NetKarma Cytoscape Visualization Plug
Contents
1. Process 17 On anode io begin an Visual Mapping Bypass edge nnd speseify tfe ipn ig en the tonget node to Use Web Services finish the edge Hide Node Specify Identifier F Linkiut vener gted E Data Provenance History Load Deta Info d empress Processes Fas Jutil acts ess Artit Cluster Meg i b ri E P Presi zu Set time interval Weipzeme to Cyt 2 amp 6 Right elici Ws DOOM Middle alio to PAN Figure 6 4 1 Display provenance as a movie The time interval on milliseconds can be configured between the appearances of two nodes in the movie 22 ji cytoscape De n x Fae Eare view sect tayon Pruga II m 40C H I i S SENI menr D Oyo K Karma H B mE nter fime imterval in ay i lj E On empty space bo create anode On a node lo begin an i Wilson be E bitip 280 Right click d abe DOOM Middle click d pees Figure 6 4 2 Continue the time interval 6 5 Saving graph as XML To save the displayed provenance in Cytoscape as an XML file that is based on the Open Provenance Model OPM right click on any node and select the menu item Export OPM The user will be prompted for the location to save the XML file The graph s structure will be based on the OPM v1 1 Open Provenance Model a rp Process 6 Visual Mapping Bypass Data Provenance History Load Detail Irfa Cur2. The abstract graph after layout The size of each node indicates the number of surrounding packets bigger node size indicates more surrounding packets User can use customized node graphics to show the statistics on traffic packets File Eda on Select meee Flug Help Tools Tucanae S Dit Karma VaMageer Es ajo Current Visual Style Defaults i O ga ETE Minde Attrixule Brewer p g ta DOCOM Mi3sHaccluck dem 35 PAH Figure 6 2 3 3 Add the Node Customized Graphics visual mapping 17 To show the statistics on Susy packets user can map the graphics to graph url drop amp sent Y Cytozcape Desktop New Session i WEM F p r EAE EE Karma TFB prewok WMmpe ede eners 0 Current Visual y Defaults D Made Lahel E Mode Shape El Urrused Proper lies Edge Font Pace Edge Font Size Erige Label Color Fidje Label Opaciy H t eun Now Welcome 1 Gy FET gaan aa D Dya K Karma E Current Visual Style I aic Description Updating Network View H Edge Color nter Progress B ma eg i Edge Label act ie Edge Target Arrow Sh O Node visual Mapping E Node Color El Mode Custom Graphics 1 grapheri droplisend Magog Type Pis 475 F e 474 Fie 475 Fide 472 Fie 539 Fie 471 F e 123 Figure 6 2 3 5 Set the mapping type to Passthrough Mapper 18 COICO S B Karma Em v Em pem
3. properties needs to be edited lt Define the Cytoscape directories gt cytoscape dir Cytoscape v2 8 2 fthe directory where Cytoscape is installed on your computer In the directory of Karma query type in the command ant If this succeeds a jar file named KarmaRetrieval jar should be generated 3 Copy the jar files into the plugins directory under Cytoscape v2 8 2 Deploy the Karma visualization plugin cp visualization OPM_visualization KarmaGraph jar Cytoscape_v2 8 2 plugins Deploy the dependent libraries for Karma visualization plugin cp visualization OPM_visualization lib Cytoscape v2 8 2 plugins Deploy the Karma provenance retrieval plugin cp visualization Karma query KarmaRetrieval jar Cytoscape v2 8 2 plugins Deploy the dependent libraries for Karma provenance retrieval plugin cp visualization Karma query lib Cytoscape v2 8 2 plugins Note some libraries are shared by Karma visualization plugin 4 Copy the configuration files into the plugins directory under Cytoscape v2 8 2 Create a new directory named config under cytoscape s plugins directory mkdir Cytoscape_v2 8 2 plugins config Deploy the configuration file for the Karma visualization plugin cp visualization OPM visualization config Cytoscape v2 8 2 plugins config Deploy the configuration file for the Karma provenance retrieval plugin cp visualization Karma_query config Cytoscape v2 8 2 plug
4. reduce the querying time For large provenance graphs we recommend retrieving without annotations since the Karma visualization plugin will load the annotations On Demand while navigating the provenance graph Note 2 While retrieving the XML file Cytoscape will appear to be blocked but will continue to work right after the file 1s retrieved successfully Please be patient while waiting for a graph to be downloaded 6 Using the Karma visualization plugin 6 1 Load the Karma provenance XML file 1 Click on the GENI toolbar 10 oo lolo 3 4 O amp J amp Q9 ag 8 B I Des Karma lig Canol Panel ZA OPM Visulizetian Plugin tot tip Te Network wastepper ajl Network Mo Ed m mpari a OPH ah ar r P a ih nnatatian v theut amp nnetatinn Asia Config Robbing cong Data Panel El 18 8 E Current Sessa all mebi alb bules vill be kak Do yeu wank ko continue OF Lance Figure 6 1 1 Click on the GENI toolbar Select whether to import the provenance xml with annotations or without annotations When importing provenance without annotations the Karma visualization plugin will set up a background connection to the Karma server and load both annotations and the registry level information On Demand when any node is selected from the provenance graph during navigation the Karma visualization will
