations and the relevant criteria for each iteration The next sections provide an overview of the interface and step by step examples of how to open edit and run different scientific workflows 5 Kepler Interface Scientific workflows are edited and built in Kepler s easily navigated drag and drop interface The major sections of the Kepler application window Figure 5 consist of the following e Menu bar provides access to all Kepler functions e Toolbar provides access to the most commonly used Kepler functions e Components Data Access and Outline area consists of three tabs The Components and Outline tabs contain search functions and display the library of available components and or search results The Outline tab provides an outline view of the workflow e Workflow canvas prov
27. e 21 Using and displaying local data in a workflow NOTE When creating a workflow remember that the limitations of the data determine which processing components are appropriate 7 Sample Scientific Workflows This section examines a small set of sample scientific workflows that come standard with Kepler and provides step by step instructions for creating these workflows 7 1 Sample Workflow 1 Simple Statistics Name Summary Statistics File name 00 StatisticalSummary xml Detailed This workflow calculates the mean standard deviation and variance of Description a set of numerical values The Constant actors contains the input data an array of values 1 2 3 4 5 6 7 8 9 10 These data are sent to the SummaryStatistics actor which calculates the statistics and then outputs the results through its output ports Results are displayed by three TextDisplay actors Assumptions The SummaryStatistics actor is a special adaptation of the RExpression actor To run this workflow R a language and environment for 33 statistical computing must be installed on the computer running the Kepler application Director SDF Director Data Data is generated in the Constant actor Actors Constant SummaryStatistics Display Parameters SDF Director iterations 1 Constant value 1 2 3 4 5 6 7 8 9 10 The Summary Statistics workflow takes a list of numbers calculates the mean variance a
28. ed in the General Purpose folder By default the RExpression actor is configured with two output ports and a simple R script Before you can use the RExpression actor in the Simple Linear Regression workflow you must add two input ports T_AIR and BARO and reconfigure the RExpression script 10 Right click the RExpression actor and select Configure Ports 11 In the Configure ports dialogue box click Add twice to add two new ports Designate the new ports as input ports by clicking the checkbox named Input beside each port 39 12 Name the new input ports by double clicking the blank box in the Name column Add the name T_AIR for one input and BARO for the other Click Commit to save the changes Figure 27 Configure Actor Customize Name Configure Ports Configure Units Open Actor Deection Documentation a DEFAULT a a DeFALALT Listen to Actor AR iv Suggest BARO Mogga a Semantic Type Annotation Save Archive KAR Comet k Apsty _ Ada J k Removes Lahi Upload to Repository O E wy a View LSID Bas Preview Convert to Class Appearance teat DEFAULT Figure 27 Adding and customizing ports 13 To configure the R script right click the RExpression actor and select Configure Actor In the R function or script dialogue box change the value of the R function or script from the default to the following res lt lm BARO 7 AIR res plot T_ AIR BARO
29. elected The Command Line 1 workflow uses Kepler s ExternalExecution actor to execute the HelloWorld application that ships with Kepler The HelloWorld application is a simple Java program that outputs a string consisting of the text Hello plus a variable usually a user name and by default the string Kepler User The ExternalExecution actor waits for the HelloWorld application to finish executing and then returns the application output which is displayed by a Display actor The ExternalExecution s directory parameter is configured to the location of the HelloWorld application All other parameters are left at the default settings To create the Command Line 1 workflow l 2 Drag and drop an SDF Director onto the workflow Drag and drop a Constant actor onto the Workflow canvas Name the actor CommandLine To name the actor right click each actor icon and select Customize Name from the drop down menu Enter a new name in the New name field and click Commit The name will be updated on the Workflow canvas Double click the CommandLine actor to open its parameters Specify java cp HelloWorld Kepler_User as the value java cp HelloWorld is the command that runs the Java application HelloWorld The cp part of the command tells Java to include the current directory in the Java classpath Kepler User is an argument passed to the command line and its value can be varied to as desired e g Katie or
30. es a cast and crew The actors take their execution instructions from the director In other words actors specify what processing occurs while the director specifies when it occurs Every workflow must have a director that controls the execution of the workflow using a particular model of computation Each model of computation in Kepler is represented by its own director For example workflow execution can be synchronous with processing occurring one component at a time in a pre calculated sequence SDF Director Alternatively workflow components can execute in parallel with one or more components running simultaneously which might be the case with a PN Director A small set of commonly used directors come pre packaged with Kepler but more are available in the underlying Ptolemy II software that can be accessed as needed For more detailed discussion of workflow models of computation please refer to the Kepler User Manual or the Ptolemy I documentation Composite actors are collections or sets of actors bundled together to perform more complex operations Composite actors can be used in workflows essentially acting as a nested or sub workflow Figure 4 An entire workflow can be represented as a composite actor and included as a component within an encapsulating workflow In more complex workflows it is possible to have different directors at different levels Input Actor Nested Workflow Output Actor e g data i e composite actor
