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1. m Br ao Step 3 Type in Task Step 1 pointWithMostHumans cell getPoint Step 4 Type in Task Step 2 Optional maxCount cell sized Step 5 Type in Task Step 3 Optional Step 6 Type in Task Step 4 Optional Step 7 Type in Task Step 5 Optional ne Figure 1 An example Repast Simphony flowchart showing the behavior for a Zombie agent North et al Complex Adaptive Systems Modeling 2013 1 3 Page 8 of 26 http www casmodeling com content 1 1 3 lines of XML Thanks to this architecture Repast Simphony exists in essence as a user selectable federation of plug in components Selected plug ins and related sets of plug ins are summarized in Table 1 It should be noted that that Repast plug ins use the Java Plug in Framework JPF Java Plug in Framework JPF Project which is separate from the Eclipse plug in architecture JPF is used at runtime by Repast models Eclipse is used at development time by the Repast design tools The next section will discuss the plug in system The following sections will consider central plug ins of particular interest Simphony application framework Repast Simphony s modular architecture is built on top of the free and open source Simphony Application Framework SAF As an application framework SAF is intended to simplify common application building tasks such as creating and configuring menus toolbars application window layout and so on SAF based app
2. complexity Both the original Piccolo based 2D and the new OpenGL based 2D as well as the current 3D implementation were guided by the need for the same agent to be displayed simultaneously in a variety of topologies networks grids and so on and a variety of styles For example a single agent could be appear in a 2D display as a red circle in a grid layout and simultaneously in a 3D display as a blue cube participating in a network with the corresponding links visualized Previous experience with agent visualization has shown that this capability is best accomplished by separating the agent s implementation from the visual representation of that agent In Repast Simphony style and layout are implemented as Java interfaces Both the 2D and 3D style interfaces consist of methods that receive an agent as a parameter and return some value typically based on some property of the agent For example there North et al Complex Adaptive Systems Modeling 2013 1 3 Page 16 of 26 http www casmodeling com content 1 1 3 are methods that return the geometric representation e g circle cube model specific polygon of the agent the agent s color rotation scale label and so forth An additional network style is used to style network edges The layout interface works in a similar fashion A location finding method takes an agent as a parameter and returns the loca tion of that agent in either 2D or 3D space Typical layouts compute the locatio
3. perform publicly and display publicly by or on behalf of the Government The authors also wish to acknowledge the many developers supporters and contributors to the Repast family of agent based modeling software Received 23 November 2012 Accepted 17 January 2013 Published 13 March 2013 References Artel A Teymour F North MJ Cinar A A multi agent approach using perceptron based learning for robust operation of distributed chemical reactor networks Int Sci J Eng App Artif Intell 2011 24 1035 1045 Bonabeau E Agent based modeling Methods and techniques for simulating human systems In Proceedings of the National Academy of Sciences Volume 99 3 Washington D C USA National Academy of Sciences Press 2002 7280 7287 Bozada T Perkins T North MJ Simunich KL Tatara E An applied approach to representing human behavior in military logistics operations In Proceedings of the fall simulation interoperability workshop September 10 15 2006 Edited by Weber R Orlando FL USA Curran Associates 2006 669 678 Branting S Wu Y Srikrishnan R Altaweel MR SHULGI A geospatial tool for modeling human movement and interaction In Proceedings of the Agent 2007 Conference on Complex Interaction and Social Emergence Edited by North M Macal C Sallach D Argonne IL Argonne National Laboratory 2007 258 273 CASOS ORA 2999 http www casos cs cmu edu projects ora Chiba S Nishizawa M An easy to use toolkit for efficient java byte
4. In Conference companion on human factors in computing systems common ground Edited by Tauber MJ New York ACM 1996 11 12 Sallach D Macal C The simulation of social agents An introduction Soc Sci Comput Rev 2001 19 3 245 248 Standish RK Going stupid with EcoLab Simulation 2008 84 611 618 Swarm license 2999 http www swarm org index php Swarm _license Tao G Minett JW Jinyun K Holland JH Wang WSY Coevolution of lexicon and syntax from a simulation perspective Research articles Complexity 2005 10 50 62 Tatara E North MJ Hood CS Teymour F Cinar A Agent based control of spatially distributed chemical reactor networks In Engineering self organising systems third international workshop revised selected papers Lecture Notes in Computer Science Series Volume 3910 Edited by Brueckner SA DiMarzo Serugendo G Hales D Zambonelli F Heidelberg Springer 2006 222 231 Tisue S Wilensky U NetLogo Design and implementation of a multi agent modeling environment In SwarmFest Edited by Riolo R Ann Arbor MI Swarm Development Group 2004 VisAD McIDAS V 2999 http www ssec wisc edu billh visad html WEKA Machine Learning Group at the University of Waikato 2999 http www cs waikato ac nz ml weka Wilensky U NetLogo Evanston IL Center for Connected Learning and Computer Based Modeling Northwestern University 2012 XStream Home Page 2999 http xstream codehaus org doi 10 1186
5. Simphony While discussing their design Minar et al 1996 states that agent based modeling toolkits or libraries are important in that they save scientists from wasting time on repetitive and error prone programming Discrete time scheduling is preferred over floating point sched uling because discrete calculations do not suffer from rounding errors Object orientation is also useful because of its close association with agents Minar et al 1996 suggests that agents should be organized into containers with schedules of activities These collections are called swarms Swarms should be inter operable to allow mixing and nesting of related models Repast 3 Repast 3 is a family of three free and open source agent based modeling libraries North et al 2006 The three libraries are Java based Repast J C based Repast NET and NQP Not Quite Python based Repast Py Repast 3 uses a new BSD Berkeley Software Distribution style license and includes third party libraries with compatible licenses Several conclusions were reached during the implementation of the libraries Object oriented design is essential to allow both the library and user models to be flex ible The use of design patterns is helpful for improving implementation quality Envir onments should allow seamless programming in different languages to help simultaneously lower barriers to entry for new users and increase flexibility for experts Choosing environ ments tha
6. select UserTurtle as the Agent Type and getInnovation for the Method Sum should be automatically selected as the default aggregate function The results of this step will direct Repast Simphony to add up all of the innovation values across all of the turtles for each time step You should choose Next and then Finish to finalize the work You can now proceed to add the chart itself To add the chart you should right click on the Charts item in the Scenario Tree in the lower left panel of the Repast Simphony runtime interface You should then choose Add Time Series Chart from the popup menu You should type in Total Innovation for the Name and then choose Next You should then click on the totalInnovation line on the chart properties wizard page and again choose Next You should type in Total Innovation for the chart title and Innovation for the Y Axis title on the next wizard page and then click Finish To complete this step you should save the chart definition by clicking on the floppy disk icon on the upper right corner of the Repast Simphony runtime interface To run the innovation model the user can select the run icon from the toolbar The run button has a green circular icon with a white triangle in the middle The model runtime window will appear and can by initialized using the Initialize Run but ton in the toolbar Thi
7. 2194 3206 1 3 Cite this article as North et al Complex adaptive systems modeling with Repast Simphony Complex Adaptive Systems Modeling 2013 1 3 Submit your manuscript to a SpringerOpen journal and benefit from gt Convenient online submission gt Rigorous peer review gt Immediate publication on acceptance gt Open access articles freely available online gt High visibility within the field gt Retaining the copyright to your article Submit your next manuscript at gt springeropen com
8. Google Summer of Code The Repast system including the source code is available directly from the Web at http repast sourceforge net Repast The Repast Suite All versions of Repast use a new BSD style license and include third party libraries with compatible licenses North et al Complex Adaptive Systems Modeling 2013 1 3 Page 5 of 26 http www casmodeling com content 1 1 3 Repast Simphony builds on the lessons of Repast 3 but uses a new code base Repast Simphony was designed from the ground up with a strong focus on well factored abstractions The resulting code has a highly modular plug in architecture that allows individual components such as networks logging and time scheduling to be replaced as needed A plug in is a software module that extends the features of a host program using a well defined programming interface The Repast Simphony code also has mul tiple layers within each plug in module to allow specific implementations at lower levels to be replaced by new implementations when required As discussed later this layering allowed the authors to replace Repast Simphony s logging and visualization implementations while maintaining backward compatibility Repast Simphony also includes many advanced features such as watchers that were not possible in Repast 3 These features are discussed later The Repast community is large and growing These users have applied Repast to a wide variety of applications that range f