5. 2 2 P Hierarchical layout of graph 2 There are several special layout algorithms developed for OPM graphs Some are designed for general OPM graphs X axis sort others are for specific category of OPM graphs Network Simulator Layout NS Layout Network Simulator Layout Extension 1 NS Layout Ext1 Those will be introduced in the following sections 6 2 1 Xaxis sort The nodes can be displayed using a layered format based on the order of the time attribute by selecting the OPM X sort option from the Layout GENI OPMLayout menu E cape De kii etm TECTA DUTETUEDT tte B Karma Seale Align and Di Zz ute ibn Cz Logs peng Decktog eap h Cun erry I amp 6 yb arii 7 E Settings Drayand Dro Y yFiles Anode shape GEHIOPMLaycut OPM X sort seh tae Cytoscape Layouts ClockwiseftinbuteCircleLayout Graph Layouts F Double click To 83d nodes and edges soecihied i SF format w n empty space fo ereaie o node E Onanode to begin an edge and specify the source node Then cic k on mw target node fo finish me edge Figure 6 2 1 1 Select the X sort algorithm 14 File Edel View Select Layout Plugint Help Took 2B 2Q0Q 8 8 84g 85 Bey Karma BL T r lure 7 ER ao networked sers meno Deskto Graph oemsentits cuti xm Drag and Drop m A nnde shape onbe the nebwerk view m An edge shape ont the spure node then ckt pn the target node Doub
6. Compress Artifact will eliminate all of the artifact nodes that link two Process nodes where the outgoing edge represents the relationship wasGeneratedBy and the incoming edge represents the relationship used The artifact will be replaced by a new edge between these two Process nodes that represents the relationship wasTriggeredBy 31 stop New Sessioni E le ET x J JE cytoscape D _ a _ Fik Edit View Select Layout Plugins Help Tools PURARA B Bg Search E B l mrn T E c em eem Instructons Orag and Drop 4 node shape ono The nelwork viens m An edge shape onin thie aouret node then chi on the target node Double click To add nodes and edges apecihed in SF format CTRL click B Cn empty apace to create Data Paral BOXE E Nade attrbute rosse Edge ARbule Browser ebore roe TE E a Middle M PAM ee a Figure 6 8 3 4 A provenance graph before ER Compress Artifact sacaa 68 BAG Karma _ ph npm mndifird md ee E bovis BF bwin AT IFAD Instructons Con 8 eim Qn Di To add nodes and edges specihed in SF fonna CTRL click d On empty apace Do crests anode Ona node lo begin an edge nnd specify te acurat nade Then chi nn the innget node tn finish the edge Zpedhr plur vestiDerreadi rom Visual Mapping Bypass Mested Networ
7. Current Visual Style m ad Default Figure 6 2 3 6 cue with auctor node graphics showing the statistic of packets been dropped and sent 2H 2828 aU BA s Karma w B Visual Mapping Browser m E Edge viaa Mapping E Edge Celer interaction E Edge Label interaction E Edge Tagel Arron interaction E Mee Visual Mapping NodeType B OE m Rigm oink drag in ZOOM MBs Hisi rpg to PAH Figure 6 2 3 7 Customized node graphic showing the statistic of packets been dropped and sent Blue line shows the number of packets dropped every 5 seconds and red line represents the number of packets sent every 5 seconds 19 To show the statistics on packets queuing time and pakcets transfer time user can map the graphics to Eos url Run ECCEPITTEEE Karma FB c Emm A MU Defaults egaanaau Bi Karma FHA Description Updating Network View Status Updating network view Please wait Purus pesas Figure 6 2 3 9 Set the mapping type to Passthrough Mapper 20 R Figure 6 2 3 10 Customized node graphic showing the statistic of average packet queuing time and packet transfer time Blue line shows the average packet queuing time and red line represents average packet transfer time 6 3 Navigating the Karma provenance graph 1 Double click on any node to see its attributes File Edit View Select Layout Plugms Help Tools was Oe CI LJ Eur Karma BL Network ae Instruct