31. ew window will open with a blank Workflow canvas In the Components Data Access and Outline area search for SDF Director Drag the SDF Director to the top of the Workflow canvas In the Components tab search for File Reader Drag the File Reader actor to the Workflow canvas Right click the File Reader actor and select Configure Actor from the menu An Edit parameters for File Reader dialog window will open 7 Click the Browse button to the right of the fileOrURL parameter and navigate to the following file mollusc_abundance txt This data file is located in the getting started directory Figure 20 Edit parameters for File Reader ON es SS firingCountLimit fileOrurL Browse newline property line separator class ptolemy actor lib io FileReader semanticType00 urn lsid locaihost onto 1 1 ReaderExternallnputActor semanticTypell urn isid localhost onto 2 1 Localinput Cancel Preferences Restore Defaults Remove 8 9 0 Open i getting started eq Name Date Modified 00 StatisticalSummary xml Thursday February 7 2008 3 20 PM 3 01 SimpleAddition xmi Thursday December 20 2007 3 05 PM 28 02 LotkaVolterraPredatorPrey xml Thursday February 7 2008 3 20 PM lt 6 03 ImageDisplay xml Thursday February 7 2008 3 20 PM 04 HelloWorld xml Thursday December 20 2007 3 48 PM 05 LinearRegression xml Friday February 1 2008 8 10 PM 2 06 WebServicesAndData
32. hides some of the complexity of the underlying operation These composites can be thought of as sub workflows that execute a potentially complex set of tasks when called Author Ilkay Altintas May 2006 SDSC Execute an External Application from Kepler ExternalExecution actor The ExternalExecution actor can be used to launch an external application from within a Kepler workflow The actor can pass values to the application and return values that can be used or displayed by downstream actors In order to use the ExternalExecution actor the invoked application must be on the local computer and in some cases configured appropriately In this section we will look at several examples of workflows that use the ExternalExecution actor Name Command Line 1 Workflow File name 07 CommandLine_ xml Detailed The 07 CommandLine xml workflow uses Kepler s Description ExternalExecution actor to execute the HelloWorld Java application that is shipped with Kepler The actor outputs 47 the application s return which is displayed by a Display actor Assumptions The HelloWorld Java application is installed on the local machine in the getting started directory Director SDF Director Data Data is generated in two Constant actors Actors Constant actor CommandLine CommandLineExec and Display Parameters CommandLineExec actor directory WorkingDir waitForProcess parameter is s
33. ides space for displaying and creating workflows e Navigation area displays the full workflow Click a section of the workflow displayed in the Navigation area to select and display that section on the Workflow canvas the small unlabeled section in the lower left in the screenshot 11 elame miej misolo Q Advanc Sources All Ontologies and Folders gt E Components gt E Projects Statistics Actors _ Directors Opendap ER Figure 5 Empty Kepler window with major sections annotated 5 1 The Toolbar The Kepler toolbar is designed to contain the most commonly used Kepler functions Figure 6 The main sections of the toolbar include e Viewing zoom in reset fit and zoom out of the workflow on the Workflow canvas e Run run pause and stop the workflow without opening the Runtime window e Ports add single black or multi white input and output ports to workflows add Relations to workflows 12 aana ilO ROM Figure 6 Annotated Kepler Toolbar 5 2 Components Data Access and Outline Area The Components Data Access and Outline area contains a library of workflow components e g directors and actors under the Components tab a search mechanism for locating and using data sets under the Data tab and an outline view of the workflow under the Outline tab When the application is first opened the Components tab i
34. ill open 2 In the Components Data Access and Outline area select the Components ontology then expand the Director category by clicking the triangle Drag the SDF Director to the top of the Workflow canvas In the Components tab search for Constant and select the Constant actor 5 Drag the Constant actor onto the Workflow canvas and place it a little below the SDF Director 6 Configure the Constant actor by right clicking the actor and selecting Configure Actor from the menu Figure 18 sar 30 onstant rhs Configure Actor Customize Name Configure Ports Configure Units Open Actor Documentation Listen to Actor Suggest Semantic Type Annotation Save Archive KAR Upload to Repository View LSID A Preview f Convert to Class firingCounttimi Appearance value class Edit parameters for Constant ptolemy actortib Const semanticType00 urn Isid localhost onto 1 1 ConstantActor semanticTypell urrcisid Jocalhostonto 2 LeConstant kar urn isid kepler peoject org kar 57 1 Cancel Preferences Restore Defaults Figure 18 Configuring the Constant actor 7 Type Hello World in the value field of the Edit parameters for Constant dialog window and click Commit to save your changes Hello World is a string value In Kepler all string values must be surrounded by quotes 8 In the Components and Data Access area search for Display and select the Display actor f
35. in the desired search string e g Datos Meteorologicos Make sure that the search string is spelled correctly You can also enter just part of the entire string e g Datos 3 Click the Search button The search may take several moments You may be prompted for log in credentials If so enter your user and password information or click Login Anonymously When the search is complete a list of search results i e Data actors will be displayed in the Components and Data Access area 4 To use one or more data actors in a workflow simply drag the desired actors to the Workflow canvas 27 Unnamed 00 0 D meee Da on Components Data Outline Workflow Search Data Qatos meteorologicos Search Sources Cancel Datos Meteorologicos Datos ee gt 1 results returned Datos eorologicos gt Figure 16 Searching for and locating Datos Meteorologicos NOTE To configure the data search click the Sources button Select the sources to be searched and the type of documents to be retrieved Information about a Data actor can be revealed in three ways 1 on the Workflow canvas roll over the Data actor s data output ports to reveal a tool tip containing the name and type of data output by each port 2 right click the Data actor and select Get Metadata to open a window containing more information about the data set 3 right click