9. North et al Complex Adaptive Systems Modeling 2013 1 3 0 Complex Ada ptive Systems Modeling http www casmodeling com content 1 1 3 a SpringerOpen Journal Complex adaptive systems modeling with Repast Simphony Michael J North Nicholson T Collier Jonathan Ozik Eric R Tatara Charles M Macal Mark Bragen and Pam Sydelko Correspondence north anl gov Decision and Information Sciences Division Argonne National Laboratory 9700 S Cass Avenue Argonne IL 60439 4867 USA University of Chicago Chicago IL USA G Springer Abstract Purpose This paper is to describe development of the features and functions of Repast Simphony the widely used free and open source agent based modeling environment that builds on the Repast 3 library Repast Simphony was designed from the ground up with a focus on well factored abstractions The resulting code has a modular architecture that allows individual components such as networks logging and time scheduling to be replaced as needed The Repast family of agent based modeling software has collectively been under continuous development for more than 10 years Method Includes reviewing other free and open source modeling libraries and environments as well as describing the architecture of Repast Simphony The architectural description includes a discussion of the Simphony application framework the core module ReLogo data collection the geographical information sy
10. a complex series of nested scapes populated by agents whose behaviors are implemented with abstracted rules Parker 2001 states that the abstraction of com plexity is a powerful way to focus design and development efforts Selective abstraction should be used to provide structure for users and reduce the complexity of user code The abstractions need to be very carefully considered to avoid limiting flexibility For Parker 2001 space should be represented with nested containers i e scapes Scapes dynamically represent space identity type and group membership Scapes should be allowed to act as agents This treatment allows complete nesting of models Agents however should not have to explicitly address the nature of scapes which greatly simplifies agent specifications and reduces the chances for errors Agent beha vior specification and scheduling should occur only at the scape level never at the indi vidual level This treatment allows behaviors to be dynamically changed and permits sophisticated behavior based designs of experiments EcoLab EcoLab Standish 2008 is a general purpose C and TCL Tk agent based modeling library Users write models in C and then invoke the models using TCL Tk can be used as needed to develop user interfaces Standish 2008 suggests that it is helpful to have standardized models with which to compare agent modeling libraries Standish states that reflection is essential for agent models Refle
11. agent models StarLogo is free and open source for non commercial use StarLogo sub stantially extended Logo by increasing the allowed number of agents i e turtles from tens to thousands by giving turtles much more interactive behaviors and by transform ing the turtle s environment from a rectangular array of pixels into a grid of first class agents i e patches Resnick 1996 notes that StarLogo is designed around a single or ganizing principle For StarLogo that principle is modeling decentralized complex sys tems There is no requirement to hide the complexity of foundational features such as parallelism if they embody the organizing principle NetLogo NetLogo Wilensky 2012 is a free and open source agent based simulation environ ment that uses a modified version of the Logo programming language NetLogo is available under the General Public License GPL NetLogo User Manual FAQ Frequently Asked Questions NetLogo s builds on the StarLogo effort Tisue and Wilensky 2004 NetLogo was designed to provide a basic laboratory for teaching com plexity concepts It can also be used to develop more sophisticated applications NetLogo provides a graphical environment to create programs that control graphic tur tles that reside in a world of patches which are monitored by an observer Links are also available to connect turtles to form networks Wilensky 2012 and Tisue and Wilensky 2004 offer several lessons from the develo
12. al 2D model viewing Provides tools for interactive three dimensional 3D model viewing Provides distributed model execution Provides tools for ordinary differential and difference equations Supports a set of independent plug ins for Geographic Resources Analysis Support System GRASS e Java Universal Network Graph Framework JUNG network analysis e ORA network analysis e Pajek network visualization e R statistics e iReport and Jasper Reports enterprise reporting e Spreadsheets e Structured Query Language SQL analysis within running simulations e VisAD scientific visualization and e Weka data mining North et al Complex Adaptive Systems Modeling 2013 1 3 Page 9 of 26 http www casmodeling com content 1 1 3 controller types of components that may or may not delegate some functionality to the application class SAF uses JPF to provide much of this functionality JPF provides a runtime engine that dynamically discovers and loads plug ins A plug in within the SAF context is a structured component that describes itself to JPF using a manifest which is an XML document with a specific schema This file contains information identifying the plug in what other plug ins this plug in depends on if any where its code is located and where any third party code that it depends on is located JPF does not provide the plug in content but rather a plug in discovery mechanism a plug in format and an ap plication prog
13. aphy Features in the geography may have either static or dynamic positions Typically landmark features such as roads buildings and streams represented by lines and polygons are static Mobile agent North et al Complex Adaptive Systems Modeling 2013 1 3 Page 15 of 26 http www casmodeling com content 1 1 3 feature types are typically represented by point features whose latitude longitude coor dinates can be updated dynamically during the course of a simulation 2D and 3D visualization The Repast Simphony 2D and 3D visualization modules provide tools for interactively viewing running models in 2D and 3D A 2D ReLogo example is shown in Figure 2 A 3D GIS example is shown in Figure 3 The initial 2D visualization code was based on the Piccolo2D graphical framework Piccolo2D A Structured 2D Graphics Framework Piccolo2D provides a 2D scene graph that allows for excellent animation layout zooming and user interaction Unfor tunately it proved to be too slow In particular it did not provide adequate perform ance for turtle and patch visualization in our new ReLogo language For efficient visualization the Repast Simphony design calls for a two phased approach where 1 all the visual representations of all of the agents are updated to reflect the current states of the agents and then 2 the entire scene is rendered The intention is that the first phase performs no graphical screen updates It is only after this first ph
14. ase that the actual display is updated to reflect the changes made in the first phase The new 2D visualization mechanism in Repast Simphony 2 0 uses OpenGL OpenGL The Industry s Foundation for High Performance Graphics via the Java Binding for the OpenGL JOGL API library jogl Java Binding for the OpenGL API and implements the two phased approach described above The abstraction provided by the multilayered Repast Simphony visualization system simplified transitioning from Piccolo2D to OpenGL while largely maintaining backward compatibility As before agent objects do not draw themselves but rather are associated with particular styles and layouts These styles and layouts are then applied to each agent to determine its display location and its visual repre sentation The actual 2D visualization is accomplished by using a lightweight 2D scene graph implemented on top of OpenGL The scene graph consists of a hierarchically arranged tree of nodes where operations on parent nodes apply to the children of those nodes This new library also allows the user to easily create a variety of geometric shapes create custom shapes import Scalable Vector Graphics based geometry import images and style these in a variety of ways It supports object selection zooming and panning via a camera implementation This new implementation has proven to be many times faster than the original Piccolo based approach when rendering simulations of similar visual
15. been identified as a candidate methodology for solving the problem the following questions can be asked e What are the modeling question s e Who are the stakeholders e What outputs are needed e What input data are available e What verification and validation V amp V is needed e What alternative techniques where tried e Who are the agents e What are the agent behaviors e What is the agent environment Each of these questions will be briefly addressed in our next section for our example CAS What Are the Modeling Question s The modeling question is how does the quality of ideas change over time in the innovation network Who Are the Stakeholders The stakeholders in this demonstration case are simply the modelers themselves What Outputs Are Needed The output will be the history of the quality of innovation This output will be displayed as a time series chart What Input Data Are Available For this model the input will be the probability of developing a new innovation on a given time step What V amp V is Needed The V amp V step is key It can be said that V amp V turns toys into tools North and Macal 2007 V amp V is like a properly prepared court case in that mode lers select a standard of evidence and then prepare arguments to meet the standard To be properly prepared countervailing facts must also be presented There are many sources of potential evidence for the arguments including by e Conduc