8. Karma Provenance Retrieval and Visualization Plugin For Cytoscape User Manual v1 2 0 Feb 24th 2012 Copyright 2012 The Trustees of Indiana University This document contains instructions for using the Karma provenance retrieval and visualization plugin version 1 2 0 which provides core capability to retrieve provenance information from a Karma provenance system and visualize the returned graph Karma provenance retrieval and visualization plugin 1S licensed under Apache License Version 2 0 the License http www apache org licenses LICENSE 2 0 The code is copyrighted and copyright owned by The Trustees of Indiana University Karma provenance retrieval and visualization plugin is a product of the Data to Insight Center at Indiana University See http pti iu edu d2i provenance for more information Contents l 2 3 4 5 6 DVO EE LUUD om 4 ON EE DE AS E E A EE EEA E E E E E IM UIIMN 4 2 1 Oe MRL de DET le S eee er ee MM I EUM MENSEM PU NE 4 2 2 Installation dependencies ea ca stones nace mt Ob Ox race senr aprum adus antep EN ed ru xe URN Eo De nsns ud dup adupu ras 5 LES BT EI stag ERR 5 3 1 Installing under Mac Lanux Unix OS wesschcsccanesegennds cparsne cutiduacenstsaascaddnes cacnetaasnaevseddataiacemavsacasnetens 5 9 2 Install under Windows OS te aueseieteirpersteeunst ssirbnen asa tos Dea atas o Sens R api um i n anaa aa 6 C onreurme pU TE ROP EUG ern iE A E E sd Mad Mein eu aves on Msc E EA E
9. at can be added to existing cyberinfrastructure for purposes of collection and representation of provenance data The Karma query plugin aims to provide a GUI component that queries provenance information of scientific experiments from the Karma provenance repository The Karma server is accessible via either a webservice API or RabbitMQ enterprise bus and our provenance retrieval plugin supports both access methods Cytoscape http www cytoscape org is an open source software platform for complex network analysis and visualization We use Cytoscape because of its support for detail and overlaying visualizations with additional annotations We developed our visualization tool as a plugin that can generate the provenance graph visualization directly from the Karma provenance information using an XML and provide control of the navigation process 2 Software Dependencies 2 1 Service dependencies The Karma plugin retrieves provenance as graphs from the Karma provenance server To use the Cytoscape plugins one will need to either setup a Karma server or process a log file using an established Karma service such Data to Insight Center s NetKarma service on the GRNOC server To set up a Karma server please refer to the Karma Provenance System user guide at http pti iu edu d2i provenance karma If an instance of Karma service either hosted as a web service or as a standalone service using the RabbitMQ messaging bus already exists contact yo
10. eane 2 8 0 Righi alik drag ig Doo Middig nlick dran in PAN Figure 6 8 2 1 The sub graph 2 By clicking on the item in the network panel on the left hand side of the screen one can go back to the parent graph 29 Ine Edit View me y jeje eua XA er Karma s0 0 T E i i metworksCr Users peng Desktop Graph opman eub xml Node Aliribxuls Erer Edge Attribute Breeser Hetwerk Attribute Browser phi cliri s p i5 ZONE Middl click drag 15 PAN Em 6 8 2 2 The parent graph 6 8 3 Compress Process Artifact Right clicking on any node in the graph will show the menu options for Compress Process and Compress Artifact Clicking on Compress Process the Cytoscape visualization plugin will eliminate all of the Process nodes that links two artifact nodes with the outgoing edge representing the relationship used and the incoming edge representing the relationship wasGeneratedBy The process node will be replaced by a new edge between these two artifact nodes that represents the relationship wasDerivedFrom J Cytoxcape Desktop New Session mm File Edit View Select Layout Plugins Help Tools DICT OE Karma m Lii rebar A pope ered fered ard lz Bi m SOs M Node Attribute Browser Edge Attribute Browser Network Attribute roweser ht elick drag bo TOOM Micdle click drag bs PAM Figure 6 8 3 1 A provenance graph before applying Compr
11. ed 2 Next click the OK button and a new dialog window will appear which prompts for the workflowID WC anope Dee Conga Panel Ta He bark m z j i meirat Vienne Heterak Hess ER enter ID here x With annotation Without Annotation lliate Retrieval with Annotation games longer Ck Data Panel ao eo Node Attribute Brewer Edge Attribute Browser Network KEtribube Grosser Walcama to Cotescapa 385 Rigtri elizk drag 1a ZOOM Middie cierh chee Figure 5 2 Enter the workflow ID Enter the workflowID of the intended graph and select whether annotations are to be included in the graph or not then press the OK button to continue 3 After the plugin has retrieved the Karma provenance XML there will be a prompt to choose the name and location to save the XML file amp amp 1 amp amp al 2 a By By d se Karma Central Pane RET a Save in ll Computer amp otc E ca READER D coe RECOVERY 0E ea OVD Drive F fo Fie names teat Save Fies ol hype onl fies anil z Cancel Mede Artrihute Eraser Edge Attribute Browser Hetiebrk Attribute Droveser Fighiclich diig bo DOM Middla click drag be PAM Figure 5 3 Save the OPM XML file Note 1 The time required to retrieve the graph varies depending on the size and complexity of the XML file Retrieving a graph without annotations can significantly