36. ing XPath composite actor by left clicking it 7 From the Edit menu select Copy or use the keyboard shortcut Ctrl C 8 Return to your workflow and paste the Sequence Getter Using XPath actor to the right of the File Reader actor using the Paste command available in the Edit menu or the keyboard shortcut Ctrl V 9 Copy and paste the HTML Generator Using XSLT actor from the Web Services and Data Transformation workflow into your workflow a a Nn NOTE To view the insides of a composite actor right click the actor and select Open Actor from the menu The composite actor will open in a new application window Figure 31 Composite actors can be thought of as sub workflows that execute a potentially complex set of tasks with a single actor 45 G ator Using XSLT Configure Actor Customize Name Configure Ports Configure Units Open Actor XML Input Documentation Listen to Actor Suggest gt Remove First Line HTML Output Semantic Type Annotation gt Save Arc hive KARS inputreplaceFirsti s MeWDOCTYPE 7 av Upload to Repository View LSIO Preview Convert to Class Appearance Figure 31 Inside the HTML Generator Using XSLT composite actor Because the File Reader actor output is required by three actors before connecting your actors you must add a relation to direct the output to multiple ports 10 Add a relation by clicking the Relation icon at the far right of the Toolbar The rel
37. l TJo2 LotkaVokerraPredatorPre 03 ImageDisplay xml OB 04 HelloWorld xml 0S LinearRegression xml a 06 WebService xml 07 CommandLine_1 xml LZ x qvyv f C O results found ay Figure 7 Accessing demonstration workflows in the Components tab 3 Double click a workflow file to open it The workflow will appear in the Workflow canvas of the application window 17 6 1 1 Example 1 Opening the Lotka Volterra Workflow In this example we will open the Lotka Volterra workflow To open this workflow Open the Demos folder in the Components tab Open the getting started folder and locate the file named 02 LotkaVolterraPredatorPrey xml 3 Double click the 02 LotkaVolterraPredatorPrey xml file The Lotka Volterra workflow appears in the Workflow canvas of the application window Figure 8 N eK Kepler File Edit View Workflow Tools Window Help D4 BD ZH Charge AOO file Users staggs keplerworkspace_ke arted 02 LotkaVolterraPredatorPrey xml TARAP Mee e oO moe Components Data Outline N f Workflow Search Components CT Director Q Search gt lt 25 SS TS Timed Plotter Advance Sources incel ed Plotte All Ontologies and Folders TA gt Components gt D Projects gt i Statistics gt Actors gt Directors gt C Openda K zal 4 p dnijdt Integrate n Qs EET f e Integrator 0 results found
38. l statistical and signal processing components and components for data input manipulation and display R or MATLAB based statistical analysis image processing and GIS functionality are available through direct links to these external packages You may also create new components or wrap existing components from other programs e g C programs for use within Kepler 2 Downloading and Installing Kepler Kepler is an open source cross platform software program that can run on Windows Macintosh or Linux based platforms Kepler can be downloaded from the project website http kepler project org Kepler releases are a continual work in progress and Kepler users are encouraged to contribute to the product by suggesting new features and notifying the designers of bugs and other problems See https kepler project org developers get involved for more information Community involvement in the on going development of Kepler has proved valuable because it allows the system to quickly adapt to the needs of practicing scientists To stay abreast of changes and updates subscribe to the Kepler users mailing list at http mercury nceas ucsb edu ecoinformatics mailman listinfo kepler users 2 1 System Requirements Recommended system requirements for running Kepler 300 MB of disk space 512 MB of RAM minimum GB or more recommended 2 GHz CPU minimum Java 1 6 Network connection optional Although a connection is not required to r
39. l rectangle though some icons such as the Data File Access icons use other colors and or shapes In the table below persistent symbols are noted For families that do not have a persistent symbol an example of one of the icons from that family is displayed A table that includes all icons for each family can be found in Chapter 5 of the Kepler User Manual Icon Family Name Description Director Stand alone component that directs the AO other components the actors in their execution Array Array actors are indicated with a curly brace Actors belonging to this family are used for general array processing e g array sorting Composite Composite actors are represented by multiple teal rectangles because they represent multiple actors Composite actors are collections of actors bundled together to perform more complex operations within an encapsulating workflow Control Control actors do not have a persistent family symbol These actors are used to control workflows e g stop pause or repeat Data File Data File Access actors do not have a Access persistent family symbol Actors belonging to this family read write and query data The icon displayed here is a data write icon NO B 14 Family Name Description Data Processing Data Processing actors assemble disassemble and update data Display Display actors are indicated by vertical bars Actors belonging