16. ccess article distributed under the terms of the Creative Commons Attribution License http creativecommons org licenses by 2 0 which permits unrestricted use distribution and reproduction in any medium provided the original work is properly cited North et al Complex Adaptive Systems Modeling 2013 1 3 Page 2 of 26 http www casmodeling com content 1 1 3 Repast Simphony is a widely used free and open source environment for agent based modeling of CAS The most recent version 2 0 was released on March 5 2012 Repast Simphony is a second generation environment that builds upon the previous Repast 3 library described in North et al 2006 This paper describes Repast Simphony and shows how to apply it to modeling CASs The next section discusses related work Section three details the architecture of Repast Simphony Section four uses a simple demonstration example to show how to model CAS with Repast Simphony Conclusions are then presented Related work This section reviews other free and open source modeling libraries and environments that are documented with published papers The review includes NetLogo StarLogo Swarm Repast 3 MASON Ascape and EcoLab StarLogo StarLogo StarLogo 2011 is a library and environment that uses a Java interpreter and interface StarLogo is an educational system that leverages the Logo language Feurzeig et al 1970 Harvey 1997 to make it easier to learn the library and to use it to develop
17. clipse a runtime engine for model execution a runtime interface for model visualization and freeze dryers for data stor age Freeze dryers are an automated way to send and retrieve the state of a simulation to and from secondary storage such as an XML extensible markup language file To implement this function Repast Simphony uses a highly modular architecture Each module is an independent plug in that can be connected or disconnected with a few Java FlowZombies src FlowZombies Zombie agent Eclipse SDK Users nick Documents workspace RepastSimphony2 Civ OQ SHG Osv SINGGOG o 7 EY Debug z I Package Exp amp S O C context xml E Zombie agent 5 a S amp 7 Zombie agent gt 5 FlowZombies Select A _ step Moved Infect Z Marquee 7 Connection A Steps Property Y Behavior E Task Grid Neighbors Find Humans Decision d Join F Loop Initialize loop amp End Loogover objects Get Object is Human save human true lt gt true I false Loop ove neighbors Braaaaaains Check count Point with most humans Found Humans 7a true true 6 neue m false false Do Tpsk 2 Problems Javadoc Declaration E Console Error Log Properties 2 Property Value Step 1 Type in a Comment that Describes this Task This is a task Step 2 Type in a Human Readable Diagram Label for the Property Point with most humans
18. code translators In Proc of 2nd international conference on generative programming and component engineering GPCE 03 Springer Lecture Notes in Computer Science 2830 Edited by Pfenning F Smaragdakis Erfurt Y Germany Springer Verlag 2003 364 376 Collier NT North MJ Repast HPC A library for large scale agent based modeling In Large Scale Computing Techniques for Complex System Simulations Edited by Dubitzky W Kurowski K Schott B Hoboken NJ Wiley IEEE Computer Society Press 2011 Collier NT North MJ Parallel agent based programming with Repast for High Performance Computing Simulation 2999 in press Collier N Howe T North MJ Onward and upward The transition to Repast 2 0 In Proceedings of the first annual North American Association for Computational Social and Organizational Science conference Edited by Carley K Pittsburgh Carnegie Mellon University 2003 Electronic Proceedings Colt Home Page 2999 http acs lbl gov software colt Eclipse Home Page 2999 http www eclipse org ESRI Understanding our world 2999 http www esri com Feurzeig W Papert S Bloom M Grant R Solomon C Programming languages as a conceptual framework for teaching mathematics Interface 1970 4 2 GeoTools The Open Source Java GIS Toolkit 2999 http geotools org GRASS GIS The world s leading Free GIS software 2999 http grass fok eu Groovy A dynamic language for the Java platform 2999 http groovy code
19. ction is the ability to examine the type information of objects dynamically that is while a program is running Stand ish also states that dynamic pointers that automatically track objects such as agents are important These pointers should automatically note the type of object being tracked and should indicate whether an object reference has been deallocated from memory Methods Repast Simphony The free and open source REcursive Porous Agent Simulation Toolkit Repast was originally developed by Sallach Collier and others Collier et al 2003 at the University of Chicago in 2000 and was subsequently expanded by Argonne National Laboratory as a reusable software infrastructure that could support rapid social science discovery based on extensive computational experimentation Sallach and Macal 2001 Successive releases of Repast have extended the system to handle large scale agent simulation applica tion development Repast is managed by the not for profit volunteer Repast Organization for Architecture and Design ROAD ROAD is led by a board of directors that includes members from a range of government academic and industrial organizations Argonne National Laboratory is especially active in maintaining and developing Repast Many other groups contribute to Repast s development For example the University of Michigan recently teamed with Argonne to add more than 20 demonstration models to Repast Simphony with support from the 2011
20. del runtime window You can double click on the UserGlobalsAndPanelFactory groovy file and modify the addGlobalsAndPanelComponents method as follows public void addGlobalsAndPanelComponents Add the needed control buttons addButton setup addToggleButton go North et al Complex Adaptive Systems Modeling 2013 1 3 Page 21 of 26 http www casmodeling com content 1 1 3 Add the model input addinput innovationProbability 0 001 The generated UserGlobalsAndPanelFactory groovy file may contain additional ex ample code that will not be activated given that it is commented Commented code lines may begin with either or and will be ignored by the simulation runtime The three new lines added above create graphical buttons in the model runtime window that provide functions to setup and run the model Changes to the UserGlobalsAndPanelFactory groovy file are now complete The UserLink groovy file does not require any modifica tions at this time Next you should open the UserObserver groovy file which will contain code that defines how to initialize the model and what happens at each simulation tick Again there will be example code in the generated UserObserver that can be ignored or deleted The UserObserver requires two methods setup and go which are listed below Define the model builder def setup Remove any existing turtles clea
21. ding display definition etc about the model and is itself a collection of extensions In addition the mechanisms by which these are manipulated e g display wizards are also extensions implementing extension points defined by the Repast Simphony run time interface In this way Repast Simphony and the Repast runtime interface are modular and easily extensible The value of Repast Simphony s modularity was demon strated when the initial library used by SAF to provide docking windows needed to be replaced to meet increasing user requirements The modular structure allowed the docking windows library to be swapped out while maintaining backward compatibility with existing user models Core The Repast Simphony core plug ins provide major simulation functions including time scheduling space management behavior activation and random number generation North et al 2007 Repast Simphony space management uses contexts and projections Repast Simphony provides a discrete event time scheduler that uses double precision real numbers for event times The scheduler also allows events with otherwise identical times to be differentiated with an optional priority ranking The Repast scheduler offers imperative scheduling and declarative scheduling for both sequential and concurrent activities as discussed later in this section North et al Complex Adaptive Systems Modeling 2013 1 3 Page 10 of 26 http www casmodeling com content 1 1 3 ADO Zo
22. e s plug in architecture is open to allow almost any kind of software to be added to the system We have used this feature to provide users with a default set of built in tools for model results analysis Some of these tools are directly embedded within the runtime interface and others are externally activated The default embedded tools are generally Java based libraries with Repast Simphony compatible licenses Examples include the JUNG network analysis system JUNG Java Universal Network Graph Framework and the SQL for Java Objects JoSQL library JoSQL What is JoSQL Repast uses JUNG for network storage and statistical analysis and uses JoSQL to allow users to query paused simulations interactively using SQL The default external tools are either not Java based or use licenses that are free and open source but incompatible with the Repast Simphony license These external pro grams are activated by wizards that go through the following sequence 1 ask users which data sets should be selected for analysis 2 export the data to a format that is readable by the external tool 3 note the licensing terms of the external program 4 start the external executable 5 automatically load the exported data into the target North et al Complex Adaptive Systems Modeling 2013 1 3 Page 18 of 26 http www casmodeling com content 1 1 3 application and then 6 switch focus to the external program The external tool loads into a separate
23. ecause it directly connects the scheduling information to the scheduled method itself rather than dividing this task among multiple locations in the model Both watch based scheduling and unconditional scheduling allow concurrent or parallel code execution This optional feature is activated by setting the duration of the activity being scheduled to a non zero value The duration is the length of time the activity is considered to take Any activities that occur between the start of the activity with non zero duration and the end of the duration are candidates to be concurrently executed with the activity having non zero duration The default duration is zero indi cating sequential execution Whether the execution is simply concurrent or actually parallel is determined by the underlying hardware the Java virtual machine in use and the interrelated details of the activities being scheduled This approach allows modelers to begin with simpler sequential execution and then scale up to concurrent or parallel execution as they continue to develop their models Many agent behaviors use random number generation for option selection The Repast Simphony core module includes a full suite of random number generation tools Repast uses the Colt library Colt Home Page to produce random numbers Colt has been widely used for scientific computation and is well validated Repast makes its Colt based random number sources accessible through a random helper cla