12. en Welcome tg Erian apa 220 n c Figure 6 7 1 Rightc click on the E in the network control panel and then select the Create WiMax DoS Vis Fa netenki ers pes 8B D 136 Misit click deg 1 PAH Figure 6 7 2 WiMax DDoS provenance graph using digit MT in differentiating attackers and users The attackers and their action event nodes are marked in blue edges connected to them are marked in red and the traffic packets surrounding attackers are marked in Cyan 25 6 8 Creating an abstract view For some experiments the complexity of the provenance relationships can result in very complicated graphs This section introduces features of the Karma visualization plug in that can be used to abstract out some of this complexity to allow visualizing specific aspects of the provenance graph 6 8 1 Clustering neighbor nodes To deal with graphs with a large number of artifact nodes the Karma visualization plugin supports extracting an abstract view by clustering neighboring nodes Figure 6 8 1 1 shows an example of a graph that has a ue ees of artifact nodes generated by a small number of Process nodes 3 ghicit s M Middle click drag io FAH Eisufe 6 8 1 1 A graph with large number of Artifact nodes The user can create an abstract view for this type of graph using the following 5 step process 1 Select the process nodes on the lower left side of the graph in Figu
13. ess Process 30 tap 5 lew Session JED Cytoscape D Fik Edit View Select Layout Plugins Help Tools DARRAR E aa Karma 1 Lot mewo E ph oprmurnodilred aril bui ale Irestructiones Drawn os ma orsa mat omen E A node shape onio ihe Dabei view dn edge shape onlo the sure exl then chek on the innget rede Double click m To ndd nodes amd edges apecified im SF inrmat CTRL click Nu wir wie Kis Visual Mapping Bypass Oo a node to begin an Mested Metwouk edge and specify the Use Web Services source rede Then click von the largat node bo Hide Node fni tht edge LinkOut Spedly Dceritifier EJ i ce ry eum Load Detail Info vessi err ated zt Compress Processes E Compress Aubilacks Expert OPM Beers o 7 o L rEEEENE Play Messe b ia La Be a Break m varrer beei nom Made Atlsibute Brower Edo Attribute Browser Network Attribute Brewer Wetssme to Cytonap 2E D Wight click aea 65 TOOM Middla clitk drag te PAM Figure 6 8 3 2 Applying Compress Process uaa a EEE Karma T B LLLI A wje mebarak CA Use peng eskbeg ara ph_opent ered tered arr wssDerneedirom imen Hede attribute Browser Edge Attribute Browser Network attribute Uroveser em TT Rightclick dag to DOOM Middle click drag bo PAN Kisute 6 8 3 3 The provenance graph after applying Compress Process Clicking on
14. he configuration panel in Cytoscape the contents in the configuration file can be modified The file karmaQueryConfig txt has identical configuration entries as the file karmaVisConfig txt Set up the configuration for connecting via the Axis2 webservice There is only one property that needs to be set when using the Axis2 server axis2 serviceURL enter the URL to the Karma v3 2 1 webservice Set up the configuration for connecting via RabbitMQ messaging system There are several properties that must be set to connect using the RabbtiMQ server messaging username username of RabbitMQ messaging password password of RabbitMQ messaging hostname hostname or IP address messaging hostport port 4 2 Updating the configuration file for Karma visualization plugin The pluginConfig xml has properties that control the labeling of nodes Karma visualization plugin automatically import all the annotations into Cytoscape graph as attributes User can choose the label of nodes from one of the imported attributes by configuring the following properties visualAttributes configuration for the properties related to the rendering of the graph includes nodeLabel for telling which attribute of the nodes to show as labels The configuration for PROCESS and ARTIFACT are separated processLabel the label of process nodes artifactLabel the label of artifact nodes Each group of configuration has a list of attribute
15. i 7 4 Updating the configuration files to connect Karma provenance retrieval and visualization plugins to Karma Service onospsceubpeteoa dmi dusiuttsdiuntpdtrb ibd buts sat es tuU ENEE SediantepdscisPdissarie cdd abad TUUM 7 4 2 Updating the configuration file for Karma visualization plugin eeeeeeerrrreeeeee 8 Using the Karma provenance retrieval plugin sseeseeeeeeeeeeeeeeeeeeeeeeeee nennen nennen nennen 8 Using the Karma visualization plugin eeeeeeeeeeeeeeeeeeeeeeeeeeeee nennen nenne nennen eene nennen 10 6 1 Load the Karma provenance XML TIE cesis eoa eae oun Ere bb beth nE o EN Nx NE nRa 10 6 2 Applying layout algorithms to the Karma provenance graph eeseeeeeeeeeeeeeeee 13 6 2 1 Ped SOU opener tice nese 14 6 2 2 Network Simulator Layout ss0ssssss0sesesssssssasssesessaseonseeseosesesesesssessssnssnsnnssnssssnsnsneseces 15 6 2 3 Network Simulator Layout Extension 1 00 00 eeeeeeeeeeeeeeeeeeeeeeeeeeeseaaaaaaaaaaaaaaaaaaaaaaaeeeeees 16 6 3 Navigating the Karma provenance STAD cissiccscsccsdsndnacssdvaneioueedvatdencnetsoavbnespontssaadundonsasuaestanaetiaes 21 D MEE II E eee een eee eee eee re 22 6 5 DUD ui A A M esac wwGS 23 6 0 Getting data provenance 11k 0 ek Gane ee ne eee ee eae eee ee 24 6 7 RB HIDE CUIR nd P M 25 6 8 Creating an abstract V