40. low and one for the director In this example you will make adjustments to both sets of parameters 3 Adjust the workflow parameters as suggested in Table 4 Parameter Value Description r 0 04 The intrinsic rate of growth of prey in the absence of predation a 0 0005 Capture efficiency of a predator or death rate of prey due to predation b 0 1 Proportion of consumed prey biomass converted into predator biomass i e efficiency of turning prey into new predators d 0 2 Death rate of the predator Table 4 Description of the suggested parameters for the Lotka Volterra workflow taken from http www stolaf edu people mckelvey envision dir lotka volt html 4 Adjust the value of the stopTime director parameter to 300 5 Inthe Runtime window click the Go button The Lotka Volterra workflow will execute with the adjusted parameters and produce two graphs 1 the TimedPlotter graph and 2 the XYPlotter graph Note that with the changes in the parameters the relationship between the predator and prey populations are still linked but the relationship has changed 23 IK file C kepler 1 0 0beta3 demos gett arted 02 LotkaVolterraPredatorPrey xml Joe File view Workflow Tools Window Help 2 BRAR Model parameters 07 3 5f ri 04 a 0 0005 3 07 b 0 1 25f 1 d 0 2 2 07 1 Director parameters 1 57 timeResolution 1E 10 1 07 i startTime 0 0 oar 4 stop
41. meters WSWithComplexTypes wsd1Ur1 http npd hgu mrc ac uk soap npd wsdl methodName geneID The Web Services workflow uses the WSWithComplexTypes actor to access a genomics database and return a gene ID from its gene name which is queried using a remote genomics data service The name of the genetic sequence i e the gene accession number is passed to the WSWithComplexTypes actor by a String Constant actor The WSWithComplexTypes actor must be configured to access the appropriate remote server Once configured the Web Service actor outputs the gene sequence obtained from the remote server In addition the workflow uses a Display actor to display errors returned by the remote server e g server down or incorrect input To create the Web Services workflow TAD Open a new Workflow canvas Drag and drop the SDF Director onto the Workflow canvas Drag and drop the String Constant actor onto the Workflow canvas Right click the String Constant actor and select Configure Actor Type ATRX the gene name into the value field and click Commit 5 To change the name of the String Constant actor right click it and select Customize Name Type a new name e g Gene Name into the Name field and click Commit Figure 28 42 rin stant Rename String Constant maae ATRX Configure Actor E r Name String Constant Configure Ports Display name String Constant Configure Units Open Actor aL Get Metadata Documen
42. mmit The data type of the Datos Meteorologicos actor must be set to As Column Vector to match the input requirements of the RExpression actor 38 ANN Edit parameters for Datos Meteorologicos EML File Data File Browse f Browse Selected Entity Datos Meteorologicos Data Output Format Ak Field r File Extension Filter As Field jl As Table Allow ow lenient data parsing As Row Check for latest version As Byte Array recordid As UnCompressed File Name As Cache File Name 5 endpoint As All Cache File Names namespace As Column Vector F 5G zi Cc py Cancel Help y Preferences z Restore Defaults Remove Add Commit Figure 25 Configuring Datos Meteorologicos NOTE Datos Meteorologicos has a series of output ports corresponding to the data attribute names e g BARO and T_AIR To locate the appropriate port mouse over the output ports and review the port tooltips Figure 26 corologicos y BARO type double a Figure 26 Identifying data ports Mouse over each output port to review the port tooltips To finish creating the workflow add the SDF Director and the remaining actors RExpression ImageJ Display 7 Locate the SDF Director and drag and drop it to the Workflow canvas 8 Click Commit for the changes to take effect 9 Locate the RExpression actor and drag and drop it to the Workflow canvas The RExpression actor is locat
43. nd standard deviation and displays the results This workflow highlights the ease and functionality of Kepler To run this workflow R a language and environment for statistical computing must be installed on the computer running the Kepler application R is included with the full Kepler installation for Windows and Macintosh R is not included with Kepler s Linux installer To create this workflow from scratch open a new blank workflow from the File menu File gt New Workflow gt Blank and follow the steps below 1 2 3 In the Components Data Access and Outline area select the Components tab Search for the SDF Director and drag and drop it to the Workflow canvas Search for the Constant actor and drag and drop it to the Workflow canvas The Constant actor can be found under Components gt Data Input gt Workflow Input gt Constant Configure the Constant actor by right clicking the actor and selecting Configure Actor In the Edit Parameters for Constant window set the value field to 1 2 3 4 5 6 7 8 9 10 and click Commit Note The braces are needed Curly braces designate an array in Kepler Search for the SummaryStatistics actor and drag and drop it to the Workflow canvas Locate the correct output ports of the SwmmaryStatistics actor by right clicking the actor and selecting Configure Ports Figure 22 In the Configure ports for SummaryStatistics dialogue box under the Show Name column click the check box f
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45. on output observational data etc and executing complex analysis on the retrieved data Each workflow consists of analytical steps that may involve database access and querying data analysis and mining and intensive computations performed on high performance cluster computers Each workflow step is represented by an actor a processing component that can be dragged and dropped into a workflow via Kepler s visual interface Connected actors and a few other components that we ll discuss in later sections form a workflow allowing scientists to inspect and display data on the fly as it is computed make parameter changes as necessary and re run and reproduce experimental results Workflows may represent theoretical models or observational analyses they can be simple and linear or complex and non linear One of the benefits of scientific workflows is that they can be nested meaning that a workflow can contain sub workflows that perform embedded tasks A nested workflow also known as a composite actor is a re usable component that performs a potentially complex task Scientific workflows in Kepler provide access to the benefits of today s grid technologies providing access to distributed resources such as data and computational services while hiding the underlying complexity of those technologies Kepler automates low level data processing tasks so that scientists can focus instead on the scientific questions of interest