24. epast Simphony network projection stores a network or graph relationship between the members of its context The members of this context can then ask to whom they are linked and who is linked to them Similarly the Repast Simphony grid projection stores a set of Cartesian coordinates for each member of the context The members of this context can ask where they are located Each context can support any mixture of projections Also projections can be declaratively visualized at runtime Contexts and projections can use watchers to activate behaviors The following example shows an agent behavior that is activated at certain times when an appropriate social network neighbor changes its contentment attribute This is an example watcher activation method Watch watcheeClassName North et al Complex Adaptive Systems Modeling 2013 1 3 Page 11 of 26 http www casmodeling com content 1 1 3 repast user models ExampleSocialAgent watcheeFieldName contentment query linked_to neighbors and not linked_from work and colocated triggerCondition watchee getContentment watcher contentment whenToTrigger WatcherTriggerSchedule LATER scheduleTriggerDelta 5 scheduleTriggerPriority 15 public void neighborMoodUpdated ExampleSocialAgent neighbor Check the contentment level if neighbor getContentment gt 0 5 Copy a neighbor this setContentment neighbor getContentment else Decide f
25. er between zero and one and checking this value against the input threshold value 1 0 innovationProbability If a new innovation is to be created then the innovation value is set based on the random value the turtle s icon color is set to the new innovation value and the turtle s existing links are destroyed In the event that a new innovation is created the turtle next asks for other turtle agents nearby located in the same patch to which the new innovation will be trans ferred The innovating turtle sets its neighboring turtles innovation and color to the new innovation value destroys the neighboring turtles existing links and gener ates a new link between the turtle and its neighbor Editing of all of the model code is now complete Next you can add a Total Innovation chart New charts begin with data sets Data sets collect data from agents As previously discussed charts files or external analysis tools can use the resulting data To begin creating the chart you can right click on the Data Sets item in the Scenario Tree in the lower left panel of the Repast Simphony runtime interface You should then type in Total Innovation as the Data Set Id You should then click Next and choose the Method Data Sources tab on the next wizard page You can click Add to add a column to the data set You should type in totalInno vation as the Source Name
26. f the Turtle agent behaviors The UserTurtle agent behavior is defined entirely within the act method and innovation parameter which are described below Define the innovation tracker int innovation 0 Define the activity def act Move forward randomly left random 15 right random 15 forward 1 1 Spontaneously create innovations if randomFloat 1 0 gt 1 0 innovationProbability Develop the new innovation innovation 10 random 11 25 setColor innovation Clear out my old links ask myLinks die Check for an innovation if innovation gt 0 Diffuse an innovation from myself to nearby turtles self ask other turtlesHere Get the innovation innovation myself innovation setColor myself getColor Clear out the old links ask myLinks die Build a new link UserLink newLink createLinkWith myself newLink setColor myself getColor The UserTurtle act method first moves the turtle forward by 1 1 units in a direc tion that is randomly determined by generating a random integer between 1 and 15 and then rotating the turtle left and right and finally moving 1 1 units forward Next Page 22 of 26 North et al Complex Adaptive Systems Modeling 2013 1 3 Page 23 of 26 http www casmodeling com content 1 1 3 spontaneous innovations are randomly created within the turtle by generating a ran dom integ
27. haus org Harvey B Computer Science Logo Style Boston MIT Press 1997 Holland JH Studying complex adaptive systems J Syst Sci Complex 2006 19 1 8 Jaspersoft Community iReport Designer 2999 http jasperforge org projects ireport Jaspersoft Community JasperReports Library 2999 http jasperforge org projects jasperreports Java Plug in Framework JPF Project 2999 http jpfsourceforge net jog Java Binding for the OpenGL API 2999 http jogamp org jog www JoSQL What is JoSQL 2999 http josql sourceforge net JUNG Java Universal Network Graph Framework 2999 http jung sourceforge net Ke J Holland JH Language origin from an emergentist perspective Applied Linguistics 2006 27 691 716 LOG4J Logging Services 2999 http logging apache org log4j Luke S Cioffi Revilla C Panait L Sullivan K Balan G MASON A multiagent simulation environment SIMULATION 2005 81 517 527 acal CM Agent based Modeling and Artificial Life In Encyclopedia of Complexity and System Science Edited by Meyers RA Springer 2009 112 131 ISBN 978 0 387 75888 6 acal CM North MJ Tutorial on agent based modeling and simulation J Simul 2010 4 151 162 ahalik MR Conzelmann G Stephan CH Mintz MM Veselka TD Tolley GS Jones DW Modeling the transition to hydrogen based transportation In Proceedings of the agent 2007 conference on complex interaction and social emergence Edited by North M Macal C Sallach D Argon
28. into common tools such as Microsoft Excel and easily edited Moreover add itional objects e g agents can be created offline by adding rows to the relevant table This tabular serialization format has worked reasonably well although it does present some maintenance difficulties In particular large changes to Repast Simphony classes such as networks grids and so forth that are serialized often require changes to the serialization code The implementation of tabular serialization also exposed some dif ferences in Java reflection implementations across operating systems XML format serialization was introduced as a simpler and more extensible serialization solution for those applications that did not need the benefits of the tabular format or had issues with it XML serialization uses the XStream XStream Home Page serialization library to serialize objects to and from XML The default serialization provided by XStream can be extended and customized by using its converter mechanism Repast Simphony takes advantage of this capability by implementing custom converters for its major components providing more efficient serialization It also allows users to provide their own custom converters for serializing their own models This functionality allows the user to handle or work around any issues in serialization without requiring any time consuming changes to Repast Simphony itself Third party applications The Repast Simphony runtime interfac
29. ion Initialization and termination occur once per run whereas recording occurs at some regular interval e g once every three ticks Crucial to the proper functioning of data collection is specification of a set of notifications associated with these phases For example when writing a row of data in tabular delimited format it is necessary to notify the writer that all of the data for that row has been collected and can now be written Similarly a histogram component requires notification that the record phase has ended and that the histogram should now be produced with the recorded data The first Repast Simphony data collection system was built upon Log4J LOG4J Log ging Services Although Log4J is a widely used for fast minimal overhead logging North et al Complex Adaptive Systems Modeling 2013 1 3 Page 14 of 26 http www casmodeling com content 1 1 3 adapting it to the requirements of Repast Simphony s data collection functionality proved to be problematic Log4J was difficult to adapt to the time stamped and time phased na ture of Repast Simphony data collection Log4J has no real user facing mechanism for re peated initialization and termination from within a single application instance Our incremental understanding of these requirements and adapting them to Log4J s system of logging levels and logging messages resulted in code that was inflexible and hard to man age The isolation available in the multilayered Repast Si
30. is of Distributed Processes with Agent Based Systems MADCABS model is a Repast Simphony simulation framework for investigating the operation and control of complex networks Artel et al 2011 Tatara et al 2006 MADCABS combines agent models with traditional differential equations models MAD CABS has been used for a variety of research pursuits including to study the effectiveness of perceptron based learning for the robust operation of distributed chemical reactor networks The Hydrogen Economy Model Mahalik et al 2007 is a Repast Simphony representa tion of the Los Angeles California metropolitan area with 5 000 square miles of detailed and geographic information system GIS sourced interstate highways and omnipresent local roads The model has driver and investor agents Driver agents use their cars to move between their demographically assigned home neighborhoods and their jobs Dri vers have a variety of characteristics including income levels environmental concerns risk North et al Complex Adaptive Systems Modeling 2013 1 3 Page 6 of 26 http www casmodeling com content 1 1 3 aversion and car type preferences e g wanting conventional fuel cars versus hydrogen cars Investor agents build own and operate hydrogen fuel stations based on the inves tor s estimates of the potential for profits at each available geolocated site The Endogenous Emergence of Coordination EndEC model Ozik and North 2010 is a Repast Simph