16. iew eeeseeseeeeeeeeeseseeeee nennen nenne nennen nenne nnsnnen enne sse esses sese esee eene 26 6 8 1 Clusterime nero DOT TOC eo sas cae ae ee sac imei t rermumsceptudaepteen ose usd Ui opm Deu EaU 26 6 8 2 Navigate between graph and SuD Praplis i25 veris ooh nrbs Saee ape sas Uphe T SbPEbP HOP nE RNA iE 29 6 8 3 Compress dare eu PE GIA RM 30 1 Introduction We have developed two plugins to Cytoscape to visualize and navigate provenance information contained in Karma provenance system The Karma provenance retrieval plugin is used to retrieve provenance graphs from a remote Karma server to your local machine In Cytoscape this plugin is executed by clicking on the blue Karma icon in the Cytoscape toolbar after the plugin is installed The second plug in is the Karma visualization plugin which allows the user to visualize and manipulate graphs downloaded using the retrieval plugin The Karma visualization plugin is displayed as an orange Geni icon in the Cytoscape toolbar Visualization of provenance data is useful for manipulating very large provenance graphs for displaying different views and for interactivity This can help a user to navigate their experiment information with a mental map of what is going on in the experiment to compare different experiment runs quantitatively and to do model selection with an effective collaboration between the user and the discovery system Karma is a standalone system th
17. ike this your graph may differ depending on your experiment s provenance Data Panel gt Node Attribute Browser drag 10 ZOOM BOS kN fi The sample OPM graph created for file C Usersipeng Desktop Graph_opmamAts_ outs rmi Edge Attribute Browser Network Attribute Browser Middle click drag to PAN Figure 6 1 4 Load the Karma provenance graph 12 5 Cytoccape Desktop New Session 3 Sans Hl File Edt View Select Layout Plugins Help Took Node Attribute Browser Edge Attribute Browser Network Attribute Eroma Vwiicoma to Gecaj a 0 0 Rigra tiick drag ta DOOM Miasta click deg 3a PAH Figure 6 1 5 Initial graph 6 2 Applying layout algorithms to the Karma provenance graph 8 Cytoscape Desktop New Session GENDOPMLayoat Cytescapelayouts Attribute Circle Layout F 3 JGraph Layouts Edge Weighted Spring Embedder Edge Weighted Force Directed BioLayeut Spring Emheclded Hierarchical Layout Circular Laycut Inverted Self Organizing Map Layout Group Attributes Lana Grid Layout Ferce D rected Layout Degree Sorted Circle Layout 1 Different layouts for the provenance graph are available from the Cytoscape Layout Cytoscape Layouts menu For example if the hierarchy layout is selected the graph will appear as shown in Figure 6 2 2 13 Node Atirbule Browser Mem rel R gri thck drag da DM LL Figure T
18. in hnesh the edge Specify Idensfler addan Ede Packed a Nudes Add a Nested Metra Waloome in Cyirecape 2 8 0 4 IIS Data Panel BEA ID D O e ny s 83 oen Karma l r Graph_ opm ari Lar i new nut1 ml ERU rie Uum a l mee herent Times new outs ccml Bl new_outhcoml B tn_eullaml B ii cutia D ts cout arl D toutan E fe BS a A Hebweork Fie name ts outa i Open Files ol Svar ed fides xml Mode Atribute Grceser Edge Altribule Brower Nebvork Atlributie Browser Aight ollos drag io Doce Middig nlipk drag in FAM Figure 6 1 3 Select the Karma provenance XML file Load the Karma provenance graph Gc ytoscape Des rie cm amp E Q amp XL a SB Ay Dn B oes Karma 3 i metwerleCAUsers pens Desktop Graph opmamits eae Control Panel fe Network MaMapper Editor 41 Instructions Drag and Drop A node shape onto fe network view An edge shape onto fe source node then chek on the target node Double click To add nodes and edges specified in SF format CTRL chick On empty space to create anode On n node to begin an edge and specify the source node Then cick On the target node to firwsh the edge Specify Identifier Add an Fdge Add Node Add a Nested Network Welcome to Cytoscape 2 8 0 Right clica The initial graph will look l