46. or xmean xstd and xvar Click Commit to save your changes The port names for the xmean xstd and xvar outputs will now display on the Workflow canvas making it easier to connect the proper ports 34 tistics Configure Actor RE Customize Name 10 11 Configure Pons E Configure Units Open Actor Documentation Listen to Actor Suggest Semantic Type Annotation Save Archive KAR Upload to Repository View LSID Preview Convert to Class Appearance Figure 22 Displaying port names Connect the output of the Constant actor to the input port of the SummaryStatistics actor Search for the text Display actor and drag and drop that to the Workflow canvas three times Note the second actor is named Disp ay2 and the third actor is named Display3 Customize the name for the three text Display actors by right clicking each and selecting Customize Name In the Rename Text Display dialogue box for the Display actor type Mean and click Commit to save your changes Name the Display2 actor Variance and the Disp ay3 actor Standard Deviation Connect the xmean xstd and xvar output ports of the SummaryStatistics actor to the input port on the corresponding Mean Standard Deviation and Variance actors You are now ready to run the workflow The resulting workflow and output are displayed in Figure 23 35 IK File Tools Help SaS SDF Director K File Tools Help Constant ics 3 0276503540975
47. ound under Textual Output 9 Drag the Display actor to the Workflow canvas 10 Connect the output port of the Constant actor to the input port of the Display actor 11 Run the model Figure 19 a00 04 HelloWorld Display Hello World SDF Director i Constant Display moser Hello World T r Figure 19 Hello World workflow and output NOTE By default the SDF Director will execute each actor in the workflow once To run Hello World a more than once double click on the SDF Director and enter the desired number of iterations into the iterations field Click the Commit button to save your changes 31 6 5 2 Example 6 Creating a Simple Workflow Using Local Data In this example we create a simple workflow using an actor that reads a local data file containing information about species abundance and then sends the data to a second actor for display Kepler can read data in many ways and from many formats In this example we will use an actor to review a data table To determine which actor is appropriate consider the format in which the data are saved In this example the data are saved in a text format As such we will use the File Reader actor to read the data in a tabular format This workflow requires two actors a File Reader actor and a Display actor to output text In addition the example requires a SDF Director 1 From the Menu bar select File then New Workflow and then Blank A n
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49. portant characteristic of scientific workflows Because Ptolemy II provides an open source mature platform for model design and execution including various models of computation and is well documented and easily extensible it was chosen as the foundation for Kepler 50 8 2 Actor Reference Documentation for actors and directors is available in the Actor Reference document Additionally this documentation is available within the Kepler interface To get documentation 1 Right click the actor or director 2 Select Documentation 3 Then select Display Figure 37 tie took Hee Garp Prediction GarpPrediction org ecoinformatics seek garp GarpPrediction Configure Actor GARP is a computer program tor predicting species beations based on verkus spatial date sets of Customize Name Crrrrorenert variaties and known spaces locations GARP It an acronym for Gerah Algorthm tor Configure Ports Ride Set Production GARP was originally coated by Deval Stockwet paces nite baa 9 on Desktop GARS hip Orww Hemmpper ae giarskiopgarp The Capreddon sctor Configure Units acapcatsnencs dade oat DPD DARA on tae nes ARAE PAISU Pea EUAN Open Actor A eee ection and the input set of errdrenesertal invert The iret layert are detorbed in a summary xi fhe id The outputs ore ether an onc grat tis or 9 herp fhe Either can be diagisyed as a btmapped image wth predcted presencesabsence Scato by perel values Cole mapped wher Customize Arpiar
50. rkflow In the differential equations used in the workflow dn1 dt r n1 a n1 n2 and dn2 dt d n2 b n1 n2 the variable nl represents prey density and the variable n2 represents predator density When changing parameters in a workflow the assumptions of the model must be kept in mind For example if creating a Lotka Volterra model with rabbits as prey and foxes as predators the following assumptions can be made with regard to how the rabbit population changes in response to fox population behavior The rabbit population grows exponentially unless it is controlled by a predator Rabbit mortality is determined by fox predation Foxes eat rabbits at a rate proportional to the number of encounters The fox population growth rate is determined by the number of rabbits they eat and their efficiency of converting the eaten rabbits into new baby foxes and e Fox mortality is determined by natural processes If you think of each run of the model in terms of the rates at which these processes would occur then you can think of changing the parameters in terms of percent of change over time To run the Lotka Volterra workflow with adjusted parameters 1 Open the workflow file named 02 LotkaVolterraPredatorPrey from the getting started directory 2 From the Menu bar select Workflow then Runtime Window The Runtime window will appear Notice there are two sets of parameters one for the 22 workf