31. its links What Is the Agent Environment The agent environment is a simple continuous 2D surface with support for a network between agents Model implementation Next we will illustrate how you can implement a Repast Simphony model The model implementation follows directly from the design questions answered in the previous section To begin you can create a new ReLogo project by clicking the new project wizard icon in the toolbar This icon has a blue folder with red RL text in the upper left corner The new project wizard dialog will appear with options for the project name and other advanced project options The only required change in this dialog is the project name which should be changed to Innovation You can click Finish to complete the new ReLogo project setup Once the project setup process is complete a new project named Innovation will appear in the left windowpane with a set of project components below Two folders are visible src which contains the model code and shape which con tains a set of optional icons that may be assigned to agents Expand the src folder to view the model components The src folder contains the package innovation relogo which itself contains the automatically generated model components such as the UserObserver UserPatch UserTurtle and others The first step is to create a set of basic user controls that will appear in the mo
32. l 2006 presented one of the first implementations the Repast watcher pattern in a large scale agent based model of military deployment logistics The execution speed of the logistics model implementation in Repast was more than an order of magnitude faster than the previous Java implementation with polling based agent behaviors Annotations can also be used for tasks such as unconditional scheduling In this usage individual methods can be called at specified times without the need for explicit Java method calls to the Repast scheduling system This approach has the potential to be both North et al Complex Adaptive Systems Modeling 2013 1 3 Page 12 of 26 http www casmodeling com content 1 1 3 E3 Geo Model Repast Simphony D00 File Run Tools view Window SEL 000o0R 1 B2 Q BA8ehe Tick Count 65 0 A S Oler dQ Layers Stars Atmosphere Fog NASA Blue Marble Image NASA Blue Marble i cubed Landsat USGS Urban Area Ortho Place Names World Map Scale bar Compass GisAgent Network Off globe Figure 3 A Repast Simphony demonstration model that combines GIS with a network more convenient than the conventional Java method of call scheduling because it requires only the setting of a few annotation parameters rather than the making of a set of method calls It is also better documented b
33. lications typically follow the model view controller design pattern with the addition of a class that mediates between various parts of the application This mediator provides a link between the user interface and the application functionality triggered by the user The Repast Simphony runtime interface implementation consists of three components the user interface proper the simulation engine infrastructure and the application class that mediates the inter action between the two The user interface is composed of other smaller model view Table 1 Selected repast simphony plug ins and plug in sets Plugin or plugin sets Function Simphony Application Framework Provides the basic runtime interface plug in system and user interface tools Eclipse Set Provides model specification and programming tools Core Set Provides central simulation functions such as scheduling ReLogo Set Provides a simple modeling language and structure GIS Provides GIS modeling and visualization Freeze Dryer Set Batch Run Set Deployment Charts Model Integration 2D Visualization Set 3D Visualization Set Terracotta System Dynamics Third Party Application Set Provides persistence in XML and text formats Provides parameter sweeps and stochastic iteration Packages user models for self contained release Provides interactive model graphing in the runtime interface Provides tools for embedding legacy models Provides tools for interactive two dimension
34. ling 2013 1 3 Page 7 of 26 http www casmodeling com content 1 1 3 These design goals have been met by the Repast Simphony architecture Eclipse Eclipse Eclipse Home Page is a widely used free and open source development envi ronment that is multilingual and integrated Eclipse can be used to develop code in many languages including Java and C Java support is particularly strong The Repast Simphony system uses Eclipse as its primary development environment Repast Simphony leverages Eclipse s plug in architecture to provide a set of develop ment options It is important to note that while Eclipse s plug in architecture is concep tually similar to that of Repast Eclipse uses a different implementation The Repast Simphony Eclipse plug ins provide tools views i e windows and per spectives i e selected sets of windows for creating a range of Repast specific model components including general Repast projects ReLogo projects flowcharts and ReLogo agents The plug ins also allow Repast models to be executed debugged and packaged into self contained installers for deployment An example flowchart that can be used to encode agent attributes and behaviors is shown in Figure 1 Repast Simphony architecture The design goal of maintaining a strict separation between model specification model execution data storage and visualization has led to creation of the multilingual Repast Simphony model development environment in E
35. ly integrates with Java Thanks to its Groovy foundations ReLogo freely interoperates with Groovy and Java ReLogo programmers can use any Java or Groovy library without special syntax They can also write Groovy or Java code fluidly at any point in a ReLogo file to gain access to the advanced features of either language A ReLogo model is compiled by using the Groovy Eclipse joint compiler The ReLogo code is first converted into its Abstract Syntax Tree AST representation The AST is then repeatedly transformed by Repast Simphony to generate model specific custom ReLogo code as needed The end result is Java byte code which is run as a regular Repast Simphony model Data collection The Repast Simphony data collection system is designed to gather and store informa tion from a simulation while it is running The system typically collects predefined sets of data from each agent at each time step a particular piece of logged data represents the state of the simulation at a particular time This logged data can contain aggregate and nonaggregate values An aggregate data value represents the result of an aggregate operation e g summation performed over some collection of individual values Typic ally these individual values correspond to agent properties A nonaggregate value is some individual value again typically an agent property Data collection in Repast Simphony consists of three phases namely initialization recording and terminat
36. mage servers Agent feature layers are placed over the underlying raster image layers and the extent of transparency colors and size of agent feature styles are fully customizable Freeze drying Repast Simphony allows the user to serialize or checkpoint the state of the simulation for later retrieval and execution Tabular and XML formats are supported The tabular format North et al Complex Adaptive Systems Modeling 2013 1 3 Page 17 of 26 http www casmodeling com content 1 1 3 writes the serialized objects to rows and columns where each row represents an object and each column a property of that object An additional column contains a unique identi fier generated by Repast Simphony for each object Objects are serialized by type with a single table holding the data for all objects of that type Additional tables record the state of the object tree For example a Map may contain agents and those agents may them selves contain additional objects These tree tables would then record the parent child relationships between the map and the agents and the agents and the objects they contain The motivation for the tabular format was two fold First we wanted to be able to load data into a variety of standard databases easily and a tabular format made that relatively straightforward Second we wanted the state of agents to be editable offline When saved to a delimited file format the state of the simulation and its agents can be loaded
37. mbies Repast Simphony B O OlO e V s e 0 y 41 8 m oN Tick Count 4090 C default_observer_context ReLogo Default Display 00x sla Setup gt Go Number of Humans 50 o Number of Zombies 5 DAR Gestation 5 o _ remainingHumans 11 Brains FA Scenario Tree 00 zo Jz aA c vd Le osi o Tp o v m 4 Parameters Scenario Tree Paused Figure 2 The Repast Simphony zombie demonstration model Repast Simphony contexts are hierarchically nested and named containers that hold model components The model components can be any type of Java object including other contexts but are typically agent objects It should be noted that contexts can be agents as well Each model component can be present in as many contexts as the mod eler desires The hierarchical nesting means that a model component that is present in a context is also present in all of that context s parent contexts Of course the converse is not true in the general case The hierarchical nesting structure can be declaratively or imperatively specified by the modeler In addition the contents of components within contexts e g agent properties can be declaratively logged at runtime In addition to supporting hierarchical nesting contexts also support projections Repast Simphony projections are named sets of relationships defined over the constituents of a context For example a R