19. ins config 5 After installing the two plugins the plugins directory under Cytoscape v2 8 2 should look like Cytoscape v2 8 2 HOME DIRECTORY plugins KarmaGraph jar KarmaRetrieval jar Other jar libraries config karmaQueryConfig txt karma VisConfig txt pluginConfig xml 3 2 Installing under Windows OS 1 Checkout the plugin package from our SVN repository svn co https karmatool svn sourceforge net svnroot karmatool karma trunk visualization visualization 2 Building from source code optional Same as step 2 in Section 3 1 3 Copy the jar files into the plugins directory under Cytoscape v2 8 2 Install Karma visualization plugin copy visualization OPM_visualization KarmaGraph jar C Program files Cytoscape_v2 8 2 plugins Deploy libraries for Karma visualization plugin copy visualization OPM_visualization lib C Program files Cytoscape_v2 8 2 plugins Deploy Karma provenance retrieval plugin copy visualization Karma_query KarmaRetrieval jar C Program files Cytoscape_v2 8 2 plugins Deploy libraries for Karma provenance retrieval plugin copy visualization Karma query lib C Program files Cytoscape_v2 8 2 plugins 4 Copy configuration files into the plugins directory under Cytoscape_v2 8 2 Create a new directory named config under cytoscape s plugins directory mkdir C Program files Cytoscape_v2 8 2 plugins config Depl
20. k F Use Web Services J Hide Node LinkOut Data Provenance History Load Detail Info Conmprest Processes Compress Artifacts Expert OPM Cluster Neighbors Play Mewar 1 i node ateaute once Ele Albe Browser Hebiork Attia Ber Welnome to Cylosonoe 2 4 0 Right click dag oo ZOOM Miadla alic amp drag bo PAN Figure 6 8 3 5 Anovi Compress Artifact 32 UG MMMETE amp Hdaeocaes 8 mE Reed Karma BL Is Network VizMapper Edta 4j p Ir amp tructons Orag and Drop LES einoiy apace bo crease anode Cn anode lo begin an ORs i ii Welcome bo Cyinsoape 23 0 Right clics fe ZOOM Middla alig amp drag ra PAH Figure 6 8 3 6 The provenance graph after applying Compress Artifact 33
21. le click A To 830 nodes and edges specified in SF format CTRI click 4 On empty amp pace to create a node On a node to begin an edge and pily lhe source ride Then chek exi fh Bagel node te iris re enn Specify Identifier WasGeneratedEy Figure 6 2 1 2 The hierarchy graph after sorting 6 2 2 Network Simulator Layout The nodes will be positioned based on their category and location coordinates if they have That is for network simulation nodes OPM PROCESS they are positioned according to location coordinates for network events actions OPM PROCESS they are positioned in a small circle surrounding the network simulation node by which they were triggered for network traffic packets OPM ARTIFACT they are positioned in a big circle surrounding the network simulation node by which they were generated ra c X few ES HOT File Edd View Select Layout Fugins Help Took Rotate By Bag meny TES T ni irc ee S3 o Karma L EN N Align and Distribute Users peng Desktop Bloomington WiklasxD Des GENNI 27 wimayl m Settings Dm iy yfile r GENI OPMLaycut N Liyeuk Cytescape Layouts OPM X sert Graph Layouts M Layer Ext j ClockwiseArtributeCirclelsyout gt Dala Panel BOs m Node Aarie Browser Bilge Alirinte Bronce Meheori Alisihube Erreser Fiigni lick drag in DOOM Missis click drag 15 PAH Ine Bove gt font Y Figure 6 2 2 1 Select the Net ag Pe
22. names listed with a priority from the highest to the lowest attributeName which attribute of the nodes to show as labels For example if the attribute objectValue or the attribute ID is to be used as the label of artifacts the following configuration can be setup where the ID attribute will be used when the objectValue attribute is not present lt artifactLabel gt lt attributeName gt objectV alue lt attributeName gt lt attributeName gt ID lt attributeName gt lt artifactLabel gt 1 Run Cytoscape and click on the Karma icon in the toolbar 2 Cytewane Tesktap f amp tQ O9 ag E Ay Pr d oes Karma Control Pane E Tg network VizMapper ei aje hetwork Ho Ed Earra Chers Karma Server Confguration 7 med Rabbit Axis Config Service IRL abis nelkarnma ies Hab orc edu S08 ae fuer vices Karma Ser vice Habbitmg contig Curent Sesiori al nebvorkiatlrbubes vell be kis Do you want lo continue Cancel UK ice Abbhibub Eroweer Gar Atribute Erosa Hir roonrk Attrbi rte Breer TESTA bo Grbic 7 ED Wagrt click 4 cem 55 ZDXJMI Miid l click 5 drag tz PAN Figure 5 1 Click on Karma toolbar Choose the connection method and configure its connection parameters Choosing Axis2 the ServiceURL in the Axis2 Config panel needs to be configured choosing Rabbitmq all parameters in the Rabbitmq config panel need to be configur
23. ng peng Karmar tus tees OPM work Simulator Layout algorithm 15 Kl Cyto pe Checkin Mew mt Fils Gat Vw Select Layout Puget tise Took suaanqe gam Karma uit B netenrle c V aers pes BA 135 Dala Panel s Oy n D O node urbe Broveser Belge Alirbuie Browder Metwrork Abiribule Erreser Riigni cilick drag in ZOOM Midde click deny 12 PAN EIL Figure 6 2 2 2 The geo graph after layout 6 2 3 Network Simulator Layout Extension 1 More than layout this extension eliminate the network events actions and network traffic packets from the graph and visualize the traffic information for individual node in a more abstract and straightforward way That is for each network simulation node it does some statistics on the surrounding packets and then removes all the packets and events actions from the graph displaying the statistic data using the size and graphic of network simulation node instead Dec pm E SS cc i H Sem B Py 3 sey Karma ciem LN Alien and Disbibule Users pene DesktepBlacmingtan Wills settings EE d yfiles 2 GEMECOPMILaycut HS Lanyisul Cytoscape Layouts OPM X sert Graph Layouts MS Lait Ext ClockwiseAttributeCirclelsyout x Ege Mirna Boner Werk Alle Browser Misie click to FAN Figure 6 2 3 1 Select the Network Simulator Layout Extension 1 16 Fi ida View Select Layout Plugins Help Took EAE Karma J Figure 6 2 3 2