51. ry components The workflow uses two composite actors Sequence Getter Using XPath and HTML Generator Using XSLT to process the returned XML data and convert it into a sequence of elements and an HTML file respectively These actors have been created for use with this workflow using existing Kepler actors Sequence Getter Using XPath and HTML Generator Using XSLT do not appear in the Components tab To see the insides of the composite actors right click the actor icon on the Workflow canvas and select Open Actor from the menu The composite actor will open in a new window The Data Transformation workflow uses two component actors designed specifically for this workflow These customized actors are not available in the Component library and rather than recreating them we will save some time by copying and pasting them from the existing workflow Open a new Workflow canvas Drag and drop the SDF Director onto the workflow canvas Drag and drop a File Reader actor onto the workflow canvas Right click on the Filer Reader actor and set fileOrUrl to the sampleEntry xml file Use the Browse button to find the file within demos getting started directory Drag and drop two Display actors onto the workflow canvas 6 Open the Data Transformation workflow 09 XMLDataTransformation xml by double clicking the file in the Demos getting started folder on Kepler component tree The workflow will open in a new window Select the Sequence Getter Us
52. s displayed Components in Kepler are arranged in three high level categorizations Components Projects and Statistics Table 1 Any given component can be classified in multiple categories appearing in multiple places in the component tree Use any instance of the actor only its categorization is different Browse for components by clicking through the trees or use the search function at the top of the Components tab to find a specific component For more information about searching for components see section 6 4 2 Category Description Components Contains a standard library of all components arranged by function Projects Contains a library of project specific components e g SEEK or CIPRes Statistics Contains a library of components for use with statistical analysis Table 1 Component Categories in Kepler Click the Data tab to reveal the Data Access area From here you can easily search the EarthGrid for remotely hosted data sets For more information about searching for data see section 6 4 1 13 5 3 Director and Actor Icons In Kepler icons provide a visual representation of each component s function Directors are represented by a single icon actors are divided into functional categories or families with each category assigned a visually related icon Table 2 Some actor families have a persistent family symbol other families do not The majority of the actor icons use a tea
53. s distribution of the species Mephitis throughout North and South America This image was created by GARP a genetic algorithm that creates an ecological niche model for a 25 species that represents the environmental conditions where that species would be able to maintain populations GARP was originally developed by David Stockwell at the San Diego Supercomputer Center For more information on GARP see http www lifemapper org desktopgarp To edit the Image Display workflow l 2 ab Open the 03 Image Display xml workflow in the Demos gt getting started folder in the Components tab Select the target component the ImageJ actor in this case The JmageJ actor will be highlighted in a thick yellow border indicating that it is selected Figure 14 SDF Director Image Filename Image Converter property outreach workflowdir dem Figure 14 Image Display workflow showing ImageJ actor highlighted Press the Delete key on your keyboard The ImageJ actor will disappear from the Workflow canvas From the Components Data Access and Outline area drag the Browser Display actor to the Workflow canvas You can find the Browser Display actor by typing Browser Display in the search field and hitting Enter in the Components tab It will appear beneath Components gt Data Output gt Workflow Output gt Textual Output Connect the output port of the ImageConverter actor to the input port of the Browser Display
54. se nodes on the EarthGrid Click Ok to confirm and save the search source changes 4 Type Datos Meteorologicos in the search box and click Search Results may take 20 seconds to return 5 From the search results click the Datos Meteorologicos icon Drag and drop the Datos Meteorologicos actor to the Workflow canvas W 37 NOTE on the To find more information about the data set right click Datos Meteorologicos Workflow canvas and select Get Metadata Figure 24 Depending upon the amount of information entered by the provider much valuable metadata can be obtained The type of value and measurement type of each attribute help you decide which statistical models are appropriate to run Datos Li Meteorologicos thot t o imb Configure Actor tle aman Datos Mo eorclogicos Customize Name yr 7 SST Configure Ports Mr Rodrigo Torrens Configure Units Open Actor RL System Bo hes j Documentation 5 rae a 5 Listen to Actor EEES Suggest Mr Rodrigo Torrens Semantic Type Annotation Save Archive KAR Upload to Reposito 5 vate LSID pe iption Dtos Estacion meteorologica La Hechicera para e 2001 Preview Convert to Class Appearance Missin Accu Value Code Report TME Figure 24 Viewing Metadata Right click the Datos Meteorologicos actor and select Configure Actor Select As Column Vector from the pull down menu beside the Data Output Format parameter Figure 25 and click Co
55. tarted from the Start menu Navigate to Start menu gt All Programs and select Kepler to start the application On a Mac the Kepler icon is created under Applications Kepler x y The icon can be dragged and dropped to the desktop or the dock if desired The main Kepler application window opens Figure 3 From this window you can access and run sample and existing scientific workflows and or create your own custom scientific workflow Each time you open an existing workflow or create a new workflow a new application window will open Multiple windows allow you to work on several workflows simultaneously and compare copy and paste components between workflows 3 2 Linux Platform To start Kepler on a Linux machine use the following steps 1 Open a shell window On some Linux systems a shell can be opened by right clicking anywhere on the desktop and selecting Open Terminal Speak to your system administrator if you need information about your system 2 Navigate to the directory in which Kepler is installed To change the directory use the cd command e g ed directory name 3 Type kepler sh to run the application The main Kepler application window opens Figure 2 3 From this window you can access and run existing scientific workflows and or create your own custom scientific workflow Each time you open an existing workflow or create a new workflow a new application window opens Multiple windows allow you to work on se