38. memory space with no direct linkage to the initiating Repast model so there are no licensing conflicts The experience is nonetheless seamless for the model user Example default external tools include the R statistics system http www 1 project org the GRASS GIS GRASS GIS The world s leading Free GIS software the ORA network analysis system CASOS ORA the Pajek network visualization system Networks Pajek Program for Large Network Analysis the iReport reporting tool Jaspersoft Community iReport Designer the JasperReports reporting tools Jaspersoft Community JasperReports Library common spreadsheets the VisAD scientific visualization system VisAD McIDAS V and the Weka data mining system WEKA Machine Learning Group at the University of Waikato Results and discussion CAS modeling example This section uses a simple demonstration example to show how to develop models of complex adaptive systems with Repast Simphony The approach presented here follows the methodology detailed in North and Macal 2007 and North and Macal 2009 The example scenario is intentionally simple so that it clearly shows the essential steps of the model design and development process The scenario is an innovation diffusion environment in which a group of people randomly circulates People occasionally com municate ideas when they encounter one another When an idea is transferred a new link is made between the transferring
39. mphony logging system made it easier for the Repast development team to transition from Log4J to custom code while largely maintaining backward compatibility Consequently the data collection mechanism was replaced by a new one built on the following abstractions data sources data sinks and data sets Data sources are just that sources of data A nonaggregate data source receives a single object e g an agent and returns some data value typically but not necessarily a property of that agent An aggregate data source receives multiple objects and performs some aggregate operation over all of the objects It then returns the result of that operation For example it might calculate the mean value of some property over all of the objects A data sink writes the output of these data sources for example to a file or a chart A data set manages a collection of sources and sinks providing the objects on which the data sources operate and directing the results to data sinks Each data source can be thought of as a column in a tabular spreadsheet type of format and each row is the result of recording data from each data source associated with a data set Crucially a data set also provides notifications to data sinks notifying them that a new row of data is being started that a row has ended and that the entire record phase for the current time period has ended It provides similar notifications to the data sources for example notifying an aggrega
40. n for an individual agent relative to the topology in which it resides The screen location of an agent in a network is determined by the incoming and outgoing links of that agent whereas an agent in a grid topology is laid out according to its grid location Conse quently the layout interface contains methods to associate it with the particular top ology or topologies being displayed Often layouts need to be recalculated as agents are added and removed from the topology and the layout interface reflects this need as well The implementation of style and layout as interfaces independent of agent implementation and the subsequent styling and layout of agents provide the required flexibility Agents can be represented differently but simultaneously in 2D and 3D displays while participating in different types of topologies Both the 2D and 3D display implementations use a scene graph architecture Individual agents are represented as geometric nodes in the scene The appearance color and so forth of the object is determined by the style and applied to the object in some scene graph specific way For example in a 3D display the color of a node s surface appearance is determined by the color returned from the style The node s ultimate screen location is the result of translating the node by the amount returned from the layout Updates to the displays occur in two stages Zooming panning and so forth are implemented as opera tions on the root
41. ne IL Argonne National Laboratory 2007 eade N Islam T Modelling and forecasting the diffusion of innovation A 25 year review Int J Forecast 2006 22 519 545 inar N Burkhart R Langton C Askenazi M The Swarm simulation system A toolkit for building multi agent simulations Santa Fe Santa Fe Institute 1996 Working Paper 96 06 042 ASA World Wind 2999 http worldwind arc nasa gov java etLogo User Manual FAQ Frequently Asked Questions 2999 http ccl northwestern edu netlogo faq html etworks Pajek Program for Large Network Analysis 2999 http vlado fmf uni lj si pub networks pajek orth MJ Macal CM Managing business complexity Discovering strategic solutions with agent based modeling and simulation Oxford U K Oxford University Press 2007 North et al Complex Adaptive Systems Modeling 2013 1 3 Page 26 of 26 http www casmodeling com content 1 1 3 orth MJ Macal CM Foundations of and recent advances in artificial life modeling with Repast 3 and Repast Simphony In Artificial Life Models in Software 2nd edition Edited by Adamatzky A Komosinski M Heidelberg Springer 2009 37 60 orth MJ Howe TR Collier NT Vos RJ The Repast Simphony runtime system In Proceedings of the agent 2005 conference on generative social processes models and mechanisms Edited by Macal C North M Sallach D Argonne L Argonne National Laboratory 2005 151 158 orth MJ Collier NT Vo
42. node or camera of the scene As mentioned above display updates are a two stage process In the first the scene graph is updated to reflect the latest styling and layout information and then in the second the scene graph is rendered GIS displays are available in both 2D and 3D implementations both of which may use the same underlying geography projection The 2D GIS display map is based on modified rendering utilities from GeoTools along with features from Piccolo2D Agent features are visible in the 2D map according to the defined GIS style which can be cre ated and modified by the user at runtime via the built in style editor or imported from an OGC styled layer descriptor SLD file OGC Making Location Count Standards The 2D GIS display can be panned and zoomed in two dimensions An additional GIS display type is based on the NASA World Wind Java WWJ soft ware development kit SDK NASA World Wind and shown in Figure 3 This WWJ display uses OpenGL to render an interactive globe on which geographical features are placed The display behavior is similar to that of the 2D GIS display such that features are represented by points lines and polygons and can be either static or dynamic The default display contains several base raster layers for terrain and satellite data which are fetched from public domain servers at runtime Depending on the level of zoom magnification finer and finer detail will be pulled automatically from the i
43. ony simulation of the endogenous emergence of coordination within a group of social agents The model demonstrates the use of a dynamic language spe cifically Groovy to represent the socially coordinated evolution of behavior The EndEC sample model is inspired in part by Holland s work on the emergence of lan guage Ke and Holland 2006 Tao et al 2005 The model consists of a set of agents each with an individual list of movement capabilities and utterances The agent s move ment capabilities and utterances are drawn from separate supersets that are available to the population as a whole The agents each maintain their own individual associations of movements with utterances As the simulation proceeds agents make utterances to announce their movements and over time adjust their associations to match the observed behavior of their neighbors These simple behavior rules result in the dynamic emergence of complex coordination between groups of agents SHULGI is a Repast Simphony model of ancient pedestrian traffic in urban environ ments Branting et al 2007 The model represents a wide range of issues that affect pedestrian route choices including source and destination locations roadway availabil ity and quality and the metabolic energy costs of candidate routes The factors can be flexibly weighted as needed to address different questions of interest The model has been successfully validated by using archaeological data from the ancien
44. or ourselves this setContentment RandomHelper nextDouble In this example the neighborMoodUpdated method will be called after another ExampleSocialAgent s contentment changes if the current agent is linked to the watched agent in the neighbor network is not linked from the watched agent in the work network is colocated with the watched agent in a context and has a contentment setting different from that of the watched agent s contentment The neighborMoodUp dated method will be called five ticks after the change and the event will be given a scheduler priority of 15 which is substantially higher than the default value of zero As shown in the example contexts work directly with watchers by allowing watcher quer ies to use context names and properties Similarly projections work directly with watchers allowing watcher queries to use projection names e g neighbors and work in Figure 3 properties and relationships e g linked_to linked_from and colocated in Figure 3 The watcher mechanism provides a listener like design pattern for reactive agent behavior which is computationally more efficient than polling a collection of agents at a fixed interval Runtime agent class instrumentation is performed with the Javassist library Chiba and Nishizawa 2003 when the agent classes are loaded by the Repast runtime which occurs automatically for classes with Watch annotations Bozada et a