24. ngress Processes Compress Artifacts Export OFM Cluster Neighbors Play Mee Miulecrm bo Cyt ape iti Rig zi Figure 6 5 1 Click on Export OPM 23 File Edd View Select Layout Plugins Help Took ERUTPIICUE Karma BE oo Netwirk e Essi Network Hass Ela Welcome to Cyicscaps 280 Righi tlick drag Figure 6 5 2 Choose the location to save the xml file 6 6 Getting data provenance history Right clicking on any artifact will display an option for Data Provenance History Selecting that option will display a new graph that includes all of the nodes involved in the generation of the selected artifact This method invokes background communications with the Karma server PARANA a BAS Karma k hetenrk Coe Drag ane Drop B node shape onto the nebwork wew WEIDE bo Opi 23 0 Right clic ie ZOOM Middle alice bo PAN Figure 6 6 1 Get data provenance history Note This functionality works best when the Karma visualization plugin is connected to Karma using Axis2 webservice instead of the RabbitMQ 24 6 7 Creating visual style User can create customized visual style through VizMapper control panel in Cytoscape We also developed a special visual style for Network Simulation graph showing WiMax DDoS experiment m Metwork Tele Create View Desire View Destroy Metwork Apply Visual Style Creabe Willan Dos Vic Meberark cormparsien DEA comparis
25. ons Orag and Drop A rode shape onlo the m An edge shape onia the acurat node then chei on the target node Double click To add nodes and edges ijj Node Attributes mE specified in SF format E Or empty apace to create Figure 6 3 1 Double click on node 2 Double click on any edge to see its attributes 21 fie Edit View Select Layout Plugins Help Tools em aaaoesaumEPD Ee Karma BL fe Network VirMapper Eder 4j p Instruchons Drag and Drop e ences ton To add nodes and edges specihed in SF tonne CTRL click T Onemndy space t create anode a On a node lo begin an edge nnd speeihy fe en the tnnget node i Panel Og 8 i uM Node Attribute Browser Edge Attribute Browser Network Attribute Broveser PAN 23 0 i Righ allai bo ZOOM Middle alicia a ug bo Figure 6 3 2 Double click on edge 6 4 Playing movie If any node is right clicked a movie displaying the provenance for the entire graph can be played The movie is based on the order of the timestep or time attributes of the nodes E Cutoscape Deran Mea tere 1 File Edit View Select Plugins Help Tools GAGA ap DAE eme i M TUER Ir tructons Orag and Drop A node shape onio the ritboezek view am An edge shape onia the apurar nade then chei on the target node E To add nodes and edges specihed in SF iormat CTRL elieke E On amot apace to crests TS
26. oy the configuration file for Karma visualization plugin copy visualization OPM visualization config C Program files Cytoscape_v2 8 2 plugins config Deploy the configuration file for Karma provenance retrieval plugin copy visualization Karma query config C Program files Cytoscape_v2 8 2 plugins config 5 After installing the two plugins the plugins directory under Cytoscape_v2 8 2 will look like Cytoscape_v2 8 2 HOME DIRECTORY plugins KarmaGraph jar KarmaRetrieval jar Other jar libraries config karmaQueryConfig txt karmaVisConfig txt pluginConfig xml 4 1 Updating the configuration files to connect Karma provenance retrieval and visualization plugins to Karma service The following describes how to configure the provenance retrieval and visualization plugins and connect them to a running Karma service There are two options Axis2 webservice or RabbitM messaging system to connect to a Karma server and all of the configuration information is stored in the file karmaQueryConfig txt for Karma Retrieval plugin and in the file karmaQueryConfig txt for Karma visualization plugin These configuration files will be loaded at the startup of either plugin and the configuration settings will be displayed in the configuration panel The default configuration settings can be modified and will be saved to the configuration files automatically Besides making configuration changes through t