56. tation gt Listen to Actor Suggest Semantic Type Annotation Save Archive KAR Upload to Repository View LSID Show name ff Preview Appearance Cancel Commit Figure 29 Customizing the name of an actor 6 Drag and drop the WSWithComplexTypes actor onto the Workflow canvas By default WSWithComplexTypes has one output port for displaying runtime errors and must be configured with a Web service URL a wsdlUrl parameter an appropriate method a methodName parameter Once the actor has been configured with this information it will automatically generate the correct input and output ports required by the Web service ve To configure the parameters required for accessing the Web service right click the WSWithComplexTypes actor and select Configure Actor Figure 29 Type http npd hgu mrc ac uk soap npd wsdl into the wsdlUrl field Click commit The WSWithComplexTypes actor should update automatically to get the available methods If you configure the actor again the methodName field will show all available methods Select genelID Click commit The WSWithComplexTypes actor ports should update automatically 8 Because the type of output port gt result is xmltoken it means the output port is a complex type The content of the complex data type can be automatically extracted by changing the outputMechanism parameter from simple to be composite Click commit after changing this configura
57. the data actor and select Preview from the drop down menu to preview the data set Figure 17 28 eorologicos Configure Actor Customize Name Configure Ports Configure Units Open Actor L Documentation AOO Datos Meteorologicos Preview A DATE TIME T_AIR RH DEW BARO WD WS RAIN ISOL SOL EE HEE 01 00 00 15 14 5 953 4 99 Suggest lOl 01 00 13 4 12 8 953 8 100 Semantic Type Annotation 01 02 00 13 4 12 8 954 114 Save Archive KAR 01 03 00 12 4 12 3 954 3 114 Upload to Repository 01 04 00 11 7 11 7 954 5 96 View LSID 01 05 00 11 4 11 2 954 7 85 n 01 06 00 11 5 11 7 954 8 114 Preview 01 07 00 11 5 11 7 954 8 88 Appearance 01 08 00 12 2 12 3 954 9 88 01 09 00 17 4 15 6 953 7 336 01 10 00 20 1 16 7 952 6 322 jO1 11 00 23 3 17 8951 7 289 01 12 00 23 1 17 8 951 2 193 01 13 00 23 5 17 8 950 7 42 01 14 00 23 5 20 6 950 3 117 01 15 00 23 1 21 7 950 3 93 01 16 00 20 19 5 950 6 156 01 17 00 18 5 17 8 951 8 34 O1 18 00 17 5 16 7 952 3 157 01 19 00 16 2 15 6 952 8 277 01 20 00 15 9 15 6 953 1 277 01 21 00 15 6 15 953 3 196 01 22 00 15 2 14 5 953 4 264 01 23 00 14 7 13 9 953 6 244 01 00 00 14 2 13 4 953 7 105 12 0 0 0 0 120 0 0 0 NN oooo soccer s oooocococococcoocococococcoao CWOM KOHN OH ee ROMUaAND EL oo Figure 17 Previewing a data set 6 4 2 Searching for Avail
58. tion A WSWithComplexTypes gt result composite actor should automatically appear after the WSWithComplexTypes actor with configured output ports The output ports of the WSWithComplexTypes gt result composite actor are simple data types extracted from the xmltoken port of the WSWithComplexTypes actor 43 Edit parameters for WSWithComplexTypes Configure Actor r wsdl http npd hgu mrc ac uk soap npd wsdl Customize Name method genelD Configure Ports inputMechanism simple Configure Units outputMechanism composite outputNil Open Actor oD Get Metadata username Documentation password timeout 600000 ignorelnvokeErrors Listen to Actor Suggest Semantic Type Annotation class org sdm spa WSWithComplexTypes Configure Save Archive KAR Upload to Repository r SEET r N 7 View LSID Cancel Preferences Defaults Remove Preview Appearance WSWithComplexTypes WSWithComplexTypes gt result hadrror zenel i A Sone _ Configured WSWithComplexTypes Actor GeneName input D Figure 30 Configuring the WSWithComplexTypes Actor 9 Connect the output of the String Constant actor Gene Name to the input of the WSWithComplexTypes actor 10 Drag and drop two Display actors onto the Workflow canvas 11 Position the two Display actors beneath and to the right of the WSWithComplexTypes gt result port 12 Connect the two output ports of the WSWithComplexT
59. to this family output the workflow in text or graphical format File Management File Management actors do not have a persistent family symbol Actors belonging to this family locate or unzip files for example The icon displayed here is a directory listing icon GAMESS GAMESS actors are used for computational chemistry workflows Jofel Jok General Actors that don t fit into one of the other families fall into the General family General actors include email file operation and transformation actors for example The icon displayed here is a filter icon GIS Spatial GIS Spatial actors are used to process geospatial information Image Processing Image Processing actors are used to manipulate graphics files Logic Logic actors have no persistent family symbol Actors in this family include Boolean switches and logic functions The icon displayed here is an equals icon Poa ae oe Qa we Math Math actors have no persistent family symbol Actors in this family include add subtract integral and statistical functions The icon displayed here is used to represent statistical functions e g the Quantizer actor E Model Model actors use a solid arrow Model actors include statistical mathematical rule based and probability models Note that icons will include additional symbols further identifying the actor function 15 Icon Family