45. parties and then any existing network links are forgotten People occasionally develop new ideas When they do so they forget all of their old links The quality of ideas is rated and tracked over time The question posed to the simulation is what is the quality of ideas over time In the sections that follow we discuss the appropriateness of using agent based model ing to simulate the problem of interest decompose the problem into components a using a series of design questions and then show how the resulting implementation proceeds step by step The combination of these steps produces a simple illustrative model When to use agent based modeling Agent based modeling is a good choice compared to other modeling techniques when the problem naturally consists of agents or when the decision makers to be modeled meet the following criteria e Must have real individual behaviors e Adapt change or learn e Form dynamically changing relationships e Form organizations e Have spatial interactions e Have arbitrarily large populations or e When structural change is an output not an input Our example satisfies two of the criteria our innovation diffusion CAS is naturally composed of agents and the agents form dynamically changing relationships North et al Complex Adaptive Systems Modeling 2013 1 3 Page 19 of 26 http www casmodeling com content 1 1 3 Essential agent based model design questions Once agent based modeling has
46. pment of NetLogo Agent based simulation environments and languages should be simple enough to allow beginners to start quickly Agent modeling libraries should in principle place no limits on what experienced users can do Agent modeling libraries should also include a large number of example simulations to help beginning and experienced users alike For Wilensky 2012 and Tisue and Wilensky 2004 programming is not something to be avoided The challenge is not to develop a programming free way to specify mod els Most people can learn to program The challenge is to simplify programming syn tax and semantics enough to make programming accessible Visual programming is not North et al Complex Adaptive Systems Modeling 2013 1 3 Page 3 of 26 http www casmodeling com content 1 1 3 necessarily the easiest way to specify models They state that working with a carefully designed text based language can sometimes be easier than a visual one Swarm Swarm is a free and open source toolkit with both Objective C and Java bindings Minar et al 1996 Swarm also uses a GPL license Swarm was originally developed as a software toolkit for the creation of simulation models in the field of Artificial Life A Life Macal 2009 Swarm provides modelers with a flexible nested approach to modeling interactions Swarm was highly influential in the development of libraries that would arrive on the scene later such as Repast 3 North et al 2006 and Repast
47. r colors and the links between these turtles indicate the innovation pedigree Clicking on the Total Innovation chart tab on the lower right shows the resulting total innovation Conclusions There are several directions for future work using the open source Repast Simphony agent based environment for modeling in CASs including to provide more scalable support for large scale modeling to simplify model specification and to provide more facilities to support model verification and validation In terms of scalability the Repast team has recently completed a C Message Passing Interface implementation of the core Repast feature set that targets supercomputer execution This new library Repast for High Performance Computing Collier and North 2011 Collier and North 2999 has recently been shown to have excellent weak scalability on Argonne National Laboratory s IBM Blue Gene P Abbreviations 2D Two dimensional 3D Three dimensional API Application programming interface AST Abstract syntax tree BSD Berkeley software distribution CAS Complex adaptive system CRS Coordinate referencing system EndEC Endogenous emergence of coordination ESRI Environmental systems research institute GIS Geographic information system GPL General public license GRASS Geographic resources analysis support system JOGL Java binding for the OpenGL JoSQL SQL for Java Objects JPF Java plug in framework JUNG Java Universal Network G
48. rAll Build a new set of turtles createTurtles 20 setShape person setColor gray forward 1 Distribute an initial innovation ask turtles first innovation yellow setColor innovation Define the model time step routine def go Give each turtle a chance to act ask turtles act The setup method is called when the setup button in the runtime window is pressed The button was previously created in the UserGlobalsAndPanelFactory and the functionality is provided in the UserObserver The setup routine first clears the model of any existing turtles using clearAll for the case when the model had already been run Next the setup method creates a set of 20 turtles sets the shape of each turtle to the person icon shape sets the initial color of the icon to gray and moves the turtle agent one step forward Finally setup retrieves the first turtle and sets its North et al Complex Adaptive Systems Modeling 2013 1 3 http www casmodeling com content 1 1 3 innovation parameter and color to yellow The go method asks each turtle agent to execute its act method once each time the simulation is stepped The turtle s ask method will be defined next The UserPatch groovy file does not require any add itional modification You should open the UserTurtle groovy file to edit the turtle agent class that will con tain all o
49. ramming interface API for working with such SAF then uses these pieces to create an application framework This plug in approach helps to make SAF applications modular Specific bits of appli cation functionality can be defined in separate plug ins and loaded at runtime Repast Simphony as a whole is simply a collection of plug ins allowing bits and pieces of Re past to be used as required The Repast Simphony runtime interface also leverages this modularity in a variety of ways For example the integration with third party applica tions such as the R statistical package that appear in the toolbar is accomplished by using the plug in mechanism Third party application integration is discussed later In addition to promoting modularity JPF also makes applications extensible by using plug in extension points and extensions An extension point functions as a generic interface that defines some specific functionality and how to invoke that functionality in an abstract way An extension is an implementation of an extension point SAF defines extension points appropriate for building applications and the Repast Simph ony runtime interface implements these as extensions Both the Repast runtime inter face and Repast Simphony define Repast specific extension points and extension implementations For example the Repast Simphony runtime interface scenario tree that appears on the lower left side of Figure 2 contains various metadata e g context loa
50. raph Framework MADCABS Monitoring analysis and diagnosis of distributed processes with agent based systems NQP Not Quite Python OGC Open geospatial consortium P amp G Procter amp gamble Repast REcursive porous agent simulation toolkit ROAD Repast organization for architecture and design SAF Simphony application framework SDK Software development kit SLD styled layer descriptor SQL Structured query language V amp V Verification and validation WWJ World wind Java XML Extensible markup language Competing interests The authors declare that they have no competing interests Authors contributions MJN NTC JO ERT MB and others developed the Repast Simphony code MJN NTC JO ERT and MB wrote parts of the paper MJN wrote the innovation demonstration model All authors MJN NTC JO ERT CMM MB and PS read and approved the final manuscript North et al Complex Adaptive Systems Modeling 2013 1 3 Page 25 of 26 http www casmodeling com content 1 1 3 Acknowledgments The submitted manuscript has been create by UChicago Argonne LLC Operator of Argonne National Laboratory Argonne Argonne a U S Department of Energy Office of Science laboratory is operated under Contract No DE AC02 06CH11357 The U S Government retains for itself and others acting on its behalf a paid up nonexclusive irrevocable worldwide license in said article to reproduce prepare derivative works distribute copies to the public and
51. rom social systems to evolutionary systems market modeling and industrial analysis A sampling of Repast applications will be pre sented next Example Repast Simphony applications This section briefly discusses several example Repast Simphony applications that illus trate the versatility of the system The examples include applications that study phe nomena related to consumer products systems engineering possible future hydrogen infrastructures social science and ancient pedestrian traffic to name a few Additional examples can be found in North and Macal 2009 The Virtual Market Learning Lab North et al 2010 is a large scale Repast Simphony model of consumer markets co developed by Argonne National Laboratory and Procter amp Gamble P amp G It represents the shopping behavior of consumer households and the busi ness behavior of retailers and manufacturers in a simulated national consumer market Argonne and P amp G successfully calibrated verified and validated the resulting agent based model using several independent real world data sets for multiple consumer product categories with more than 60 comparison tests per data set First Repast and then later Repast Simphony were used to implement the model P amp G has successfully applied the model to several challenging business problems where it has directly influenced manager ial decision making and has produced substantial cost savings The Monitoring Analysis and Diagnos
52. s RJ Experiences creating three implementations of the Repast agent modeling toolkit ACM Transactions on Modeling and Computer Simulation 16 1 th edition New York ACM 2006 1 25 orth MJ Howe TR Collier NT Vos JR A declarative model assembly infrastructure for verification and validation In Advancing social simulation the first world congress Edited by Takahashi S Sallach DL Rouchier J Heidelberg Springer 2007 129 140 orth MJ Macal CM St Aubin J Thimmapuram P Bragen M Hahn J Karr J Brigham N Lacy ME Hampton D Multi scale agent based consumer market modeling Complexity 2010 15 5 37 47 OGC Making Location Count Standards 2999 http www opengeospatial org standards sld OGC Making location count 2999 http www opengeospatial org OpenGL The Industry s Foundation for High Performance Graphics 2999 http www opengl org Ozik J North MJ Modeling endogenous coordination with a dynamic language In Simulating interacting agents and social phenomenon the second world congress on social simulationEdited by Takadama K Cioffi Revilla C Deffuant G Heidelberg FRG Springer 2010 265 276 Parker MT Ascape Abstracting complexity Nat Res Environ Issues 2001 8 21 30 Piccolo2D A Structured 2D Graphics Framework 2999 http www piccolo2d org Repast The Repast Suite 2999 http repast sourceforge net Resnick M StarLogo An environment for decentralized modeling and decentralized thinking