27. re 6 8 1 2 26 Fr a a ine ap et tt uae ea ieu SOLEC Karma ss T BB E Drag and Drape m A node shape onic the neharerk vier a An dji shape ants the soured nada then click nn ihe target node Conable click m To odd nodes and edges Data Paral E JE Right click drag be ZA Middle click drag ia FAH Figure 6 8 1 2 Select processes 2 Click zoom selected region icon from the toolbar highlighted magnifying glass icon the Figure 6 8 1 3 euaadaepuUa R Karma TIB T TES i HOE amp ea one ERE REGE Tee Ra Figure 6 8 1 3 Zoom into process region 3 Right click on one of the nodes with a large out degree a significant number of edges 27 le Serene Perap ci Ti File Edit View Select amp Help Tools eala ada sua an rH er Karma T xm come H TT Process 12 source node Then click Visual Mapping Bypass irish the edor En Mested Network Use Web Services Hide Node WersGererabedBy lpowe e LinkOut h 5m amp i m SIL Mode Abate Bromenr Edge Attribute Browser Network Attribute Browser Wierik a 2 10 Aight clieg drag to ZOO Middie tlinic drag 1 PAN Figure 6 8 1 4 Right click on node 4 E the neighbors of the node selected in step 3 F e Edit View Select ugins Help Tools euaaaas na EU Karma T UE c Instructions Drag and Drope A node shape onto ihe netwo
28. retrieve more information for it 2 If the provenance graph is imported without annotations the background connection method needs to be chosen and the connection parameters need to be configured KY Cytoseape Desktop Blew See Ble SH QQQQ a E303 Sy Sq SG oes Karma Control Panel E tr Netek VisMapper afr H amp bwork N Ed gt gt Inmet an OPH Graph from ma fie mia or D valfrou Leo ao LEEF y Rabbeed L Axis Config Rabbitmg contig LETTVMTES FRAME peeved quest haiam 156 5 2 M M hastpart 5672 0 ban B a virtusibeost fo E E ID enchangename Kanmmsbxchange guaeuenames Cama uur rnutingke ys Karmakry Current Session nebork aktributes wil be lost Do vou want te contnoes Cancel UK Neve Attribute Browser Edge Attribute Browser Network Attribute Browser Weloorten bo Cyleecee 12D Right click dens bo ZOXDM Middle clict Gag be FAM Figure 6 1 2 Configure the connection to Karma Server 11 amp 3 Q amp C1 amp T Control Panel J fg Network VrMapper Editor 4 Instructions Drag and Drap B A node shape ate the network view m An eige shape onte the snuree node then tkk on the target node Double click To Bdd nodes and edges pitied in Sa Pamat C TRA click B Un empty space to create anode On anoda io begn an pigi nne specify the shure nie Then cick nn ine wget nnde
29. rk view e An edge shape onis the source node then click nn the target node Double click m To nde neces and edges specified in SF feemar CTRL click m On empty space ip create anode a On anode to begn an S node Abbe Brome ripe Attribute Browser Network Altribute Browser Wacome t Cyc 2 100 Right click drag te ZOOM Middie click drag to PAN Figure 6 8 1 5 Cluster nodes 5 Repeat step 4 until an abstract graph is obtained showing only the smaller set of nodes that the user intends to visualize 28 tj Bua anam na Br e Karma esL DD Mode Abite Brave Edge Attriite Browser Network Attribute Browser Walcam ti Cyteiecape 2 0 Hight elick drag ti SEEMA Middls clizk drag 15 PAN Figure 6 8 1 6 Create abstract graph 6 8 2 Navigate between graph and sub graphs Once an abstract view is created one can navigate between the parent abstract view and the sub graph for any collapsed node 1 Double dann on any abstract node will show the view of the collapsed sub graph Ji Cytoscape E Deseo Mew Se joa adque na Syri iei Karma LL qum XP ni Drag and rape m An edge shape cto the apuce rade then cick on the target node a To 83d nodes and edges Spec ited in SUP foemar CTRL click On empty space lo create anode 10 rede Attribute Browser Edge Attribute Browser Network Attribute Browser Welcome in Cvipr
30. ur system administrator for obtaining access 2 2 Installation dependencies The Karma provenance retrieval and visualization plugin v1 1 0 has been tested with the following software packages on which it has a dependency These packages will need to be installed before using the visualization plugin 1 Java Development Kit JDK v5 or v6 http java sun com 2 Cytoscape v2 8 2 http www cytoscape org 3 Installing Plugin Download the plugin package as a zip file from http pti iu edu d2i provenance karma 3 1 Installing under Mac Linux Unix OS 1 Check out the plugin package from our SVN repository svn co https karmatool svn sourceforge net svnroot karmatool karma trunk visualization visualization 2 Building from source code optional This step can be skipped since the plugin package already includes pre build plugin jar files If one wants to build from source code the ant properties in the file build properties needs to be set To build the Karma visualization plugin the file visualization OPM visualization build properties needs to be edited lt Define the Cytoscape directories gt cytoscape dir Cytoscape v2 8 2 the directory where Cytoscape is installed on your computer In the directory of OPM visualization type in the command ant If this succeeds a jar file named KarmaGraph jar should be generated To build the Karma retrieval plugin the file visualization Karma query build
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