60. troduces the main components and functionality of Kepler and contains step by step instructions for using modifying and creating your own scientific workflows The Guide provides a brief introduction to the application interface as well as to application specific terminology and concepts Once you are familiar with the general principles of Kepler we recommend that you work through a couple of the sample workflows covered in Section 7 to get a feel for how easy it is to use and modify workflow components and how components can be combined to form powerful workflows 1 1 What is Kepler Kepler is a software application for the analysis and modeling of scientific data Kepler simplifies the effort required to create executable models by using a visual representation of these processes These representations or scientific workflows display the flow of data among discrete analysis and modeling components Figure 1 K File Tools Help 5 5 SDF Director K File Tools Help Constant 3 0276503540975 K Variance File Tools Help 9 1666666666667 Figure 1 A simple scientific workflow developed in Kepler Kepler allows scientists to create their own executable scientific workflows by simply dragging and dropping components onto a workflow creation area and connecting the components to construct a specific data flow creating a visual model of the analytical portion of their research Kepler represents the overall
61. ultaneously and compare copy and paste components between Workflow canvases 6 Basic Operations in Kepler This section covers the basic operations in Kepler opening and running an existing workflow and some techniques for editing designing and creating your own workflows 16 6 1 Opening an Existing Scientific Workflow In Kepler workflows may be written as XML MoML or KAR files A KAR is an archive file a JAR that aggregates many files into one A workflow KAR is one that contains a MoML workflow file To open or save a workflow KAR use File gt Open File gt Save and File gt Save As To save a workflow as XML only use File gt Export As gt XML The demo workflows discussed here can be opened from the Components tab as shown in Figure 7 1 Open the yellow folder named Demos to see the different categories of workflow demos 2 Open the getting started folder to see the introductory workflow demos Unnamed1 alaale Mme a a Components Data Outline gt f Workflow Search Components q Search N lt oo Advanced Sources Cancel a All Ontologies and Folders B gt Components Projects i Statistics E Demos gt E Branching gt 3 Database gt 53 Looping gt E Matlab gt E MultipleTabDisplay E Python gt 5 RESTService gt E SEEK v E getting started 00 Statisticalsummary xml 01 SimpleAddition xm
62. un Kepler many workflows require a connection to access networked resources e R software optional R is a language and environment for statistical computing and graphics and it is required for some common Kepler functionality To download and install Kepler follow the instructions for your system Downloading the installer files may be time consuming depending upon your connection NOTE Java 1 6 is required and can be obtained from Sun s Java website at http java sun com j2se downloads or from your system administrator Kepler has many actors that utilize R so installing R is recommended http www r project org 2 2 Installing on Windows The Windows installer will install the Kepler application on your system Java 1 6 or greater is required in order to run Kepler Kepler has many actors that utilize R so installing R is recommended http www r project org Follow these steps to download and install Kepler for Windows 1 Click the following link https kepler project org users downloads and select the Windows installer 2 Save the install file to your computer 3 Double click the install file to open the install wizard 4 Follow the steps presented to complete the Kepler installation process Once the installation process is complete a Kepler shortcut icon will appear on your desktop Figure 2 and or in the Start Menu K Kepler Figure 2 Kepler shortcut icon 2 3 Installing on Macintosh
63. veral workflows simultaneously and compare copy and paste components between workflows 4 Basic Components in Kepler Scientific workflows consist of customizable components directors actors and parameters as well as relations and ports which facilitate communication between the components keplerworkspace_ke arted 02 LotkaVolterraPredatorPrey xml manar Meson Components Daa Outine Workfiow CT Director r Search Components a Advance Sources Cancel TimedPiotter All Ontologies and Folders E gt Components gt Projects gt F Statistics gt Actors gt Directors gt gt La Opendap E R This model shows the solution to the classic Lotka Volterra predator prey dynamics model It uses the Continuous Time domain to solve two coupled differential equations one that models the predator population and one that models the prey population The results are plotted as they are calculated showing both population change and a phase diagram of the dynamics 0 results found Rich Williams 2003 NCEAS a Y gt ees lt Figure 3 Main window of Kepler with some of the major workflow components highlighted 4 1 Director and Actors Kepler uses a director actor metaphor to visually represent the various components of a workflow A director controls or directs the execution of a workflow just as a film director overse
64. ypes actor to the input port of the two Display actors You may now run the workflow and view its output in the two Display actors 7 4 Sample Workflow 4 XML Data Transformation Name XML Data Transformation workflow File name 09 XMLDataTransformation xml Detailed This workflow demonstrates the use of the data Description transformation actors to process a genetic Sequence and display the data as XML a sequence and HTML Assumptions The sampleEntry xml file exists in your getting started directory Director SDF Director Data A genetic sequence in XML format in a file Actors File Reader XSLTActor Expression XPath StringToXML Display Parameters FileReader fileOrURL sampleEntry xml This workflow demonstrates the use of the data transformation actors to process a genetic sequence The sequence is displayed in three different ways first in its native format 44 XML second as a sequence element that has been extracted from the XML format and third as an HTML document that might be used for display on a web site Both of the latter two operations are performed using a composite actor that hides some of the complexity of the underlying operation These composites can be thought of as sub workflows that execute a potentially complex set of tasks when called A Relation is used to branch the data output by the File Reader actor so that it can be shared by all of the necessa

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