53. s button has a blue circular icon with a white circular on symbol in the middle After the model has been initialized the User Panel pane of the model runtime window will contain the setup and go buttons used to control the model Clicking the setup button executes the setup method of the UserObserver described above which creates an initial population of turtles in a circular arrangement in the center of the display panel on the right side of the simulation runtime window One of the turtle icons is a different color than the others since the UserObserver set its innovation value to the nonzero value Selecting the go button runs the model continuously The turtles start to spread out in a circular pattern and some additional turtles near the initial innovator may be colored according to the adopted innovation The runtime window for a model that was run continuously for several hundred time North et al Complex Adaptive Systems Modeling 2013 1 3 Page 24 of 26 http www casmodeling com content 1 1 3 eoo Innovation Repast Simphony ooo ACCAC Tick Count 161 0 User Panel 00 ReLogo ReLogo Default Display setup go innovationProbability 0 001 Scenario Tree 00 Total Innovation Paused Figure 4 The example Repast Simphony innovation model steps is shown in Figure 4 Turtles that share the same innovation value are simila
54. ss with a supporting internal registry The internal registry supports efficient reuse of random streams It also allows all random streams to be simultaneously reset when a user changes the default random seed North et al Complex Adaptive Systems Modeling 2013 1 3 Page 13 of 26 http www casmodeling com content 1 1 3 ReLogo ReLogo wraps much of the Repast Simphony library s functionality into a semantically simple but powerful package The goal is to provide a fast track so modelers can quickly develop simulations that can later be scaled up as needed using the features of the full Repast Simphony library A tool for automatically converting NetLogo models into ReLogo models is also included ReLogo semantics are drawn from the venerable Logo lineage of software Harvey 1997 informed especially by the previously discussed StarLogo Resnick 1996 and NetLogo Wilensky 2012 variants while maintaining the object oriented nature of Repast Simphony ReLogo provides a streamlined Eclipse perspective to create Repast Simphony models with turtles links patches and observers An example is shown in the Innovation model discussed later ReLogo models are programmed using a Logo style syntax the ReLogo domain specific language based on the Groovy Groovy A dynamic language for the Java platform dynamic language Groovy itself is a widely used free and open source Java Virtual Machine language that both compiles to Java bytecode and tight
55. stem visualization freeze drying and third party application integration Results Include a review of several Repast Simphony applications and brief tutorial on how to use Repast Simphony to model a simple complex adaptive system Conclusions We discuss opportunities for future work including plans to provide support for increasingly large scale modeling efforts Keywords Complex adaptive systems modeling Agent based modeling Java Groovy Background Introduction Complex adaptive systems CASs are composed of interacting autonomous agents Holland 2006 CAS agents have properties and behaviors They interact with and influ ence each other learn from their experiences and adapt their behaviors so they are better suited to their environment s By modeling these agents individually the full effects of the diversity that exists among agents with respect to their attributes and behaviors can be observed as they give rise to the dynamic behavior of the system as a whole Agent based modeling provides a mechanism for modeling CASs Bonabeau 2002 Macal and North 2010 Agent based modeling has been used successfully to model complex adaptive systems in many disciplines including archaeology biology ecology supply chains consumer market analysis military planning and economics North and Macal 2007 North and Macal 2009 Some examples are reviewed in section three 2013 North et al licensee Springer This is an Open A
56. t Turkish city of Kerkenes Dag Repast Simphony design goals The design goals of Repast Simphony are as follows North et al 2005 e All of the core features and capabilities of the previous versions of Repast should be available These features are detailed in North et al 2006 The lessons learned from developing the original Repast series of libraries are summarized above in the related work section e There should be a strict separation between model specification model execution model visualization and data storage e All user model components should be plain unadorned Java objects that are accessible to and replaceable with external software e g legacy models and enterprise information systems e Tasks that are commonly performed by model developers should be automated when possible e Imperative boilerplate code should be eliminated or replaced with declarative runtime configuration settings when possible Much like boilerplate text in standard English boilerplate code is moderate to large sized pieces of code that are used again and again in model after model An example in Repast 3 1 is code to setup a master time schedule or configure a network display e Idiomatic code expressions should be simple and direct Idiomatic code expressions are short pieces of code that act as slang terms or shorthand An example is code to update the weight on a network edge between agents North et al Complex Adaptive Systems Mode
57. t are cross library makes systems usable for a wider audience compared to single library approaches Modular construction is essential Library developers should be keenly aware of differences in the fundamental details of the candidate implementation environ ments such as differences in mathematics libraries Library developers should also consider the availability and capability of the ecosystem surrounding an implementation environ ment when making their selections MASON MASON is a free and open source agent based modeling library that provides core ser vices that can be mixed easily with other libraries Luke et al 2005 Luke et al 2005 recommends that libraries should be developed from first principles derived from spe cific domains Another key attribute is that libraries should be minimal and mix well with third party libraries Only essential features should be provided to increase inter operability and simplify learning There should be complete separation between mod els user interfaces and offline storage A large number of agents e g millions should be supported All model runs should be reproducible Furthermore checkpointing i e saving and restoring model runs midstream should be supported North et al Complex Adaptive Systems Modeling 2013 1 3 Page 4 of 26 http www casmodeling com content 1 1 3 Ascape Ascape Parker 2001 is a free and open source agent based modeling library that repre sents models as
58. te data source that the current row has started and thus any previous aggregate values should be reset The new code embodying these abstractions is proving to be much more flexible than the previous Log4J code and has provided the basis for a more simple and more efficient user interface GIS Geographic referencing is provided through geography projections that like the other spatial projections in Repast Simphony correlate the agents to positions in space An agent s representation in a geography projection corresponds to a specific geographical feature such as points lines and polygons Repast Simphony uses GeoTools GeoTools The Open Source Java GIS Toolkit an Open Geospatial Consortium OGC compliant library OGC Making location count to provide support for the feature types described above along with additional GIS data types and functions Repast Simphony s GIS capabil ities also include providing support for Environmental Systems Research Institute ESRI shapefiles esri Understanding our world and a range of raster data files The geography projection is associated with a coordinate referencing system CRS which is based on the OGC standards and can be used to execute geographical queries on the topology of the agent features in the geography Agents can query the geography to determine whether agent features overlap or are within a certain distance of inter sect with or border other agent features in the geogr
59. ting design and code walkthroughs e Performing unit testing e Conducting face validity checks e Docking against other models e Trying real world and tricky artificial cases and e Conducting parameter sweeps and sensitivity analyses Simple face validity checks will be used for the innovation model North et al Complex Adaptive Systems Modeling 2013 1 3 Page 20 of 26 http www casmodeling com content 1 1 3 What Alternative Techniques Were Tried Many models of innovation diffusion have been developed Meade and Islam 2006 Our model offers a simple agent based approach to this problem Much more detail would be needed to translate this tutorial model into a full scale model for studying innovation diffusion Who Are the Agents The agents are individual people in the innovation network What Are the Agent Behaviors The agents will randomly circulate on a continuous two dimensional surface When an agent with an innovation comes close enough to another agent they will transfer their ideas When an idea is transferred a new link is made between the transferring parties Any existing network links in the recipient will be deleted Agents develop at the rate given by the input innovation probability When they do so they delete all of their links Each idea is represented using a number The value of the number represents the relative quality of the idea The value also automatically maps into a display color for the agent and

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